Starting phenix.real_space_refine
on Thu Jul  2 00:44:45 2026 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/9iy7_60987/07_2026/9iy7_60987.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/9iy7_60987/07_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 {
    real_map_files = "/net/cci-nas-00/data/ceres_data/9iy7_60987/07_2026/9iy7_60987.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/9iy7_60987/07_2026/9iy7_60987.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/9iy7_60987/07_2026/9iy7_60987.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/9iy7_60987/07_2026/9iy7_60987.cif"
  }
  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-dev-6108/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, 347
          Ad-hoc single atom residues: {' CL': 1, ' NA': 2}
          Unusual residues: {'D10': 2, 'D12': 6, 'DD9': 5, 'JC9': 1, 'LMT': 1, 'NAG': 1, 'OCT': 5, 'Y01': 3}
          Classifications: {'undetermined': 24}
          Link IDs: {None: 23}
          Chain breaks: 3
          Unresolved non-hydrogen bonds: 1
          Unresolved non-hydrogen angles: 2
          Unresolved non-hydrogen dihedrals: 3
          Unresolved non-hydrogen chiralities: 1
  Time building chain proxies: 1.03, per 1000 atoms: 0.22
  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: 0.44
  Conformation dependent library (CDL) restraints added in 131.2 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: 0.07
  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: 0.45

  Time building geometry restraints manager: 0.53 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 3.210
  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 3.270
  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:             0.760
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.010
  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:                     4.990
  Find NCS groups from input model:        0.010
  Set up NCS constraints:                  0.010
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.000
  Load rotamer database and sin/cos tables:0.910
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:    6.810
-------------------------------------------------------------------------------
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  : 0.153 
Fit side-chains
   revert: symmetry clash
  outliers start: 1
  outliers final: 1
  residues processed: 49
  average time/residue: 0.0323
  time to fit residues: 2.5103
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  : 0.146 
-------------------------------------------------------------------------------
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:    0.6980
   chunk 16 optimal weight:    0.9990
   chunk 32 optimal weight:    6.9990
   chunk 31 optimal weight:    0.0470
   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:    0.6078

-------------------------------------------------------------------------------
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 = 0.3504 r_free = 0.3504 target = 0.143734 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.3261 r_free = 0.3261 target = 0.121952 restraints weight = 4942.443|
|-----------------------------------------------------------------------------|
r_work (start): 0.3316 rms_B_bonded: 1.49
r_work: 0.3201 rms_B_bonded: 2.21 restraints_weight: 0.5000
r_work: 0.3053 rms_B_bonded: 3.75 restraints_weight: 0.2500
r_work (final): 0.3053
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7369
moved from start:          0.1023

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= 0.158
  Angle     :  0.640   7.950   6484  Z= 0.316
  Chirality :  0.044   0.185    721
  Planarity :  0.005   0.063    747
  Dihedral  : 11.270  58.730   1029
  Min Nonbonded Distance : 2.523

Molprobity Statistics.
  All-atom Clashscore : 8.04
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.90 %
    Favored  : 96.10 %
  Rotamer:
    Outliers :  1.74 %
    Allowed  : 16.12 %
    Favored  : 82.14 %
  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: -0.43 (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   0.009   0.001   TRP A 103 
 HIS   0.002   0.001   HIS A 143 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00363 /  0.16 ( 4792)
  covalent geometry    : angle       0.63437 /  0.31 ( 6479)
  SS BOND              : bond        0.00122 /  0.06 (    1)
  SS BOND              : angle       2.26013 /  1.20 (    2)
  hydrogen bonds       : bond        0.05380 /  3.45 (  268)
  hydrogen bonds       : angle       4.80435 /  3.26 (  780)
  Misc. bond           : bond        0.00212 /  0.11 (    3)
  link_NAG-ASN         : bond        0.00328 /  0.17 (    1)
  link_NAG-ASN         : angle       3.41835 /  1.86 (    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
  55 residues out of total 459 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 47
  time to evaluate  : 0.104 
Fit side-chains
REVERT: A  229 GLU cc_start: 0.6824 (tt0) cc_final: 0.6542 (tt0)
REVERT: A  241 ARG cc_start: 0.7717 (mtp180) cc_final: 0.7378 (mtp85)
REVERT: A  310 LEU cc_start: 0.7510 (tp) cc_final: 0.7301 (tt)
  outliers start: 8
  outliers final: 3
  residues processed: 53
  average time/residue: 0.0505
  time to fit residues: 3.6635
Evaluate side-chains
  49 residues out of total 459 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 3
    poor density    : 46
  time to evaluate  : 0.092 
-------------------------------------------------------------------------------
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
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:    0.9980
   chunk 6 optimal weight:    0.8980
   chunk 13 optimal weight:    0.8980
   chunk 47 optimal weight:    0.8980
   chunk 19 optimal weight:    0.6980
   chunk 52 optimal weight:    0.7980
   chunk 25 optimal weight:    0.6980
   chunk 11 optimal weight:    0.6980
   chunk 33 optimal weight:    0.2980
   chunk 28 optimal weight:    2.9990
   overall best weight:    0.6380

