Starting phenix.real_space_refine
on Tue Mar  3 12:26:19 2026 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/7y0o_33551/03_2026/7y0o_33551.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/7y0o_33551/03_2026/7y0o_33551.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=4.4
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    model {
      file = "/net/cci-nas-00/data/ceres_data/7y0o_33551/03_2026/7y0o_33551.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/7y0o_33551/03_2026/7y0o_33551.cif"
    real_map_files = "/net/cci-nas-00/data/ceres_data/7y0o_33551/03_2026/7y0o_33551.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/7y0o_33551/03_2026/7y0o_33551.map"
  }
  resolution = 4.4
  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=   0.042 sd=   1.426
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      19      5.16       5
     C    2644      2.51       5
     N     701      2.21       5
     O     821      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 11 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: 4185
  Number of models: 1
  Model: ""
    Number of chains: 6
    Chain: "A"
      Number of atoms: 1513
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 194, 1513
          Classifications: {'peptide': 194}
          Incomplete info: {'truncation_to_alanine': 6}
          Link IDs: {'PTRANS': 11, 'TRANS': 182}
          Unresolved non-hydrogen bonds: 23
          Unresolved non-hydrogen angles: 29
          Unresolved non-hydrogen dihedrals: 17
          Planarities with less than four sites: {'ARG:plan': 1, 'ASP:plan': 3, 'GLU:plan': 2}
          Unresolved non-hydrogen planarities: 22
    Chain: "H"
      Number of atoms: 889
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 116, 889
          Classifications: {'peptide': 116}
          Link IDs: {'PTRANS': 4, 'TRANS': 111}
    Chain: "L"
      Number of atoms: 818
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 108, 818
          Classifications: {'peptide': 108}
          Incomplete info: {'truncation_to_alanine': 1}
          Link IDs: {'PCIS': 2, 'PTRANS': 4, 'TRANS': 101}
          Unresolved non-hydrogen bonds: 3
          Unresolved non-hydrogen angles: 4
          Unresolved non-hydrogen dihedrals: 2
          Planarities with less than four sites: {'ASP:plan': 1}
          Unresolved non-hydrogen planarities: 3
    Chain: "B"
      Number of atoms: 947
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 123, 947
          Classifications: {'peptide': 123}
          Link IDs: {'PTRANS': 5, 'TRANS': 117}
    Chain: "A"
      Number of atoms: 1
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 1, 1
          Classifications: {'water': 1}
    Chain: "B"
      Number of atoms: 17
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 17, 17
          Classifications: {'water': 17}
          Link IDs: {None: 16}
  Time building chain proxies: 0.96, per 1000 atoms: 0.23
  Number of scatterers: 4185
  At special positions: 0
  Unit cell: (85.6, 87.74, 111.28, 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      19     16.00
     O     821      8.00
     N     701      7.00
     C    2644      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=7, symmetry=0
    Simple disulfide: pdb=" SG  CYS A 336 " - pdb=" SG  CYS A 361 " distance=2.03
    Simple disulfide: pdb=" SG  CYS A 379 " - pdb=" SG  CYS A 432 " distance=2.05
    Simple disulfide: pdb=" SG  CYS A 391 " - pdb=" SG  CYS A 525 " distance=2.03
    Simple disulfide: pdb=" SG  CYS A 480 " - pdb=" SG  CYS A 488 " distance=2.04
    Simple disulfide: pdb=" SG  CYS H  22 " - pdb=" SG  CYS H  95 " distance=2.03
    Simple disulfide: pdb=" SG  CYS L  23 " - pdb=" SG  CYS L  88 " distance=2.04
    Simple disulfide: pdb=" SG  CYS B  22 " - pdb=" SG  CYS B  96 " distance=2.04

  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: 0.21
  Conformation dependent library (CDL) restraints added in 121.1 milliseconds
  

  1066 Ramachandran restraints generated.
    533 Oldfield, 0 Emsley, 533 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  980

  Finding SS restraints...
    Secondary structure from input PDB file:
      7 helices and 11 sheets defined
      7.4% alpha, 22.2% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.10
  Creating SS restraints...
    Processing helix  chain 'A' and resid 338 through 343
    Processing helix  chain 'A' and resid 365 through 371
    Processing helix  chain 'A' and resid 383 through 387
      removed outlier: 3.521A  pdb=" N   LEU A 387 " --> pdb=" O   PRO A 384 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 405 through 410
      removed outlier: 5.878A  pdb=" N   ARG A 408 " --> pdb=" O   ASP A 405 " (cutoff:3.500A)
      removed outlier: 3.547A  pdb=" N   ILE A 410 " --> pdb=" O   VAL A 407 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 417 through 422
      removed outlier: 3.824A  pdb=" N   ASN A 422 " --> pdb=" O   ILE A 418 " (cutoff:3.500A)
    Processing helix  chain 'H' and resid 61 through 65
      removed outlier: 3.673A  pdb=" N   GLN H  65 " --> pdb=" O   GLN H  62 " (cutoff:3.500A)
    Processing helix  chain 'L' and resid 79 through 83
    Processing sheet with id=AA1, first strand: chain 'A' and resid 356 through 358
      removed outlier: 4.393A  pdb=" N   ASN A 394 " --> pdb=" O   GLU A 516 " (cutoff:3.500A)
      removed outlier: 4.222A  pdb=" N   GLU A 516 " --> pdb=" O   ASN A 394 " (cutoff:3.500A)
      removed outlier: 3.529A  pdb=" N   ASP A 398 " --> pdb=" O   VAL A 512 " (cutoff:3.500A)
      removed outlier: 3.599A  pdb=" N   VAL A 512 " --> pdb=" O   ASP A 398 " (cutoff:3.500A)
      removed outlier: 3.608A  pdb=" N   TYR A 508 " --> pdb=" O   ILE A 402 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'A' and resid 452 through 454
    Processing sheet with id=AA3, first strand: chain 'H' and resid 16 through 17
      removed outlier: 3.942A  pdb=" N   ALA H  16 " --> pdb=" O   SER H  85 " (cutoff:3.500A)
      removed outlier: 3.917A  pdb=" N   SER H  85 " --> pdb=" O   ALA H  16 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AA3
    Processing sheet with id=AA4, first strand: chain 'H' and resid 22 through 23
      removed outlier: 3.827A  pdb=" N   GLU H  82 " --> pdb=" O   THR H  69 " (cutoff:3.500A)
    Processing sheet with id=AA5, first strand: chain 'H' and resid 45 through 51
      removed outlier: 4.998A  pdb=" N   TRP H  47 " --> pdb=" O   ARG H  38 " (cutoff:3.500A)
      removed outlier: 6.383A  pdb=" N   ARG H  38 " --> pdb=" O   TRP H  47 " (cutoff:3.500A)
      removed outlier: 4.242A  pdb=" N   GLY H  49 " --> pdb=" O   TRP H  36 " (cutoff:3.500A)
      removed outlier: 3.532A  pdb=" N   SER H  35 " --> pdb=" O   ALA H  96 " (cutoff:3.500A)
    Processing sheet with id=AA6, first strand: chain 'L' and resid 5 through 7
    Processing sheet with id=AA7, first strand: chain 'L' and resid 10 through 13
      removed outlier: 3.617A  pdb=" N   ALA L  13 " --> pdb=" O   GLU L 105 " (cutoff:3.500A)
      removed outlier: 3.531A  pdb=" N   THR L 102 " --> pdb=" O   TYR L  86 " (cutoff:3.500A)
      removed outlier: 6.831A  pdb=" N   LEU L  33 " --> pdb=" O   TYR L  49 " (cutoff:3.500A)
      removed outlier: 5.398A  pdb=" N   TYR L  49 " --> pdb=" O   LEU L  33 " (cutoff:3.500A)
      removed outlier: 6.950A  pdb=" N   TRP L  35 " --> pdb=" O   LEU L  47 " (cutoff:3.500A)
      removed outlier: 3.647A  pdb=" N   TYR L  49 " --> pdb=" O   SER L  53 " (cutoff:3.500A)
    Processing sheet with id=AA8, first strand: chain 'L' and resid 62 through 67
      removed outlier: 3.623A  pdb=" N   SER L  65 " --> pdb=" O   THR L  72 " (cutoff:3.500A)
      removed outlier: 3.862A  pdb=" N   THR L  72 " --> pdb=" O   SER L  65 " (cutoff:3.500A)
      removed outlier: 3.765A  pdb=" N   SER L  67 " --> pdb=" O   ASP L  70 " (cutoff:3.500A)
      removed outlier: 3.956A  pdb=" N   ASP L  70 " --> pdb=" O   SER L  67 " (cutoff:3.500A)
    Processing sheet with id=AA9, first strand: chain 'B' and resid 6 through 7
      removed outlier: 3.904A  pdb=" N   CYS B  22 " --> pdb=" O   VAL B  79 " (cutoff:3.500A)
      removed outlier: 3.722A  pdb=" N   VAL B  79 " --> pdb=" O   CYS B  22 " (cutoff:3.500A)
    Processing sheet with id=AB1, first strand: chain 'B' and resid 11 through 12
    Processing sheet with id=AB2, first strand: chain 'B' and resid 58 through 60
      removed outlier: 3.666A  pdb=" N   ARG B  59 " --> pdb=" O   ASP B  50 " (cutoff:3.500A)
      removed outlier: 5.392A  pdb=" N   ALA B  44 " --> pdb=" O   ALA B  40 " (cutoff:3.500A)
      removed outlier: 5.126A  pdb=" N   ALA B  40 " --> pdb=" O   ALA B  44 " (cutoff:3.500A)
      removed outlier: 7.114A  pdb=" N   TRP B  36 " --> pdb=" O   VAL B  48 " (cutoff:3.500A)

