Starting phenix.real_space_refine
on Fri Aug 22 19:58:53 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/7y49_33604/08_2025/7y49_33604.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/7y49_33604/08_2025/7y49_33604.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.67
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/7y49_33604/08_2025/7y49_33604.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/7y49_33604/08_2025/7y49_33604.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/7y49_33604/08_2025/7y49_33604.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/7y49_33604/08_2025/7y49_33604.cif"
  }
  resolution = 3.67
  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=   0.016
Set stop_for_unknowns flag
  Set to: True
Assert model is a single copy model
Assert all atoms have isotropic ADPs
  Anisotropic ADP refinement not supported. Converting 4095 atoms to isotropic.
Construct map_model_manager
Extract box with map and model
Check model and map are aligned
Set scattering table
  Set to: electron
  Number of scattering types: 4
    Type Number    sf(0)   Gaussians
     S      16      5.16       5
     C    2670      2.51       5
     N     722      2.21       5
     O     761      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 1 residue(s): 0.00s

  Monomer Library directory:
    "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/chem_data/mon_lib"
  Total number of atoms: 4169
  Number of models: 1
  Model: ""
    Number of chains: 1
    Chain: "A"
      Number of atoms: 4169
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 565, 4169
          Classifications: {'peptide': 565}
          Incomplete info: {'truncation_to_alanine': 37}
          Link IDs: {'PTRANS': 20, 'TRANS': 544}
          Chain breaks: 2
          Unresolved non-hydrogen bonds: 153
          Unresolved non-hydrogen angles: 185
          Unresolved non-hydrogen dihedrals: 124
          Unresolved non-hydrogen chiralities: 6
          Planarities with less than four sites: {'GLU:plan': 13, 'ARG:plan': 5, 'ASP:plan': 3, 'TYR:plan': 1, 'GLN:plan1': 1, 'ASN:plan1': 1}
          Unresolved non-hydrogen planarities: 98
  Time building chain proxies: 1.41, per 1000 atoms: 0.34
  Number of scatterers: 4169
  At special positions: 0
  Unit cell: (67.15, 98.6, 143.65, 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      16     16.00
     O     761      8.00
     N     722      7.00
     C    2670      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=0, symmetry=0

  Automatic linking
    Parameters for automatic linking
      Linking & cutoffs
        Metal                : Auto  - 3.00
        Amino acid           : True  - 1.90
        Carbohydrate         : True  - 1.99
        Ligands              : True  - 1.99
        Small molecules      : False - 1.98
        Amino acid - RNA/DNA : False
      
  Number of custom bonds: simple=0, symmetry=0
  Time building additional restraints: 0.36
  Conformation dependent library (CDL) restraints added in 158.6 milliseconds
  
  Enol-peptide restraints added in 476.8 nanoseconds
  

  1118 Ramachandran restraints generated.
    559 Oldfield, 0 Emsley, 559 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  1036

