Starting phenix.real_space_refine
on Tue Feb  3 18:53:25 2026 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/9leq_63032/02_2026/9leq_63032.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/9leq_63032/02_2026/9leq_63032.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.23
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    model {
      file = "/net/cci-nas-00/data/ceres_data/9leq_63032/02_2026/9leq_63032.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/9leq_63032/02_2026/9leq_63032.cif"
    real_map_files = "/net/cci-nas-00/data/ceres_data/9leq_63032/02_2026/9leq_63032.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/9leq_63032/02_2026/9leq_63032.map"
  }
  resolution = 3.23
  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=   0.062
Set stop_for_unknowns flag
  Set to: True
Assert model is a single copy model
Assert all atoms have isotropic ADPs
Construct map_model_manager
Extract box with map and model
Check model and map are aligned
Set scattering table
  Set to: electron
  Number of scattering types: 4
    Type Number    sf(0)   Gaussians
     S      21      5.16       5
     C    4044      2.51       5
     N    1028      2.21       5
     O    1202      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model
  Monomer Library directory:
    "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5952/lib/python3.9/site-packages/chem_data/mon_lib"
  Total number of atoms: 6295
  Number of models: 1
  Model: ""
    Number of chains: 2
    Chain: "A"
      Number of atoms: 1192
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 149, 1192
          Classifications: {'peptide': 149}
          Link IDs: {'PTRANS': 6, 'TRANS': 142}
    Chain: "B"
      Number of atoms: 5103
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 633, 5103
          Classifications: {'peptide': 633}
          Link IDs: {'PTRANS': 12, 'TRANS': 620}
          Chain breaks: 1
  Time building chain proxies: 1.39, per 1000 atoms: 0.22
  Number of scatterers: 6295
  At special positions: 0
  Unit cell: (68.53, 82.77, 134.39, 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      21     16.00
     O    1202      8.00
     N    1028      7.00
     C    4044      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=1, symmetry=0
    Simple disulfide: pdb=" SG  CYS A  44 " - pdb=" SG  CYS A  57 " distance=2.03

  Automatic linking
    Parameters for automatic linking
      Linking & cutoffs
        Metal                : Auto  - 3.00
        Amino acid           : True  - 1.90
        Carbohydrate         : True  - 1.99
        Ligands              : True  - 1.99
        Small molecules      : False - 1.98
        Amino acid - RNA/DNA : False
      
  Number of custom bonds: simple=0, symmetry=0
  Time building additional restraints: 0.48
  Conformation dependent library (CDL) restraints added in 409.2 milliseconds
  

  1552 Ramachandran restraints generated.
    776 Oldfield, 0 Emsley, 776 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  1522

  Finding SS restraints...
    Secondary structure from input PDB file:
      41 helices and 4 sheets defined
      64.3% alpha, 11.0% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.18
  Creating SS restraints...
    Processing helix  chain 'B' and resid 179 through 189
    Processing helix  chain 'B' and resid 193 through 207
    Processing helix  chain 'B' and resid 209 through 224
      removed outlier: 3.527A  pdb=" N   LEU B 224 " --> pdb=" O   CYS B 220 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 226 through 240
      removed outlier: 3.541A  pdb=" N   PHE B 230 " --> pdb=" O   ASP B 226 " (cutoff:3.500A)
      removed outlier: 3.881A  pdb=" N   GLN B 238 " --> pdb=" O   ILE B 234 " (cutoff:3.500A)
      removed outlier: 4.329A  pdb=" N   VAL B 239 " --> pdb=" O   ASP B 235 " (cutoff:3.500A)
      removed outlier: 4.107A  pdb=" N   TYR B 240 " --> pdb=" O   LEU B 236 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 241 through 245
    Processing helix  chain 'B' and resid 249 through 261
    Processing helix  chain 'B' and resid 263 through 272
      removed outlier: 3.967A  pdb=" N   GLN B 272 " --> pdb=" O   LEU B 268 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 279 through 294
    Processing helix  chain 'B' and resid 296 through 306
    Processing helix  chain 'B' and resid 312 through 324
    Processing helix  chain 'B' and resid 325 through 338
      removed outlier: 3.769A  pdb=" N   VAL B 331 " --> pdb=" O   ALA B 327 " (cutoff:3.500A)
      removed outlier: 4.173A  pdb=" N   LYS B 338 " --> pdb=" O   SER B 334 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 342 through 358
      removed outlier: 3.573A  pdb=" N   SER B 346 " --> pdb=" O   ASP B 342 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 359 through 369
      removed outlier: 3.735A  pdb=" N   MET B 363 " --> pdb=" O   ASN B 359 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 374 through 381
      removed outlier: 3.607A  pdb=" N   ILE B 380 " --> pdb=" O   ASP B 376 " (cutoff:3.500A)
      removed outlier: 4.169A  pdb=" N   LEU B 381 " --> pdb=" O   ARG B 377 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 392 through 395
    Processing helix  chain 'B' and resid 396 through 406
      removed outlier: 3.574A  pdb=" N   LYS B 406 " --> pdb=" O   ASN B 402 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 411 through 423
    Processing helix  chain 'B' and resid 429 through 435
      removed outlier: 3.746A  pdb=" N   LEU B 435 " --> pdb=" O   LYS B 431 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 441 through 445
      removed outlier: 3.600A  pdb=" N   PHE B 445 " --> pdb=" O   ASN B 441 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'B' and resid 441 through 445'
    Processing helix  chain 'B' and resid 463 through 478
    Processing helix  chain 'B' and resid 480 through 493
      removed outlier: 3.946A  pdb=" N   ALA B 484 " --> pdb=" O   LYS B 480 " (cutoff:3.500A)
      removed outlier: 3.711A  pdb=" N   LYS B 493 " --> pdb=" O   GLN B 489 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 498 through 512
      removed outlier: 3.506A  pdb=" N   HIS B 502 " --> pdb=" O   HIS B 498 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 514 through 529
      removed outlier: 3.546A  pdb=" N   ALA B 518 " --> pdb=" O   ASN B 514 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 532 through 546
    Processing helix  chain 'B' and resid 550 through 563
    Processing helix  chain 'B' and resid 569 through 576
      removed outlier: 4.288A  pdb=" N   LYS B 573 " --> pdb=" O   ALA B 569 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 577 through 579
      No H-bonds generated for 'chain 'B' and resid 577 through 579'
    Processing helix  chain 'B' and resid 583 through 591
      removed outlier: 3.540A  pdb=" N   MET B 586 " --> pdb=" O   TYR B 583 " (cutoff:3.500A)
      Proline residue:  B 588  - end of helix
    Processing helix  chain 'B' and resid 597 through 610
    Processing helix  chain 'B' and resid 615 through 628
      removed outlier: 4.029A  pdb=" N   VAL B 619 " --> pdb=" O   ASN B 615 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 631 through 643
    Processing helix  chain 'B' and resid 647 through 661
      removed outlier: 3.582A  pdb=" N   ASN B 661 " --> pdb=" O   ILE B 657 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 665 through 670
      removed outlier: 4.500A  pdb=" N   PHE B 670 " --> pdb=" O   TYR B 666 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 673 through 687
      removed outlier: 4.270A  pdb=" N   ARG B 677 " --> pdb=" O   PRO B 673 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 689 through 704
      removed outlier: 4.042A  pdb=" N   SER B 704 " --> pdb=" O   LEU B 700 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 708 through 722
      removed outlier: 4.164A  pdb=" N   LEU B 712 " --> pdb=" O   ASP B 708 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 724 through 739
      removed outlier: 3.638A  pdb=" N   ALA B 728 " --> pdb=" O   GLN B 724 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 743 through 757
    Processing helix  chain 'B' and resid 759 through 772
      removed outlier: 3.592A  pdb=" N   ALA B 765 " --> pdb=" O   ASN B 761 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 777 through 791
      removed outlier: 3.783A  pdb=" N   ALA B 782 " --> pdb=" O   LYS B 778 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 793 through 802
      removed outlier: 3.564A  pdb=" N   ILE B 798 " --> pdb=" O   TYR B 794 " (cutoff:3.500A)
      removed outlier: 4.020A  pdb=" N   SER B 799 " --> pdb=" O   GLU B 795 " (cutoff:3.500A)
    Processing sheet with id=AA1, first strand: chain 'A' and resid 17 through 24
      removed outlier: 3.559A  pdb=" N   LYS A  85 " --> pdb=" O   GLU A  82 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'A' and resid 17 through 24
      removed outlier: 3.505A  pdb=" N   ASN A  38 " --> pdb=" O   LYS A 120 " (cutoff:3.500A)
      removed outlier: 5.545A  pdb=" N   LYS A 120 " --> pdb=" O   ASN A  38 " (cutoff:3.500A)
      removed outlier: 10.827A  pdb=" N   LEU A  40 " --> pdb=" O   LYS A 118 " (cutoff:3.500A)
      removed outlier: 9.688A  pdb=" N   LYS A 118 " --> pdb=" O   LEU A  40 " (cutoff:3.500A)
    Processing sheet with id=AA3, first strand: chain 'B' and resid 386 through 390
    Processing sheet with id=AA4, first strand: chain 'B' and resid 425 through 426
      removed outlier: 6.217A  pdb=" N   TYR B 425 " --> pdb=" O   ASP B 447 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AA4

