Starting phenix.real_space_refine
on Wed Sep 17 04:54:46 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/9n95_49160/09_2025/9n95_49160.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/9n95_49160/09_2025/9n95_49160.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.65
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/9n95_49160/09_2025/9n95_49160.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/9n95_49160/09_2025/9n95_49160.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/9n95_49160/09_2025/9n95_49160.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/9n95_49160/09_2025/9n95_49160.cif"
  }
  resolution = 3.65
  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=   0.002
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      26      5.16       5
     C    3038      2.51       5
     N     715      2.21       5
     O     780      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 4 residue(s): 0.01s

  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: 4559
  Number of models: 1
  Model: ""
    Number of chains: 1
    Chain: "A"
      Number of atoms: 4559
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 570, 4559
          Classifications: {'peptide': 570}
          Incomplete info: {'truncation_to_alanine': 30}
          Link IDs: {'PTRANS': 22, 'TRANS': 547}
          Chain breaks: 5
          Unresolved non-hydrogen bonds: 134
          Unresolved non-hydrogen angles: 156
          Unresolved non-hydrogen dihedrals: 117
          Unresolved non-hydrogen chiralities: 3
          Planarities with less than four sites: {'TYR:plan': 1, 'ARG:plan': 7, 'ASP:plan': 3, 'GLU:plan': 2, 'GLN:plan1': 2, 'PHE:plan': 1}
          Unresolved non-hydrogen planarities: 73
  Time building chain proxies: 1.36, per 1000 atoms: 0.30
  Number of scatterers: 4559
  At special positions: 0
  Unit cell: (86.87, 86.14, 81.76, 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      26     16.00
     O     780      8.00
     N     715      7.00
     C    3038      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: 0.32
  Conformation dependent library (CDL) restraints added in 156.2 milliseconds
  
  Enol-peptide restraints added in 238.4 nanoseconds
  

  1116 Ramachandran restraints generated.
    558 Oldfield, 0 Emsley, 558 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  1096

  Finding SS restraints...
    Secondary structure from input PDB file:
      30 helices and 1 sheets defined
      71.4% alpha, 0.4% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.17
  Creating SS restraints...
    Processing helix  chain 'A' and resid 46 through 48
      No H-bonds generated for 'chain 'A' and resid 46 through 48'
    Processing helix  chain 'A' and resid 49 through 72
    Processing helix  chain 'A' and resid 116 through 123
    Processing helix  chain 'A' and resid 126 through 131
    Processing helix  chain 'A' and resid 133 through 159
      removed outlier: 3.707A  pdb=" N   ILE A 137 " --> pdb=" O   GLY A 133 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 160 through 167
    Processing helix  chain 'A' and resid 192 through 218
    Processing helix  chain 'A' and resid 241 through 249
    Processing helix  chain 'A' and resid 272 through 274
      No H-bonds generated for 'chain 'A' and resid 272 through 274'
    Processing helix  chain 'A' and resid 275 through 283
    Processing helix  chain 'A' and resid 325 through 342
      removed outlier: 3.643A  pdb=" N   THR A 336 " --> pdb=" O   LEU A 332 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 356 through 368
      removed outlier: 3.872A  pdb=" N   ALA A 360 " --> pdb=" O   GLU A 356 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 386 through 391
    Processing helix  chain 'A' and resid 392 through 395
      removed outlier: 3.758A  pdb=" N   TRP A 395 " --> pdb=" O   THR A 392 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'A' and resid 392 through 395'
    Processing helix  chain 'A' and resid 409 through 414
      removed outlier: 3.985A  pdb=" N   SER A 412 " --> pdb=" O   LYS A 409 " (cutoff:3.500A)
      removed outlier: 4.650A  pdb=" N   GLN A 414 " --> pdb=" O   LEU A 411 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 415 through 446
      removed outlier: 3.600A  pdb=" N   TRP A 419 " --> pdb=" O   GLY A 415 " (cutoff:3.500A)
      removed outlier: 3.861A  pdb=" N   THR A 438 " --> pdb=" O   PHE A 434 " (cutoff:3.500A)
      Proline residue:  A 439  - end of helix
    Processing helix  chain 'A' and resid 447 through 450
      removed outlier: 3.793A  pdb=" N   ASN A 450 " --> pdb=" O   ASP A 447 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'A' and resid 447 through 450'
    Processing helix  chain 'A' and resid 465 through 491
      Proline residue:  A 480  - end of helix
    Processing helix  chain 'A' and resid 495 through 498
    Processing helix  chain 'A' and resid 499 through 515
    Processing helix  chain 'A' and resid 515 through 532
      removed outlier: 3.599A  pdb=" N   SER A 519 " --> pdb=" O   LEU A 515 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 543 through 547
    Processing helix  chain 'A' and resid 553 through 565
    Processing helix  chain 'A' and resid 565 through 574
    Processing helix  chain 'A' and resid 574 through 587
    Processing helix  chain 'A' and resid 606 through 624
      removed outlier: 3.703A  pdb=" N   TYR A 624 " --> pdb=" O   VAL A 620 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 630 through 653
      removed outlier: 4.114A  pdb=" N   PHE A 634 " --> pdb=" O   ILE A 630 " (cutoff:3.500A)
      removed outlier: 4.202A  pdb=" N   TYR A 651 " --> pdb=" O   ARG A 647 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 660 through 672
      removed outlier: 4.200A  pdb=" N   HIS A 664 " --> pdb=" O   GLU A 660 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 672 through 690
      removed outlier: 3.858A  pdb=" N   ILE A 676 " --> pdb=" O   LEU A 672 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 694 through 710
      removed outlier: 4.110A  pdb=" N   LEU A 702 " --> pdb=" O   LEU A 698 " (cutoff:3.500A)
    Processing sheet with id=AA1, first strand: chain 'A' and resid 231 through 232

    274 hydrogen bonds defined for protein.
    807 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: 0.66

