Starting phenix.real_space_refine
on Tue Aug  4 16:18:52 2026 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/9iy7_60987/08_2026/9iy7_60987.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/9iy7_60987/08_2026/9iy7_60987.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.27
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    model {
      file = "/net/cci-nas-00/data/ceres_data/9iy7_60987/08_2026/9iy7_60987.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/9iy7_60987/08_2026/9iy7_60987.cif"
    real_map_files = "/net/cci-nas-00/data/ceres_data/9iy7_60987/08_2026/9iy7_60987.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/9iy7_60987/08_2026/9iy7_60987.map"
  }
  resolution = 3.27
  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=   0.066
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: 6
    Type Number    sf(0)   Gaussians
     S      26      5.16       5
     Cl      2      4.86       5
     Na      2      4.78       5
     C    3200      2.51       5
     N     670      2.21       5
     O     764      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 9 residue(s): 0.00s

  Monomer Library directory:
    "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.2rc3-6140/lib/python3.11/site-packages/chem_data/mon_lib"
  Total number of atoms: 4664
  Number of models: 1
  Model: ""
    Number of chains: 2
    Chain: "A"
      Number of atoms: 4314
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 540, 4314
          Classifications: {'peptide': 540}
          Link IDs: {'PTRANS': 23, 'TRANS': 516}
    Chain: "A"
      Number of atoms: 350
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 27, 350
          Unusual residues: {' CL': 1, ' NA': 2, 'D10': 2, 'D12': 6, 'DD9': 5, 'JC9': 1, 'LMT': 1, 'NAG': 1, 'OCT': 5, 'Y01': 3}
          Classifications: {'undetermined': 27}
          Link IDs: {None: 26}
          Unresolved non-hydrogen bonds: 1
          Unresolved non-hydrogen angles: 2
          Unresolved non-hydrogen dihedrals: 3
          Unresolved non-hydrogen chiralities: 1
  Time building chain proxies: 1.34, per 1000 atoms: 0.29
  Number of scatterers: 4664
  At special positions: 0
  Unit cell: (85.455, 80.18, 73.85, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 6
    Type Number    sf(0)
     Cl      2     17.00
     S      26     16.00
     Na      2     11.00
     O     764      8.00
     N     670      7.00
     C    3200      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=1, symmetry=0
    Simple disulfide: pdb=" SG  CYS A 200 " - pdb=" SG  CYS A 209 " distance=2.03

  Automatic linking
    Parameters for automatic linking
      Linking & cutoffs
        Metal                : Auto  - 3.00
        Amino acid           : True  - 1.90
        Carbohydrate         : True  - 1.99
        Ligands              : True  - 1.99
        Small molecules      : False - 1.98
        Amino acid - RNA/DNA : False
      
  Number of custom bonds: simple=3, symmetry=0
  Links applied
    NAG-ASN
      " NAG A 707 " - " ASN A 208 "
  Number of additional bonds: simple=3, symmetry=0
  Coordination:
  Other bonds:
  Time building additional restraints: 0.42
  Conformation dependent library (CDL) restraints added in 143.0 milliseconds
  

  1076 Ramachandran restraints generated.
    538 Oldfield, 0 Emsley, 538 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  998

  Finding SS restraints...
    Secondary structure from input PDB file:
      29 helices and 0 sheets defined
      75.7% alpha, 0.0% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.12
  Creating SS restraints...
    Processing helix  chain 'A' and resid 84 through 97
      removed outlier: 3.688A  pdb=" N   PHE A  88 " --> pdb=" O   LYS A  84 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 99 through 112
      removed outlier: 4.033A  pdb=" N   TRP A 103 " --> pdb=" O   LEU A  99 " (cutoff:3.500A)
      removed outlier: 4.161A  pdb=" N   PHE A 105 " --> pdb=" O   ASN A 101 " (cutoff:3.500A)
      Proline residue:  A 106  - end of helix
    Processing helix  chain 'A' and resid 117 through 127
    Processing helix  chain 'A' and resid 128 through 144
    Processing helix  chain 'A' and resid 149 through 153
    Processing helix  chain 'A' and resid 155 through 158
    Processing helix  chain 'A' and resid 159 through 190
      removed outlier: 3.910A  pdb=" N   TYR A 163 " --> pdb=" O   LYS A 159 " (cutoff:3.500A)
      removed outlier: 4.068A  pdb=" N   ASN A 177 " --> pdb=" O   ALA A 173 " (cutoff:3.500A)
      removed outlier: 4.228A  pdb=" N   THR A 178 " --> pdb=" O   SER A 174 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 226 through 235
    Processing helix  chain 'A' and resid 238 through 242
    Processing helix  chain 'A' and resid 252 through 271
      removed outlier: 3.799A  pdb=" N   ILE A 262 " --> pdb=" O   CYS A 258 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 276 through 285
      removed outlier: 3.982A  pdb=" N   VAL A 281 " --> pdb=" O   SER A 277 " (cutoff:3.500A)
      removed outlier: 4.397A  pdb=" N   TRP A 282 " --> pdb=" O   GLY A 278 " (cutoff:3.500A)
      removed outlier: 4.716A  pdb=" N   VAL A 283 " --> pdb=" O   LYS A 279 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 286 through 301
      removed outlier: 3.720A  pdb=" N   VAL A 294 " --> pdb=" O   ILE A 290 " (cutoff:3.500A)
      removed outlier: 3.592A  pdb=" N   THR A 301 " --> pdb=" O   VAL A 297 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 304 through 311
    Processing helix  chain 'A' and resid 316 through 321
    Processing helix  chain 'A' and resid 322 through 338
      removed outlier: 4.045A  pdb=" N   TRP A 326 " --> pdb=" O   GLU A 322 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 342 through 350
      removed outlier: 3.842A  pdb=" N   ALA A 346 " --> pdb=" O   GLY A 342 " (cutoff:3.500A)
      removed outlier: 4.059A  pdb=" N   TYR A 350 " --> pdb=" O   ALA A 346 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 356 through 390
      removed outlier: 3.505A  pdb=" N   ASP A 360 " --> pdb=" O   ASN A 356 " (cutoff:3.500A)
      removed outlier: 3.779A  pdb=" N   ASN A 368 " --> pdb=" O   THR A 364 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 403 through 408
    Processing helix  chain 'A' and resid 408 through 416
    Processing helix  chain 'A' and resid 419 through 454
      removed outlier: 4.077A  pdb=" N   ASP A 437 " --> pdb=" O   THR A 433 " (cutoff:3.500A)
      removed outlier: 4.276A  pdb=" N   SER A 438 " --> pdb=" O   LEU A 434 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 461 through 477
    Processing helix  chain 'A' and resid 484 through 495
    Processing helix  chain 'A' and resid 498 through 514
    Processing helix  chain 'A' and resid 517 through 530
    Processing helix  chain 'A' and resid 534 through 543
    Processing helix  chain 'A' and resid 545 through 559
      removed outlier: 4.209A  pdb=" N   PHE A 551 " --> pdb=" O   LEU A 547 " (cutoff:3.500A)
      removed outlier: 3.941A  pdb=" N   MET A 558 " --> pdb=" O   CYS A 554 " (cutoff:3.500A)
      removed outlier: 3.889A  pdb=" N   SER A 559 " --> pdb=" O   SER A 555 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 571 through 587
      removed outlier: 4.164A  pdb=" N   ILE A 575 " --> pdb=" O   PRO A 571 " (cutoff:3.500A)
      removed outlier: 3.950A  pdb=" N   ILE A 576 " --> pdb=" O   TYR A 572 " (cutoff:3.500A)
      removed outlier: 3.621A  pdb=" N   SER A 585 " --> pdb=" O   ILE A 581 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 587 through 600
    Processing helix  chain 'A' and resid 605 through 613
      removed outlier: 3.648A  pdb=" N   THR A 613 " --> pdb=" O   ILE A 609 " (cutoff:3.500A)