    357 hydrogen bonds defined for protein.
    1047 hydrogen bond angles defined for protein.
    Restraints generated for nucleic acids:
      0 hydrogen bonds
      0 hydrogen bond angles
      0 basepair planarities
      0 basepair parallelities
      0 stacking parallelities
  Total time for adding SS restraints: 0.66

  Time building geometry restraints manager: 0.67 seconds

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

  Histogram of bond lengths:
        1.20 -     1.32: 1126
        1.32 -     1.45: 1627
        1.45 -     1.57: 3623
        1.57 -     1.69: 0
        1.69 -     1.81: 38
  Bond restraints: 6414
  Sorted by residual:
  bond pdb=" C   ARG B 677 "
       pdb=" O   ARG B 677 "
    ideal  model  delta    sigma   weight residual
    1.236  1.203  0.033 1.16e-02 7.43e+03 8.05e+00
  bond pdb=" N   MET A  88 "
       pdb=" CA  MET A  88 "
    ideal  model  delta    sigma   weight residual
    1.457  1.486 -0.029 1.23e-02 6.61e+03 5.40e+00
  bond pdb=" C   ALA A 131 "
       pdb=" N   PRO A 132 "
    ideal  model  delta    sigma   weight residual
    1.329  1.358 -0.028 1.25e-02 6.40e+03 5.14e+00
  bond pdb=" N   ASN B 643 "
       pdb=" CA  ASN B 643 "
    ideal  model  delta    sigma   weight residual
    1.459  1.482 -0.024 1.19e-02 7.06e+03 3.94e+00
  bond pdb=" C   LEU B 804 "
       pdb=" N   PRO B 805 "
    ideal  model  delta    sigma   weight residual
    1.326  1.354 -0.028 1.44e-02 4.82e+03 3.81e+00
  ... (remaining 6409 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     2.01: 8525
        2.01 -     4.03: 108
        4.03 -     6.04: 18
        6.04 -     8.05: 6
        8.05 -    10.07: 2
  Bond angle restraints: 8659
  Sorted by residual:
  angle pdb=" C   ARG B 677 "
        pdb=" CA  ARG B 677 "
        pdb=" CB  ARG B 677 "
      ideal   model   delta    sigma   weight residual
     110.92  100.85   10.07 1.59e+00 3.96e-01 4.01e+01
  angle pdb=" N   LYS B 698 "
        pdb=" CA  LYS B 698 "
        pdb=" C   LYS B 698 "
      ideal   model   delta    sigma   weight residual
     110.97  105.59    5.38 1.09e+00 8.42e-01 2.44e+01
  angle pdb=" C   LYS B 698 "
        pdb=" CA  LYS B 698 "
        pdb=" CB  LYS B 698 "
      ideal   model   delta    sigma   weight residual
     110.96  117.82   -6.86 1.54e+00 4.22e-01 1.99e+01
  angle pdb=" N   ASN B 654 "
        pdb=" CA  ASN B 654 "
        pdb=" C   ASN B 654 "
      ideal   model   delta    sigma   weight residual
     111.07  106.92    4.15 1.07e+00 8.73e-01 1.51e+01
  angle pdb=" N   ARG B 677 "
        pdb=" CA  ARG B 677 "
        pdb=" CB  ARG B 677 "
      ideal   model   delta    sigma   weight residual
     109.82  115.25   -5.43 1.52e+00 4.33e-01 1.28e+01
  ... (remaining 8654 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    17.85: 3478
       17.85 -    35.70: 346
       35.70 -    53.55: 70
       53.55 -    71.40: 9
       71.40 -    89.25: 4
  Dihedral angle restraints: 3907
    sinusoidal: 1557
      harmonic: 2350
  Sorted by residual:
  dihedral pdb=" CA  THR B 593 "
           pdb=" C   THR B 593 "
           pdb=" N   LYS B 594 "
           pdb=" CA  LYS B 594 "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00 -155.83  -24.17     0      5.00e+00 4.00e-02 2.34e+01
  dihedral pdb=" C   ARG B 677 "
           pdb=" N   ARG B 677 "
           pdb=" CA  ARG B 677 "
           pdb=" CB  ARG B 677 "
      ideal   model   delta  harmonic     sigma   weight residual
    -122.60 -111.84  -10.76     0      2.50e+00 1.60e-01 1.85e+01
  dihedral pdb=" CB  GLU B 244 "
           pdb=" CG  GLU B 244 "
           pdb=" CD  GLU B 244 "
           pdb=" OE1 GLU B 244 "
      ideal   model   delta sinusoidal    sigma   weight residual
       0.00   89.25  -89.25     1      3.00e+01 1.11e-03 1.05e+01
  ... (remaining 3904 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.042: 711
       0.042 -    0.083: 200
       0.083 -    0.125: 42
       0.125 -    0.167: 4
       0.167 -    0.209: 1
  Chirality restraints: 958
  Sorted by residual:
  chirality pdb=" CA  ARG B 677 "
            pdb=" N   ARG B 677 "
            pdb=" C   ARG B 677 "
            pdb=" CB  ARG B 677 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.72   -0.21 2.00e-01 2.50e+01 1.09e+00
  chirality pdb=" CA  ILE A  59 "
            pdb=" N   ILE A  59 "
            pdb=" C   ILE A  59 "
            pdb=" CB  ILE A  59 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.43    2.60   -0.16 2.00e-01 2.50e+01 6.77e-01
  chirality pdb=" CA  MET A  88 "
            pdb=" N   MET A  88 "
            pdb=" C   MET A  88 "
            pdb=" CB  MET A  88 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.64   -0.13 2.00e-01 2.50e+01 4.37e-01
  ... (remaining 955 not shown)

  Planarity restraints: 1119
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CD  ARG B 677 "    0.323 9.50e-02 1.11e+02   1.45e-01 1.28e+01
        pdb=" NE  ARG B 677 "   -0.019 2.00e-02 2.50e+03
        pdb=" CZ  ARG B 677 "   -0.004 2.00e-02 2.50e+03
        pdb=" NH1 ARG B 677 "   -0.003 2.00e-02 2.50e+03
        pdb=" NH2 ARG B 677 "    0.011 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CB  PHE A  17 "   -0.010 2.00e-02 2.50e+03   1.45e-02 3.67e+00
        pdb=" CG  PHE A  17 "    0.032 2.00e-02 2.50e+03
        pdb=" CD1 PHE A  17 "   -0.006 2.00e-02 2.50e+03
        pdb=" CD2 PHE A  17 "   -0.016 2.00e-02 2.50e+03
        pdb=" CE1 PHE A  17 "   -0.005 2.00e-02 2.50e+03
        pdb=" CE2 PHE A  17 "    0.005 2.00e-02 2.50e+03
        pdb=" CZ  PHE A  17 "   -0.000 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  LYS B 698 "   -0.008 2.00e-02 2.50e+03   1.66e-02 2.74e+00
        pdb=" C   LYS B 698 "    0.029 2.00e-02 2.50e+03
        pdb=" O   LYS B 698 "   -0.011 2.00e-02 2.50e+03
        pdb=" N   GLU B 699 "   -0.010 2.00e-02 2.50e+03
  ... (remaining 1116 not shown)

  Histogram of nonbonded interaction distances:
        2.22 -     2.75: 949
        2.75 -     3.29: 5853
        3.29 -     3.83: 9924
        3.83 -     4.36: 11551
        4.36 -     4.90: 20233
  Nonbonded interactions: 48510
  Sorted by model distance:
  nonbonded pdb=" OD1 ASN B 640 "
            pdb=" OH  TYR B 651 "
     model   vdw
     2.215 3.040
  nonbonded pdb=" OD2 ASP B 354 "
            pdb=" NH2 ARG B 366 "
     model   vdw
     2.218 3.120
  nonbonded pdb=" OH  TYR B 666 "
            pdb=" OE1 GLU B 693 "
     model   vdw
     2.228 3.040
  nonbonded pdb=" O   ASN B 471 "
            pdb=" CD2 TYR B 475 "
     model   vdw
     2.237 3.340
  nonbonded pdb=" CE2 PHE B 567 "
            pdb=" OD1 ASN B 570 "
     model   vdw
     2.244 3.340
  ... (remaining 48505 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 individual isotropic
Make a string to write initial .geo file
Internal consistency checks
Time:
  Set random seed:                         0.000
  Set model cs if undefined:               0.000
  Decide on map wrapping:                  0.000
  Normalize map: mean=0, sd=1:             0.920
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.000
  Construct map_model_manager:             0.010
  Extract box with map and model:          0.140
  Check model and map are aligned:         0.020
  Set scattering table:                    0.020
  Process input model:                     6.880
  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:1.050
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:    9.080
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7661
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      :  0.004   0.038   6415  Z= 0.182
  Angle     :  0.597  10.066   8661  Z= 0.332
  Chirality :  0.040   0.209    958
  Planarity :  0.005   0.145   1119
  Dihedral  : 14.725  89.254   2382
  Min Nonbonded Distance : 2.215