  Time building geometry restraints manager: 0.40 seconds

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

  Histogram of bond lengths:
        1.23 -     1.34: 1364
        1.34 -     1.46: 1181
        1.46 -     1.58: 2101
        1.58 -     1.70: 0
        1.70 -     1.81: 41
  Bond restraints: 4687
  Sorted by residual:
  bond pdb=" N   VAL A 257 "
       pdb=" CA  VAL A 257 "
    ideal  model  delta    sigma   weight residual
    1.452  1.495 -0.043 1.18e-02 7.18e+03 1.32e+01
  bond pdb=" N   VAL A 258 "
       pdb=" CA  VAL A 258 "
    ideal  model  delta    sigma   weight residual
    1.459  1.501 -0.042 1.25e-02 6.40e+03 1.15e+01
  bond pdb=" N   ILE A 321 "
       pdb=" CA  ILE A 321 "
    ideal  model  delta    sigma   weight residual
    1.459  1.498 -0.039 1.25e-02 6.40e+03 9.65e+00
  bond pdb=" N   ASP A 259 "
       pdb=" CA  ASP A 259 "
    ideal  model  delta    sigma   weight residual
    1.458  1.491 -0.034 1.16e-02 7.43e+03 8.42e+00
  bond pdb=" N   VAL A 260 "
       pdb=" CA  VAL A 260 "
    ideal  model  delta    sigma   weight residual
    1.459  1.495 -0.036 1.25e-02 6.40e+03 8.25e+00
  ... (remaining 4682 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     1.85: 6171
        1.85 -     3.69: 174
        3.69 -     5.54: 36
        5.54 -     7.39: 7
        7.39 -     9.23: 3
  Bond angle restraints: 6391
  Sorted by residual:
  angle pdb=" C   THR A 229 "
        pdb=" CA  THR A 229 "
        pdb=" CB  THR A 229 "
      ideal   model   delta    sigma   weight residual
     115.79  109.08    6.71 1.19e+00 7.06e-01 3.18e+01
  angle pdb=" C   TYR A 324 "
        pdb=" CA  TYR A 324 "
        pdb=" CB  TYR A 324 "
      ideal   model   delta    sigma   weight residual
     115.89  109.21    6.68 1.32e+00 5.74e-01 2.56e+01
  angle pdb=" C   GLN A 552 "
        pdb=" CA  GLN A 552 "
        pdb=" CB  GLN A 552 "
      ideal   model   delta    sigma   weight residual
     115.79  110.29    5.50 1.19e+00 7.06e-01 2.13e+01
  angle pdb=" C   TYR A 252 "
        pdb=" CA  TYR A 252 "
        pdb=" CB  TYR A 252 "
      ideal   model   delta    sigma   weight residual
     110.17  101.49    8.68 1.97e+00 2.58e-01 1.94e+01
  angle pdb=" N   VAL A 257 "
        pdb=" CA  VAL A 257 "
        pdb=" C   VAL A 257 "
      ideal   model   delta    sigma   weight residual
     112.96  109.08    3.88 1.00e+00 1.00e+00 1.51e+01
  ... (remaining 6386 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    17.21: 2303
       17.21 -    34.42: 294
       34.42 -    51.63: 78
       51.63 -    68.84: 21
       68.84 -    86.05: 2
  Dihedral angle restraints: 2698
    sinusoidal: 1015
      harmonic: 1683
  Sorted by residual:
  dihedral pdb=" C   TYR A 252 "
           pdb=" N   TYR A 252 "
           pdb=" CA  TYR A 252 "
           pdb=" CB  TYR A 252 "
      ideal   model   delta  harmonic     sigma   weight residual
    -122.60 -114.10   -8.50     0      2.50e+00 1.60e-01 1.16e+01
  dihedral pdb=" CA  ASP A 447 "
           pdb=" CB  ASP A 447 "
           pdb=" CG  ASP A 447 "
           pdb=" OD1 ASP A 447 "
      ideal   model   delta sinusoidal    sigma   weight residual
     -30.00  -85.66   55.66     1      2.00e+01 2.50e-03 1.05e+01
  dihedral pdb=" CA  GLU A 223 "
           pdb=" C   GLU A 223 "
           pdb=" N   ASN A 224 "
           pdb=" CA  ASN A 224 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  164.02   15.98     0      5.00e+00 4.00e-02 1.02e+01
  ... (remaining 2695 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.043: 554
       0.043 -    0.087: 156
       0.087 -    0.130: 30
       0.130 -    0.173: 5
       0.173 -    0.216: 2
  Chirality restraints: 747
  Sorted by residual:
  chirality pdb=" CA  VAL A 257 "
            pdb=" N   VAL A 257 "
            pdb=" C   VAL A 257 "
            pdb=" CB  VAL A 257 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.44    2.66   -0.22 2.00e-01 2.50e+01 1.17e+00
  chirality pdb=" CA  TYR A 252 "
            pdb=" N   TYR A 252 "
            pdb=" C   TYR A 252 "
            pdb=" CB  TYR A 252 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.69   -0.18 2.00e-01 2.50e+01 8.01e-01
  chirality pdb=" CA  ILE A 321 "
            pdb=" N   ILE A 321 "
            pdb=" C   ILE A 321 "
            pdb=" CB  ILE A 321 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.43    2.59   -0.15 2.00e-01 2.50e+01 5.98e-01
  ... (remaining 744 not shown)

  Planarity restraints: 778
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  LYS A 241 "    0.019 2.00e-02 2.50e+03   3.70e-02 1.37e+01
        pdb=" C   LYS A 241 "   -0.064 2.00e-02 2.50e+03
        pdb=" O   LYS A 241 "    0.024 2.00e-02 2.50e+03
        pdb=" N   GLU A 242 "    0.022 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  THR A 325 "   -0.013 2.00e-02 2.50e+03   2.69e-02 7.24e+00
        pdb=" C   THR A 325 "    0.047 2.00e-02 2.50e+03
        pdb=" O   THR A 325 "   -0.017 2.00e-02 2.50e+03
        pdb=" N   ARG A 326 "   -0.016 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  CYS A 255 "    0.009 2.00e-02 2.50e+03   1.76e-02 3.09e+00
        pdb=" C   CYS A 255 "   -0.030 2.00e-02 2.50e+03
        pdb=" O   CYS A 255 "    0.012 2.00e-02 2.50e+03
        pdb=" N   GLU A 256 "    0.010 2.00e-02 2.50e+03
  ... (remaining 775 not shown)

  Histogram of nonbonded interaction distances:
        2.20 -     2.74: 442
        2.74 -     3.28: 4946
        3.28 -     3.82: 7814
        3.82 -     4.36: 8954
        4.36 -     4.90: 14785
  Nonbonded interactions: 36941
  Sorted by model distance:
  nonbonded pdb=" OH  TYR A 139 "
            pdb=" OD2 ASP A 646 "
     model   vdw
     2.201 3.040
  nonbonded pdb=" O   PHE A 434 "
            pdb=" OG1 THR A 438 "
     model   vdw
     2.242 3.040
  nonbonded pdb=" O   PRO A 253 "
            pdb=" OG1 THR A 254 "
     model   vdw
     2.313 3.040
  nonbonded pdb=" OD2 ASP A 172 "
            pdb=" OG  SER A 177 "
     model   vdw
     2.341 3.040
  nonbonded pdb=" OD2 ASP A 135 "
            pdb=" N   LEU A 659 "
     model   vdw
     2.347 3.120
  ... (remaining 36936 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 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:             2.900
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.000
  Construct map_model_manager:             0.010
  Extract box with map and model:          0.080
  Check model and map are aligned:         0.010
  Set scattering table:                    0.010
  Process input model:                     6.200
  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:1.240
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   10.480
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7186
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      :  0.004   0.043   4687  Z= 0.235
  Angle     :  0.774   9.234   6391  Z= 0.457
  Chirality :  0.043   0.216    747
  Planarity :  0.004   0.037    778
  Dihedral  : 16.875  86.054   1602
  Min Nonbonded Distance : 2.201

Molprobity Statistics.
  All-atom Clashscore : 15.12
  Ramachandran Plot:
    Outliers :  0.54 %
    Allowed  :  7.89 %
    Favored  : 91.58 %
  Rotamer:
    Outliers :  0.41 %
    Allowed  : 23.30 %
    Favored  : 76.29 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z 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:  0.00 (0.38), residues: 558
  helix:  0.95 (0.27), residues: 377
  sheet:  None (None), residues: 0
  loop : -2.06 (0.50), residues: 181

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.001   ARG A 647 
 TYR   0.011   0.001   TYR A 264 
 PHE   0.016   0.001   PHE A 665 
 TRP   0.021   0.001   TRP A 681 
 HIS   0.007   0.001   HIS A 247 

