Starting phenix.real_space_refine
on Thu Sep 10 23:55:51 2026 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/8iew_35374/09_2026/8iew_35374.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/8iew_35374/09_2026/8iew_35374.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.1
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    model {
      file = "/net/cci-nas-00/data/ceres_data/8iew_35374/09_2026/8iew_35374.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/8iew_35374/09_2026/8iew_35374.cif"
    real_map_files = "/net/cci-nas-00/data/ceres_data/8iew_35374/09_2026/8iew_35374.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/8iew_35374/09_2026/8iew_35374.map"
  }
  resolution = 3.1
  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=   0.001 sd=   0.018
Set stop_for_unknowns flag
  Set to: True
Assert model is a single copy model
Assert all atoms have isotropic ADPs
  Anisotropic ADP refinement not supported. Converting 546 atoms to isotropic.
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      65      5.49       5
     S       8      5.16       5
     C    3141      2.51       5
     N     969      2.21       5
     O    1138      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 2 residue(s): 0.00s

  Monomer Library directory:
    "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.2.1-6174/lib/python3.11/site-packages/chem_data/mon_lib"
  Total number of atoms: 5321
  Number of models: 1
  Model: ""
    Number of chains: 4
    Chain: "A"
      Number of atoms: 3966
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 498, 3966
          Classifications: {'peptide': 498}
          Link IDs: {'PTRANS': 37, 'TRANS': 460}
          Chain breaks: 2
    Chain: "B"
      Number of atoms: 753
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 36, 753
          Classifications: {'RNA': 36}
          Modifications used: {'rna2p_pur': 1, 'rna2p_pyr': 8, 'rna3p_pur': 11, 'rna3p_pyr': 16}
          Link IDs: {'rna2p': 9, 'rna3p': 26}
    Chain: "C"
      Number of atoms: 463
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 22, 463
          Classifications: {'DNA': 22}
          Link IDs: {'rna3p': 21}
    Chain: "D"
      Number of atoms: 139
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 7, 139
          Classifications: {'DNA': 7}
          Link IDs: {'rna3p': 6}
  Time building chain proxies: 1.41, per 1000 atoms: 0.26
  Number of scatterers: 5321
  At special positions: 0
  Unit cell: (85.8, 90.42, 97.02, 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       8     16.00
     P      65     15.00
     O    1138      8.00
     N     969      7.00
     C    3141      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: 0.53
  Conformation dependent library (CDL) restraints added in 151.9 milliseconds
  

  984 Ramachandran restraints generated.
    492 Oldfield, 0 Emsley, 492 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  932

  Finding SS restraints...
    Secondary structure from input PDB file:
      18 helices and 2 sheets defined
      49.4% alpha, 8.2% beta
      19 base pairs and 40 stacking pairs defined.
    Time for finding SS restraints: 0.60
  Creating SS restraints...
    Processing helix  chain 'A' and resid 71 through 74
    Processing helix  chain 'A' and resid 75 through 90
      removed outlier: 3.571A  pdb=" N   GLY A  90 " --> pdb=" O   GLU A  86 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 92 through 99
      removed outlier: 4.091A  pdb=" N   GLU A  97 " --> pdb=" O   ALA A  93 " (cutoff:3.500A)
      removed outlier: 4.034A  pdb=" N   ALA A  98 " --> pdb=" O   ALA A  94 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 105 through 116
    Processing helix  chain 'A' and resid 125 through 141
      removed outlier: 6.579A  pdb=" N   LEU A 131 " --> pdb=" O   GLN A 127 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 142 through 168
      removed outlier: 3.680A  pdb=" N   LYS A 146 " --> pdb=" O   GLY A 142 " (cutoff:3.500A)
      removed outlier: 3.664A  pdb=" N   VAL A 147 " --> pdb=" O   VAL A 143 " (cutoff:3.500A)
      removed outlier: 3.658A  pdb=" N   VAL A 163 " --> pdb=" O   THR A 159 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 201 through 205
    Processing helix  chain 'A' and resid 234 through 238
      removed outlier: 3.878A  pdb=" N   ILE A 238 " --> pdb=" O   ARG A 235 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 266 through 270
    Processing helix  chain 'A' and resid 281 through 291
      removed outlier: 3.910A  pdb=" N   LEU A 285 " --> pdb=" O   ASP A 281 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 309 through 319
      removed outlier: 3.559A  pdb=" N   ARG A 319 " --> pdb=" O   ALA A 315 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 327 through 334
    Processing helix  chain 'A' and resid 367 through 380
      removed outlier: 4.158A  pdb=" N   LYS A 371 " --> pdb=" O   GLY A 367 " (cutoff:3.500A)
      removed outlier: 3.950A  pdb=" N   GLU A 372 " --> pdb=" O   LYS A 368 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 422 through 450
      removed outlier: 3.525A  pdb=" N   GLU A 441 " --> pdb=" O   ASP A 437 " (cutoff:3.500A)
      removed outlier: 3.738A  pdb=" N   GLN A 442 " --> pdb=" O   ALA A 438 " (cutoff:3.500A)
      removed outlier: 3.778A  pdb=" N   ALA A 445 " --> pdb=" O   GLU A 441 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 452 through 464
      removed outlier: 3.842A  pdb=" N   GLU A 458 " --> pdb=" O   GLU A 454 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 543 through 558
    Processing helix  chain 'A' and resid 558 through 586
      removed outlier: 3.851A  pdb=" N   LYS A 568 " --> pdb=" O   LEU A 564 " (cutoff:3.500A)
      removed outlier: 3.784A  pdb=" N   THR A 569 " --> pdb=" O   SER A 565 " (cutoff:3.500A)
      removed outlier: 3.551A  pdb=" N   LYS A 584 " --> pdb=" O   VAL A 580 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 627 through 642
      removed outlier: 3.906A  pdb=" N   LEU A 638 " --> pdb=" O   ALA A 634 " (cutoff:3.500A)
      removed outlier: 4.805A  pdb=" N   ALA A 639 " --> pdb=" O   PHE A 635 " (cutoff:3.500A)
      removed outlier: 4.260A  pdb=" N   LEU A 640 " --> pdb=" O   SER A 636 " (cutoff:3.500A)
    Processing sheet with id=AA1, first strand: chain 'A' and resid 198 through 199
      removed outlier: 3.914A  pdb=" N   ILE A 347 " --> pdb=" O   ASP A 342 " (cutoff:3.500A)
      removed outlier: 4.096A  pdb=" N   ASN A  64 " --> pdb=" O   ASP A 308 " (cutoff:3.500A)
      removed outlier: 6.661A  pdb=" N   VAL A 306 " --> pdb=" O   LEU A  66 " (cutoff:3.500A)
      removed outlier: 4.864A  pdb=" N   GLN A  68 " --> pdb=" O   TRP A 304 " (cutoff:3.500A)
      removed outlier: 6.884A  pdb=" N   TRP A 304 " --> pdb=" O   GLN A  68 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'A' and resid 417 through 420
      removed outlier: 4.117A  pdb=" N   GLY A 417 " --> pdb=" O   PHE A 401 " (cutoff:3.500A)

    185 hydrogen bonds defined for protein.
    525 hydrogen bond angles defined for protein.
    Restraints generated for nucleic acids:
      48 hydrogen bonds
      88 hydrogen bond angles
      0 basepair planarities
      19 basepair parallelities
      40 stacking parallelities
  Total time for adding SS restraints: 0.89

