Starting phenix.real_space_refine
on Tue Feb  3 14:34:17 2026 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/9juq_61834/02_2026/9juq_61834.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/9juq_61834/02_2026/9juq_61834.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.2
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/9juq_61834/02_2026/9juq_61834.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/9juq_61834/02_2026/9juq_61834.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/9juq_61834/02_2026/9juq_61834.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/9juq_61834/02_2026/9juq_61834.cif"
  }
  resolution = 3.2
  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=   0.033
Set stop_for_unknowns flag
  Set to: True
Assert model is a single copy model
Assert all atoms have isotropic ADPs
Construct map_model_manager
Extract box with map and model
Check model and map are aligned
Set scattering table
  Set to: electron
  Number of scattering types: 4
    Type Number    sf(0)   Gaussians
     S      35      5.16       5
     C    2492      2.51       5
     N     594      2.21       5
     O     623      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 4 residue(s): 0.00s

  Monomer Library directory:
    "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5952/lib/python3.9/site-packages/chem_data/mon_lib"
  Total number of atoms: 3744
  Number of models: 1
  Model: ""
    Number of chains: 1
    Chain: "A"
      Number of atoms: 3744
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 494, 3744
          Classifications: {'peptide': 494}
          Incomplete info: {'backbone_only': 1, 'truncation_to_alanine': 26}
          Link IDs: {'PTRANS': 29, 'TRANS': 464}
          Chain breaks: 9
          Unresolved non-hydrogen bonds: 100
          Unresolved non-hydrogen angles: 122
          Unresolved non-hydrogen dihedrals: 80
          Unresolved non-hydrogen chiralities: 5
          Planarities with less than four sites: {'ASN:plan1': 2, 'GLU:plan': 3, 'GLN:plan1': 2, 'ASP:plan': 4, 'ARG:plan': 4, 'PHE:plan': 1}
          Unresolved non-hydrogen planarities: 64
  Time building chain proxies: 0.75, per 1000 atoms: 0.20
  Number of scatterers: 3744
  At special positions: 0
  Unit cell: (93.5, 68.85, 73.1, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 4
    Type Number    sf(0)
     S      35     16.00
     O     623      8.00
     N     594      7.00
     C    2492      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=7, symmetry=0
    Simple disulfide: pdb=" SG  CYS A 143 " - pdb=" SG  CYS A 448 " distance=2.03
    Simple disulfide: pdb=" SG  CYS A 420 " - pdb=" SG  CYS A 511 " distance=2.03
    Simple disulfide: pdb=" SG  CYS A 444 " - pdb=" SG  CYS A 494 " distance=2.03
    Simple disulfide: pdb=" SG  CYS A 450 " - pdb=" SG  CYS A 470 " distance=2.03
    Simple disulfide: pdb=" SG  CYS A 459 " - pdb=" SG  CYS A 507 " distance=2.03
    Simple disulfide: pdb=" SG  CYS A 474 " - pdb=" SG  CYS A 492 " distance=2.03
    Simple disulfide: pdb=" SG  CYS A 580 " - pdb=" SG  CYS A 594 " 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=0, symmetry=0
  Time building additional restraints: 0.17
  Conformation dependent library (CDL) restraints added in 87.1 milliseconds
  

  948 Ramachandran restraints generated.
    474 Oldfield, 0 Emsley, 474 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  916

  Finding SS restraints...
    Secondary structure from input PDB file:
      26 helices and 2 sheets defined
      73.3% alpha, 1.8% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.09
  Creating SS restraints...
    Processing helix  chain 'A' and resid 30 through 63
      removed outlier: 4.956A  pdb=" N   THR A  57 " --> pdb=" O   LYS A  53 " (cutoff:3.500A)
      removed outlier: 4.709A  pdb=" N   THR A  58 " --> pdb=" O   SER A  54 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 77 through 91
      removed outlier: 4.888A  pdb=" N   ILE A  86 " --> pdb=" O   ALA A  82 " (cutoff:3.500A)
      removed outlier: 5.105A  pdb=" N   PHE A  87 " --> pdb=" O   ILE A  83 " (cutoff:3.500A)
      removed outlier: 3.769A  pdb=" N   PHE A  91 " --> pdb=" O   PHE A  87 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 92 through 94
      No H-bonds generated for 'chain 'A' and resid 92 through 94'
    Processing helix  chain 'A' and resid 96 through 122
      Proline residue:  A 118  - end of helix
    Processing helix  chain 'A' and resid 170 through 184
      removed outlier: 3.524A  pdb=" N   VAL A 175 " --> pdb=" O   GLY A 171 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 187 through 198
      removed outlier: 3.657A  pdb=" N   SER A 193 " --> pdb=" O   PRO A 189 " (cutoff:3.500A)
      removed outlier: 3.934A  pdb=" N   TYR A 194 " --> pdb=" O   PHE A 190 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 203 through 215
    Processing helix  chain 'A' and resid 217 through 230
    Processing helix  chain 'A' and resid 256 through 273
      removed outlier: 3.745A  pdb=" N   GLY A 260 " --> pdb=" O   ALA A 256 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 274 through 277
    Processing helix  chain 'A' and resid 308 through 314
      removed outlier: 3.585A  pdb=" N   ILE A 312 " --> pdb=" O   LEU A 308 " (cutoff:3.500A)
      removed outlier: 3.664A  pdb=" N   LYS A 313 " --> pdb=" O   VAL A 309 " (cutoff:3.500A)
      removed outlier: 3.548A  pdb=" N   ARG A 314 " --> pdb=" O   ASP A 310 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'A' and resid 308 through 314'
    Processing helix  chain 'A' and resid 314 through 324
      removed outlier: 3.501A  pdb=" N   ARG A 321 " --> pdb=" O   CYS A 317 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 325 through 336
    Processing helix  chain 'A' and resid 338 through 348
      removed outlier: 3.646A  pdb=" N   ILE A 342 " --> pdb=" O   PHE A 338 " (cutoff:3.500A)
      removed outlier: 3.537A  pdb=" N   GLY A 344 " --> pdb=" O   SER A 340 " (cutoff:3.500A)
      removed outlier: 3.826A  pdb=" N   PHE A 348 " --> pdb=" O   GLY A 344 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 348 through 358
    Processing helix  chain 'A' and resid 360 through 371
      removed outlier: 3.809A  pdb=" N   ASN A 365 " --> pdb=" O   ALA A 361 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 371 through 390
      removed outlier: 3.601A  pdb=" N   GLY A 384 " --> pdb=" O   MET A 380 " (cutoff:3.500A)
      removed outlier: 3.606A  pdb=" N   MET A 387 " --> pdb=" O   GLY A 383 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 396 through 411
      removed outlier: 4.021A  pdb=" N   THR A 403 " --> pdb=" O   ARG A 399 " (cutoff:3.500A)
      removed outlier: 3.895A  pdb=" N   ILE A 410 " --> pdb=" O   THR A 406 " (cutoff:3.500A)
      removed outlier: 3.850A  pdb=" N   LEU A 411 " --> pdb=" O   ILE A 407 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 412 through 417
    Processing helix  chain 'A' and resid 468 through 473
    Processing helix  chain 'A' and resid 511 through 513
      No H-bonds generated for 'chain 'A' and resid 511 through 513'
    Processing helix  chain 'A' and resid 514 through 530
    Processing helix  chain 'A' and resid 532 through 543
      removed outlier: 3.572A  pdb=" N   VAL A 540 " --> pdb=" O   LEU A 536 " (cutoff:3.500A)
      removed outlier: 3.744A  pdb=" N   LEU A 541 " --> pdb=" O   TYR A 537 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 548 through 564
    Processing helix  chain 'A' and resid 566 through 577
      removed outlier: 4.115A  pdb=" N   ALA A 570 " --> pdb=" O   LEU A 566 " (cutoff:3.500A)
      removed outlier: 3.537A  pdb=" N   THR A 575 " --> pdb=" O   LEU A 571 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 598 through 631
      removed outlier: 3.600A  pdb=" N   ASP A 604 " --> pdb=" O   ASP A 600 " (cutoff:3.500A)
      removed outlier: 3.540A  pdb=" N   GLN A 610 " --> pdb=" O   TYR A 606 " (cutoff:3.500A)
      removed outlier: 3.625A  pdb=" N   TYR A 613 " --> pdb=" O   LEU A 609 " (cutoff:3.500A)
      removed outlier: 3.833A  pdb=" N   LYS A 614 " --> pdb=" O   GLN A 610 " (cutoff:3.500A)
      removed outlier: 3.644A  pdb=" N   LEU A 621 " --> pdb=" O   GLY A 617 " (cutoff:3.500A)
      removed outlier: 3.657A  pdb=" N   LYS A 630 " --> pdb=" O   TRP A 626 " (cutoff:3.500A)
    Processing sheet with id=AA1, first strand: chain 'A' and resid 465 through 466
      removed outlier: 3.555A  pdb=" N   LYS A 503 " --> pdb=" O   CYS A 459 " (cutoff:3.500A)
      removed outlier: 3.755A  pdb=" N   ALA A 502 " --> pdb=" O   TYR A 489 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'A' and resid 582 through 583
      removed outlier: 6.896A  pdb=" N   ARG A 582 " --> pdb=" O   ALA A 595 " (cutoff:3.500A)