Details of bonding type rmsd
  covalent geometry    : bond        0.00408 ( 4687)
  covalent geometry    : angle       0.77412 ( 6391)
  hydrogen bonds       : bond        0.11784 (  274)
  hydrogen bonds       : angle       5.48031 (  807)

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

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

  1116 Ramachandran restraints generated.
    558 Oldfield, 0 Emsley, 558 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1116 Ramachandran restraints generated.
    558 Oldfield, 0 Emsley, 558 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  51 residues out of total 515 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 2
    poor density    : 49
  time to evaluate  : 0.155 
Fit side-chains
REVERT: A  125 ASP cc_start: 0.6767 (t0) cc_final: 0.6282 (t0)
REVERT: A  264 TYR cc_start: 0.4170 (OUTLIER) cc_final: 0.2941 (p90)
REVERT: A  502 MET cc_start: 0.8049 (tpp) cc_final: 0.7256 (tmm)
  outliers start: 2
  outliers final: 0
  residues processed: 51
  average time/residue: 0.0610
  time to fit residues: 4.2588
Evaluate side-chains
  47 residues out of total 515 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 46
  time to evaluate  : 0.197 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  264 TYR
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 57
   random chunks:
   chunk 54 optimal weight:    0.9990
   chunk 24 optimal weight:    2.9990
   chunk 48 optimal weight:    0.9980
   chunk 56 optimal weight:    0.6980
   chunk 26 optimal weight:    3.9990
   chunk 2 optimal weight:    0.7980
   chunk 16 optimal weight:    0.0570
   chunk 32 optimal weight:    1.9990
   chunk 31 optimal weight:    0.0980
   chunk 25 optimal weight:    0.3980
   chunk 50 optimal weight:    0.5980
   overall best weight:    0.3698

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

Flipped N/Q/H residues before XYZ refinement:
** A 261 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 568 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 643 HIS

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3979 r_free = 0.3979 target = 0.183659 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 77)----------------|
| r_work = 0.3742 r_free = 0.3742 target = 0.159045 restraints weight = 5065.634|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 34)----------------|
| r_work = 0.3751 r_free = 0.3751 target = 0.159927 restraints weight = 4122.762|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 31)----------------|
| r_work = 0.3759 r_free = 0.3759 target = 0.160675 restraints weight = 3627.111|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 25)----------------|
| r_work = 0.3760 r_free = 0.3760 target = 0.160802 restraints weight = 3276.925|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 37)----------------|
| r_work = 0.3767 r_free = 0.3767 target = 0.161497 restraints weight = 3184.387|
|-----------------------------------------------------------------------------|
r_work (final): 0.3928
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7182
moved from start:          0.0971

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.031   4687  Z= 0.130
  Angle     :  0.604   6.821   6391  Z= 0.312
  Chirality :  0.039   0.145    747
  Planarity :  0.004   0.037    778
  Dihedral  :  4.956  43.420    608
  Min Nonbonded Distance : 2.482

Molprobity Statistics.
  All-atom Clashscore : 9.05
  Ramachandran Plot:
    Outliers :  0.36 %
    Allowed  :  7.71 %
    Favored  : 91.94 %
  Rotamer:
    Outliers :  3.09 %
    Allowed  : 21.44 %
    Favored  : 75.46 %
  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:  0.30 (0.38), residues: 558
  helix:  1.21 (0.27), residues: 380
  sheet:  None (None), residues: 0
  loop : -2.06 (0.51), residues: 178

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.001   ARG A 647 
 TYR   0.012   0.001   TYR A 638 
 PHE   0.011   0.001   PHE A 665 
 TRP   0.016   0.001   TRP A 681 
 HIS   0.004   0.001   HIS A 138 

Details of bonding type rmsd
  covalent geometry    : bond        0.00284 ( 4687)
  covalent geometry    : angle       0.60367 ( 6391)
  hydrogen bonds       : bond        0.03655 (  274)
  hydrogen bonds       : angle       4.50611 (  807)

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

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

  1116 Ramachandran restraints generated.
    558 Oldfield, 0 Emsley, 558 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1116 Ramachandran restraints generated.
    558 Oldfield, 0 Emsley, 558 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  63 residues out of total 515 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 48
  time to evaluate  : 0.170 
Fit side-chains
REVERT: A  125 ASP cc_start: 0.6590 (t0) cc_final: 0.6103 (t0)
REVERT: A  169 ASP cc_start: 0.7096 (m-30) cc_final: 0.6879 (t70)
REVERT: A  264 TYR cc_start: 0.4171 (OUTLIER) cc_final: 0.3081 (p90)
REVERT: A  502 MET cc_start: 0.8054 (tpp) cc_final: 0.7165 (tmm)
  outliers start: 15
  outliers final: 5
  residues processed: 60
  average time/residue: 0.0521
  time to fit residues: 4.5428
Evaluate side-chains
  49 residues out of total 515 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 43
  time to evaluate  : 0.172 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  124 HIS
Chi-restraints excluded: chain A residue  264 TYR
Chi-restraints excluded: chain A residue  327 MET
Chi-restraints excluded: chain A residue  514 VAL
Chi-restraints excluded: chain A residue  606 GLU
Chi-restraints excluded: chain A residue  703 VAL
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 57
   random chunks:
   chunk 42 optimal weight:    1.9990
   chunk 19 optimal weight:    0.3980
   chunk 37 optimal weight:    0.9990
   chunk 23 optimal weight:    0.5980
   chunk 11 optimal weight:    0.5980
   chunk 49 optimal weight:    0.6980
   chunk 0 optimal weight:    1.9990
   chunk 48 optimal weight:    0.9990
   chunk 30 optimal weight:    0.7980
   chunk 25 optimal weight:    3.9990
   chunk 40 optimal weight:    0.6980
   overall best weight:    0.5980

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

Flipped N/Q/H residues before XYZ refinement:
A 185 ASN
** A 568 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 596 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3959 r_free = 0.3959 target = 0.180696 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 87)----------------|
| r_work = 0.3702 r_free = 0.3702 target = 0.153572 restraints weight = 5031.068|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 45)----------------|
| r_work = 0.3717 r_free = 0.3717 target = 0.154967 restraints weight = 4000.665|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 28)----------------|
| r_work = 0.3725 r_free = 0.3725 target = 0.155737 restraints weight = 3413.426|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 36)----------------|
| r_work = 0.3735 r_free = 0.3735 target = 0.156665 restraints weight = 3088.820|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 16)----------------|
| r_work = 0.3735 r_free = 0.3735 target = 0.156666 restraints weight = 2875.693|
|-----------------------------------------------------------------------------|
r_work (final): 0.3868
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7301
moved from start:          0.1506

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.036   4687  Z= 0.149
  Angle     :  0.602   6.306   6391  Z= 0.310
  Chirality :  0.041   0.140    747
  Planarity :  0.004   0.032    778
  Dihedral  :  4.990  46.841    608
  Min Nonbonded Distance : 2.473

Molprobity Statistics.
  All-atom Clashscore : 7.73
  Ramachandran Plot:
    Outliers :  0.18 %
    Allowed  :  8.42 %
    Favored  : 91.40 %
  Rotamer:
    Outliers :  3.30 %
    Allowed  : 21.65 %
    Favored  : 75.05 %
  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:  0.31 (0.37), residues: 558
  helix:  1.20 (0.27), residues: 382
  sheet:  None (None), residues: 0
  loop : -2.05 (0.50), residues: 176

