Starting phenix.real_space_refine
on Wed Jan 15 18:10:40 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/8xvz_38724/01_2025/8xvz_38724.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/8xvz_38724/01_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_38724/01_2025/8xvz_38724.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/8xvz_38724/01_2025/8xvz_38724.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/8xvz_38724/01_2025/8xvz_38724.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/8xvz_38724/01_2025/8xvz_38724.cif"
  }
  resolution = 3.78
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }
  qi {
    qm_restraints {
      package {
        program = *test
      }
    }
  }


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): 0.02s

  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/modules/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: {'GLN:plan1': 9, 'TYR:plan': 7, 'ASN:plan1': 5, 'TRP:plan': 4, 'ASP:plan': 4, 'PHE:plan': 10, 'GLU:plan': 19, 'ARG:plan': 15}
          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: {'GLN:plan1': 9, 'TYR:plan': 8, 'ASN:plan1': 5, 'TRP:plan': 4, 'ASP:plan': 4, 'PHE:plan': 10, 'GLU:plan': 20, 'ARG:plan': 16}
          Unresolved non-hydrogen planarities: 375
  Time building chain proxies: 5.25, per 1000 atoms: 0.60
  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: 2.48
  Conformation dependent library (CDL) restraints added in 1.1 seconds
  

  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: 0.90
  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: 2.44

  Time building geometry restraints manager: 2.80 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:             0.880
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.000
  Construct map_model_manager:             0.000
  Extract box with map and model:          0.370
  Check model and map are aligned:         0.070
  Set scattering table:                    0.090
  Process input model:                     22.550
  Find NCS groups from input model:        0.330
  Set up NCS constraints:                  0.030
  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:             0.010
  Load rotamer database and sin/cos tables:2.840
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   27.170
-------------------------------------------------------------------------------
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= 0.699
  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 (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  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
 TRP   0.116   0.005   TRP A 336 
 HIS   0.007   0.002   HIS A 617 
 PHE   0.041   0.003   PHE A 640 
 TYR   0.072   0.003   TYR A 171 
 ARG   0.007   0.001   ARG B 661 

*********************** 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  : 1.022 
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: 0.1702
  time to fit residues: 41.7027
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  : 0.920 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 122
   random chunks:
   chunk 103 optimal weight:    0.9980
   chunk 92 optimal weight:    0.9980
   chunk 51 optimal weight:    0.9980
   chunk 31 optimal weight:    1.9990
   chunk 62 optimal weight:    5.9990
   chunk 49 optimal weight:    0.7980
   chunk 95 optimal weight:    2.9990
   chunk 37 optimal weight:    0.0970
   chunk 58 optimal weight:    0.5980
   chunk 71 optimal weight:    1.9990
   chunk 110 optimal weight:    5.9990
   overall best weight:    0.6978

-------------------------------------------------------------------------------
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 = 0.3772 r_free = 0.3772 target = 0.145959 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 43)----------------|
| r_work = 0.3312 r_free = 0.3312 target = 0.112366 restraints weight = 15347.376|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 42)----------------|
| r_work = 0.3347 r_free = 0.3347 target = 0.114731 restraints weight = 9625.683|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 28)----------------|
| r_work = 0.3364 r_free = 0.3364 target = 0.116029 restraints weight = 7229.955|
|-----------------------------------------------------------------------------|
r_work (final): 0.3356
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7802
moved from start:          0.1571

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.048   8909  Z= 0.246
  Angle     :  0.805  14.782  12239  Z= 0.422
  Chirality :  0.044   0.226   1516
  Planarity :  0.007   0.098   1520
  Dihedral  :  7.207  71.742   1271
  Min Nonbonded Distance : 2.493