    232 hydrogen bonds defined for protein.
    681 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: 0.39

  Time building geometry restraints manager: 0.25 seconds

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

  Histogram of bond lengths:
        1.23 -     1.34: 1115
        1.34 -     1.46: 949
        1.46 -     1.58: 1729
        1.58 -     1.69: 0
        1.69 -     1.81: 49
  Bond restraints: 3842
  Sorted by residual:
  bond pdb=" CA  LEU A 117 "
       pdb=" C   LEU A 117 "
    ideal  model  delta    sigma   weight residual
    1.521  1.531 -0.009 1.17e-02 7.31e+03 6.12e-01
  bond pdb=" CG1 ILE A 101 "
       pdb=" CD1 ILE A 101 "
    ideal  model  delta    sigma   weight residual
    1.513  1.483  0.030 3.90e-02 6.57e+02 5.74e-01
  bond pdb=" N   MET A 229 "
       pdb=" CA  MET A 229 "
    ideal  model  delta    sigma   weight residual
    1.456  1.466 -0.010 1.32e-02 5.74e+03 5.49e-01
  bond pdb=" CA  VAL A 413 "
       pdb=" CB  VAL A 413 "
    ideal  model  delta    sigma   weight residual
    1.539  1.535  0.004 5.40e-03 3.43e+04 5.17e-01
  bond pdb=" C   LEU A 566 "
       pdb=" N   PRO A 567 "
    ideal  model  delta    sigma   weight residual
    1.334  1.351 -0.017 2.34e-02 1.83e+03 5.12e-01
  ... (remaining 3837 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     1.40: 5101
        1.40 -     2.80: 88
        2.80 -     4.20: 22
        4.20 -     5.60: 15
        5.60 -     7.00: 2
  Bond angle restraints: 5228
  Sorted by residual:
  angle pdb=" C   THR A 184 "
        pdb=" N   VAL A 185 "
        pdb=" CA  VAL A 185 "
      ideal   model   delta    sigma   weight residual
     120.33  122.85   -2.52 8.00e-01 1.56e+00 9.92e+00
  angle pdb=" C   VAL A 185 "
        pdb=" CA  VAL A 185 "
        pdb=" CB  VAL A 185 "
      ideal   model   delta    sigma   weight residual
     114.00  110.01    3.99 1.31e+00 5.83e-01 9.27e+00
  angle pdb=" N   MET A 418 "
        pdb=" CA  MET A 418 "
        pdb=" C   MET A 418 "
      ideal   model   delta    sigma   weight residual
     112.97  109.92    3.05 1.06e+00 8.90e-01 8.27e+00
  angle pdb=" C   ALA A 426 "
        pdb=" N   GLU A 427 "
        pdb=" CA  GLU A 427 "
      ideal   model   delta    sigma   weight residual
     121.54  126.17   -4.63 1.91e+00 2.74e-01 5.87e+00
  angle pdb=" C   MET A 229 "
        pdb=" N   LEU A 230 "
        pdb=" CA  LEU A 230 "
      ideal   model   delta    sigma   weight residual
     122.27  118.50    3.77 1.85e+00 2.92e-01 4.16e+00
  ... (remaining 5223 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    12.05: 1902
       12.05 -    24.09: 220
       24.09 -    36.14: 88
       36.14 -    48.19: 26
       48.19 -    60.23: 10
  Dihedral angle restraints: 2246
    sinusoidal: 827
      harmonic: 1419
  Sorted by residual:
  dihedral pdb=" CA  VAL A 185 "
           pdb=" C   VAL A 185 "
           pdb=" N   PRO A 186 "
           pdb=" CA  PRO A 186 "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00 -164.47  -15.53     0      5.00e+00 4.00e-02 9.65e+00
  dihedral pdb=" CB  MET A 282 "
           pdb=" CG  MET A 282 "
           pdb=" SD  MET A 282 "
           pdb=" CE  MET A 282 "
      ideal   model   delta sinusoidal    sigma   weight residual
     -60.00 -111.57   51.57     3      1.50e+01 4.44e-03 9.03e+00
  dihedral pdb=" CG  ARG A 399 "
           pdb=" CD  ARG A 399 "
           pdb=" NE  ARG A 399 "
           pdb=" CZ  ARG A 399 "
      ideal   model   delta sinusoidal    sigma   weight residual
     -90.00 -128.65   38.65     2      1.50e+01 4.44e-03 8.32e+00
  ... (remaining 2243 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.029: 377
       0.029 -    0.058: 150
       0.058 -    0.087: 51
       0.087 -    0.116: 33
       0.116 -    0.145: 3
  Chirality restraints: 614
  Sorted by residual:
  chirality pdb=" CA  MET A 229 "
            pdb=" N   MET A 229 "
            pdb=" C   MET A 229 "
            pdb=" CB  MET A 229 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.37    0.15 2.00e-01 2.50e+01 5.26e-01
  chirality pdb=" CA  SER A 568 "
            pdb=" N   SER A 568 "
            pdb=" C   SER A 568 "
            pdb=" CB  SER A 568 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.38    0.13 2.00e-01 2.50e+01 4.54e-01
  chirality pdb=" CA  PRO A 118 "
            pdb=" N   PRO A 118 "
            pdb=" C   PRO A 118 "
            pdb=" CB  PRO A 118 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.72    2.60    0.12 2.00e-01 2.50e+01 3.59e-01
  ... (remaining 611 not shown)

