Starting phenix.real_space_refine
on Wed Sep 17 12:27:23 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/8xvz_38724/09_2025/8xvz_38724.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/8xvz_38724/09_2025/8xvz_38724.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.78
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/8xvz_38724/09_2025/8xvz_38724.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/8xvz_38724/09_2025/8xvz_38724.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/8xvz_38724/09_2025/8xvz_38724.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/8xvz_38724/09_2025/8xvz_38724.cif"
  }
  resolution = 3.78
  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=   0.008 sd=   0.059
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      26      5.16       5
     C    5745      2.51       5
     N    1389      2.21       5
     O    1530      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 21 residue(s): 0.01s

  Monomer Library directory:
    "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5805/lib/python3.9/site-packages/chem_data/mon_lib"
  Total number of atoms: 8690
  Number of models: 1
  Model: ""
    Number of chains: 2
    Chain: "A"
      Number of atoms: 4438
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 622, 4438
          Classifications: {'peptide': 622}
          Incomplete info: {'truncation_to_alanine': 138}
          Link IDs: {'PTRANS': 29, 'TRANS': 592}
          Chain breaks: 3
          Unresolved non-hydrogen bonds: 600
          Unresolved non-hydrogen angles: 750
          Unresolved non-hydrogen dihedrals: 519
          Unresolved non-hydrogen chiralities: 37
          Planarities with less than four sites: {'PHE:plan': 10, 'TRP:plan': 4, 'ARG:plan': 15, 'TYR:plan': 7, 'ASN:plan1': 5, 'GLU:plan': 19, 'GLN:plan1': 9, 'ASP:plan': 4}
          Unresolved non-hydrogen planarities: 359
    Chain: "B"
      Number of atoms: 4252
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 601, 4252
          Classifications: {'peptide': 601}
          Incomplete info: {'truncation_to_alanine': 141}
          Link IDs: {'CIS': 1, 'PTRANS': 27, 'TRANS': 572}
          Chain breaks: 4
          Unresolved non-hydrogen bonds: 618
          Unresolved non-hydrogen angles: 773
          Unresolved non-hydrogen dihedrals: 535
          Unresolved non-hydrogen chiralities: 37
          Planarities with less than four sites: {'PHE:plan': 10, 'TRP:plan': 4, 'ARG:plan': 16, 'TYR:plan': 8, 'ASN:plan1': 5, 'GLU:plan': 20, 'GLN:plan1': 9, 'ASP:plan': 4}
          Unresolved non-hydrogen planarities: 375
  Time building chain proxies: 2.32, per 1000 atoms: 0.27
  Number of scatterers: 8690
  At special positions: 0
  Unit cell: (75.96, 133.985, 98.115, 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      26     16.00
     O    1530      8.00
     N    1389      7.00
     C    5745      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=0, symmetry=0

  Automatic linking
    Parameters for automatic linking
      Linking & cutoffs
        Metal                : Auto  - 3.00
        Amino acid           : True  - 1.90
        Carbohydrate         : True  - 1.99
        Ligands              : True  - 1.99
        Small molecules      : False - 1.98
        Amino acid - RNA/DNA : False
      
  Number of custom bonds: simple=0, symmetry=0
  Time building additional restraints: 0.89
  Conformation dependent library (CDL) restraints added in 401.0 milliseconds
  
  Enol-peptide restraints added in 953.7 nanoseconds
  

  2410 Ramachandran restraints generated.
    1205 Oldfield, 0 Emsley, 1205 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  2338

  Finding SS restraints...
    Secondary structure from input PDB file:
      52 helices and 2 sheets defined
      68.6% alpha, 1.6% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.27
  Creating SS restraints...
    Processing helix  chain 'A' and resid 3 through 26
      removed outlier: 4.132A  pdb=" N   LEU A   7 " --> pdb=" O   PHE A   3 " (cutoff:3.500A)
      removed outlier: 3.760A  pdb=" N   SER A  13 " --> pdb=" O   SER A   9 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 36 through 42
    Processing helix  chain 'A' and resid 56 through 67
      removed outlier: 3.562A  pdb=" N   TRP A  61 " --> pdb=" O   ASN A  57 " (cutoff:3.500A)
      removed outlier: 3.514A  pdb=" N   ARG A  63 " --> pdb=" O   PHE A  59 " (cutoff:3.500A)
      removed outlier: 4.267A  pdb=" N   GLU A  64 " --> pdb=" O   ALA A  60 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 69 through 77
    Processing helix  chain 'A' and resid 78 through 98
      removed outlier: 3.791A  pdb=" N   ALA A  82 " --> pdb=" O   GLY A  78 " (cutoff:3.500A)
      removed outlier: 3.663A  pdb=" N   ILE A  94 " --> pdb=" O   THR A  90 " (cutoff:3.500A)
      removed outlier: 3.755A  pdb=" N   SER A  98 " --> pdb=" O   ILE A  94 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 102 through 107
    Processing helix  chain 'A' and resid 151 through 185
      removed outlier: 4.101A  pdb=" N   SER A 175 " --> pdb=" O   TYR A 171 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 207 through 220
    Processing helix  chain 'A' and resid 233 through 248
    Processing helix  chain 'A' and resid 291 through 305
      removed outlier: 3.516A  pdb=" N   GLU A 305 " --> pdb=" O   ALA A 301 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 317 through 326
    Processing helix  chain 'A' and resid 355 through 378
      removed outlier: 3.524A  pdb=" N   ARG A 359 " --> pdb=" O   LYS A 355 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 379 through 388
    Processing helix  chain 'A' and resid 390 through 395
      removed outlier: 3.696A  pdb=" N   ARG A 395 " --> pdb=" O   LYS A 391 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 396 through 405
      removed outlier: 5.269A  pdb=" N   LYS A 401 " --> pdb=" O   PRO A 398 " (cutoff:3.500A)
      Proline residue:  A 402  - end of helix
    Processing helix  chain 'A' and resid 409 through 439
      removed outlier: 3.898A  pdb=" N   LEU A 413 " --> pdb=" O   ILE A 409 " (cutoff:3.500A)
      Proline residue:  A 418  - end of helix
      Proline residue:  A 430  - end of helix
      removed outlier: 3.569A  pdb=" N   LEU A 436 " --> pdb=" O   LEU A 432 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 445 through 465
    Processing helix  chain 'A' and resid 465 through 476
    Processing helix  chain 'A' and resid 489 through 525
      Proline residue:  A 499  - end of helix
    Processing helix  chain 'A' and resid 525 through 537
      removed outlier: 3.539A  pdb=" N   LYS A 533 " --> pdb=" O   ILE A 529 " (cutoff:3.500A)
      removed outlier: 3.635A  pdb=" N   LYS A 534 " --> pdb=" O   PHE A 530 " (cutoff:3.500A)
      removed outlier: 4.125A  pdb=" N   LYS A 535 " --> pdb=" O   HIS A 531 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 557 through 572
      removed outlier: 3.530A  pdb=" N   GLY A 561 " --> pdb=" O   THR A 557 " (cutoff:3.500A)
      removed outlier: 4.175A  pdb=" N   ILE A 565 " --> pdb=" O   GLY A 561 " (cutoff:3.500A)
      removed outlier: 4.155A  pdb=" N   LEU A 566 " --> pdb=" O   ASP A 562 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 576 through 578
      No H-bonds generated for 'chain 'A' and resid 576 through 578'
    Processing helix  chain 'A' and resid 579 through 596
    Processing helix  chain 'A' and resid 612 through 637
      removed outlier: 3.515A  pdb=" N   ILE A 616 " --> pdb=" O   MET A 612 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 646 through 662
    Processing helix  chain 'A' and resid 672 through 679
      removed outlier: 3.656A  pdb=" N   GLU A 679 " --> pdb=" O   VAL A 675 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 686 through 694
      removed outlier: 3.854A  pdb=" N   ARG A 691 " --> pdb=" O   GLU A 687 " (cutoff:3.500A)
      removed outlier: 4.865A  pdb=" N   ALA A 692 " --> pdb=" O   GLU A 688 " (cutoff:3.500A)
      removed outlier: 3.762A  pdb=" N   TYR A 693 " --> pdb=" O   ILE A 689 " (cutoff:3.500A)
      removed outlier: 3.572A  pdb=" N   ILE A 694 " --> pdb=" O   PHE A 690 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 4 through 27
      removed outlier: 3.737A  pdb=" N   VAL B   8 " --> pdb=" O   GLY B   4 " (cutoff:3.500A)
      removed outlier: 4.301A  pdb=" N   LEU B  27 " --> pdb=" O   LEU B  23 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 28 through 33
      removed outlier: 3.671A  pdb=" N   SER B  31 " --> pdb=" O   SER B  28 " (cutoff:3.500A)
      removed outlier: 4.141A  pdb=" N   GLY B  32 " --> pdb=" O   ARG B  29 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 69 through 77
      removed outlier: 3.967A  pdb=" N   VAL B  74 " --> pdb=" O   GLU B  70 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 78 through 98
      removed outlier: 3.695A  pdb=" N   ALA B  82 " --> pdb=" O   GLY B  78 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 102 through 107
      removed outlier: 3.602A  pdb=" N   LEU B 106 " --> pdb=" O   LEU B 102 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 148 through 184
      removed outlier: 3.566A  pdb=" N   PHE B 152 " --> pdb=" O   ARG B 148 " (cutoff:3.500A)
      removed outlier: 3.898A  pdb=" N   TYR B 164 " --> pdb=" O   SER B 160 " (cutoff:3.500A)
      removed outlier: 3.617A  pdb=" N   SER B 184 " --> pdb=" O   GLN B 180 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 207 through 220
    Processing helix  chain 'B' and resid 237 through 250
      removed outlier: 3.530A  pdb=" N   LEU B 250 " --> pdb=" O   TYR B 246 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 288 through 303
    Processing helix  chain 'B' and resid 317 through 326
      removed outlier: 3.797A  pdb=" N   GLN B 326 " --> pdb=" O   ALA B 322 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 343 through 347
      removed outlier: 3.717A  pdb=" N   LEU B 347 " --> pdb=" O   PRO B 344 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 355 through 379
      removed outlier: 3.737A  pdb=" N   ILE B 360 " --> pdb=" O   LEU B 356 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 379 through 386
    Processing helix  chain 'B' and resid 411 through 428
      Proline residue:  B 418  - end of helix
      removed outlier: 3.743A  pdb=" N   MET B 428 " --> pdb=" O   VAL B 424 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 430 through 439
    Processing helix  chain 'B' and resid 444 through 477
      removed outlier: 4.270A  pdb=" N   ARG B 450 " --> pdb=" O   SER B 446 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 489 through 513
      Proline residue:  B 499  - end of helix
      removed outlier: 4.454A  pdb=" N   LEU B 506 " --> pdb=" O   ALA B 502 " (cutoff:3.500A)
      removed outlier: 4.059A  pdb=" N   VAL B 509 " --> pdb=" O   PHE B 505 " (cutoff:3.500A)
      removed outlier: 3.911A  pdb=" N   ALA B 510 " --> pdb=" O   LEU B 506 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 514 through 523
      removed outlier: 3.578A  pdb=" N   SER B 522 " --> pdb=" O   GLY B 518 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 523 through 536
    Processing helix  chain 'B' and resid 560 through 571
      removed outlier: 4.316A  pdb=" N   ILE B 565 " --> pdb=" O   GLY B 561 " (cutoff:3.500A)
      removed outlier: 4.973A  pdb=" N   LEU B 566 " --> pdb=" O   ASP B 562 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 576 through 601
      removed outlier: 4.013A  pdb=" N   LEU B 580 " --> pdb=" O   ALA B 576 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 612 through 638
    Processing helix  chain 'B' and resid 642 through 664
      Proline residue:  B 648  - end of helix
    Processing helix  chain 'B' and resid 672 through 678
    Processing helix  chain 'B' and resid 685 through 692
      removed outlier: 3.884A  pdb=" N   ILE B 689 " --> pdb=" O   ASP B 685 " (cutoff:3.500A)
    Processing sheet with id=AA1, first strand: chain 'A' and resid 193 through 194
      removed outlier: 3.590A  pdb=" N   VAL A 313 " --> pdb=" O   ILE A 194 " (cutoff:3.500A)
      removed outlier: 5.839A  pdb=" N   ALA A 310 " --> pdb=" O   ALA A 230 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'B' and resid 194 through 196
      removed outlier: 3.680A  pdb=" N   ARG B 226 " --> pdb=" O   PHE B 314 " (cutoff:3.500A)