  Time building geometry restraints manager: 0.67 seconds

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

  Histogram of bond lengths:
        1.21 -     1.33: 1351
        1.33 -     1.45: 1300
        1.45 -     1.57: 2780
        1.57 -     1.69: 127
        1.69 -     1.81: 11
  Bond restraints: 5569
  Sorted by residual:
  bond pdb=" C   TYR A  87 "
       pdb=" N   VAL A  88 "
    ideal  model  delta    sigma   weight residual
    1.334  1.291  0.043 1.26e-02 6.30e+03 1.16e+01
  bond pdb=" C3'  DT D  -2 "
       pdb=" O3'  DT D  -2 "
    ideal  model  delta    sigma   weight residual
    1.435  1.401  0.034 1.30e-02 5.92e+03 6.98e+00
  bond pdb=" C3'  DA D  -4 "
       pdb=" O3'  DA D  -4 "
    ideal  model  delta    sigma   weight residual
    1.435  1.401  0.034 1.30e-02 5.92e+03 6.70e+00
  bond pdb=" C3'  DG C   0 "
       pdb=" O3'  DG C   0 "
    ideal  model  delta    sigma   weight residual
    1.435  1.402  0.033 1.30e-02 5.92e+03 6.55e+00
  bond pdb=" C3'  DA C  -1 "
       pdb=" O3'  DA C  -1 "
    ideal  model  delta    sigma   weight residual
    1.435  1.405  0.030 1.30e-02 5.92e+03 5.40e+00
  ... (remaining 5564 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     2.35: 7669
        2.35 -     4.71: 148
        4.71 -     7.06: 13
        7.06 -     9.41: 2
        9.41 -    11.76: 1
  Bond angle restraints: 7833
  Sorted by residual:
  angle pdb=" O   GLU A  86 "
        pdb=" C   GLU A  86 "
        pdb=" N   TYR A  87 "
      ideal   model   delta    sigma   weight residual
     122.12  117.45    4.67 1.06e+00 8.90e-01 1.94e+01
  angle pdb=" N3   DT D  -2 "
        pdb=" C4   DT D  -2 "
        pdb=" O4   DT D  -2 "
      ideal   model   delta    sigma   weight residual
     119.90  122.42   -2.52 6.00e-01 2.78e+00 1.77e+01
  angle pdb=" C   TYR A  87 "
        pdb=" N   VAL A  88 "
        pdb=" CA  VAL A  88 "
      ideal   model   delta    sigma   weight residual
     120.42  114.47    5.95 1.42e+00 4.96e-01 1.76e+01
  angle pdb=" N3   DT C  -7 "
        pdb=" C4   DT C  -7 "
        pdb=" O4   DT C  -7 "
      ideal   model   delta    sigma   weight residual
     119.90  122.39   -2.49 6.00e-01 2.78e+00 1.73e+01
  angle pdb=" N3   DT C   4 "
        pdb=" C4   DT C   4 "
        pdb=" O4   DT C   4 "
      ideal   model   delta    sigma   weight residual
     119.90  122.36   -2.46 6.00e-01 2.78e+00 1.68e+01
  ... (remaining 7828 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    35.44: 3067
       35.44 -    70.88: 304
       70.88 -   106.32: 20
      106.32 -   141.76: 0
      141.76 -   177.20: 2
  Dihedral angle restraints: 3393
    sinusoidal: 1953
      harmonic: 1440
  Sorted by residual:
  dihedral pdb=" O4'   C B   8 "
           pdb=" C1'   C B   8 "
           pdb=" N1    C B   8 "
           pdb=" C2    C B   8 "
      ideal   model   delta sinusoidal    sigma   weight residual
     232.00   54.80  177.20     1      1.70e+01 3.46e-03 6.64e+01
  dihedral pdb=" O4'   U B  -9 "
           pdb=" C1'   U B  -9 "
           pdb=" N1    U B  -9 "
           pdb=" C2    U B  -9 "
      ideal   model   delta sinusoidal    sigma   weight residual
     232.00   65.11  166.89     1      1.70e+01 3.46e-03 6.56e+01
  dihedral pdb=" CA  PRO A 295 "
           pdb=" C   PRO A 295 "
           pdb=" N   ILE A 296 "
           pdb=" CA  ILE A 296 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  161.42   18.58     0      5.00e+00 4.00e-02 1.38e+01
  ... (remaining 3390 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.080: 780
       0.080 -    0.159: 116
       0.159 -    0.239: 1
       0.239 -    0.319: 0
       0.319 -    0.398: 1
  Chirality restraints: 898
  Sorted by residual:
  chirality pdb=" P     C B   8 "
            pdb=" OP1   C B   8 "
            pdb=" OP2   C B   8 "
            pdb=" O5'   C B   8 "
    both_signs  ideal   model   delta    sigma   weight residual
      True       2.41   -2.81   -0.40 2.00e-01 2.50e+01 3.97e+00
  chirality pdb=" C3'  DA D  -4 "
            pdb=" C4'  DA D  -4 "
            pdb=" O3'  DA D  -4 "
            pdb=" C2'  DA D  -4 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.73   -2.54   -0.19 2.00e-01 2.50e+01 8.87e-01
  chirality pdb=" CA  ILE A 419 "
            pdb=" N   ILE A 419 "
            pdb=" C   ILE A 419 "
            pdb=" CB  ILE A 419 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.43    2.58   -0.15 2.00e-01 2.50e+01 5.54e-01
  ... (remaining 895 not shown)

  Planarity restraints: 775
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   GLN A 242 "    0.060 5.00e-02 4.00e+02   9.03e-02 1.31e+01
        pdb=" N   PRO A 243 "   -0.156 5.00e-02 4.00e+02
        pdb=" CA  PRO A 243 "    0.048 5.00e-02 4.00e+02
        pdb=" CD  PRO A 243 "    0.049 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C1'   C B  -5 "   -0.027 2.00e-02 2.50e+03   1.49e-02 4.98e+00
        pdb=" N1    C B  -5 "    0.034 2.00e-02 2.50e+03
        pdb=" C2    C B  -5 "    0.005 2.00e-02 2.50e+03
        pdb=" O2    C B  -5 "   -0.001 2.00e-02 2.50e+03
        pdb=" N3    C B  -5 "   -0.003 2.00e-02 2.50e+03
        pdb=" C4    C B  -5 "    0.002 2.00e-02 2.50e+03
        pdb=" N4    C B  -5 "   -0.009 2.00e-02 2.50e+03
        pdb=" C5    C B  -5 "   -0.003 2.00e-02 2.50e+03
        pdb=" C6    C B  -5 "    0.002 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   TRP A  75 "   -0.031 5.00e-02 4.00e+02   4.64e-02 3.45e+00
        pdb=" N   PRO A  76 "    0.080 5.00e-02 4.00e+02
        pdb=" CA  PRO A  76 "   -0.024 5.00e-02 4.00e+02
        pdb=" CD  PRO A  76 "   -0.026 5.00e-02 4.00e+02
  ... (remaining 772 not shown)

  Histogram of nonbonded interaction distances:
        2.16 -     2.71: 266
        2.71 -     3.25: 4939
        3.25 -     3.80: 9255
        3.80 -     4.35: 11477
        4.35 -     4.90: 17293
  Nonbonded interactions: 43230
  Sorted by model distance:
  nonbonded pdb=" OD1 ASP A 185 "
            pdb=" N   GLY A 186 "
     model   vdw
     2.156 3.120
  nonbonded pdb=" O2'   U B -10 "
            pdb=" O2    U B  -9 "
     model   vdw
     2.211 3.040
  nonbonded pdb=" ND2 ASN A  56 "
            pdb=" O   HIS A 360 "
     model   vdw
     2.226 3.120
  nonbonded pdb=" OG1 THR A 394 "
            pdb=" N   ASN A 395 "
     model   vdw
     2.232 3.120
  nonbonded pdb=" OH  TYR A 209 "
            pdb=" O   HIS A 214 "
     model   vdw
     2.246 3.040
  ... (remaining 43225 not shown)

  NOTE: a complete listing of the restraints can be obtained by requesting
        output of .geo file.
Find NCS groups from input model
Time spend for trying shortcut: 0.00
========== WARNING! ============

  No NCS relation were found !!!