    77 hydrogen bonds defined for protein.
    171 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: 0.50

  Time building geometry restraints manager: 0.30 seconds

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

  Histogram of bond lengths:
        1.23 -     1.35: 1337
        1.35 -     1.47: 1148
        1.47 -     1.59: 1764
        1.59 -     1.71: 0
        1.71 -     1.83: 24
  Bond restraints: 4273
  Sorted by residual:
  bond pdb=" CB  GLN L  38 "
       pdb=" CG  GLN L  38 "
    ideal  model  delta    sigma   weight residual
    1.520  1.566 -0.046 3.00e-02 1.11e+03 2.31e+00
  bond pdb=" C   SER A 477 "
       pdb=" N   THR A 478 "
    ideal  model  delta    sigma   weight residual
    1.331  1.311  0.021 1.63e-02 3.76e+03 1.61e+00
  bond pdb=" CA  VAL A 483 "
       pdb=" CB  VAL A 483 "
    ideal  model  delta    sigma   weight residual
    1.547  1.568 -0.021 1.68e-02 3.54e+03 1.56e+00
  bond pdb=" CG  GLN L  38 "
       pdb=" CD  GLN L  38 "
    ideal  model  delta    sigma   weight residual
    1.516  1.546 -0.030 2.50e-02 1.60e+03 1.47e+00
  bond pdb=" C   GLY H  26 "
       pdb=" N   TYR H  27 "
    ideal  model  delta    sigma   weight residual
    1.325  1.339 -0.014 1.14e-02 7.69e+03 1.47e+00
  ... (remaining 4268 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     2.55: 5635
        2.55 -     5.10: 150
        5.10 -     7.66: 16
        7.66 -    10.21: 2
       10.21 -    12.76: 2
  Bond angle restraints: 5805
  Sorted by residual:
  angle pdb=" C   TYR H  27 "
        pdb=" CA  TYR H  27 "
        pdb=" CB  TYR H  27 "
      ideal   model   delta    sigma   weight residual
     115.79  109.40    6.39 1.19e+00 7.06e-01 2.88e+01
  angle pdb=" CB  GLN L  38 "
        pdb=" CG  GLN L  38 "
        pdb=" CD  GLN L  38 "
      ideal   model   delta    sigma   weight residual
     112.60  118.45   -5.85 1.70e+00 3.46e-01 1.19e+01
  angle pdb=" CA  LEU B 119 "
        pdb=" CB  LEU B 119 "
        pdb=" CG  LEU B 119 "
      ideal   model   delta    sigma   weight residual
     116.30  127.53  -11.23 3.50e+00 8.16e-02 1.03e+01
  angle pdb=" C   ALA L  50 "
        pdb=" N   ALA L  51 "
        pdb=" CA  ALA L  51 "
      ideal   model   delta    sigma   weight residual
     121.54  127.42   -5.88 1.91e+00 2.74e-01 9.49e+00
  angle pdb=" C   ASN A 354 "
        pdb=" N   ARG A 355 "
        pdb=" CA  ARG A 355 "
      ideal   model   delta    sigma   weight residual
     122.59  127.38   -4.79 1.57e+00 4.06e-01 9.30e+00
  ... (remaining 5800 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    16.92: 2189
       16.92 -    33.83: 248
       33.83 -    50.75: 55
       50.75 -    67.66: 8
       67.66 -    84.57: 8
  Dihedral angle restraints: 2508
    sinusoidal: 954
      harmonic: 1554
  Sorted by residual:
  dihedral pdb=" CB  CYS A 391 "
           pdb=" SG  CYS A 391 "
           pdb=" SG  CYS A 525 "
           pdb=" CB  CYS A 525 "
      ideal   model   delta sinusoidal    sigma   weight residual
      93.00   11.68   81.32     1      1.00e+01 1.00e-02 8.15e+01
  dihedral pdb=" CB  CYS L  23 "
           pdb=" SG  CYS L  23 "
           pdb=" SG  CYS L  88 "
           pdb=" CB  CYS L  88 "
      ideal   model   delta sinusoidal    sigma   weight residual
      93.00  161.12  -68.12     1      1.00e+01 1.00e-02 6.02e+01
  dihedral pdb=" CA  ASN A 481 "
           pdb=" C   ASN A 481 "
           pdb=" N   GLY A 482 "
           pdb=" CA  GLY A 482 "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00 -151.38  -28.62     0      5.00e+00 4.00e-02 3.28e+01
  ... (remaining 2505 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.085: 539
       0.085 -    0.170: 72
       0.170 -    0.254: 2
       0.254 -    0.339: 2
       0.339 -    0.424: 1
  Chirality restraints: 616
  Sorted by residual:
  chirality pdb=" CB  ILE A 410 "
            pdb=" CA  ILE A 410 "
            pdb=" CG1 ILE A 410 "
            pdb=" CG2 ILE A 410 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.64    2.22    0.42 2.00e-01 2.50e+01 4.49e+00
  chirality pdb=" CB  ILE H  52 "
            pdb=" CA  ILE H  52 "
            pdb=" CG1 ILE H  52 "
            pdb=" CG2 ILE H  52 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.64    2.36    0.28 2.00e-01 2.50e+01 1.96e+00
  chirality pdb=" CB  VAL B  98 "
            pdb=" CA  VAL B  98 "
            pdb=" CG1 VAL B  98 "
            pdb=" CG2 VAL B  98 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.63   -2.35   -0.28 2.00e-01 2.50e+01 1.94e+00
  ... (remaining 613 not shown)