  Finding SS restraints...
    Secondary structure from input PDB file:
      24 helices and 3 sheets defined
      65.5% alpha, 2.5% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.25
  Creating SS restraints...
    Processing helix  chain 'A' and resid 156 through 164
      removed outlier: 3.747A  pdb=" N   LEU A 161 " --> pdb=" O   ALA A 157 " (cutoff:3.500A)
      removed outlier: 3.794A  pdb=" N   GLY A 162 " --> pdb=" O   ARG A 158 " (cutoff:3.500A)
      removed outlier: 3.840A  pdb=" N   ALA A 164 " --> pdb=" O   LEU A 160 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 168 through 184
      removed outlier: 3.829A  pdb=" N   ALA A 172 " --> pdb=" O   ARG A 168 " (cutoff:3.500A)
      removed outlier: 3.632A  pdb=" N   ALA A 173 " --> pdb=" O   ARG A 169 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 187 through 200
      removed outlier: 3.875A  pdb=" N   PHE A 191 " --> pdb=" O   SER A 187 " (cutoff:3.500A)
      removed outlier: 3.580A  pdb=" N   LYS A 194 " --> pdb=" O   PHE A 190 " (cutoff:3.500A)
      removed outlier: 3.682A  pdb=" N   ILE A 199 " --> pdb=" O   ILE A 195 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 211 through 257
      removed outlier: 3.953A  pdb=" N   ALA A 220 " --> pdb=" O   LEU A 216 " (cutoff:3.500A)
      removed outlier: 3.705A  pdb=" N   VAL A 221 " --> pdb=" O   GLY A 217 " (cutoff:3.500A)
      removed outlier: 4.149A  pdb=" N   ARG A 246 " --> pdb=" O   ARG A 242 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 261 through 266
      removed outlier: 4.131A  pdb=" N   LYS A 265 " --> pdb=" O   ALA A 261 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 267 through 285
      removed outlier: 3.707A  pdb=" N   LEU A 271 " --> pdb=" O   ARG A 267 " (cutoff:3.500A)
      removed outlier: 4.079A  pdb=" N   ASP A 278 " --> pdb=" O   ARG A 274 " (cutoff:3.500A)
      removed outlier: 5.255A  pdb=" N   THR A 279 " --> pdb=" O   LEU A 275 " (cutoff:3.500A)
      removed outlier: 3.952A  pdb=" N   ALA A 280 " --> pdb=" O   SER A 276 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 289 through 311
      removed outlier: 3.613A  pdb=" N   PHE A 308 " --> pdb=" O   ILE A 304 " (cutoff:3.500A)
      removed outlier: 4.085A  pdb=" N   PHE A 309 " --> pdb=" O   SER A 305 " (cutoff:3.500A)
      removed outlier: 3.792A  pdb=" N   VAL A 310 " --> pdb=" O   MET A 306 " (cutoff:3.500A)
      removed outlier: 3.997A  pdb=" N   SER A 311 " --> pdb=" O   MET A 307 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 311 through 360
      removed outlier: 3.659A  pdb=" N   PHE A 317 " --> pdb=" O   ASN A 313 " (cutoff:3.500A)
      removed outlier: 3.736A  pdb=" N   SER A 320 " --> pdb=" O   THR A 316 " (cutoff:3.500A)
      removed outlier: 3.663A  pdb=" N   VAL A 321 " --> pdb=" O   PHE A 317 " (cutoff:3.500A)
      removed outlier: 3.792A  pdb=" N   VAL A 322 " --> pdb=" O   VAL A 318 " (cutoff:3.500A)
      Proline residue:  A 323  - end of helix
      removed outlier: 3.668A  pdb=" N   ILE A 328 " --> pdb=" O   PRO A 324 " (cutoff:3.500A)
      removed outlier: 3.694A  pdb=" N   ARG A 334 " --> pdb=" O   VAL A 330 " (cutoff:3.500A)
      removed outlier: 4.025A  pdb=" N   TYR A 335 " --> pdb=" O   ILE A 331 " (cutoff:3.500A)
      removed outlier: 3.883A  pdb=" N   LEU A 336 " --> pdb=" O   TYR A 332 " (cutoff:3.500A)
      removed outlier: 3.581A  pdb=" N   ARG A 337 " --> pdb=" O   GLY A 333 " (cutoff:3.500A)
      removed outlier: 3.524A  pdb=" N   LEU A 353 " --> pdb=" O   GLN A 349 " (cutoff:3.500A)
      removed outlier: 3.574A  pdb=" N   ALA A 354 " --> pdb=" O   ALA A 350 " (cutoff:3.500A)
      removed outlier: 3.730A  pdb=" N   GLU A 356 " --> pdb=" O   GLN A 352 " (cutoff:3.500A)
      removed outlier: 3.640A  pdb=" N   ARG A 357 " --> pdb=" O   LEU A 353 " (cutoff:3.500A)
      removed outlier: 3.851A  pdb=" N   ILE A 358 " --> pdb=" O   ALA A 354 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 360 through 367
      removed outlier: 3.569A  pdb=" N   ALA A 366 " --> pdb=" O   ARG A 362 " (cutoff:3.500A)
      removed outlier: 4.320A  pdb=" N   PHE A 367 " --> pdb=" O   THR A 363 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 370 through 417
      removed outlier: 3.551A  pdb=" N   ILE A 374 " --> pdb=" O   GLU A 370 " (cutoff:3.500A)
      removed outlier: 4.053A  pdb=" N   LYS A 390 " --> pdb=" O   GLN A 386 " (cutoff:3.500A)
      removed outlier: 3.841A  pdb=" N   GLU A 391 " --> pdb=" O   LEU A 387 " (cutoff:3.500A)
      removed outlier: 3.541A  pdb=" N   ALA A 392 " --> pdb=" O   ALA A 388 " (cutoff:3.500A)
      removed outlier: 3.798A  pdb=" N   ALA A 394 " --> pdb=" O   LYS A 390 " (cutoff:3.500A)
      removed outlier: 3.592A  pdb=" N   GLY A 417 " --> pdb=" O   VAL A 413 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 427 through 466
      removed outlier: 3.573A  pdb=" N   LEU A 431 " --> pdb=" O   THR A 427 " (cutoff:3.500A)
      removed outlier: 3.860A  pdb=" N   GLY A 446 " --> pdb=" O   GLY A 442 " (cutoff:3.500A)
      removed outlier: 3.703A  pdb=" N   ARG A 464 " --> pdb=" O   GLY A 460 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 467 through 471
      removed outlier: 3.503A  pdb=" N   ARG A 471 " --> pdb=" O   LEU A 468 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 532 through 534
      No H-bonds generated for 'chain 'A' and resid 532 through 534'
    Processing helix  chain 'A' and resid 535 through 541
      removed outlier: 3.632A  pdb=" N   LEU A 541 " --> pdb=" O   LEU A 537 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 562 through 569
    Processing helix  chain 'A' and resid 583 through 588
    Processing helix  chain 'A' and resid 589 through 591
      No H-bonds generated for 'chain 'A' and resid 589 through 591'
    Processing helix  chain 'A' and resid 599 through 610
      removed outlier: 3.936A  pdb=" N   ILE A 603 " --> pdb=" O   THR A 599 " (cutoff:3.500A)
      removed outlier: 3.678A  pdb=" N   GLN A 604 " --> pdb=" O   ALA A 600 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 612 through 617
    Processing helix  chain 'A' and resid 621 through 625
      removed outlier: 3.789A  pdb=" N   ASN A 624 " --> pdb=" O   GLN A 621 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 635 through 647
      removed outlier: 3.850A  pdb=" N   ALA A 643 " --> pdb=" O   LYS A 639 " (cutoff:3.500A)
      removed outlier: 3.574A  pdb=" N   ALA A 647 " --> pdb=" O   ALA A 643 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 668 through 674
      removed outlier: 3.612A  pdb=" N   VAL A 672 " --> pdb=" O   ASN A 668 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 691 through 697
      removed outlier: 3.614A  pdb=" N   ILE A 695 " --> pdb=" O   ARG A 691 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 714 through 720
      removed outlier: 3.946A  pdb=" N   SER A 720 " --> pdb=" O   GLU A 716 " (cutoff:3.500A)
    Processing sheet with id=AA1, first strand: chain 'A' and resid 516 through 517
      removed outlier: 3.669A  pdb=" N   LEU A 492 " --> pdb=" O   ILE A 517 " (cutoff:3.500A)
      removed outlier: 3.551A  pdb=" N   HIS A 556 " --> pdb=" O   LEU A 553 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'A' and resid 570 through 572
    Processing sheet with id=AA3, first strand: chain 'A' and resid 703 through 704
      removed outlier: 6.749A  pdb=" N   VAL A 703 " --> pdb=" O   THR A 710 " (cutoff:3.500A)

    228 hydrogen bonds defined for protein.
    678 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: 0.59