Molprobity Statistics.
  All-atom Clashscore : 12.91
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.61 %
    Favored  : 96.39 %
  Rotamer:
    Outliers :  0.29 %
    Allowed  :  7.18 %
    Favored  : 92.52 %
  Cbeta Deviations :  0.13 %
  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:  0.31 (0.30), residues: 776
  helix:  1.62 (0.24), residues: 448
  sheet:  0.24 (0.62), residues: 68
  loop : -2.47 (0.34), residues: 260

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG B 341 
 TYR   0.014   0.001   TYR B 240 
 PHE   0.032   0.001   PHE A  17 
 HIS   0.003   0.001   HIS A  35 

Details of bonding type rmsd
  covalent geometry    : bond        0.00371 ( 6414)
  covalent geometry    : angle       0.59723 ( 8659)
  SS BOND              : bond        0.00188 (    1)
  SS BOND              : angle       0.14768 (    2)
  hydrogen bonds       : bond        0.14159 (  349)
  hydrogen bonds       : angle       4.51160 ( 1047)

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

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

  1552 Ramachandran restraints generated.
    776 Oldfield, 0 Emsley, 776 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1552 Ramachandran restraints generated.
    776 Oldfield, 0 Emsley, 776 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  166 residues out of total 682 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 2
    poor density    : 164
  time to evaluate  : 0.138 
Fit side-chains
   revert: symmetry clash
REVERT: A  118 LYS cc_start: 0.8469 (ttmm) cc_final: 0.8249 (tttp)
REVERT: A  120 LYS cc_start: 0.8902 (mtpp) cc_final: 0.8623 (mttt)
REVERT: B  188 MET cc_start: 0.7429 (tmm) cc_final: 0.6632 (ttt)
REVERT: B  192 LYS cc_start: 0.8234 (mttt) cc_final: 0.7895 (mmtp)
REVERT: B  229 LYS cc_start: 0.8598 (ttmm) cc_final: 0.8392 (tttt)
REVERT: B  341 ARG cc_start: 0.8684 (ttp80) cc_final: 0.8307 (ttp80)
REVERT: B  385 LYS cc_start: 0.7868 (mttt) cc_final: 0.7403 (mmtm)
REVERT: B  758 ASN cc_start: 0.7223 (m-40) cc_final: 0.6889 (m-40)
REVERT: B  811 GLU cc_start: 0.7524 (mt-10) cc_final: 0.7139 (tp30)
  outliers start: 2
  outliers final: 1
  residues processed: 166
  average time/residue: 0.0625
  time to fit residues: 13.9550
Evaluate side-chains
  101 residues out of total 682 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 100
  time to evaluate  : 0.136 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue  643 ASN
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 77
   random chunks:
   chunk 49 optimal weight:    2.9990
   chunk 53 optimal weight:    8.9990
   chunk 5 optimal weight:    6.9990
   chunk 33 optimal weight:    5.9990
   chunk 65 optimal weight:    0.6980
   chunk 62 optimal weight:    3.9990
   chunk 51 optimal weight:    6.9990
   chunk 38 optimal weight:    0.0770
   chunk 61 optimal weight:    1.9990
   chunk 45 optimal weight:    0.9980
   chunk 74 optimal weight:    0.7980
   overall best weight:    0.9140

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

Flipped N/Q/H residues before XYZ refinement:
A 144 ASN
B 187 GLN
B 209 ASN
** B 307 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 532 ASN
B 654 ASN

Total number of N/Q/H flips: 5

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3977 r_free = 0.3977 target = 0.178520 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.3572 r_free = 0.3572 target = 0.139481 restraints weight = 7200.026|
|-----------------------------------------------------------------------------|
r_work (start): 0.3565 rms_B_bonded: 2.32
r_work: 0.3420 rms_B_bonded: 3.20 restraints_weight: 0.5000
r_work (final): 0.3420
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7948
moved from start:          0.1965

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.052   6415  Z= 0.126
  Angle     :  0.504   7.700   8661  Z= 0.257
  Chirality :  0.038   0.151    958
  Planarity :  0.004   0.058   1119
  Dihedral  :  3.934  21.754    844
  Min Nonbonded Distance : 2.533

Molprobity Statistics.
  All-atom Clashscore : 5.02
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.22 %
    Favored  : 96.78 %
  Rotamer:
    Outliers :  3.08 %
    Allowed  :  8.80 %
    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:  0.74 (0.30), residues: 776
  helix:  1.83 (0.24), residues: 458
  sheet:  0.65 (0.64), residues: 67
  loop : -2.23 (0.35), residues: 251

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.001   ARG B 341 
 TYR   0.019   0.001   TYR B 475 
 PHE   0.007   0.001   PHE B 721 
 HIS   0.003   0.001   HIS B 521 

Details of bonding type rmsd
  covalent geometry    : bond        0.00300 ( 6414)
  covalent geometry    : angle       0.50357 ( 8659)
  SS BOND              : bond        0.01161 (    1)
  SS BOND              : angle       1.13332 (    2)
  hydrogen bonds       : bond        0.03310 (  349)
  hydrogen bonds       : angle       3.44733 ( 1047)

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

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

  1552 Ramachandran restraints generated.
    776 Oldfield, 0 Emsley, 776 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1552 Ramachandran restraints generated.
    776 Oldfield, 0 Emsley, 776 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  127 residues out of total 682 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 106
  time to evaluate  : 0.137 
Fit side-chains
REVERT: A  118 LYS cc_start: 0.8428 (ttmm) cc_final: 0.8206 (tttp)
REVERT: A  120 LYS cc_start: 0.8883 (mtpp) cc_final: 0.8580 (mttt)
REVERT: B  188 MET cc_start: 0.7305 (tmm) cc_final: 0.6462 (ttt)
REVERT: B  192 LYS cc_start: 0.7773 (mttt) cc_final: 0.7459 (mmtp)
REVERT: B  385 LYS cc_start: 0.7997 (mttt) cc_final: 0.7680 (mptt)
REVERT: B  666 TYR cc_start: 0.7652 (m-80) cc_final: 0.7329 (m-80)
REVERT: B  743 ASP cc_start: 0.8217 (m-30) cc_final: 0.8004 (m-30)
REVERT: B  811 GLU cc_start: 0.7698 (mt-10) cc_final: 0.7288 (tp30)
  outliers start: 21
  outliers final: 11
  residues processed: 117
  average time/residue: 0.0518
  time to fit residues: 8.3947
Evaluate side-chains
  104 residues out of total 682 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 93
  time to evaluate  : 0.135 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   20 VAL
Chi-restraints excluded: chain A residue   53 VAL
Chi-restraints excluded: chain A residue   94 ILE
Chi-restraints excluded: chain A residue  144 ASN
Chi-restraints excluded: chain B residue  211 SER
Chi-restraints excluded: chain B residue  239 VAL
Chi-restraints excluded: chain B residue  323 ILE
Chi-restraints excluded: chain B residue  363 MET
Chi-restraints excluded: chain B residue  532 ASN
Chi-restraints excluded: chain B residue  601 LEU
Chi-restraints excluded: chain B residue  669 VAL
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 77
   random chunks:
   chunk 15 optimal weight:    7.9990
   chunk 1 optimal weight:    6.9990
   chunk 67 optimal weight:    3.9990
   chunk 12 optimal weight:    3.9990
   chunk 73 optimal weight:    5.9990
   chunk 69 optimal weight:    3.9990
   chunk 4 optimal weight:    4.9990
   chunk 27 optimal weight:    3.9990
   chunk 75 optimal weight:    1.9990
   chunk 74 optimal weight:    0.9980
   chunk 52 optimal weight:    4.9990
   overall best weight:    2.9988

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

Flipped N/Q/H residues before XYZ refinement:
A 144 ASN
B 187 GLN
B 209 ASN
B 307 GLN
B 415 GLN
B 560 ASN
B 610 ASN
B 654 ASN

Total number of N/Q/H flips: 8

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3876 r_free = 0.3876 target = 0.167693 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.3461 r_free = 0.3461 target = 0.129579 restraints weight = 7283.503|
|-----------------------------------------------------------------------------|
r_work (start): 0.3381 rms_B_bonded: 2.20
r_work: 0.3235 rms_B_bonded: 3.03 restraints_weight: 0.5000
r_work: 0.3078 rms_B_bonded: 4.86 restraints_weight: 0.2500
r_work (final): 0.3078
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8242
moved from start:          0.2868