  Planarity restraints: 755
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CB  TRP B  36 "   -0.018 2.00e-02 2.50e+03   1.98e-02 9.80e+00
        pdb=" CG  TRP B  36 "    0.050 2.00e-02 2.50e+03
        pdb=" CD1 TRP B  36 "   -0.027 2.00e-02 2.50e+03
        pdb=" CD2 TRP B  36 "    0.001 2.00e-02 2.50e+03
        pdb=" NE1 TRP B  36 "   -0.006 2.00e-02 2.50e+03
        pdb=" CE2 TRP B  36 "    0.013 2.00e-02 2.50e+03
        pdb=" CE3 TRP B  36 "   -0.001 2.00e-02 2.50e+03
        pdb=" CZ2 TRP B  36 "    0.000 2.00e-02 2.50e+03
        pdb=" CZ3 TRP B  36 "   -0.012 2.00e-02 2.50e+03
        pdb=" CH2 TRP B  36 "   -0.001 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   LEU A 425 "    0.044 5.00e-02 4.00e+02   6.74e-02 7.26e+00
        pdb=" N   PRO A 426 "   -0.117 5.00e-02 4.00e+02
        pdb=" CA  PRO A 426 "    0.036 5.00e-02 4.00e+02
        pdb=" CD  PRO A 426 "    0.037 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CB  TRP A 353 "    0.014 2.00e-02 2.50e+03   1.70e-02 7.20e+00
        pdb=" CG  TRP A 353 "   -0.042 2.00e-02 2.50e+03
        pdb=" CD1 TRP A 353 "    0.028 2.00e-02 2.50e+03
        pdb=" CD2 TRP A 353 "   -0.002 2.00e-02 2.50e+03
        pdb=" NE1 TRP A 353 "   -0.003 2.00e-02 2.50e+03
        pdb=" CE2 TRP A 353 "   -0.003 2.00e-02 2.50e+03
        pdb=" CE3 TRP A 353 "   -0.001 2.00e-02 2.50e+03
        pdb=" CZ2 TRP A 353 "   -0.003 2.00e-02 2.50e+03
        pdb=" CZ3 TRP A 353 "    0.011 2.00e-02 2.50e+03
        pdb=" CH2 TRP A 353 "    0.001 2.00e-02 2.50e+03
  ... (remaining 752 not shown)

  Histogram of nonbonded interaction distances:
        2.25 -     2.78: 911
        2.78 -     3.31: 3769
        3.31 -     3.84: 7051
        3.84 -     4.37: 7661
        4.37 -     4.90: 12927
  Nonbonded interactions: 32319
  Sorted by model distance:
  nonbonded pdb=" O   PRO B 111 "
            pdb=" O   HOH B 201 "
     model   vdw
     2.254 3.040
  nonbonded pdb=" O   LYS H  12 "
            pdb=" OG  SER H  87 "
     model   vdw
     2.268 3.040
  nonbonded pdb=" OG  SER B 123 "
            pdb=" O   HOH B 202 "
     model   vdw
     2.302 3.040
  nonbonded pdb=" OG1 THR B 118 "
            pdb=" O   HOH B 203 "
     model   vdw
     2.304 3.040
  nonbonded pdb=" O   VAL A 367 "
            pdb=" OG  SER A 371 "
     model   vdw
     2.309 3.040
  ... (remaining 32314 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:             4.430
  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:             0.000
  Extract box with map and model:          0.080
  Check model and map are aligned:         0.010
  Set scattering table:                    0.020
  Process input model:                     5.690
  Find NCS groups from input model:        0.010
  Set up NCS constraints:                  0.010
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.000
  Load rotamer database and sin/cos tables:1.320
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   11.570
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.5619
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   0.046   4280  Z= 0.193
  Angle     :  0.931  12.762   5819  Z= 0.481
  Chirality :  0.058   0.424    616
  Planarity :  0.006   0.067    755
  Dihedral  : 15.066  84.574   1507
  Min Nonbonded Distance : 2.254

Molprobity Statistics.
  All-atom Clashscore : 9.72
  Ramachandran Plot:
    Outliers :  0.19 %
    Allowed  :  9.76 %
    Favored  : 90.06 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.90 %
    Favored  : 99.10 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 7.69 %
    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: -3.24 (0.32), residues: 533
  helix: -4.20 (0.65), residues: 30
  sheet: -1.83 (0.42), residues: 144
  loop : -2.21 (0.29), residues: 359

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.011   0.001   ARG A 355 
 TYR   0.022   0.002   TYR B  95 
 PHE   0.014   0.002   PHE B  27 
 TRP   0.050   0.004   TRP B  36 
 HIS   0.006   0.004   HIS A 519 

Details of bonding type rmsd
  covalent geometry    : bond        0.00411 ( 4273)
  covalent geometry    : angle       0.92746 ( 5805)
  SS BOND              : bond        0.00925 (    7)
  SS BOND              : angle       1.97770 (   14)
  hydrogen bonds       : bond        0.31887 (   77)
  hydrogen bonds       : angle      11.64770 (  171)

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

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

  1066 Ramachandran restraints generated.
    533 Oldfield, 0 Emsley, 533 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1066 Ramachandran restraints generated.
    533 Oldfield, 0 Emsley, 533 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  58 residues out of total 449 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 58
  time to evaluate  : 0.155 
Fit side-chains
REVERT: A  353 TRP cc_start: 0.4437 (p-90) cc_final: 0.4105 (p-90)
REVERT: H   48 MET cc_start: 0.6276 (mpp) cc_final: 0.5899 (mpp)
REVERT: B   83 MET cc_start: 0.7793 (mpp) cc_final: 0.7583 (mpp)
  outliers start: 0
  outliers final: 0
  residues processed: 58
  average time/residue: 0.0645
  time to fit residues: 4.9237
Evaluate side-chains
  43 residues out of total 449 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 43
  time to evaluate  : 0.163 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 52
   random chunks:
   chunk 24 optimal weight:    0.0470
   chunk 48 optimal weight:    3.9990
   chunk 26 optimal weight:    2.9990
   chunk 2 optimal weight:    0.0770
   chunk 16 optimal weight:    5.9990
   chunk 32 optimal weight:    0.8980
   chunk 31 optimal weight:    1.9990
   chunk 25 optimal weight:    0.0970
   chunk 50 optimal weight:    2.9990
   chunk 19 optimal weight:    0.6980
   chunk 30 optimal weight:    0.0870
   overall best weight:    0.2012

