Starting phenix.real_space_refine
on Wed Mar  4 02:57:30 2026 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/7pmx_13543/03_2026/7pmx_13543.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/7pmx_13543/03_2026/7pmx_13543.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.5
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/7pmx_13543/03_2026/7pmx_13543.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/7pmx_13543/03_2026/7pmx_13543.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/7pmx_13543/03_2026/7pmx_13543.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/7pmx_13543/03_2026/7pmx_13543.cif"
  }
  resolution = 3.5
  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=   0.000 sd=   1.000
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: 5
    Type Number    sf(0)   Gaussians
     S      32      5.16       5
     C    3384      2.51       5
     N     830      2.21       5
     O     918      1.98       5
     H    5253      0.53       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 10 residue(s): 0.00s

  Monomer Library directory:
    "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/chem_data/mon_lib"
  Total number of atoms: 10417
  Number of models: 1
  Model: ""
    Number of chains: 2
    Chain: "A"
      Number of atoms: 10384
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 657, 10384
          Classifications: {'peptide': 657}
          Link IDs: {'PTRANS': 30, 'TRANS': 626}
          Chain breaks: 3
    Chain: "B"
      Number of atoms: 33
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 2, 33
          Classifications: {'peptide': 2}
          Modifications used: {'COO': 1, 'NH3': 1}
          Link IDs: {'TRANS': 1}
  Time building chain proxies: 1.80, per 1000 atoms: 0.17
  Number of scatterers: 10417
  At special positions: 0
  Unit cell: (85.09, 89.11, 121.94, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 5
    Type Number    sf(0)
     S      32     16.00
     O     918      8.00
     N     830      7.00
     C    3384      6.00
     H    5253      1.00
    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: 0.91
  Conformation dependent library (CDL) restraints added in 315.1 milliseconds
  

  1298 Ramachandran restraints generated.
    649 Oldfield, 0 Emsley, 649 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  1234