  Planarity restraints: 641
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   PHE A 278 "   -0.029 5.00e-02 4.00e+02   4.41e-02 3.11e+00
        pdb=" N   PRO A 279 "    0.076 5.00e-02 4.00e+02
        pdb=" CA  PRO A 279 "   -0.023 5.00e-02 4.00e+02
        pdb=" CD  PRO A 279 "   -0.024 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   VAL A 413 "    0.023 5.00e-02 4.00e+02   3.41e-02 1.86e+00
        pdb=" N   PRO A 414 "   -0.059 5.00e-02 4.00e+02
        pdb=" CA  PRO A 414 "    0.017 5.00e-02 4.00e+02
        pdb=" CD  PRO A 414 "    0.019 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   LEU A 516 "    0.019 5.00e-02 4.00e+02   2.85e-02 1.30e+00
        pdb=" N   PRO A 517 "   -0.049 5.00e-02 4.00e+02
        pdb=" CA  PRO A 517 "    0.014 5.00e-02 4.00e+02
        pdb=" CD  PRO A 517 "    0.016 5.00e-02 4.00e+02
  ... (remaining 638 not shown)

  Histogram of nonbonded interaction distances:
        2.28 -     2.80: 991
        2.80 -     3.33: 3513
        3.33 -     3.85: 5693
        3.85 -     4.38: 6557
        4.38 -     4.90: 11569
  Nonbonded interactions: 28323
  Sorted by model distance:
  nonbonded pdb=" O   LEU A 574 "
            pdb=" ND1 HIS A 578 "
     model   vdw
     2.279 3.120
  nonbonded pdb=" O   ILE A  85 "
            pdb=" OG  SER A  89 "
     model   vdw
     2.303 3.040
  nonbonded pdb=" O   GLY A 344 "
            pdb=" OH  TYR A 606 "
     model   vdw
     2.303 3.040
  nonbonded pdb=" O   ARG A  94 "
            pdb=" NH2 ARG A 280 "
     model   vdw
     2.351 3.120
  nonbonded pdb=" NH2 ARG A 321 "
            pdb=" OE2 GLU A 548 "
     model   vdw
     2.375 3.120
  ... (remaining 28318 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:             2.010
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.000
  Construct map_model_manager:             0.010
  Extract box with map and model:          0.050
  Check model and map are aligned:         0.010
  Set scattering table:                    0.010
  Process input model:                     4.340
  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:1.360
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:    7.810
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7288
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      :  0.002   0.030   3849  Z= 0.109
  Angle     :  0.546   7.005   5242  Z= 0.274
  Chirality :  0.040   0.145    614
  Planarity :  0.004   0.044    641
  Dihedral  : 13.173  60.232   1309
  Min Nonbonded Distance : 2.279

Molprobity Statistics.
  All-atom Clashscore : 5.08
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.01 %
    Favored  : 95.99 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.25 %
    Favored  : 99.75 %
  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:  0.69 (0.40), residues: 474
  helix:  0.91 (0.30), residues: 318
  sheet:  None (None), residues: 0
  loop : -0.31 (0.52), residues: 156

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.001   0.000   ARG A 603 
 TYR   0.012   0.001   TYR A 223 
 PHE   0.006   0.001   PHE A 277 
 TRP   0.007   0.001   TRP A 170 
 HIS   0.002   0.001   HIS A  96 

Details of bonding type rmsd
  covalent geometry    : bond        0.00238 ( 3842)
  covalent geometry    : angle       0.54591 ( 5228)
  SS BOND              : bond        0.00230 (    7)
  SS BOND              : angle       0.65863 (   14)
  hydrogen bonds       : bond        0.24394 (  232)
  hydrogen bonds       : angle       6.75811 (  681)

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

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

  948 Ramachandran restraints generated.
    474 Oldfield, 0 Emsley, 474 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  948 Ramachandran restraints generated.
    474 Oldfield, 0 Emsley, 474 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  46 residues out of total 422 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 46
  time to evaluate  : 0.135 
Fit side-chains
   revert: symmetry clash
  outliers start: 0
  outliers final: 0
  residues processed: 46
  average time/residue: 0.0626
  time to fit residues: 3.7669
Evaluate side-chains
  41 residues out of total 422 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 41
  time to evaluate  : 0.134 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 49
   random chunks:
   chunk 24 optimal weight:    0.9990
   chunk 48 optimal weight:    0.8980
   chunk 26 optimal weight:    0.6980
   chunk 2 optimal weight:    0.1980
   chunk 16 optimal weight:    0.8980
   chunk 32 optimal weight:    0.0970
   chunk 31 optimal weight:    0.0770
   chunk 25 optimal weight:    0.8980
   chunk 19 optimal weight:    0.5980
   chunk 30 optimal weight:    0.7980
   chunk 22 optimal weight:    0.3980
   overall best weight:    0.2736