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

Flipped N/Q/H residues before XYZ refinement:
A 481 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3511 r_free = 0.3511 target = 0.051263 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 43)----------------|
| r_work = 0.3242 r_free = 0.3242 target = 0.042007 restraints weight = 36981.478|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 31)----------------|
| r_work = 0.3274 r_free = 0.3274 target = 0.043200 restraints weight = 25292.649|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 39)----------------|
| r_work = 0.3299 r_free = 0.3299 target = 0.044087 restraints weight = 18802.701|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 27)----------------|
| r_work = 0.3315 r_free = 0.3315 target = 0.044689 restraints weight = 14854.314|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 35)----------------|
| r_work = 0.3329 r_free = 0.3329 target = 0.045186 restraints weight = 12431.535|
|-----------------------------------------------------------------------------|
r_work (final): 0.3315
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.5704
moved from start:          0.1319

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.037   4280  Z= 0.102
  Angle     :  0.613   5.525   5819  Z= 0.320
  Chirality :  0.045   0.183    616
  Planarity :  0.004   0.055    755
  Dihedral  :  5.521  27.229    599
  Min Nonbonded Distance : 2.551

Molprobity Statistics.
  All-atom Clashscore : 8.61
  Ramachandran Plot:
    Outliers :  0.19 %
    Allowed  :  8.07 %
    Favored  : 91.74 %
  Rotamer:
    Outliers :  0.23 %
    Allowed  :  4.98 %
    Favored  : 94.80 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 7.69 %
    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: -3.15 (0.33), residues: 533
  helix: -3.89 (0.68), residues: 31
  sheet: -1.98 (0.41), residues: 145
  loop : -2.06 (0.29), residues: 357

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.001   ARG H  50 
 TYR   0.017   0.001   TYR A 449 
 PHE   0.025   0.001   PHE L  98 
 TRP   0.011   0.002   TRP L  35 
 HIS   0.001   0.001   HIS A 519 

Details of bonding type rmsd
  covalent geometry    : bond        0.00232 ( 4273)
  covalent geometry    : angle       0.61008 ( 5805)
  SS BOND              : bond        0.00366 (    7)
  SS BOND              : angle       1.30820 (   14)
  hydrogen bonds       : bond        0.04472 (   77)
  hydrogen bonds       : angle       8.70474 (  171)

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

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

  1066 Ramachandran restraints generated.
    533 Oldfield, 0 Emsley, 533 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1066 Ramachandran restraints generated.
    533 Oldfield, 0 Emsley, 533 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  59 residues out of total 449 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 58
  time to evaluate  : 0.165 
Fit side-chains
REVERT: A  351 TYR cc_start: 0.7845 (p90) cc_final: 0.7540 (p90)
REVERT: A  353 TRP cc_start: 0.4661 (p-90) cc_final: 0.4403 (p-90)
REVERT: H   48 MET cc_start: 0.6650 (mpp) cc_final: 0.6317 (mpp)
REVERT: L   98 PHE cc_start: 0.4758 (m-10) cc_final: 0.4188 (m-80)
  outliers start: 1
  outliers final: 0
  residues processed: 59
  average time/residue: 0.0705
  time to fit residues: 5.3996
Evaluate side-chains
  43 residues out of total 449 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 43
  time to evaluate  : 0.161 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 52
   random chunks:
   chunk 39 optimal weight:    0.0370
   chunk 2 optimal weight:    0.2980
   chunk 9 optimal weight:    0.7980
   chunk 38 optimal weight:    0.9990
   chunk 10 optimal weight:    0.9980
   chunk 30 optimal weight:    0.6980
   chunk 41 optimal weight:    3.9990
   chunk 5 optimal weight:    1.9990
   chunk 37 optimal weight:    3.9990
   chunk 8 optimal weight:    0.7980
   chunk 1 optimal weight:    0.6980
   overall best weight:    0.5058

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

Flipped N/Q/H residues before XYZ refinement:
A 440 ASN
A 481 ASN
** L   3 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3493 r_free = 0.3493 target = 0.050688 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 32)----------------|
| r_work = 0.3221 r_free = 0.3221 target = 0.041561 restraints weight = 36992.653|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 37)----------------|
| r_work = 0.3254 r_free = 0.3254 target = 0.042783 restraints weight = 24942.011|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 31)----------------|
| r_work = 0.3279 r_free = 0.3279 target = 0.043664 restraints weight = 18355.364|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 27)----------------|
| r_work = 0.3295 r_free = 0.3295 target = 0.044285 restraints weight = 14397.727|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 34)----------------|
| r_work = 0.3310 r_free = 0.3310 target = 0.044794 restraints weight = 11963.172|
|-----------------------------------------------------------------------------|
r_work (final): 0.3299
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.5708
moved from start:          0.1567

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.040   4280  Z= 0.118
  Angle     :  0.648  10.372   5819  Z= 0.335
  Chirality :  0.045   0.173    616
  Planarity :  0.005   0.052    755
  Dihedral  :  5.712  26.567    599
  Min Nonbonded Distance : 2.383

Molprobity Statistics.
  All-atom Clashscore : 9.59
  Ramachandran Plot:
    Outliers :  0.19 %
    Allowed  :  9.38 %
    Favored  : 90.43 %
  Rotamer:
    Outliers :  0.23 %
    Allowed  :  6.56 %
    Favored  : 93.21 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 7.69 %
    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: -3.02 (0.33), residues: 533
  helix: -3.30 (0.92), residues: 25
  sheet: -1.82 (0.40), residues: 151
  loop : -2.08 (0.30), residues: 357

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.001   ARG A 355 
 TYR   0.035   0.002   TYR A 449 
 PHE   0.020   0.002   PHE L  98 
 TRP   0.011   0.002   TRP B  47 
 HIS   0.001   0.001   HIS A 519 

Details of bonding type rmsd
  covalent geometry    : bond        0.00271 ( 4273)
  covalent geometry    : angle       0.64315 ( 5805)
  SS BOND              : bond        0.00432 (    7)
  SS BOND              : angle       1.68276 (   14)
  hydrogen bonds       : bond        0.04128 (   77)
  hydrogen bonds       : angle       8.26842 (  171)