  Time building geometry restraints manager: 0.49 seconds

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

  Histogram of bond lengths:
        1.22 -     1.34: 1364
        1.34 -     1.46: 546
        1.46 -     1.57: 2300
        1.57 -     1.69: 0
        1.69 -     1.81: 29
  Bond restraints: 4239
  Sorted by residual:
  bond pdb=" C   VAL A 286 "
       pdb=" O   VAL A 286 "
    ideal  model  delta    sigma   weight residual
    1.242  1.228  0.014 1.17e-02 7.31e+03 1.42e+00
  bond pdb=" C   ALA A 438 "
       pdb=" N   PHE A 439 "
    ideal  model  delta    sigma   weight residual
    1.334  1.320  0.015 1.27e-02 6.20e+03 1.37e+00
  bond pdb=" N   PHE A 439 "
       pdb=" CA  PHE A 439 "
    ideal  model  delta    sigma   weight residual
    1.459  1.447  0.013 1.19e-02 7.06e+03 1.12e+00
  bond pdb=" N   THR A 402 "
       pdb=" CA  THR A 402 "
    ideal  model  delta    sigma   weight residual
    1.459  1.472 -0.013 1.23e-02 6.61e+03 1.08e+00
  bond pdb=" C   SER A 285 "
       pdb=" O   SER A 285 "
    ideal  model  delta    sigma   weight residual
    1.235  1.222  0.013 1.33e-02 5.65e+03 1.02e+00
  ... (remaining 4234 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     1.22: 5505
        1.22 -     2.44: 181
        2.44 -     3.66: 46
        3.66 -     4.88: 15
        4.88 -     6.10: 7
  Bond angle restraints: 5754
  Sorted by residual:
  angle pdb=" N   GLN A 659 "
        pdb=" CA  GLN A 659 "
        pdb=" C   GLN A 659 "
      ideal   model   delta    sigma   weight residual
     108.90  113.97   -5.07 1.63e+00 3.76e-01 9.66e+00
  angle pdb=" N   ASN A 202 "
        pdb=" CA  ASN A 202 "
        pdb=" C   ASN A 202 "
      ideal   model   delta    sigma   weight residual
     109.81  104.00    5.81 2.21e+00 2.05e-01 6.91e+00
  angle pdb=" N   PRO A 505 "
        pdb=" CA  PRO A 505 "
        pdb=" C   PRO A 505 "
      ideal   model   delta    sigma   weight residual
     114.80  111.09    3.71 1.42e+00 4.96e-01 6.82e+00
  angle pdb=" N   VAL A 286 "
        pdb=" CA  VAL A 286 "
        pdb=" C   VAL A 286 "
      ideal   model   delta    sigma   weight residual
     113.53  111.01    2.52 9.80e-01 1.04e+00 6.61e+00
  angle pdb=" CA  LYS A 369 "
        pdb=" CB  LYS A 369 "
        pdb=" CG  LYS A 369 "
      ideal   model   delta    sigma   weight residual
     114.10  119.22   -5.12 2.00e+00 2.50e-01 6.55e+00
  ... (remaining 5749 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    15.26: 2213
       15.26 -    30.52: 226
       30.52 -    45.78: 78
       45.78 -    61.04: 9
       61.04 -    76.31: 5
  Dihedral angle restraints: 2531
    sinusoidal: 919
      harmonic: 1612
  Sorted by residual:
  dihedral pdb=" CA  ARG A 337 "
           pdb=" CB  ARG A 337 "
           pdb=" CG  ARG A 337 "
           pdb=" CD  ARG A 337 "
      ideal   model   delta sinusoidal    sigma   weight residual
     180.00  120.18   59.82     3      1.50e+01 4.44e-03 9.48e+00
  dihedral pdb=" CA  GLN A 659 "
           pdb=" CB  GLN A 659 "
           pdb=" CG  GLN A 659 "
           pdb=" CD  GLN A 659 "
      ideal   model   delta sinusoidal    sigma   weight residual
    -180.00 -130.84  -49.16     3      1.50e+01 4.44e-03 8.74e+00
  dihedral pdb=" N   ARG A 357 "
           pdb=" CA  ARG A 357 "
           pdb=" CB  ARG A 357 "
           pdb=" CG  ARG A 357 "
      ideal   model   delta sinusoidal    sigma   weight residual
     -60.00 -107.15   47.15     3      1.50e+01 4.44e-03 8.45e+00
  ... (remaining 2528 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.029: 414
       0.029 -    0.059: 197
       0.059 -    0.088: 48
       0.088 -    0.117: 20
       0.117 -    0.147: 12
  Chirality restraints: 691
  Sorted by residual:
  chirality pdb=" CB  VAL A 364 "
            pdb=" CA  VAL A 364 "
            pdb=" CG1 VAL A 364 "
            pdb=" CG2 VAL A 364 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.63   -2.48   -0.15 2.00e-01 2.50e+01 5.39e-01
  chirality pdb=" CA  TYR A 200 "
            pdb=" N   TYR A 200 "
            pdb=" C   TYR A 200 "
            pdb=" CB  TYR A 200 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.36    0.15 2.00e-01 2.50e+01 5.29e-01
  chirality pdb=" CB  THR A 204 "
            pdb=" CA  THR A 204 "
            pdb=" OG1 THR A 204 "
            pdb=" CG2 THR A 204 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.55    2.69   -0.14 2.00e-01 2.50e+01 4.83e-01
  ... (remaining 688 not shown)

  Planarity restraints: 734
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   VAL A 322 "   -0.025 5.00e-02 4.00e+02   3.76e-02 2.27e+00
        pdb=" N   PRO A 323 "    0.065 5.00e-02 4.00e+02
        pdb=" CA  PRO A 323 "   -0.019 5.00e-02 4.00e+02
        pdb=" CD  PRO A 323 "   -0.021 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  LYS A 369 "   -0.006 2.00e-02 2.50e+03   1.28e-02 1.63e+00
        pdb=" C   LYS A 369 "    0.022 2.00e-02 2.50e+03
        pdb=" O   LYS A 369 "   -0.008 2.00e-02 2.50e+03
        pdb=" N   GLU A 370 "   -0.007 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   TYR A 165 "   -0.020 5.00e-02 4.00e+02   3.06e-02 1.50e+00
        pdb=" N   PRO A 166 "    0.053 5.00e-02 4.00e+02
        pdb=" CA  PRO A 166 "   -0.015 5.00e-02 4.00e+02
        pdb=" CD  PRO A 166 "   -0.017 5.00e-02 4.00e+02
  ... (remaining 731 not shown)

  Histogram of nonbonded interaction distances:
        2.32 -     2.83: 1295
        2.83 -     3.35: 4043
        3.35 -     3.87: 6370
        3.87 -     4.38: 6579
        4.38 -     4.90: 11724
  Nonbonded interactions: 30011
  Sorted by model distance:
  nonbonded pdb=" O   SER A 311 "
            pdb=" OG  SER A 311 "
     model   vdw
     2.317 3.040
  nonbonded pdb=" O   ALA A 296 "
            pdb=" OG  SER A 444 "
     model   vdw
     2.328 3.040
  nonbonded pdb=" O   SER A 516 "
            pdb=" OH  TYR A 712 "
     model   vdw
     2.392 3.040
  nonbonded pdb=" O   MET A 371 "
            pdb=" OE1 GLU A 375 "
     model   vdw
     2.468 3.040
  nonbonded pdb=" O   GLY A 622 "
            pdb=" OG1 THR A 625 "
     model   vdw
     2.519 3.040
  ... (remaining 30006 not shown)

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

  No NCS relation were found !!!

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

Found NCS groups:
  found none.
Set up NCS constraints
  No NCS constraints will be used in refinement.
Set refine NCS operators
Adjust number of macro_cycles
  Number of macro_cycles: 10
Reset NCS operators
Extract rigid body selections
Check and reset occupancies
  Occupancies: min=1.00 max=1.00 mean=1.00
Load rotamer database and sin/cos tables
Set ADP refinement strategy
  ADPs will be refined as group one per residue
Make a string to write initial .geo file
Internal consistency checks
Time:
  Set random seed:                         0.000
  Set model cs if undefined:               0.000
  Decide on map wrapping:                  0.000
  Normalize map: mean=0, sd=1:             3.630
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.030
  Construct map_model_manager:             0.000
  Extract box with map and model:          0.120
  Check model and map are aligned:         0.010
  Set scattering table:                    0.010
  Process input model:                     6.260
  Find NCS groups from input model:        0.020
  Set up NCS constraints:                  0.010
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.000
  Load rotamer database and sin/cos tables:1.160
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   11.250
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6209
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      :  0.003   0.036   4239  Z= 0.177
  Angle     :  0.590   6.099   5754  Z= 0.325
  Chirality :  0.040   0.147    691
  Planarity :  0.003   0.038    734
  Dihedral  : 14.272  76.306   1495
  Min Nonbonded Distance : 2.317

Molprobity Statistics.
  All-atom Clashscore : 4.91
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.76 %
    Favored  : 96.24 %
  Rotamer:
    Outliers :  0.47 %
    Allowed  :  0.71 %
    Favored  : 98.82 %
  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 aren not related in a simple way.
  whole:  0.44 (0.36), residues: 559
  helix:  1.79 (0.30), residues: 302
  sheet:  None (None), residues: 0
  loop : -1.65 (0.35), residues: 257

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG A 295 
 TYR   0.010   0.001   TYR A 501 
 PHE   0.018   0.001   PHE A 619 
 TRP   0.006   0.001   TRP A 565 
 HIS   0.005   0.001   HIS A 498 

Details of bonding type rmsd
  covalent geometry    : bond        0.00346 ( 4239)
  covalent geometry    : angle       0.59001 ( 5754)
  hydrogen bonds       : bond        0.19557 (  228)
  hydrogen bonds       : angle       5.36755 (  678)