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.007   0.074   6415  Z= 0.291
  Angle     :  0.655   7.295   8661  Z= 0.329
  Chirality :  0.043   0.143    958
  Planarity :  0.004   0.043   1119
  Dihedral  :  4.424  25.305    842
  Min Nonbonded Distance : 2.552

Molprobity Statistics.
  All-atom Clashscore : 5.82
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.64 %
    Favored  : 95.36 %
  Rotamer:
    Outliers :  3.08 %
    Allowed  : 12.46 %
    Favored  : 84.46 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  0.13 (0.30), residues: 776
  helix:  1.33 (0.24), residues: 456
  sheet:  0.35 (0.63), residues: 67
  loop : -2.39 (0.34), residues: 253

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.001   ARG B 322 
 TYR   0.024   0.002   TYR B 519 
 PHE   0.022   0.002   PHE B 721 
 HIS   0.006   0.002   HIS A 147 

Details of bonding type rmsd
  covalent geometry    : bond        0.00724 ( 6414)
  covalent geometry    : angle       0.65447 ( 8659)
  SS BOND              : bond        0.02073 (    1)
  SS BOND              : angle       2.19896 (    2)
  hydrogen bonds       : bond        0.04673 (  349)
  hydrogen bonds       : angle       3.81665 ( 1047)

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

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

  1552 Ramachandran restraints generated.
    776 Oldfield, 0 Emsley, 776 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1552 Ramachandran restraints generated.
    776 Oldfield, 0 Emsley, 776 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  124 residues out of total 682 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 103
  time to evaluate  : 0.223 
Fit side-chains
REVERT: A   31 PHE cc_start: 0.7014 (t80) cc_final: 0.6773 (t80)
REVERT: A   70 GLN cc_start: 0.7996 (mp10) cc_final: 0.7767 (mp10)
REVERT: A  106 TYR cc_start: 0.8487 (p90) cc_final: 0.8243 (p90)
REVERT: A  118 LYS cc_start: 0.8595 (ttmm) cc_final: 0.8206 (tttp)
REVERT: A  120 LYS cc_start: 0.8983 (mtpp) cc_final: 0.8732 (mttt)
REVERT: A  144 ASN cc_start: 0.8784 (OUTLIER) cc_final: 0.8405 (m110)
REVERT: A  161 ASP cc_start: 0.7825 (m-30) cc_final: 0.7518 (m-30)
REVERT: B  188 MET cc_start: 0.7733 (tmm) cc_final: 0.7105 (ttt)
REVERT: B  328 LYS cc_start: 0.8581 (mttt) cc_final: 0.8329 (mtmt)
REVERT: B  368 GLN cc_start: 0.8319 (mm-40) cc_final: 0.8018 (mm-40)
REVERT: B  385 LYS cc_start: 0.8176 (mttt) cc_final: 0.7838 (mptt)
REVERT: B  396 ASN cc_start: 0.8274 (t0) cc_final: 0.7961 (t0)
REVERT: B  497 GLU cc_start: 0.7703 (tm-30) cc_final: 0.7222 (pm20)
REVERT: B  654 ASN cc_start: 0.7623 (OUTLIER) cc_final: 0.7026 (t0)
REVERT: B  669 VAL cc_start: 0.8940 (OUTLIER) cc_final: 0.8638 (p)
REVERT: B  811 GLU cc_start: 0.8158 (mt-10) cc_final: 0.7565 (tp30)
  outliers start: 21
  outliers final: 11
  residues processed: 117
  average time/residue: 0.0591
  time to fit residues: 9.5444
Evaluate side-chains
  106 residues out of total 682 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 92
  time to evaluate  : 0.150 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   23 THR
Chi-restraints excluded: chain A residue   53 VAL
Chi-restraints excluded: chain A residue   94 ILE
Chi-restraints excluded: chain A residue  140 ASP
Chi-restraints excluded: chain A residue  144 ASN
Chi-restraints excluded: chain B residue  211 SER
Chi-restraints excluded: chain B residue  239 VAL
Chi-restraints excluded: chain B residue  323 ILE
Chi-restraints excluded: chain B residue  340 GLU
Chi-restraints excluded: chain B residue  363 MET
Chi-restraints excluded: chain B residue  601 LEU
Chi-restraints excluded: chain B residue  642 LEU
Chi-restraints excluded: chain B residue  654 ASN
Chi-restraints excluded: chain B residue  669 VAL
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 77
   random chunks:
   chunk 69 optimal weight:    3.9990
   chunk 30 optimal weight:    2.9990
   chunk 32 optimal weight:    0.9980
   chunk 73 optimal weight:    0.6980
   chunk 61 optimal weight:    2.9990
   chunk 17 optimal weight:    9.9990
   chunk 62 optimal weight:    0.9980
   chunk 31 optimal weight:    0.7980
   chunk 3 optimal weight:    2.9990
   chunk 42 optimal weight:    0.6980
   chunk 9 optimal weight:    0.9990
   overall best weight:    0.8380

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

Flipped N/Q/H residues before XYZ refinement:
B 187 GLN
B 209 ASN
B 466 ASN
** B 532 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 560 ASN
B 654 ASN

Total number of N/Q/H flips: 5

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3927 r_free = 0.3927 target = 0.173065 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 42)----------------|
| r_work = 0.3510 r_free = 0.3510 target = 0.134495 restraints weight = 7223.553|
|-----------------------------------------------------------------------------|
r_work (start): 0.3470 rms_B_bonded: 2.27
r_work: 0.3327 rms_B_bonded: 3.10 restraints_weight: 0.5000
r_work (final): 0.3327
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8019
moved from start:          0.2975

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.034   6415  Z= 0.114
  Angle     :  0.481   7.597   8661  Z= 0.246
  Chirality :  0.037   0.142    958
  Planarity :  0.003   0.044   1119
  Dihedral  :  4.013  21.923    842
  Min Nonbonded Distance : 2.589

Molprobity Statistics.
  All-atom Clashscore : 5.26
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.48 %
    Favored  : 96.52 %
  Rotamer:
    Outliers :  2.35 %
    Allowed  : 12.76 %
    Favored  : 84.90 %
  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:  0.55 (0.30), residues: 776
  helix:  1.69 (0.24), residues: 464
  sheet:  0.44 (0.64), residues: 67
  loop : -2.37 (0.35), residues: 245

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG B 322 
 TYR   0.013   0.001   TYR B 436 
 PHE   0.017   0.001   PHE B 567 
 HIS   0.003   0.001   HIS A 147 

Details of bonding type rmsd
  covalent geometry    : bond        0.00271 ( 6414)
  covalent geometry    : angle       0.48071 ( 8659)
  SS BOND              : bond        0.00719 (    1)
  SS BOND              : angle       0.97430 (    2)
  hydrogen bonds       : bond        0.03057 (  349)
  hydrogen bonds       : angle       3.42593 ( 1047)

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

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

  1552 Ramachandran restraints generated.
    776 Oldfield, 0 Emsley, 776 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1552 Ramachandran restraints generated.
    776 Oldfield, 0 Emsley, 776 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  115 residues out of total 682 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 99
  time to evaluate  : 0.196 
Fit side-chains
   revert: symmetry clash
REVERT: A   31 PHE cc_start: 0.6975 (t80) cc_final: 0.6728 (t80)
REVERT: A   70 GLN cc_start: 0.7926 (mp10) cc_final: 0.7709 (mp10)
REVERT: A  118 LYS cc_start: 0.8450 (ttmm) cc_final: 0.8225 (tttp)
REVERT: A  120 LYS cc_start: 0.8849 (mtpp) cc_final: 0.8596 (mttt)
REVERT: A  152 TYR cc_start: 0.8883 (p90) cc_final: 0.8530 (p90)
REVERT: A  161 ASP cc_start: 0.7778 (m-30) cc_final: 0.7445 (m-30)
REVERT: B  188 MET cc_start: 0.7639 (tmm) cc_final: 0.7068 (ttt)
REVERT: B  228 GLU cc_start: 0.7379 (tm-30) cc_final: 0.6748 (pt0)
REVERT: B  270 MET cc_start: 0.8664 (mmm) cc_final: 0.8266 (tmm)
REVERT: B  328 LYS cc_start: 0.8308 (mttt) cc_final: 0.8081 (mtmt)
REVERT: B  385 LYS cc_start: 0.7999 (mttt) cc_final: 0.7707 (mptt)
REVERT: B  497 GLU cc_start: 0.7576 (tm-30) cc_final: 0.7213 (pm20)
REVERT: B  654 ASN cc_start: 0.7593 (OUTLIER) cc_final: 0.7155 (t0)
REVERT: B  669 VAL cc_start: 0.8817 (OUTLIER) cc_final: 0.8476 (p)
REVERT: B  811 GLU cc_start: 0.7941 (mt-10) cc_final: 0.7513 (tp30)
  outliers start: 16
  outliers final: 8
  residues processed: 107
  average time/residue: 0.0518
  time to fit residues: 7.8949
Evaluate side-chains
  103 residues out of total 682 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 93
  time to evaluate  : 0.230 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   53 VAL
Chi-restraints excluded: chain A residue   58 ASP
Chi-restraints excluded: chain A residue   94 ILE
Chi-restraints excluded: chain B residue  211 SER
Chi-restraints excluded: chain B residue  312 SER
Chi-restraints excluded: chain B residue  323 ILE
Chi-restraints excluded: chain B residue  363 MET
Chi-restraints excluded: chain B residue  601 LEU
Chi-restraints excluded: chain B residue  654 ASN
Chi-restraints excluded: chain B residue  669 VAL
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 77
   random chunks:
   chunk 59 optimal weight:    5.9990
   chunk 41 optimal weight:   10.0000
   chunk 38 optimal weight:    1.9990
   chunk 56 optimal weight:    4.9990
   chunk 64 optimal weight:    3.9990
   chunk 6 optimal weight:    6.9990
   chunk 74 optimal weight:    2.9990
   chunk 46 optimal weight:    2.9990
   chunk 60 optimal weight:    0.8980
   chunk 61 optimal weight:    3.9990
   chunk 29 optimal weight:    0.9990
   overall best weight:    1.9788