    574 hydrogen bonds defined for protein.
    1698 hydrogen bond angles defined for protein.
    Restraints generated for nucleic acids:
      0 hydrogen bonds
      0 hydrogen bond angles
      0 basepair planarities
      0 basepair parallelities
      0 stacking parallelities
  Total time for adding SS restraints: 1.45

  Time building geometry restraints manager: 1.16 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: 1517
        1.32 -     1.45: 2333
        1.45 -     1.57: 5019
        1.57 -     1.69: 0
        1.69 -     1.81: 40
  Bond restraints: 8909
  Sorted by residual:
  bond pdb=" CB  VAL A 313 "
       pdb=" CG2 VAL A 313 "
    ideal  model  delta    sigma   weight residual
    1.521  1.439  0.082 3.30e-02 9.18e+02 6.15e+00
  bond pdb=" C   ASN A 596 "
       pdb=" O   ASN A 596 "
    ideal  model  delta    sigma   weight residual
    1.234  1.202  0.033 1.38e-02 5.25e+03 5.64e+00
  bond pdb=" CB  VAL B  15 "
       pdb=" CG2 VAL B  15 "
    ideal  model  delta    sigma   weight residual
    1.521  1.443  0.078 3.30e-02 9.18e+02 5.64e+00
  bond pdb=" CB  GLU A 619 "
       pdb=" CG  GLU A 619 "
    ideal  model  delta    sigma   weight residual
    1.520  1.455  0.065 3.00e-02 1.11e+03 4.63e+00
  bond pdb=" CB  TRP A 336 "
       pdb=" CG  TRP A 336 "
    ideal  model  delta    sigma   weight residual
    1.498  1.432  0.066 3.10e-02 1.04e+03 4.49e+00
  ... (remaining 8904 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     2.58: 11823
        2.58 -     5.15: 360
        5.15 -     7.73: 47
        7.73 -    10.31: 6
       10.31 -    12.89: 3
  Bond angle restraints: 12239
  Sorted by residual:
  angle pdb=" N   ASN B 237 "
        pdb=" CA  ASN B 237 "
        pdb=" C   ASN B 237 "
      ideal   model   delta    sigma   weight residual
     113.18  102.45   10.73 1.33e+00 5.65e-01 6.50e+01
  angle pdb=" CA  ASN B 237 "
        pdb=" C   ASN B 237 "
        pdb=" N   LYS B 238 "
      ideal   model   delta    sigma   weight residual
     118.22  113.55    4.67 1.03e+00 9.43e-01 2.06e+01
  angle pdb=" N   ILE A 525 "
        pdb=" CA  ILE A 525 "
        pdb=" C   ILE A 525 "
      ideal   model   delta    sigma   weight residual
     112.35  117.58   -5.23 1.20e+00 6.94e-01 1.90e+01
  angle pdb=" CG1 ILE A 379 "
        pdb=" CB  ILE A 379 "
        pdb=" CG2 ILE A 379 "
      ideal   model   delta    sigma   weight residual
     110.70   97.81   12.89 3.00e+00 1.11e-01 1.85e+01
  angle pdb=" C   MET A 378 "
        pdb=" N   ILE A 379 "
        pdb=" CA  ILE A 379 "
      ideal   model   delta    sigma   weight residual
     122.13  129.60   -7.47 1.85e+00 2.92e-01 1.63e+01
  ... (remaining 12234 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    17.96: 4750
       17.96 -    35.91: 323
       35.91 -    53.87: 57
       53.87 -    71.83: 5
       71.83 -    89.78: 7
  Dihedral angle restraints: 5142
    sinusoidal: 1547
      harmonic: 3595
  Sorted by residual:
  dihedral pdb=" CA  LYS B 235 "
           pdb=" C   LYS B 235 "
           pdb=" N   VAL B 236 "
           pdb=" CA  VAL B 236 "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00 -106.14  -73.86     0      5.00e+00 4.00e-02 2.18e+02
  dihedral pdb=" CA  VAL B 236 "
           pdb=" C   VAL B 236 "
           pdb=" N   ASN B 237 "
           pdb=" CA  ASN B 237 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  126.39   53.61     0      5.00e+00 4.00e-02 1.15e+02
  dihedral pdb=" CA  PHE B 513 "
           pdb=" C   PHE B 513 "
           pdb=" N   PHE B 514 "
           pdb=" CA  PHE B 514 "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00 -130.36  -49.64     0      5.00e+00 4.00e-02 9.85e+01
  ... (remaining 5139 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.059: 1127
       0.059 -    0.117: 338
       0.117 -    0.176: 42
       0.176 -    0.234: 6
       0.234 -    0.293: 3
  Chirality restraints: 1516
  Sorted by residual:
  chirality pdb=" CG  LEU B  22 "
            pdb=" CB  LEU B  22 "
            pdb=" CD1 LEU B  22 "
            pdb=" CD2 LEU B  22 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.59   -2.30   -0.29 2.00e-01 2.50e+01 2.14e+00
  chirality pdb=" CB  ILE A 379 "
            pdb=" CA  ILE A 379 "
            pdb=" CG1 ILE A 379 "
            pdb=" CG2 ILE A 379 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.64    2.92   -0.27 2.00e-01 2.50e+01 1.86e+00
  chirality pdb=" CB  VAL A 313 "
            pdb=" CA  VAL A 313 "
            pdb=" CG1 VAL A 313 "
            pdb=" CG2 VAL A 313 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.63   -2.37   -0.26 2.00e-01 2.50e+01 1.65e+00
  ... (remaining 1513 not shown)

  Planarity restraints: 1520
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CB  TRP A 336 "   -0.024 2.00e-02 2.50e+03   5.05e-02 6.37e+01
        pdb=" CG  TRP A 336 "    0.116 2.00e-02 2.50e+03
        pdb=" CD1 TRP A 336 "   -0.099 2.00e-02 2.50e+03
        pdb=" CD2 TRP A 336 "    0.011 2.00e-02 2.50e+03
        pdb=" NE1 TRP A 336 "    0.023 2.00e-02 2.50e+03
        pdb=" CE2 TRP A 336 "    0.007 2.00e-02 2.50e+03
        pdb=" CE3 TRP A 336 "   -0.015 2.00e-02 2.50e+03
        pdb=" CZ2 TRP A 336 "    0.003 2.00e-02 2.50e+03
        pdb=" CZ3 TRP A 336 "   -0.025 2.00e-02 2.50e+03
        pdb=" CH2 TRP A 336 "    0.005 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   ILE A 525 "   -0.075 5.00e-02 4.00e+02   1.12e-01 1.99e+01
        pdb=" N   PRO A 526 "    0.193 5.00e-02 4.00e+02
        pdb=" CA  PRO A 526 "   -0.056 5.00e-02 4.00e+02
        pdb=" CD  PRO A 526 "   -0.062 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CB  TYR A 171 "    0.036 2.00e-02 2.50e+03   2.95e-02 1.74e+01
        pdb=" CG  TYR A 171 "   -0.072 2.00e-02 2.50e+03
        pdb=" CD1 TYR A 171 "    0.017 2.00e-02 2.50e+03
        pdb=" CD2 TYR A 171 "   -0.000 2.00e-02 2.50e+03
        pdb=" CE1 TYR A 171 "   -0.000 2.00e-02 2.50e+03
        pdb=" CE2 TYR A 171 "    0.017 2.00e-02 2.50e+03
        pdb=" CZ  TYR A 171 "    0.003 2.00e-02 2.50e+03
        pdb=" OH  TYR A 171 "   -0.000 2.00e-02 2.50e+03
  ... (remaining 1517 not shown)