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

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

  1118 Ramachandran restraints generated.
    559 Oldfield, 0 Emsley, 559 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1118 Ramachandran restraints generated.
    559 Oldfield, 0 Emsley, 559 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  48 residues out of total 464 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 2
    poor density    : 46
  time to evaluate  : 0.149 
Fit side-chains
REVERT: A  187 SER cc_start: 0.8089 (m) cc_final: 0.7652 (p)
  outliers start: 2
  outliers final: 1
  residues processed: 48
  average time/residue: 0.1115
  time to fit residues: 6.4601
Evaluate side-chains
  45 residues out of total 464 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 44
  time to evaluate  : 0.173 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  586 GLU
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 56
   random chunks:
   chunk 54 optimal weight:    6.9990
   chunk 24 optimal weight:    0.0970
   chunk 48 optimal weight:    0.9980
   chunk 26 optimal weight:    0.3980
   chunk 2 optimal weight:    0.5980
   chunk 16 optimal weight:    0.2980
   chunk 32 optimal weight:    0.9990
   chunk 31 optimal weight:    0.5980
   chunk 25 optimal weight:    0.0980
   chunk 50 optimal weight:   50.0000
   chunk 53 optimal weight:    5.9990
   overall best weight:    0.2978

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

Flipped N/Q/H residues before XYZ refinement:
A 556 HIS

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4313 r_free = 0.4313 target = 0.189225 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 51)----------------|
| r_work = 0.4237 r_free = 0.4237 target = 0.182560 restraints weight = 5895.458|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 60)----------------|
| r_work = 0.4126 r_free = 0.4126 target = 0.176538 restraints weight = 12315.438|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 32)----------------|
| r_work = 0.4101 r_free = 0.4101 target = 0.173577 restraints weight = 8995.394|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 41)----------------|
| r_work = 0.4100 r_free = 0.4100 target = 0.173232 restraints weight = 8687.830|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 29)----------------|
| r_work = 0.4096 r_free = 0.4096 target = 0.173068 restraints weight = 8205.165|
|-----------------------------------------------------------------------------|
r_work (final): 0.4084
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6453
moved from start:          0.1279

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.032   4239  Z= 0.141
  Angle     :  0.521   7.621   5754  Z= 0.263
  Chirality :  0.038   0.127    691
  Planarity :  0.004   0.037    734
  Dihedral  :  4.246  49.271    608
  Min Nonbonded Distance : 2.556

Molprobity Statistics.
  All-atom Clashscore : 4.43
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.58 %
    Favored  : 96.42 %
  Rotamer:
    Outliers :  0.94 %
    Allowed  :  8.24 %
    Favored  : 90.82 %
  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 aren not related in a simple way.
  whole:  0.74 (0.36), residues: 559
  helix:  1.92 (0.29), residues: 330
  sheet:  0.05 (2.90), residues: 5
  loop : -1.81 (0.37), residues: 224

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG A 295 
 TYR   0.023   0.001   TYR A 207 
 PHE   0.016   0.001   PHE A 619 
 TRP   0.006   0.001   TRP A 565 
 HIS   0.004   0.001   HIS A 498 

Details of bonding type rmsd
  covalent geometry    : bond        0.00278 ( 4239)
  covalent geometry    : angle       0.52111 ( 5754)
  hydrogen bonds       : bond        0.07184 (  228)
  hydrogen bonds       : angle       3.95956 (  678)

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

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

  1118 Ramachandran restraints generated.
    559 Oldfield, 0 Emsley, 559 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1118 Ramachandran restraints generated.
    559 Oldfield, 0 Emsley, 559 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  54 residues out of total 464 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 4
    poor density    : 50
  time to evaluate  : 0.152 
Fit side-chains
REVERT: A  285 SER cc_start: 0.8185 (p) cc_final: 0.7939 (t)
  outliers start: 4
  outliers final: 1
  residues processed: 51
  average time/residue: 0.1182
  time to fit residues: 7.1347
Evaluate side-chains
  45 residues out of total 464 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 44
  time to evaluate  : 0.149 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  459 LEU
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 56
   random chunks:
   chunk 29 optimal weight:    0.9980
   chunk 40 optimal weight:    0.4980
   chunk 19 optimal weight:    0.6980
   chunk 35 optimal weight:    0.9980
   chunk 13 optimal weight:    0.6980
   chunk 24 optimal weight:    0.5980
   chunk 4 optimal weight:    0.0980
   chunk 27 optimal weight:    0.1980
   chunk 2 optimal weight:    0.4980
   chunk 50 optimal weight:    5.9990
   chunk 5 optimal weight:    0.3980
   overall best weight:    0.3380

-------------------------------------------------------------------------------
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 = 0.4307 r_free = 0.4307 target = 0.188456 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 42)----------------|
| r_work = 0.4228 r_free = 0.4228 target = 0.181645 restraints weight = 5863.776|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 47)----------------|
| r_work = 0.4103 r_free = 0.4103 target = 0.175561 restraints weight = 12964.611|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 38)----------------|
| r_work = 0.4074 r_free = 0.4074 target = 0.171821 restraints weight = 9016.201|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 27)----------------|
| r_work = 0.4074 r_free = 0.4074 target = 0.171729 restraints weight = 8651.708|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 42)----------------|
| r_work = 0.4079 r_free = 0.4079 target = 0.172119 restraints weight = 6830.953|
|-----------------------------------------------------------------------------|
r_work (final): 0.4067
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6482
moved from start:          0.1601

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.030   4239  Z= 0.142
  Angle     :  0.495   7.384   5754  Z= 0.250
  Chirality :  0.038   0.129    691
  Planarity :  0.003   0.037    734
  Dihedral  :  3.350  11.855    605
  Min Nonbonded Distance : 2.591

Molprobity Statistics.
  All-atom Clashscore : 3.83
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.22 %
    Favored  : 96.78 %
  Rotamer:
    Outliers :  0.94 %
    Allowed  : 12.71 %
    Favored  : 86.35 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  0.85 (0.36), residues: 559
  helix:  2.03 (0.29), residues: 329
  sheet: -0.13 (2.66), residues: 5
  loop : -1.77 (0.37), residues: 225

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG A 284 
 TYR   0.019   0.001   TYR A 207 
 PHE   0.023   0.001   PHE A 317 
 TRP   0.007   0.001   TRP A 565 
 HIS   0.004   0.001   HIS A 498 

Details of bonding type rmsd
  covalent geometry    : bond        0.00285 ( 4239)
  covalent geometry    : angle       0.49540 ( 5754)
  hydrogen bonds       : bond        0.07141 (  228)
  hydrogen bonds       : angle       3.71964 (  678)