  Finding SS restraints...
    Secondary structure from input PDB file:
      29 helices and 6 sheets defined
      61.2% alpha, 13.5% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.27
  Creating SS restraints...
    Processing helix  chain 'A' and resid 12 through 45
      removed outlier: 4.214A  pdb=" N   PHE A  18 " --> pdb=" O   LEU A  14 " (cutoff:3.500A)
      removed outlier: 4.088A  pdb=" N   ILE A  19 " --> pdb=" O   SER A  15 " (cutoff:3.500A)
      removed outlier: 3.606A  pdb=" N   ALA A  35 " --> pdb=" O   TYR A  31 " (cutoff:3.500A)
      removed outlier: 3.701A  pdb=" N   ILE A  36 " --> pdb=" O   GLY A  32 " (cutoff:3.500A)
      removed outlier: 3.704A  pdb=" N   LEU A  39 " --> pdb=" O   ALA A  35 " (cutoff:3.500A)
      removed outlier: 3.643A  pdb=" N   PHE A  41 " --> pdb=" O   LEU A  37 " (cutoff:3.500A)
      removed outlier: 3.966A  pdb=" N   THR A  42 " --> pdb=" O   ILE A  38 " (cutoff:3.500A)
      removed outlier: 4.086A  pdb=" N   ASN A  43 " --> pdb=" O   LEU A  39 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 51 through 56
    Processing helix  chain 'A' and resid 61 through 66
    Processing helix  chain 'A' and resid 66 through 75
      removed outlier: 3.532A  pdb=" N   GLY A  70 " --> pdb=" O   THR A  66 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 78 through 108
      removed outlier: 3.737A  pdb=" N   LYS A  82 " --> pdb=" O   LEU A  78 " (cutoff:3.500A)
      removed outlier: 3.995A  pdb=" N   THR A  83 " --> pdb=" O   GLY A  79 " (cutoff:3.500A)
      removed outlier: 3.599A  pdb=" N   VAL A  85 " --> pdb=" O   PHE A  81 " (cutoff:3.500A)
      removed outlier: 3.608A  pdb=" N   ILE A 103 " --> pdb=" O   SER A  99 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 118 through 149
      removed outlier: 3.942A  pdb=" N   LEU A 124 " --> pdb=" O   VAL A 120 " (cutoff:3.500A)
      removed outlier: 3.912A  pdb=" N   SER A 125 " --> pdb=" O   HIS A 121 " (cutoff:3.500A)
      removed outlier: 3.732A  pdb=" N   LEU A 134 " --> pdb=" O   ALA A 130 " (cutoff:3.500A)
      removed outlier: 3.829A  pdb=" N   GLY A 135 " --> pdb=" O   LEU A 131 " (cutoff:3.500A)
      removed outlier: 3.667A  pdb=" N   ILE A 139 " --> pdb=" O   GLY A 135 " (cutoff:3.500A)
      removed outlier: 4.197A  pdb=" N   LYS A 140 " --> pdb=" O   THR A 136 " (cutoff:3.500A)
      Proline residue:  A 141  - end of helix
      removed outlier: 3.537A  pdb=" N   SER A 144 " --> pdb=" O   LYS A 140 " (cutoff:3.500A)
      removed outlier: 3.806A  pdb=" N   GLY A 148 " --> pdb=" O   SER A 144 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 155 through 185
      removed outlier: 3.560A  pdb=" N   SER A 164 " --> pdb=" O   ASN A 160 " (cutoff:3.500A)
      removed outlier: 3.958A  pdb=" N   ASN A 171 " --> pdb=" O   TYR A 167 " (cutoff:3.500A)
      Proline residue:  A 182  - end of helix
    Processing helix  chain 'A' and resid 197 through 219
      Proline residue:  A 205  - end of helix
      removed outlier: 3.529A  pdb=" N   VAL A 211 " --> pdb=" O   ALA A 207 " (cutoff:3.500A)
      removed outlier: 3.624A  pdb=" N   GLY A 219 " --> pdb=" O   VAL A 215 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 231 through 249
      removed outlier: 3.505A  pdb=" N   LYS A 245 " --> pdb=" O   GLY A 241 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 261 through 266
    Processing helix  chain 'A' and resid 270 through 286
      removed outlier: 3.876A  pdb=" N   LEU A 286 " --> pdb=" O   ARG A 282 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 287 through 288
      No H-bonds generated for 'chain 'A' and resid 287 through 288'
    Processing helix  chain 'A' and resid 289 through 291
      No H-bonds generated for 'chain 'A' and resid 289 through 291'
    Processing helix  chain 'A' and resid 292 through 298
      removed outlier: 3.565A  pdb=" N   ASP A 298 " --> pdb=" O   TRP A 294 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 298 through 311
      removed outlier: 4.157A  pdb=" N   SER A 302 " --> pdb=" O   ASP A 298 " (cutoff:3.500A)
      removed outlier: 4.209A  pdb=" N   TRP A 304 " --> pdb=" O   GLN A 300 " (cutoff:3.500A)
      removed outlier: 4.163A  pdb=" N   THR A 305 " --> pdb=" O   GLY A 301 " (cutoff:3.500A)
      removed outlier: 3.512A  pdb=" N   GLN A 307 " --> pdb=" O   ARG A 303 " (cutoff:3.500A)
      removed outlier: 3.575A  pdb=" N   THR A 309 " --> pdb=" O   THR A 305 " (cutoff:3.500A)
      removed outlier: 3.703A  pdb=" N   THR A 310 " --> pdb=" O   LEU A 306 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 321 through 325
      removed outlier: 3.720A  pdb=" N   MET A 325 " --> pdb=" O   PRO A 322 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 326 through 343
      removed outlier: 4.238A  pdb=" N   ALA A 330 " --> pdb=" O   GLN A 326 " (cutoff:3.500A)
      removed outlier: 3.653A  pdb=" N   ILE A 335 " --> pdb=" O   ILE A 331 " (cutoff:3.500A)
      removed outlier: 3.675A  pdb=" N   VAL A 337 " --> pdb=" O   ILE A 333 " (cutoff:3.500A)
      Proline residue:  A 338  - end of helix
    Processing helix  chain 'A' and resid 343 through 351
    Processing helix  chain 'A' and resid 356 through 384
      removed outlier: 3.697A  pdb=" N   VAL A 366 " --> pdb=" O   ALA A 362 " (cutoff:3.500A)
      removed outlier: 3.592A  pdb=" N   VAL A 374 " --> pdb=" O   MET A 370 " (cutoff:3.500A)
      removed outlier: 3.804A  pdb=" N   ALA A 375 " --> pdb=" O   ALA A 371 " (cutoff:3.500A)
      removed outlier: 3.763A  pdb=" N   LYS A 384 " --> pdb=" O   VAL A 380 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 433 through 435
      No H-bonds generated for 'chain 'A' and resid 433 through 435'
    Processing helix  chain 'A' and resid 481 through 485
    Processing helix  chain 'A' and resid 580 through 583
      removed outlier: 3.671A  pdb=" N   LEU A 583 " --> pdb=" O   ASN A 580 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'A' and resid 580 through 583'
    Processing helix  chain 'A' and resid 584 through 610
      removed outlier: 3.580A  pdb=" N   LEU A 591 " --> pdb=" O   GLN A 587 " (cutoff:3.500A)
      removed outlier: 3.749A  pdb=" N   VAL A 597 " --> pdb=" O   CYS A 593 " (cutoff:3.500A)
      removed outlier: 3.923A  pdb=" N   THR A 601 " --> pdb=" O   VAL A 597 " (cutoff:3.500A)
      removed outlier: 4.095A  pdb=" N   TYR A 607 " --> pdb=" O   LEU A 603 " (cutoff:3.500A)
      removed outlier: 3.802A  pdb=" N   ALA A 610 " --> pdb=" O   SER A 606 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 614 through 637
      removed outlier: 3.639A  pdb=" N   LEU A 618 " --> pdb=" O   MET A 614 " (cutoff:3.500A)
      removed outlier: 3.545A  pdb=" N   THR A 625 " --> pdb=" O   GLY A 621 " (cutoff:3.500A)
      removed outlier: 3.832A  pdb=" N   VAL A 626 " --> pdb=" O   TRP A 622 " (cutoff:3.500A)
      removed outlier: 3.804A  pdb=" N   ILE A 631 " --> pdb=" O   ALA A 627 " (cutoff:3.500A)
      removed outlier: 3.555A  pdb=" N   ILE A 632 " --> pdb=" O   VAL A 628 " (cutoff:3.500A)
      removed outlier: 3.776A  pdb=" N   VAL A 633 " --> pdb=" O   GLY A 629 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 643 through 651
      removed outlier: 3.556A  pdb=" N   ALA A 647 " --> pdb=" O   SER A 643 " (cutoff:3.500A)
      removed outlier: 4.162A  pdb=" N   TYR A 649 " --> pdb=" O   GLN A 645 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 655 through 668
    Processing helix  chain 'A' and resid 669 through 674
      removed outlier: 5.739A  pdb=" N   TYR A 672 " --> pdb=" O   PHE A 669 " (cutoff:3.500A)
      removed outlier: 4.224A  pdb=" N   ASN A 674 " --> pdb=" O   THR A 671 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 675 through 680
      removed outlier: 4.322A  pdb=" N   ALA A 680 " --> pdb=" O   ALA A 676 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 681 through 683
      No H-bonds generated for 'chain 'A' and resid 681 through 683'
    Processing sheet with id=AA1, first strand: chain 'A' and resid 422 through 423
    Processing sheet with id=AA2, first strand: chain 'A' and resid 422 through 423
      removed outlier: 6.723A  pdb=" N   HIS A 469 " --> pdb=" O   TRP A 465 " (cutoff:3.500A)
    Processing sheet with id=AA3, first strand: chain 'A' and resid 414 through 418
    Processing sheet with id=AA4, first strand: chain 'A' and resid 514 through 515
      removed outlier: 3.653A  pdb=" N   ASN A 514 " --> pdb=" O   ASN A 492 " (cutoff:3.500A)
    Processing sheet with id=AA5, first strand: chain 'A' and resid 514 through 515
      removed outlier: 3.653A  pdb=" N   ASN A 514 " --> pdb=" O   ASN A 492 " (cutoff:3.500A)
      removed outlier: 6.497A  pdb=" N   GLY A 487 " --> pdb=" O   TYR A 554 " (cutoff:3.500A)
      removed outlier: 7.670A  pdb=" N   TYR A 556 " --> pdb=" O   GLY A 487 " (cutoff:3.500A)
      removed outlier: 6.426A  pdb=" N   ARG A 489 " --> pdb=" O   TYR A 556 " (cutoff:3.500A)
      removed outlier: 7.599A  pdb=" N   VAL A 558 " --> pdb=" O   ARG A 489 " (cutoff:3.500A)
      removed outlier: 6.388A  pdb=" N   VAL A 491 " --> pdb=" O   VAL A 558 " (cutoff:3.500A)
      removed outlier: 8.556A  pdb=" N   ARG A 560 " --> pdb=" O   VAL A 491 " (cutoff:3.500A)
      removed outlier: 6.543A  pdb=" N   ALA A 553 " --> pdb=" O   ASP A 573 " (cutoff:3.500A)
    Processing sheet with id=AA6, first strand: chain 'A' and resid 505 through 510
      removed outlier: 5.889A  pdb=" N   ILE A 498 " --> pdb=" O   ASN A 509 " (cutoff:3.500A)

    279 hydrogen bonds defined for protein.
    795 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: 1.99