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

Flipped N/Q/H residues before XYZ refinement:
** A 534 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 = 0.3961 r_free = 0.3961 target = 0.173031 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 46)----------------|
| r_work = 0.3743 r_free = 0.3743 target = 0.149154 restraints weight = 3996.532|
|-----------------------------------------------------------------------------|
r_work (start): 0.3801 rms_B_bonded: 1.37
r_work: 0.3722 rms_B_bonded: 1.87 restraints_weight: 0.5000
r_work: 0.3614 rms_B_bonded: 3.32 restraints_weight: 0.2500
r_work (final): 0.3614
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7398
moved from start:          0.1278

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.023   3849  Z= 0.123
  Angle     :  0.575   8.899   5242  Z= 0.280
  Chirality :  0.040   0.122    614
  Planarity :  0.004   0.034    641
  Dihedral  :  3.810  17.275    518
  Min Nonbonded Distance : 2.560

Molprobity Statistics.
  All-atom Clashscore : 4.41
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.38 %
    Favored  : 96.62 %
  Rotamer:
    Outliers :  0.25 %
    Allowed  :  4.56 %
    Favored  : 95.19 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  1.64 (0.40), residues: 474
  helix:  1.58 (0.29), residues: 327
  sheet:  None (None), residues: 0
  loop :  0.10 (0.54), residues: 147

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.001   0.000   ARG A 582 
 TYR   0.018   0.001   TYR A  48 
 PHE   0.009   0.001   PHE A 190 
 TRP   0.003   0.000   TRP A 626 
 HIS   0.002   0.001   HIS A 533 

Details of bonding type rmsd
  covalent geometry    : bond        0.00253 ( 3842)
  covalent geometry    : angle       0.57527 ( 5228)
  SS BOND              : bond        0.00242 (    7)
  SS BOND              : angle       0.59416 (   14)
  hydrogen bonds       : bond        0.04596 (  232)
  hydrogen bonds       : angle       4.26200 (  681)

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

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

  948 Ramachandran restraints generated.
    474 Oldfield, 0 Emsley, 474 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  948 Ramachandran restraints generated.
    474 Oldfield, 0 Emsley, 474 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  42 residues out of total 422 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 41
  time to evaluate  : 0.137 
Fit side-chains
   revert: symmetry clash
REVERT: A  561 ARG cc_start: 0.7594 (tpt170) cc_final: 0.7291 (tpt170)
REVERT: A  616 LEU cc_start: 0.8070 (tt) cc_final: 0.7506 (mp)
  outliers start: 1
  outliers final: 0
  residues processed: 41
  average time/residue: 0.0630
  time to fit residues: 3.4295
Evaluate side-chains
  37 residues out of total 422 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 37
  time to evaluate  : 0.136 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 49
   random chunks:
   chunk 2 optimal weight:    0.7980
   chunk 45 optimal weight:    0.6980
   chunk 4 optimal weight:    0.2980
   chunk 9 optimal weight:    0.0980
   chunk 28 optimal weight:    0.9980
   chunk 3 optimal weight:    0.0050
   chunk 22 optimal weight:    0.3980
   chunk 21 optimal weight:    0.9990
   chunk 16 optimal weight:    0.0770
   chunk 40 optimal weight:    1.9990
   chunk 26 optimal weight:    0.8980
   overall best weight:    0.1752

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

Flipped N/Q/H residues before XYZ refinement:
** A 534 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 = 0.3989 r_free = 0.3989 target = 0.175706 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 45)----------------|
| r_work = 0.3761 r_free = 0.3761 target = 0.150790 restraints weight = 3928.027|
|-----------------------------------------------------------------------------|
r_work (start): 0.3818 rms_B_bonded: 1.46
r_work: 0.3736 rms_B_bonded: 2.02 restraints_weight: 0.5000
r_work: 0.3622 rms_B_bonded: 3.62 restraints_weight: 0.2500
r_work (final): 0.3622
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7373
moved from start:          0.1614

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.023   3849  Z= 0.103
  Angle     :  0.524   8.259   5242  Z= 0.250
  Chirality :  0.039   0.126    614
  Planarity :  0.004   0.027    641
  Dihedral  :  3.613  18.625    518
  Min Nonbonded Distance : 2.574

Molprobity Statistics.
  All-atom Clashscore : 3.74
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.95 %
    Favored  : 97.05 %
  Rotamer:
    Outliers :  0.51 %
    Allowed  :  6.33 %
    Favored  : 93.16 %
  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:  2.11 (0.40), residues: 474
  helix:  1.96 (0.30), residues: 329
  sheet:  None (None), residues: 0
  loop :  0.18 (0.55), residues: 145

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.001   0.000   ARG A 603 
 TYR   0.009   0.001   TYR A 194 
 PHE   0.007   0.001   PHE A 190 
 TRP   0.002   0.000   TRP A 258 
 HIS   0.001   0.000   HIS A 456 

Details of bonding type rmsd
  covalent geometry    : bond        0.00212 ( 3842)
  covalent geometry    : angle       0.52387 ( 5228)
  SS BOND              : bond        0.00223 (    7)
  SS BOND              : angle       0.46362 (   14)
  hydrogen bonds       : bond        0.03757 (  232)
  hydrogen bonds       : angle       3.76288 (  681)

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

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

  948 Ramachandran restraints generated.
    474 Oldfield, 0 Emsley, 474 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  948 Ramachandran restraints generated.
    474 Oldfield, 0 Emsley, 474 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  41 residues out of total 422 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 2
    poor density    : 39
  time to evaluate  : 0.137 
Fit side-chains
   revert: symmetry clash
REVERT: A  230 LEU cc_start: 0.6417 (OUTLIER) cc_final: 0.5767 (tt)
REVERT: A  561 ARG cc_start: 0.7678 (tpt170) cc_final: 0.7405 (tpt170)
REVERT: A  616 LEU cc_start: 0.7981 (tt) cc_final: 0.7493 (mp)
  outliers start: 2
  outliers final: 0
  residues processed: 41
  average time/residue: 0.0544
  time to fit residues: 3.0397
Evaluate side-chains
  37 residues out of total 422 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 36
  time to evaluate  : 0.152 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  230 LEU
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 49
   random chunks:
   chunk 23 optimal weight:    1.9990
   chunk 33 optimal weight:    8.9990
   chunk 38 optimal weight:    0.8980
   chunk 6 optimal weight:    1.9990
   chunk 40 optimal weight:    0.9990
   chunk 20 optimal weight:    0.9990
   chunk 25 optimal weight:    2.9990
   chunk 7 optimal weight:    0.5980
   chunk 34 optimal weight:    1.9990
   chunk 9 optimal weight:    0.4980
   chunk 39 optimal weight:    0.7980
   overall best weight:    0.7582