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

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

  1066 Ramachandran restraints generated.
    533 Oldfield, 0 Emsley, 533 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1066 Ramachandran restraints generated.
    533 Oldfield, 0 Emsley, 533 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  55 residues out of total 449 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 54
  time to evaluate  : 0.158 
Fit side-chains
REVERT: A  351 TYR cc_start: 0.7703 (p90) cc_final: 0.7427 (p90)
REVERT: H   48 MET cc_start: 0.6541 (mpp) cc_final: 0.6157 (mpp)
REVERT: L   98 PHE cc_start: 0.4643 (m-80) cc_final: 0.4194 (m-80)
  outliers start: 1
  outliers final: 0
  residues processed: 55
  average time/residue: 0.0604
  time to fit residues: 4.4501
Evaluate side-chains
  42 residues out of total 449 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 42
  time to evaluate  : 0.179 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 52
   random chunks:
   chunk 2 optimal weight:    0.0070
   chunk 21 optimal weight:    0.9990
   chunk 22 optimal weight:    3.9990
   chunk 49 optimal weight:    0.5980
   chunk 30 optimal weight:    5.9990
   chunk 19 optimal weight:    0.7980
   chunk 50 optimal weight:    1.9990
   chunk 36 optimal weight:    7.9990
   chunk 20 optimal weight:    0.8980
   chunk 5 optimal weight:    2.9990
   chunk 40 optimal weight:    0.7980
   overall best weight:    0.6198

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

Flipped N/Q/H residues before XYZ refinement:
A 481 ASN
** L   3 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3494 r_free = 0.3494 target = 0.050695 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 31)----------------|
| r_work = 0.3224 r_free = 0.3224 target = 0.041335 restraints weight = 36724.749|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 30)----------------|
| r_work = 0.3259 r_free = 0.3259 target = 0.042570 restraints weight = 24579.401|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 29)----------------|
| r_work = 0.3284 r_free = 0.3284 target = 0.043487 restraints weight = 18088.086|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 29)----------------|
| r_work = 0.3303 r_free = 0.3303 target = 0.044166 restraints weight = 14169.009|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 37)----------------|
| r_work = 0.3318 r_free = 0.3318 target = 0.044692 restraints weight = 11675.457|
|-----------------------------------------------------------------------------|
r_work (final): 0.3305
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.5724
moved from start:          0.1947

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.048   4280  Z= 0.130
  Angle     :  0.670  11.646   5819  Z= 0.345
  Chirality :  0.046   0.178    616
  Planarity :  0.005   0.052    755
  Dihedral  :  5.815  26.677    599
  Min Nonbonded Distance : 2.367

Molprobity Statistics.
  All-atom Clashscore : 10.82
  Ramachandran Plot:
    Outliers :  0.19 %
    Allowed  :  9.57 %
    Favored  : 90.24 %
  Rotamer:
    Outliers :  0.23 %
    Allowed  :  3.85 %
    Favored  : 95.93 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 7.69 %
    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: -3.15 (0.33), residues: 533
  helix: -3.19 (0.95), residues: 25
  sheet: -2.13 (0.38), residues: 155
  loop : -2.07 (0.30), residues: 353

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.001   ARG H  38 
 TYR   0.030   0.002   TYR A 449 
 PHE   0.021   0.002   PHE L  98 
 TRP   0.017   0.002   TRP B  47 
 HIS   0.002   0.001   HIS A 519 

Details of bonding type rmsd
  covalent geometry    : bond        0.00299 ( 4273)
  covalent geometry    : angle       0.66653 ( 5805)
  SS BOND              : bond        0.00542 (    7)
  SS BOND              : angle       1.62669 (   14)
  hydrogen bonds       : bond        0.03922 (   77)
  hydrogen bonds       : angle       7.92754 (  171)

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

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

  1066 Ramachandran restraints generated.
    533 Oldfield, 0 Emsley, 533 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1066 Ramachandran restraints generated.
    533 Oldfield, 0 Emsley, 533 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  57 residues out of total 449 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 56
  time to evaluate  : 0.163 
Fit side-chains
REVERT: A  351 TYR cc_start: 0.7772 (p90) cc_final: 0.7338 (p90)
REVERT: H    3 GLN cc_start: 0.6223 (pp30) cc_final: 0.5952 (pp30)
REVERT: H   47 TRP cc_start: 0.5566 (t60) cc_final: 0.5314 (t60)
REVERT: H   48 MET cc_start: 0.6518 (mpp) cc_final: 0.6280 (mpp)
  outliers start: 1
  outliers final: 1
  residues processed: 57
  average time/residue: 0.0703
  time to fit residues: 5.1518
Evaluate side-chains
  45 residues out of total 449 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 44
  time to evaluate  : 0.161 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 52
   random chunks:
   chunk 47 optimal weight:    4.9990
   chunk 41 optimal weight:    0.5980
   chunk 26 optimal weight:    1.9990
   chunk 4 optimal weight:    0.0770
   chunk 40 optimal weight:    2.9990
   chunk 35 optimal weight:    0.7980
   chunk 51 optimal weight:    0.2980
   chunk 32 optimal weight:    0.9980
   chunk 24 optimal weight:    0.9980
   chunk 23 optimal weight:    0.0270
   chunk 39 optimal weight:    0.9990
   overall best weight:    0.3596

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

Flipped N/Q/H residues before XYZ refinement:
A 481 ASN
H   1 GLN
** L   3 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3486 r_free = 0.3486 target = 0.050492 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.3212 r_free = 0.3212 target = 0.041368 restraints weight = 36074.060|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 31)----------------|
| r_work = 0.3245 r_free = 0.3245 target = 0.042556 restraints weight = 24433.629|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 31)----------------|
| r_work = 0.3270 r_free = 0.3270 target = 0.043457 restraints weight = 18048.146|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 37)----------------|
| r_work = 0.3288 r_free = 0.3288 target = 0.044111 restraints weight = 14169.565|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 24)----------------|
| r_work = 0.3301 r_free = 0.3301 target = 0.044577 restraints weight = 11694.998|
|-----------------------------------------------------------------------------|
r_work (final): 0.3289
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.5707
moved from start:          0.2124

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.041   4280  Z= 0.103
  Angle     :  0.616   9.502   5819  Z= 0.319
  Chirality :  0.045   0.185    616
  Planarity :  0.004   0.049    755
  Dihedral  :  5.430  25.539    599
  Min Nonbonded Distance : 2.475

Molprobity Statistics.
  All-atom Clashscore : 11.31
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  8.82 %
    Favored  : 91.18 %
  Rotamer:
    Outliers :  0.23 %
    Allowed  :  2.71 %
    Favored  : 97.06 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 7.69 %
    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: -3.04 (0.33), residues: 533
  helix: -3.16 (0.94), residues: 25
  sheet: -2.04 (0.38), residues: 155
  loop : -1.99 (0.30), residues: 353

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.001   ARG B  85 
 TYR   0.022   0.001   TYR A 449 
 PHE   0.010   0.001   PHE A 490 
 TRP   0.006   0.001   TRP L  35 
 HIS   0.001   0.000   HIS A 519 

Details of bonding type rmsd
  covalent geometry    : bond        0.00236 ( 4273)
  covalent geometry    : angle       0.61269 ( 5805)
  SS BOND              : bond        0.00468 (    7)
  SS BOND              : angle       1.37257 (   14)
  hydrogen bonds       : bond        0.03416 (   77)
  hydrogen bonds       : angle       7.58358 (  171)