-------------------------------------------------------------------------------
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 = 0.3516 r_free = 0.3516 target = 0.144474 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.3271 r_free = 0.3271 target = 0.122387 restraints weight = 4907.409|
|-----------------------------------------------------------------------------|
r_work (start): 0.3299 rms_B_bonded: 1.51
r_work: 0.3182 rms_B_bonded: 2.24 restraints_weight: 0.5000
r_work: 0.3031 rms_B_bonded: 3.82 restraints_weight: 0.2500
r_work (final): 0.3031
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7408
moved from start:          0.1195

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= 0.154
  Angle     :  0.580   5.448   6484  Z= 0.295
  Chirality :  0.042   0.171    721
  Planarity :  0.004   0.053    747
  Dihedral  :  9.456  55.153   1027
  Min Nonbonded Distance : 2.494

Molprobity Statistics.
  All-atom Clashscore : 7.83
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.72 %
    Favored  : 96.28 %
  Rotamer:
    Outliers :  2.40 %
    Allowed  : 15.03 %
    Favored  : 82.57 %
  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 (0.38), residues: 538
  helix:  0.64 (0.27), residues: 369
  sheet:  None (None), residues: 0
  loop : -1.47 (0.55), residues: 169

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG A 607 
 TYR   0.015   0.001   TYR A 267 
 PHE   0.019   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        0.00362 /  0.15 ( 4792)
  covalent geometry    : angle       0.57526 /  0.29 ( 6479)
  SS BOND              : bond        0.00013 /  0.01 (    1)
  SS BOND              : angle       2.31988 /  1.24 (    2)
  hydrogen bonds       : bond        0.05201 /  3.33 (  268)
  hydrogen bonds       : angle       4.55412 /  3.07 (  780)
  Misc. bond           : bond        0.00221 /  0.12 (    3)
  link_NAG-ASN         : bond        0.00379 /  0.20 (    1)
  link_NAG-ASN         : angle       3.03550 /  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
  49 residues out of total 459 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 38
  time to evaluate  : 0.151 
Fit side-chains
REVERT: A  229 GLU cc_start: 0.6879 (tt0) cc_final: 0.6621 (tt0)
REVERT: A  241 ARG cc_start: 0.7712 (mtp180) cc_final: 0.7462 (mtp85)
REVERT: A  310 LEU cc_start: 0.7552 (tp) cc_final: 0.7344 (tt)
  outliers start: 11
  outliers final: 6
  residues processed: 48
  average time/residue: 0.0438
  time to fit residues: 3.0210
Evaluate side-chains
  42 residues out of total 459 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 36
  time to evaluate  : 0.109 
-------------------------------------------------------------------------------
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  585 SER
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 54
   random chunks:
   chunk 12 optimal weight:    3.9990
   chunk 45 optimal weight:    0.0170
   chunk 48 optimal weight:    0.7980
   chunk 9 optimal weight:    1.9990
   chunk 14 optimal weight:    3.9990
   chunk 30 optimal weight:    0.7980
   chunk 39 optimal weight:    0.7980
   chunk 26 optimal weight:    0.0070
   chunk 19 optimal weight:    0.7980
   chunk 22 optimal weight:    0.9980
   chunk 10 optimal weight:    0.5980
   overall best weight:    0.4436