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

Flipped N/Q/H residues before XYZ refinement:
A 144 ASN
B 209 ASN
** B 532 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 560 ASN
B 654 ASN

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3890 r_free = 0.3890 target = 0.169425 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.3476 r_free = 0.3476 target = 0.131201 restraints weight = 7365.019|
|-----------------------------------------------------------------------------|
r_work (start): 0.3465 rms_B_bonded: 2.23
r_work: 0.3323 rms_B_bonded: 3.03 restraints_weight: 0.5000
r_work: 0.3164 rms_B_bonded: 4.92 restraints_weight: 0.2500
r_work (final): 0.3164
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8209
moved from start:          0.3151

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.067   6415  Z= 0.200
  Angle     :  0.546   7.364   8661  Z= 0.275
  Chirality :  0.040   0.139    958
  Planarity :  0.003   0.043   1119
  Dihedral  :  4.113  23.091    842
  Min Nonbonded Distance : 2.570

Molprobity Statistics.
  All-atom Clashscore : 5.34
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.38 %
    Favored  : 95.62 %
  Rotamer:
    Outliers :  2.64 %
    Allowed  : 13.78 %
    Favored  : 83.58 %
  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:  0.32 (0.30), residues: 776
  helix:  1.52 (0.24), residues: 463
  sheet: -0.16 (0.61), residues: 75
  loop : -2.38 (0.35), residues: 238

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG B 322 
 TYR   0.013   0.002   TYR B 680 
 PHE   0.019   0.001   PHE B 567 
 HIS   0.004   0.001   HIS A 147 

Details of bonding type rmsd
  covalent geometry    : bond        0.00499 ( 6414)
  covalent geometry    : angle       0.54537 ( 8659)
  SS BOND              : bond        0.00940 (    1)
  SS BOND              : angle       1.33403 (    2)
  hydrogen bonds       : bond        0.03797 (  349)
  hydrogen bonds       : angle       3.56593 ( 1047)

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

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

  1552 Ramachandran restraints generated.
    776 Oldfield, 0 Emsley, 776 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1552 Ramachandran restraints generated.
    776 Oldfield, 0 Emsley, 776 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  111 residues out of total 682 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 93
  time to evaluate  : 0.143 
Fit side-chains
REVERT: A   31 PHE cc_start: 0.7189 (t80) cc_final: 0.6873 (t80)
REVERT: A   70 GLN cc_start: 0.7926 (mp10) cc_final: 0.7641 (mp10)
REVERT: A  118 LYS cc_start: 0.8563 (ttmm) cc_final: 0.8167 (tttp)
REVERT: A  120 LYS cc_start: 0.8941 (mtpp) cc_final: 0.8725 (mttt)
REVERT: A  161 ASP cc_start: 0.7822 (m-30) cc_final: 0.7467 (m-30)
REVERT: B  188 MET cc_start: 0.7693 (tmm) cc_final: 0.7089 (ttt)
REVERT: B  202 LYS cc_start: 0.8303 (OUTLIER) cc_final: 0.8066 (mttp)
REVERT: B  328 LYS cc_start: 0.8533 (mttt) cc_final: 0.8289 (mtmt)
REVERT: B  385 LYS cc_start: 0.8135 (mttt) cc_final: 0.7790 (mptt)
REVERT: B  431 LYS cc_start: 0.8182 (mmmt) cc_final: 0.7941 (mmmt)
REVERT: B  497 GLU cc_start: 0.7770 (tm-30) cc_final: 0.7277 (pm20)
REVERT: B  654 ASN cc_start: 0.7629 (OUTLIER) cc_final: 0.7020 (t0)
REVERT: B  669 VAL cc_start: 0.8893 (OUTLIER) cc_final: 0.8584 (p)
REVERT: B  811 GLU cc_start: 0.8201 (mt-10) cc_final: 0.7585 (tp30)
  outliers start: 18
  outliers final: 8
  residues processed: 106
  average time/residue: 0.0612
  time to fit residues: 8.8677
Evaluate side-chains
  100 residues out of total 682 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 89
  time to evaluate  : 0.282 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   53 VAL
Chi-restraints excluded: chain A residue   58 ASP
Chi-restraints excluded: chain A residue   94 ILE
Chi-restraints excluded: chain B residue  202 LYS
Chi-restraints excluded: chain B residue  211 SER
Chi-restraints excluded: chain B residue  323 ILE
Chi-restraints excluded: chain B residue  363 MET
Chi-restraints excluded: chain B residue  601 LEU
Chi-restraints excluded: chain B residue  654 ASN
Chi-restraints excluded: chain B residue  669 VAL
Chi-restraints excluded: chain B residue  711 ILE
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 77
   random chunks:
   chunk 2 optimal weight:    3.9990
   chunk 60 optimal weight:    0.9990
   chunk 52 optimal weight:    4.9990
   chunk 73 optimal weight:    1.9990
   chunk 34 optimal weight:    3.9990
   chunk 17 optimal weight:    8.9990
   chunk 47 optimal weight:    3.9990
   chunk 41 optimal weight:   10.0000
   chunk 62 optimal weight:    2.9990
   chunk 26 optimal weight:    0.9990
   chunk 33 optimal weight:    4.9990
   overall best weight:    2.1990

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

Flipped N/Q/H residues before XYZ refinement:
B 209 ASN
** B 532 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 560 ASN
B 654 ASN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3880 r_free = 0.3880 target = 0.168364 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 44)----------------|
| r_work = 0.3461 r_free = 0.3461 target = 0.129956 restraints weight = 7300.497|
|-----------------------------------------------------------------------------|
r_work (start): 0.3432 rms_B_bonded: 2.25
r_work: 0.3294 rms_B_bonded: 3.02 restraints_weight: 0.5000
r_work: 0.3130 rms_B_bonded: 4.94 restraints_weight: 0.2500
r_work (final): 0.3130
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8220
moved from start:          0.3298

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.046   6415  Z= 0.217
  Angle     :  0.565   7.172   8661  Z= 0.285
  Chirality :  0.040   0.141    958
  Planarity :  0.003   0.043   1119
  Dihedral  :  4.177  23.761    842
  Min Nonbonded Distance : 2.565

Molprobity Statistics.
  All-atom Clashscore : 5.34
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.51 %
    Favored  : 95.49 %
  Rotamer:
    Outliers :  2.79 %
    Allowed  : 14.96 %
    Favored  : 82.26 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  0.20 (0.30), residues: 776
  helix:  1.40 (0.24), residues: 463
  sheet: -0.24 (0.60), residues: 75
  loop : -2.35 (0.34), residues: 238

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.001   ARG B 322 
 TYR   0.014   0.002   TYR B 680 
 PHE   0.023   0.002   PHE B 567 
 HIS   0.004   0.001   HIS A 147 

Details of bonding type rmsd
  covalent geometry    : bond        0.00538 ( 6414)
  covalent geometry    : angle       0.56484 ( 8659)
  SS BOND              : bond        0.00966 (    1)
  SS BOND              : angle       1.36606 (    2)
  hydrogen bonds       : bond        0.03908 (  349)
  hydrogen bonds       : angle       3.61470 ( 1047)