    268 hydrogen bonds defined for protein.
    780 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: 0.52 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: 711
        1.33 -     1.45: 1359
        1.45 -     1.57: 2684
        1.57 -     1.69: 0
        1.69 -     1.81: 38
  Bond restraints: 4792
  Sorted by residual:
  bond pdb=" C5  JC9 A 708 "
       pdb=" O1  JC9 A 708 "
    ideal  model  delta    sigma   weight residual
    1.217  1.411 -0.194 2.00e-02 2.50e+03 9.44e+01
  bond pdb=" C8  JC9 A 708 "
       pdb="CL1  JC9 A 708 "
    ideal  model  delta    sigma   weight residual
    1.735  1.788 -0.053 2.00e-02 2.50e+03 7.14e+00
  bond pdb=" C3' LMT A 706 "
       pdb=" O3' LMT A 706 "
    ideal  model  delta    sigma   weight residual
    1.404  1.361  0.043 2.00e-02 2.50e+03 4.62e+00
  bond pdb=" C6' LMT A 706 "
       pdb=" O6' LMT A 706 "
    ideal  model  delta    sigma   weight residual
    1.407  1.364  0.043 2.00e-02 2.50e+03 4.52e+00
  bond pdb=" C2B LMT A 706 "
       pdb=" O2B LMT A 706 "
    ideal  model  delta    sigma   weight residual
    1.410  1.368  0.042 2.00e-02 2.50e+03 4.38e+00
  ... (remaining 4787 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     2.62: 6365
        2.62 -     5.23: 93
        5.23 -     7.85: 15
        7.85 -    10.46: 3
       10.46 -    13.08: 3
  Bond angle restraints: 6479
  Sorted by residual:
  angle pdb=" C6  JC9 A 708 "
        pdb=" C5  JC9 A 708 "
        pdb=" O1  JC9 A 708 "
      ideal   model   delta    sigma   weight residual
     121.29  108.21   13.08 3.00e+00 1.11e-01 1.90e+01
  angle pdb=" C1  JC9 A 708 "
        pdb=" C5  JC9 A 708 "
        pdb=" O1  JC9 A 708 "
      ideal   model   delta    sigma   weight residual
     121.39  108.36   13.03 3.00e+00 1.11e-01 1.89e+01
  angle pdb=" C2  LMT A 706 "
        pdb=" C3  LMT A 706 "
        pdb=" C4  LMT A 706 "
      ideal   model   delta    sigma   weight residual
     117.09  106.99   10.10 3.00e+00 1.11e-01 1.13e+01
  angle pdb=" CA  CYS A 200 "
        pdb=" CB  CYS A 200 "
        pdb=" SG  CYS A 200 "
      ideal   model   delta    sigma   weight residual
     114.40  121.36   -6.96 2.30e+00 1.89e-01 9.16e+00
  angle pdb=" C   SER A 199 "
        pdb=" N   CYS A 200 "
        pdb=" CA  CYS A 200 "
      ideal   model   delta    sigma   weight residual
     123.34  117.90    5.44 1.80e+00 3.09e-01 9.13e+00
  ... (remaining 6474 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    22.12: 2596
       22.12 -    44.24: 284
       44.24 -    66.36: 51
       66.36 -    88.48: 12
       88.48 -   110.59: 15
  Dihedral angle restraints: 2958
    sinusoidal: 1391
      harmonic: 1567
  Sorted by residual:
  dihedral pdb=" CB  CYS A 200 "
           pdb=" SG  CYS A 200 "
           pdb=" SG  CYS A 209 "
           pdb=" CB  CYS A 209 "
      ideal   model   delta sinusoidal    sigma   weight residual
     -86.00 -146.75   60.75     1      1.00e+01 1.00e-02 4.91e+01
  dihedral pdb=" C4B LMT A 706 "
           pdb=" C2B LMT A 706 "
           pdb=" C3B LMT A 706 "
           pdb=" O2B LMT A 706 "
      ideal   model   delta sinusoidal    sigma   weight residual
     174.48   63.89  110.59     1      3.00e+01 1.11e-03 1.44e+01
  dihedral pdb=" C1' LMT A 706 "
           pdb=" C2' LMT A 706 "
           pdb=" C3' LMT A 706 "
           pdb=" O3' LMT A 706 "
      ideal   model   delta sinusoidal    sigma   weight residual
    -176.68  -66.30 -110.38     1      3.00e+01 1.11e-03 1.44e+01
  ... (remaining 2955 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.049: 531
       0.049 -    0.097: 154
       0.097 -    0.146: 29
       0.146 -    0.195: 3
       0.195 -    0.243: 4
  Chirality restraints: 721
  Sorted by residual:
  chirality pdb=" CBF Y01 A 722 "
            pdb=" CAS Y01 A 722 "
            pdb=" CBD Y01 A 722 "
            pdb=" CBH Y01 A 722 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.45   -2.20   -0.24 2.00e-01 2.50e+01 1.48e+00
  chirality pdb=" CB  ILE A 609 "
            pdb=" CA  ILE A 609 "
            pdb=" CG1 ILE A 609 "
            pdb=" CG2 ILE A 609 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.64    2.41    0.24 2.00e-01 2.50e+01 1.39e+00
  chirality pdb=" CB  ILE A 150 "
            pdb=" CA  ILE A 150 "
            pdb=" CG1 ILE A 150 "
            pdb=" CG2 ILE A 150 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.64    2.43    0.22 2.00e-01 2.50e+01 1.16e+00
  ... (remaining 718 not shown)

  Planarity restraints: 748
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C1  JC9 A 708 "    0.117 2.00e-02 2.50e+03   2.03e-01 4.10e+02
        pdb=" C5  JC9 A 708 "   -0.351 2.00e-02 2.50e+03
        pdb=" C6  JC9 A 708 "    0.116 2.00e-02 2.50e+03
        pdb=" O1  JC9 A 708 "    0.118 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   THR A 600 "   -0.052 5.00e-02 4.00e+02   7.94e-02 1.01e+01
        pdb=" N   PRO A 601 "    0.137 5.00e-02 4.00e+02
        pdb=" CA  PRO A 601 "   -0.042 5.00e-02 4.00e+02
        pdb=" CD  PRO A 601 "   -0.044 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CB  TYR A 267 "   -0.020 2.00e-02 2.50e+03   1.20e-02 2.89e+00
        pdb=" CG  TYR A 267 "    0.021 2.00e-02 2.50e+03
        pdb=" CD1 TYR A 267 "   -0.000 2.00e-02 2.50e+03
        pdb=" CD2 TYR A 267 "    0.000 2.00e-02 2.50e+03
        pdb=" CE1 TYR A 267 "    0.005 2.00e-02 2.50e+03
        pdb=" CE2 TYR A 267 "    0.006 2.00e-02 2.50e+03
        pdb=" CZ  TYR A 267 "    0.003 2.00e-02 2.50e+03
        pdb=" OH  TYR A 267 "   -0.015 2.00e-02 2.50e+03
  ... (remaining 745 not shown)