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

Flipped N/Q/H residues before XYZ refinement:
A  45 GLN
A 534 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3946 r_free = 0.3946 target = 0.170265 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 45)----------------|
| r_work = 0.3715 r_free = 0.3715 target = 0.145874 restraints weight = 3942.836|
|-----------------------------------------------------------------------------|
r_work (start): 0.3719 rms_B_bonded: 1.41
r_work: 0.3637 rms_B_bonded: 1.96 restraints_weight: 0.5000
r_work: 0.3524 rms_B_bonded: 3.52 restraints_weight: 0.2500
r_work (final): 0.3524
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7510
moved from start:          0.1746

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.030   3849  Z= 0.152
  Angle     :  0.619  13.383   5242  Z= 0.293
  Chirality :  0.042   0.135    614
  Planarity :  0.004   0.026    641
  Dihedral  :  3.914  20.046    518
  Min Nonbonded Distance : 2.478

Molprobity Statistics.
  All-atom Clashscore : 4.95
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.95 %
    Favored  : 97.05 %
  Rotamer:
    Outliers :  0.76 %
    Allowed  :  9.87 %
    Favored  : 89.37 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  1.89 (0.40), residues: 474
  helix:  1.82 (0.29), residues: 329
  sheet:  None (None), residues: 0
  loop :  0.02 (0.53), residues: 145

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG A  62 
 TYR   0.014   0.001   TYR A 194 
 PHE   0.014   0.001   PHE A 198 
 TRP   0.004   0.001   TRP A 253 
 HIS   0.003   0.001   HIS A  96 

Details of bonding type rmsd
  covalent geometry    : bond        0.00362 ( 3842)
  covalent geometry    : angle       0.61372 ( 5228)
  SS BOND              : bond        0.00450 (    7)
  SS BOND              : angle       1.62501 (   14)
  hydrogen bonds       : bond        0.04816 (  232)
  hydrogen bonds       : angle       3.83450 (  681)

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

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

  948 Ramachandran restraints generated.
    474 Oldfield, 0 Emsley, 474 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  948 Ramachandran restraints generated.
    474 Oldfield, 0 Emsley, 474 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  39 residues out of total 422 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 3
    poor density    : 36
  time to evaluate  : 0.135 
Fit side-chains
   revert: symmetry clash
REVERT: A  230 LEU cc_start: 0.6920 (OUTLIER) cc_final: 0.6318 (tt)
REVERT: A  616 LEU cc_start: 0.7999 (tt) cc_final: 0.7512 (mp)
  outliers start: 3
  outliers final: 1
  residues processed: 37
  average time/residue: 0.0576
  time to fit residues: 2.8941
Evaluate side-chains
  37 residues out of total 422 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 2
    poor density    : 35
  time to evaluate  : 0.133 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  230 LEU
Chi-restraints excluded: chain A residue  312 ILE
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 49
   random chunks:
   chunk 43 optimal weight:    0.5980
   chunk 20 optimal weight:    2.9990
   chunk 11 optimal weight:    0.9990
   chunk 12 optimal weight:    0.7980
   chunk 37 optimal weight:    0.0070
   chunk 15 optimal weight:    1.9990
   chunk 24 optimal weight:    2.9990
   chunk 6 optimal weight:    0.6980
   chunk 35 optimal weight:    0.0970
   chunk 40 optimal weight:    0.5980
   chunk 38 optimal weight:    3.9990
   overall best weight:    0.3996

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3931 r_free = 0.3931 target = 0.170205 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 43)----------------|
| r_work = 0.3690 r_free = 0.3690 target = 0.144821 restraints weight = 3940.105|
|-----------------------------------------------------------------------------|
r_work (start): 0.3749 rms_B_bonded: 1.49
r_work: 0.3664 rms_B_bonded: 2.04 restraints_weight: 0.5000
r_work: 0.3550 rms_B_bonded: 3.59 restraints_weight: 0.2500
r_work (final): 0.3550
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7434
moved from start:          0.1850

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.024   3849  Z= 0.112
  Angle     :  0.553  11.712   5242  Z= 0.261
  Chirality :  0.040   0.130    614
  Planarity :  0.004   0.026    641
  Dihedral  :  3.749  18.101    518
  Min Nonbonded Distance : 2.501

Molprobity Statistics.
  All-atom Clashscore : 4.15
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.32 %
    Favored  : 97.68 %
  Rotamer:
    Outliers :  0.51 %
    Allowed  : 10.63 %
    Favored  : 88.86 %
  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:  2.17 (0.40), residues: 474
  helix:  2.06 (0.29), residues: 330
  sheet:  None (None), residues: 0
  loop :  0.05 (0.52), residues: 144

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG A  62 
 TYR   0.016   0.001   TYR A 223 
 PHE   0.007   0.001   PHE A 198 
 TRP   0.002   0.000   TRP A 626 
 HIS   0.001   0.000   HIS A 456 

Details of bonding type rmsd
  covalent geometry    : bond        0.00251 ( 3842)
  covalent geometry    : angle       0.55250 ( 5228)
  SS BOND              : bond        0.00364 (    7)
  SS BOND              : angle       0.81011 (   14)
  hydrogen bonds       : bond        0.03862 (  232)
  hydrogen bonds       : angle       3.61500 (  681)