================================

Found NCS groups:
  found none.
Set up NCS constraints
  No NCS constraints will be used in refinement.
Set refine NCS operators
Adjust number of macro_cycles
  Number of macro_cycles: 10
Reset NCS operators
Extract rigid body selections
Check and reset occupancies
  Occupancies: min=1.00 max=1.00 mean=1.00
Load rotamer database and sin/cos tables
Set ADP refinement strategy
  ADPs will be refined as 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:             3.890
  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:          0.120
  Check model and map are aligned:         0.010
  Set scattering table:                    0.010
  Process input model:                     7.220
  Find NCS groups from input model:        0.020
  Set up NCS constraints:                  0.000
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.010
  Load rotamer database and sin/cos tables:0.980
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   12.270
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7603
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      :  0.005   0.043   5569  Z= 0.376
  Angle     :  0.748  11.764   7833  Z= 0.541
  Chirality :  0.052   0.398    898
  Planarity :  0.006   0.090    775
  Dihedral  : 22.785 177.199   2461
  Min Nonbonded Distance : 2.156

Molprobity Statistics.
  All-atom Clashscore : 9.70
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  9.35 %
    Favored  : 90.65 %
  Rotamer:
    Outliers :  0.47 %
    Allowed  : 30.02 %
    Favored  : 69.50 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -0.52 (0.38), residues: 492
  helix:  0.38 (0.34), residues: 224
  sheet: -0.54 (0.76), residues: 54
  loop : -1.00 (0.45), residues: 214

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.001   ARG A 111 
 TYR   0.016   0.002   TYR A 317 
 PHE   0.006   0.001   PHE A 102 
 TRP   0.015   0.002   TRP A 552 
 HIS   0.005   0.001   HIS A 214 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00518 /  0.38 ( 5569)
  covalent geometry    : angle       0.74780 /  0.54 ( 7833)
  hydrogen bonds       : bond        0.16323 / 10.59 (  233)
  hydrogen bonds       : angle       5.55970 /  3.90 (  613)

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

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

  984 Ramachandran restraints generated.
    492 Oldfield, 0 Emsley, 492 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  984 Ramachandran restraints generated.
    492 Oldfield, 0 Emsley, 492 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  98 residues out of total 423 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 2
    poor density    : 96
  time to evaluate  : 0.104 
Fit side-chains
   revert: symmetry clash
  outliers start: 2
  outliers final: 0
  residues processed: 98
  average time/residue: 0.1076
  time to fit residues: 12.8379
Evaluate side-chains
  95 residues out of total 423 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 95
  time to evaluate  : 0.208 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 54
   random chunks:
   chunk 24 optimal weight:    0.9980
   chunk 48 optimal weight:    1.9990
   chunk 26 optimal weight:    0.6980
   chunk 2 optimal weight:    0.5980
   chunk 16 optimal weight:    0.0980
   chunk 32 optimal weight:    0.7980
   chunk 31 optimal weight:    1.9990
   chunk 25 optimal weight:    0.8980
   chunk 50 optimal weight:    3.9990
   chunk 53 optimal weight:    3.9990
   chunk 19 optimal weight:    0.6980
   overall best weight:    0.5780

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
A 203 GLN
A 395 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3694 r_free = 0.3694 target = 0.134160 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 63)----------------|
| r_work = 0.3379 r_free = 0.3379 target = 0.111372 restraints weight = 7837.178|
|-----------------------------------------------------------------------------|
r_work (start): 0.3372 rms_B_bonded: 1.66
r_work: 0.3273 rms_B_bonded: 2.33 restraints_weight: 0.5000
r_work: 0.3139 rms_B_bonded: 4.04 restraints_weight: 0.2500
r_work (final): 0.3139
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7799
moved from start:          0.0657

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.035   5569  Z= 0.175
  Angle     :  0.617   7.329   7833  Z= 0.341
  Chirality :  0.044   0.214    898
  Planarity :  0.006   0.066    775
  Dihedral  : 23.549 177.411   1447
  Min Nonbonded Distance : 2.554

Molprobity Statistics.
  All-atom Clashscore : 7.82
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  8.54 %
    Favored  : 91.46 %
  Rotamer:
    Outliers :  3.31 %
    Allowed  : 28.61 %
    Favored  : 68.09 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -0.12 (0.38), residues: 492
  helix:  0.95 (0.34), residues: 213
  sheet: -0.32 (0.76), residues: 54
  loop : -0.99 (0.43), residues: 225

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.001   ARG A 345 
 TYR   0.016   0.002   TYR A 432 
 PHE   0.011   0.001   PHE A 137 
 TRP   0.013   0.002   TRP A 318 
 HIS   0.005   0.001   HIS A 214 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00367 /  0.18 ( 5569)
  covalent geometry    : angle       0.61709 /  0.34 ( 7833)
  hydrogen bonds       : bond        0.06724 /  4.75 (  233)
  hydrogen bonds       : angle       4.07798 /  2.87 (  613)

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

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

  984 Ramachandran restraints generated.
    492 Oldfield, 0 Emsley, 492 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  984 Ramachandran restraints generated.
    492 Oldfield, 0 Emsley, 492 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  121 residues out of total 423 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 107
  time to evaluate  : 0.173 
Fit side-chains
   revert: symmetry clash
REVERT: A  195 ASN cc_start: 0.7805 (t0) cc_final: 0.7439 (t0)
REVERT: A  197 SER cc_start: 0.8504 (m) cc_final: 0.8297 (m)
REVERT: A  280 LEU cc_start: 0.7093 (OUTLIER) cc_final: 0.6551 (tp)
REVERT: A  282 GLU cc_start: 0.7558 (tp30) cc_final: 0.7220 (tp30)
REVERT: A  383 HIS cc_start: 0.5685 (OUTLIER) cc_final: 0.5198 (t-90)
REVERT: A  395 ASN cc_start: 0.5456 (OUTLIER) cc_final: 0.4943 (p0)
REVERT: A  588 GLN cc_start: 0.8110 (mp10) cc_final: 0.7767 (mp10)
REVERT: A  647 ILE cc_start: 0.7448 (mt) cc_final: 0.7195 (pt)
  outliers start: 14
  outliers final: 5
  residues processed: 115
  average time/residue: 0.0990
  time to fit residues: 13.8300
Evaluate side-chains
  112 residues out of total 423 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 104
  time to evaluate  : 0.160 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   68 GLN
Chi-restraints excluded: chain A residue  180 THR
Chi-restraints excluded: chain A residue  253 HIS
Chi-restraints excluded: chain A residue  280 LEU
Chi-restraints excluded: chain A residue  347 ILE
Chi-restraints excluded: chain A residue  359 VAL
Chi-restraints excluded: chain A residue  383 HIS
Chi-restraints excluded: chain A residue  395 ASN
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 54
   random chunks:
   chunk 51 optimal weight:    3.9990
   chunk 45 optimal weight:    0.5980
   chunk 12 optimal weight:    1.9990
   chunk 32 optimal weight:    2.9990
   chunk 19 optimal weight:    0.5980
   chunk 47 optimal weight:    1.9990
   chunk 5 optimal weight:    0.9990
   chunk 6 optimal weight:    1.9990
   chunk 27 optimal weight:    0.5980
   chunk 43 optimal weight:    0.7980
   chunk 35 optimal weight:    0.0070
   overall best weight:    0.5198

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
A  78 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3701 r_free = 0.3701 target = 0.134753 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 53)----------------|
| r_work = 0.3386 r_free = 0.3386 target = 0.111916 restraints weight = 7755.027|
|-----------------------------------------------------------------------------|
r_work (start): 0.3379 rms_B_bonded: 1.65
r_work: 0.3280 rms_B_bonded: 2.32 restraints_weight: 0.5000
r_work: 0.3147 rms_B_bonded: 4.01 restraints_weight: 0.2500
r_work (final): 0.3147
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7789
moved from start:          0.0855

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.078   5569  Z= 0.164
  Angle     :  0.593   7.330   7833  Z= 0.329
  Chirality :  0.042   0.210    898
  Planarity :  0.006   0.057    775
  Dihedral  : 23.425 177.601   1447
  Min Nonbonded Distance : 2.548