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

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

  1118 Ramachandran restraints generated.
    559 Oldfield, 0 Emsley, 559 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1118 Ramachandran restraints generated.
    559 Oldfield, 0 Emsley, 559 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  45 residues out of total 464 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 4
    poor density    : 41
  time to evaluate  : 0.150 
Fit side-chains
REVERT: A  285 SER cc_start: 0.8201 (p) cc_final: 0.7922 (t)
REVERT: A  654 ILE cc_start: 0.7626 (mp) cc_final: 0.7215 (mt)
  outliers start: 4
  outliers final: 3
  residues processed: 43
  average time/residue: 0.1107
  time to fit residues: 5.7067
Evaluate side-chains
  43 residues out of total 464 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 3
    poor density    : 40
  time to evaluate  : 0.142 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  459 LEU
Chi-restraints excluded: chain A residue  499 PHE
Chi-restraints excluded: chain A residue  648 LEU
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 56
   random chunks:
   chunk 34 optimal weight:    0.9990
   chunk 24 optimal weight:    0.7980
   chunk 44 optimal weight:    1.9990
   chunk 19 optimal weight:    0.6980
   chunk 14 optimal weight:    0.9990
   chunk 7 optimal weight:    0.5980
   chunk 33 optimal weight:    0.6980
   chunk 46 optimal weight:    1.9990
   chunk 29 optimal weight:    0.3980
   chunk 50 optimal weight:   10.0000
   chunk 26 optimal weight:    0.0770
   overall best weight:    0.4938

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

Flipped N/Q/H residues before XYZ refinement:
A 556 HIS

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4288 r_free = 0.4288 target = 0.186695 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 42)----------------|
| r_work = 0.4207 r_free = 0.4207 target = 0.179724 restraints weight = 5740.629|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 41)----------------|
| r_work = 0.4082 r_free = 0.4082 target = 0.172336 restraints weight = 13260.357|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 32)----------------|
| r_work = 0.4062 r_free = 0.4062 target = 0.169931 restraints weight = 10981.546|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 33)----------------|
| r_work = 0.4058 r_free = 0.4058 target = 0.169819 restraints weight = 12558.444|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 39)----------------|
| r_work = 0.4069 r_free = 0.4069 target = 0.170641 restraints weight = 8093.675|
|-----------------------------------------------------------------------------|
r_work (final): 0.4059
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6481
moved from start:          0.1764

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.038   4239  Z= 0.172
  Angle     :  0.517   7.615   5754  Z= 0.262
  Chirality :  0.039   0.130    691
  Planarity :  0.003   0.038    734
  Dihedral  :  3.435  14.044    605
  Min Nonbonded Distance : 2.584

Molprobity Statistics.
  All-atom Clashscore : 3.71
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.11 %
    Favored  : 95.89 %
  Rotamer:
    Outliers :  1.88 %
    Allowed  : 13.65 %
    Favored  : 84.47 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  0.71 (0.36), residues: 559
  helix:  1.92 (0.29), residues: 329
  sheet:  None (None), residues: 0
  loop : -1.81 (0.37), residues: 230

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG A 242 
 TYR   0.016   0.002   TYR A 207 
 PHE   0.014   0.001   PHE A 317 
 TRP   0.007   0.001   TRP A 565 
 HIS   0.004   0.001   HIS A 498 

Details of bonding type rmsd
  covalent geometry    : bond        0.00371 ( 4239)
  covalent geometry    : angle       0.51735 ( 5754)
  hydrogen bonds       : bond        0.07935 (  228)
  hydrogen bonds       : angle       3.82337 (  678)

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

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

  1118 Ramachandran restraints generated.
    559 Oldfield, 0 Emsley, 559 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1118 Ramachandran restraints generated.
    559 Oldfield, 0 Emsley, 559 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  51 residues out of total 464 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 43
  time to evaluate  : 0.148 
Fit side-chains
REVERT: A  187 SER cc_start: 0.7729 (m) cc_final: 0.7329 (p)
REVERT: A  285 SER cc_start: 0.8226 (p) cc_final: 0.7961 (t)
REVERT: A  443 ILE cc_start: 0.8355 (mm) cc_final: 0.8090 (mt)
  outliers start: 8
  outliers final: 4
  residues processed: 48
  average time/residue: 0.0893
  time to fit residues: 5.3061
Evaluate side-chains
  47 residues out of total 464 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 4
    poor density    : 43
  time to evaluate  : 0.106 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  427 THR
Chi-restraints excluded: chain A residue  648 LEU
Chi-restraints excluded: chain A residue  687 VAL
Chi-restraints excluded: chain A residue  700 MET
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 56
   random chunks:
   chunk 51 optimal weight:    0.0070
   chunk 34 optimal weight:    0.7980
   chunk 35 optimal weight:    0.9990
   chunk 5 optimal weight:    0.9980
   chunk 13 optimal weight:    0.9990
   chunk 22 optimal weight:    0.0980
   chunk 47 optimal weight:    0.0010
   chunk 50 optimal weight:    3.9990
   chunk 42 optimal weight:    0.7980
   chunk 4 optimal weight:    0.0980
   chunk 2 optimal weight:    0.7980
   overall best weight:    0.2004

-------------------------------------------------------------------------------
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 = 0.4343 r_free = 0.4343 target = 0.192978 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 68)----------------|
| r_work = 0.4267 r_free = 0.4267 target = 0.186172 restraints weight = 5895.409|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 57)----------------|
| r_work = 0.4168 r_free = 0.4168 target = 0.181117 restraints weight = 12116.019|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 36)----------------|
| r_work = 0.4140 r_free = 0.4140 target = 0.177878 restraints weight = 8383.913|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 31)----------------|
| r_work = 0.4140 r_free = 0.4140 target = 0.177732 restraints weight = 8232.903|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 31)----------------|
| r_work = 0.4143 r_free = 0.4143 target = 0.177950 restraints weight = 6412.917|
|-----------------------------------------------------------------------------|
r_work (final): 0.4128
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6400
moved from start:          0.1971

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.025   4239  Z= 0.122
  Angle     :  0.477   7.306   5754  Z= 0.240
  Chirality :  0.037   0.126    691
  Planarity :  0.003   0.037    734
  Dihedral  :  3.195  11.836    605
  Min Nonbonded Distance : 2.577

Molprobity Statistics.
  All-atom Clashscore : 3.47
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.22 %
    Favored  : 96.78 %
  Rotamer:
    Outliers :  2.12 %
    Allowed  : 15.06 %
    Favored  : 82.82 %
  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 aren not related in a simple way.
  whole:  1.02 (0.36), residues: 559
  helix:  2.23 (0.29), residues: 330
  sheet:  None (None), residues: 0
  loop : -1.80 (0.37), residues: 229

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG A 242 
 TYR   0.013   0.001   TYR A 207 
 PHE   0.007   0.001   PHE A 619 
 TRP   0.008   0.001   TRP A 565 
 HIS   0.003   0.001   HIS A 498 

Details of bonding type rmsd
  covalent geometry    : bond        0.00227 ( 4239)
  covalent geometry    : angle       0.47678 ( 5754)
  hydrogen bonds       : bond        0.06246 (  228)
  hydrogen bonds       : angle       3.46728 (  678)