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.001   ARG A 647 
 TYR   0.011   0.001   TYR A 139 
 PHE   0.011   0.001   PHE A 665 
 TRP   0.016   0.001   TRP A 681 
 HIS   0.003   0.001   HIS A 386 

Details of bonding type rmsd
  covalent geometry    : bond        0.00341 ( 4687)
  covalent geometry    : angle       0.60211 ( 6391)
  hydrogen bonds       : bond        0.03565 (  274)
  hydrogen bonds       : angle       4.40069 (  807)

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

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

  1116 Ramachandran restraints generated.
    558 Oldfield, 0 Emsley, 558 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1116 Ramachandran restraints generated.
    558 Oldfield, 0 Emsley, 558 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  64 residues out of total 515 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 48
  time to evaluate  : 0.155 
Fit side-chains
REVERT: A  125 ASP cc_start: 0.6494 (t0) cc_final: 0.6010 (t0)
REVERT: A  174 ASP cc_start: 0.6386 (t0) cc_final: 0.6163 (m-30)
REVERT: A  185 ASN cc_start: 0.8191 (t0) cc_final: 0.7884 (t0)
REVERT: A  192 LEU cc_start: 0.8571 (OUTLIER) cc_final: 0.8295 (mt)
REVERT: A  264 TYR cc_start: 0.4658 (OUTLIER) cc_final: 0.3478 (p90)
REVERT: A  446 MET cc_start: 0.6208 (tpt) cc_final: 0.5994 (tpt)
  outliers start: 16
  outliers final: 10
  residues processed: 60
  average time/residue: 0.0447
  time to fit residues: 4.0054
Evaluate side-chains
  58 residues out of total 515 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 46
  time to evaluate  : 0.116 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  124 HIS
Chi-restraints excluded: chain A residue  192 LEU
Chi-restraints excluded: chain A residue  226 VAL
Chi-restraints excluded: chain A residue  264 TYR
Chi-restraints excluded: chain A residue  359 MET
Chi-restraints excluded: chain A residue  428 THR
Chi-restraints excluded: chain A residue  464 SER
Chi-restraints excluded: chain A residue  504 THR
Chi-restraints excluded: chain A residue  514 VAL
Chi-restraints excluded: chain A residue  606 GLU
Chi-restraints excluded: chain A residue  652 PHE
Chi-restraints excluded: chain A residue  672 LEU
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 57
   random chunks:
   chunk 42 optimal weight:    1.9990
   chunk 29 optimal weight:    0.6980
   chunk 18 optimal weight:    0.3980
   chunk 8 optimal weight:    0.0050
   chunk 6 optimal weight:    0.5980
   chunk 36 optimal weight:    2.9990
   chunk 11 optimal weight:    0.6980
   chunk 16 optimal weight:    0.6980
   chunk 49 optimal weight:    0.5980
   chunk 17 optimal weight:    0.0980
   chunk 20 optimal weight:    0.0020
   overall best weight:    0.2202

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

Flipped N/Q/H residues before XYZ refinement:
** A 196 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 568 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 596 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3974 r_free = 0.3974 target = 0.183873 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 69)----------------|
| r_work = 0.3762 r_free = 0.3762 target = 0.161785 restraints weight = 5001.511|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 37)----------------|
| r_work = 0.3749 r_free = 0.3749 target = 0.160460 restraints weight = 4568.759|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 31)----------------|
| r_work = 0.3752 r_free = 0.3752 target = 0.160667 restraints weight = 4126.453|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 29)----------------|
| r_work = 0.3752 r_free = 0.3752 target = 0.160722 restraints weight = 3817.041|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 27)----------------|
| r_work = 0.3753 r_free = 0.3753 target = 0.160780 restraints weight = 3739.815|
|-----------------------------------------------------------------------------|
r_work (final): 0.3934
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7194
moved from start:          0.1784

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.035   4687  Z= 0.109
  Angle     :  0.554   6.593   6391  Z= 0.282
  Chirality :  0.038   0.128    747
  Planarity :  0.004   0.029    778
  Dihedral  :  4.797  47.628    608
  Min Nonbonded Distance : 2.481

Molprobity Statistics.
  All-atom Clashscore : 7.29
  Ramachandran Plot:
    Outliers :  0.36 %
    Allowed  :  8.24 %
    Favored  : 91.40 %
  Rotamer:
    Outliers :  2.68 %
    Allowed  : 22.47 %
    Favored  : 74.85 %
  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:  0.69 (0.38), residues: 558
  helix:  1.49 (0.27), residues: 383
  sheet:  None (None), residues: 0
  loop : -1.93 (0.51), residues: 175

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG A 647 
 TYR   0.009   0.001   TYR A 638 
 PHE   0.009   0.001   PHE A 665 
 TRP   0.013   0.001   TRP A 473 
 HIS   0.003   0.001   HIS A 386 

Details of bonding type rmsd
  covalent geometry    : bond        0.00230 ( 4687)
  covalent geometry    : angle       0.55354 ( 6391)
  hydrogen bonds       : bond        0.03098 (  274)
  hydrogen bonds       : angle       4.22070 (  807)

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

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

  1116 Ramachandran restraints generated.
    558 Oldfield, 0 Emsley, 558 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1116 Ramachandran restraints generated.
    558 Oldfield, 0 Emsley, 558 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  62 residues out of total 515 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 49
  time to evaluate  : 0.212 
Fit side-chains
REVERT: A  125 ASP cc_start: 0.6212 (t0) cc_final: 0.5757 (t0)
REVERT: A  174 ASP cc_start: 0.6205 (t0) cc_final: 0.5995 (m-30)
REVERT: A  264 TYR cc_start: 0.4219 (OUTLIER) cc_final: 0.3268 (p90)
  outliers start: 13
  outliers final: 7
  residues processed: 59
  average time/residue: 0.0441
  time to fit residues: 3.9713
Evaluate side-chains
  55 residues out of total 515 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 47
  time to evaluate  : 0.163 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  124 HIS
Chi-restraints excluded: chain A residue  264 TYR
Chi-restraints excluded: chain A residue  352 VAL
Chi-restraints excluded: chain A residue  359 MET
Chi-restraints excluded: chain A residue  431 LEU
Chi-restraints excluded: chain A residue  514 VAL
Chi-restraints excluded: chain A residue  606 GLU
Chi-restraints excluded: chain A residue  672 LEU
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 57
   random chunks:
   chunk 41 optimal weight:    0.0980
   chunk 39 optimal weight:    0.9990
   chunk 34 optimal weight:    0.5980
   chunk 31 optimal weight:    2.9990
   chunk 27 optimal weight:    4.9990
   chunk 46 optimal weight:    0.5980
   chunk 36 optimal weight:    0.7980
   chunk 48 optimal weight:    0.9980
   chunk 11 optimal weight:    0.4980
   chunk 45 optimal weight:    0.9990
   chunk 14 optimal weight:    0.4980
   overall best weight:    0.4580