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

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

  948 Ramachandran restraints generated.
    474 Oldfield, 0 Emsley, 474 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  948 Ramachandran restraints generated.
    474 Oldfield, 0 Emsley, 474 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  40 residues out of total 422 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 2
    poor density    : 38
  time to evaluate  : 0.141 
Fit side-chains
   revert: symmetry clash
REVERT: A  230 LEU cc_start: 0.6651 (OUTLIER) cc_final: 0.6075 (tt)
REVERT: A  616 LEU cc_start: 0.7798 (tt) cc_final: 0.7356 (mp)
  outliers start: 2
  outliers final: 1
  residues processed: 38
  average time/residue: 0.0580
  time to fit residues: 2.9822
Evaluate side-chains
  40 residues out of total 422 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 2
    poor density    : 38
  time to evaluate  : 0.149 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  230 LEU
Chi-restraints excluded: chain A residue  312 ILE
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 49
   random chunks:
   chunk 7 optimal weight:    0.5980
   chunk 46 optimal weight:    0.9980
   chunk 24 optimal weight:    0.5980
   chunk 6 optimal weight:    0.8980
   chunk 17 optimal weight:    2.9990
   chunk 9 optimal weight:    0.8980
   chunk 34 optimal weight:    0.4980
   chunk 12 optimal weight:    0.6980
   chunk 26 optimal weight:    0.6980
   chunk 15 optimal weight:    0.7980
   chunk 13 optimal weight:    0.5980
   overall best weight:    0.5980

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3914 r_free = 0.3914 target = 0.168311 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 44)----------------|
| r_work = 0.3676 r_free = 0.3676 target = 0.143775 restraints weight = 3999.765|
|-----------------------------------------------------------------------------|
r_work (start): 0.3723 rms_B_bonded: 1.38
r_work: 0.3645 rms_B_bonded: 1.87 restraints_weight: 0.5000
r_work: 0.3539 rms_B_bonded: 3.22 restraints_weight: 0.2500
r_work (final): 0.3539
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7462
moved from start:          0.1900

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.027   3849  Z= 0.131
  Angle     :  0.573  10.657   5242  Z= 0.273
  Chirality :  0.041   0.132    614
  Planarity :  0.004   0.026    641
  Dihedral  :  3.783  18.491    518
  Min Nonbonded Distance : 2.522

Molprobity Statistics.
  All-atom Clashscore : 4.28
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.74 %
    Favored  : 97.26 %
  Rotamer:
    Outliers :  0.76 %
    Allowed  : 11.14 %
    Favored  : 88.10 %
  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:  2.05 (0.39), residues: 474
  helix:  2.01 (0.29), residues: 325
  sheet:  None (None), residues: 0
  loop : -0.03 (0.51), residues: 149

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG A  62 
 TYR   0.016   0.001   TYR A 223 
 PHE   0.011   0.001   PHE A 198 
 TRP   0.003   0.001   TRP A 626 
 HIS   0.002   0.001   HIS A  96 

Details of bonding type rmsd
  covalent geometry    : bond        0.00309 ( 3842)
  covalent geometry    : angle       0.57232 ( 5228)
  SS BOND              : bond        0.00357 (    7)
  SS BOND              : angle       0.89701 (   14)
  hydrogen bonds       : bond        0.04287 (  232)
  hydrogen bonds       : angle       3.68812 (  681)

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

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

  948 Ramachandran restraints generated.
    474 Oldfield, 0 Emsley, 474 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  948 Ramachandran restraints generated.
    474 Oldfield, 0 Emsley, 474 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  43 residues out of total 422 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 3
    poor density    : 40
  time to evaluate  : 0.132 
Fit side-chains
   revert: symmetry clash
REVERT: A  230 LEU cc_start: 0.6808 (OUTLIER) cc_final: 0.6241 (tt)
REVERT: A  616 LEU cc_start: 0.7830 (tt) cc_final: 0.7375 (mp)
  outliers start: 3
  outliers final: 1
  residues processed: 41
  average time/residue: 0.0538
  time to fit residues: 3.0128
Evaluate side-chains
  42 residues out of total 422 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 2
    poor density    : 40
  time to evaluate  : 0.129 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  230 LEU
Chi-restraints excluded: chain A residue  312 ILE
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 49
   random chunks:
   chunk 15 optimal weight:    0.0980
   chunk 48 optimal weight:    0.6980
   chunk 28 optimal weight:    0.5980
   chunk 37 optimal weight:    0.8980
   chunk 5 optimal weight:    1.9990
   chunk 3 optimal weight:    0.9980
   chunk 36 optimal weight:    0.9990
   chunk 13 optimal weight:    0.6980
   chunk 10 optimal weight:    0.7980
   chunk 39 optimal weight:    0.9990
   chunk 34 optimal weight:    0.9980
   overall best weight:    0.5780

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3910 r_free = 0.3910 target = 0.167976 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 43)----------------|
| r_work = 0.3672 r_free = 0.3672 target = 0.143360 restraints weight = 4051.109|
|-----------------------------------------------------------------------------|
r_work (start): 0.3717 rms_B_bonded: 1.39
r_work: 0.3639 rms_B_bonded: 1.85 restraints_weight: 0.5000
r_work: 0.3535 rms_B_bonded: 3.18 restraints_weight: 0.2500
r_work (final): 0.3535
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7468
moved from start:          0.2023

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.027   3849  Z= 0.126
  Angle     :  0.561  10.233   5242  Z= 0.266
  Chirality :  0.040   0.132    614
  Planarity :  0.004   0.027    641
  Dihedral  :  3.772  17.796    518
  Min Nonbonded Distance : 2.531

Molprobity Statistics.
  All-atom Clashscore : 3.61
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.53 %
    Favored  : 97.47 %
  Rotamer:
    Outliers :  0.51 %
    Allowed  : 12.15 %
    Favored  : 87.34 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  2.03 (0.39), residues: 474
  helix:  2.06 (0.30), residues: 323
  sheet:  None (None), residues: 0
  loop : -0.20 (0.50), residues: 151

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG A  62 
 TYR   0.015   0.001   TYR A 223 
 PHE   0.010   0.001   PHE A 198 
 TRP   0.004   0.001   TRP A 253 
 HIS   0.002   0.001   HIS A  96 

Details of bonding type rmsd
  covalent geometry    : bond        0.00297 ( 3842)
  covalent geometry    : angle       0.55961 ( 5228)
  SS BOND              : bond        0.00334 (    7)
  SS BOND              : angle       0.84019 (   14)
  hydrogen bonds       : bond        0.04166 (  232)
  hydrogen bonds       : angle       3.65093 (  681)