  Histogram of nonbonded interaction distances:
        1.97 -     2.56: 87
        2.56 -     3.14: 8262
        3.14 -     3.73: 13565
        3.73 -     4.31: 17219
        4.31 -     4.90: 28035
  Nonbonded interactions: 67168
  Sorted by model distance:
  nonbonded pdb=" O   VAL A 593 "
            pdb=" O   ASN A 596 "
     model   vdw
     1.969 3.040
  nonbonded pdb=" OH  TYR A 157 "
            pdb=" O   LEU A 645 "
     model   vdw
     2.118 3.040
  nonbonded pdb=" OE2 GLU B 343 "
            pdb=" OG  SER B 446 "
     model   vdw
     2.141 3.040
  nonbonded pdb=" OH  TYR B 157 "
            pdb=" O   LEU B 645 "
     model   vdw
     2.147 3.040
  nonbonded pdb=" OG1 THR A 207 "
            pdb=" OE1 GLU A 210 "
     model   vdw
     2.170 3.040
  ... (remaining 67163 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
Found NCS groups:
ncs_group {
  reference = (chain 'A' and (resid 3 through 388 or (resid 410 and (name N or name CA or name \ 
 C or name O or name CB )) or resid 411 through 413 or (resid 414 and (name N or \ 
 name CA or name C or name O or name CB )) or resid 415 through 664 or (resid 66 \ 
5 and (name N or name CA or name C or name O or name CB )) or resid 666 through  \ 
696))
  selection = chain 'B'
}

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:             1.290
  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:          0.130
  Check model and map are aligned:         0.030
  Set scattering table:                    0.020
  Process input model:                     9.900
  Find NCS groups from input model:        0.290
  Set up NCS constraints:                  0.020
  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:1.230
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   12.920
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8002
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      :  0.011   0.082   8909  Z= 0.465
  Angle     :  1.046  12.887  12239  Z= 0.576
  Chirality :  0.054   0.293   1516
  Planarity :  0.008   0.112   1520
  Dihedral  : 13.535  89.783   2804
  Min Nonbonded Distance : 1.969

Molprobity Statistics.
  All-atom Clashscore : 17.84
  Ramachandran Plot:
    Outliers :  0.33 %
    Allowed  : 16.18 %
    Favored  : 83.49 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.51 %
    Favored  : 99.49 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.09 %
    Twisted Proline : 5.36 %
    Twisted General : 0.60 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -2.09 (0.24), residues: 1205
  helix: -0.02 (0.19), residues: 762
  sheet: -2.57 (1.12), residues: 26
  loop : -4.02 (0.27), residues: 417

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.001   ARG B 661 
 TYR   0.072   0.003   TYR A 171 
 PHE   0.041   0.003   PHE A 640 
 TRP   0.116   0.005   TRP A 336 
 HIS   0.007   0.002   HIS A 617 

Details of bonding type rmsd
  covalent geometry    : bond        0.01058 ( 8909)
  covalent geometry    : angle       1.04645 (12239)
  hydrogen bonds       : bond        0.13070 (  574)
  hydrogen bonds       : angle       6.50248 ( 1698)

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

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

  2410 Ramachandran restraints generated.
    1205 Oldfield, 0 Emsley, 1205 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2410 Ramachandran restraints generated.
    1205 Oldfield, 0 Emsley, 1205 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  168 residues out of total 1064 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 168
  time to evaluate  : 0.337 
Fit side-chains
REVERT: A  465 PHE cc_start: 0.7191 (t80) cc_final: 0.6981 (t80)
REVERT: B  618 GLN cc_start: 0.8411 (tm-30) cc_final: 0.8109 (tm-30)
  outliers start: 0
  outliers final: 0
  residues processed: 168
  average time/residue: 0.0734
  time to fit residues: 18.2566
Evaluate side-chains
  142 residues out of total 1064 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 142
  time to evaluate  : 0.266 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 122
   random chunks:
   chunk 108 optimal weight:    2.9990
   chunk 49 optimal weight:    0.6980
   chunk 97 optimal weight:    8.9990
   chunk 113 optimal weight:    0.9980
   chunk 53 optimal weight:    0.9980
   chunk 5 optimal weight:    0.4980
   chunk 33 optimal weight:    7.9990
   chunk 65 optimal weight:   10.0000
   chunk 62 optimal weight:    4.9990
   chunk 51 optimal weight:    0.6980
   chunk 117 optimal weight:    0.8980
   overall best weight:    0.7580

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

Flipped N/Q/H residues before XYZ refinement:
A 463 ASN
B 351 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3768 r_free = 0.3768 target = 0.145656 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 48)----------------|
| r_work = 0.3306 r_free = 0.3306 target = 0.111982 restraints weight = 15539.318|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 46)----------------|
| r_work = 0.3341 r_free = 0.3341 target = 0.114350 restraints weight = 9789.762|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 33)----------------|
| r_work = 0.3360 r_free = 0.3360 target = 0.115776 restraints weight = 7348.543|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 47)----------------|
| r_work = 0.3377 r_free = 0.3377 target = 0.116813 restraints weight = 6205.945|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 28)----------------|
| r_work = 0.3383 r_free = 0.3383 target = 0.117258 restraints weight = 5616.111|
|-----------------------------------------------------------------------------|
r_work (final): 0.3378
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7837
moved from start:          0.1535

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.049   8909  Z= 0.178
  Angle     :  0.807  14.795  12239  Z= 0.423
  Chirality :  0.045   0.226   1516
  Planarity :  0.007   0.098   1520
  Dihedral  :  7.235  71.714   1271
  Min Nonbonded Distance : 2.476

Molprobity Statistics.
  All-atom Clashscore : 11.37
  Ramachandran Plot:
    Outliers :  0.33 %
    Allowed  : 13.20 %
    Favored  : 86.47 %
  Rotamer:
    Outliers :  2.17 %
    Allowed  : 11.72 %
    Favored  : 86.11 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.09 %
    Twisted Proline : 5.36 %
    Twisted General : 0.52 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -1.41 (0.25), residues: 1205
  helix:  0.42 (0.19), residues: 791
  sheet: -1.26 (1.76), residues: 12
  loop : -3.83 (0.28), residues: 402

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.001   ARG A 450 
 TYR   0.039   0.002   TYR A 171 
 PHE   0.036   0.002   PHE B 513 
 TRP   0.063   0.003   TRP A 336 
 HIS   0.005   0.001   HIS B 615 

Details of bonding type rmsd
  covalent geometry    : bond        0.00380 ( 8909)
  covalent geometry    : angle       0.80702 (12239)
  hydrogen bonds       : bond        0.05603 (  574)
  hydrogen bonds       : angle       5.31036 ( 1698)

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

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

  2410 Ramachandran restraints generated.
    1205 Oldfield, 0 Emsley, 1205 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2410 Ramachandran restraints generated.
    1205 Oldfield, 0 Emsley, 1205 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  184 residues out of total 1064 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 167
  time to evaluate  : 0.330 
Fit side-chains
REVERT: A  215 TYR cc_start: 0.8314 (t80) cc_final: 0.7951 (t80)
REVERT: A  369 PHE cc_start: 0.8932 (t80) cc_final: 0.8668 (t80)
REVERT: A  374 ILE cc_start: 0.8337 (OUTLIER) cc_final: 0.8074 (mp)
REVERT: A  378 MET cc_start: 0.4402 (OUTLIER) cc_final: 0.3708 (tmm)
REVERT: A  437 SER cc_start: 0.9137 (m) cc_final: 0.8582 (p)
REVERT: B  210 GLU cc_start: 0.8638 (pm20) cc_final: 0.8364 (pm20)
REVERT: B  447 HIS cc_start: 0.8853 (m90) cc_final: 0.8487 (m170)
REVERT: B  618 GLN cc_start: 0.8274 (tm-30) cc_final: 0.7874 (tm-30)
REVERT: B  649 LEU cc_start: 0.8747 (mt) cc_final: 0.8537 (mt)
  outliers start: 17
  outliers final: 6
  residues processed: 176
  average time/residue: 0.0728
  time to fit residues: 19.1199
Evaluate side-chains
  151 residues out of total 1064 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 143
  time to evaluate  : 0.322 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  374 ILE
Chi-restraints excluded: chain A residue  378 MET
Chi-restraints excluded: chain A residue  641 PHE
Chi-restraints excluded: chain B residue  212 ILE
Chi-restraints excluded: chain B residue  515 ILE
Chi-restraints excluded: chain B residue  579 ILE
Chi-restraints excluded: chain B residue  589 LEU
Chi-restraints excluded: chain B residue  601 VAL
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 122
   random chunks:
   chunk 13 optimal weight:    0.9980
   chunk 24 optimal weight:    3.9990
   chunk 77 optimal weight:    0.0020
   chunk 93 optimal weight:    1.9990
   chunk 65 optimal weight:    9.9990
   chunk 71 optimal weight:    0.8980
   chunk 1 optimal weight:    0.9980
   chunk 103 optimal weight:    0.7980
   chunk 29 optimal weight:    0.9990
   chunk 21 optimal weight:    7.9990
   chunk 73 optimal weight:    0.0030
   overall best weight:    0.5398