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

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

  1552 Ramachandran restraints generated.
    776 Oldfield, 0 Emsley, 776 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1552 Ramachandran restraints generated.
    776 Oldfield, 0 Emsley, 776 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  113 residues out of total 682 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 94
  time to evaluate  : 0.234 
Fit side-chains
REVERT: A   31 PHE cc_start: 0.7226 (t80) cc_final: 0.6964 (t80)
REVERT: A   39 ASP cc_start: 0.8356 (t0) cc_final: 0.8125 (p0)
REVERT: A   70 GLN cc_start: 0.7881 (mp10) cc_final: 0.7563 (mp10)
REVERT: A  118 LYS cc_start: 0.8562 (ttmm) cc_final: 0.8148 (tttp)
REVERT: A  120 LYS cc_start: 0.8949 (mtpp) cc_final: 0.8712 (mttt)
REVERT: B  188 MET cc_start: 0.7699 (tmm) cc_final: 0.7011 (ttt)
REVERT: B  202 LYS cc_start: 0.8276 (OUTLIER) cc_final: 0.8018 (mttp)
REVERT: B  228 GLU cc_start: 0.7709 (tm-30) cc_final: 0.7111 (pt0)
REVERT: B  270 MET cc_start: 0.8846 (mmm) cc_final: 0.8513 (tmm)
REVERT: B  328 LYS cc_start: 0.8578 (mttt) cc_final: 0.8327 (mtmt)
REVERT: B  385 LYS cc_start: 0.8140 (mttt) cc_final: 0.7787 (mptt)
REVERT: B  497 GLU cc_start: 0.7755 (tm-30) cc_final: 0.7276 (pm20)
REVERT: B  654 ASN cc_start: 0.7631 (OUTLIER) cc_final: 0.7179 (t0)
REVERT: B  669 VAL cc_start: 0.8890 (OUTLIER) cc_final: 0.8580 (p)
REVERT: B  684 MET cc_start: 0.8682 (OUTLIER) cc_final: 0.8354 (mmt)
REVERT: B  811 GLU cc_start: 0.8250 (mt-10) cc_final: 0.7670 (tp30)
  outliers start: 19
  outliers final: 10
  residues processed: 105
  average time/residue: 0.0585
  time to fit residues: 8.4483
Evaluate side-chains
  102 residues out of total 682 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 88
  time to evaluate  : 0.161 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   53 VAL
Chi-restraints excluded: chain A residue   94 ILE
Chi-restraints excluded: chain B residue  202 LYS
Chi-restraints excluded: chain B residue  211 SER
Chi-restraints excluded: chain B residue  239 VAL
Chi-restraints excluded: chain B residue  323 ILE
Chi-restraints excluded: chain B residue  340 GLU
Chi-restraints excluded: chain B residue  363 MET
Chi-restraints excluded: chain B residue  548 ILE
Chi-restraints excluded: chain B residue  601 LEU
Chi-restraints excluded: chain B residue  654 ASN
Chi-restraints excluded: chain B residue  669 VAL
Chi-restraints excluded: chain B residue  684 MET
Chi-restraints excluded: chain B residue  711 ILE
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 77
   random chunks:
   chunk 65 optimal weight:    0.7980
   chunk 13 optimal weight:    0.8980
   chunk 39 optimal weight:    9.9990
   chunk 74 optimal weight:    0.9980
   chunk 19 optimal weight:    6.9990
   chunk 61 optimal weight:    0.6980
   chunk 66 optimal weight:    1.9990
   chunk 56 optimal weight:    5.9990
   chunk 52 optimal weight:    3.9990
   chunk 1 optimal weight:    5.9990
   chunk 76 optimal weight:    2.9990
   overall best weight:    1.0782

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

Flipped N/Q/H residues before XYZ refinement:
B 209 ASN
** B 532 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 560 ASN
B 654 ASN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3911 r_free = 0.3911 target = 0.171630 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.3514 r_free = 0.3514 target = 0.134542 restraints weight = 7263.613|
|-----------------------------------------------------------------------------|
r_work (start): 0.3507 rms_B_bonded: 2.11
r_work: 0.3370 rms_B_bonded: 2.86 restraints_weight: 0.5000
r_work: 0.3215 rms_B_bonded: 4.63 restraints_weight: 0.2500
r_work (final): 0.3215
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8116
moved from start:          0.3348

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.032   6415  Z= 0.130
  Angle     :  0.495   6.617   8661  Z= 0.251
  Chirality :  0.039   0.274    958
  Planarity :  0.003   0.044   1119
  Dihedral  :  3.955  21.781    842
  Min Nonbonded Distance : 2.587

Molprobity Statistics.
  All-atom Clashscore : 5.34
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.99 %
    Favored  : 96.01 %
  Rotamer:
    Outliers :  2.20 %
    Allowed  : 15.10 %
    Favored  : 82.70 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  0.52 (0.30), residues: 776
  helix:  1.68 (0.24), residues: 463
  sheet: -0.15 (0.60), residues: 75
  loop : -2.28 (0.34), residues: 238

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG B 322 
 TYR   0.013   0.001   TYR B 680 
 PHE   0.026   0.001   PHE B 567 
 HIS   0.003   0.001   HIS B 521 

Details of bonding type rmsd
  covalent geometry    : bond        0.00314 ( 6414)
  covalent geometry    : angle       0.49422 ( 8659)
  SS BOND              : bond        0.01646 (    1)
  SS BOND              : angle       1.26642 (    2)
  hydrogen bonds       : bond        0.03147 (  349)
  hydrogen bonds       : angle       3.45335 ( 1047)

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

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

  1552 Ramachandran restraints generated.
    776 Oldfield, 0 Emsley, 776 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1552 Ramachandran restraints generated.
    776 Oldfield, 0 Emsley, 776 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  110 residues out of total 682 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 95
  time to evaluate  : 0.201 
Fit side-chains
   revert: symmetry clash
REVERT: A   31 PHE cc_start: 0.7302 (t80) cc_final: 0.7028 (t80)
REVERT: A   39 ASP cc_start: 0.8302 (t0) cc_final: 0.8071 (p0)
REVERT: A   70 GLN cc_start: 0.7823 (mp10) cc_final: 0.7486 (mp10)
REVERT: A  118 LYS cc_start: 0.8513 (ttmm) cc_final: 0.8117 (tttp)
REVERT: A  119 SER cc_start: 0.9119 (p) cc_final: 0.8876 (m)
REVERT: A  120 LYS cc_start: 0.8928 (mtpp) cc_final: 0.8653 (mttt)
REVERT: B  188 MET cc_start: 0.7660 (tmm) cc_final: 0.6931 (ttt)
REVERT: B  202 LYS cc_start: 0.8233 (OUTLIER) cc_final: 0.7986 (mttp)
REVERT: B  270 MET cc_start: 0.8784 (mmm) cc_final: 0.8386 (tmm)
REVERT: B  328 LYS cc_start: 0.8452 (mttt) cc_final: 0.8168 (mtmt)
REVERT: B  385 LYS cc_start: 0.8044 (mttt) cc_final: 0.7666 (mptt)
REVERT: B  497 GLU cc_start: 0.7731 (tm-30) cc_final: 0.7288 (pm20)
REVERT: B  654 ASN cc_start: 0.7613 (OUTLIER) cc_final: 0.7181 (t0)
REVERT: B  666 TYR cc_start: 0.7333 (m-80) cc_final: 0.7121 (m-80)
REVERT: B  669 VAL cc_start: 0.8780 (OUTLIER) cc_final: 0.8432 (p)
REVERT: B  811 GLU cc_start: 0.8222 (mt-10) cc_final: 0.7563 (tp30)
  outliers start: 15
  outliers final: 9
  residues processed: 103
  average time/residue: 0.0642
  time to fit residues: 9.1179
Evaluate side-chains
  100 residues out of total 682 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 88
  time to evaluate  : 0.143 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   53 VAL
Chi-restraints excluded: chain A residue   58 ASP
Chi-restraints excluded: chain A residue   94 ILE
Chi-restraints excluded: chain B residue  202 LYS
Chi-restraints excluded: chain B residue  211 SER
Chi-restraints excluded: chain B residue  323 ILE
Chi-restraints excluded: chain B residue  363 MET
Chi-restraints excluded: chain B residue  512 MET
Chi-restraints excluded: chain B residue  548 ILE
Chi-restraints excluded: chain B residue  601 LEU
Chi-restraints excluded: chain B residue  654 ASN
Chi-restraints excluded: chain B residue  669 VAL
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 77
   random chunks:
   chunk 64 optimal weight:    1.9990
   chunk 11 optimal weight:    1.9990
   chunk 16 optimal weight:    2.9990
   chunk 33 optimal weight:    5.9990
   chunk 40 optimal weight:    2.9990
   chunk 47 optimal weight:    4.9990
   chunk 60 optimal weight:    9.9990
   chunk 70 optimal weight:    3.9990
   chunk 55 optimal weight:    2.9990
   chunk 61 optimal weight:    4.9990
   chunk 54 optimal weight:    0.0870
   overall best weight:    2.0166

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

Flipped N/Q/H residues before XYZ refinement:
** B 532 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 560 ASN
B 654 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3883 r_free = 0.3883 target = 0.168854 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.3483 r_free = 0.3483 target = 0.131864 restraints weight = 7293.712|
|-----------------------------------------------------------------------------|
r_work (start): 0.3475 rms_B_bonded: 2.09
r_work: 0.3337 rms_B_bonded: 2.85 restraints_weight: 0.5000
r_work: 0.3182 rms_B_bonded: 4.60 restraints_weight: 0.2500
r_work (final): 0.3182
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8164
moved from start:          0.3446