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

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

  1066 Ramachandran restraints generated.
    533 Oldfield, 0 Emsley, 533 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1066 Ramachandran restraints generated.
    533 Oldfield, 0 Emsley, 533 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  58 residues out of total 449 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 57
  time to evaluate  : 0.197 
Fit side-chains
REVERT: A  351 TYR cc_start: 0.7795 (p90) cc_final: 0.7324 (p90)
REVERT: H   47 TRP cc_start: 0.5697 (t60) cc_final: 0.5368 (t60)
REVERT: B   34 MET cc_start: 0.6647 (mtt) cc_final: 0.6272 (mtt)
  outliers start: 1
  outliers final: 0
  residues processed: 58
  average time/residue: 0.0658
  time to fit residues: 4.8845
Evaluate side-chains
  45 residues out of total 449 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 45
  time to evaluate  : 0.109 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 52
   random chunks:
   chunk 11 optimal weight:    1.9990
   chunk 32 optimal weight:    1.9990
   chunk 44 optimal weight:    4.9990
   chunk 16 optimal weight:    0.7980
   chunk 28 optimal weight:    6.9990
   chunk 47 optimal weight:    0.9990
   chunk 6 optimal weight:    0.5980
   chunk 4 optimal weight:    0.7980
   chunk 29 optimal weight:    0.0270
   chunk 22 optimal weight:    0.8980
   chunk 18 optimal weight:    0.9980
   overall best weight:    0.6238

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

Flipped N/Q/H residues before XYZ refinement:
A 448 ASN
A 481 ASN
** L   3 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3490 r_free = 0.3490 target = 0.050625 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.3222 r_free = 0.3222 target = 0.041435 restraints weight = 38382.549|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 30)----------------|
| r_work = 0.3257 r_free = 0.3257 target = 0.042670 restraints weight = 25299.980|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 33)----------------|
| r_work = 0.3284 r_free = 0.3284 target = 0.043597 restraints weight = 18418.668|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 28)----------------|
| r_work = 0.3302 r_free = 0.3302 target = 0.044265 restraints weight = 14334.317|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 38)----------------|
| r_work = 0.3317 r_free = 0.3317 target = 0.044778 restraints weight = 11754.483|
|-----------------------------------------------------------------------------|
r_work (final): 0.3304
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.5718
moved from start:          0.2256

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.046   4280  Z= 0.129
  Angle     :  0.668  12.876   5819  Z= 0.341
  Chirality :  0.046   0.195    616
  Planarity :  0.005   0.051    755
  Dihedral  :  5.764  26.659    599
  Min Nonbonded Distance : 2.438

Molprobity Statistics.
  All-atom Clashscore : 12.79
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  : 10.32 %
    Favored  : 89.68 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  4.52 %
    Favored  : 95.48 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 7.69 %
    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: -3.05 (0.33), residues: 533
  helix: -2.42 (1.20), residues: 19
  sheet: -2.08 (0.38), residues: 155
  loop : -2.07 (0.30), residues: 359

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.001   ARG H  38 
 TYR   0.025   0.002   TYR A 449 
 PHE   0.012   0.002   PHE B 105 
 TRP   0.006   0.002   TRP H  47 
 HIS   0.001   0.001   HIS A 519 

Details of bonding type rmsd
  covalent geometry    : bond        0.00295 ( 4273)
  covalent geometry    : angle       0.66043 ( 5805)
  SS BOND              : bond        0.00664 (    7)
  SS BOND              : angle       2.08942 (   14)
  hydrogen bonds       : bond        0.03525 (   77)
  hydrogen bonds       : angle       7.60629 (  171)

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

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

  1066 Ramachandran restraints generated.
    533 Oldfield, 0 Emsley, 533 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1066 Ramachandran restraints generated.
    533 Oldfield, 0 Emsley, 533 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  55 residues out of total 449 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 55
  time to evaluate  : 0.141 
Fit side-chains
REVERT: A  351 TYR cc_start: 0.7644 (p90) cc_final: 0.7204 (p90)
REVERT: H   47 TRP cc_start: 0.5633 (t60) cc_final: 0.5357 (t60)
REVERT: H   48 MET cc_start: 0.6604 (mpp) cc_final: 0.6384 (mpp)
REVERT: B   34 MET cc_start: 0.6670 (mtt) cc_final: 0.6356 (mtt)
  outliers start: 0
  outliers final: 0
  residues processed: 55
  average time/residue: 0.0729
  time to fit residues: 5.0811
Evaluate side-chains
  41 residues out of total 449 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 41
  time to evaluate  : 0.190 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 52
   random chunks:
   chunk 23 optimal weight:    2.9990
   chunk 42 optimal weight:    1.9990
   chunk 46 optimal weight:    0.0770
   chunk 14 optimal weight:    0.9980
   chunk 19 optimal weight:    0.9980
   chunk 10 optimal weight:    1.9990
   chunk 31 optimal weight:    3.9990
   chunk 9 optimal weight:    0.5980
   chunk 0 optimal weight:    1.9990
   chunk 51 optimal weight:    2.9990
   chunk 12 optimal weight:    0.0980
   overall best weight:    0.5538

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

Flipped N/Q/H residues before XYZ refinement:
A 481 ASN
** H  59 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** L   3 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3485 r_free = 0.3485 target = 0.050188 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.3208 r_free = 0.3208 target = 0.041186 restraints weight = 37742.771|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 29)----------------|
| r_work = 0.3244 r_free = 0.3244 target = 0.042406 restraints weight = 25105.960|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 36)----------------|
| r_work = 0.3269 r_free = 0.3269 target = 0.043295 restraints weight = 18389.232|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 33)----------------|
| r_work = 0.3288 r_free = 0.3288 target = 0.043966 restraints weight = 14347.862|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 34)----------------|
| r_work = 0.3304 r_free = 0.3304 target = 0.044474 restraints weight = 11769.594|
|-----------------------------------------------------------------------------|
r_work (final): 0.3293
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.5708
moved from start:          0.2349

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.045   4280  Z= 0.122
  Angle     :  0.667  11.035   5819  Z= 0.341
  Chirality :  0.046   0.201    616
  Planarity :  0.005   0.050    755
  Dihedral  :  5.761  26.073    599
  Min Nonbonded Distance : 2.439

Molprobity Statistics.
  All-atom Clashscore : 11.68
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  9.76 %
    Favored  : 90.24 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  1.58 %
    Favored  : 98.42 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 7.69 %
    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: -3.09 (0.33), residues: 533
  helix: -3.23 (0.92), residues: 25
  sheet: -2.09 (0.38), residues: 155
  loop : -2.02 (0.30), residues: 353

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.001   ARG H  38 
 TYR   0.023   0.002   TYR A 449 
 PHE   0.012   0.002   PHE A 400 
 TRP   0.030   0.002   TRP B  36 
 HIS   0.001   0.001   HIS A 519 

Details of bonding type rmsd
  covalent geometry    : bond        0.00280 ( 4273)
  covalent geometry    : angle       0.65734 ( 5805)
  SS BOND              : bond        0.00672 (    7)
  SS BOND              : angle       2.34328 (   14)
  hydrogen bonds       : bond        0.03389 (   77)
  hydrogen bonds       : angle       7.55819 (  171)