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3786 r_free = 0.3786 target = 0.146776 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 53)----------------|
| r_work = 0.3293 r_free = 0.3293 target = 0.110691 restraints weight = 15619.825|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 43)----------------|
| r_work = 0.3337 r_free = 0.3337 target = 0.113645 restraints weight = 8988.846|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 41)----------------|
| r_work = 0.3365 r_free = 0.3365 target = 0.115562 restraints weight = 6408.131|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 33)----------------|
| r_work = 0.3378 r_free = 0.3378 target = 0.116520 restraints weight = 5204.937|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 31)----------------|
| r_work = 0.3387 r_free = 0.3387 target = 0.117212 restraints weight = 4654.656|
|-----------------------------------------------------------------------------|
r_work (final): 0.3386
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7713
moved from start:          0.2135

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.050   8909  Z= 0.159
  Angle     :  0.756  13.688  12239  Z= 0.393
  Chirality :  0.043   0.184   1516
  Planarity :  0.006   0.102   1520
  Dihedral  :  6.785  70.425   1271
  Min Nonbonded Distance : 2.498

Molprobity Statistics.
  All-atom Clashscore : 10.95
  Ramachandran Plot:
    Outliers :  0.33 %
    Allowed  : 12.86 %
    Favored  : 86.80 %
  Rotamer:
    Outliers :  3.44 %
    Allowed  : 17.07 %
    Favored  : 79.49 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.09 %
    Twisted Proline : 3.57 %
    Twisted General : 0.43 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -1.16 (0.25), residues: 1205
  helix:  0.56 (0.19), residues: 794
  sheet:  0.38 (1.82), residues: 10
  loop : -3.69 (0.28), residues: 401

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.001   ARG B 661 
 TYR   0.029   0.001   TYR A 171 
 PHE   0.043   0.002   PHE B 513 
 TRP   0.045   0.002   TRP A 336 
 HIS   0.006   0.001   HIS B 615 

Details of bonding type rmsd
  covalent geometry    : bond        0.00340 ( 8909)
  covalent geometry    : angle       0.75562 (12239)
  hydrogen bonds       : bond        0.05015 (  574)
  hydrogen bonds       : angle       5.01539 ( 1698)

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

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

  2410 Ramachandran restraints generated.
    1205 Oldfield, 0 Emsley, 1205 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2410 Ramachandran restraints generated.
    1205 Oldfield, 0 Emsley, 1205 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  193 residues out of total 1064 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 27
    poor density    : 166
  time to evaluate  : 0.329 
Fit side-chains
   revert: symmetry clash
REVERT: A  190 GLU cc_start: 0.8535 (pp20) cc_final: 0.8252 (pp20)
REVERT: A  308 GLN cc_start: 0.8052 (mt0) cc_final: 0.7368 (mm-40)
REVERT: A  353 ASN cc_start: 0.8848 (t0) cc_final: 0.8360 (m-40)
REVERT: A  378 MET cc_start: 0.4308 (OUTLIER) cc_final: 0.3611 (tmm)
REVERT: A  425 PHE cc_start: 0.7613 (t80) cc_final: 0.7206 (t80)
REVERT: A  436 LEU cc_start: 0.8971 (mp) cc_final: 0.8590 (mt)
REVERT: A  437 SER cc_start: 0.9078 (m) cc_final: 0.8499 (p)
REVERT: A  620 ILE cc_start: 0.7966 (tt) cc_final: 0.7613 (tp)
REVERT: B   72 ASP cc_start: 0.8317 (t0) cc_final: 0.8059 (t0)
REVERT: B  353 ASN cc_start: 0.8482 (t0) cc_final: 0.8107 (m-40)
REVERT: B  369 PHE cc_start: 0.8285 (t80) cc_final: 0.8018 (t80)
REVERT: B  447 HIS cc_start: 0.8870 (m90) cc_final: 0.8542 (m170)
REVERT: B  563 MET cc_start: 0.8543 (ttp) cc_final: 0.8319 (ttp)
REVERT: B  618 GLN cc_start: 0.8346 (tm-30) cc_final: 0.7966 (tm-30)
REVERT: B  649 LEU cc_start: 0.8712 (mt) cc_final: 0.8461 (mt)
  outliers start: 27
  outliers final: 10
  residues processed: 181
  average time/residue: 0.0712
  time to fit residues: 19.4087
Evaluate side-chains
  162 residues out of total 1064 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 151
  time to evaluate  : 0.305 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  157 TYR
Chi-restraints excluded: chain A residue  187 VAL
Chi-restraints excluded: chain A residue  319 VAL
Chi-restraints excluded: chain A residue  378 MET
Chi-restraints excluded: chain A residue  458 TYR
Chi-restraints excluded: chain A residue  463 ASN
Chi-restraints excluded: chain B residue  515 ILE
Chi-restraints excluded: chain B residue  572 TYR
Chi-restraints excluded: chain B residue  579 ILE
Chi-restraints excluded: chain B residue  589 LEU
Chi-restraints excluded: chain B residue  601 VAL
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 122
   random chunks:
   chunk 12 optimal weight:    2.9990
   chunk 115 optimal weight:    0.6980
   chunk 87 optimal weight:    3.9990
   chunk 16 optimal weight:    1.9990
   chunk 7 optimal weight:    0.4980
   chunk 26 optimal weight:    4.9990
   chunk 4 optimal weight:    2.9990
   chunk 112 optimal weight:    0.8980
   chunk 22 optimal weight:   10.0000
   chunk 8 optimal weight:    0.6980
   chunk 71 optimal weight:    3.9990
   overall best weight:    0.9582

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3784 r_free = 0.3784 target = 0.146793 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 49)----------------|
| r_work = 0.3284 r_free = 0.3284 target = 0.110072 restraints weight = 15982.715|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 41)----------------|
| r_work = 0.3328 r_free = 0.3328 target = 0.113024 restraints weight = 9169.883|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 42)----------------|
| r_work = 0.3355 r_free = 0.3355 target = 0.114932 restraints weight = 6533.022|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 28)----------------|
| r_work = 0.3367 r_free = 0.3367 target = 0.115750 restraints weight = 5322.359|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 41)----------------|
| r_work = 0.3378 r_free = 0.3378 target = 0.116618 restraints weight = 4790.924|
|-----------------------------------------------------------------------------|
r_work (final): 0.3375
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7734
moved from start:          0.2346

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.039   8909  Z= 0.170
  Angle     :  0.759  12.906  12239  Z= 0.390
  Chirality :  0.044   0.209   1516
  Planarity :  0.006   0.103   1520
  Dihedral  :  6.620  69.776   1271
  Min Nonbonded Distance : 2.503

Molprobity Statistics.
  All-atom Clashscore : 10.47
  Ramachandran Plot:
    Outliers :  0.33 %
    Allowed  : 12.28 %
    Favored  : 87.39 %
  Rotamer:
    Outliers :  2.42 %
    Allowed  : 21.02 %
    Favored  : 76.56 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.09 %
    Twisted Proline : 3.57 %
    Twisted General : 0.43 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -1.08 (0.25), residues: 1205
  helix:  0.58 (0.19), residues: 801
  sheet: -0.10 (1.68), residues: 10
  loop : -3.58 (0.29), residues: 394

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG A 450 
 TYR   0.025   0.001   TYR A 171 
 PHE   0.039   0.002   PHE B 513 
 TRP   0.037   0.002   TRP A 336 
 HIS   0.005   0.001   HIS B 615 

Details of bonding type rmsd
  covalent geometry    : bond        0.00374 ( 8909)
  covalent geometry    : angle       0.75916 (12239)
  hydrogen bonds       : bond        0.04887 (  574)
  hydrogen bonds       : angle       4.92115 ( 1698)

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

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

  2410 Ramachandran restraints generated.
    1205 Oldfield, 0 Emsley, 1205 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2410 Ramachandran restraints generated.
    1205 Oldfield, 0 Emsley, 1205 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  181 residues out of total 1064 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 162
  time to evaluate  : 0.314 
Fit side-chains
   revert: symmetry clash
REVERT: A  190 GLU cc_start: 0.8489 (pp20) cc_final: 0.8257 (pp20)
REVERT: A  378 MET cc_start: 0.4307 (tmm) cc_final: 0.3599 (tmm)
REVERT: A  425 PHE cc_start: 0.7600 (t80) cc_final: 0.7288 (t80)
REVERT: A  437 SER cc_start: 0.9074 (m) cc_final: 0.8491 (p)
REVERT: A  563 MET cc_start: 0.8781 (ttp) cc_final: 0.8420 (ttt)
REVERT: B   72 ASP cc_start: 0.8343 (t0) cc_final: 0.8058 (t0)
REVERT: B   92 LEU cc_start: 0.9115 (tt) cc_final: 0.8915 (tt)
REVERT: B  308 GLN cc_start: 0.7572 (mt0) cc_final: 0.7084 (mt0)
REVERT: B  353 ASN cc_start: 0.8492 (t0) cc_final: 0.8186 (m-40)
REVERT: B  369 PHE cc_start: 0.8321 (t80) cc_final: 0.8106 (t80)
REVERT: B  376 PHE cc_start: 0.8177 (t80) cc_final: 0.7892 (t80)
REVERT: B  447 HIS cc_start: 0.8893 (m90) cc_final: 0.8568 (m170)
REVERT: B  618 GLN cc_start: 0.8328 (tm-30) cc_final: 0.7933 (tm-30)
REVERT: B  631 MET cc_start: 0.9180 (mmp) cc_final: 0.8834 (mmp)
REVERT: B  649 LEU cc_start: 0.8768 (mt) cc_final: 0.8490 (mt)
  outliers start: 19
  outliers final: 11
  residues processed: 173
  average time/residue: 0.0709
  time to fit residues: 18.3502
Evaluate side-chains
  158 residues out of total 1064 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 147
  time to evaluate  : 0.318 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  157 TYR
Chi-restraints excluded: chain A residue  319 VAL
Chi-restraints excluded: chain A residue  458 TYR
Chi-restraints excluded: chain A residue  463 ASN
Chi-restraints excluded: chain A residue  511 LEU
Chi-restraints excluded: chain A residue  559 VAL
Chi-restraints excluded: chain A residue  599 LEU
Chi-restraints excluded: chain B residue  212 ILE
Chi-restraints excluded: chain B residue  515 ILE
Chi-restraints excluded: chain B residue  579 ILE
Chi-restraints excluded: chain B residue  601 VAL
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 122
   random chunks:
   chunk 69 optimal weight:    0.7980
   chunk 72 optimal weight:    0.0470
   chunk 16 optimal weight:    0.8980
   chunk 43 optimal weight:    5.9990
   chunk 100 optimal weight:    1.9990
   chunk 71 optimal weight:    1.9990
   chunk 32 optimal weight:    2.9990
   chunk 11 optimal weight:    3.9990
   chunk 42 optimal weight:   10.0000
   chunk 60 optimal weight:    7.9990
   chunk 79 optimal weight:    1.9990
   overall best weight:    1.1482