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

Flipped N/Q/H residues before XYZ refinement:
** A 196 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 568 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 596 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3947 r_free = 0.3947 target = 0.180601 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 76)----------------|
| r_work = 0.3705 r_free = 0.3705 target = 0.155652 restraints weight = 5046.026|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 40)----------------|
| r_work = 0.3715 r_free = 0.3715 target = 0.156564 restraints weight = 4181.576|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 26)----------------|
| r_work = 0.3718 r_free = 0.3718 target = 0.156949 restraints weight = 3603.749|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 26)----------------|
| r_work = 0.3720 r_free = 0.3720 target = 0.157056 restraints weight = 3378.807|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 32)----------------|
| r_work = 0.3727 r_free = 0.3727 target = 0.157785 restraints weight = 3320.218|
|-----------------------------------------------------------------------------|
r_work (final): 0.3720
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7267
moved from start:          0.2032

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.036   4687  Z= 0.128
  Angle     :  0.577   7.155   6391  Z= 0.293
  Chirality :  0.039   0.140    747
  Planarity :  0.004   0.029    778
  Dihedral  :  4.874  50.578    608
  Min Nonbonded Distance : 2.499

Molprobity Statistics.
  All-atom Clashscore : 8.39
  Ramachandran Plot:
    Outliers :  0.36 %
    Allowed  :  7.89 %
    Favored  : 91.76 %
  Rotamer:
    Outliers :  2.68 %
    Allowed  : 22.68 %
    Favored  : 74.64 %
  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:  0.62 (0.37), residues: 558
  helix:  1.45 (0.27), residues: 383
  sheet:  None (None), residues: 0
  loop : -2.02 (0.50), residues: 175

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG A 647 
 TYR   0.010   0.001   TYR A 139 
 PHE   0.009   0.001   PHE A 665 
 TRP   0.042   0.002   TRP A 395 
 HIS   0.004   0.001   HIS A 386 

Details of bonding type rmsd
  covalent geometry    : bond        0.00289 ( 4687)
  covalent geometry    : angle       0.57672 ( 6391)
  hydrogen bonds       : bond        0.03266 (  274)
  hydrogen bonds       : angle       4.20105 (  807)

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

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

  1116 Ramachandran restraints generated.
    558 Oldfield, 0 Emsley, 558 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1116 Ramachandran restraints generated.
    558 Oldfield, 0 Emsley, 558 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  59 residues out of total 515 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 46
  time to evaluate  : 0.120 
Fit side-chains
REVERT: A  125 ASP cc_start: 0.6237 (t0) cc_final: 0.5778 (t0)
REVERT: A  185 ASN cc_start: 0.8097 (t0) cc_final: 0.7677 (t0)
REVERT: A  264 TYR cc_start: 0.4723 (OUTLIER) cc_final: 0.3642 (p90)
REVERT: A  502 MET cc_start: 0.8111 (tpp) cc_final: 0.7236 (tmm)
  outliers start: 13
  outliers final: 8
  residues processed: 56
  average time/residue: 0.0462
  time to fit residues: 3.8764
Evaluate side-chains
  53 residues out of total 515 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 44
  time to evaluate  : 0.168 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  124 HIS
Chi-restraints excluded: chain A residue  264 TYR
Chi-restraints excluded: chain A residue  352 VAL
Chi-restraints excluded: chain A residue  359 MET
Chi-restraints excluded: chain A residue  464 SER
Chi-restraints excluded: chain A residue  514 VAL
Chi-restraints excluded: chain A residue  606 GLU
Chi-restraints excluded: chain A residue  627 THR
Chi-restraints excluded: chain A residue  672 LEU
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 57
   random chunks:
   chunk 30 optimal weight:    0.7980
   chunk 42 optimal weight:    0.9980
   chunk 9 optimal weight:    0.0980
   chunk 56 optimal weight:    2.9990
   chunk 18 optimal weight:    0.6980
   chunk 48 optimal weight:    0.8980
   chunk 5 optimal weight:    0.6980
   chunk 51 optimal weight:    0.6980
   chunk 28 optimal weight:    1.9990
   chunk 8 optimal weight:    0.0970
   chunk 55 optimal weight:    0.9980
   overall best weight:    0.4578

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

Flipped N/Q/H residues before XYZ refinement:
** A 196 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 568 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 596 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3951 r_free = 0.3951 target = 0.180256 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 79)----------------|
| r_work = 0.3694 r_free = 0.3694 target = 0.153354 restraints weight = 5142.655|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 48)----------------|
| r_work = 0.3712 r_free = 0.3712 target = 0.154953 restraints weight = 3963.658|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 33)----------------|
| r_work = 0.3720 r_free = 0.3720 target = 0.155789 restraints weight = 3329.898|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 44)----------------|
| r_work = 0.3729 r_free = 0.3729 target = 0.156677 restraints weight = 2993.854|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 36)----------------|
| r_work = 0.3733 r_free = 0.3733 target = 0.157088 restraints weight = 2783.890|
|-----------------------------------------------------------------------------|
r_work (final): 0.3718
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7230
moved from start:          0.2290

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.034   4687  Z= 0.127
  Angle     :  0.571   6.943   6391  Z= 0.290
  Chirality :  0.039   0.131    747
  Planarity :  0.004   0.029    778
  Dihedral  :  4.839  50.584    608
  Min Nonbonded Distance : 2.508

Molprobity Statistics.
  All-atom Clashscore : 8.50
  Ramachandran Plot:
    Outliers :  0.36 %
    Allowed  :  9.14 %
    Favored  : 90.50 %
  Rotamer:
    Outliers :  3.51 %
    Allowed  : 23.09 %
    Favored  : 73.40 %
  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:  0.61 (0.37), residues: 558
  helix:  1.46 (0.27), residues: 383
  sheet:  None (None), residues: 0
  loop : -2.05 (0.50), residues: 175

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG A 647 
 TYR   0.009   0.001   TYR A 139 
 PHE   0.009   0.001   PHE A 665 
 TRP   0.023   0.001   TRP A 395 
 HIS   0.003   0.001   HIS A 386 

Details of bonding type rmsd
  covalent geometry    : bond        0.00283 ( 4687)
  covalent geometry    : angle       0.57058 ( 6391)
  hydrogen bonds       : bond        0.03188 (  274)
  hydrogen bonds       : angle       4.16898 (  807)

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

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

  1116 Ramachandran restraints generated.
    558 Oldfield, 0 Emsley, 558 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1116 Ramachandran restraints generated.
    558 Oldfield, 0 Emsley, 558 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  63 residues out of total 515 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 46
  time to evaluate  : 0.127 
Fit side-chains
REVERT: A  125 ASP cc_start: 0.6375 (t0) cc_final: 0.5887 (t0)
REVERT: A  185 ASN cc_start: 0.8177 (t0) cc_final: 0.7690 (t0)
REVERT: A  264 TYR cc_start: 0.4467 (OUTLIER) cc_final: 0.3550 (p90)
REVERT: A  408 TRP cc_start: 0.9257 (m-90) cc_final: 0.8977 (m-90)
REVERT: A  652 PHE cc_start: 0.8383 (OUTLIER) cc_final: 0.8116 (t80)
  outliers start: 17
  outliers final: 11
  residues processed: 59
  average time/residue: 0.0399
  time to fit residues: 3.5335
Evaluate side-chains
  58 residues out of total 515 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 45
  time to evaluate  : 0.096 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  124 HIS
Chi-restraints excluded: chain A residue  264 TYR
Chi-restraints excluded: chain A residue  327 MET
Chi-restraints excluded: chain A residue  352 VAL
Chi-restraints excluded: chain A residue  359 MET
Chi-restraints excluded: chain A residue  431 LEU
Chi-restraints excluded: chain A residue  464 SER
Chi-restraints excluded: chain A residue  504 THR
Chi-restraints excluded: chain A residue  514 VAL
Chi-restraints excluded: chain A residue  606 GLU
Chi-restraints excluded: chain A residue  627 THR
Chi-restraints excluded: chain A residue  652 PHE
Chi-restraints excluded: chain A residue  672 LEU
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 57
   random chunks:
   chunk 21 optimal weight:    0.9980
   chunk 32 optimal weight:    4.9990
   chunk 39 optimal weight:    2.9990
   chunk 42 optimal weight:    0.9980
   chunk 41 optimal weight:    0.5980
   chunk 13 optimal weight:    0.7980
   chunk 27 optimal weight:    1.9990
   chunk 14 optimal weight:    0.7980
   chunk 10 optimal weight:    0.0970
   chunk 46 optimal weight:    1.9990
   chunk 12 optimal weight:    0.6980
   overall best weight:    0.5978