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

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

  1118 Ramachandran restraints generated.
    559 Oldfield, 0 Emsley, 559 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1118 Ramachandran restraints generated.
    559 Oldfield, 0 Emsley, 559 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  53 residues out of total 464 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 44
  time to evaluate  : 0.128 
Fit side-chains
REVERT: A  285 SER cc_start: 0.8243 (p) cc_final: 0.7955 (t)
REVERT: A  443 ILE cc_start: 0.8262 (mm) cc_final: 0.8026 (mt)
  outliers start: 9
  outliers final: 6
  residues processed: 49
  average time/residue: 0.1000
  time to fit residues: 5.8947
Evaluate side-chains
  49 residues out of total 464 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 43
  time to evaluate  : 0.149 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  427 THR
Chi-restraints excluded: chain A residue  499 PHE
Chi-restraints excluded: chain A residue  539 LEU
Chi-restraints excluded: chain A residue  648 LEU
Chi-restraints excluded: chain A residue  687 VAL
Chi-restraints excluded: chain A residue  700 MET
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 56
   random chunks:
   chunk 52 optimal weight:    0.5980
   chunk 18 optimal weight:    0.5980
   chunk 21 optimal weight:    0.0170
   chunk 20 optimal weight:    0.1980
   chunk 41 optimal weight:    0.8980
   chunk 47 optimal weight:    6.9990
   chunk 48 optimal weight:    0.9980
   chunk 5 optimal weight:    0.3980
   chunk 15 optimal weight:    0.4980
   chunk 16 optimal weight:    0.1980
   chunk 55 optimal weight:    0.0470
   overall best weight:    0.1716

-------------------------------------------------------------------------------
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 = 0.4216 r_free = 0.4216 target = 0.183627 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 187)---------------|
| r_work = 0.4070 r_free = 0.4070 target = 0.170180 restraints weight = 5981.556|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 55)----------------|
| r_work = 0.4028 r_free = 0.4028 target = 0.166713 restraints weight = 8970.604|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 59)----------------|
| r_work = 0.4017 r_free = 0.4017 target = 0.165781 restraints weight = 10068.242|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 35)----------------|
| r_work = 0.4018 r_free = 0.4018 target = 0.165823 restraints weight = 9193.013|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 29)----------------|
| r_work = 0.4018 r_free = 0.4018 target = 0.165850 restraints weight = 7469.586|
|-----------------------------------------------------------------------------|
r_work (final): 0.4017
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6295
moved from start:          0.2201

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.025   4239  Z= 0.114
  Angle     :  0.463   7.195   5754  Z= 0.232
  Chirality :  0.037   0.126    691
  Planarity :  0.003   0.037    734
  Dihedral  :  3.040  11.794    605
  Min Nonbonded Distance : 2.562

Molprobity Statistics.
  All-atom Clashscore : 3.47
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.40 %
    Favored  : 96.60 %
  Rotamer:
    Outliers :  1.88 %
    Allowed  : 15.53 %
    Favored  : 82.59 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  1.21 (0.37), residues: 559
  helix:  2.35 (0.29), residues: 334
  sheet: -1.38 (1.62), residues: 10
  loop : -1.74 (0.39), residues: 215

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG A 257 
 TYR   0.010   0.001   TYR A 207 
 PHE   0.007   0.001   PHE A 619 
 TRP   0.007   0.001   TRP A 565 
 HIS   0.003   0.000   HIS A 498 

Details of bonding type rmsd
  covalent geometry    : bond        0.00214 ( 4239)
  covalent geometry    : angle       0.46277 ( 5754)
  hydrogen bonds       : bond        0.05697 (  228)
  hydrogen bonds       : angle       3.28655 (  678)

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

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

  1118 Ramachandran restraints generated.
    559 Oldfield, 0 Emsley, 559 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1118 Ramachandran restraints generated.
    559 Oldfield, 0 Emsley, 559 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  53 residues out of total 464 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 45
  time to evaluate  : 0.149 
Fit side-chains
REVERT: A  426 MET cc_start: 0.7484 (mmm) cc_final: 0.7017 (mmm)
REVERT: A  443 ILE cc_start: 0.8178 (mm) cc_final: 0.7953 (mt)
  outliers start: 8
  outliers final: 7
  residues processed: 50
  average time/residue: 0.0946
  time to fit residues: 5.7877
Evaluate side-chains
  52 residues out of total 464 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 45
  time to evaluate  : 0.148 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  247 LEU
Chi-restraints excluded: chain A residue  307 MET
Chi-restraints excluded: chain A residue  427 THR
Chi-restraints excluded: chain A residue  499 PHE
Chi-restraints excluded: chain A residue  539 LEU
Chi-restraints excluded: chain A residue  648 LEU
Chi-restraints excluded: chain A residue  687 VAL
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 56
   random chunks:
   chunk 17 optimal weight:    0.5980
   chunk 15 optimal weight:    0.0970
   chunk 55 optimal weight:    0.4980
   chunk 53 optimal weight:    7.9990
   chunk 44 optimal weight:    0.9980
   chunk 24 optimal weight:    0.7980
   chunk 39 optimal weight:    3.9990
   chunk 12 optimal weight:    1.9990
   chunk 33 optimal weight:    1.9990
   chunk 10 optimal weight:    0.8980
   chunk 34 optimal weight:    0.0870
   overall best weight:    0.4156

-------------------------------------------------------------------------------
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 = 0.4169 r_free = 0.4169 target = 0.179070 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 62)----------------|
| r_work = 0.4021 r_free = 0.4021 target = 0.165598 restraints weight = 5931.469|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 53)----------------|
| r_work = 0.3984 r_free = 0.3984 target = 0.162521 restraints weight = 9878.217|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 91)----------------|
| r_work = 0.3976 r_free = 0.3976 target = 0.161828 restraints weight = 9998.216|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 126)---------------|
| r_work = 0.3966 r_free = 0.3966 target = 0.160951 restraints weight = 8540.262|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 28)----------------|
| r_work = 0.3965 r_free = 0.3965 target = 0.160863 restraints weight = 9467.239|
|-----------------------------------------------------------------------------|
r_work (final): 0.3964
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6374
moved from start:          0.2090

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.033   4239  Z= 0.155
  Angle     :  0.500   7.627   5754  Z= 0.256
  Chirality :  0.039   0.182    691
  Planarity :  0.003   0.038    734
  Dihedral  :  3.219  13.063    605
  Min Nonbonded Distance : 2.565

Molprobity Statistics.
  All-atom Clashscore : 4.07
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.94 %
    Favored  : 96.06 %
  Rotamer:
    Outliers :  1.65 %
    Allowed  : 16.24 %
    Favored  : 82.12 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  1.03 (0.36), residues: 559
  helix:  2.21 (0.29), residues: 331
  sheet:  None (None), residues: 0
  loop : -1.75 (0.38), residues: 228

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG A 242 
 TYR   0.010   0.001   TYR A 207 
 PHE   0.008   0.001   PHE A 619 
 TRP   0.005   0.001   TRP A 565 
 HIS   0.004   0.001   HIS A 498 

Details of bonding type rmsd
  covalent geometry    : bond        0.00325 ( 4239)
  covalent geometry    : angle       0.49959 ( 5754)
  hydrogen bonds       : bond        0.07383 (  228)
  hydrogen bonds       : angle       3.58793 (  678)