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

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

  1066 Ramachandran restraints generated.
    533 Oldfield, 0 Emsley, 533 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1066 Ramachandran restraints generated.
    533 Oldfield, 0 Emsley, 533 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  53 residues out of total 449 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 53
  time to evaluate  : 0.166 
Fit side-chains
REVERT: A  351 TYR cc_start: 0.7601 (p90) cc_final: 0.7115 (p90)
REVERT: H   47 TRP cc_start: 0.5579 (t60) cc_final: 0.5245 (t60)
  outliers start: 0
  outliers final: 0
  residues processed: 53
  average time/residue: 0.0764
  time to fit residues: 5.1359
Evaluate side-chains
  39 residues out of total 449 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 39
  time to evaluate  : 0.173 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 52
   random chunks:
   chunk 2 optimal weight:    0.7980
   chunk 45 optimal weight:    0.7980
   chunk 15 optimal weight:    0.4980
   chunk 17 optimal weight:    0.8980
   chunk 38 optimal weight:    5.9990
   chunk 21 optimal weight:    0.9990
   chunk 25 optimal weight:    0.8980
   chunk 36 optimal weight:    5.9990
   chunk 6 optimal weight:    0.5980
   chunk 46 optimal weight:    0.7980
   chunk 18 optimal weight:    0.0170
   overall best weight:    0.5418

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

Flipped N/Q/H residues before XYZ refinement:
A 481 ASN
** L   3 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3482 r_free = 0.3482 target = 0.050152 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 23)----------------|
| r_work = 0.3207 r_free = 0.3207 target = 0.041177 restraints weight = 37084.250|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 30)----------------|
| r_work = 0.3241 r_free = 0.3241 target = 0.042384 restraints weight = 25122.996|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 29)----------------|
| r_work = 0.3266 r_free = 0.3266 target = 0.043278 restraints weight = 18380.416|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 30)----------------|
| r_work = 0.3284 r_free = 0.3284 target = 0.043930 restraints weight = 14343.250|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 29)----------------|
| r_work = 0.3298 r_free = 0.3298 target = 0.044422 restraints weight = 11789.057|
|-----------------------------------------------------------------------------|
r_work (final): 0.3286
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.5715
moved from start:          0.2476

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.045   4280  Z= 0.121
  Angle     :  0.659  10.632   5819  Z= 0.338
  Chirality :  0.046   0.206    616
  Planarity :  0.005   0.049    755
  Dihedral  :  5.777  25.808    599
  Min Nonbonded Distance : 2.433

Molprobity Statistics.
  All-atom Clashscore : 12.05
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  : 11.44 %
    Favored  : 88.56 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  2.49 %
    Favored  : 97.51 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 7.69 %
    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: -3.08 (0.33), residues: 533
  helix: -2.66 (1.10), residues: 19
  sheet: -2.04 (0.38), residues: 154
  loop : -2.10 (0.30), residues: 360

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.001   ARG H  38 
 TYR   0.033   0.002   TYR A 449 
 PHE   0.012   0.002   PHE B 105 
 TRP   0.006   0.001   TRP H  47 
 HIS   0.001   0.001   HIS A 519 

Details of bonding type rmsd
  covalent geometry    : bond        0.00277 ( 4273)
  covalent geometry    : angle       0.65197 ( 5805)
  SS BOND              : bond        0.00674 (    7)
  SS BOND              : angle       2.12119 (   14)
  hydrogen bonds       : bond        0.03297 (   77)
  hydrogen bonds       : angle       7.48547 (  171)

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

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

  1066 Ramachandran restraints generated.
    533 Oldfield, 0 Emsley, 533 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1066 Ramachandran restraints generated.
    533 Oldfield, 0 Emsley, 533 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  53 residues out of total 449 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 53
  time to evaluate  : 0.168 
Fit side-chains
REVERT: A  351 TYR cc_start: 0.7641 (p90) cc_final: 0.7075 (p90)
REVERT: H   47 TRP cc_start: 0.5594 (t60) cc_final: 0.5333 (t60)
REVERT: H   48 MET cc_start: 0.6711 (mpp) cc_final: 0.6484 (mpp)
  outliers start: 0
  outliers final: 0
  residues processed: 53
  average time/residue: 0.0683
  time to fit residues: 4.6900
Evaluate side-chains
  40 residues out of total 449 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 40
  time to evaluate  : 0.151 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 52
   random chunks:
   chunk 23 optimal weight:    3.9990
   chunk 2 optimal weight:    0.5980
   chunk 40 optimal weight:    2.9990
   chunk 6 optimal weight:    0.8980
   chunk 48 optimal weight:    0.7980
   chunk 14 optimal weight:    0.5980
   chunk 13 optimal weight:    0.3980
   chunk 20 optimal weight:    0.9980
   chunk 16 optimal weight:    0.7980
   chunk 8 optimal weight:    1.9990
   chunk 46 optimal weight:    0.6980
   overall best weight:    0.6180

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

Flipped N/Q/H residues before XYZ refinement:
A 481 ASN
** L   3 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 116 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3474 r_free = 0.3474 target = 0.050087 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.3201 r_free = 0.3201 target = 0.040837 restraints weight = 38405.588|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 36)----------------|
| r_work = 0.3237 r_free = 0.3237 target = 0.042084 restraints weight = 25299.422|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 28)----------------|
| r_work = 0.3262 r_free = 0.3262 target = 0.042980 restraints weight = 18420.605|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 31)----------------|
| r_work = 0.3281 r_free = 0.3281 target = 0.043648 restraints weight = 14416.686|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 30)----------------|
| r_work = 0.3296 r_free = 0.3296 target = 0.044161 restraints weight = 11837.442|
|-----------------------------------------------------------------------------|
r_work (final): 0.3279
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.5717
moved from start:          0.2614

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.046   4280  Z= 0.136
  Angle     :  0.697  11.713   5819  Z= 0.358
  Chirality :  0.047   0.205    616
  Planarity :  0.005   0.049    755
  Dihedral  :  5.931  25.895    599
  Min Nonbonded Distance : 2.427

Molprobity Statistics.
  All-atom Clashscore : 13.53
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  : 11.26 %
    Favored  : 88.74 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  1.13 %
    Favored  : 98.87 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 7.69 %
    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: -3.17 (0.33), residues: 533
  helix: -3.35 (0.86), residues: 25
  sheet: -2.13 (0.38), residues: 154
  loop : -2.08 (0.30), residues: 354

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.001   ARG H  38 
 TYR   0.038   0.002   TYR A 449 
 PHE   0.031   0.002   PHE L  98 
 TRP   0.037   0.002   TRP B  36 
 HIS   0.001   0.001   HIS A 519 

Details of bonding type rmsd
  covalent geometry    : bond        0.00310 ( 4273)
  covalent geometry    : angle       0.69063 ( 5805)
  SS BOND              : bond        0.00654 (    7)
  SS BOND              : angle       2.09897 (   14)
  hydrogen bonds       : bond        0.03525 (   77)
  hydrogen bonds       : angle       7.56969 (  171)