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

Flipped N/Q/H residues before XYZ refinement:
** A 196 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 568 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 596 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3930 r_free = 0.3930 target = 0.177705 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 88)----------------|
| r_work = 0.3679 r_free = 0.3679 target = 0.151405 restraints weight = 5142.205|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 32)----------------|
| r_work = 0.3691 r_free = 0.3691 target = 0.152514 restraints weight = 4050.965|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 41)----------------|
| r_work = 0.3701 r_free = 0.3701 target = 0.153524 restraints weight = 3479.117|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 42)----------------|
| r_work = 0.3709 r_free = 0.3709 target = 0.154321 restraints weight = 3089.270|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 22)----------------|
| r_work = 0.3709 r_free = 0.3709 target = 0.154321 restraints weight = 2849.977|
|-----------------------------------------------------------------------------|
r_work (final): 0.3676
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7308
moved from start:          0.2500

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.034   4687  Z= 0.146
  Angle     :  0.598   8.275   6391  Z= 0.303
  Chirality :  0.040   0.131    747
  Planarity :  0.004   0.029    778
  Dihedral  :  4.942  53.814    608
  Min Nonbonded Distance : 2.518

Molprobity Statistics.
  All-atom Clashscore : 9.60
  Ramachandran Plot:
    Outliers :  0.36 %
    Allowed  :  8.96 %
    Favored  : 90.68 %
  Rotamer:
    Outliers :  3.71 %
    Allowed  : 23.09 %
    Favored  : 73.20 %
  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:  0.50 (0.37), residues: 558
  helix:  1.37 (0.26), residues: 383
  sheet:  None (None), residues: 0
  loop : -2.06 (0.49), residues: 175

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.001   ARG A 647 
 TYR   0.012   0.001   TYR A 252 
 PHE   0.010   0.001   PHE A 665 
 TRP   0.018   0.001   TRP A 395 
 HIS   0.004   0.001   HIS A 145 

Details of bonding type rmsd
  covalent geometry    : bond        0.00335 ( 4687)
  covalent geometry    : angle       0.59842 ( 6391)
  hydrogen bonds       : bond        0.03392 (  274)
  hydrogen bonds       : angle       4.20336 (  807)

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

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

  1116 Ramachandran restraints generated.
    558 Oldfield, 0 Emsley, 558 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1116 Ramachandran restraints generated.
    558 Oldfield, 0 Emsley, 558 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  65 residues out of total 515 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 47
  time to evaluate  : 0.174 
Fit side-chains
REVERT: A  125 ASP cc_start: 0.6419 (t0) cc_final: 0.5942 (t0)
REVERT: A  185 ASN cc_start: 0.8151 (t0) cc_final: 0.7651 (t0)
REVERT: A  264 TYR cc_start: 0.4923 (OUTLIER) cc_final: 0.3786 (p90)
REVERT: A  408 TRP cc_start: 0.9287 (m-90) cc_final: 0.9050 (m-90)
REVERT: A  502 MET cc_start: 0.8097 (tpp) cc_final: 0.7238 (tmm)
REVERT: A  652 PHE cc_start: 0.8473 (OUTLIER) cc_final: 0.8182 (t80)
  outliers start: 18
  outliers final: 14
  residues processed: 60
  average time/residue: 0.0458
  time to fit residues: 4.1260
Evaluate side-chains
  64 residues out of total 515 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 48
  time to evaluate  : 0.170 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  124 HIS
Chi-restraints excluded: chain A residue  160 VAL
Chi-restraints excluded: chain A residue  201 VAL
Chi-restraints excluded: chain A residue  264 TYR
Chi-restraints excluded: chain A residue  327 MET
Chi-restraints excluded: chain A residue  352 VAL
Chi-restraints excluded: chain A residue  359 MET
Chi-restraints excluded: chain A residue  464 SER
Chi-restraints excluded: chain A residue  504 THR
Chi-restraints excluded: chain A residue  511 ILE
Chi-restraints excluded: chain A residue  514 VAL
Chi-restraints excluded: chain A residue  579 ILE
Chi-restraints excluded: chain A residue  606 GLU
Chi-restraints excluded: chain A residue  627 THR
Chi-restraints excluded: chain A residue  652 PHE
Chi-restraints excluded: chain A residue  672 LEU
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 57
   random chunks:
   chunk 5 optimal weight:    0.8980
   chunk 43 optimal weight:    0.9980
   chunk 47 optimal weight:    1.9990
   chunk 8 optimal weight:    0.6980
   chunk 49 optimal weight:    0.4980
   chunk 10 optimal weight:    0.5980
   chunk 7 optimal weight:    0.9990
   chunk 41 optimal weight:    0.6980
   chunk 35 optimal weight:    0.6980
   chunk 9 optimal weight:    0.9990
   chunk 6 optimal weight:    0.5980
   overall best weight:    0.6180

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

Flipped N/Q/H residues before XYZ refinement:
** A 196 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 568 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 596 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3991 r_free = 0.3991 target = 0.180387 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 50)----------------|
| r_work = 0.3708 r_free = 0.3708 target = 0.151286 restraints weight = 5112.804|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 39)----------------|
| r_work = 0.3735 r_free = 0.3735 target = 0.153941 restraints weight = 3287.549|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 34)----------------|
| r_work = 0.3753 r_free = 0.3753 target = 0.155803 restraints weight = 2461.771|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 28)----------------|
| r_work = 0.3762 r_free = 0.3762 target = 0.156743 restraints weight = 2047.481|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 37)----------------|
| r_work = 0.3770 r_free = 0.3770 target = 0.157513 restraints weight = 1836.704|
|-----------------------------------------------------------------------------|
r_work (final): 0.3764
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7089
moved from start:          0.2769

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.035   4687  Z= 0.145
  Angle     :  0.597   9.040   6391  Z= 0.301
  Chirality :  0.040   0.131    747
  Planarity :  0.004   0.029    778
  Dihedral  :  4.940  52.491    608
  Min Nonbonded Distance : 2.527