  Histogram of nonbonded interaction distances:
        1.86 -     2.47: 22
        2.47 -     3.08: 3321
        3.08 -     3.68: 6775
        3.68 -     4.29: 10759
        4.29 -     4.90: 18098
  Nonbonded interactions: 38975
  Sorted by model distance:
  nonbonded pdb=" OD2 ASP A 437 "
            pdb="NA    NA A 703 "
     model   vdw
     1.860 2.470
  nonbonded pdb=" OG1 THR A 284 "
            pdb=" OD1 ASP A 437 "
     model   vdw
     2.209 3.040
  nonbonded pdb=" OH  TYR A 121 "
            pdb="CL    CL A 701 "
     model   vdw
     2.231 3.190
  nonbonded pdb=" O   ARG A 596 "
            pdb=" OG1 THR A 600 "
     model   vdw
     2.262 3.040
  nonbonded pdb=" O   ILE A 587 "
            pdb=" OG1 THR A 591 "
     model   vdw
     2.264 3.040
  ... (remaining 38970 not shown)

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

  No NCS relation were found !!!

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

Found NCS groups:
  found none.
Set up NCS constraints
  No NCS constraints will be used in refinement.
Set refine NCS operators
Adjust number of macro_cycles
  Number of macro_cycles: 10
Reset NCS operators
Extract rigid body selections
Check and reset occupancies
  Occupancies: min=1.00 max=1.00 mean=1.00
Load rotamer database and sin/cos tables
Set ADP refinement strategy
  ADPs will be refined as individual isotropic
Make a string to write initial .geo file
Internal consistency checks
Time:
  Set random seed:                         0.000
  Set model cs if undefined:               0.000
  Decide on map wrapping:                  0.000
  Normalize map: mean=0, sd=1:             1.300
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.000
  Construct map_model_manager:             0.000
  Extract box with map and model:          0.090
  Check model and map are aligned:         0.010
  Set scattering table:                    0.020
  Process input model:                     6.010
  Find NCS groups from input model:        0.030
  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:             0.000
  Load rotamer database and sin/cos tables:1.170
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:    8.630
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7849
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      :  0.008   0.194   4797  Z= 0.341
  Angle     :  0.841  13.080   6484  Z= 0.402
  Chirality :  0.049   0.243    721
  Planarity :  0.010   0.203    747
  Dihedral  : 19.705 110.595   1957
  Min Nonbonded Distance : 1.860

Molprobity Statistics.
  All-atom Clashscore : 11.59
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.02 %
    Favored  : 94.98 %
  Rotamer:
    Outliers :  0.22 %
    Allowed  : 19.39 %
    Favored  : 80.39 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -1.45 (0.36), residues: 538
  helix: -0.42 (0.26), residues: 366
  sheet:  None (None), residues: 0
  loop : -1.96 (0.52), residues: 172

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.001   ARG A 152 
 TYR   0.021   0.002   TYR A 267 
 PHE   0.023   0.002   PHE A 548 
 TRP   0.013   0.002   TRP A 271 
 HIS   0.004   0.001   HIS A 143 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00764 /  0.34 ( 4792)
  covalent geometry    : angle       0.83778 /  0.40 ( 6479)
  SS BOND              : bond        0.00033 /  0.02 (    1)
  SS BOND              : angle       3.18339 /  1.68 (    2)
  hydrogen bonds       : bond        0.16688 / 10.26 (  268)
  hydrogen bonds       : angle       6.88973 /  4.92 (  780)
  Misc. bond           : bond        0.00325 /  0.17 (    3)
  link_NAG-ASN         : bond        0.00529 /  0.28 (    1)
  link_NAG-ASN         : angle       2.44022 /  1.35 (    3)

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

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

  1076 Ramachandran restraints generated.
    538 Oldfield, 0 Emsley, 538 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1076 Ramachandran restraints generated.
    538 Oldfield, 0 Emsley, 538 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  49 residues out of total 459 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 48
  time to evaluate  : 0.150 
Fit side-chains
   revert: symmetry clash
  outliers start: 1
  outliers final: 1
  residues processed: 49
  average time/residue: 0.0399
  time to fit residues: 3.0560
Evaluate side-chains
  48 residues out of total 459 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 47
  time to evaluate  : 0.153 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  539 ILE
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 54
   random chunks:
   chunk 24 optimal weight:    0.7980
   chunk 48 optimal weight:    0.7980
   chunk 26 optimal weight:    0.8980
   chunk 2 optimal weight:    0.8980
   chunk 16 optimal weight:    0.9990
   chunk 32 optimal weight:    0.0670
   chunk 31 optimal weight:    8.9990
   chunk 25 optimal weight:    0.6980
   chunk 50 optimal weight:    0.9980
   chunk 53 optimal weight:    1.9990
   chunk 19 optimal weight:    0.7980
   overall best weight:    0.6318

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
** A 145 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 = 0.3493 r_free = 0.3493 target = 0.143009 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 32)----------------|
| r_work = 0.3252 r_free = 0.3252 target = 0.121506 restraints weight = 4949.537|
|-----------------------------------------------------------------------------|
r_work (start): 0.3313 rms_B_bonded: 1.48
r_work: 0.3199 rms_B_bonded: 2.19 restraints_weight: 0.5000
r_work: 0.3051 rms_B_bonded: 3.73 restraints_weight: 0.2500
r_work (final): 0.3051
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7384
moved from start:          0.0993

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.041   4797  Z= 0.160
  Angle     :  0.643   8.046   6484  Z= 0.317
  Chirality :  0.044   0.186    721
  Planarity :  0.005   0.063    747
  Dihedral  : 11.336  58.488   1029
  Min Nonbonded Distance : 2.351

Molprobity Statistics.
  All-atom Clashscore : 8.35
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.90 %
    Favored  : 96.10 %
  Rotamer:
    Outliers :  1.74 %
    Allowed  : 16.78 %
    Favored  : 81.48 %
  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: -0.44 (0.37), residues: 538
  helix:  0.32 (0.26), residues: 370
  sheet:  None (None), residues: 0
  loop : -1.52 (0.56), residues: 168

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.001   ARG A 607 
 TYR   0.015   0.001   TYR A 267 
 PHE   0.017   0.001   PHE A 548 
 TRP   0.008   0.001   TRP A 103 
 HIS   0.002   0.001   HIS A 143 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00369 /  0.16 ( 4792)
  covalent geometry    : angle       0.63766 /  0.32 ( 6479)
  SS BOND              : bond        0.00148 /  0.08 (    1)
  SS BOND              : angle       2.35780 /  1.26 (    2)
  hydrogen bonds       : bond        0.05436 /  3.50 (  268)
  hydrogen bonds       : angle       4.81252 /  3.27 (  780)
  Misc. bond           : bond        0.00219 /  0.11 (    3)
  link_NAG-ASN         : bond        0.00329 /  0.17 (    1)
  link_NAG-ASN         : angle       3.39176 /  1.85 (    3)