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
A 145 ASN
A 368 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3518 r_free = 0.3518 target = 0.145488 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 46)----------------|
| r_work = 0.3280 r_free = 0.3280 target = 0.123700 restraints weight = 4870.586|
|-----------------------------------------------------------------------------|
r_work (start): 0.3340 rms_B_bonded: 1.51
r_work: 0.3223 rms_B_bonded: 2.25 restraints_weight: 0.5000
r_work: 0.3070 rms_B_bonded: 3.89 restraints_weight: 0.2500
r_work (final): 0.3070
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7468
moved from start:          0.1508

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= 0.129
  Angle     :  0.543   5.377   6484  Z= 0.277
  Chirality :  0.040   0.147    721
  Planarity :  0.004   0.045    747
  Dihedral  :  8.752  59.477   1027
  Min Nonbonded Distance : 2.502

Molprobity Statistics.
  All-atom Clashscore : 7.93
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.90 %
    Favored  : 96.10 %
  Rotamer:
    Outliers :  2.40 %
    Allowed  : 15.47 %
    Favored  : 82.14 %
  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:  0.13 (0.37), residues: 538
  helix:  0.83 (0.27), residues: 372
  sheet:  None (None), residues: 0
  loop : -1.57 (0.53), residues: 166

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG A 564 
 TYR   0.014   0.001   TYR A 267 
 PHE   0.018   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        0.00297 /  0.13 ( 4792)
  covalent geometry    : angle       0.53844 /  0.28 ( 6479)
  SS BOND              : bond        0.00069 /  0.04 (    1)
  SS BOND              : angle       1.95239 /  1.05 (    2)
  hydrogen bonds       : bond        0.04705 /  3.03 (  268)
  hydrogen bonds       : angle       4.35424 /  2.93 (  780)
  Misc. bond           : bond        0.00180 /  0.09 (    3)
  link_NAG-ASN         : bond        0.00306 /  0.16 (    1)
  link_NAG-ASN         : angle       2.92868 /  1.62 (    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
  52 residues out of total 459 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 41
  time to evaluate  : 0.098 
Fit side-chains
REVERT: A  229 GLU cc_start: 0.7007 (tt0) cc_final: 0.6741 (tt0)
REVERT: A  310 LEU cc_start: 0.7552 (tp) cc_final: 0.7304 (tt)
  outliers start: 11
  outliers final: 7
  residues processed: 50
  average time/residue: 0.0454
  time to fit residues: 3.2247
Evaluate side-chains
  42 residues out of total 459 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 35
  time to evaluate  : 0.163 
-------------------------------------------------------------------------------
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  527 GLU
Chi-restraints excluded: chain A residue  528 MET
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 54
   random chunks:
   chunk 48 optimal weight:    0.0040
   chunk 23 optimal weight:    4.9990
   chunk 43 optimal weight:    0.5980
   chunk 6 optimal weight:    2.9990
   chunk 17 optimal weight:    0.9980
   chunk 46 optimal weight:    0.3980
   chunk 40 optimal weight:    0.9990
   chunk 53 optimal weight:    0.9990
   chunk 0 optimal weight:    2.9990
   chunk 39 optimal weight:    0.5980
   chunk 45 optimal weight:    1.9990
   overall best weight:    0.5192

-------------------------------------------------------------------------------
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 = 0.3514 r_free = 0.3514 target = 0.145226 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.3283 r_free = 0.3283 target = 0.124215 restraints weight = 4911.595|
|-----------------------------------------------------------------------------|
r_work (start): 0.3349 rms_B_bonded: 1.41
r_work: 0.3237 rms_B_bonded: 2.11 restraints_weight: 0.5000
r_work: 0.3091 rms_B_bonded: 3.61 restraints_weight: 0.2500
r_work (final): 0.3091
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7412
moved from start:          0.1636

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= 0.136
  Angle     :  0.556   7.041   6484  Z= 0.283
  Chirality :  0.041   0.148    721
  Planarity :  0.004   0.040    747
  Dihedral  :  8.483  59.265   1027
  Min Nonbonded Distance : 2.497