Molprobity Statistics.
  All-atom Clashscore : 8.12
  Ramachandran Plot:
    Outliers :  0.20 %
    Allowed  :  8.74 %
    Favored  : 91.06 %
  Rotamer:
    Outliers :  4.49 %
    Allowed  : 27.42 %
    Favored  : 68.09 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -0.04 (0.38), residues: 492
  helix:  1.18 (0.35), residues: 212
  sheet: -0.37 (0.71), residues: 55
  loop : -1.11 (0.42), residues: 225

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG A 345 
 TYR   0.016   0.002   TYR A 432 
 PHE   0.007   0.001   PHE A 350 
 TRP   0.013   0.002   TRP A 318 
 HIS   0.008   0.001   HIS A 214 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00352 /  0.16 ( 5569)
  covalent geometry    : angle       0.59271 /  0.33 ( 7833)
  hydrogen bonds       : bond        0.04872 /  3.31 (  233)
  hydrogen bonds       : angle       3.90860 /  2.75 (  613)

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

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

  984 Ramachandran restraints generated.
    492 Oldfield, 0 Emsley, 492 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  984 Ramachandran restraints generated.
    492 Oldfield, 0 Emsley, 492 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  123 residues out of total 423 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 104
  time to evaluate  : 0.174 
Fit side-chains
REVERT: A  195 ASN cc_start: 0.7788 (t0) cc_final: 0.7505 (t0)
REVERT: A  197 SER cc_start: 0.8490 (m) cc_final: 0.8271 (m)
REVERT: A  260 ARG cc_start: 0.8165 (OUTLIER) cc_final: 0.7803 (ttt180)
REVERT: A  280 LEU cc_start: 0.7096 (OUTLIER) cc_final: 0.6683 (tp)
REVERT: A  375 LEU cc_start: 0.7955 (mm) cc_final: 0.7748 (mt)
REVERT: A  383 HIS cc_start: 0.5633 (OUTLIER) cc_final: 0.5193 (t-90)
REVERT: A  582 GLU cc_start: 0.6897 (mp0) cc_final: 0.6254 (mp0)
REVERT: A  588 GLN cc_start: 0.8097 (mp10) cc_final: 0.7767 (mp10)
REVERT: A  647 ILE cc_start: 0.7438 (mt) cc_final: 0.7200 (pt)
  outliers start: 19
  outliers final: 11
  residues processed: 116
  average time/residue: 0.1077
  time to fit residues: 15.1818
Evaluate side-chains
  116 residues out of total 423 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 102
  time to evaluate  : 0.187 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   68 GLN
Chi-restraints excluded: chain A residue   91 LEU
Chi-restraints excluded: chain A residue  118 VAL
Chi-restraints excluded: chain A residue  180 THR
Chi-restraints excluded: chain A residue  246 VAL
Chi-restraints excluded: chain A residue  253 HIS
Chi-restraints excluded: chain A residue  260 ARG
Chi-restraints excluded: chain A residue  280 LEU
Chi-restraints excluded: chain A residue  302 LYS
Chi-restraints excluded: chain A residue  347 ILE
Chi-restraints excluded: chain A residue  354 LEU
Chi-restraints excluded: chain A residue  359 VAL
Chi-restraints excluded: chain A residue  383 HIS
Chi-restraints excluded: chain A residue  638 LEU
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 54
   random chunks:
   chunk 24 optimal weight:    0.6980
   chunk 53 optimal weight:    3.9990
   chunk 52 optimal weight:    7.9990
   chunk 22 optimal weight:    0.0020
   chunk 38 optimal weight:    2.9990
   chunk 31 optimal weight:    0.6980
   chunk 50 optimal weight:    2.9990
   chunk 30 optimal weight:    0.7980
   chunk 45 optimal weight:    0.3980
   chunk 23 optimal weight:    0.9980
   chunk 35 optimal weight:    0.8980
   overall best weight:    0.5188

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
A  56 ASN
** A 395 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 = 0.3704 r_free = 0.3704 target = 0.134926 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 49)----------------|
| r_work = 0.3388 r_free = 0.3388 target = 0.112081 restraints weight = 7809.998|
|-----------------------------------------------------------------------------|
r_work (start): 0.3381 rms_B_bonded: 1.65
r_work: 0.3283 rms_B_bonded: 2.33 restraints_weight: 0.5000
r_work: 0.3150 rms_B_bonded: 4.02 restraints_weight: 0.2500
r_work (final): 0.3150
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7786
moved from start:          0.1002

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.031   5569  Z= 0.158
  Angle     :  0.572   7.226   7833  Z= 0.314
  Chirality :  0.042   0.213    898
  Planarity :  0.006   0.053    775
  Dihedral  : 23.367 178.214   1447
  Min Nonbonded Distance : 2.537

Molprobity Statistics.
  All-atom Clashscore : 7.13
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  8.33 %
    Favored  : 91.67 %
  Rotamer:
    Outliers :  4.73 %
    Allowed  : 27.42 %
    Favored  : 67.85 %
  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 are not related in a simple way.
  whole:  0.09 (0.38), residues: 492
  helix:  1.25 (0.35), residues: 212
  sheet: -0.19 (0.71), residues: 55
  loop : -1.02 (0.42), residues: 225

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG A 581 
 TYR   0.015   0.002   TYR A 432 
 PHE   0.007   0.001   PHE A 350 
 TRP   0.014   0.002   TRP A 318 
 HIS   0.010   0.001   HIS A 214 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00332 /  0.16 ( 5569)
  covalent geometry    : angle       0.57158 /  0.31 ( 7833)
  hydrogen bonds       : bond        0.04502 /  3.05 (  233)
  hydrogen bonds       : angle       3.80411 /  2.68 (  613)

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

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

  984 Ramachandran restraints generated.
    492 Oldfield, 0 Emsley, 492 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  984 Ramachandran restraints generated.
    492 Oldfield, 0 Emsley, 492 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  126 residues out of total 423 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 106
  time to evaluate  : 0.162 
Fit side-chains
REVERT: A  195 ASN cc_start: 0.7762 (t0) cc_final: 0.7441 (t0)
REVERT: A  197 SER cc_start: 0.8464 (m) cc_final: 0.8213 (m)
REVERT: A  260 ARG cc_start: 0.8166 (OUTLIER) cc_final: 0.7794 (ttt180)
REVERT: A  271 ARG cc_start: 0.7825 (ptt-90) cc_final: 0.7553 (ptt-90)
REVERT: A  280 LEU cc_start: 0.7129 (OUTLIER) cc_final: 0.6662 (tp)
REVERT: A  308 ASP cc_start: 0.7875 (t0) cc_final: 0.7556 (t70)
REVERT: A  383 HIS cc_start: 0.5696 (OUTLIER) cc_final: 0.5267 (t-90)
REVERT: A  582 GLU cc_start: 0.6907 (mp0) cc_final: 0.6325 (mp0)
REVERT: A  585 ARG cc_start: 0.7626 (OUTLIER) cc_final: 0.7342 (ttp-110)
REVERT: A  647 ILE cc_start: 0.7444 (mt) cc_final: 0.7224 (pt)
  outliers start: 20
  outliers final: 12
  residues processed: 118
  average time/residue: 0.1101
  time to fit residues: 15.6926
Evaluate side-chains
  122 residues out of total 423 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 106
  time to evaluate  : 0.166 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   68 GLN
Chi-restraints excluded: chain A residue   91 LEU
Chi-restraints excluded: chain A residue  118 VAL
Chi-restraints excluded: chain A residue  144 ILE
Chi-restraints excluded: chain A residue  180 THR
Chi-restraints excluded: chain A residue  246 VAL
Chi-restraints excluded: chain A residue  253 HIS
Chi-restraints excluded: chain A residue  256 THR
Chi-restraints excluded: chain A residue  260 ARG
Chi-restraints excluded: chain A residue  280 LEU
Chi-restraints excluded: chain A residue  302 LYS
Chi-restraints excluded: chain A residue  347 ILE
Chi-restraints excluded: chain A residue  354 LEU
Chi-restraints excluded: chain A residue  359 VAL
Chi-restraints excluded: chain A residue  383 HIS
Chi-restraints excluded: chain A residue  585 ARG
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 54
   random chunks:
   chunk 46 optimal weight:    0.5980
   chunk 30 optimal weight:    0.9980
   chunk 17 optimal weight:    0.7980
   chunk 5 optimal weight:    0.8980
   chunk 4 optimal weight:    0.1980
   chunk 11 optimal weight:   20.0000
   chunk 12 optimal weight:    0.8980
   chunk 53 optimal weight:    3.9990
   chunk 41 optimal weight:    3.9990
   chunk 21 optimal weight:    0.9980
   chunk 13 optimal weight:    0.7980
   overall best weight:    0.6580