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

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

  1118 Ramachandran restraints generated.
    559 Oldfield, 0 Emsley, 559 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1118 Ramachandran restraints generated.
    559 Oldfield, 0 Emsley, 559 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  53 residues out of total 464 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 46
  time to evaluate  : 0.164 
Fit side-chains
REVERT: A  362 ARG cc_start: 0.5747 (mmt180) cc_final: 0.2660 (mtt180)
REVERT: A  443 ILE cc_start: 0.8284 (mm) cc_final: 0.8039 (mt)
  outliers start: 7
  outliers final: 4
  residues processed: 50
  average time/residue: 0.1016
  time to fit residues: 6.1142
Evaluate side-chains
  50 residues out of total 464 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 4
    poor density    : 46
  time to evaluate  : 0.149 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  427 THR
Chi-restraints excluded: chain A residue  499 PHE
Chi-restraints excluded: chain A residue  648 LEU
Chi-restraints excluded: chain A residue  687 VAL
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 56
   random chunks:
   chunk 12 optimal weight:    1.9990
   chunk 6 optimal weight:    0.3980
   chunk 45 optimal weight:    4.9990
   chunk 11 optimal weight:    0.8980
   chunk 37 optimal weight:    0.0010
   chunk 2 optimal weight:    0.6980
   chunk 36 optimal weight:    1.9990
   chunk 49 optimal weight:    0.5980
   chunk 32 optimal weight:    0.4980
   chunk 17 optimal weight:    0.6980
   chunk 51 optimal weight:    3.9990
   overall best weight:    0.4386

-------------------------------------------------------------------------------
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 = 0.4167 r_free = 0.4167 target = 0.178908 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 45)----------------|
| r_work = 0.4021 r_free = 0.4021 target = 0.165718 restraints weight = 5845.923|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 78)----------------|
| r_work = 0.3988 r_free = 0.3988 target = 0.162979 restraints weight = 8574.707|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 67)----------------|
| r_work = 0.3967 r_free = 0.3967 target = 0.161170 restraints weight = 11040.355|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 58)----------------|
| r_work = 0.3962 r_free = 0.3962 target = 0.160731 restraints weight = 10840.887|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 44)----------------|
| r_work = 0.3953 r_free = 0.3953 target = 0.160010 restraints weight = 10158.401|
|-----------------------------------------------------------------------------|
r_work (final): 0.3950
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6403
moved from start:          0.2153

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.035   4239  Z= 0.160
  Angle     :  0.499   7.602   5754  Z= 0.256
  Chirality :  0.039   0.164    691
  Planarity :  0.003   0.038    734
  Dihedral  :  3.276  14.224    605
  Min Nonbonded Distance : 2.561

Molprobity Statistics.
  All-atom Clashscore : 3.83
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.76 %
    Favored  : 96.24 %
  Rotamer:
    Outliers :  1.65 %
    Allowed  : 15.76 %
    Favored  : 82.59 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  0.85 (0.36), residues: 559
  helix:  2.07 (0.29), residues: 333
  sheet:  None (None), residues: 0
  loop : -1.89 (0.37), residues: 226

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG A 542 
 TYR   0.011   0.001   TYR A 207 
 PHE   0.009   0.001   PHE A 619 
 TRP   0.006   0.001   TRP A 565 
 HIS   0.004   0.001   HIS A 498 

Details of bonding type rmsd
  covalent geometry    : bond        0.00339 ( 4239)
  covalent geometry    : angle       0.49937 ( 5754)
  hydrogen bonds       : bond        0.07508 (  228)
  hydrogen bonds       : angle       3.63683 (  678)

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

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

  1118 Ramachandran restraints generated.
    559 Oldfield, 0 Emsley, 559 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1118 Ramachandran restraints generated.
    559 Oldfield, 0 Emsley, 559 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  54 residues out of total 464 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 47
  time to evaluate  : 0.151 
Fit side-chains
REVERT: A  362 ARG cc_start: 0.5712 (mmt180) cc_final: 0.2988 (mmt180)
REVERT: A  443 ILE cc_start: 0.8301 (mm) cc_final: 0.8046 (mt)
  outliers start: 7
  outliers final: 6
  residues processed: 52
  average time/residue: 0.1173
  time to fit residues: 7.2243
Evaluate side-chains
  53 residues out of total 464 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 47
  time to evaluate  : 0.156 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  285 SER
Chi-restraints excluded: chain A residue  427 THR
Chi-restraints excluded: chain A residue  499 PHE
Chi-restraints excluded: chain A residue  539 LEU
Chi-restraints excluded: chain A residue  648 LEU
Chi-restraints excluded: chain A residue  687 VAL
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 56
   random chunks:
   chunk 22 optimal weight:    0.0980
   chunk 43 optimal weight:    0.3980
   chunk 40 optimal weight:    0.9980
   chunk 12 optimal weight:    0.8980
   chunk 17 optimal weight:    0.5980
   chunk 6 optimal weight:    0.9990
   chunk 41 optimal weight:    0.9980
   chunk 25 optimal weight:    0.9980
   chunk 1 optimal weight:    0.6980
   chunk 24 optimal weight:    0.5980
   chunk 20 optimal weight:    0.0980
   overall best weight:    0.3580

-------------------------------------------------------------------------------
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 = 0.4168 r_free = 0.4168 target = 0.178998 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 49)----------------|
| r_work = 0.4033 r_free = 0.4033 target = 0.166713 restraints weight = 5840.000|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 54)----------------|
| r_work = 0.3991 r_free = 0.3991 target = 0.163398 restraints weight = 9360.190|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 41)----------------|
| r_work = 0.3980 r_free = 0.3980 target = 0.162368 restraints weight = 10730.127|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 67)----------------|
| r_work = 0.3966 r_free = 0.3966 target = 0.161110 restraints weight = 9969.005|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 36)----------------|
| r_work = 0.3960 r_free = 0.3960 target = 0.160668 restraints weight = 9869.300|
|-----------------------------------------------------------------------------|
r_work (final): 0.3961
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6372
moved from start:          0.2211

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.032   4239  Z= 0.145
  Angle     :  0.496   7.980   5754  Z= 0.251
  Chirality :  0.038   0.137    691
  Planarity :  0.003   0.037    734
  Dihedral  :  3.224  13.818    605
  Min Nonbonded Distance : 2.548

Molprobity Statistics.
  All-atom Clashscore : 3.95
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.94 %
    Favored  : 96.06 %
  Rotamer:
    Outliers :  1.88 %
    Allowed  : 15.53 %
    Favored  : 82.59 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  0.98 (0.36), residues: 559
  helix:  2.18 (0.29), residues: 334
  sheet:  None (None), residues: 0
  loop : -1.86 (0.38), residues: 225

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG A 542 
 TYR   0.010   0.001   TYR A 207 
 PHE   0.008   0.001   PHE A 619 
 TRP   0.007   0.001   TRP A 565 
 HIS   0.004   0.001   HIS A 498 

Details of bonding type rmsd
  covalent geometry    : bond        0.00297 ( 4239)
  covalent geometry    : angle       0.49553 ( 5754)
  hydrogen bonds       : bond        0.07116 (  228)
  hydrogen bonds       : angle       3.57579 (  678)