Molprobity Statistics.
  All-atom Clashscore : 8.14
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.35 %
    Favored  : 96.65 %
  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:  0.23 (0.37), residues: 538
  helix:  0.90 (0.27), residues: 372
  sheet:  None (None), residues: 0
  loop : -1.50 (0.54), residues: 166

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.000   ARG A 241 
 TYR   0.026   0.001   TYR A 267 
 PHE   0.018   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        0.00320 /  0.14 ( 4792)
  covalent geometry    : angle       0.55204 /  0.28 ( 6479)
  SS BOND              : bond        0.00139 /  0.07 (    1)
  SS BOND              : angle       1.93729 /  1.03 (    2)
  hydrogen bonds       : bond        0.04745 /  3.05 (  268)
  hydrogen bonds       : angle       4.32620 /  2.91 (  780)
  Misc. bond           : bond        0.00187 /  0.10 (    3)
  link_NAG-ASN         : bond        0.00309 /  0.16 (    1)
  link_NAG-ASN         : angle       2.72268 /  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
  52 residues out of total 459 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 37
  time to evaluate  : 0.090 
Fit side-chains
REVERT: A  229 GLU cc_start: 0.6977 (tt0) cc_final: 0.6714 (tt0)
REVERT: A  241 ARG cc_start: 0.7823 (mtp85) cc_final: 0.7226 (mtp180)
REVERT: A  310 LEU cc_start: 0.7472 (tp) cc_final: 0.7243 (tt)
REVERT: A  430 MET cc_start: 0.7672 (OUTLIER) cc_final: 0.7451 (ttp)
  outliers start: 15
  outliers final: 9
  residues processed: 48
  average time/residue: 0.0401
  time to fit residues: 2.6599
Evaluate side-chains
  45 residues out of total 459 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 35
  time to evaluate  : 0.092 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
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  527 GLU
Chi-restraints excluded: chain A residue  528 MET
Chi-restraints excluded: chain A residue  585 SER
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 54
   random chunks:
   chunk 37 optimal weight:    0.5980
   chunk 6 optimal weight:    1.9990
   chunk 49 optimal weight:    0.5980
   chunk 52 optimal weight:    0.9980
   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:    1.9990
   chunk 10 optimal weight:    0.9990
   chunk 40 optimal weight:    0.9980
   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 = 0.3509 r_free = 0.3509 target = 0.144577 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 45)----------------|
| r_work = 0.3269 r_free = 0.3269 target = 0.122834 restraints weight = 4936.951|
|-----------------------------------------------------------------------------|
r_work (start): 0.3333 rms_B_bonded: 1.47
r_work: 0.3215 rms_B_bonded: 2.22 restraints_weight: 0.5000
r_work: 0.3067 rms_B_bonded: 3.76 restraints_weight: 0.2500
r_work (final): 0.3067
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7413
moved from start:          0.1609

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     :  0.568   6.597   6484  Z= 0.291
  Chirality :  0.042   0.146    721
  Planarity :  0.004   0.042    747
  Dihedral  :  8.395  56.828   1027
  Min Nonbonded Distance : 2.512

Molprobity Statistics.
  All-atom Clashscore : 7.93
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.28 %
    Favored  : 95.72 %
  Rotamer:
    Outliers :  2.83 %
    Allowed  : 15.90 %
    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:  0.20 (0.37), residues: 538
  helix:  0.89 (0.26), residues: 371
  sheet:  None (None), residues: 0
  loop : -1.53 (0.54), residues: 167