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
A  56 ASN
A  78 ASN
** A 395 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3699 r_free = 0.3699 target = 0.134411 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 49)----------------|
| r_work = 0.3379 r_free = 0.3379 target = 0.111477 restraints weight = 7890.047|
|-----------------------------------------------------------------------------|
r_work (start): 0.3372 rms_B_bonded: 1.66
r_work: 0.3272 rms_B_bonded: 2.34 restraints_weight: 0.5000
r_work: 0.3138 rms_B_bonded: 4.05 restraints_weight: 0.2500
r_work (final): 0.3138
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7796
moved from start:          0.1061

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.033   5569  Z= 0.181
  Angle     :  0.595   8.380   7833  Z= 0.322
  Chirality :  0.043   0.216    898
  Planarity :  0.006   0.052    775
  Dihedral  : 23.343 177.883   1447
  Min Nonbonded Distance : 2.542

Molprobity Statistics.
  All-atom Clashscore : 7.23
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  8.94 %
    Favored  : 91.06 %
  Rotamer:
    Outliers :  5.20 %
    Allowed  : 28.13 %
    Favored  : 66.67 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  0.07 (0.38), residues: 492
  helix:  1.22 (0.35), residues: 212
  sheet: -0.15 (0.72), residues: 55
  loop : -1.03 (0.42), residues: 225

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG A 573 
 TYR   0.015   0.002   TYR A 432 
 PHE   0.007   0.001   PHE A 350 
 TRP   0.014   0.002   TRP A 318 
 HIS   0.008   0.001   HIS A 214 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00387 /  0.18 ( 5569)
  covalent geometry    : angle       0.59472 /  0.32 ( 7833)
  hydrogen bonds       : bond        0.04581 /  3.09 (  233)
  hydrogen bonds       : angle       3.80614 /  2.67 (  613)

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

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

  984 Ramachandran restraints generated.
    492 Oldfield, 0 Emsley, 492 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  984 Ramachandran restraints generated.
    492 Oldfield, 0 Emsley, 492 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  130 residues out of total 423 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 22
    poor density    : 108
  time to evaluate  : 0.177 
Fit side-chains
REVERT: A  260 ARG cc_start: 0.8196 (OUTLIER) cc_final: 0.7831 (ttt180)
REVERT: A  271 ARG cc_start: 0.7832 (ptt-90) cc_final: 0.7558 (ptt-90)
REVERT: A  280 LEU cc_start: 0.7147 (OUTLIER) cc_final: 0.6644 (tp)
REVERT: A  308 ASP cc_start: 0.7849 (t0) cc_final: 0.7594 (t70)
REVERT: A  582 GLU cc_start: 0.6941 (mp0) cc_final: 0.6305 (mp0)
REVERT: A  588 GLN cc_start: 0.8070 (mp10) cc_final: 0.7748 (mp10)
REVERT: A  647 ILE cc_start: 0.7439 (mt) cc_final: 0.7238 (pt)
  outliers start: 22
  outliers final: 16
  residues processed: 122
  average time/residue: 0.1068
  time to fit residues: 15.7871
Evaluate side-chains
  123 residues out of total 423 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 105
  time to evaluate  : 0.102 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   68 GLN
Chi-restraints excluded: chain A residue   91 LEU
Chi-restraints excluded: chain A residue  118 VAL
Chi-restraints excluded: chain A residue  144 ILE
Chi-restraints excluded: chain A residue  180 THR
Chi-restraints excluded: chain A residue  222 VAL
Chi-restraints excluded: chain A residue  228 LEU
Chi-restraints excluded: chain A residue  246 VAL
Chi-restraints excluded: chain A residue  253 HIS
Chi-restraints excluded: chain A residue  260 ARG
Chi-restraints excluded: chain A residue  280 LEU
Chi-restraints excluded: chain A residue  302 LYS
Chi-restraints excluded: chain A residue  347 ILE
Chi-restraints excluded: chain A residue  354 LEU
Chi-restraints excluded: chain A residue  359 VAL
Chi-restraints excluded: chain A residue  418 GLN
Chi-restraints excluded: chain A residue  425 LEU
Chi-restraints excluded: chain A residue  638 LEU
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 54
   random chunks:
   chunk 26 optimal weight:    0.9990
   chunk 38 optimal weight:    2.9990
   chunk 29 optimal weight:    0.7980
   chunk 5 optimal weight:    0.9980
   chunk 25 optimal weight:    1.9990
   chunk 36 optimal weight:    0.3980
   chunk 11 optimal weight:    7.9990
   chunk 21 optimal weight:    0.7980
   chunk 28 optimal weight:    0.5980
   chunk 35 optimal weight:    3.9990
   chunk 49 optimal weight:    2.9990
   overall best weight:    0.7180

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
A  56 ASN
A  78 ASN
A  99 ASN
** A 395 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3708 r_free = 0.3708 target = 0.134969 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 51)----------------|
| r_work = 0.3394 r_free = 0.3394 target = 0.112295 restraints weight = 7850.244|
|-----------------------------------------------------------------------------|
r_work (start): 0.3392 rms_B_bonded: 1.60
r_work: 0.3294 rms_B_bonded: 2.27 restraints_weight: 0.5000
r_work: 0.3164 rms_B_bonded: 3.92 restraints_weight: 0.2500
r_work (final): 0.3164
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7797
moved from start:          0.1100

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.035   5569  Z= 0.193
  Angle     :  0.604   7.334   7833  Z= 0.330
  Chirality :  0.043   0.220    898
  Planarity :  0.006   0.051    775
  Dihedral  : 23.341 177.561   1447
  Min Nonbonded Distance : 2.396

Molprobity Statistics.
  All-atom Clashscore : 7.62
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  8.54 %
    Favored  : 91.46 %
  Rotamer:
    Outliers :  6.15 %
    Allowed  : 27.42 %
    Favored  : 66.43 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  0.12 (0.38), residues: 492
  helix:  1.10 (0.35), residues: 218
  sheet: -0.09 (0.73), residues: 55
  loop : -0.89 (0.43), residues: 219

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG A 345 
 TYR   0.016   0.002   TYR A 432 
 PHE   0.007   0.001   PHE A 137 
 TRP   0.014   0.002   TRP A 318 
 HIS   0.012   0.002   HIS A 214 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00414 /  0.19 ( 5569)
  covalent geometry    : angle       0.60407 /  0.33 ( 7833)
  hydrogen bonds       : bond        0.04646 /  3.13 (  233)
  hydrogen bonds       : angle       3.79977 /  2.67 (  613)