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.043   6415  Z= 0.202
  Angle     :  0.564   7.121   8661  Z= 0.283
  Chirality :  0.041   0.237    958
  Planarity :  0.003   0.043   1119
  Dihedral  :  4.110  23.252    842
  Min Nonbonded Distance : 2.572

Molprobity Statistics.
  All-atom Clashscore : 5.58
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.90 %
    Favored  : 95.10 %
  Rotamer:
    Outliers :  2.49 %
    Allowed  : 15.25 %
    Favored  : 82.26 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  0.28 (0.30), residues: 776
  helix:  1.47 (0.24), residues: 466
  sheet: -0.24 (0.59), residues: 75
  loop : -2.36 (0.34), residues: 235

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.001   ARG B 322 
 TYR   0.014   0.001   TYR B 680 
 PHE   0.020   0.001   PHE B 567 
 HIS   0.003   0.001   HIS B 521 

Details of bonding type rmsd
  covalent geometry    : bond        0.00502 ( 6414)
  covalent geometry    : angle       0.56348 ( 8659)
  SS BOND              : bond        0.01136 (    1)
  SS BOND              : angle       1.40861 (    2)
  hydrogen bonds       : bond        0.03764 (  349)
  hydrogen bonds       : angle       3.58012 ( 1047)

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

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

  1552 Ramachandran restraints generated.
    776 Oldfield, 0 Emsley, 776 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1552 Ramachandran restraints generated.
    776 Oldfield, 0 Emsley, 776 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  108 residues out of total 682 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 91
  time to evaluate  : 0.232 
Fit side-chains
REVERT: A   39 ASP cc_start: 0.8303 (t0) cc_final: 0.8085 (p0)
REVERT: A   70 GLN cc_start: 0.7887 (mp10) cc_final: 0.7531 (mp10)
REVERT: A  118 LYS cc_start: 0.8539 (ttmm) cc_final: 0.8301 (tttp)
REVERT: A  120 LYS cc_start: 0.8924 (mtpp) cc_final: 0.8700 (mttt)
REVERT: B  188 MET cc_start: 0.7657 (tmm) cc_final: 0.6995 (ttt)
REVERT: B  202 LYS cc_start: 0.8255 (OUTLIER) cc_final: 0.8000 (mttp)
REVERT: B  228 GLU cc_start: 0.7693 (tm-30) cc_final: 0.7072 (pt0)
REVERT: B  270 MET cc_start: 0.8766 (mmm) cc_final: 0.8355 (tmm)
REVERT: B  328 LYS cc_start: 0.8544 (mttt) cc_final: 0.8266 (mtmt)
REVERT: B  385 LYS cc_start: 0.8123 (mttt) cc_final: 0.7752 (mptt)
REVERT: B  497 GLU cc_start: 0.7770 (tm-30) cc_final: 0.7322 (pm20)
REVERT: B  654 ASN cc_start: 0.7498 (OUTLIER) cc_final: 0.6962 (t0)
REVERT: B  669 VAL cc_start: 0.8869 (OUTLIER) cc_final: 0.8556 (p)
REVERT: B  811 GLU cc_start: 0.8291 (mt-10) cc_final: 0.7653 (tp30)
  outliers start: 17
  outliers final: 9
  residues processed: 101
  average time/residue: 0.0587
  time to fit residues: 8.2023
Evaluate side-chains
  99 residues out of total 682 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 87
  time to evaluate  : 0.226 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   53 VAL
Chi-restraints excluded: chain A residue   94 ILE
Chi-restraints excluded: chain B residue  202 LYS
Chi-restraints excluded: chain B residue  211 SER
Chi-restraints excluded: chain B residue  239 VAL
Chi-restraints excluded: chain B residue  323 ILE
Chi-restraints excluded: chain B residue  363 MET
Chi-restraints excluded: chain B residue  548 ILE
Chi-restraints excluded: chain B residue  601 LEU
Chi-restraints excluded: chain B residue  654 ASN
Chi-restraints excluded: chain B residue  669 VAL
Chi-restraints excluded: chain B residue  711 ILE
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 77
   random chunks:
   chunk 35 optimal weight:    1.9990
   chunk 25 optimal weight:    0.5980
   chunk 8 optimal weight:    1.9990
   chunk 23 optimal weight:    4.9990
   chunk 75 optimal weight:    0.7980
   chunk 74 optimal weight:    0.9990
   chunk 2 optimal weight:    1.9990
   chunk 20 optimal weight:    0.7980
   chunk 47 optimal weight:    3.9990
   chunk 53 optimal weight:    0.7980
   chunk 9 optimal weight:    0.6980
   overall best weight:    0.7380

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

Flipped N/Q/H residues before XYZ refinement:
B 373 ASN
** B 532 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 560 ASN
B 654 ASN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3923 r_free = 0.3923 target = 0.173063 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 49)----------------|
| r_work = 0.3532 r_free = 0.3532 target = 0.136173 restraints weight = 7291.221|
|-----------------------------------------------------------------------------|
r_work (start): 0.3461 rms_B_bonded: 2.11
r_work: 0.3323 rms_B_bonded: 2.86 restraints_weight: 0.5000
r_work: 0.3165 rms_B_bonded: 4.65 restraints_weight: 0.2500
r_work (final): 0.3165
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8085
moved from start:          0.3456

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.028   6415  Z= 0.108
  Angle     :  0.484   8.106   8661  Z= 0.247
  Chirality :  0.037   0.149    958
  Planarity :  0.003   0.044   1119
  Dihedral  :  3.857  20.880    842
  Min Nonbonded Distance : 2.594

Molprobity Statistics.
  All-atom Clashscore : 5.34
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.48 %
    Favored  : 96.52 %
  Rotamer:
    Outliers :  2.49 %
    Allowed  : 15.25 %
    Favored  : 82.26 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  0.68 (0.30), residues: 776
  helix:  1.79 (0.24), residues: 466
  sheet: -0.08 (0.60), residues: 75
  loop : -2.21 (0.35), residues: 235

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG B 322 
 TYR   0.013   0.001   TYR B 680 
 PHE   0.006   0.001   PHE B 721 
 HIS   0.002   0.001   HIS B 658 

Details of bonding type rmsd
  covalent geometry    : bond        0.00253 ( 6414)
  covalent geometry    : angle       0.48429 ( 8659)
  SS BOND              : bond        0.00151 (    1)
  SS BOND              : angle       0.91505 (    2)
  hydrogen bonds       : bond        0.02859 (  349)
  hydrogen bonds       : angle       3.39354 ( 1047)

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

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

  1552 Ramachandran restraints generated.
    776 Oldfield, 0 Emsley, 776 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1552 Ramachandran restraints generated.
    776 Oldfield, 0 Emsley, 776 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  109 residues out of total 682 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 92
  time to evaluate  : 0.232 
Fit side-chains
REVERT: A   39 ASP cc_start: 0.8257 (t0) cc_final: 0.8047 (p0)
REVERT: A   70 GLN cc_start: 0.7803 (mp10) cc_final: 0.7442 (mp10)
REVERT: A  118 LYS cc_start: 0.8505 (ttmm) cc_final: 0.8119 (tttp)
REVERT: A  119 SER cc_start: 0.9153 (p) cc_final: 0.8828 (m)
REVERT: A  120 LYS cc_start: 0.8908 (mtpp) cc_final: 0.8657 (mttt)
REVERT: A  152 TYR cc_start: 0.8892 (p90) cc_final: 0.8599 (p90)
REVERT: B  188 MET cc_start: 0.7645 (tmm) cc_final: 0.7020 (ttt)
REVERT: B  202 LYS cc_start: 0.8240 (OUTLIER) cc_final: 0.7988 (mttp)
REVERT: B  228 GLU cc_start: 0.7521 (tm-30) cc_final: 0.6883 (pt0)
REVERT: B  270 MET cc_start: 0.8753 (mmm) cc_final: 0.8330 (tmm)
REVERT: B  385 LYS cc_start: 0.8063 (mttt) cc_final: 0.7677 (mptt)
REVERT: B  497 GLU cc_start: 0.7700 (tm-30) cc_final: 0.7284 (pm20)
REVERT: B  601 LEU cc_start: 0.8207 (OUTLIER) cc_final: 0.8000 (mm)
REVERT: B  654 ASN cc_start: 0.7514 (OUTLIER) cc_final: 0.7028 (t0)
REVERT: B  669 VAL cc_start: 0.8752 (OUTLIER) cc_final: 0.8414 (p)
REVERT: B  811 GLU cc_start: 0.8232 (mt-10) cc_final: 0.7535 (tp30)
  outliers start: 17
  outliers final: 11
  residues processed: 101
  average time/residue: 0.0625
  time to fit residues: 8.8098
Evaluate side-chains
  104 residues out of total 682 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 89
  time to evaluate  : 0.222 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   20 VAL
Chi-restraints excluded: chain A residue   53 VAL
Chi-restraints excluded: chain A residue   58 ASP
Chi-restraints excluded: chain A residue   94 ILE
Chi-restraints excluded: chain B residue  202 LYS
Chi-restraints excluded: chain B residue  204 ILE
Chi-restraints excluded: chain B residue  211 SER
Chi-restraints excluded: chain B residue  239 VAL
Chi-restraints excluded: chain B residue  323 ILE
Chi-restraints excluded: chain B residue  363 MET
Chi-restraints excluded: chain B residue  548 ILE
Chi-restraints excluded: chain B residue  601 LEU
Chi-restraints excluded: chain B residue  654 ASN
Chi-restraints excluded: chain B residue  669 VAL
Chi-restraints excluded: chain B residue  711 ILE
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 77
   random chunks:
   chunk 68 optimal weight:    1.9990
   chunk 21 optimal weight:    3.9990
   chunk 24 optimal weight:    0.9980
   chunk 33 optimal weight:    7.9990
   chunk 1 optimal weight:    5.9990
   chunk 26 optimal weight:    1.9990
   chunk 11 optimal weight:    0.9980
   chunk 45 optimal weight:    2.9990
   chunk 34 optimal weight:    2.9990
   chunk 67 optimal weight:    0.7980
   chunk 9 optimal weight:    0.0170
   overall best weight:    0.9620