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.000   ARG A 241 
 TYR   0.024   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        0.00366 /  0.15 ( 4792)
  covalent geometry    : angle       0.56449 /  0.29 ( 6479)
  SS BOND              : bond        0.00205 /  0.11 (    1)
  SS BOND              : angle       2.09615 /  1.11 (    2)
  hydrogen bonds       : bond        0.04902 /  3.14 (  268)
  hydrogen bonds       : angle       4.38523 /  2.96 (  780)
  Misc. bond           : bond        0.00217 /  0.11 (    3)
  link_NAG-ASN         : bond        0.00277 /  0.15 (    1)
  link_NAG-ASN         : angle       2.59726 /  1.45 (    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: 13
    poor density    : 40
  time to evaluate  : 0.156 
Fit side-chains
REVERT: A  229 GLU cc_start: 0.6990 (tt0) cc_final: 0.6714 (tt0)
REVERT: A  241 ARG cc_start: 0.7792 (mtp85) cc_final: 0.7252 (mtp180)
REVERT: A  310 LEU cc_start: 0.7501 (tp) cc_final: 0.7265 (tt)
REVERT: A  430 MET cc_start: 0.7628 (OUTLIER) cc_final: 0.7404 (ttp)
REVERT: A  444 GLU cc_start: 0.6624 (OUTLIER) cc_final: 0.6291 (tp30)
  outliers start: 13
  outliers final: 9
  residues processed: 50
  average time/residue: 0.0508
  time to fit residues: 3.5539
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  : 0.119 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
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  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=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 54
   random chunks:
   chunk 46 optimal weight:    0.5980
   chunk 22 optimal weight:    0.4980
   chunk 50 optimal weight:    4.9990
   chunk 12 optimal weight:    2.9990
   chunk 27 optimal weight:    0.0060
   chunk 53 optimal weight:    2.9990
   chunk 17 optimal weight:    0.0870
   chunk 44 optimal weight:    0.6980
   chunk 5 optimal weight:    0.9980
   chunk 52 optimal weight:    0.9990
   chunk 20 optimal weight:    0.9990
   overall best weight:    0.3774

-------------------------------------------------------------------------------
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 = 0.3584 r_free = 0.3584 target = 0.150078 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.3338 r_free = 0.3338 target = 0.127256 restraints weight = 4845.070|
|-----------------------------------------------------------------------------|
r_work (start): 0.3366 rms_B_bonded: 1.57
r_work: 0.3243 rms_B_bonded: 2.43 restraints_weight: 0.5000
r_work: 0.3090 rms_B_bonded: 4.18 restraints_weight: 0.2500
r_work (final): 0.3090
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7665
moved from start:          0.1882

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.039   4797  Z= 0.119
  Angle     :  0.530   6.033   6484  Z= 0.271
  Chirality :  0.041   0.215    721
  Planarity :  0.004   0.043    747
  Dihedral  :  7.807  58.265   1027
  Min Nonbonded Distance : 2.496

Molprobity Statistics.
  All-atom Clashscore : 7.62
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.72 %
    Favored  : 96.28 %
  Rotamer:
    Outliers :  2.61 %
    Allowed  : 15.90 %
    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:  1.10 (0.27), residues: 369
  sheet:  None (None), residues: 0
  loop : -1.49 (0.53), residues: 169

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG A 241 
 TYR   0.019   0.001   TYR A 267 
 PHE   0.015   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        0.00274 /  0.12 ( 4792)
  covalent geometry    : angle       0.52639 /  0.27 ( 6479)
  SS BOND              : bond        0.00080 /  0.04 (    1)
  SS BOND              : angle       1.63659 /  0.88 (    2)
  hydrogen bonds       : bond        0.04453 /  2.87 (  268)
  hydrogen bonds       : angle       4.20895 /  2.83 (  780)
  Misc. bond           : bond        0.00164 /  0.09 (    3)
  link_NAG-ASN         : bond        0.00330 /  0.17 (    1)
  link_NAG-ASN         : angle       2.49501 /  1.39 (    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
  52 residues out of total 459 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 40
  time to evaluate  : 0.136 
Fit side-chains
REVERT: A  229 GLU cc_start: 0.7344 (tt0) cc_final: 0.7101 (tt0)
REVERT: A  310 LEU cc_start: 0.7773 (tp) cc_final: 0.7547 (tt)
REVERT: A  430 MET cc_start: 0.7877 (OUTLIER) cc_final: 0.7663 (ttp)
  outliers start: 12
  outliers final: 7
  residues processed: 49
  average time/residue: 0.0459
  time to fit residues: 3.1557
Evaluate side-chains
  47 residues out of total 459 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 39
  time to evaluate  : 0.152 
-------------------------------------------------------------------------------
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  430 MET
Chi-restraints excluded: chain A residue  527 GLU
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:    0.3980
   chunk 41 optimal weight:    0.9990
   chunk 11 optimal weight:    0.9980
   chunk 29 optimal weight:    0.5980
   chunk 31 optimal weight:    1.9990
   chunk 19 optimal weight:    1.9990
   chunk 50 optimal weight:    0.9990
   chunk 13 optimal weight:    2.9990
   chunk 36 optimal weight:    1.9990
   chunk 40 optimal weight:    0.8980
   chunk 0 optimal weight:    2.9990
   overall best weight:    0.7782