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

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

  984 Ramachandran restraints generated.
    492 Oldfield, 0 Emsley, 492 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  984 Ramachandran restraints generated.
    492 Oldfield, 0 Emsley, 492 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  130 residues out of total 423 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 26
    poor density    : 104
  time to evaluate  : 0.162 
Fit side-chains
REVERT: A   95 GLU cc_start: 0.8000 (OUTLIER) cc_final: 0.7317 (pt0)
REVERT: A  260 ARG cc_start: 0.8215 (OUTLIER) cc_final: 0.7846 (ttt180)
REVERT: A  271 ARG cc_start: 0.7801 (ptt-90) cc_final: 0.7539 (ptt-90)
REVERT: A  280 LEU cc_start: 0.7132 (OUTLIER) cc_final: 0.6606 (tp)
REVERT: A  308 ASP cc_start: 0.7831 (t0) cc_final: 0.7602 (t70)
REVERT: A  552 TRP cc_start: 0.7339 (OUTLIER) cc_final: 0.6570 (m100)
REVERT: A  582 GLU cc_start: 0.6923 (mp0) cc_final: 0.6359 (mp0)
REVERT: A  585 ARG cc_start: 0.7634 (OUTLIER) cc_final: 0.7342 (ttp-110)
REVERT: A  588 GLN cc_start: 0.8091 (mp10) cc_final: 0.7766 (mp10)
  outliers start: 26
  outliers final: 15
  residues processed: 122
  average time/residue: 0.1070
  time to fit residues: 15.7410
Evaluate side-chains
  123 residues out of total 423 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 103
  time to evaluate  : 0.161 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   68 GLN
Chi-restraints excluded: chain A residue   91 LEU
Chi-restraints excluded: chain A residue   95 GLU
Chi-restraints excluded: chain A residue  118 VAL
Chi-restraints excluded: chain A residue  144 ILE
Chi-restraints excluded: chain A residue  180 THR
Chi-restraints excluded: chain A residue  222 VAL
Chi-restraints excluded: chain A residue  246 VAL
Chi-restraints excluded: chain A residue  253 HIS
Chi-restraints excluded: chain A residue  256 THR
Chi-restraints excluded: chain A residue  260 ARG
Chi-restraints excluded: chain A residue  280 LEU
Chi-restraints excluded: chain A residue  302 LYS
Chi-restraints excluded: chain A residue  347 ILE
Chi-restraints excluded: chain A residue  354 LEU
Chi-restraints excluded: chain A residue  359 VAL
Chi-restraints excluded: chain A residue  418 GLN
Chi-restraints excluded: chain A residue  425 LEU
Chi-restraints excluded: chain A residue  552 TRP
Chi-restraints excluded: chain A residue  585 ARG
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 54
   random chunks:
   chunk 53 optimal weight:    3.9990
   chunk 9 optimal weight:    1.9990
   chunk 31 optimal weight:    1.9990
   chunk 27 optimal weight:    0.6980
   chunk 35 optimal weight:    4.9990
   chunk 6 optimal weight:    0.5980
   chunk 28 optimal weight:    0.8980
   chunk 17 optimal weight:    0.5980
   chunk 38 optimal weight:    2.9990
   chunk 19 optimal weight:    0.0570
   chunk 30 optimal weight:    0.9980
   overall best weight:    0.5698

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
A  56 ASN
A  78 ASN
** A 395 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3716 r_free = 0.3716 target = 0.135461 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 49)----------------|
| r_work = 0.3401 r_free = 0.3401 target = 0.112837 restraints weight = 7941.945|
|-----------------------------------------------------------------------------|
r_work (start): 0.3397 rms_B_bonded: 1.62
r_work: 0.3301 rms_B_bonded: 2.28 restraints_weight: 0.5000
r_work: 0.3170 rms_B_bonded: 3.94 restraints_weight: 0.2500
r_work (final): 0.3170
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7789
moved from start:          0.1194

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.033   5569  Z= 0.169
  Angle     :  0.587   7.177   7833  Z= 0.321
  Chirality :  0.042   0.220    898
  Planarity :  0.006   0.051    775
  Dihedral  : 23.305 177.572   1447
  Min Nonbonded Distance : 2.478

Molprobity Statistics.
  All-atom Clashscore : 7.23
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  8.54 %
    Favored  : 91.46 %
  Rotamer:
    Outliers :  6.15 %
    Allowed  : 27.42 %
    Favored  : 66.43 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  0.18 (0.38), residues: 492
  helix:  1.17 (0.35), residues: 219
  sheet: -0.10 (0.73), residues: 55
  loop : -0.88 (0.43), residues: 218

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG A 345 
 TYR   0.016   0.002   TYR A 432 
 PHE   0.007   0.001   PHE A 350 
 TRP   0.014   0.002   TRP A 318 
 HIS   0.012   0.001   HIS A 214 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00359 /  0.17 ( 5569)
  covalent geometry    : angle       0.58678 /  0.32 ( 7833)
  hydrogen bonds       : bond        0.04493 /  3.03 (  233)
  hydrogen bonds       : angle       3.75331 /  2.64 (  613)

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

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

  984 Ramachandran restraints generated.
    492 Oldfield, 0 Emsley, 492 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  984 Ramachandran restraints generated.
    492 Oldfield, 0 Emsley, 492 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  132 residues out of total 423 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 26
    poor density    : 106
  time to evaluate  : 0.230 
Fit side-chains
REVERT: A   95 GLU cc_start: 0.7999 (OUTLIER) cc_final: 0.7323 (pt0)
REVERT: A  260 ARG cc_start: 0.8198 (OUTLIER) cc_final: 0.7824 (ttt180)
REVERT: A  271 ARG cc_start: 0.7804 (ptt-90) cc_final: 0.7553 (ptt-90)
REVERT: A  280 LEU cc_start: 0.7108 (OUTLIER) cc_final: 0.6584 (tp)
REVERT: A  308 ASP cc_start: 0.7830 (t0) cc_final: 0.7558 (t70)
REVERT: A  383 HIS cc_start: 0.5609 (OUTLIER) cc_final: 0.5233 (t-90)
REVERT: A  582 GLU cc_start: 0.6929 (mp0) cc_final: 0.6365 (mp0)
REVERT: A  585 ARG cc_start: 0.7621 (OUTLIER) cc_final: 0.7346 (ttp-110)
REVERT: A  588 GLN cc_start: 0.8095 (mp10) cc_final: 0.7752 (mp10)
  outliers start: 26
  outliers final: 17
  residues processed: 123
  average time/residue: 0.1227
  time to fit residues: 17.9893
Evaluate side-chains
  126 residues out of total 423 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 22
    poor density    : 104
  time to evaluate  : 0.183 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   68 GLN
Chi-restraints excluded: chain A residue   91 LEU
Chi-restraints excluded: chain A residue   95 GLU
Chi-restraints excluded: chain A residue  118 VAL
Chi-restraints excluded: chain A residue  144 ILE
Chi-restraints excluded: chain A residue  180 THR
Chi-restraints excluded: chain A residue  222 VAL
Chi-restraints excluded: chain A residue  246 VAL
Chi-restraints excluded: chain A residue  253 HIS
Chi-restraints excluded: chain A residue  256 THR
Chi-restraints excluded: chain A residue  260 ARG
Chi-restraints excluded: chain A residue  280 LEU
Chi-restraints excluded: chain A residue  302 LYS
Chi-restraints excluded: chain A residue  347 ILE
Chi-restraints excluded: chain A residue  354 LEU
Chi-restraints excluded: chain A residue  359 VAL
Chi-restraints excluded: chain A residue  383 HIS
Chi-restraints excluded: chain A residue  386 LEU
Chi-restraints excluded: chain A residue  418 GLN
Chi-restraints excluded: chain A residue  425 LEU
Chi-restraints excluded: chain A residue  585 ARG
Chi-restraints excluded: chain A residue  638 LEU
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 54
   random chunks:
   chunk 39 optimal weight:    0.6980
   chunk 36 optimal weight:    1.9990
   chunk 28 optimal weight:    0.0980
   chunk 29 optimal weight:    0.4980
   chunk 41 optimal weight:    0.8980
   chunk 18 optimal weight:    0.7980
   chunk 31 optimal weight:    0.1980
   chunk 5 optimal weight:    0.9980
   chunk 43 optimal weight:    0.6980
   chunk 0 optimal weight:    0.9990
   chunk 45 optimal weight:    0.9980
   overall best weight:    0.4380

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
A  56 ASN
A  78 ASN
** A 395 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3724 r_free = 0.3724 target = 0.136088 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 54)----------------|
| r_work = 0.3413 r_free = 0.3413 target = 0.113585 restraints weight = 7868.126|
|-----------------------------------------------------------------------------|
r_work (start): 0.3409 rms_B_bonded: 1.62
r_work: 0.3312 rms_B_bonded: 2.29 restraints_weight: 0.5000
r_work: 0.3182 rms_B_bonded: 3.95 restraints_weight: 0.2500
r_work (final): 0.3182
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7777
moved from start:          0.1290