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

Flipped N/Q/H residues before XYZ refinement:
B 466 ASN
** B 532 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 560 ASN
B 654 ASN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3919 r_free = 0.3919 target = 0.172473 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 46)----------------|
| r_work = 0.3523 r_free = 0.3523 target = 0.135508 restraints weight = 7214.625|
|-----------------------------------------------------------------------------|
r_work (start): 0.3470 rms_B_bonded: 2.11
r_work: 0.3331 rms_B_bonded: 2.88 restraints_weight: 0.5000
r_work: 0.3173 rms_B_bonded: 4.65 restraints_weight: 0.2500
r_work (final): 0.3173
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8099
moved from start:          0.3505

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.028   6415  Z= 0.121
  Angle     :  0.507   8.014   8661  Z= 0.255
  Chirality :  0.038   0.158    958
  Planarity :  0.003   0.044   1119
  Dihedral  :  3.844  20.740    842
  Min Nonbonded Distance : 2.595

Molprobity Statistics.
  All-atom Clashscore : 5.90
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.48 %
    Favored  : 96.52 %
  Rotamer:
    Outliers :  2.20 %
    Allowed  : 16.13 %
    Favored  : 81.67 %
  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:  0.74 (0.30), residues: 776
  helix:  1.80 (0.24), residues: 466
  sheet:  0.45 (0.63), residues: 67
  loop : -2.23 (0.35), residues: 243

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG B 322 
 TYR   0.008   0.001   TYR A 106 
 PHE   0.034   0.001   PHE A  17 
 HIS   0.002   0.001   HIS B 521 

Details of bonding type rmsd
  covalent geometry    : bond        0.00293 ( 6414)
  covalent geometry    : angle       0.50649 ( 8659)
  SS BOND              : bond        0.00769 (    1)
  SS BOND              : angle       0.74307 (    2)
  hydrogen bonds       : bond        0.03014 (  349)
  hydrogen bonds       : angle       3.38570 ( 1047)

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

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

  1552 Ramachandran restraints generated.
    776 Oldfield, 0 Emsley, 776 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1552 Ramachandran restraints generated.
    776 Oldfield, 0 Emsley, 776 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  103 residues out of total 682 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 88
  time to evaluate  : 0.214 
Fit side-chains
REVERT: A   39 ASP cc_start: 0.8270 (t0) cc_final: 0.8060 (p0)
REVERT: A   70 GLN cc_start: 0.7893 (mp10) cc_final: 0.7535 (mp10)
REVERT: A  118 LYS cc_start: 0.8533 (ttmm) cc_final: 0.8152 (tttp)
REVERT: A  119 SER cc_start: 0.9162 (p) cc_final: 0.8866 (m)
REVERT: A  120 LYS cc_start: 0.8900 (mtpp) cc_final: 0.8649 (mttt)
REVERT: A  152 TYR cc_start: 0.8922 (p90) cc_final: 0.8640 (p90)
REVERT: B  188 MET cc_start: 0.7639 (tmm) cc_final: 0.7005 (ttt)
REVERT: B  202 LYS cc_start: 0.8282 (OUTLIER) cc_final: 0.8023 (mttp)
REVERT: B  228 GLU cc_start: 0.7523 (tm-30) cc_final: 0.6892 (pt0)
REVERT: B  270 MET cc_start: 0.8748 (mmm) cc_final: 0.8329 (tmm)
REVERT: B  337 MET cc_start: 0.8787 (ttm) cc_final: 0.8582 (mtp)
REVERT: B  385 LYS cc_start: 0.8061 (mttt) cc_final: 0.7693 (mptt)
REVERT: B  497 GLU cc_start: 0.7840 (tm-30) cc_final: 0.7366 (pm20)
REVERT: B  654 ASN cc_start: 0.7545 (OUTLIER) cc_final: 0.7034 (t0)
REVERT: B  666 TYR cc_start: 0.7339 (m-80) cc_final: 0.7091 (m-80)
REVERT: B  669 VAL cc_start: 0.8776 (OUTLIER) cc_final: 0.8432 (p)
REVERT: B  811 GLU cc_start: 0.8255 (mt-10) cc_final: 0.7565 (tp30)
  outliers start: 15
  outliers final: 11
  residues processed: 97
  average time/residue: 0.0666
  time to fit residues: 8.9606
Evaluate side-chains
  97 residues out of total 682 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 83
  time to evaluate  : 0.227 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   53 VAL
Chi-restraints excluded: chain A residue   58 ASP
Chi-restraints excluded: chain A residue   94 ILE
Chi-restraints excluded: chain B residue  202 LYS
Chi-restraints excluded: chain B residue  204 ILE
Chi-restraints excluded: chain B residue  211 SER
Chi-restraints excluded: chain B residue  239 VAL
Chi-restraints excluded: chain B residue  323 ILE
Chi-restraints excluded: chain B residue  363 MET
Chi-restraints excluded: chain B residue  548 ILE
Chi-restraints excluded: chain B residue  601 LEU
Chi-restraints excluded: chain B residue  654 ASN
Chi-restraints excluded: chain B residue  669 VAL
Chi-restraints excluded: chain B residue  711 ILE
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 77
   random chunks:
   chunk 74 optimal weight:    2.9990
   chunk 62 optimal weight:    3.9990
   chunk 64 optimal weight:    3.9990
   chunk 60 optimal weight:    0.9990
   chunk 24 optimal weight:    1.9990
   chunk 38 optimal weight:    0.6980
   chunk 12 optimal weight:    0.4980
   chunk 20 optimal weight:    0.7980
   chunk 6 optimal weight:    6.9990
   chunk 5 optimal weight:    5.9990
   chunk 10 optimal weight:    6.9990
   overall best weight:    0.9984

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

Flipped N/Q/H residues before XYZ refinement:
B 373 ASN
** B 532 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 560 ASN
B 654 ASN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3918 r_free = 0.3918 target = 0.172478 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.3524 r_free = 0.3524 target = 0.135522 restraints weight = 7226.455|
|-----------------------------------------------------------------------------|
r_work (start): 0.3469 rms_B_bonded: 2.11
r_work: 0.3333 rms_B_bonded: 2.86 restraints_weight: 0.5000
r_work: 0.3173 rms_B_bonded: 4.64 restraints_weight: 0.2500
r_work (final): 0.3173
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8098
moved from start:          0.3520

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.027   6415  Z= 0.123
  Angle     :  0.512  10.524   8661  Z= 0.258
  Chirality :  0.038   0.163    958
  Planarity :  0.003   0.043   1119
  Dihedral  :  3.832  20.651    842
  Min Nonbonded Distance : 2.595

Molprobity Statistics.
  All-atom Clashscore : 5.58
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.87 %
    Favored  : 96.13 %
  Rotamer:
    Outliers :  2.35 %
    Allowed  : 16.13 %
    Favored  : 81.52 %
  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:  0.75 (0.30), residues: 776
  helix:  1.82 (0.24), residues: 466
  sheet:  0.47 (0.63), residues: 67
  loop : -2.24 (0.35), residues: 243

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG B 322 
 TYR   0.008   0.001   TYR B 233 
 PHE   0.029   0.001   PHE A  17 
 HIS   0.002   0.001   HIS B 521 

Details of bonding type rmsd
  covalent geometry    : bond        0.00297 ( 6414)
  covalent geometry    : angle       0.51216 ( 8659)
  SS BOND              : bond        0.00762 (    1)
  SS BOND              : angle       0.70170 (    2)
  hydrogen bonds       : bond        0.03005 (  349)
  hydrogen bonds       : angle       3.37522 ( 1047)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 1373.86 seconds
wall clock time: 24 minutes 11.60 seconds (1451.60 seconds total)