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

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

  1076 Ramachandran restraints generated.
    538 Oldfield, 0 Emsley, 538 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1076 Ramachandran restraints generated.
    538 Oldfield, 0 Emsley, 538 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  53 residues out of total 459 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 45
  time to evaluate  : 0.158 
Fit side-chains
REVERT: A  229 GLU cc_start: 0.6849 (tt0) cc_final: 0.6570 (tt0)
REVERT: A  241 ARG cc_start: 0.7720 (mtp180) cc_final: 0.7395 (mtp85)
REVERT: A  310 LEU cc_start: 0.7517 (tp) cc_final: 0.7306 (tt)
  outliers start: 8
  outliers final: 4
  residues processed: 51
  average time/residue: 0.0690
  time to fit residues: 4.7641
Evaluate side-chains
  48 residues out of total 459 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 4
    poor density    : 44
  time to evaluate  : 0.141 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  296 LEU
Chi-restraints excluded: chain A residue  377 PHE
Chi-restraints excluded: chain A residue  426 ILE
Chi-restraints excluded: chain A residue  437 ASP
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 54
   random chunks:
   chunk 36 optimal weight:    1.9990
   chunk 37 optimal weight:    0.0470
   chunk 6 optimal weight:    0.6980
   chunk 13 optimal weight:    0.8980
   chunk 47 optimal weight:    1.9990
   chunk 19 optimal weight:    0.5980
   chunk 52 optimal weight:    0.0980
   chunk 25 optimal weight:    0.8980
   chunk 11 optimal weight:    0.0030
   chunk 33 optimal weight:    0.2980
   chunk 28 optimal weight:    2.9990
   overall best weight:    0.2088

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
** A 145 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 = 0.3550 r_free = 0.3550 target = 0.148335 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.3317 r_free = 0.3317 target = 0.126916 restraints weight = 4848.876|
|-----------------------------------------------------------------------------|
r_work (start): 0.3347 rms_B_bonded: 1.46
r_work: 0.3236 rms_B_bonded: 2.17 restraints_weight: 0.5000
r_work: 0.3087 rms_B_bonded: 3.74 restraints_weight: 0.2500
r_work (final): 0.3087
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7367
moved from start:          0.1530

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.038   4797  Z= 0.114
  Angle     :  0.536   5.392   6484  Z= 0.272
  Chirality :  0.040   0.169    721
  Planarity :  0.004   0.055    747
  Dihedral  :  8.908  55.290   1027
  Min Nonbonded Distance : 2.335

Molprobity Statistics.
  All-atom Clashscore : 7.72
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.53 %
    Favored  : 96.47 %
  Rotamer:
    Outliers :  2.40 %
    Allowed  : 15.90 %
    Favored  : 81.70 %
  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:  0.28 (0.38), residues: 538
  helix:  0.93 (0.27), residues: 369
  sheet:  None (None), residues: 0
  loop : -1.43 (0.55), residues: 169

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG A 607 
 TYR   0.011   0.001   TYR A 267 
 PHE   0.016   0.001   PHE A 548 
 TRP   0.011   0.001   TRP A 458 
 HIS   0.001   0.000   HIS A 240 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00250 /  0.11 ( 4792)
  covalent geometry    : angle       0.53087 /  0.27 ( 6479)
  SS BOND              : bond        0.00102 /  0.05 (    1)
  SS BOND              : angle       1.93819 /  1.05 (    2)
  hydrogen bonds       : bond        0.04622 /  2.97 (  268)
  hydrogen bonds       : angle       4.33301 /  2.92 (  780)
  Misc. bond           : bond        0.00134 /  0.07 (    3)
  link_NAG-ASN         : bond        0.00440 /  0.23 (    1)
  link_NAG-ASN         : angle       3.04681 /  1.67 (    3)

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

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

  1076 Ramachandran restraints generated.
    538 Oldfield, 0 Emsley, 538 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1076 Ramachandran restraints generated.
    538 Oldfield, 0 Emsley, 538 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  52 residues out of total 459 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 41
  time to evaluate  : 0.160 
Fit side-chains
REVERT: A  377 PHE cc_start: 0.7496 (OUTLIER) cc_final: 0.6941 (t80)
  outliers start: 11
  outliers final: 4
  residues processed: 51
  average time/residue: 0.0478
  time to fit residues: 3.5167
Evaluate side-chains
  41 residues out of total 459 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 5
    poor density    : 36
  time to evaluate  : 0.145 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  377 PHE
Chi-restraints excluded: chain A residue  386 MET
Chi-restraints excluded: chain A residue  426 ILE
Chi-restraints excluded: chain A residue  437 ASP
Chi-restraints excluded: chain A residue  585 SER
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 54
   random chunks:
   chunk 12 optimal weight:    2.9990
   chunk 45 optimal weight:    1.9990
   chunk 48 optimal weight:    0.4980
   chunk 9 optimal weight:    1.9990
   chunk 14 optimal weight:    2.9990
   chunk 30 optimal weight:    1.9990
   chunk 39 optimal weight:    1.9990
   chunk 26 optimal weight:    0.6980
   chunk 19 optimal weight:    1.9990
   chunk 22 optimal weight:    0.9980
   chunk 10 optimal weight:    0.6980
   overall best weight:    0.9782

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
A 145 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3471 r_free = 0.3471 target = 0.141497 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 53)----------------|
| r_work = 0.3227 r_free = 0.3227 target = 0.119628 restraints weight = 4944.506|
|-----------------------------------------------------------------------------|
r_work (start): 0.3291 rms_B_bonded: 1.51
r_work: 0.3174 rms_B_bonded: 2.26 restraints_weight: 0.5000
r_work: 0.3024 rms_B_bonded: 3.84 restraints_weight: 0.2500
r_work (final): 0.3024
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7506
moved from start:          0.1265

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.041   4797  Z= 0.194
  Angle     :  0.614   5.547   6484  Z= 0.314
  Chirality :  0.044   0.154    721
  Planarity :  0.005   0.050    747
  Dihedral  :  9.192  57.132   1027
  Min Nonbonded Distance : 2.201

Molprobity Statistics.
  All-atom Clashscore : 7.83
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.90 %
    Favored  : 96.10 %
  Rotamer:
    Outliers :  2.18 %
    Allowed  : 17.21 %
    Favored  : 80.61 %
  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: -0.05 (0.37), residues: 538
  helix:  0.70 (0.26), residues: 370
  sheet:  None (None), residues: 0
  loop : -1.61 (0.54), residues: 168