  Time building geometry restraints manager: 1.27 seconds

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

  Histogram of bond lengths:
        0.84 -     1.03: 5243
        1.03 -     1.23: 10
        1.23 -     1.42: 2199
        1.42 -     1.61: 3033
        1.61 -     1.81: 54
  Bond restraints: 10539
  Sorted by residual:
  bond pdb=" C   GLN A 609 "
       pdb=" N   ALA A 610 "
    ideal  model  delta    sigma   weight residual
    1.330  1.285  0.045 1.47e-02 4.63e+03 9.42e+00
  bond pdb=" CA  VAL A 204 "
       pdb=" CB  VAL A 204 "
    ideal  model  delta    sigma   weight residual
    1.539  1.533  0.006 5.40e-03 3.43e+04 1.10e+00
  bond pdb=" C   ILE A 320 "
       pdb=" N   GLN A 321 "
    ideal  model  delta    sigma   weight residual
    1.329  1.360 -0.031 3.03e-02 1.09e+03 1.06e+00
  bond pdb=" CA  PRO A 536 "
       pdb=" C   PRO A 536 "
    ideal  model  delta    sigma   weight residual
    1.514  1.519 -0.005 5.50e-03 3.31e+04 6.72e-01
  bond pdb=" CA  ILE A 585 "
       pdb=" CB  ILE A 585 "
    ideal  model  delta    sigma   weight residual
    1.539  1.535  0.004 5.40e-03 3.43e+04 6.67e-01
  ... (remaining 10534 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     7.06: 19071
        7.06 -    14.12: 0
       14.12 -    21.18: 0
       21.18 -    28.24: 0
       28.24 -    35.30: 3
  Bond angle restraints: 19074
  Sorted by residual:
  angle pdb=" C   GLN A 609 "
        pdb=" CA  GLN A 609 "
        pdb=" HA  GLN A 609 "
      ideal   model   delta    sigma   weight residual
     109.00   73.70   35.30 3.00e+00 1.11e-01 1.38e+02
  angle pdb=" N   GLN A 609 "
        pdb=" CA  GLN A 609 "
        pdb=" HA  GLN A 609 "
      ideal   model   delta    sigma   weight residual
     110.00   75.41   34.59 3.00e+00 1.11e-01 1.33e+02
  angle pdb=" CB  GLN A 609 "
        pdb=" CA  GLN A 609 "
        pdb=" HA  GLN A 609 "
      ideal   model   delta    sigma   weight residual
     109.00   76.17   32.83 3.00e+00 1.11e-01 1.20e+02
  angle pdb=" N   GLN A 609 "
        pdb=" CA  GLN A 609 "
        pdb=" C   GLN A 609 "
      ideal   model   delta    sigma   weight residual
     113.18  116.37   -3.19 1.21e+00 6.83e-01 6.94e+00
  angle pdb=" N   VAL A 334 "
        pdb=" CA  VAL A 334 "
        pdb=" C   VAL A 334 "
      ideal   model   delta    sigma   weight residual
     113.07  109.63    3.44 1.37e+00 5.33e-01 6.30e+00
  ... (remaining 19069 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    16.85: 4628
       16.85 -    33.70: 240
       33.70 -    50.56: 63
       50.56 -    67.41: 46
       67.41 -    84.26: 9
  Dihedral angle restraints: 4986
    sinusoidal: 2660
      harmonic: 2326
  Sorted by residual:
  dihedral pdb=" C   GLN A 609 "
           pdb=" N   GLN A 609 "
           pdb=" CA  GLN A 609 "
           pdb=" CB  GLN A 609 "
      ideal   model   delta  harmonic     sigma   weight residual
    -122.60 -131.27    8.67     0      2.50e+00 1.60e-01 1.20e+01
  dihedral pdb=" CA  LYS A 257 "
           pdb=" C   LYS A 257 "
           pdb=" N   ARG A 258 "
           pdb=" CA  ARG A 258 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  162.87   17.13     0      5.00e+00 4.00e-02 1.17e+01
  dihedral pdb=" N   GLN A 609 "
           pdb=" C   GLN A 609 "
           pdb=" CA  GLN A 609 "
           pdb=" CB  GLN A 609 "
      ideal   model   delta  harmonic     sigma   weight residual
     122.80  131.07   -8.27     0      2.50e+00 1.60e-01 1.09e+01
  ... (remaining 4983 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.076: 775
       0.076 -    0.153: 53
       0.153 -    0.229: 0
       0.229 -    0.305: 0
       0.305 -    0.381: 1
  Chirality restraints: 829
  Sorted by residual:
  chirality pdb=" CA  GLN A 609 "
            pdb=" N   GLN A 609 "
            pdb=" C   GLN A 609 "
            pdb=" CB  GLN A 609 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.13    0.38 2.00e-01 2.50e+01 3.63e+00
  chirality pdb=" CA  PRO A 291 "
            pdb=" N   PRO A 291 "
            pdb=" C   PRO A 291 "
            pdb=" CB  PRO A 291 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.72    2.59    0.12 2.00e-01 2.50e+01 3.81e-01
  chirality pdb=" CA  ILE A 438 "
            pdb=" N   ILE A 438 "
            pdb=" C   ILE A 438 "
            pdb=" CB  ILE A 438 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.43    2.56   -0.12 2.00e-01 2.50e+01 3.72e-01
  ... (remaining 826 not shown)

  Planarity restraints: 1522
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   TYR A 345 "    0.028 5.00e-02 4.00e+02   4.20e-02 2.82e+00
        pdb=" N   PRO A 346 "   -0.073 5.00e-02 4.00e+02
        pdb=" CA  PRO A 346 "    0.021 5.00e-02 4.00e+02
        pdb=" CD  PRO A 346 "    0.024 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   ILE A 288 "    0.022 5.00e-02 4.00e+02   3.32e-02 1.77e+00
        pdb=" N   PRO A 289 "   -0.057 5.00e-02 4.00e+02
        pdb=" CA  PRO A 289 "    0.017 5.00e-02 4.00e+02
        pdb=" CD  PRO A 289 "    0.019 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   GLN A 540 "    0.021 5.00e-02 4.00e+02   3.11e-02 1.55e+00
        pdb=" N   PRO A 541 "   -0.054 5.00e-02 4.00e+02
        pdb=" CA  PRO A 541 "    0.016 5.00e-02 4.00e+02
        pdb=" CD  PRO A 541 "    0.017 5.00e-02 4.00e+02
  ... (remaining 1519 not shown)

  Histogram of nonbonded interaction distances:
        1.61 -     2.21: 637
        2.21 -     2.81: 21876
        2.81 -     3.40: 27998
        3.40 -     4.00: 35922
        4.00 -     4.60: 55672
  Nonbonded interactions: 142105
  Sorted by model distance:
  nonbonded pdb=" OE1 GLU A 271 "
            pdb=" H   GLU A 271 "
     model   vdw
     1.609 2.450
  nonbonded pdb=" O   GLY A 419 "
            pdb=" HG  SER A 422 "
     model   vdw
     1.615 2.450
  nonbonded pdb=" OD1 ASN A 486 "
            pdb=" HG  SER A 552 "
     model   vdw
     1.649 2.450
  nonbonded pdb=" O   PHE A 652 "
            pdb=" H   LEU A 656 "
     model   vdw
     1.652 2.450
  nonbonded pdb=" O   GLU A 156 "
            pdb="HD22 ASN A 160 "
     model   vdw
     1.653 2.450
  ... (remaining 142100 not shown)

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

  No NCS relation were found !!!

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

Found NCS groups:
  found none.
Set up NCS constraints
  No NCS constraints will be used in refinement.
Set refine NCS operators
Adjust number of macro_cycles
  Number of macro_cycles: 10
Reset NCS operators
Extract rigid body selections
Check and reset occupancies
  Occupancies: min=1.00 max=1.00 mean=1.00
Load rotamer database and sin/cos tables
Set ADP refinement strategy
  ADPs will be refined as 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:             2.380
  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:             0.060
  Extract box with map and model:          0.190
  Check model and map are aligned:         0.030
  Set scattering table:                    0.030
  Process input model:                     10.590
  Find NCS groups from input model:        0.030
  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:1.040
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   14.360
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8014
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   0.045   5286  Z= 0.153
  Angle     :  0.536   5.749   7178  Z= 0.313
  Chirality :  0.040   0.381    829
  Planarity :  0.003   0.042    898
  Dihedral  : 10.516  84.261   1885
  Min Nonbonded Distance : 2.134

Molprobity Statistics.
  All-atom Clashscore : 6.34
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.24 %
    Favored  : 96.76 %
  Rotamer:
    Outliers :  2.13 %
    Allowed  :  4.08 %
    Favored  : 93.79 %
  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:  0.60 (0.33), residues: 649
  helix:  0.56 (0.30), residues: 318
  sheet:  2.02 (0.61), residues: 64
  loop : -0.07 (0.38), residues: 267

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG A 159 
 TYR   0.007   0.001   TYR A  12 
 PHE   0.009   0.001   PHE A 598 
 TRP   0.010   0.001   TRP A 264 
 HIS   0.001   0.000   HIS A 260 