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
A 240 HIS

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3504 r_free = 0.3504 target = 0.144080 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 43)----------------|
| r_work = 0.3259 r_free = 0.3259 target = 0.122115 restraints weight = 4981.011|
|-----------------------------------------------------------------------------|
r_work (start): 0.3299 rms_B_bonded: 1.52
r_work: 0.3180 rms_B_bonded: 2.30 restraints_weight: 0.5000
r_work: 0.3028 rms_B_bonded: 3.91 restraints_weight: 0.2500
r_work (final): 0.3028
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7394
moved from start:          0.1772

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.051   4797  Z= 0.168
  Angle     :  0.580   6.489   6484  Z= 0.297
  Chirality :  0.043   0.195    721
  Planarity :  0.004   0.043    747
  Dihedral  :  8.048  59.112   1027
  Min Nonbonded Distance : 2.496

Molprobity Statistics.
  All-atom Clashscore : 8.04
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.28 %
    Favored  : 95.72 %
  Rotamer:
    Outliers :  1.96 %
    Allowed  : 16.56 %
    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:  0.29 (0.37), residues: 538
  helix:  0.97 (0.26), residues: 371
  sheet:  None (None), residues: 0
  loop : -1.55 (0.54), residues: 167

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.000   ARG A 241 
 TYR   0.026   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        0.00406 /  0.17 ( 4792)
  covalent geometry    : angle       0.57642 /  0.30 ( 6479)
  SS BOND              : bond        0.00294 /  0.15 (    1)
  SS BOND              : angle       2.17645 /  1.15 (    2)
  hydrogen bonds       : bond        0.04944 /  3.16 (  268)
  hydrogen bonds       : angle       4.38850 /  2.98 (  780)
  Misc. bond           : bond        0.00241 /  0.13 (    3)
  link_NAG-ASN         : bond        0.00284 /  0.15 (    1)
  link_NAG-ASN         : angle       2.44858 /  1.37 (    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: 9
    poor density    : 40
  time to evaluate  : 0.143 
Fit side-chains
REVERT: A  229 GLU cc_start: 0.6978 (tt0) cc_final: 0.6704 (tt0)
REVERT: A  241 ARG cc_start: 0.7755 (mtp85) cc_final: 0.7042 (mtp180)
REVERT: A  310 LEU cc_start: 0.7535 (tp) cc_final: 0.7293 (tt)
REVERT: A  430 MET cc_start: 0.7614 (ttm) cc_final: 0.7390 (ttp)
  outliers start: 9
  outliers final: 9
  residues processed: 47
  average time/residue: 0.0455
  time to fit residues: 3.0782
Evaluate side-chains
  49 residues out of total 459 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 40
  time to evaluate  : 0.143 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
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  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:    0.7980
   chunk 5 optimal weight:    1.9990
   chunk 28 optimal weight:    1.9990
   chunk 22 optimal weight:    0.5980
   chunk 40 optimal weight:    0.1980
   chunk 50 optimal weight:    3.9990
   chunk 1 optimal weight:    0.6980
   chunk 8 optimal weight:    0.7980
   chunk 3 optimal weight:    3.9990
   chunk 47 optimal weight:    0.8980
   chunk 17 optimal weight:    0.5980
   overall best weight:    0.5780