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.001   ARG A 241 
 TYR   0.029   0.002   TYR A 267 
 PHE   0.021   0.002   PHE A 548 
 TRP   0.009   0.001   TRP A 458 
 HIS   0.003   0.001   HIS A 143 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00465 /  0.19 ( 4792)
  covalent geometry    : angle       0.60935 /  0.31 ( 6479)
  SS BOND              : bond        0.00222 /  0.12 (    1)
  SS BOND              : angle       2.48352 /  1.31 (    2)
  hydrogen bonds       : bond        0.05397 /  3.45 (  268)
  hydrogen bonds       : angle       4.56554 /  3.08 (  780)
  Misc. bond           : bond        0.00264 /  0.14 (    3)
  link_NAG-ASN         : bond        0.00224 /  0.12 (    1)
  link_NAG-ASN         : angle       2.88309 /  1.60 (    3)

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

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

  1076 Ramachandran restraints generated.
    538 Oldfield, 0 Emsley, 538 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1076 Ramachandran restraints generated.
    538 Oldfield, 0 Emsley, 538 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  51 residues out of total 459 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 41
  time to evaluate  : 0.113 
Fit side-chains
REVERT: A  229 GLU cc_start: 0.7003 (tt0) cc_final: 0.6738 (tt0)
  outliers start: 10
  outliers final: 8
  residues processed: 49
  average time/residue: 0.0470
  time to fit residues: 3.3491
Evaluate side-chains
  48 residues out of total 459 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 40
  time to evaluate  : 0.148 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  274 VAL
Chi-restraints excluded: chain A residue  296 LEU
Chi-restraints excluded: chain A residue  377 PHE
Chi-restraints excluded: chain A residue  386 MET
Chi-restraints excluded: chain A residue  426 ILE
Chi-restraints excluded: chain A residue  437 ASP
Chi-restraints excluded: chain A residue  528 MET
Chi-restraints excluded: chain A residue  585 SER
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 54
   random chunks:
   chunk 48 optimal weight:    0.9980
   chunk 23 optimal weight:    0.6980
   chunk 43 optimal weight:    0.8980
   chunk 6 optimal weight:    1.9990
   chunk 17 optimal weight:    0.8980
   chunk 46 optimal weight:    0.4980
   chunk 40 optimal weight:    0.9980
   chunk 53 optimal weight:    0.9980
   chunk 0 optimal weight:    2.9990
   chunk 39 optimal weight:    0.5980
   chunk 45 optimal weight:    0.6980
   overall best weight:    0.6780

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

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3494 r_free = 0.3494 target = 0.143334 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 42)----------------|
| r_work = 0.3254 r_free = 0.3254 target = 0.121727 restraints weight = 4937.664|
|-----------------------------------------------------------------------------|
r_work (start): 0.3317 rms_B_bonded: 1.47
r_work: 0.3203 rms_B_bonded: 2.18 restraints_weight: 0.5000
r_work: 0.3054 rms_B_bonded: 3.72 restraints_weight: 0.2500
r_work (final): 0.3054
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7362
moved from start:          0.1431

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.040   4797  Z= 0.154
  Angle     :  0.571   7.854   6484  Z= 0.292
  Chirality :  0.042   0.193    721
  Planarity :  0.004   0.042    747
  Dihedral  :  8.775  58.822   1027
  Min Nonbonded Distance : 2.246

Molprobity Statistics.
  All-atom Clashscore : 8.25
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.90 %
    Favored  : 96.10 %
  Rotamer:
    Outliers :  3.05 %
    Allowed  : 16.12 %
    Favored  : 80.83 %
  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:  0.06 (0.37), residues: 538
  helix:  0.75 (0.26), residues: 373
  sheet:  None (None), residues: 0
  loop : -1.52 (0.54), residues: 165

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG A 241 
 TYR   0.021   0.001   TYR A 267 
 PHE   0.019   0.001   PHE A 548 
 TRP   0.010   0.001   TRP A 458 
 HIS   0.002   0.001   HIS A 143 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00365 /  0.15 ( 4792)
  covalent geometry    : angle       0.56728 /  0.29 ( 6479)
  SS BOND              : bond        0.00138 /  0.07 (    1)
  SS BOND              : angle       2.11347 /  1.13 (    2)
  hydrogen bonds       : bond        0.05005 /  3.22 (  268)
  hydrogen bonds       : angle       4.41906 /  2.97 (  780)
  Misc. bond           : bond        0.00219 /  0.12 (    3)
  link_NAG-ASN         : bond        0.00299 /  0.16 (    1)
  link_NAG-ASN         : angle       2.73025 /  1.51 (    3)

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

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

  1076 Ramachandran restraints generated.
    538 Oldfield, 0 Emsley, 538 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1076 Ramachandran restraints generated.
    538 Oldfield, 0 Emsley, 538 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  53 residues out of total 459 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 39
  time to evaluate  : 0.200 
Fit side-chains
REVERT: A  229 GLU cc_start: 0.6820 (tt0) cc_final: 0.6572 (tt0)
REVERT: A  430 MET cc_start: 0.7544 (OUTLIER) cc_final: 0.7342 (ttp)
  outliers start: 14
  outliers final: 10
  residues processed: 49
  average time/residue: 0.0644
  time to fit residues: 4.3099
Evaluate side-chains
  47 residues out of total 459 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 36
  time to evaluate  : 0.150 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   98 ASP
Chi-restraints excluded: chain A residue  153 LYS
Chi-restraints excluded: chain A residue  274 VAL
Chi-restraints excluded: chain A residue  296 LEU
Chi-restraints excluded: chain A residue  377 PHE
Chi-restraints excluded: chain A residue  386 MET
Chi-restraints excluded: chain A residue  426 ILE
Chi-restraints excluded: chain A residue  430 MET
Chi-restraints excluded: chain A residue  437 ASP
Chi-restraints excluded: chain A residue  527 GLU
Chi-restraints excluded: chain A residue  528 MET
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 54
   random chunks:
   chunk 37 optimal weight:    0.0980
   chunk 6 optimal weight:    1.9990
   chunk 49 optimal weight:    1.9990
   chunk 52 optimal weight:    0.9990
   chunk 17 optimal weight:    0.5980
   chunk 25 optimal weight:    2.9990
   chunk 23 optimal weight:    2.9990
   chunk 36 optimal weight:    0.5980
   chunk 44 optimal weight:    0.9990
   chunk 10 optimal weight:    0.7980
   chunk 40 optimal weight:    1.9990
   overall best weight:    0.6182

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

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3501 r_free = 0.3501 target = 0.143875 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.3259 r_free = 0.3259 target = 0.122109 restraints weight = 4956.853|
|-----------------------------------------------------------------------------|
r_work (start): 0.3304 rms_B_bonded: 1.49
r_work: 0.3190 rms_B_bonded: 2.21 restraints_weight: 0.5000
r_work: 0.3040 rms_B_bonded: 3.78 restraints_weight: 0.2500
r_work (final): 0.3040
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7332
moved from start:          0.1528

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.040   4797  Z= 0.148
  Angle     :  0.561   6.828   6484  Z= 0.288
  Chirality :  0.041   0.171    721
  Planarity :  0.004   0.042    747
  Dihedral  :  8.530  57.972   1027
  Min Nonbonded Distance : 2.247

Molprobity Statistics.
  All-atom Clashscore : 8.14
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.72 %
    Favored  : 96.28 %
  Rotamer:
    Outliers :  3.27 %
    Allowed  : 15.69 %
    Favored  : 81.05 %
  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 are not related in a simple way.
  whole:  0.11 (0.37), residues: 538
  helix:  0.81 (0.26), residues: 372
  sheet:  None (None), residues: 0
  loop : -1.54 (0.54), residues: 166