Details of bonding type rmsd
  covalent geometry    : bond        0.00315 ( 5286)
  covalent geometry    : angle       0.53628 ( 7178)
  hydrogen bonds       : bond        0.27867 (  276)
  hydrogen bonds       : angle       8.33202 (  795)

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

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

  1298 Ramachandran restraints generated.
    649 Oldfield, 0 Emsley, 649 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1298 Ramachandran restraints generated.
    649 Oldfield, 0 Emsley, 649 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  107 residues out of total 564 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 95
  time to evaluate  : 0.279 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   37 LEU cc_start: 0.9155 (tt) cc_final: 0.8799 (tt)
REVERT: A  255 PHE cc_start: 0.5399 (t80) cc_final: 0.5187 (t80)
REVERT: A  296 LEU cc_start: 0.8938 (mm) cc_final: 0.8726 (mm)
REVERT: A  397 ILE cc_start: 0.9220 (mt) cc_final: 0.8168 (mp)
REVERT: A  407 MET cc_start: 0.7532 (mmt) cc_final: 0.7247 (mmm)
REVERT: A  609 GLN cc_start: 0.9074 (OUTLIER) cc_final: 0.8206 (mp10)
  outliers start: 12
  outliers final: 4
  residues processed: 104
  average time/residue: 0.1604
  time to fit residues: 21.6554
Evaluate side-chains
  69 residues out of total 564 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 5
    poor density    : 64
  time to evaluate  : 0.260 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  257 LYS
Chi-restraints excluded: chain A residue  311 MET
Chi-restraints excluded: chain A residue  355 PHE
Chi-restraints excluded: chain A residue  577 ASN
Chi-restraints excluded: chain A residue  609 GLN
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 65
   random chunks:
   chunk 49 optimal weight:    0.6980
   chunk 53 optimal weight:   10.0000
   chunk 5 optimal weight:    0.9980
   chunk 33 optimal weight:    2.9990
   chunk 62 optimal weight:    4.9990
   chunk 51 optimal weight:    0.0060
   chunk 38 optimal weight:    9.9990
   chunk 61 optimal weight:    0.9990
   chunk 45 optimal weight:    0.8980
   chunk 27 optimal weight:    2.9990
   chunk 64 optimal weight:    0.9980
   overall best weight:    0.7196

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

Flipped N/Q/H residues before XYZ refinement:
** A 299 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 326 GLN
A 393 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4014 r_free = 0.4014 target = 0.121306 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 47)----------------|
| r_work = 0.3410 r_free = 0.3410 target = 0.087237 restraints weight = 36903.428|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 36)----------------|
| r_work = 0.3491 r_free = 0.3491 target = 0.091436 restraints weight = 16166.851|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 40)----------------|
| r_work = 0.3538 r_free = 0.3538 target = 0.093912 restraints weight = 10594.005|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 29)----------------|
| r_work = 0.3557 r_free = 0.3557 target = 0.095048 restraints weight = 8549.662|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 39)----------------|
| r_work = 0.3577 r_free = 0.3577 target = 0.095980 restraints weight = 7710.453|
|-----------------------------------------------------------------------------|
r_work (final): 0.3569
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7925
moved from start:          0.2203

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.029   5286  Z= 0.177
  Angle     :  0.638   6.950   7178  Z= 0.349
  Chirality :  0.044   0.407    829
  Planarity :  0.005   0.045    898
  Dihedral  :  6.114  56.381    711
  Min Nonbonded Distance : 2.409

Molprobity Statistics.
  All-atom Clashscore : 5.86
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.24 %
    Favored  : 96.76 %
  Rotamer:
    Outliers :  1.60 %
    Allowed  :  8.69 %
    Favored  : 89.72 %
  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:  0.85 (0.34), residues: 649
  helix:  0.80 (0.28), residues: 341
  sheet:  1.50 (0.56), residues: 85
  loop : -0.01 (0.44), residues: 223

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG A 161 
 TYR   0.013   0.001   TYR A  12 
 PHE   0.017   0.001   PHE A 166 
 TRP   0.007   0.001   TRP A 264 
 HIS   0.003   0.001   HIS A 121 

Details of bonding type rmsd
  covalent geometry    : bond        0.00340 ( 5286)
  covalent geometry    : angle       0.63803 ( 7178)
  hydrogen bonds       : bond        0.08768 (  276)
  hydrogen bonds       : angle       5.67289 (  795)

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

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

  1298 Ramachandran restraints generated.
    649 Oldfield, 0 Emsley, 649 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1298 Ramachandran restraints generated.
    649 Oldfield, 0 Emsley, 649 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  85 residues out of total 564 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 76
  time to evaluate  : 0.261 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  407 MET cc_start: 0.7509 (mmt) cc_final: 0.7213 (mmm)
  outliers start: 9
  outliers final: 9
  residues processed: 80
  average time/residue: 0.1038
  time to fit residues: 11.9907
Evaluate side-chains
  74 residues out of total 564 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 65
  time to evaluate  : 0.238 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  124 LEU
Chi-restraints excluded: chain A residue  126 LEU
Chi-restraints excluded: chain A residue  132 ILE
Chi-restraints excluded: chain A residue  257 LYS
Chi-restraints excluded: chain A residue  311 MET
Chi-restraints excluded: chain A residue  355 PHE
Chi-restraints excluded: chain A residue  411 LEU
Chi-restraints excluded: chain A residue  491 VAL
Chi-restraints excluded: chain A residue  577 ASN
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 65
   random chunks:
   chunk 59 optimal weight:    2.9990
   chunk 30 optimal weight:    0.7980
   chunk 45 optimal weight:    1.9990
   chunk 1 optimal weight:    3.9990
   chunk 28 optimal weight:    4.9990
   chunk 9 optimal weight:   20.0000
   chunk 31 optimal weight:    0.4980
   chunk 11 optimal weight:    5.9990
   chunk 22 optimal weight:    5.9990
   chunk 53 optimal weight:    9.9990
   chunk 56 optimal weight:    0.5980
   overall best weight:    1.3784

-------------------------------------------------------------------------------
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 = 0.4018 r_free = 0.4018 target = 0.121716 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 42)----------------|
| r_work = 0.3429 r_free = 0.3429 target = 0.088277 restraints weight = 35580.669|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 52)----------------|
| r_work = 0.3508 r_free = 0.3508 target = 0.092296 restraints weight = 15497.417|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 34)----------------|
| r_work = 0.3555 r_free = 0.3555 target = 0.094785 restraints weight = 10122.268|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 36)----------------|
| r_work = 0.3574 r_free = 0.3574 target = 0.095955 restraints weight = 8079.102|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 26)----------------|
| r_work = 0.3584 r_free = 0.3584 target = 0.096492 restraints weight = 7240.711|
|-----------------------------------------------------------------------------|
r_work (final): 0.3581
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7917
moved from start:          0.2737

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.026   5286  Z= 0.148
  Angle     :  0.564   6.121   7178  Z= 0.306
  Chirality :  0.043   0.399    829
  Planarity :  0.004   0.047    898
  Dihedral  :  5.904  54.787    708
  Min Nonbonded Distance : 2.363

Molprobity Statistics.
  All-atom Clashscore : 5.09
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.24 %
    Favored  : 96.76 %
  Rotamer:
    Outliers :  1.77 %
    Allowed  :  9.93 %
    Favored  : 88.30 %
  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:  0.63 (0.33), residues: 649
  helix:  0.90 (0.28), residues: 344
  sheet:  1.12 (0.63), residues: 69
  loop : -0.39 (0.41), residues: 236

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG A  34 
 TYR   0.008   0.001   TYR A 507 
 PHE   0.017   0.001   PHE A 166 
 TRP   0.008   0.001   TRP A 264 
 HIS   0.002   0.001   HIS A 260 