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.033   5569  Z= 0.145
  Angle     :  0.567   7.074   7833  Z= 0.310
  Chirality :  0.041   0.215    898
  Planarity :  0.006   0.050    775
  Dihedral  : 23.261 178.391   1447
  Min Nonbonded Distance : 2.528

Molprobity Statistics.
  All-atom Clashscore : 7.33
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  8.33 %
    Favored  : 91.67 %
  Rotamer:
    Outliers :  5.44 %
    Allowed  : 27.90 %
    Favored  : 66.67 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  0.32 (0.39), residues: 492
  helix:  1.47 (0.35), residues: 213
  sheet: -0.07 (0.73), residues: 55
  loop : -0.94 (0.43), residues: 224

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG A 154 
 TYR   0.015   0.001   TYR A 432 
 PHE   0.007   0.001   PHE A 350 
 TRP   0.015   0.001   TRP A 249 
 HIS   0.011   0.001   HIS A 214 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00302 /  0.14 ( 5569)
  covalent geometry    : angle       0.56708 /  0.31 ( 7833)
  hydrogen bonds       : bond        0.04299 /  2.90 (  233)
  hydrogen bonds       : angle       3.64708 /  2.56 (  613)

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

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

  984 Ramachandran restraints generated.
    492 Oldfield, 0 Emsley, 492 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  984 Ramachandran restraints generated.
    492 Oldfield, 0 Emsley, 492 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  126 residues out of total 423 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 23
    poor density    : 103
  time to evaluate  : 0.209 
Fit side-chains
REVERT: A   95 GLU cc_start: 0.7986 (OUTLIER) cc_final: 0.7284 (pt0)
REVERT: A  260 ARG cc_start: 0.8178 (OUTLIER) cc_final: 0.7801 (ttt180)
REVERT: A  271 ARG cc_start: 0.7807 (ptt-90) cc_final: 0.7574 (ptt-90)
REVERT: A  280 LEU cc_start: 0.7065 (OUTLIER) cc_final: 0.6575 (tp)
REVERT: A  308 ASP cc_start: 0.7782 (t0) cc_final: 0.7542 (t70)
REVERT: A  383 HIS cc_start: 0.5631 (OUTLIER) cc_final: 0.5226 (t-90)
REVERT: A  582 GLU cc_start: 0.6915 (mp0) cc_final: 0.6267 (mp0)
REVERT: A  588 GLN cc_start: 0.8097 (mp10) cc_final: 0.7753 (mp10)
  outliers start: 23
  outliers final: 15
  residues processed: 118
  average time/residue: 0.1181
  time to fit residues: 16.7665
Evaluate side-chains
  123 residues out of total 423 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 104
  time to evaluate  : 0.168 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   68 GLN
Chi-restraints excluded: chain A residue   91 LEU
Chi-restraints excluded: chain A residue   95 GLU
Chi-restraints excluded: chain A residue  118 VAL
Chi-restraints excluded: chain A residue  144 ILE
Chi-restraints excluded: chain A residue  180 THR
Chi-restraints excluded: chain A residue  246 VAL
Chi-restraints excluded: chain A residue  253 HIS
Chi-restraints excluded: chain A residue  256 THR
Chi-restraints excluded: chain A residue  260 ARG
Chi-restraints excluded: chain A residue  280 LEU
Chi-restraints excluded: chain A residue  302 LYS
Chi-restraints excluded: chain A residue  347 ILE
Chi-restraints excluded: chain A residue  354 LEU
Chi-restraints excluded: chain A residue  359 VAL
Chi-restraints excluded: chain A residue  383 HIS
Chi-restraints excluded: chain A residue  386 LEU
Chi-restraints excluded: chain A residue  425 LEU
Chi-restraints excluded: chain A residue  638 LEU
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 54
   random chunks:
   chunk 47 optimal weight:    1.9990
   chunk 7 optimal weight:    0.1980
   chunk 6 optimal weight:    0.3980
   chunk 8 optimal weight:    0.5980
   chunk 40 optimal weight:    1.9990
   chunk 36 optimal weight:    2.9990
   chunk 19 optimal weight:    0.3980
   chunk 49 optimal weight:    3.9990
   chunk 39 optimal weight:    1.9990
   chunk 44 optimal weight:    0.6980
   chunk 37 optimal weight:    0.5980
   overall best weight:    0.4380

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
A  56 ASN
A  78 ASN
A  99 ASN
** A 395 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3727 r_free = 0.3727 target = 0.136333 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 55)----------------|
| r_work = 0.3415 r_free = 0.3415 target = 0.113811 restraints weight = 7843.728|
|-----------------------------------------------------------------------------|
r_work (start): 0.3412 rms_B_bonded: 1.61
r_work: 0.3315 rms_B_bonded: 2.29 restraints_weight: 0.5000
r_work: 0.3184 rms_B_bonded: 3.97 restraints_weight: 0.2500
r_work (final): 0.3184
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7776
moved from start:          0.1385

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.032   5569  Z= 0.146
  Angle     :  0.566   7.162   7833  Z= 0.308
  Chirality :  0.041   0.210    898
  Planarity :  0.006   0.050    775
  Dihedral  : 23.238 178.365   1447
  Min Nonbonded Distance : 2.529

Molprobity Statistics.
  All-atom Clashscore : 7.03
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  8.54 %
    Favored  : 91.46 %
  Rotamer:
    Outliers :  4.73 %
    Allowed  : 29.08 %
    Favored  : 66.19 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  0.37 (0.39), residues: 492
  helix:  1.51 (0.35), residues: 213
  sheet: -0.09 (0.73), residues: 55
  loop : -0.90 (0.43), residues: 224

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.000   ARG A 585 
 TYR   0.015   0.002   TYR A 432 
 PHE   0.007   0.001   PHE A 350 
 TRP   0.015   0.002   TRP A 318 
 HIS   0.010   0.001   HIS A 214 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00305 /  0.15 ( 5569)
  covalent geometry    : angle       0.56587 /  0.31 ( 7833)
  hydrogen bonds       : bond        0.04307 /  2.89 (  233)
  hydrogen bonds       : angle       3.61935 /  2.55 (  613)

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

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

  984 Ramachandran restraints generated.
    492 Oldfield, 0 Emsley, 492 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  984 Ramachandran restraints generated.
    492 Oldfield, 0 Emsley, 492 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  125 residues out of total 423 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 105
  time to evaluate  : 0.173 
Fit side-chains
REVERT: A   95 GLU cc_start: 0.7981 (OUTLIER) cc_final: 0.7284 (pt0)
REVERT: A  260 ARG cc_start: 0.8173 (OUTLIER) cc_final: 0.7803 (ttt180)
REVERT: A  280 LEU cc_start: 0.7050 (OUTLIER) cc_final: 0.6564 (tp)
REVERT: A  308 ASP cc_start: 0.7788 (t0) cc_final: 0.7553 (t70)
REVERT: A  383 HIS cc_start: 0.5619 (OUTLIER) cc_final: 0.5215 (t-90)
REVERT: A  582 GLU cc_start: 0.6937 (mp0) cc_final: 0.6290 (mp0)
  outliers start: 20
  outliers final: 15
  residues processed: 118
  average time/residue: 0.1141
  time to fit residues: 16.1247
Evaluate side-chains
  121 residues out of total 423 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 102
  time to evaluate  : 0.164 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   68 GLN
Chi-restraints excluded: chain A residue   91 LEU
Chi-restraints excluded: chain A residue   95 GLU
Chi-restraints excluded: chain A residue  118 VAL
Chi-restraints excluded: chain A residue  144 ILE
Chi-restraints excluded: chain A residue  180 THR
Chi-restraints excluded: chain A residue  246 VAL
Chi-restraints excluded: chain A residue  253 HIS
Chi-restraints excluded: chain A residue  256 THR
Chi-restraints excluded: chain A residue  260 ARG
Chi-restraints excluded: chain A residue  280 LEU
Chi-restraints excluded: chain A residue  302 LYS
Chi-restraints excluded: chain A residue  347 ILE
Chi-restraints excluded: chain A residue  354 LEU
Chi-restraints excluded: chain A residue  359 VAL
Chi-restraints excluded: chain A residue  383 HIS
Chi-restraints excluded: chain A residue  386 LEU
Chi-restraints excluded: chain A residue  425 LEU
Chi-restraints excluded: chain A residue  638 LEU
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 54
   random chunks:
   chunk 9 optimal weight:    1.9990
   chunk 7 optimal weight:    0.0980
   chunk 25 optimal weight:    1.9990
   chunk 3 optimal weight:    0.7980
   chunk 40 optimal weight:    0.9980
   chunk 30 optimal weight:    1.9990
   chunk 37 optimal weight:    0.9990
   chunk 29 optimal weight:    0.6980
   chunk 18 optimal weight:    0.9990
   chunk 35 optimal weight:    0.2980
   chunk 5 optimal weight:    0.9980
   overall best weight:    0.5780