Molprobity Statistics.
  All-atom Clashscore : 8.61
  Ramachandran Plot:
    Outliers :  0.36 %
    Allowed  :  9.14 %
    Favored  : 90.50 %
  Rotamer:
    Outliers :  3.51 %
    Allowed  : 24.12 %
    Favored  : 72.37 %
  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:  0.45 (0.37), residues: 558
  helix:  1.42 (0.26), residues: 378
  sheet:  None (None), residues: 0
  loop : -2.22 (0.48), residues: 180

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.001   ARG A 647 
 TYR   0.012   0.001   TYR A 252 
 PHE   0.010   0.001   PHE A 665 
 TRP   0.020   0.001   TRP A 395 
 HIS   0.003   0.001   HIS A 145 

Details of bonding type rmsd
  covalent geometry    : bond        0.00333 ( 4687)
  covalent geometry    : angle       0.59652 ( 6391)
  hydrogen bonds       : bond        0.03364 (  274)
  hydrogen bonds       : angle       4.22705 (  807)

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

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

  1116 Ramachandran restraints generated.
    558 Oldfield, 0 Emsley, 558 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1116 Ramachandran restraints generated.
    558 Oldfield, 0 Emsley, 558 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  65 residues out of total 515 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 48
  time to evaluate  : 0.160 
Fit side-chains
REVERT: A  169 ASP cc_start: 0.6356 (t70) cc_final: 0.6135 (t70)
REVERT: A  185 ASN cc_start: 0.8282 (t0) cc_final: 0.7655 (t0)
REVERT: A  264 TYR cc_start: 0.4573 (OUTLIER) cc_final: 0.3637 (p90)
REVERT: A  408 TRP cc_start: 0.9247 (m-90) cc_final: 0.8823 (m-90)
REVERT: A  652 PHE cc_start: 0.8598 (OUTLIER) cc_final: 0.8185 (t80)
  outliers start: 17
  outliers final: 14
  residues processed: 60
  average time/residue: 0.0457
  time to fit residues: 4.0465
Evaluate side-chains
  63 residues out of total 515 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 47
  time to evaluate  : 0.165 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  124 HIS
Chi-restraints excluded: chain A residue  129 LEU
Chi-restraints excluded: chain A residue  160 VAL
Chi-restraints excluded: chain A residue  201 VAL
Chi-restraints excluded: chain A residue  264 TYR
Chi-restraints excluded: chain A residue  327 MET
Chi-restraints excluded: chain A residue  352 VAL
Chi-restraints excluded: chain A residue  431 LEU
Chi-restraints excluded: chain A residue  464 SER
Chi-restraints excluded: chain A residue  504 THR
Chi-restraints excluded: chain A residue  514 VAL
Chi-restraints excluded: chain A residue  579 ILE
Chi-restraints excluded: chain A residue  606 GLU
Chi-restraints excluded: chain A residue  627 THR
Chi-restraints excluded: chain A residue  652 PHE
Chi-restraints excluded: chain A residue  672 LEU
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 57
   random chunks:
   chunk 13 optimal weight:    2.9990
   chunk 56 optimal weight:    0.9990
   chunk 39 optimal weight:    0.7980
   chunk 36 optimal weight:    1.9990
   chunk 28 optimal weight:    0.7980
   chunk 29 optimal weight:    0.5980
   chunk 41 optimal weight:    0.5980
   chunk 18 optimal weight:    0.8980
   chunk 31 optimal weight:    0.7980
   chunk 5 optimal weight:    0.7980
   chunk 43 optimal weight:    0.9990
   overall best weight:    0.7180

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

Flipped N/Q/H residues before XYZ refinement:
** A 196 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 568 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 596 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3958 r_free = 0.3958 target = 0.176955 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 61)----------------|
| r_work = 0.3672 r_free = 0.3672 target = 0.148144 restraints weight = 5034.762|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 38)----------------|
| r_work = 0.3700 r_free = 0.3700 target = 0.150872 restraints weight = 3261.939|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 34)----------------|
| r_work = 0.3717 r_free = 0.3717 target = 0.152501 restraints weight = 2485.232|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 32)----------------|
| r_work = 0.3727 r_free = 0.3727 target = 0.153602 restraints weight = 2086.026|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 32)----------------|
| r_work = 0.3735 r_free = 0.3735 target = 0.154359 restraints weight = 1856.630|
|-----------------------------------------------------------------------------|
r_work (final): 0.3742
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7155
moved from start:          0.2924

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.033   4687  Z= 0.160
  Angle     :  0.610   7.556   6391  Z= 0.310
  Chirality :  0.041   0.129    747
  Planarity :  0.004   0.029    778
  Dihedral  :  5.065  55.912    608
  Min Nonbonded Distance : 2.534

Molprobity Statistics.
  All-atom Clashscore : 9.72
  Ramachandran Plot:
    Outliers :  0.36 %
    Allowed  :  8.96 %
    Favored  : 90.68 %
  Rotamer:
    Outliers :  3.09 %
    Allowed  : 24.12 %
    Favored  : 72.78 %
  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:  0.41 (0.37), residues: 558
  helix:  1.36 (0.26), residues: 378
  sheet:  None (None), residues: 0
  loop : -2.17 (0.48), residues: 180

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.001   ARG A 689 
 TYR   0.014   0.001   TYR A 252 
 PHE   0.010   0.001   PHE A 665 
 TRP   0.027   0.002   TRP A 395 
 HIS   0.004   0.001   HIS A 145 

Details of bonding type rmsd
  covalent geometry    : bond        0.00374 ( 4687)
  covalent geometry    : angle       0.60976 ( 6391)
  hydrogen bonds       : bond        0.03524 (  274)
  hydrogen bonds       : angle       4.27885 (  807)

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

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

  1116 Ramachandran restraints generated.
    558 Oldfield, 0 Emsley, 558 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1116 Ramachandran restraints generated.
    558 Oldfield, 0 Emsley, 558 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  75 residues out of total 515 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 60
  time to evaluate  : 0.140 
Fit side-chains
REVERT: A  185 ASN cc_start: 0.8340 (t0) cc_final: 0.8138 (t0)
REVERT: A  264 TYR cc_start: 0.4922 (OUTLIER) cc_final: 0.3693 (p90)
REVERT: A  408 TRP cc_start: 0.9280 (m-90) cc_final: 0.8870 (m-90)
REVERT: A  502 MET cc_start: 0.7946 (tpp) cc_final: 0.7050 (tmm)
REVERT: A  652 PHE cc_start: 0.8632 (OUTLIER) cc_final: 0.8160 (t80)
  outliers start: 15
  outliers final: 12
  residues processed: 71
  average time/residue: 0.0429
  time to fit residues: 4.5247
Evaluate side-chains
  70 residues out of total 515 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 56
  time to evaluate  : 0.153 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  124 HIS
Chi-restraints excluded: chain A residue  129 LEU
Chi-restraints excluded: chain A residue  160 VAL
Chi-restraints excluded: chain A residue  201 VAL
Chi-restraints excluded: chain A residue  264 TYR
Chi-restraints excluded: chain A residue  327 MET
Chi-restraints excluded: chain A residue  464 SER
Chi-restraints excluded: chain A residue  504 THR
Chi-restraints excluded: chain A residue  511 ILE
Chi-restraints excluded: chain A residue  514 VAL
Chi-restraints excluded: chain A residue  606 GLU
Chi-restraints excluded: chain A residue  627 THR
Chi-restraints excluded: chain A residue  652 PHE
Chi-restraints excluded: chain A residue  672 LEU
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 57
   random chunks:
   chunk 54 optimal weight:    0.9980
   chunk 47 optimal weight:    0.5980
   chunk 13 optimal weight:    2.9990
   chunk 53 optimal weight:    0.2980
   chunk 4 optimal weight:    0.7980
   chunk 0 optimal weight:    1.9990
   chunk 17 optimal weight:    0.5980
   chunk 1 optimal weight:    1.9990
   chunk 35 optimal weight:    0.3980
   chunk 39 optimal weight:    0.6980
   chunk 16 optimal weight:    0.4980
   overall best weight:    0.4780