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

Flipped N/Q/H residues before XYZ refinement:
** A 392 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3778 r_free = 0.3778 target = 0.146375 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 56)----------------|
| r_work = 0.3280 r_free = 0.3280 target = 0.109900 restraints weight = 15728.775|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 45)----------------|
| r_work = 0.3323 r_free = 0.3323 target = 0.112779 restraints weight = 9119.550|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 34)----------------|
| r_work = 0.3350 r_free = 0.3350 target = 0.114614 restraints weight = 6519.457|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 30)----------------|
| r_work = 0.3363 r_free = 0.3363 target = 0.115580 restraints weight = 5334.015|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 23)----------------|
| r_work = 0.3366 r_free = 0.3366 target = 0.115827 restraints weight = 4782.023|
|-----------------------------------------------------------------------------|
r_work (final): 0.3363
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7708
moved from start:          0.2489

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.073   8909  Z= 0.179
  Angle     :  0.752  13.144  12239  Z= 0.389
  Chirality :  0.043   0.196   1516
  Planarity :  0.006   0.104   1520
  Dihedral  :  6.514  69.262   1271
  Min Nonbonded Distance : 2.509

Molprobity Statistics.
  All-atom Clashscore : 10.77
  Ramachandran Plot:
    Outliers :  0.33 %
    Allowed  : 12.95 %
    Favored  : 86.72 %
  Rotamer:
    Outliers :  3.95 %
    Allowed  : 22.42 %
    Favored  : 73.63 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.09 %
    Twisted Proline : 3.57 %
    Twisted General : 0.43 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -0.95 (0.25), residues: 1205
  helix:  0.69 (0.19), residues: 800
  sheet: -0.01 (1.75), residues: 10
  loop : -3.55 (0.29), residues: 395

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG A 450 
 TYR   0.021   0.001   TYR A 171 
 PHE   0.046   0.002   PHE B 513 
 TRP   0.032   0.002   TRP A 336 
 HIS   0.005   0.001   HIS B 615 

Details of bonding type rmsd
  covalent geometry    : bond        0.00400 ( 8909)
  covalent geometry    : angle       0.75204 (12239)
  hydrogen bonds       : bond        0.04785 (  574)
  hydrogen bonds       : angle       4.88609 ( 1698)

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

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

  2410 Ramachandran restraints generated.
    1205 Oldfield, 0 Emsley, 1205 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2410 Ramachandran restraints generated.
    1205 Oldfield, 0 Emsley, 1205 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  183 residues out of total 1064 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 31
    poor density    : 152
  time to evaluate  : 0.324 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  336 TRP cc_start: 0.7546 (m-10) cc_final: 0.7066 (m-10)
REVERT: A  378 MET cc_start: 0.4359 (OUTLIER) cc_final: 0.3595 (tmm)
REVERT: A  425 PHE cc_start: 0.7526 (t80) cc_final: 0.7236 (t80)
REVERT: A  437 SER cc_start: 0.9052 (m) cc_final: 0.8473 (p)
REVERT: A  563 MET cc_start: 0.8767 (OUTLIER) cc_final: 0.8509 (ttt)
REVERT: A  620 ILE cc_start: 0.7994 (tt) cc_final: 0.7623 (tp)
REVERT: B   72 ASP cc_start: 0.8446 (t0) cc_final: 0.8151 (t0)
REVERT: B  308 GLN cc_start: 0.7569 (mt0) cc_final: 0.7072 (mt0)
REVERT: B  353 ASN cc_start: 0.8464 (t0) cc_final: 0.8168 (m-40)
REVERT: B  376 PHE cc_start: 0.8289 (t80) cc_final: 0.7977 (t80)
REVERT: B  447 HIS cc_start: 0.8926 (m90) cc_final: 0.8570 (m170)
REVERT: B  618 GLN cc_start: 0.8410 (tm-30) cc_final: 0.8011 (tm-30)
REVERT: B  649 LEU cc_start: 0.8758 (mt) cc_final: 0.8489 (mt)
  outliers start: 31
  outliers final: 17
  residues processed: 171
  average time/residue: 0.0689
  time to fit residues: 17.6056
Evaluate side-chains
  162 residues out of total 1064 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 143
  time to evaluate  : 0.363 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  157 TYR
Chi-restraints excluded: chain A residue  319 VAL
Chi-restraints excluded: chain A residue  378 MET
Chi-restraints excluded: chain A residue  458 TYR
Chi-restraints excluded: chain A residue  463 ASN
Chi-restraints excluded: chain A residue  511 LEU
Chi-restraints excluded: chain A residue  559 VAL
Chi-restraints excluded: chain A residue  563 MET
Chi-restraints excluded: chain A residue  564 LEU
Chi-restraints excluded: chain B residue  212 ILE
Chi-restraints excluded: chain B residue  338 VAL
Chi-restraints excluded: chain B residue  366 ILE
Chi-restraints excluded: chain B residue  377 TYR
Chi-restraints excluded: chain B residue  416 PHE
Chi-restraints excluded: chain B residue  444 SER
Chi-restraints excluded: chain B residue  515 ILE
Chi-restraints excluded: chain B residue  579 ILE
Chi-restraints excluded: chain B residue  589 LEU
Chi-restraints excluded: chain B residue  601 VAL
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 122
   random chunks:
   chunk 111 optimal weight:    0.6980
   chunk 106 optimal weight:    7.9990
   chunk 109 optimal weight:    0.7980
   chunk 34 optimal weight:    7.9990
   chunk 118 optimal weight:    0.9990
   chunk 121 optimal weight:    4.9990
   chunk 2 optimal weight:    9.9990
   chunk 51 optimal weight:    0.6980
   chunk 53 optimal weight:    0.9990
   chunk 14 optimal weight:    0.6980
   chunk 96 optimal weight:    0.9990
   overall best weight:    0.7782

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

Flipped N/Q/H residues before XYZ refinement:
** A 392 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3798 r_free = 0.3798 target = 0.148110 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 57)----------------|
| r_work = 0.3314 r_free = 0.3314 target = 0.112221 restraints weight = 15677.764|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 40)----------------|
| r_work = 0.3353 r_free = 0.3353 target = 0.114866 restraints weight = 9535.948|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 36)----------------|
| r_work = 0.3379 r_free = 0.3379 target = 0.116645 restraints weight = 7031.091|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 26)----------------|
| r_work = 0.3388 r_free = 0.3388 target = 0.117339 restraints weight = 5829.647|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 31)----------------|
| r_work = 0.3395 r_free = 0.3395 target = 0.117874 restraints weight = 5314.677|
|-----------------------------------------------------------------------------|
r_work (final): 0.3388
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7658
moved from start:          0.2714

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.059   8909  Z= 0.159
  Angle     :  0.742  12.905  12239  Z= 0.381
  Chirality :  0.043   0.182   1516
  Planarity :  0.006   0.104   1520
  Dihedral  :  6.426  68.435   1271
  Min Nonbonded Distance : 2.507

Molprobity Statistics.
  All-atom Clashscore : 11.19
  Ramachandran Plot:
    Outliers :  0.25 %
    Allowed  : 12.37 %
    Favored  : 87.39 %
  Rotamer:
    Outliers :  3.44 %
    Allowed  : 23.44 %
    Favored  : 73.12 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.09 %
    Twisted Proline : 3.57 %
    Twisted General : 0.43 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -0.83 (0.25), residues: 1205
  helix:  0.79 (0.19), residues: 797
  sheet: -0.06 (1.77), residues: 10
  loop : -3.48 (0.29), residues: 398

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG B 661 
 TYR   0.018   0.001   TYR A 171 
 PHE   0.043   0.002   PHE B 513 
 TRP   0.028   0.001   TRP A 336 
 HIS   0.004   0.001   HIS B 615 

Details of bonding type rmsd
  covalent geometry    : bond        0.00345 ( 8909)
  covalent geometry    : angle       0.74226 (12239)
  hydrogen bonds       : bond        0.04650 (  574)
  hydrogen bonds       : angle       4.81160 ( 1698)