Details of bonding type rmsd
  covalent geometry    : bond        0.00311 ( 5286)
  covalent geometry    : angle       0.56439 ( 7178)
  hydrogen bonds       : bond        0.07234 (  276)
  hydrogen bonds       : angle       5.05625 (  795)

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

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

  1298 Ramachandran restraints generated.
    649 Oldfield, 0 Emsley, 649 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1298 Ramachandran restraints generated.
    649 Oldfield, 0 Emsley, 649 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  77 residues out of total 564 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 67
  time to evaluate  : 0.288 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   23 GLU cc_start: 0.7938 (tp30) cc_final: 0.7707 (tp30)
REVERT: A  407 MET cc_start: 0.7532 (mmt) cc_final: 0.7228 (mmm)
  outliers start: 10
  outliers final: 7
  residues processed: 73
  average time/residue: 0.1149
  time to fit residues: 12.1558
Evaluate side-chains
  69 residues out of total 564 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 62
  time to evaluate  : 0.262 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  124 LEU
Chi-restraints excluded: chain A residue  132 ILE
Chi-restraints excluded: chain A residue  257 LYS
Chi-restraints excluded: chain A residue  311 MET
Chi-restraints excluded: chain A residue  355 PHE
Chi-restraints excluded: chain A residue  411 LEU
Chi-restraints excluded: chain A residue  577 ASN
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 65
   random chunks:
   chunk 0 optimal weight:    4.9990
   chunk 56 optimal weight:    0.9990
   chunk 43 optimal weight:   10.0000
   chunk 44 optimal weight:    0.6980
   chunk 35 optimal weight:    1.9990
   chunk 11 optimal weight:    3.9990
   chunk 17 optimal weight:    0.7980
   chunk 45 optimal weight:    7.9990
   chunk 13 optimal weight:    0.7980
   chunk 50 optimal weight:    3.9990
   chunk 23 optimal weight:    1.9990
   overall best weight:    1.0584

-------------------------------------------------------------------------------
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 = 0.4030 r_free = 0.4030 target = 0.122667 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 31)----------------|
| r_work = 0.3491 r_free = 0.3491 target = 0.092011 restraints weight = 35642.506|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 26)----------------|
| r_work = 0.3521 r_free = 0.3521 target = 0.093649 restraints weight = 14721.926|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 26)----------------|
| r_work = 0.3550 r_free = 0.3550 target = 0.095634 restraints weight = 11039.075|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 29)----------------|
| r_work = 0.3559 r_free = 0.3559 target = 0.095907 restraints weight = 10229.000|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 23)----------------|
| r_work = 0.3558 r_free = 0.3558 target = 0.095875 restraints weight = 8976.265|
|-----------------------------------------------------------------------------|
r_work (final): 0.3555
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7933
moved from start:          0.3003

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.025   5286  Z= 0.125
  Angle     :  0.539   6.000   7178  Z= 0.288
  Chirality :  0.042   0.382    829
  Planarity :  0.004   0.047    898
  Dihedral  :  5.796  55.581    708
  Min Nonbonded Distance : 2.347

Molprobity Statistics.
  All-atom Clashscore : 4.71
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.24 %
    Favored  : 96.76 %
  Rotamer:
    Outliers :  1.42 %
    Allowed  : 10.82 %
    Favored  : 87.77 %
  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:  0.79 (0.34), residues: 649
  helix:  1.08 (0.29), residues: 344
  sheet:  0.93 (0.56), residues: 85
  loop : -0.42 (0.44), residues: 220

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG A  34 
 TYR   0.008   0.001   TYR A 507 
 PHE   0.016   0.001   PHE A 166 
 TRP   0.007   0.001   TRP A 264 
 HIS   0.002   0.000   HIS A 260 

Details of bonding type rmsd
  covalent geometry    : bond        0.00258 ( 5286)
  covalent geometry    : angle       0.53863 ( 7178)
  hydrogen bonds       : bond        0.06085 (  276)
  hydrogen bonds       : angle       4.66152 (  795)

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

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

  1298 Ramachandran restraints generated.
    649 Oldfield, 0 Emsley, 649 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1298 Ramachandran restraints generated.
    649 Oldfield, 0 Emsley, 649 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  72 residues out of total 564 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 64
  time to evaluate  : 0.283 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   23 GLU cc_start: 0.7979 (tp30) cc_final: 0.7726 (tp30)
REVERT: A  407 MET cc_start: 0.7609 (mmt) cc_final: 0.7296 (mmm)
  outliers start: 8
  outliers final: 7
  residues processed: 69
  average time/residue: 0.1147
  time to fit residues: 11.4059
Evaluate side-chains
  69 residues out of total 564 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 62
  time to evaluate  : 0.256 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  124 LEU
Chi-restraints excluded: chain A residue  126 LEU
Chi-restraints excluded: chain A residue  257 LYS
Chi-restraints excluded: chain A residue  311 MET
Chi-restraints excluded: chain A residue  355 PHE
Chi-restraints excluded: chain A residue  411 LEU
Chi-restraints excluded: chain A residue  577 ASN
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 65
   random chunks:
   chunk 13 optimal weight:    1.9990
   chunk 50 optimal weight:    1.9990
   chunk 15 optimal weight:    2.9990
   chunk 32 optimal weight:    0.0020
   chunk 7 optimal weight:    2.9990
   chunk 3 optimal weight:    9.9990
   chunk 12 optimal weight:    0.9980
   chunk 21 optimal weight:    3.9990
   chunk 26 optimal weight:    0.8980
   chunk 16 optimal weight:    5.9990
   chunk 23 optimal weight:    1.9990
   overall best weight:    1.1792

-------------------------------------------------------------------------------
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 = 0.4028 r_free = 0.4028 target = 0.122237 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.3484 r_free = 0.3484 target = 0.091175 restraints weight = 35398.203|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 30)----------------|
| r_work = 0.3517 r_free = 0.3517 target = 0.093244 restraints weight = 15195.990|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 23)----------------|
| r_work = 0.3532 r_free = 0.3532 target = 0.094215 restraints weight = 10886.539|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 28)----------------|
| r_work = 0.3539 r_free = 0.3539 target = 0.094596 restraints weight = 10360.270|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 26)----------------|
| r_work = 0.3544 r_free = 0.3544 target = 0.094934 restraints weight = 9561.268|
|-----------------------------------------------------------------------------|
r_work (final): 0.3539
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7939
moved from start:          0.3236

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.028   5286  Z= 0.124
  Angle     :  0.529   7.355   7178  Z= 0.281
  Chirality :  0.042   0.390    829
  Planarity :  0.004   0.046    898
  Dihedral  :  5.708  54.030    708
  Min Nonbonded Distance : 2.358

Molprobity Statistics.
  All-atom Clashscore : 3.75
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.08 %
    Favored  : 96.92 %
  Rotamer:
    Outliers :  2.48 %
    Allowed  :  9.57 %
    Favored  : 87.94 %
  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:  0.83 (0.34), residues: 649
  helix:  1.14 (0.29), residues: 349
  sheet:  0.78 (0.56), residues: 85
  loop : -0.40 (0.44), residues: 215

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.001   0.000   ARG A  34 
 TYR   0.013   0.001   TYR A  56 
 PHE   0.015   0.001   PHE A 166 
 TRP   0.008   0.001   TRP A 264 
 HIS   0.003   0.001   HIS A  57 

Details of bonding type rmsd
  covalent geometry    : bond        0.00269 ( 5286)
  covalent geometry    : angle       0.52864 ( 7178)
  hydrogen bonds       : bond        0.05552 (  276)
  hydrogen bonds       : angle       4.46324 (  795)