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

Flipped N/Q/H residues before XYZ refinement:
** A 196 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 568 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 = 0.3986 r_free = 0.3986 target = 0.179861 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 64)----------------|
| r_work = 0.3706 r_free = 0.3706 target = 0.150853 restraints weight = 4994.479|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 33)----------------|
| r_work = 0.3732 r_free = 0.3732 target = 0.153501 restraints weight = 3257.812|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 42)----------------|
| r_work = 0.3751 r_free = 0.3751 target = 0.155467 restraints weight = 2476.447|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 30)----------------|
| r_work = 0.3760 r_free = 0.3760 target = 0.156377 restraints weight = 2078.630|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 27)----------------|
| r_work = 0.3765 r_free = 0.3765 target = 0.156894 restraints weight = 1875.807|
|-----------------------------------------------------------------------------|
r_work (final): 0.3833
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7120
moved from start:          0.3062

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.035   4687  Z= 0.136
  Angle     :  0.610   8.466   6391  Z= 0.301
  Chirality :  0.040   0.127    747
  Planarity :  0.004   0.029    778
  Dihedral  :  4.960  55.341    608
  Min Nonbonded Distance : 2.542

Molprobity Statistics.
  All-atom Clashscore : 10.05
  Ramachandran Plot:
    Outliers :  0.36 %
    Allowed  :  9.14 %
    Favored  : 90.50 %
  Rotamer:
    Outliers :  2.89 %
    Allowed  : 25.77 %
    Favored  : 71.34 %
  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:  0.59 (0.37), residues: 558
  helix:  1.53 (0.27), residues: 378
  sheet:  None (None), residues: 0
  loop : -2.18 (0.48), residues: 180

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG A 647 
 TYR   0.015   0.001   TYR A 654 
 PHE   0.010   0.001   PHE A 665 
 TRP   0.025   0.001   TRP A 395 
 HIS   0.003   0.001   HIS A 145 

Details of bonding type rmsd
  covalent geometry    : bond        0.00309 ( 4687)
  covalent geometry    : angle       0.61031 ( 6391)
  hydrogen bonds       : bond        0.03357 (  274)
  hydrogen bonds       : angle       4.20832 (  807)

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

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

  1116 Ramachandran restraints generated.
    558 Oldfield, 0 Emsley, 558 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1116 Ramachandran restraints generated.
    558 Oldfield, 0 Emsley, 558 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  64 residues out of total 515 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 50
  time to evaluate  : 0.160 
Fit side-chains
REVERT: A  264 TYR cc_start: 0.4612 (OUTLIER) cc_final: 0.3531 (p90)
REVERT: A  408 TRP cc_start: 0.9240 (m-90) cc_final: 0.8833 (m-90)
REVERT: A  502 MET cc_start: 0.8011 (tpp) cc_final: 0.7062 (tmm)
REVERT: A  652 PHE cc_start: 0.8534 (OUTLIER) cc_final: 0.8101 (t80)
  outliers start: 14
  outliers final: 11
  residues processed: 60
  average time/residue: 0.0442
  time to fit residues: 3.9827
Evaluate side-chains
  62 residues out of total 515 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 49
  time to evaluate  : 0.135 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  124 HIS
Chi-restraints excluded: chain A residue  129 LEU
Chi-restraints excluded: chain A residue  160 VAL
Chi-restraints excluded: chain A residue  201 VAL
Chi-restraints excluded: chain A residue  264 TYR
Chi-restraints excluded: chain A residue  327 MET
Chi-restraints excluded: chain A residue  431 LEU
Chi-restraints excluded: chain A residue  464 SER
Chi-restraints excluded: chain A residue  514 VAL
Chi-restraints excluded: chain A residue  606 GLU
Chi-restraints excluded: chain A residue  627 THR
Chi-restraints excluded: chain A residue  652 PHE
Chi-restraints excluded: chain A residue  672 LEU
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 57
   random chunks:
   chunk 28 optimal weight:    0.8980
   chunk 11 optimal weight:    0.9980
   chunk 2 optimal weight:    0.7980
   chunk 47 optimal weight:    0.5980
   chunk 45 optimal weight:    0.0270
   chunk 31 optimal weight:    0.5980
   chunk 36 optimal weight:    1.9990
   chunk 15 optimal weight:    3.9990
   chunk 5 optimal weight:    0.3980
   chunk 56 optimal weight:    0.8980
   chunk 17 optimal weight:    0.7980
   overall best weight:    0.4838

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

Flipped N/Q/H residues before XYZ refinement:
A 185 ASN
** A 196 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 568 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4053 r_free = 0.4053 target = 0.186903 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 48)----------------|
| r_work = 0.3770 r_free = 0.3770 target = 0.157191 restraints weight = 5008.323|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 36)----------------|
| r_work = 0.3799 r_free = 0.3799 target = 0.160301 restraints weight = 3045.752|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 31)----------------|
| r_work = 0.3819 r_free = 0.3819 target = 0.162473 restraints weight = 2220.710|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 32)----------------|
| r_work = 0.3830 r_free = 0.3830 target = 0.163569 restraints weight = 1806.915|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 29)----------------|
| r_work = 0.3839 r_free = 0.3839 target = 0.164524 restraints weight = 1603.330|
|-----------------------------------------------------------------------------|
r_work (final): 0.3787
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7047
moved from start:          0.3123

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.035   4687  Z= 0.135
  Angle     :  0.616  10.518   6391  Z= 0.305
  Chirality :  0.040   0.165    747
  Planarity :  0.004   0.028    778
  Dihedral  :  5.019  57.604    608
  Min Nonbonded Distance : 2.550

Molprobity Statistics.
  All-atom Clashscore : 9.83
  Ramachandran Plot:
    Outliers :  0.36 %
    Allowed  :  8.78 %
    Favored  : 90.86 %
  Rotamer:
    Outliers :  3.09 %
    Allowed  : 25.57 %
    Favored  : 71.34 %
  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:  0.62 (0.37), residues: 558
  helix:  1.45 (0.27), residues: 380
  sheet:  None (None), residues: 0
  loop : -1.95 (0.50), residues: 178

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG A 647 
 TYR   0.011   0.001   TYR A 654 
 PHE   0.010   0.001   PHE A 665 
 TRP   0.025   0.001   TRP A 395 
 HIS   0.003   0.001   HIS A 145 

Details of bonding type rmsd
  covalent geometry    : bond        0.00308 ( 4687)
  covalent geometry    : angle       0.61580 ( 6391)
  hydrogen bonds       : bond        0.03324 (  274)
  hydrogen bonds       : angle       4.17166 (  807)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 954.74 seconds
wall clock time: 17 minutes 8.74 seconds (1028.74 seconds total)