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

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

  2410 Ramachandran restraints generated.
    1205 Oldfield, 0 Emsley, 1205 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2410 Ramachandran restraints generated.
    1205 Oldfield, 0 Emsley, 1205 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  185 residues out of total 1064 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 27
    poor density    : 158
  time to evaluate  : 0.325 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  336 TRP cc_start: 0.7605 (m-10) cc_final: 0.7148 (m-10)
REVERT: A  378 MET cc_start: 0.4353 (OUTLIER) cc_final: 0.3654 (tmm)
REVERT: A  437 SER cc_start: 0.9014 (m) cc_final: 0.8415 (p)
REVERT: A  563 MET cc_start: 0.8731 (ttp) cc_final: 0.8437 (ttt)
REVERT: A  572 TYR cc_start: 0.8551 (m-10) cc_final: 0.8257 (m-10)
REVERT: B   72 ASP cc_start: 0.8428 (t0) cc_final: 0.8121 (t0)
REVERT: B  308 GLN cc_start: 0.7560 (mt0) cc_final: 0.6826 (mt0)
REVERT: B  353 ASN cc_start: 0.8459 (t0) cc_final: 0.8015 (m-40)
REVERT: B  376 PHE cc_start: 0.8382 (t80) cc_final: 0.8032 (t80)
REVERT: B  447 HIS cc_start: 0.8923 (m90) cc_final: 0.8568 (m170)
REVERT: B  618 GLN cc_start: 0.8368 (tm-30) cc_final: 0.7973 (tm-30)
REVERT: B  649 LEU cc_start: 0.8708 (mt) cc_final: 0.8429 (mt)
REVERT: B  661 ARG cc_start: 0.7388 (tpt170) cc_final: 0.6976 (tpt170)
  outliers start: 27
  outliers final: 17
  residues processed: 174
  average time/residue: 0.0710
  time to fit residues: 18.5457
Evaluate side-chains
  165 residues out of total 1064 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 147
  time to evaluate  : 0.319 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  157 TYR
Chi-restraints excluded: chain A residue  319 VAL
Chi-restraints excluded: chain A residue  378 MET
Chi-restraints excluded: chain A residue  458 TYR
Chi-restraints excluded: chain A residue  463 ASN
Chi-restraints excluded: chain A residue  511 LEU
Chi-restraints excluded: chain A residue  559 VAL
Chi-restraints excluded: chain A residue  564 LEU
Chi-restraints excluded: chain A residue  594 LEU
Chi-restraints excluded: chain B residue  212 ILE
Chi-restraints excluded: chain B residue  377 TYR
Chi-restraints excluded: chain B residue  416 PHE
Chi-restraints excluded: chain B residue  444 SER
Chi-restraints excluded: chain B residue  463 ASN
Chi-restraints excluded: chain B residue  515 ILE
Chi-restraints excluded: chain B residue  579 ILE
Chi-restraints excluded: chain B residue  589 LEU
Chi-restraints excluded: chain B residue  601 VAL
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 122
   random chunks:
   chunk 81 optimal weight:    3.9990
   chunk 6 optimal weight:   10.0000
   chunk 36 optimal weight:    0.9990
   chunk 75 optimal weight:    0.6980
   chunk 4 optimal weight:    6.9990
   chunk 56 optimal weight:    7.9990
   chunk 89 optimal weight:    2.9990
   chunk 28 optimal weight:    0.0980
   chunk 76 optimal weight:    0.6980
   chunk 29 optimal weight:    1.9990
   chunk 3 optimal weight:    6.9990
   overall best weight:    0.8984

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3797 r_free = 0.3797 target = 0.147881 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 51)----------------|
| r_work = 0.3319 r_free = 0.3319 target = 0.112438 restraints weight = 15671.497|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 42)----------------|
| r_work = 0.3357 r_free = 0.3357 target = 0.115043 restraints weight = 9479.437|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 42)----------------|
| r_work = 0.3381 r_free = 0.3381 target = 0.116724 restraints weight = 6954.668|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 34)----------------|
| r_work = 0.3393 r_free = 0.3393 target = 0.117654 restraints weight = 5789.148|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 26)----------------|
| r_work = 0.3398 r_free = 0.3398 target = 0.118021 restraints weight = 5222.854|
|-----------------------------------------------------------------------------|
r_work (final): 0.3391
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7666
moved from start:          0.2839

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.052   8909  Z= 0.162
  Angle     :  0.747  14.005  12239  Z= 0.382
  Chirality :  0.043   0.217   1516
  Planarity :  0.006   0.106   1520
  Dihedral  :  6.360  67.375   1271
  Min Nonbonded Distance : 2.505

Molprobity Statistics.
  All-atom Clashscore : 10.24
  Ramachandran Plot:
    Outliers :  0.33 %
    Allowed  : 12.61 %
    Favored  : 87.05 %
  Rotamer:
    Outliers :  3.69 %
    Allowed  : 24.20 %
    Favored  : 72.10 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.09 %
    Twisted Proline : 3.57 %
    Twisted General : 0.43 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -0.83 (0.25), residues: 1205
  helix:  0.82 (0.19), residues: 798
  sheet: -1.90 (1.14), residues: 22
  loop : -3.56 (0.29), residues: 385

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG A 450 
 TYR   0.019   0.001   TYR A 364 
 PHE   0.043   0.002   PHE B 513 
 TRP   0.027   0.002   TRP B 548 
 HIS   0.004   0.001   HIS B 615 

Details of bonding type rmsd
  covalent geometry    : bond        0.00355 ( 8909)
  covalent geometry    : angle       0.74726 (12239)
  hydrogen bonds       : bond        0.04602 (  574)
  hydrogen bonds       : angle       4.78915 ( 1698)

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

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

  2410 Ramachandran restraints generated.
    1205 Oldfield, 0 Emsley, 1205 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2410 Ramachandran restraints generated.
    1205 Oldfield, 0 Emsley, 1205 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  188 residues out of total 1064 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 29
    poor density    : 159
  time to evaluate  : 0.376 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  378 MET cc_start: 0.4306 (OUTLIER) cc_final: 0.3602 (tmm)
REVERT: A  437 SER cc_start: 0.9014 (m) cc_final: 0.8434 (p)
REVERT: A  563 MET cc_start: 0.8728 (OUTLIER) cc_final: 0.8455 (ttt)
REVERT: A  572 TYR cc_start: 0.8554 (m-10) cc_final: 0.8295 (m-10)
REVERT: A  620 ILE cc_start: 0.7995 (tt) cc_final: 0.7514 (tp)
REVERT: B   72 ASP cc_start: 0.8404 (t0) cc_final: 0.8105 (t0)
REVERT: B  234 SER cc_start: 0.6564 (p) cc_final: 0.6332 (p)
REVERT: B  351 ASN cc_start: 0.8981 (OUTLIER) cc_final: 0.8370 (t0)
REVERT: B  447 HIS cc_start: 0.8912 (m90) cc_final: 0.8561 (m170)
REVERT: B  618 GLN cc_start: 0.8241 (tm-30) cc_final: 0.7869 (tm-30)
REVERT: B  661 ARG cc_start: 0.7363 (tpt170) cc_final: 0.7005 (tpt170)
  outliers start: 29
  outliers final: 19
  residues processed: 176
  average time/residue: 0.0654
  time to fit residues: 17.3308
Evaluate side-chains
  171 residues out of total 1064 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 22
    poor density    : 149
  time to evaluate  : 0.256 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  157 TYR
Chi-restraints excluded: chain A residue  319 VAL
Chi-restraints excluded: chain A residue  378 MET
Chi-restraints excluded: chain A residue  458 TYR
Chi-restraints excluded: chain A residue  463 ASN
Chi-restraints excluded: chain A residue  511 LEU
Chi-restraints excluded: chain A residue  559 VAL
Chi-restraints excluded: chain A residue  563 MET
Chi-restraints excluded: chain A residue  564 LEU
Chi-restraints excluded: chain A residue  594 LEU
Chi-restraints excluded: chain B residue  338 VAL
Chi-restraints excluded: chain B residue  351 ASN
Chi-restraints excluded: chain B residue  366 ILE
Chi-restraints excluded: chain B residue  377 TYR
Chi-restraints excluded: chain B residue  416 PHE
Chi-restraints excluded: chain B residue  444 SER
Chi-restraints excluded: chain B residue  463 ASN
Chi-restraints excluded: chain B residue  515 ILE
Chi-restraints excluded: chain B residue  579 ILE
Chi-restraints excluded: chain B residue  589 LEU
Chi-restraints excluded: chain B residue  594 LEU
Chi-restraints excluded: chain B residue  601 VAL
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 122
   random chunks:
   chunk 63 optimal weight:    0.8980
   chunk 95 optimal weight:    1.9990
   chunk 34 optimal weight:    0.7980
   chunk 60 optimal weight:    1.9990
   chunk 120 optimal weight:    0.0770
   chunk 72 optimal weight:    0.0270
   chunk 49 optimal weight:    0.9980
   chunk 42 optimal weight:    7.9990
   chunk 1 optimal weight:    0.8980
   chunk 86 optimal weight:    0.0370
   chunk 5 optimal weight:    3.9990
   overall best weight:    0.3674

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3835 r_free = 0.3835 target = 0.150856 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 45)----------------|
| r_work = 0.3355 r_free = 0.3355 target = 0.114772 restraints weight = 15489.791|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 38)----------------|
| r_work = 0.3398 r_free = 0.3398 target = 0.117714 restraints weight = 8861.538|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 39)----------------|
| r_work = 0.3425 r_free = 0.3425 target = 0.119589 restraints weight = 6301.751|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 32)----------------|
| r_work = 0.3438 r_free = 0.3438 target = 0.120597 restraints weight = 5136.661|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 41)----------------|
| r_work = 0.3451 r_free = 0.3451 target = 0.121464 restraints weight = 4582.123|
|-----------------------------------------------------------------------------|
r_work (final): 0.3443
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7651
moved from start:          0.3169