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

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

  1298 Ramachandran restraints generated.
    649 Oldfield, 0 Emsley, 649 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1298 Ramachandran restraints generated.
    649 Oldfield, 0 Emsley, 649 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  77 residues out of total 564 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 63
  time to evaluate  : 0.220 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  407 MET cc_start: 0.7642 (mmt) cc_final: 0.7334 (mmm)
  outliers start: 14
  outliers final: 9
  residues processed: 72
  average time/residue: 0.1100
  time to fit residues: 11.4377
Evaluate side-chains
  70 residues out of total 564 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 61
  time to evaluate  : 0.206 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   37 LEU
Chi-restraints excluded: chain A residue   66 THR
Chi-restraints excluded: chain A residue  124 LEU
Chi-restraints excluded: chain A residue  257 LYS
Chi-restraints excluded: chain A residue  311 MET
Chi-restraints excluded: chain A residue  355 PHE
Chi-restraints excluded: chain A residue  372 PHE
Chi-restraints excluded: chain A residue  411 LEU
Chi-restraints excluded: chain A residue  577 ASN
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 65
   random chunks:
   chunk 41 optimal weight:   10.0000
   chunk 40 optimal weight:   10.0000
   chunk 44 optimal weight:    0.7980
   chunk 35 optimal weight:    1.9990
   chunk 59 optimal weight:    1.9990
   chunk 13 optimal weight:    1.9990
   chunk 57 optimal weight:    1.9990
   chunk 60 optimal weight:    1.9990
   chunk 51 optimal weight:    3.9990
   chunk 26 optimal weight:    0.9980
   chunk 12 optimal weight:    0.8980
   overall best weight:    1.3384

-------------------------------------------------------------------------------
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 = 0.4031 r_free = 0.4031 target = 0.122280 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 42)----------------|
| r_work = 0.3447 r_free = 0.3447 target = 0.089166 restraints weight = 35868.152|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 42)----------------|
| r_work = 0.3527 r_free = 0.3527 target = 0.093261 restraints weight = 15603.035|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 40)----------------|
| r_work = 0.3574 r_free = 0.3574 target = 0.095775 restraints weight = 10139.436|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 24)----------------|
| r_work = 0.3598 r_free = 0.3598 target = 0.097095 restraints weight = 8061.039|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 28)----------------|
| r_work = 0.3609 r_free = 0.3609 target = 0.097720 restraints weight = 7157.972|
|-----------------------------------------------------------------------------|
r_work (final): 0.3604
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7878
moved from start:          0.3326

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.027   5286  Z= 0.127
  Angle     :  0.530   7.383   7178  Z= 0.284
  Chirality :  0.042   0.388    829
  Planarity :  0.004   0.046    898
  Dihedral  :  5.663  53.475    708
  Min Nonbonded Distance : 2.342

Molprobity Statistics.
  All-atom Clashscore : 4.23
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.54 %
    Favored  : 96.46 %
  Rotamer:
    Outliers :  1.60 %
    Allowed  : 10.46 %
    Favored  : 87.94 %
  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:  0.92 (0.34), residues: 649
  helix:  1.24 (0.29), residues: 344
  sheet:  0.72 (0.56), residues: 85
  loop : -0.34 (0.45), residues: 220

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.001   0.000   ARG A  34 
 TYR   0.007   0.001   TYR A  12 
 PHE   0.023   0.001   PHE A 297 
 TRP   0.007   0.001   TRP A 264 
 HIS   0.002   0.000   HIS A 260 

Details of bonding type rmsd
  covalent geometry    : bond        0.00278 ( 5286)
  covalent geometry    : angle       0.52956 ( 7178)
  hydrogen bonds       : bond        0.05399 (  276)
  hydrogen bonds       : angle       4.36391 (  795)

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

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

  1298 Ramachandran restraints generated.
    649 Oldfield, 0 Emsley, 649 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1298 Ramachandran restraints generated.
    649 Oldfield, 0 Emsley, 649 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  70 residues out of total 564 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 61
  time to evaluate  : 0.262 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  407 MET cc_start: 0.7528 (mmt) cc_final: 0.7231 (mmm)
REVERT: A  577 ASN cc_start: 0.8513 (OUTLIER) cc_final: 0.8244 (m-40)
  outliers start: 9
  outliers final: 7
  residues processed: 68
  average time/residue: 0.1135
  time to fit residues: 11.0668
Evaluate side-chains
  67 residues out of total 564 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 59
  time to evaluate  : 0.267 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   66 THR
Chi-restraints excluded: chain A residue  126 LEU
Chi-restraints excluded: chain A residue  257 LYS
Chi-restraints excluded: chain A residue  311 MET
Chi-restraints excluded: chain A residue  355 PHE
Chi-restraints excluded: chain A residue  372 PHE
Chi-restraints excluded: chain A residue  411 LEU
Chi-restraints excluded: chain A residue  577 ASN
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 65
   random chunks:
   chunk 34 optimal weight:    1.9990
   chunk 49 optimal weight:    2.9990
   chunk 61 optimal weight:    7.9990
   chunk 57 optimal weight:    2.9990
   chunk 22 optimal weight:    9.9990
   chunk 60 optimal weight:    0.9990
   chunk 58 optimal weight:    2.9990
   chunk 53 optimal weight:    3.9990
   chunk 48 optimal weight:    6.9990
   chunk 25 optimal weight:    0.6980
   chunk 45 optimal weight:    0.9980
   overall best weight:    1.5386

-------------------------------------------------------------------------------
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 = 0.4028 r_free = 0.4028 target = 0.122161 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.3479 r_free = 0.3479 target = 0.090912 restraints weight = 35154.482|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 30)----------------|
| r_work = 0.3513 r_free = 0.3513 target = 0.093060 restraints weight = 15100.297|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 23)----------------|
| r_work = 0.3523 r_free = 0.3523 target = 0.093795 restraints weight = 10967.425|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 28)----------------|
| r_work = 0.3530 r_free = 0.3530 target = 0.094172 restraints weight = 10721.724|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 26)----------------|
| r_work = 0.3537 r_free = 0.3537 target = 0.094585 restraints weight = 9684.645|
|-----------------------------------------------------------------------------|
r_work (final): 0.3532
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7951
moved from start:          0.3401

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.031   5286  Z= 0.130
  Angle     :  0.527   6.423   7178  Z= 0.282
  Chirality :  0.042   0.387    829
  Planarity :  0.004   0.045    898
  Dihedral  :  5.661  51.871    708
  Min Nonbonded Distance : 2.322

Molprobity Statistics.
  All-atom Clashscore : 4.32
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.54 %
    Favored  : 96.46 %
  Rotamer:
    Outliers :  1.77 %
    Allowed  : 10.11 %
    Favored  : 88.12 %
  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 are not related in a simple way.
  whole:  0.95 (0.34), residues: 649
  helix:  1.31 (0.29), residues: 344
  sheet:  0.71 (0.56), residues: 85
  loop : -0.39 (0.44), residues: 220

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.001   0.000   ARG A  34 
 TYR   0.007   0.001   TYR A  12 
 PHE   0.018   0.001   PHE A 166 
 TRP   0.008   0.001   TRP A 264 
 HIS   0.002   0.000   HIS A 260 

Details of bonding type rmsd
  covalent geometry    : bond        0.00292 ( 5286)
  covalent geometry    : angle       0.52748 ( 7178)
  hydrogen bonds       : bond        0.05252 (  276)
  hydrogen bonds       : angle       4.31071 (  795)