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

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

  1118 Ramachandran restraints generated.
    559 Oldfield, 0 Emsley, 559 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1118 Ramachandran restraints generated.
    559 Oldfield, 0 Emsley, 559 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  55 residues out of total 464 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 47
  time to evaluate  : 0.164 
Fit side-chains
REVERT: A  362 ARG cc_start: 0.5803 (mmt180) cc_final: 0.3165 (mmt180)
REVERT: A  443 ILE cc_start: 0.8282 (mm) cc_final: 0.8036 (mt)
  outliers start: 8
  outliers final: 8
  residues processed: 52
  average time/residue: 0.1121
  time to fit residues: 7.0449
Evaluate side-chains
  53 residues out of total 464 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 45
  time to evaluate  : 0.159 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  285 SER
Chi-restraints excluded: chain A residue  363 THR
Chi-restraints excluded: chain A residue  427 THR
Chi-restraints excluded: chain A residue  499 PHE
Chi-restraints excluded: chain A residue  515 LEU
Chi-restraints excluded: chain A residue  539 LEU
Chi-restraints excluded: chain A residue  648 LEU
Chi-restraints excluded: chain A residue  687 VAL
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 56
   random chunks:
   chunk 3 optimal weight:    0.3980
   chunk 13 optimal weight:    0.9980
   chunk 1 optimal weight:    0.5980
   chunk 9 optimal weight:    0.5980
   chunk 33 optimal weight:    1.9990
   chunk 11 optimal weight:    0.5980
   chunk 18 optimal weight:    0.7980
   chunk 19 optimal weight:    0.7980
   chunk 26 optimal weight:    0.0370
   chunk 27 optimal weight:    0.0870
   chunk 34 optimal weight:    0.2980
   overall best weight:    0.2836

-------------------------------------------------------------------------------
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 = 0.4181 r_free = 0.4181 target = 0.180244 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 52)----------------|
| r_work = 0.4044 r_free = 0.4044 target = 0.167674 restraints weight = 5833.204|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 56)----------------|
| r_work = 0.4007 r_free = 0.4007 target = 0.164785 restraints weight = 9885.089|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 64)----------------|
| r_work = 0.3993 r_free = 0.3993 target = 0.163473 restraints weight = 11098.601|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 41)----------------|
| r_work = 0.3986 r_free = 0.3986 target = 0.162825 restraints weight = 9555.258|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 43)----------------|
| r_work = 0.3977 r_free = 0.3977 target = 0.162051 restraints weight = 9843.911|
|-----------------------------------------------------------------------------|
r_work (final): 0.3987
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6344
moved from start:          0.2308

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.028   4239  Z= 0.131
  Angle     :  0.481   8.797   5754  Z= 0.243
  Chirality :  0.038   0.130    691
  Planarity :  0.003   0.037    734
  Dihedral  :  3.130  12.496    605
  Min Nonbonded Distance : 2.546

Molprobity Statistics.
  All-atom Clashscore : 4.07
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.58 %
    Favored  : 96.42 %
  Rotamer:
    Outliers :  1.41 %
    Allowed  : 16.24 %
    Favored  : 82.35 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  1.14 (0.36), residues: 559
  helix:  2.30 (0.29), residues: 334
  sheet: -1.90 (1.47), residues: 10
  loop : -1.74 (0.39), residues: 215

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG A 542 
 TYR   0.010   0.001   TYR A 207 
 PHE   0.008   0.001   PHE A 619 
 TRP   0.007   0.001   TRP A 565 
 HIS   0.003   0.001   HIS A 498 

Details of bonding type rmsd
  covalent geometry    : bond        0.00259 ( 4239)
  covalent geometry    : angle       0.48086 ( 5754)
  hydrogen bonds       : bond        0.06547 (  228)
  hydrogen bonds       : angle       3.45943 (  678)

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

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

  1118 Ramachandran restraints generated.
    559 Oldfield, 0 Emsley, 559 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1118 Ramachandran restraints generated.
    559 Oldfield, 0 Emsley, 559 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  53 residues out of total 464 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 47
  time to evaluate  : 0.167 
Fit side-chains
REVERT: A  362 ARG cc_start: 0.5864 (mmt180) cc_final: 0.5036 (mmt180)
REVERT: A  426 MET cc_start: 0.7533 (mmm) cc_final: 0.7095 (mmm)
REVERT: A  443 ILE cc_start: 0.8245 (mm) cc_final: 0.8007 (mt)
REVERT: A  459 LEU cc_start: 0.7666 (mt) cc_final: 0.7401 (tp)
  outliers start: 6
  outliers final: 6
  residues processed: 50
  average time/residue: 0.1120
  time to fit residues: 6.6794
Evaluate side-chains
  53 residues out of total 464 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 47
  time to evaluate  : 0.152 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  427 THR
Chi-restraints excluded: chain A residue  499 PHE
Chi-restraints excluded: chain A residue  515 LEU
Chi-restraints excluded: chain A residue  539 LEU
Chi-restraints excluded: chain A residue  648 LEU
Chi-restraints excluded: chain A residue  687 VAL
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 56
   random chunks:
   chunk 33 optimal weight:    1.9990
   chunk 2 optimal weight:    0.6980
   chunk 14 optimal weight:    1.9990
   chunk 35 optimal weight:    0.9990
   chunk 4 optimal weight:    0.6980
   chunk 55 optimal weight:    0.9990
   chunk 40 optimal weight:    0.5980
   chunk 47 optimal weight:    0.9990
   chunk 6 optimal weight:    0.5980
   chunk 22 optimal weight:    0.2980
   chunk 48 optimal weight:    0.9990
   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 = 0.4143 r_free = 0.4143 target = 0.176767 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 96)----------------|
| r_work = 0.3962 r_free = 0.3962 target = 0.160571 restraints weight = 5872.842|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 79)----------------|
| r_work = 0.3915 r_free = 0.3915 target = 0.156694 restraints weight = 9612.147|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 43)----------------|
| r_work = 0.3906 r_free = 0.3906 target = 0.155864 restraints weight = 9076.821|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 84)----------------|
| r_work = 0.3908 r_free = 0.3908 target = 0.156097 restraints weight = 6742.321|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 59)----------------|
| r_work = 0.3893 r_free = 0.3893 target = 0.154762 restraints weight = 6340.662|
|-----------------------------------------------------------------------------|
r_work (final): 0.3893
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6510
moved from start:          0.2279

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.041   4239  Z= 0.189
  Angle     :  0.530   9.095   5754  Z= 0.272
  Chirality :  0.040   0.149    691
  Planarity :  0.003   0.039    734
  Dihedral  :  3.375  15.865    605
  Min Nonbonded Distance : 2.552

Molprobity Statistics.
  All-atom Clashscore : 4.31
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.94 %
    Favored  : 96.06 %
  Rotamer:
    Outliers :  2.12 %
    Allowed  : 15.53 %
    Favored  : 82.35 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  0.87 (0.36), residues: 559
  helix:  2.07 (0.28), residues: 330
  sheet:  None (None), residues: 0
  loop : -1.80 (0.37), residues: 229

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG A 542 
 TYR   0.010   0.002   TYR A 207 
 PHE   0.016   0.001   PHE A 309 
 TRP   0.005   0.001   TRP A 565 
 HIS   0.005   0.001   HIS A 498 

Details of bonding type rmsd
  covalent geometry    : bond        0.00420 ( 4239)
  covalent geometry    : angle       0.53011 ( 5754)
  hydrogen bonds       : bond        0.08088 (  228)
  hydrogen bonds       : angle       3.75397 (  678)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 1072.80 seconds
wall clock time: 19 minutes 0.31 seconds (1140.31 seconds total)