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.043   8909  Z= 0.146
  Angle     :  0.745  13.274  12239  Z= 0.377
  Chirality :  0.042   0.230   1516
  Planarity :  0.006   0.106   1520
  Dihedral  :  6.231  65.431   1271
  Min Nonbonded Distance : 2.507

Molprobity Statistics.
  All-atom Clashscore : 10.53
  Ramachandran Plot:
    Outliers :  0.25 %
    Allowed  : 11.70 %
    Favored  : 88.05 %
  Rotamer:
    Outliers :  3.06 %
    Allowed  : 24.20 %
    Favored  : 72.74 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.09 %
    Twisted Proline : 3.57 %
    Twisted General : 0.43 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -0.74 (0.25), residues: 1205
  helix:  0.88 (0.19), residues: 798
  sheet: -1.86 (1.17), residues: 22
  loop : -3.49 (0.29), residues: 385

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.001   0.000   ARG B 450 
 TYR   0.020   0.001   TYR A 364 
 PHE   0.041   0.001   PHE B 513 
 TRP   0.038   0.001   TRP A 336 
 HIS   0.006   0.001   HIS B 615 

Details of bonding type rmsd
  covalent geometry    : bond        0.00308 ( 8909)
  covalent geometry    : angle       0.74491 (12239)
  hydrogen bonds       : bond        0.04393 (  574)
  hydrogen bonds       : angle       4.71632 ( 1698)

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

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

  2410 Ramachandran restraints generated.
    1205 Oldfield, 0 Emsley, 1205 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2410 Ramachandran restraints generated.
    1205 Oldfield, 0 Emsley, 1205 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  195 residues out of total 1064 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 24
    poor density    : 171
  time to evaluate  : 0.371 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  336 TRP cc_start: 0.7449 (m-10) cc_final: 0.7214 (m-10)
REVERT: A  378 MET cc_start: 0.4273 (OUTLIER) cc_final: 0.3595 (tmm)
REVERT: A  437 SER cc_start: 0.8970 (m) cc_final: 0.8380 (p)
REVERT: A  563 MET cc_start: 0.8607 (OUTLIER) cc_final: 0.8327 (ttt)
REVERT: A  572 TYR cc_start: 0.8533 (m-10) cc_final: 0.8290 (m-10)
REVERT: A  620 ILE cc_start: 0.8073 (tt) cc_final: 0.7583 (tp)
REVERT: B   72 ASP cc_start: 0.8201 (t0) cc_final: 0.7906 (t0)
REVERT: B  308 GLN cc_start: 0.7144 (mt0) cc_final: 0.6826 (mt0)
REVERT: B  351 ASN cc_start: 0.8957 (t0) cc_final: 0.8479 (t0)
REVERT: B  376 PHE cc_start: 0.8367 (t80) cc_final: 0.8031 (t80)
REVERT: B  447 HIS cc_start: 0.8872 (m90) cc_final: 0.8551 (m170)
REVERT: B  618 GLN cc_start: 0.8280 (tm-30) cc_final: 0.7966 (tm-30)
REVERT: B  661 ARG cc_start: 0.7268 (tpt170) cc_final: 0.6947 (tpt170)
  outliers start: 24
  outliers final: 15
  residues processed: 183
  average time/residue: 0.0635
  time to fit residues: 17.8586
Evaluate side-chains
  177 residues out of total 1064 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 160
  time to evaluate  : 0.353 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  157 TYR
Chi-restraints excluded: chain A residue  319 VAL
Chi-restraints excluded: chain A residue  378 MET
Chi-restraints excluded: chain A residue  397 ILE
Chi-restraints excluded: chain A residue  458 TYR
Chi-restraints excluded: chain A residue  463 ASN
Chi-restraints excluded: chain A residue  511 LEU
Chi-restraints excluded: chain A residue  559 VAL
Chi-restraints excluded: chain A residue  563 MET
Chi-restraints excluded: chain A residue  564 LEU
Chi-restraints excluded: chain B residue  338 VAL
Chi-restraints excluded: chain B residue  366 ILE
Chi-restraints excluded: chain B residue  416 PHE
Chi-restraints excluded: chain B residue  444 SER
Chi-restraints excluded: chain B residue  515 ILE
Chi-restraints excluded: chain B residue  579 ILE
Chi-restraints excluded: chain B residue  601 VAL
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 122
   random chunks:
   chunk 74 optimal weight:    3.9990
   chunk 29 optimal weight:    2.9990
   chunk 67 optimal weight:    0.0670
   chunk 22 optimal weight:    9.9990
   chunk 48 optimal weight:    0.0980
   chunk 53 optimal weight:    0.0570
   chunk 105 optimal weight:    6.9990
   chunk 39 optimal weight:    1.9990
   chunk 17 optimal weight:    7.9990
   chunk 65 optimal weight:    0.0870
   chunk 43 optimal weight:    2.9990
   overall best weight:    0.4616

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

Flipped N/Q/H residues before XYZ refinement:
** B 208 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3843 r_free = 0.3843 target = 0.151554 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 56)----------------|
| r_work = 0.3372 r_free = 0.3372 target = 0.115999 restraints weight = 15468.329|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 48)----------------|
| r_work = 0.3410 r_free = 0.3410 target = 0.118684 restraints weight = 9425.020|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 34)----------------|
| r_work = 0.3431 r_free = 0.3431 target = 0.120187 restraints weight = 6908.026|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 50)----------------|
| r_work = 0.3450 r_free = 0.3450 target = 0.121468 restraints weight = 5773.445|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 26)----------------|
| r_work = 0.3456 r_free = 0.3456 target = 0.121907 restraints weight = 5145.701|
|-----------------------------------------------------------------------------|
r_work (final): 0.3451
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7634
moved from start:          0.3364

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.042   8909  Z= 0.148
  Angle     :  0.769  17.292  12239  Z= 0.382
  Chirality :  0.043   0.231   1516
  Planarity :  0.006   0.106   1520
  Dihedral  :  6.104  64.781   1271
  Min Nonbonded Distance : 2.497

Molprobity Statistics.
  All-atom Clashscore : 10.89
  Ramachandran Plot:
    Outliers :  0.33 %
    Allowed  : 12.20 %
    Favored  : 87.47 %
  Rotamer:
    Outliers :  2.55 %
    Allowed  : 25.22 %
    Favored  : 72.23 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.09 %
    Twisted Proline : 3.57 %
    Twisted General : 0.43 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -0.72 (0.25), residues: 1205
  helix:  0.89 (0.19), residues: 792
  sheet: -1.86 (1.16), residues: 22
  loop : -3.39 (0.29), residues: 391

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.001   0.000   ARG A 450 
 TYR   0.019   0.001   TYR A 364 
 PHE   0.042   0.001   PHE B 513 
 TRP   0.028   0.001   TRP A 336 
 HIS   0.004   0.001   HIS B 615 

Details of bonding type rmsd
  covalent geometry    : bond        0.00317 ( 8909)
  covalent geometry    : angle       0.76855 (12239)
  hydrogen bonds       : bond        0.04400 (  574)
  hydrogen bonds       : angle       4.70027 ( 1698)

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

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

  2410 Ramachandran restraints generated.
    1205 Oldfield, 0 Emsley, 1205 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2410 Ramachandran restraints generated.
    1205 Oldfield, 0 Emsley, 1205 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  184 residues out of total 1064 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 164
  time to evaluate  : 0.316 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  336 TRP cc_start: 0.7518 (m-10) cc_final: 0.7288 (m-10)
REVERT: A  369 PHE cc_start: 0.8790 (t80) cc_final: 0.8539 (t80)
REVERT: A  373 THR cc_start: 0.7144 (m) cc_final: 0.6774 (m)
REVERT: A  378 MET cc_start: 0.4294 (OUTLIER) cc_final: 0.3699 (tmm)
REVERT: A  436 LEU cc_start: 0.8926 (mp) cc_final: 0.8477 (mt)
REVERT: A  437 SER cc_start: 0.8965 (m) cc_final: 0.8386 (p)
REVERT: A  572 TYR cc_start: 0.8643 (m-10) cc_final: 0.8433 (m-10)
REVERT: A  620 ILE cc_start: 0.8109 (tt) cc_final: 0.7528 (tp)
REVERT: B   72 ASP cc_start: 0.8234 (t0) cc_final: 0.7933 (t0)
REVERT: B  351 ASN cc_start: 0.8820 (t0) cc_final: 0.8143 (t0)
REVERT: B  376 PHE cc_start: 0.8366 (t80) cc_final: 0.8032 (t80)
REVERT: B  381 ILE cc_start: 0.7947 (mm) cc_final: 0.7689 (mm)
REVERT: B  447 HIS cc_start: 0.8895 (m90) cc_final: 0.8571 (m170)
REVERT: B  570 PHE cc_start: 0.8501 (OUTLIER) cc_final: 0.6991 (t80)
REVERT: B  618 GLN cc_start: 0.8302 (tm-30) cc_final: 0.7922 (tm-30)
REVERT: B  661 ARG cc_start: 0.7250 (tpt170) cc_final: 0.6973 (tpt170)
  outliers start: 20
  outliers final: 15
  residues processed: 174
  average time/residue: 0.0622
  time to fit residues: 16.6535
Evaluate side-chains
  173 residues out of total 1064 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 156
  time to evaluate  : 0.306 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  157 TYR
Chi-restraints excluded: chain A residue  319 VAL
Chi-restraints excluded: chain A residue  378 MET
Chi-restraints excluded: chain A residue  397 ILE
Chi-restraints excluded: chain A residue  458 TYR
Chi-restraints excluded: chain A residue  463 ASN
Chi-restraints excluded: chain A residue  511 LEU
Chi-restraints excluded: chain A residue  559 VAL
Chi-restraints excluded: chain A residue  564 LEU
Chi-restraints excluded: chain B residue  302 VAL
Chi-restraints excluded: chain B residue  338 VAL
Chi-restraints excluded: chain B residue  366 ILE
Chi-restraints excluded: chain B residue  444 SER
Chi-restraints excluded: chain B residue  515 ILE
Chi-restraints excluded: chain B residue  570 PHE
Chi-restraints excluded: chain B residue  579 ILE
Chi-restraints excluded: chain B residue  601 VAL
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 122
   random chunks:
   chunk 50 optimal weight:    0.0770
   chunk 69 optimal weight:    0.9980
   chunk 87 optimal weight:    0.6980
   chunk 110 optimal weight:    0.6980
   chunk 62 optimal weight:   20.0000
   chunk 71 optimal weight:    0.7980
   chunk 80 optimal weight:    0.6980
   chunk 4 optimal weight:    3.9990
   chunk 96 optimal weight:    0.0270
   chunk 98 optimal weight:    2.9990
   chunk 28 optimal weight:    1.9990
   overall best weight:    0.4396