-------------------------------------------------------------------------------
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 = 0.3516 r_free = 0.3516 target = 0.145399 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 45)----------------|
| r_work = 0.3286 r_free = 0.3286 target = 0.124612 restraints weight = 4899.293|
|-----------------------------------------------------------------------------|
r_work (start): 0.3317 rms_B_bonded: 1.39
r_work: 0.3208 rms_B_bonded: 2.09 restraints_weight: 0.5000
r_work: 0.3065 rms_B_bonded: 3.59 restraints_weight: 0.2500
r_work (final): 0.3065
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7426
moved from start:          0.1854

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.047   4797  Z= 0.142
  Angle     :  0.554   6.102   6484  Z= 0.284
  Chirality :  0.041   0.218    721
  Planarity :  0.004   0.044    747
  Dihedral  :  7.887  59.970   1027
  Min Nonbonded Distance : 2.507

Molprobity Statistics.
  All-atom Clashscore : 7.93
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.72 %
    Favored  : 96.28 %
  Rotamer:
    Outliers :  2.40 %
    Allowed  : 16.56 %
    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:  0.34 (0.37), residues: 538
  helix:  1.01 (0.26), residues: 370
  sheet:  None (None), residues: 0
  loop : -1.53 (0.52), residues: 168

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.000   ARG A 241 
 TYR   0.022   0.001   TYR A 267 
 PHE   0.016   0.001   PHE A 548 
 TRP   0.008   0.001   TRP A 458 
 HIS   0.002   0.001   HIS A 143 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00338 /  0.14 ( 4792)
  covalent geometry    : angle       0.55096 /  0.28 ( 6479)
  SS BOND              : bond        0.00192 /  0.10 (    1)
  SS BOND              : angle       1.86384 /  0.99 (    2)
  hydrogen bonds       : bond        0.04753 /  3.05 (  268)
  hydrogen bonds       : angle       4.32993 /  2.93 (  780)
  Misc. bond           : bond        0.00207 /  0.11 (    3)
  link_NAG-ASN         : bond        0.00323 /  0.17 (    1)
  link_NAG-ASN         : angle       2.40395 /  1.34 (    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
  54 residues out of total 459 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 43
  time to evaluate  : 0.147 
Fit side-chains
REVERT: A  241 ARG cc_start: 0.7719 (mtp85) cc_final: 0.7040 (mtp180)
REVERT: A  310 LEU cc_start: 0.7610 (tp) cc_final: 0.7366 (tt)
REVERT: A  430 MET cc_start: 0.7650 (OUTLIER) cc_final: 0.7430 (ttp)
  outliers start: 11
  outliers final: 9
  residues processed: 51
  average time/residue: 0.0548
  time to fit residues: 3.9522
Evaluate side-chains
  52 residues out of total 459 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 42
  time to evaluate  : 0.119 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
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  430 MET
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:    0.6980
   chunk 9 optimal weight:    1.9990
   chunk 0 optimal weight:    2.9990
   chunk 16 optimal weight:    0.7980
   chunk 46 optimal weight:    0.5980
   chunk 14 optimal weight:    0.0870
   chunk 29 optimal weight:    0.7980
   chunk 38 optimal weight:    0.8980
   chunk 51 optimal weight:    0.5980
   chunk 28 optimal weight:    0.7980
   chunk 41 optimal weight:    0.8980
   overall best weight:    0.5558

-------------------------------------------------------------------------------
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 = 0.145746 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 46)----------------|
| r_work = 0.3288 r_free = 0.3288 target = 0.124825 restraints weight = 4950.424|
|-----------------------------------------------------------------------------|
r_work (start): 0.3321 rms_B_bonded: 1.40
r_work: 0.3211 rms_B_bonded: 2.11 restraints_weight: 0.5000
r_work: 0.3067 rms_B_bonded: 3.61 restraints_weight: 0.2500
r_work (final): 0.3067
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7429
moved from start:          0.1906

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.045   4797  Z= 0.140
  Angle     :  0.554   6.104   6484  Z= 0.284
  Chirality :  0.041   0.215    721
  Planarity :  0.004   0.043    747
  Dihedral  :  7.808  59.658   1027
  Min Nonbonded Distance : 2.510

Molprobity Statistics.
  All-atom Clashscore : 7.93
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.28 %
    Favored  : 95.72 %
  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:  0.36 (0.37), residues: 538
  helix:  1.04 (0.27), residues: 370
  sheet:  None (None), residues: 0
  loop : -1.53 (0.52), residues: 168