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.000   ARG A 241 
 TYR   0.020   0.001   TYR A 267 
 PHE   0.015   0.001   PHE A 548 
 TRP   0.009   0.001   TRP A 458 
 HIS   0.002   0.001   HIS A 143 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00352 /  0.15 ( 4792)
  covalent geometry    : angle       0.55770 /  0.29 ( 6479)
  SS BOND              : bond        0.00112 /  0.06 (    1)
  SS BOND              : angle       1.98447 /  1.06 (    2)
  hydrogen bonds       : bond        0.04903 /  3.15 (  268)
  hydrogen bonds       : angle       4.39291 /  2.96 (  780)
  Misc. bond           : bond        0.00212 /  0.11 (    3)
  link_NAG-ASN         : bond        0.00327 /  0.17 (    1)
  link_NAG-ASN         : angle       2.63495 /  1.46 (    3)

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

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

  1076 Ramachandran restraints generated.
    538 Oldfield, 0 Emsley, 538 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1076 Ramachandran restraints generated.
    538 Oldfield, 0 Emsley, 538 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  53 residues out of total 459 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 38
  time to evaluate  : 0.151 
Fit side-chains
REVERT: A  229 GLU cc_start: 0.6829 (tt0) cc_final: 0.6553 (tt0)
REVERT: A  241 ARG cc_start: 0.7776 (mtp85) cc_final: 0.7035 (mtp180)
  outliers start: 15
  outliers final: 11
  residues processed: 50
  average time/residue: 0.0514
  time to fit residues: 3.6160
Evaluate side-chains
  49 residues out of total 459 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 38
  time to evaluate  : 0.165 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   98 ASP
Chi-restraints excluded: chain A residue  153 LYS
Chi-restraints excluded: chain A residue  242 SER
Chi-restraints excluded: chain A residue  274 VAL
Chi-restraints excluded: chain A residue  296 LEU
Chi-restraints excluded: chain A residue  377 PHE
Chi-restraints excluded: chain A residue  386 MET
Chi-restraints excluded: chain A residue  426 ILE
Chi-restraints excluded: chain A residue  437 ASP
Chi-restraints excluded: chain A residue  527 GLU
Chi-restraints excluded: chain A residue  585 SER
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 54
   random chunks:
   chunk 46 optimal weight:    0.8980
   chunk 22 optimal weight:    0.9990
   chunk 50 optimal weight:    4.9990
   chunk 12 optimal weight:    2.9990
   chunk 27 optimal weight:    1.9990
   chunk 53 optimal weight:    0.8980
   chunk 17 optimal weight:    0.0770
   chunk 44 optimal weight:    0.6980
   chunk 5 optimal weight:    0.6980
   chunk 52 optimal weight:    0.9980
   chunk 20 optimal weight:    1.9990
   overall best weight:    0.6538

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

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3507 r_free = 0.3507 target = 0.144214 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 44)----------------|
| r_work = 0.3261 r_free = 0.3261 target = 0.122067 restraints weight = 4928.692|
|-----------------------------------------------------------------------------|
r_work (start): 0.3320 rms_B_bonded: 1.52
r_work: 0.3196 rms_B_bonded: 2.38 restraints_weight: 0.5000
r_work: 0.3045 rms_B_bonded: 4.07 restraints_weight: 0.2500
r_work (final): 0.3045
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7720
moved from start:          0.1587

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.040   4797  Z= 0.150
  Angle     :  0.555   5.456   6484  Z= 0.286
  Chirality :  0.042   0.205    721
  Planarity :  0.004   0.044    747
  Dihedral  :  8.388  57.548   1027
  Min Nonbonded Distance : 2.241

Molprobity Statistics.
  All-atom Clashscore : 7.41
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.09 %
    Favored  : 95.91 %
  Rotamer:
    Outliers :  3.05 %
    Allowed  : 15.69 %
    Favored  : 81.26 %
  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:  0.16 (0.37), residues: 538
  helix:  0.85 (0.26), residues: 372
  sheet:  None (None), residues: 0
  loop : -1.54 (0.54), residues: 166

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.000   ARG A 241 
 TYR   0.020   0.001   TYR A 267 
 PHE   0.016   0.001   PHE A 548 
 TRP   0.009   0.001   TRP A 458 
 HIS   0.002   0.001   HIS A 143 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00355 /  0.15 ( 4792)
  covalent geometry    : angle       0.55148 /  0.29 ( 6479)
  SS BOND              : bond        0.00155 /  0.08 (    1)
  SS BOND              : angle       1.98971 /  1.06 (    2)
  hydrogen bonds       : bond        0.04912 /  3.15 (  268)
  hydrogen bonds       : angle       4.35929 /  2.94 (  780)
  Misc. bond           : bond        0.00216 /  0.11 (    3)
  link_NAG-ASN         : bond        0.00303 /  0.16 (    1)
  link_NAG-ASN         : angle       2.59456 /  1.44 (    3)

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

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

  1076 Ramachandran restraints generated.
    538 Oldfield, 0 Emsley, 538 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1076 Ramachandran restraints generated.
    538 Oldfield, 0 Emsley, 538 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  50 residues out of total 459 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 36
  time to evaluate  : 0.153 
Fit side-chains
REVERT: A  229 GLU cc_start: 0.7344 (tt0) cc_final: 0.7062 (tt0)
REVERT: A  241 ARG cc_start: 0.7958 (mtp85) cc_final: 0.7298 (mtp180)
REVERT: A  444 GLU cc_start: 0.6973 (OUTLIER) cc_final: 0.6715 (tp30)
  outliers start: 14
  outliers final: 12
  residues processed: 48
  average time/residue: 0.0586
  time to fit residues: 3.9490
Evaluate side-chains
  48 residues out of total 459 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 35
  time to evaluate  : 0.152 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   98 ASP
Chi-restraints excluded: chain A residue  153 LYS
Chi-restraints excluded: chain A residue  242 SER
Chi-restraints excluded: chain A residue  274 VAL
Chi-restraints excluded: chain A residue  296 LEU
Chi-restraints excluded: chain A residue  377 PHE
Chi-restraints excluded: chain A residue  386 MET
Chi-restraints excluded: chain A residue  426 ILE
Chi-restraints excluded: chain A residue  437 ASP
Chi-restraints excluded: chain A residue  444 GLU
Chi-restraints excluded: chain A residue  527 GLU
Chi-restraints excluded: chain A residue  528 MET
Chi-restraints excluded: chain A residue  585 SER
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 54
   random chunks:
   chunk 17 optimal weight:    0.7980
   chunk 41 optimal weight:    0.8980
   chunk 11 optimal weight:    0.7980
   chunk 29 optimal weight:    0.6980
   chunk 31 optimal weight:    0.0970
   chunk 19 optimal weight:    1.9990
   chunk 50 optimal weight:    0.7980
   chunk 13 optimal weight:    0.9980
   chunk 36 optimal weight:    1.9990
   chunk 40 optimal weight:    0.9990
   chunk 0 optimal weight:    2.9990
   overall best weight:    0.6378