Molprobity Statistics.
  All-atom Clashscore : 10.89
  Ramachandran Plot:
    Outliers :  0.33 %
    Allowed  : 13.36 %
    Favored  : 86.31 %
  Rotamer:
    Outliers :  2.04 %
    Allowed  : 11.72 %
    Favored  : 86.24 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.09 %
    Twisted Proline : 5.36 %
    Twisted General : 0.43 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -1.39 (0.25), residues: 1205
  helix:  0.43 (0.19), residues: 791
  sheet: -1.22 (1.77), residues: 12
  loop : -3.81 (0.28), residues: 402

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.057   0.002   TRP A 336 
 HIS   0.005   0.001   HIS B 615 
 PHE   0.036   0.002   PHE B 513 
 TYR   0.036   0.002   TYR A 171 
 ARG   0.005   0.001   ARG A 450 

*********************** 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
  182 residues out of total 1064 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 166
  time to evaluate  : 0.975 
Fit side-chains
REVERT: A  215 TYR cc_start: 0.8322 (t80) cc_final: 0.8065 (t80)
REVERT: A  374 ILE cc_start: 0.8220 (OUTLIER) cc_final: 0.7972 (mp)
REVERT: A  378 MET cc_start: 0.4490 (OUTLIER) cc_final: 0.3801 (tmm)
REVERT: A  437 SER cc_start: 0.9117 (m) cc_final: 0.8551 (p)
REVERT: B  210 GLU cc_start: 0.8636 (pm20) cc_final: 0.8295 (pm20)
REVERT: B  447 HIS cc_start: 0.8876 (m90) cc_final: 0.8527 (m170)
REVERT: B  618 GLN cc_start: 0.8274 (tm-30) cc_final: 0.7813 (tm-30)
  outliers start: 16
  outliers final: 6
  residues processed: 175
  average time/residue: 0.1609
  time to fit residues: 41.4003
Evaluate side-chains
  154 residues out of total 1064 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 146
  time to evaluate  : 0.937 
-------------------------------------------------------------------------------
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 39 optimal weight:    0.9980
   chunk 28 optimal weight:    0.7980
   chunk 30 optimal weight:    0.9980
   chunk 58 optimal weight:    0.6980
   chunk 103 optimal weight:    0.7980
   chunk 99 optimal weight:    0.6980
   chunk 12 optimal weight:    0.8980
   chunk 86 optimal weight:    2.9990
   chunk 20 optimal weight:    4.9990
   chunk 83 optimal weight:    5.9990
   chunk 60 optimal weight:    4.9990
   overall best weight:    0.7780

-------------------------------------------------------------------------------
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 = 0.3779 r_free = 0.3779 target = 0.146903 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 44)----------------|
| r_work = 0.3304 r_free = 0.3304 target = 0.112170 restraints weight = 15660.023|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 39)----------------|
| r_work = 0.3344 r_free = 0.3344 target = 0.114918 restraints weight = 9281.164|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 44)----------------|
| r_work = 0.3371 r_free = 0.3371 target = 0.116738 restraints weight = 6722.161|
|-----------------------------------------------------------------------------|
r_work (final): 0.3370
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7798
moved from start:          0.2055

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.050   8909  Z= 0.240
  Angle     :  0.762  13.734  12239  Z= 0.397
  Chirality :  0.043   0.182   1516
  Planarity :  0.006   0.102   1520
  Dihedral  :  6.827  70.346   1271
  Min Nonbonded Distance : 2.497

Molprobity Statistics.
  All-atom Clashscore : 11.37
  Ramachandran Plot:
    Outliers :  0.33 %
    Allowed  : 13.20 %
    Favored  : 86.47 %
  Rotamer:
    Outliers :  3.57 %
    Allowed  : 17.07 %
    Favored  : 79.36 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.09 %
    Twisted Proline : 3.57 %
    Twisted General : 0.52 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -1.15 (0.25), residues: 1205
  helix:  0.57 (0.19), residues: 798
  sheet:  0.42 (1.83), residues: 10
  loop : -3.71 (0.28), residues: 397