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

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

  948 Ramachandran restraints generated.
    474 Oldfield, 0 Emsley, 474 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  948 Ramachandran restraints generated.
    474 Oldfield, 0 Emsley, 474 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  41 residues out of total 422 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 2
    poor density    : 39
  time to evaluate  : 0.080 
Fit side-chains
   revert: symmetry clash
REVERT: A  230 LEU cc_start: 0.6820 (OUTLIER) cc_final: 0.6263 (tt)
REVERT: A  616 LEU cc_start: 0.7812 (tt) cc_final: 0.7365 (mp)
  outliers start: 2
  outliers final: 1
  residues processed: 39
  average time/residue: 0.0329
  time to fit residues: 1.7758
Evaluate side-chains
  41 residues out of total 422 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 2
    poor density    : 39
  time to evaluate  : 0.081 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  230 LEU
Chi-restraints excluded: chain A residue  312 ILE
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 49
   random chunks:
   chunk 31 optimal weight:    0.0370
   chunk 35 optimal weight:    0.9980
   chunk 6 optimal weight:    0.7980
   chunk 7 optimal weight:    0.7980
   chunk 22 optimal weight:    0.5980
   chunk 10 optimal weight:    0.7980
   chunk 27 optimal weight:    2.9990
   chunk 48 optimal weight:    0.3980
   chunk 46 optimal weight:    0.9990
   chunk 13 optimal weight:    0.7980
   chunk 21 optimal weight:    0.5980
   overall best weight:    0.4858

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3914 r_free = 0.3914 target = 0.168430 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 45)----------------|
| r_work = 0.3668 r_free = 0.3668 target = 0.142647 restraints weight = 4028.987|
|-----------------------------------------------------------------------------|
r_work (start): 0.3717 rms_B_bonded: 1.52
r_work: 0.3631 rms_B_bonded: 2.07 restraints_weight: 0.5000
r_work: 0.3517 rms_B_bonded: 3.62 restraints_weight: 0.2500
r_work (final): 0.3517
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7463
moved from start:          0.2071

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.027   3849  Z= 0.119
  Angle     :  0.554   9.534   5242  Z= 0.264
  Chirality :  0.040   0.131    614
  Planarity :  0.004   0.027    641
  Dihedral  :  3.737  17.821    518
  Min Nonbonded Distance : 2.546

Molprobity Statistics.
  All-atom Clashscore : 4.01
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.53 %
    Favored  : 97.47 %
  Rotamer:
    Outliers :  0.76 %
    Allowed  : 12.91 %
    Favored  : 86.33 %
  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:  2.21 (0.39), residues: 474
  helix:  2.18 (0.29), residues: 324
  sheet:  None (None), residues: 0
  loop : -0.07 (0.50), residues: 150

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG A  62 
 TYR   0.014   0.001   TYR A 223 
 PHE   0.009   0.001   PHE A 198 
 TRP   0.003   0.001   TRP A 626 
 HIS   0.001   0.001   HIS A 456 

Details of bonding type rmsd
  covalent geometry    : bond        0.00277 ( 3842)
  covalent geometry    : angle       0.55336 ( 5228)
  SS BOND              : bond        0.00305 (    7)
  SS BOND              : angle       0.74597 (   14)
  hydrogen bonds       : bond        0.03951 (  232)
  hydrogen bonds       : angle       3.60087 (  681)

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

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

  948 Ramachandran restraints generated.
    474 Oldfield, 0 Emsley, 474 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  948 Ramachandran restraints generated.
    474 Oldfield, 0 Emsley, 474 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  42 residues out of total 422 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 3
    poor density    : 39
  time to evaluate  : 0.091 
Fit side-chains
   revert: symmetry clash
REVERT: A  230 LEU cc_start: 0.6764 (OUTLIER) cc_final: 0.6237 (tt)
REVERT: A  616 LEU cc_start: 0.7767 (tt) cc_final: 0.7326 (mp)
  outliers start: 3
  outliers final: 0
  residues processed: 40
  average time/residue: 0.0385
  time to fit residues: 2.0530
Evaluate side-chains
  40 residues out of total 422 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 39
  time to evaluate  : 0.078 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  230 LEU
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 49
   random chunks:
   chunk 44 optimal weight:    2.9990
   chunk 3 optimal weight:    0.7980
   chunk 10 optimal weight:    0.7980
   chunk 21 optimal weight:    0.0670
   chunk 20 optimal weight:    0.6980
   chunk 29 optimal weight:    0.8980
   chunk 2 optimal weight:    0.9990
   chunk 17 optimal weight:    0.5980
   chunk 45 optimal weight:    1.9990
   chunk 24 optimal weight:    0.6980
   chunk 26 optimal weight:    0.6980
   overall best weight:    0.5518

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3819 r_free = 0.3819 target = 0.161811 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 43)----------------|
| r_work = 0.3566 r_free = 0.3566 target = 0.136610 restraints weight = 3949.258|
|-----------------------------------------------------------------------------|
r_work (start): 0.3707 rms_B_bonded: 1.51
r_work: 0.3620 rms_B_bonded: 2.05 restraints_weight: 0.5000
r_work: 0.3509 rms_B_bonded: 3.58 restraints_weight: 0.2500
r_work (final): 0.3509
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7481
moved from start:          0.2162

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.027   3849  Z= 0.125
  Angle     :  0.561   9.348   5242  Z= 0.266
  Chirality :  0.041   0.131    614
  Planarity :  0.004   0.027    641
  Dihedral  :  3.757  17.565    518
  Min Nonbonded Distance : 2.550

Molprobity Statistics.
  All-atom Clashscore : 3.88
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.74 %
    Favored  : 97.26 %
  Rotamer:
    Outliers :  0.51 %
    Allowed  : 13.16 %
    Favored  : 86.33 %
  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:  2.25 (0.39), residues: 474
  helix:  2.26 (0.30), residues: 318
  sheet:  None (None), residues: 0
  loop : -0.09 (0.50), residues: 156

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG A  62 
 TYR   0.012   0.001   TYR A 194 
 PHE   0.009   0.001   PHE A 198 
 TRP   0.005   0.001   TRP A 253 
 HIS   0.001   0.001   HIS A 456 

Details of bonding type rmsd
  covalent geometry    : bond        0.00292 ( 3842)
  covalent geometry    : angle       0.55977 ( 5228)
  SS BOND              : bond        0.00319 (    7)
  SS BOND              : angle       0.80392 (   14)
  hydrogen bonds       : bond        0.04097 (  232)
  hydrogen bonds       : angle       3.62346 (  681)