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.000   ARG A 241 
 TYR   0.023   0.001   TYR A 267 
 PHE   0.016   0.001   PHE A 548 
 TRP   0.008   0.001   TRP A 458 
 HIS   0.002   0.001   HIS A 143 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00333 /  0.14 ( 4792)
  covalent geometry    : angle       0.55056 /  0.28 ( 6479)
  SS BOND              : bond        0.00267 /  0.14 (    1)
  SS BOND              : angle       1.83801 /  0.98 (    2)
  hydrogen bonds       : bond        0.04723 /  3.03 (  268)
  hydrogen bonds       : angle       4.32175 /  2.93 (  780)
  Misc. bond           : bond        0.00207 /  0.11 (    3)
  link_NAG-ASN         : bond        0.00258 /  0.14 (    1)
  link_NAG-ASN         : angle       2.36996 /  1.32 (    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
  51 residues out of total 459 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 41
  time to evaluate  : 0.156 
Fit side-chains
REVERT: A  241 ARG cc_start: 0.7725 (mtp85) cc_final: 0.7058 (mtp180)
REVERT: A  310 LEU cc_start: 0.7538 (tp) cc_final: 0.7309 (tt)
  outliers start: 10
  outliers final: 9
  residues processed: 48
  average time/residue: 0.0436
  time to fit residues: 3.0100
Evaluate side-chains
  50 residues out of total 459 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 41
  time to evaluate  : 0.152 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
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  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:    0.2980
   chunk 30 optimal weight:    0.9990
   chunk 28 optimal weight:    0.9990
   chunk 49 optimal weight:    0.4980
   chunk 13 optimal weight:    2.9990
   chunk 17 optimal weight:    0.7980
   chunk 8 optimal weight:    0.6980
   chunk 39 optimal weight:    0.5980
   chunk 34 optimal weight:    1.9990
   chunk 10 optimal weight:    0.5980
   chunk 52 optimal weight:    0.0970
   overall best weight:    0.4178

-------------------------------------------------------------------------------
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 = 0.3540 r_free = 0.3540 target = 0.147463 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 44)----------------|
| r_work = 0.3305 r_free = 0.3305 target = 0.125844 restraints weight = 4923.398|
|-----------------------------------------------------------------------------|
r_work (start): 0.3348 rms_B_bonded: 1.45
r_work: 0.3240 rms_B_bonded: 2.15 restraints_weight: 0.5000
r_work: 0.3093 rms_B_bonded: 3.68 restraints_weight: 0.2500
r_work (final): 0.3093
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7289
moved from start:          0.2051

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.039   4797  Z= 0.125
  Angle     :  0.538   6.670   6484  Z= 0.276
  Chirality :  0.040   0.213    721
  Planarity :  0.004   0.044    747
  Dihedral  :  7.563  59.970   1027
  Min Nonbonded Distance : 2.482

Molprobity Statistics.
  All-atom Clashscore : 7.31
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.90 %
    Favored  : 96.10 %
  Rotamer:
    Outliers :  1.96 %
    Allowed  : 17.21 %
    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:  0.47 (0.37), residues: 538
  helix:  1.13 (0.27), residues: 369
  sheet:  None (None), residues: 0
  loop : -1.50 (0.52), residues: 169

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   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        0.00295 /  0.13 ( 4792)
  covalent geometry    : angle       0.53482 /  0.28 ( 6479)
  SS BOND              : bond        0.00201 /  0.11 (    1)
  SS BOND              : angle       1.61340 /  0.86 (    2)
  hydrogen bonds       : bond        0.04481 /  2.88 (  268)
  hydrogen bonds       : angle       4.24840 /  2.88 (  780)
  Misc. bond           : bond        0.00180 /  0.09 (    3)
  link_NAG-ASN         : bond        0.00311 /  0.16 (    1)
  link_NAG-ASN         : angle       2.38822 /  1.33 (    3)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 1003.55 seconds
wall clock time: 17 minutes 55.85 seconds (1075.85 seconds total)