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

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3505 r_free = 0.3505 target = 0.144268 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 48)----------------|
| r_work = 0.3264 r_free = 0.3264 target = 0.122502 restraints weight = 4989.928|
|-----------------------------------------------------------------------------|
r_work (start): 0.3325 rms_B_bonded: 1.48
r_work: 0.3211 rms_B_bonded: 2.19 restraints_weight: 0.5000
r_work: 0.3062 rms_B_bonded: 3.74 restraints_weight: 0.2500
r_work (final): 0.3062
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7312
moved from start:          0.1623

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.040   4797  Z= 0.148
  Angle     :  0.557   5.456   6484  Z= 0.285
  Chirality :  0.042   0.199    721
  Planarity :  0.004   0.044    747
  Dihedral  :  8.233  58.401   1027
  Min Nonbonded Distance : 2.246

Molprobity Statistics.
  All-atom Clashscore : 7.52
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.90 %
    Favored  : 96.10 %
  Rotamer:
    Outliers :  2.61 %
    Allowed  : 16.12 %
    Favored  : 81.26 %
  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:  0.19 (0.37), residues: 538
  helix:  0.87 (0.26), residues: 372
  sheet:  None (None), residues: 0
  loop : -1.52 (0.54), residues: 166

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.000   ARG A 241 
 TYR   0.019   0.001   TYR A 267 
 PHE   0.016   0.001   PHE A 548 
 TRP   0.009   0.001   TRP A 458 
 HIS   0.002   0.001   HIS A 143 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00351 /  0.15 ( 4792)
  covalent geometry    : angle       0.55309 /  0.28 ( 6479)
  SS BOND              : bond        0.00163 /  0.09 (    1)
  SS BOND              : angle       1.92978 /  1.03 (    2)
  hydrogen bonds       : bond        0.04859 /  3.12 (  268)
  hydrogen bonds       : angle       4.36321 /  2.94 (  780)
  Misc. bond           : bond        0.00216 /  0.11 (    3)
  link_NAG-ASN         : bond        0.00309 /  0.16 (    1)
  link_NAG-ASN         : angle       2.51994 /  1.40 (    3)

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

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

  1076 Ramachandran restraints generated.
    538 Oldfield, 0 Emsley, 538 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1076 Ramachandran restraints generated.
    538 Oldfield, 0 Emsley, 538 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  49 residues out of total 459 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 37
  time to evaluate  : 0.163 
Fit side-chains
REVERT: A  229 GLU cc_start: 0.6799 (tt0) cc_final: 0.6523 (tt0)
REVERT: A  241 ARG cc_start: 0.7704 (mtp85) cc_final: 0.6997 (mtp180)
REVERT: A  444 GLU cc_start: 0.6524 (OUTLIER) cc_final: 0.6163 (tp30)
  outliers start: 12
  outliers final: 11
  residues processed: 47
  average time/residue: 0.0505
  time to fit residues: 3.3793
Evaluate side-chains
  49 residues out of total 459 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 37
  time to evaluate  : 0.160 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   98 ASP
Chi-restraints excluded: chain A residue  153 LYS
Chi-restraints excluded: chain A residue  274 VAL
Chi-restraints excluded: chain A residue  296 LEU
Chi-restraints excluded: chain A residue  377 PHE
Chi-restraints excluded: chain A residue  386 MET
Chi-restraints excluded: chain A residue  426 ILE
Chi-restraints excluded: chain A residue  437 ASP
Chi-restraints excluded: chain A residue  444 GLU
Chi-restraints excluded: chain A residue  527 GLU
Chi-restraints excluded: chain A residue  528 MET
Chi-restraints excluded: chain A residue  585 SER
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 54
   random chunks:
   chunk 27 optimal weight:    0.2980
   chunk 5 optimal weight:    0.8980
   chunk 28 optimal weight:    0.7980
   chunk 22 optimal weight:    0.3980
   chunk 40 optimal weight:    0.6980
   chunk 50 optimal weight:    2.9990
   chunk 1 optimal weight:    0.8980
   chunk 8 optimal weight:    0.5980
   chunk 3 optimal weight:    3.9990
   chunk 47 optimal weight:    0.0070
   chunk 17 optimal weight:    0.0970
   overall best weight:    0.2796

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
A 112 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3591 r_free = 0.3591 target = 0.150649 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 42)----------------|
| r_work = 0.3344 r_free = 0.3344 target = 0.127717 restraints weight = 4820.878|
|-----------------------------------------------------------------------------|
r_work (start): 0.3389 rms_B_bonded: 1.58
r_work: 0.3271 rms_B_bonded: 2.36 restraints_weight: 0.5000
r_work: 0.3119 rms_B_bonded: 4.04 restraints_weight: 0.2500
r_work (final): 0.3119
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7473
moved from start:          0.1958

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.040   4797  Z= 0.113
  Angle     :  0.521   6.890   6484  Z= 0.267
  Chirality :  0.040   0.196    721
  Planarity :  0.004   0.044    747
  Dihedral  :  7.620  59.501   1027
  Min Nonbonded Distance : 2.314

Molprobity Statistics.
  All-atom Clashscore : 7.52
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.53 %
    Favored  : 96.47 %
  Rotamer:
    Outliers :  2.40 %
    Allowed  : 16.34 %
    Favored  : 81.26 %
  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:  0.49 (0.38), residues: 538
  helix:  1.14 (0.27), residues: 370
  sheet:  None (None), residues: 0
  loop : -1.48 (0.54), residues: 168

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.000   ARG A 241 
 TYR   0.014   0.001   TYR A 267 
 PHE   0.014   0.001   PHE A 548 
 TRP   0.011   0.001   TRP A 458 
 HIS   0.002   0.001   HIS A 143 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00256 /  0.11 ( 4792)
  covalent geometry    : angle       0.51826 /  0.27 ( 6479)
  SS BOND              : bond        0.00066 /  0.03 (    1)
  SS BOND              : angle       1.48928 /  0.81 (    2)
  hydrogen bonds       : bond        0.04341 /  2.80 (  268)
  hydrogen bonds       : angle       4.16961 /  2.80 (  780)
  Misc. bond           : bond        0.00149 /  0.08 (    3)
  link_NAG-ASN         : bond        0.00357 /  0.19 (    1)
  link_NAG-ASN         : angle       2.40681 /  1.33 (    3)