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

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

  948 Ramachandran restraints generated.
    474 Oldfield, 0 Emsley, 474 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  948 Ramachandran restraints generated.
    474 Oldfield, 0 Emsley, 474 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  40 residues out of total 422 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 2
    poor density    : 38
  time to evaluate  : 0.082 
Fit side-chains
   revert: symmetry clash
REVERT: A  230 LEU cc_start: 0.6846 (OUTLIER) cc_final: 0.6318 (tt)
REVERT: A  616 LEU cc_start: 0.7801 (tt) cc_final: 0.7381 (mp)
  outliers start: 2
  outliers final: 1
  residues processed: 38
  average time/residue: 0.0462
  time to fit residues: 2.3636
Evaluate side-chains
  40 residues out of total 422 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 2
    poor density    : 38
  time to evaluate  : 0.132 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  230 LEU
Chi-restraints excluded: chain A residue  539 MET
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 49
   random chunks:
   chunk 27 optimal weight:    2.9990
   chunk 43 optimal weight:    0.7980
   chunk 41 optimal weight:    0.9980
   chunk 22 optimal weight:    0.6980
   chunk 12 optimal weight:    0.0070
   chunk 24 optimal weight:    0.6980
   chunk 17 optimal weight:    0.2980
   chunk 32 optimal weight:    0.2980
   chunk 21 optimal weight:    0.7980
   chunk 14 optimal weight:    1.9990
   chunk 25 optimal weight:    0.6980
   overall best weight:    0.3998

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3888 r_free = 0.3888 target = 0.167112 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.3647 r_free = 0.3647 target = 0.142238 restraints weight = 4026.565|
|-----------------------------------------------------------------------------|
r_work (start): 0.3732 rms_B_bonded: 1.39
r_work: 0.3653 rms_B_bonded: 1.88 restraints_weight: 0.5000
r_work: 0.3549 rms_B_bonded: 3.26 restraints_weight: 0.2500
r_work (final): 0.3549
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7455
moved from start:          0.2168

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.030   3849  Z= 0.112
  Angle     :  0.547   8.929   5242  Z= 0.261
  Chirality :  0.040   0.129    614
  Planarity :  0.004   0.027    641
  Dihedral  :  3.706  17.328    518
  Min Nonbonded Distance : 2.523

Molprobity Statistics.
  All-atom Clashscore : 3.88
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.74 %
    Favored  : 97.26 %
  Rotamer:
    Outliers :  0.51 %
    Allowed  : 13.67 %
    Favored  : 85.82 %
  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:  2.40 (0.40), residues: 474
  helix:  2.36 (0.30), residues: 320
  sheet:  None (None), residues: 0
  loop : -0.05 (0.50), residues: 154

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.001   0.000   ARG A  62 
 TYR   0.013   0.001   TYR A 223 
 PHE   0.008   0.001   PHE A 198 
 TRP   0.003   0.000   TRP A 626 
 HIS   0.001   0.001   HIS A 456 

Details of bonding type rmsd
  covalent geometry    : bond        0.00256 ( 3842)
  covalent geometry    : angle       0.54682 ( 5228)
  SS BOND              : bond        0.00292 (    7)
  SS BOND              : angle       0.67501 (   14)
  hydrogen bonds       : bond        0.03736 (  232)
  hydrogen bonds       : angle       3.52965 (  681)

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

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

  948 Ramachandran restraints generated.
    474 Oldfield, 0 Emsley, 474 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  948 Ramachandran restraints generated.
    474 Oldfield, 0 Emsley, 474 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  39 residues out of total 422 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 2
    poor density    : 37
  time to evaluate  : 0.133 
Fit side-chains
   revert: symmetry clash
REVERT: A  230 LEU cc_start: 0.6859 (OUTLIER) cc_final: 0.6346 (tt)
REVERT: A  616 LEU cc_start: 0.7789 (tt) cc_final: 0.7326 (mp)
REVERT: A  626 TRP cc_start: 0.7483 (t60) cc_final: 0.7241 (t60)
  outliers start: 2
  outliers final: 0
  residues processed: 37
  average time/residue: 0.0562
  time to fit residues: 2.8299
Evaluate side-chains
  37 residues out of total 422 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 36
  time to evaluate  : 0.132 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  230 LEU
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 49
   random chunks:
   chunk 8 optimal weight:    0.1980
   chunk 41 optimal weight:    0.4980
   chunk 6 optimal weight:    0.7980
   chunk 38 optimal weight:    0.9980
   chunk 25 optimal weight:    2.9990
   chunk 28 optimal weight:    0.2980
   chunk 47 optimal weight:    2.9990
   chunk 39 optimal weight:    0.7980
   chunk 3 optimal weight:    0.2980
   chunk 11 optimal weight:    0.0170
   chunk 42 optimal weight:    0.5980
   overall best weight:    0.2618

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3913 r_free = 0.3913 target = 0.169457 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 44)----------------|
| r_work = 0.3673 r_free = 0.3673 target = 0.144383 restraints weight = 3905.348|
|-----------------------------------------------------------------------------|
r_work (start): 0.3752 rms_B_bonded: 1.43
r_work: 0.3672 rms_B_bonded: 1.93 restraints_weight: 0.5000
r_work: 0.3565 rms_B_bonded: 3.37 restraints_weight: 0.2500
r_work (final): 0.3565
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7408
moved from start:          0.2310

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.024   3849  Z= 0.101
  Angle     :  0.523   8.267   5242  Z= 0.248
  Chirality :  0.040   0.128    614
  Planarity :  0.004   0.028    641
  Dihedral  :  3.609  17.187    518
  Min Nonbonded Distance : 2.575

Molprobity Statistics.
  All-atom Clashscore : 3.34
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.11 %
    Favored  : 97.89 %
  Rotamer:
    Outliers :  0.25 %
    Allowed  : 14.18 %
    Favored  : 85.57 %
  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:  2.56 (0.40), residues: 474
  helix:  2.49 (0.30), residues: 321
  sheet:  None (None), residues: 0
  loop : -0.02 (0.51), residues: 153

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.001   0.000   ARG A  62 
 TYR   0.008   0.001   TYR A 194 
 PHE   0.007   0.001   PHE A 198 
 TRP   0.003   0.000   TRP A 253 
 HIS   0.001   0.000   HIS A 456 

Details of bonding type rmsd
  covalent geometry    : bond        0.00217 ( 3842)
  covalent geometry    : angle       0.52270 ( 5228)
  SS BOND              : bond        0.00251 (    7)
  SS BOND              : angle       0.57694 (   14)
  hydrogen bonds       : bond        0.03300 (  232)
  hydrogen bonds       : angle       3.41441 (  681)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 1072.97 seconds
wall clock time: 19 minutes 3.21 seconds (1143.21 seconds total)