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

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

  1298 Ramachandran restraints generated.
    649 Oldfield, 0 Emsley, 649 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1298 Ramachandran restraints generated.
    649 Oldfield, 0 Emsley, 649 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  70 residues out of total 564 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 60
  time to evaluate  : 0.233 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  407 MET cc_start: 0.7647 (mmt) cc_final: 0.7340 (mmm)
REVERT: A  577 ASN cc_start: 0.8507 (OUTLIER) cc_final: 0.8222 (m-40)
  outliers start: 10
  outliers final: 8
  residues processed: 68
  average time/residue: 0.1187
  time to fit residues: 11.5409
Evaluate side-chains
  67 residues out of total 564 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 58
  time to evaluate  : 0.341 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   66 THR
Chi-restraints excluded: chain A residue  178 THR
Chi-restraints excluded: chain A residue  257 LYS
Chi-restraints excluded: chain A residue  311 MET
Chi-restraints excluded: chain A residue  355 PHE
Chi-restraints excluded: chain A residue  372 PHE
Chi-restraints excluded: chain A residue  411 LEU
Chi-restraints excluded: chain A residue  577 ASN
Chi-restraints excluded: chain A residue  603 LEU
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 65
   random chunks:
   chunk 46 optimal weight:    8.9990
   chunk 58 optimal weight:    3.9990
   chunk 32 optimal weight:    1.9990
   chunk 3 optimal weight:    9.9990
   chunk 26 optimal weight:    0.5980
   chunk 14 optimal weight:    2.9990
   chunk 45 optimal weight:    1.9990
   chunk 42 optimal weight:    6.9990
   chunk 10 optimal weight:    5.9990
   chunk 61 optimal weight:    4.9990
   chunk 39 optimal weight:    7.9990
   overall best weight:    2.3188

-------------------------------------------------------------------------------
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 = 0.4013 r_free = 0.4013 target = 0.121071 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.3452 r_free = 0.3452 target = 0.089571 restraints weight = 35718.693|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 28)----------------|
| r_work = 0.3488 r_free = 0.3488 target = 0.091921 restraints weight = 16038.934|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 28)----------------|
| r_work = 0.3504 r_free = 0.3504 target = 0.092877 restraints weight = 11270.041|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 26)----------------|
| r_work = 0.3508 r_free = 0.3508 target = 0.093087 restraints weight = 10295.885|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 26)----------------|
| r_work = 0.3517 r_free = 0.3517 target = 0.093582 restraints weight = 9849.647|
|-----------------------------------------------------------------------------|
r_work (final): 0.3507
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7982
moved from start:          0.3435

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.037   5286  Z= 0.167
  Angle     :  0.543   6.024   7178  Z= 0.294
  Chirality :  0.042   0.389    829
  Planarity :  0.004   0.044    898
  Dihedral  :  5.768  51.920    708
  Min Nonbonded Distance : 2.318

Molprobity Statistics.
  All-atom Clashscore : 4.71
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.16 %
    Favored  : 95.84 %
  Rotamer:
    Outliers :  1.77 %
    Allowed  : 10.28 %
    Favored  : 87.94 %
  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:  0.79 (0.34), residues: 649
  helix:  1.20 (0.29), residues: 350
  sheet:  0.65 (0.56), residues: 85
  loop : -0.56 (0.45), residues: 214

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.001   0.000   ARG A 159 
 TYR   0.008   0.001   TYR A 588 
 PHE   0.018   0.001   PHE A 166 
 TRP   0.009   0.001   TRP A 646 
 HIS   0.002   0.001   HIS A 260 

Details of bonding type rmsd
  covalent geometry    : bond        0.00375 ( 5286)
  covalent geometry    : angle       0.54317 ( 7178)
  hydrogen bonds       : bond        0.05445 (  276)
  hydrogen bonds       : angle       4.38870 (  795)

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

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

  1298 Ramachandran restraints generated.
    649 Oldfield, 0 Emsley, 649 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1298 Ramachandran restraints generated.
    649 Oldfield, 0 Emsley, 649 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  73 residues out of total 564 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 63
  time to evaluate  : 0.265 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  577 ASN cc_start: 0.8559 (OUTLIER) cc_final: 0.8217 (m-40)
REVERT: A  646 TRP cc_start: 0.5785 (m100) cc_final: 0.5353 (t-100)
  outliers start: 10
  outliers final: 9
  residues processed: 71
  average time/residue: 0.1154
  time to fit residues: 11.8451
Evaluate side-chains
  70 residues out of total 564 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 60
  time to evaluate  : 0.268 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   66 THR
Chi-restraints excluded: chain A residue  126 LEU
Chi-restraints excluded: chain A residue  178 THR
Chi-restraints excluded: chain A residue  257 LYS
Chi-restraints excluded: chain A residue  311 MET
Chi-restraints excluded: chain A residue  355 PHE
Chi-restraints excluded: chain A residue  372 PHE
Chi-restraints excluded: chain A residue  411 LEU
Chi-restraints excluded: chain A residue  577 ASN
Chi-restraints excluded: chain A residue  603 LEU
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 65
   random chunks:
   chunk 17 optimal weight:    0.9980
   chunk 20 optimal weight:    2.9990
   chunk 39 optimal weight:    9.9990
   chunk 6 optimal weight:    0.9980
   chunk 10 optimal weight:    5.9990
   chunk 52 optimal weight:    3.9990
   chunk 64 optimal weight:    1.9990
   chunk 21 optimal weight:    5.9990
   chunk 47 optimal weight:    0.0570
   chunk 48 optimal weight:    0.9990
   chunk 54 optimal weight:    1.9990
   overall best weight:    1.0102

-------------------------------------------------------------------------------
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 = 0.4033 r_free = 0.4033 target = 0.122604 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.3484 r_free = 0.3484 target = 0.091314 restraints weight = 35357.634|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 32)----------------|
| r_work = 0.3521 r_free = 0.3521 target = 0.093667 restraints weight = 15191.723|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 23)----------------|
| r_work = 0.3530 r_free = 0.3530 target = 0.094321 restraints weight = 11017.398|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 28)----------------|
| r_work = 0.3538 r_free = 0.3538 target = 0.094727 restraints weight = 10758.860|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 26)----------------|
| r_work = 0.3545 r_free = 0.3545 target = 0.095135 restraints weight = 9706.363|
|-----------------------------------------------------------------------------|
r_work (final): 0.3536
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7937
moved from start:          0.3573

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.025   5286  Z= 0.113
  Angle     :  0.522   5.929   7178  Z= 0.277
  Chirality :  0.042   0.390    829
  Planarity :  0.004   0.045    898
  Dihedral  :  5.636  52.317    708
  Min Nonbonded Distance : 2.326

Molprobity Statistics.
  All-atom Clashscore : 4.51
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.93 %
    Favored  : 97.07 %
  Rotamer:
    Outliers :  1.77 %
    Allowed  : 10.46 %
    Favored  : 87.77 %
  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:  1.05 (0.35), residues: 649
  helix:  1.43 (0.29), residues: 344
  sheet:  0.72 (0.57), residues: 85
  loop : -0.40 (0.45), residues: 220

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.001   0.000   ARG A  34 
 TYR   0.007   0.001   TYR A  56 
 PHE   0.018   0.001   PHE A 166 
 TRP   0.007   0.001   TRP A 264 
 HIS   0.002   0.001   HIS A 260 

Details of bonding type rmsd
  covalent geometry    : bond        0.00249 ( 5286)
  covalent geometry    : angle       0.52152 ( 7178)
  hydrogen bonds       : bond        0.04962 (  276)
  hydrogen bonds       : angle       4.15036 (  795)