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

Flipped N/Q/H residues before XYZ refinement:
B  33 ASN
** B 208 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 353 ASN ** 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 = 0.3868 r_free = 0.3868 target = 0.152219 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 54)----------------|
| r_work = 0.3380 r_free = 0.3380 target = 0.115740 restraints weight = 15616.613|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 40)----------------|
| r_work = 0.3425 r_free = 0.3425 target = 0.118769 restraints weight = 8854.665|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 36)----------------|
| r_work = 0.3448 r_free = 0.3448 target = 0.120492 restraints weight = 6257.396|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 43)----------------|
| r_work = 0.3471 r_free = 0.3471 target = 0.121926 restraints weight = 5129.360|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 28)----------------|
| r_work = 0.3478 r_free = 0.3478 target = 0.122494 restraints weight = 4511.590|
|-----------------------------------------------------------------------------|
r_work (final): 0.3474
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7612
moved from start:          0.3532

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.043   8909  Z= 0.148
  Angle     :  0.769  14.403  12239  Z= 0.381
  Chirality :  0.043   0.243   1516
  Planarity :  0.006   0.106   1520
  Dihedral  :  6.034  63.018   1271
  Min Nonbonded Distance : 2.478

Molprobity Statistics.
  All-atom Clashscore : 10.95
  Ramachandran Plot:
    Outliers :  0.33 %
    Allowed  : 10.95 %
    Favored  : 88.71 %
  Rotamer:
    Outliers :  2.29 %
    Allowed  : 25.86 %
    Favored  : 71.85 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.09 %
    Twisted Proline : 3.57 %
    Twisted General : 0.43 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -0.58 (0.25), residues: 1205
  helix:  0.99 (0.19), residues: 800
  sheet: -1.74 (1.20), residues: 22
  loop : -3.42 (0.29), residues: 383

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.001   0.000   ARG B 450 
 TYR   0.017   0.001   TYR B 364 
 PHE   0.041   0.001   PHE B 513 
 TRP   0.026   0.001   TRP A 336 
 HIS   0.004   0.001   HIS B 615 

Details of bonding type rmsd
  covalent geometry    : bond        0.00318 ( 8909)
  covalent geometry    : angle       0.76881 (12239)
  hydrogen bonds       : bond        0.04357 (  574)
  hydrogen bonds       : angle       4.64095 ( 1698)

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

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

  2410 Ramachandran restraints generated.
    1205 Oldfield, 0 Emsley, 1205 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2410 Ramachandran restraints generated.
    1205 Oldfield, 0 Emsley, 1205 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  185 residues out of total 1064 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 167
  time to evaluate  : 0.340 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  199 MET cc_start: 0.8178 (mmm) cc_final: 0.7659 (mmt)
REVERT: A  336 TRP cc_start: 0.7436 (m-10) cc_final: 0.7025 (m-10)
REVERT: A  369 PHE cc_start: 0.8815 (t80) cc_final: 0.8283 (t80)
REVERT: A  373 THR cc_start: 0.7062 (m) cc_final: 0.6617 (m)
REVERT: A  378 MET cc_start: 0.4151 (OUTLIER) cc_final: 0.3599 (tmm)
REVERT: A  436 LEU cc_start: 0.8894 (mp) cc_final: 0.8431 (mt)
REVERT: A  437 SER cc_start: 0.8956 (m) cc_final: 0.8377 (p)
REVERT: A  572 TYR cc_start: 0.8508 (m-10) cc_final: 0.8294 (m-10)
REVERT: A  620 ILE cc_start: 0.8002 (tt) cc_final: 0.7591 (tp)
REVERT: B   72 ASP cc_start: 0.8237 (t0) cc_final: 0.7936 (t0)
REVERT: B  105 THR cc_start: 0.8626 (m) cc_final: 0.8375 (m)
REVERT: B  351 ASN cc_start: 0.8837 (t0) cc_final: 0.8378 (t0)
REVERT: B  376 PHE cc_start: 0.8379 (t80) cc_final: 0.8050 (t80)
REVERT: B  381 ILE cc_start: 0.7980 (mm) cc_final: 0.7719 (mm)
REVERT: B  447 HIS cc_start: 0.8843 (m90) cc_final: 0.8552 (m170)
REVERT: B  570 PHE cc_start: 0.8443 (OUTLIER) cc_final: 0.7282 (t80)
REVERT: B  618 GLN cc_start: 0.8144 (tm-30) cc_final: 0.7847 (tm-30)
REVERT: B  661 ARG cc_start: 0.7223 (tpt170) cc_final: 0.7008 (tpt170)
  outliers start: 18
  outliers final: 15
  residues processed: 177
  average time/residue: 0.0624
  time to fit residues: 17.1886
Evaluate side-chains
  177 residues out of total 1064 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 160
  time to evaluate  : 0.329 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  157 TYR
Chi-restraints excluded: chain A residue  378 MET
Chi-restraints excluded: chain A residue  397 ILE
Chi-restraints excluded: chain A residue  412 VAL
Chi-restraints excluded: chain A residue  458 TYR
Chi-restraints excluded: chain A residue  463 ASN
Chi-restraints excluded: chain A residue  511 LEU
Chi-restraints excluded: chain A residue  559 VAL
Chi-restraints excluded: chain A residue  564 LEU
Chi-restraints excluded: chain B residue  302 VAL
Chi-restraints excluded: chain B residue  338 VAL
Chi-restraints excluded: chain B residue  366 ILE
Chi-restraints excluded: chain B residue  444 SER
Chi-restraints excluded: chain B residue  515 ILE
Chi-restraints excluded: chain B residue  570 PHE
Chi-restraints excluded: chain B residue  579 ILE
Chi-restraints excluded: chain B residue  601 VAL
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 122
   random chunks:
   chunk 120 optimal weight:    0.3980
   chunk 33 optimal weight:    8.9990
   chunk 56 optimal weight:    0.7980
   chunk 114 optimal weight:    1.9990
   chunk 79 optimal weight:    1.9990
   chunk 16 optimal weight:    0.8980
   chunk 23 optimal weight:    6.9990
   chunk 105 optimal weight:    4.9990
   chunk 41 optimal weight:    6.9990
   chunk 5 optimal weight:    0.0040
   chunk 20 optimal weight:    3.9990
   overall best weight:    0.8194

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

Flipped N/Q/H residues before XYZ refinement:
** B 208 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 308 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3852 r_free = 0.3852 target = 0.150903 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.3355 r_free = 0.3355 target = 0.114080 restraints weight = 15673.545|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 40)----------------|
| r_work = 0.3399 r_free = 0.3399 target = 0.117023 restraints weight = 9014.838|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 35)----------------|
| r_work = 0.3422 r_free = 0.3422 target = 0.118678 restraints weight = 6429.179|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 51)----------------|
| r_work = 0.3444 r_free = 0.3444 target = 0.120017 restraints weight = 5305.635|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 26)----------------|
| r_work = 0.3450 r_free = 0.3450 target = 0.120515 restraints weight = 4703.541|
|-----------------------------------------------------------------------------|
r_work (final): 0.3447
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7649
moved from start:          0.3524

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.041   8909  Z= 0.160
  Angle     :  0.774  14.214  12239  Z= 0.386
  Chirality :  0.043   0.225   1516
  Planarity :  0.006   0.106   1520
  Dihedral  :  5.973  61.531   1271
  Min Nonbonded Distance : 2.436

Molprobity Statistics.
  All-atom Clashscore : 11.97
  Ramachandran Plot:
    Outliers :  0.33 %
    Allowed  : 11.78 %
    Favored  : 87.88 %
  Rotamer:
    Outliers :  2.29 %
    Allowed  : 26.24 %
    Favored  : 71.46 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.09 %
    Twisted Proline : 3.57 %
    Twisted General : 0.43 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -0.50 (0.25), residues: 1205
  helix:  1.14 (0.19), residues: 792
  sheet: -1.60 (1.24), residues: 22
  loop : -3.51 (0.28), residues: 391

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG A 450 
 TYR   0.018   0.001   TYR A 364 
 PHE   0.041   0.001   PHE B 513 
 TRP   0.027   0.001   TRP B 548 
 HIS   0.005   0.001   HIS B 615 

Details of bonding type rmsd
  covalent geometry    : bond        0.00355 ( 8909)
  covalent geometry    : angle       0.77425 (12239)
  hydrogen bonds       : bond        0.04418 (  574)
  hydrogen bonds       : angle       4.68640 ( 1698)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 1442.23 seconds
wall clock time: 25 minutes 39.01 seconds (1539.01 seconds total)