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

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

  1066 Ramachandran restraints generated.
    533 Oldfield, 0 Emsley, 533 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1066 Ramachandran restraints generated.
    533 Oldfield, 0 Emsley, 533 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  52 residues out of total 449 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 52
  time to evaluate  : 0.167 
Fit side-chains
REVERT: A  351 TYR cc_start: 0.7713 (p90) cc_final: 0.7167 (p90)
REVERT: H    3 GLN cc_start: 0.6623 (pp30) cc_final: 0.6417 (pp30)
REVERT: H   48 MET cc_start: 0.6647 (mpp) cc_final: 0.6447 (mpp)
REVERT: L   98 PHE cc_start: 0.4338 (m-10) cc_final: 0.3803 (m-80)
REVERT: B   34 MET cc_start: 0.6392 (mtt) cc_final: 0.6097 (mtt)
  outliers start: 0
  outliers final: 0
  residues processed: 52
  average time/residue: 0.0730
  time to fit residues: 4.8313
Evaluate side-chains
  39 residues out of total 449 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 39
  time to evaluate  : 0.141 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 52
   random chunks:
   chunk 20 optimal weight:    0.9980
   chunk 2 optimal weight:    0.6980
   chunk 25 optimal weight:    0.8980
   chunk 29 optimal weight:    1.9990
   chunk 50 optimal weight:    0.0770
   chunk 18 optimal weight:    0.8980
   chunk 38 optimal weight:    0.9980
   chunk 42 optimal weight:    0.0970
   chunk 13 optimal weight:    0.4980
   chunk 51 optimal weight:    0.8980
   chunk 9 optimal weight:    0.5980
   overall best weight:    0.3936

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

Flipped N/Q/H residues before XYZ refinement:
** A 439 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 481 ASN
** L   3 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3477 r_free = 0.3477 target = 0.050050 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.3202 r_free = 0.3202 target = 0.041004 restraints weight = 36812.057|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 28)----------------|
| r_work = 0.3236 r_free = 0.3236 target = 0.042207 restraints weight = 24547.641|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 37)----------------|
| r_work = 0.3262 r_free = 0.3262 target = 0.043113 restraints weight = 17994.579|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 32)----------------|
| r_work = 0.3280 r_free = 0.3280 target = 0.043744 restraints weight = 14079.635|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 27)----------------|
| r_work = 0.3292 r_free = 0.3292 target = 0.044187 restraints weight = 11592.463|
|-----------------------------------------------------------------------------|
r_work (final): 0.3281
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.5709
moved from start:          0.2672

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.044   4280  Z= 0.112
  Angle     :  0.655   9.362   5819  Z= 0.338
  Chirality :  0.046   0.217    616
  Planarity :  0.004   0.046    755
  Dihedral  :  5.647  25.482    599
  Min Nonbonded Distance : 2.426

Molprobity Statistics.
  All-atom Clashscore : 11.68
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  : 10.13 %
    Favored  : 89.87 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.90 %
    Favored  : 99.10 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 7.69 %
    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: -3.15 (0.33), residues: 533
  helix: -3.61 (0.71), residues: 31
  sheet: -1.76 (0.40), residues: 142
  loop : -2.20 (0.30), residues: 360

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.001   ARG B  85 
 TYR   0.030   0.002   TYR A 449 
 PHE   0.027   0.002   PHE L  98 
 TRP   0.010   0.001   TRP H  47 
 HIS   0.001   0.001   HIS A 519 

Details of bonding type rmsd
  covalent geometry    : bond        0.00260 ( 4273)
  covalent geometry    : angle       0.64940 ( 5805)
  SS BOND              : bond        0.00566 (    7)
  SS BOND              : angle       1.84378 (   14)
  hydrogen bonds       : bond        0.03410 (   77)
  hydrogen bonds       : angle       7.43186 (  171)

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

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

  1066 Ramachandran restraints generated.
    533 Oldfield, 0 Emsley, 533 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1066 Ramachandran restraints generated.
    533 Oldfield, 0 Emsley, 533 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  56 residues out of total 449 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 56
  time to evaluate  : 0.171 
Fit side-chains
   revert: symmetry clash
REVERT: L   98 PHE cc_start: 0.4922 (m-10) cc_final: 0.4334 (m-80)
REVERT: B    2 GLU cc_start: 0.5659 (mp0) cc_final: 0.4807 (mm-30)
  outliers start: 0
  outliers final: 0
  residues processed: 56
  average time/residue: 0.0626
  time to fit residues: 4.5803
Evaluate side-chains
  39 residues out of total 449 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 39
  time to evaluate  : 0.153 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 52
   random chunks:
   chunk 47 optimal weight:    2.9990
   chunk 32 optimal weight:    2.9990
   chunk 7 optimal weight:    0.8980
   chunk 21 optimal weight:    0.9980
   chunk 19 optimal weight:    1.9990
   chunk 11 optimal weight:    2.9990
   chunk 40 optimal weight:    2.9990
   chunk 48 optimal weight:    0.9990
   chunk 5 optimal weight:    0.0470
   chunk 51 optimal weight:    0.9990
   chunk 0 optimal weight:    1.9990
   overall best weight:    0.7882

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

Flipped N/Q/H residues before XYZ refinement:
** A 439 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 481 ASN
** L   3 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3460 r_free = 0.3460 target = 0.049304 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 43)----------------|
| r_work = 0.3176 r_free = 0.3176 target = 0.040289 restraints weight = 37448.943|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 32)----------------|
| r_work = 0.3210 r_free = 0.3210 target = 0.041447 restraints weight = 25114.127|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 29)----------------|
| r_work = 0.3235 r_free = 0.3235 target = 0.042323 restraints weight = 18536.443|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 29)----------------|
| r_work = 0.3254 r_free = 0.3254 target = 0.042963 restraints weight = 14540.998|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 28)----------------|
| r_work = 0.3268 r_free = 0.3268 target = 0.043431 restraints weight = 11985.760|
|-----------------------------------------------------------------------------|
r_work (final): 0.3256
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.5721
moved from start:          0.2837

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.049   4280  Z= 0.153
  Angle     :  0.746  12.935   5819  Z= 0.383
  Chirality :  0.048   0.227    616
  Planarity :  0.005   0.048    755
  Dihedral  :  6.205  26.398    599
  Min Nonbonded Distance : 2.421

Molprobity Statistics.
  All-atom Clashscore : 14.27
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  : 12.20 %
    Favored  : 87.80 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  1.13 %
    Favored  : 98.87 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 7.69 %
    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: -3.34 (0.32), residues: 533
  helix: -2.87 (1.08), residues: 19
  sheet: -2.15 (0.38), residues: 149
  loop : -2.34 (0.29), residues: 365

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.001   ARG H  38 
 TYR   0.040   0.002   TYR A 449 
 PHE   0.030   0.002   PHE L  98 
 TRP   0.020   0.002   TRP H  47 
 HIS   0.002   0.001   HIS A 519 

Details of bonding type rmsd
  covalent geometry    : bond        0.00348 ( 4273)
  covalent geometry    : angle       0.73454 ( 5805)
  SS BOND              : bond        0.00828 (    7)
  SS BOND              : angle       2.71832 (   14)
  hydrogen bonds       : bond        0.03865 (   77)
  hydrogen bonds       : angle       7.72648 (  171)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 966.87 seconds
wall clock time: 17 minutes 18.05 seconds (1038.05 seconds total)