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
A  56 ASN
** A 395 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 = 0.3722 r_free = 0.3722 target = 0.135966 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 50)----------------|
| r_work = 0.3408 r_free = 0.3408 target = 0.113232 restraints weight = 7921.473|
|-----------------------------------------------------------------------------|
r_work (start): 0.3401 rms_B_bonded: 1.64
r_work: 0.3302 rms_B_bonded: 2.32 restraints_weight: 0.5000
r_work: 0.3170 rms_B_bonded: 4.01 restraints_weight: 0.2500
r_work (final): 0.3170
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7787
moved from start:          0.1395

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.032   5569  Z= 0.167
  Angle     :  0.584   7.300   7833  Z= 0.317
  Chirality :  0.042   0.210    898
  Planarity :  0.006   0.050    775
  Dihedral  : 23.257 178.554   1447
  Min Nonbonded Distance : 2.535

Molprobity Statistics.
  All-atom Clashscore : 7.03
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  8.54 %
    Favored  : 91.46 %
  Rotamer:
    Outliers :  5.20 %
    Allowed  : 28.61 %
    Favored  : 66.19 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  0.35 (0.39), residues: 492
  helix:  1.34 (0.35), residues: 219
  sheet: -0.09 (0.74), residues: 55
  loop : -0.79 (0.43), residues: 218

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG A 251 
 TYR   0.016   0.002   TYR A 432 
 PHE   0.014   0.001   PHE A 352 
 TRP   0.014   0.002   TRP A 249 
 HIS   0.011   0.001   HIS A 214 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00358 /  0.17 ( 5569)
  covalent geometry    : angle       0.58352 /  0.32 ( 7833)
  hydrogen bonds       : bond        0.04425 /  2.95 (  233)
  hydrogen bonds       : angle       3.65767 /  2.58 (  613)

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

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

  984 Ramachandran restraints generated.
    492 Oldfield, 0 Emsley, 492 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  984 Ramachandran restraints generated.
    492 Oldfield, 0 Emsley, 492 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  126 residues out of total 423 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 22
    poor density    : 104
  time to evaluate  : 0.227 
Fit side-chains
REVERT: A   95 GLU cc_start: 0.8001 (OUTLIER) cc_final: 0.7299 (pt0)
REVERT: A  195 ASN cc_start: 0.7744 (t0) cc_final: 0.7543 (t0)
REVERT: A  260 ARG cc_start: 0.8189 (OUTLIER) cc_final: 0.7824 (ttt180)
REVERT: A  276 ARG cc_start: 0.7330 (ttm170) cc_final: 0.6917 (mtt90)
REVERT: A  280 LEU cc_start: 0.7073 (OUTLIER) cc_final: 0.6563 (tp)
REVERT: A  308 ASP cc_start: 0.7821 (t0) cc_final: 0.7556 (t70)
REVERT: A  383 HIS cc_start: 0.5738 (OUTLIER) cc_final: 0.5307 (t-90)
REVERT: A  582 GLU cc_start: 0.6953 (mp0) cc_final: 0.6309 (mp0)
  outliers start: 22
  outliers final: 17
  residues processed: 117
  average time/residue: 0.1183
  time to fit residues: 16.4781
Evaluate side-chains
  124 residues out of total 423 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 103
  time to evaluate  : 0.169 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   68 GLN
Chi-restraints excluded: chain A residue   91 LEU
Chi-restraints excluded: chain A residue   95 GLU
Chi-restraints excluded: chain A residue  118 VAL
Chi-restraints excluded: chain A residue  144 ILE
Chi-restraints excluded: chain A residue  180 THR
Chi-restraints excluded: chain A residue  222 VAL
Chi-restraints excluded: chain A residue  246 VAL
Chi-restraints excluded: chain A residue  253 HIS
Chi-restraints excluded: chain A residue  256 THR
Chi-restraints excluded: chain A residue  260 ARG
Chi-restraints excluded: chain A residue  280 LEU
Chi-restraints excluded: chain A residue  302 LYS
Chi-restraints excluded: chain A residue  347 ILE
Chi-restraints excluded: chain A residue  354 LEU
Chi-restraints excluded: chain A residue  359 VAL
Chi-restraints excluded: chain A residue  383 HIS
Chi-restraints excluded: chain A residue  386 LEU
Chi-restraints excluded: chain A residue  418 GLN
Chi-restraints excluded: chain A residue  425 LEU
Chi-restraints excluded: chain A residue  638 LEU
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 54
   random chunks:
   chunk 42 optimal weight:    0.9990
   chunk 53 optimal weight:    3.9990
   chunk 28 optimal weight:    0.0980
   chunk 12 optimal weight:    0.0270
   chunk 21 optimal weight:    0.8980
   chunk 22 optimal weight:    2.9990
   chunk 46 optimal weight:    0.0470
   chunk 34 optimal weight:    0.6980
   chunk 7 optimal weight:    0.2980
   chunk 52 optimal weight:    7.9990
   chunk 32 optimal weight:    0.8980
   overall best weight:    0.2336

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
A  56 ASN
** A 395 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 = 0.3750 r_free = 0.3750 target = 0.137917 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 51)----------------|
| r_work = 0.3440 r_free = 0.3440 target = 0.115395 restraints weight = 7912.078|
|-----------------------------------------------------------------------------|
r_work (start): 0.3435 rms_B_bonded: 1.63
r_work: 0.3336 rms_B_bonded: 2.33 restraints_weight: 0.5000
r_work: 0.3205 rms_B_bonded: 4.02 restraints_weight: 0.2500
r_work (final): 0.3205
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7748
moved from start:          0.1573

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.032   5569  Z= 0.120
  Angle     :  0.545   6.844   7833  Z= 0.298
  Chirality :  0.040   0.203    898
  Planarity :  0.006   0.049    775
  Dihedral  : 23.153 179.095   1447
  Min Nonbonded Distance : 2.518

Molprobity Statistics.
  All-atom Clashscore : 6.43
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  8.54 %
    Favored  : 91.46 %
  Rotamer:
    Outliers :  4.73 %
    Allowed  : 29.08 %
    Favored  : 66.19 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  0.56 (0.39), residues: 492
  helix:  1.69 (0.36), residues: 216
  sheet: -0.17 (0.70), residues: 60
  loop : -0.81 (0.44), residues: 216

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG A 154 
 TYR   0.016   0.001   TYR A 432 
 PHE   0.010   0.001   PHE A 352 
 TRP   0.016   0.001   TRP A 318 
 HIS   0.008   0.001   HIS A 214 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00241 /  0.12 ( 5569)
  covalent geometry    : angle       0.54473 /  0.30 ( 7833)
  hydrogen bonds       : bond        0.04038 /  2.72 (  233)
  hydrogen bonds       : angle       3.49952 /  2.47 (  613)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 1743.63 seconds
wall clock time: 30 minutes 35.66 seconds (1835.66 seconds total)