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

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

  1076 Ramachandran restraints generated.
    538 Oldfield, 0 Emsley, 538 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1076 Ramachandran restraints generated.
    538 Oldfield, 0 Emsley, 538 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  52 residues out of total 459 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 41
  time to evaluate  : 0.188 
Fit side-chains
REVERT: A  241 ARG cc_start: 0.7804 (mtp85) cc_final: 0.7163 (mtp180)
REVERT: A  377 PHE cc_start: 0.7685 (OUTLIER) cc_final: 0.7100 (t80)
REVERT: A  444 GLU cc_start: 0.6596 (OUTLIER) cc_final: 0.6238 (tp30)
  outliers start: 11
  outliers final: 7
  residues processed: 50
  average time/residue: 0.0618
  time to fit residues: 4.3457
Evaluate side-chains
  47 residues out of total 459 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 38
  time to evaluate  : 0.189 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   98 ASP
Chi-restraints excluded: chain A residue  242 SER
Chi-restraints excluded: chain A residue  274 VAL
Chi-restraints excluded: chain A residue  377 PHE
Chi-restraints excluded: chain A residue  386 MET
Chi-restraints excluded: chain A residue  426 ILE
Chi-restraints excluded: chain A residue  444 GLU
Chi-restraints excluded: chain A residue  527 GLU
Chi-restraints excluded: chain A residue  585 SER
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 54
   random chunks:
   chunk 15 optimal weight:    0.7980
   chunk 9 optimal weight:    1.9990
   chunk 0 optimal weight:    3.9990
   chunk 16 optimal weight:    2.9990
   chunk 46 optimal weight:    0.7980
   chunk 14 optimal weight:    4.9990
   chunk 29 optimal weight:    0.6980
   chunk 38 optimal weight:    0.4980
   chunk 51 optimal weight:    0.7980
   chunk 28 skipped: trial refinement blew up (Bond distance > max_reasonable_bond_distance: 56.2038 > 50:)
   chunk 41 optimal weight:    0.8980
   overall best weight:    0.7180

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

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3520 r_free = 0.3520 target = 0.145288 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 44)----------------|
| r_work = 0.3277 r_free = 0.3277 target = 0.123373 restraints weight = 4964.705|
|-----------------------------------------------------------------------------|
r_work (start): 0.3300 rms_B_bonded: 1.47
r_work: 0.3186 rms_B_bonded: 2.21 restraints_weight: 0.5000
r_work: 0.3039 rms_B_bonded: 3.77 restraints_weight: 0.2500
r_work (final): 0.3039
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7460
moved from start:          0.1769

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.039   4797  Z= 0.158
  Angle     :  0.569   7.187   6484  Z= 0.291
  Chirality :  0.042   0.188    721
  Planarity :  0.004   0.043    747
  Dihedral  :  7.921  59.647   1027
  Min Nonbonded Distance : 2.227

Molprobity Statistics.
  All-atom Clashscore : 7.62
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.46 %
    Favored  : 95.54 %
  Rotamer:
    Outliers :  2.40 %
    Allowed  : 15.90 %
    Favored  : 81.70 %
  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:  0.39 (0.37), residues: 538
  helix:  1.04 (0.26), residues: 371
  sheet:  None (None), residues: 0
  loop : -1.48 (0.54), residues: 167

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG A 241 
 TYR   0.025   0.001   TYR A 267 
 PHE   0.017   0.001   PHE A 548 
 TRP   0.007   0.001   TRP A 458 
 HIS   0.003   0.001   HIS A 143 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00376 /  0.16 ( 4792)
  covalent geometry    : angle       0.56588 /  0.29 ( 6479)
  SS BOND              : bond        0.00276 /  0.15 (    1)
  SS BOND              : angle       2.07510 /  1.10 (    2)
  hydrogen bonds       : bond        0.04878 /  3.13 (  268)
  hydrogen bonds       : angle       4.34615 /  2.93 (  780)
  Misc. bond           : bond        0.00227 /  0.12 (    3)
  link_NAG-ASN         : bond        0.00282 /  0.15 (    1)
  link_NAG-ASN         : angle       2.38736 /  1.33 (    3)

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

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

  1076 Ramachandran restraints generated.
    538 Oldfield, 0 Emsley, 538 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1076 Ramachandran restraints generated.
    538 Oldfield, 0 Emsley, 538 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  50 residues out of total 459 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 39
  time to evaluate  : 0.146 
Fit side-chains
REVERT: A  241 ARG cc_start: 0.7789 (mtp85) cc_final: 0.7127 (mtp180)
REVERT: A  444 GLU cc_start: 0.6712 (OUTLIER) cc_final: 0.6423 (tp30)
  outliers start: 11
  outliers final: 8
  residues processed: 49
  average time/residue: 0.0820
  time to fit residues: 5.1932
Evaluate side-chains
  47 residues out of total 459 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 38
  time to evaluate  : 0.151 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   98 ASP
Chi-restraints excluded: chain A residue  242 SER
Chi-restraints excluded: chain A residue  274 VAL
Chi-restraints excluded: chain A residue  377 PHE
Chi-restraints excluded: chain A residue  386 MET
Chi-restraints excluded: chain A residue  426 ILE
Chi-restraints excluded: chain A residue  444 GLU
Chi-restraints excluded: chain A residue  527 GLU
Chi-restraints excluded: chain A residue  585 SER
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 54
   random chunks:
   chunk 37 optimal weight:    0.7980
   chunk 30 optimal weight:    0.5980
   chunk 28 optimal weight:    0.7980
   chunk 49 optimal weight:    0.4980
   chunk 13 optimal weight:    0.9980
   chunk 17 optimal weight:    0.6980
   chunk 8 optimal weight:    0.9980
   chunk 39 optimal weight:    0.5980
   chunk 34 optimal weight:    0.5980
   chunk 10 optimal weight:    0.2980
   chunk 52 optimal weight:    1.9990
   overall best weight:    0.5180

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

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3522 r_free = 0.3522 target = 0.145867 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 46)----------------|
| r_work = 0.3279 r_free = 0.3279 target = 0.123887 restraints weight = 4951.761|
|-----------------------------------------------------------------------------|
r_work (start): 0.3309 rms_B_bonded: 1.50
r_work: 0.3196 rms_B_bonded: 2.22 restraints_weight: 0.5000
r_work: 0.3048 rms_B_bonded: 3.80 restraints_weight: 0.2500
r_work (final): 0.3048
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7341
moved from start:          0.1865

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.040   4797  Z= 0.135
  Angle     :  0.549   6.872   6484  Z= 0.281
  Chirality :  0.041   0.186    721
  Planarity :  0.004   0.045    747
  Dihedral  :  7.767  59.850   1027
  Min Nonbonded Distance : 2.264

Molprobity Statistics.
  All-atom Clashscore : 7.62
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.90 %
    Favored  : 96.10 %
  Rotamer:
    Outliers :  2.18 %
    Allowed  : 16.99 %
    Favored  : 80.83 %
  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:  0.42 (0.37), residues: 538
  helix:  1.06 (0.27), residues: 370
  sheet:  None (None), residues: 0
  loop : -1.46 (0.53), residues: 168

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.001   ARG A 390 
 TYR   0.022   0.001   TYR A 267 
 PHE   0.016   0.001   PHE A 548 
 TRP   0.009   0.001   TRP A 458 
 HIS   0.002   0.001   HIS A 143 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00317 /  0.14 ( 4792)
  covalent geometry    : angle       0.54648 /  0.28 ( 6479)
  SS BOND              : bond        0.00214 /  0.11 (    1)
  SS BOND              : angle       1.80722 /  0.96 (    2)
  hydrogen bonds       : bond        0.04681 /  3.00 (  268)
  hydrogen bonds       : angle       4.28769 /  2.89 (  780)
  Misc. bond           : bond        0.00197 /  0.10 (    3)
  link_NAG-ASN         : bond        0.00311 /  0.16 (    1)
  link_NAG-ASN         : angle       2.33015 /  1.29 (    3)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 1231.78 seconds
wall clock time: 21 minutes 49.68 seconds (1309.68 seconds total)