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

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

  1298 Ramachandran restraints generated.
    649 Oldfield, 0 Emsley, 649 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1298 Ramachandran restraints generated.
    649 Oldfield, 0 Emsley, 649 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  69 residues out of total 564 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 59
  time to evaluate  : 0.269 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  577 ASN cc_start: 0.8500 (OUTLIER) cc_final: 0.8216 (m-40)
  outliers start: 10
  outliers final: 9
  residues processed: 66
  average time/residue: 0.1171
  time to fit residues: 11.0346
Evaluate side-chains
  68 residues out of total 564 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 58
  time to evaluate  : 0.320 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   37 LEU
Chi-restraints excluded: chain A residue   66 THR
Chi-restraints excluded: chain A residue  126 LEU
Chi-restraints excluded: chain A residue  257 LYS
Chi-restraints excluded: chain A residue  311 MET
Chi-restraints excluded: chain A residue  355 PHE
Chi-restraints excluded: chain A residue  372 PHE
Chi-restraints excluded: chain A residue  411 LEU
Chi-restraints excluded: chain A residue  577 ASN
Chi-restraints excluded: chain A residue  603 LEU
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 65
   random chunks:
   chunk 37 optimal weight:    9.9990
   chunk 35 optimal weight:    0.8980
   chunk 1 optimal weight:    3.9990
   chunk 11 optimal weight:    5.9990
   chunk 19 optimal weight:    4.9990
   chunk 51 optimal weight:    8.9990
   chunk 17 optimal weight:    0.7980
   chunk 41 optimal weight:   20.0000
   chunk 26 optimal weight:    0.7980
   chunk 16 optimal weight:    0.6980
   chunk 33 optimal weight:    2.9990
   overall best weight:    1.2382

-------------------------------------------------------------------------------
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 = 0.4032 r_free = 0.4032 target = 0.122291 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.3482 r_free = 0.3482 target = 0.091143 restraints weight = 35396.346|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 26)----------------|
| r_work = 0.3518 r_free = 0.3518 target = 0.093471 restraints weight = 15156.999|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 26)----------------|
| r_work = 0.3534 r_free = 0.3534 target = 0.094567 restraints weight = 11156.455|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 26)----------------|
| r_work = 0.3547 r_free = 0.3547 target = 0.095126 restraints weight = 10636.411|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 23)----------------|
| r_work = 0.3550 r_free = 0.3550 target = 0.095357 restraints weight = 9466.204|
|-----------------------------------------------------------------------------|
r_work (final): 0.3542
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7932
moved from start:          0.3648

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.041   5286  Z= 0.122
  Angle     :  0.533   6.096   7178  Z= 0.283
  Chirality :  0.042   0.389    829
  Planarity :  0.004   0.045    898
  Dihedral  :  5.622  53.008    708
  Min Nonbonded Distance : 2.318

Molprobity Statistics.
  All-atom Clashscore : 4.80
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.54 %
    Favored  : 96.46 %
  Rotamer:
    Outliers :  1.42 %
    Allowed  : 11.17 %
    Favored  : 87.41 %
  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:  1.05 (0.34), residues: 649
  helix:  1.44 (0.29), residues: 344
  sheet:  0.68 (0.57), residues: 85
  loop : -0.41 (0.44), residues: 220

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.001   0.000   ARG A 258 
 TYR   0.007   0.001   TYR A  56 
 PHE   0.018   0.001   PHE A 166 
 TRP   0.007   0.001   TRP A 264 
 HIS   0.002   0.000   HIS A 260 

Details of bonding type rmsd
  covalent geometry    : bond        0.00275 ( 5286)
  covalent geometry    : angle       0.53284 ( 7178)
  hydrogen bonds       : bond        0.04858 (  276)
  hydrogen bonds       : angle       4.12270 (  795)

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

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

  1298 Ramachandran restraints generated.
    649 Oldfield, 0 Emsley, 649 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1298 Ramachandran restraints generated.
    649 Oldfield, 0 Emsley, 649 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  66 residues out of total 564 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 58
  time to evaluate  : 0.262 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  577 ASN cc_start: 0.8500 (OUTLIER) cc_final: 0.8222 (m-40)
  outliers start: 8
  outliers final: 7
  residues processed: 65
  average time/residue: 0.1194
  time to fit residues: 11.0024
Evaluate side-chains
  66 residues out of total 564 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 58
  time to evaluate  : 0.405 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   66 THR
Chi-restraints excluded: chain A residue  126 LEU
Chi-restraints excluded: chain A residue  257 LYS
Chi-restraints excluded: chain A residue  355 PHE
Chi-restraints excluded: chain A residue  372 PHE
Chi-restraints excluded: chain A residue  411 LEU
Chi-restraints excluded: chain A residue  577 ASN
Chi-restraints excluded: chain A residue  603 LEU
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 65
   random chunks:
   chunk 3 optimal weight:   10.0000
   chunk 47 optimal weight:    0.9990
   chunk 48 optimal weight:    2.9990
   chunk 56 optimal weight:    0.5980
   chunk 36 optimal weight:    3.9990
   chunk 43 optimal weight:    4.9990
   chunk 7 optimal weight:    0.6980
   chunk 6 optimal weight:    1.9990
   chunk 23 optimal weight:    4.9990
   chunk 10 optimal weight:    5.9990
   chunk 51 optimal weight:    0.0070
   overall best weight:    0.8602

-------------------------------------------------------------------------------
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 = 0.4044 r_free = 0.4044 target = 0.123297 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 43)----------------|
| r_work = 0.3468 r_free = 0.3468 target = 0.090405 restraints weight = 35645.524|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 46)----------------|
| r_work = 0.3547 r_free = 0.3547 target = 0.094550 restraints weight = 15490.552|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 44)----------------|
| r_work = 0.3594 r_free = 0.3594 target = 0.097076 restraints weight = 10047.931|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 29)----------------|
| r_work = 0.3613 r_free = 0.3613 target = 0.098270 restraints weight = 7972.038|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 32)----------------|
| r_work = 0.3632 r_free = 0.3632 target = 0.099213 restraints weight = 7117.856|
|-----------------------------------------------------------------------------|
r_work (final): 0.3626
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7852
moved from start:          0.3754

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.034   5286  Z= 0.110
  Angle     :  0.520   5.927   7178  Z= 0.275
  Chirality :  0.042   0.386    829
  Planarity :  0.004   0.045    898
  Dihedral  :  5.202  54.199    705
  Min Nonbonded Distance : 2.308

Molprobity Statistics.
  All-atom Clashscore : 4.71
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.24 %
    Favored  : 96.76 %
  Rotamer:
    Outliers :  1.60 %
    Allowed  : 10.82 %
    Favored  : 87.59 %
  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 are not related in a simple way.
  whole:  1.06 (0.34), residues: 649
  helix:  1.51 (0.29), residues: 346
  sheet:  0.72 (0.57), residues: 85
  loop : -0.54 (0.43), residues: 218

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.001   0.000   ARG A 251 
 TYR   0.007   0.001   TYR A 507 
 PHE   0.018   0.001   PHE A 166 
 TRP   0.007   0.001   TRP A 264 
 HIS   0.002   0.000   HIS A 260 

Details of bonding type rmsd
  covalent geometry    : bond        0.00246 ( 5286)
  covalent geometry    : angle       0.52032 ( 7178)
  hydrogen bonds       : bond        0.04588 (  276)
  hydrogen bonds       : angle       4.01268 (  795)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 1958.55 seconds
wall clock time: 33 minutes 58.19 seconds (2038.19 seconds total)