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.049   0.002   TRP A 336 
 HIS   0.005   0.001   HIS B 615 
 PHE   0.044   0.002   PHE B 513 
 TYR   0.029   0.001   TYR A 171 
 ARG   0.004   0.000   ARG B 661 

*********************** 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
  196 residues out of total 1064 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 28
    poor density    : 168
  time to evaluate  : 0.965 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  190 GLU cc_start: 0.8443 (pp20) cc_final: 0.8175 (pp20)
REVERT: A  378 MET cc_start: 0.4330 (OUTLIER) cc_final: 0.3595 (tmm)
REVERT: A  425 PHE cc_start: 0.7761 (t80) cc_final: 0.7393 (t80)
REVERT: A  437 SER cc_start: 0.9121 (m) cc_final: 0.8552 (p)
REVERT: A  620 ILE cc_start: 0.8183 (tt) cc_final: 0.7812 (tp)
REVERT: B   72 ASP cc_start: 0.8223 (t0) cc_final: 0.7973 (t0)
REVERT: B  369 PHE cc_start: 0.8299 (t80) cc_final: 0.8077 (t80)
REVERT: B  416 PHE cc_start: 0.7645 (OUTLIER) cc_final: 0.7330 (t80)
REVERT: B  447 HIS cc_start: 0.8868 (m90) cc_final: 0.8540 (m170)
REVERT: B  618 GLN cc_start: 0.8378 (tm-30) cc_final: 0.8008 (tm-30)
REVERT: B  649 LEU cc_start: 0.8802 (mt) cc_final: 0.8570 (mt)
  outliers start: 28
  outliers final: 12
  residues processed: 182
  average time/residue: 0.1657
  time to fit residues: 44.4896
Evaluate side-chains
  164 residues out of total 1064 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 150
  time to evaluate  : 0.947 
-------------------------------------------------------------------------------
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 A residue  599 LEU
Chi-restraints excluded: chain B residue  212 ILE
Chi-restraints excluded: chain B residue  416 PHE
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 73 optimal weight:    6.9990
   chunk 30 optimal weight:    5.9990
   chunk 107 optimal weight:    3.9990
   chunk 69 optimal weight:    0.8980
   chunk 15 optimal weight:    2.9990
   chunk 95 optimal weight:    0.9980
   chunk 31 optimal weight:    6.9990
   chunk 40 optimal weight:    0.7980
   chunk 57 optimal weight:    0.0670
   chunk 3 optimal weight:    4.9990
   chunk 50 optimal weight:    0.7980
   overall best weight:    0.7118

-------------------------------------------------------------------------------
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 = 0.3785 r_free = 0.3785 target = 0.146894 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 46)----------------|
| r_work = 0.3292 r_free = 0.3292 target = 0.110712 restraints weight = 15619.076|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 40)----------------|
| r_work = 0.3335 r_free = 0.3335 target = 0.113604 restraints weight = 8975.188|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 29)----------------|
| r_work = 0.3360 r_free = 0.3360 target = 0.115376 restraints weight = 6382.031|
|-----------------------------------------------------------------------------|
r_work (final): 0.3356
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7696
moved from start:          0.2340

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= 0.231
  Angle     :  0.756  13.041  12239  Z= 0.389
  Chirality :  0.043   0.225   1516
  Planarity :  0.006   0.103   1520
  Dihedral  :  6.647  69.629   1271
  Min Nonbonded Distance : 2.502

Molprobity Statistics.
  All-atom Clashscore : 10.77
  Ramachandran Plot:
    Outliers :  0.33 %
    Allowed  : 12.61 %
    Favored  : 87.05 %
  Rotamer:
    Outliers :  2.42 %
    Allowed  : 20.89 %
    Favored  : 76.69 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.09 %
    Twisted Proline : 3.57 %
    Twisted General : 0.43 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -1.06 (0.25), residues: 1205
  helix:  0.63 (0.19), residues: 794
  sheet:  0.13 (1.75), residues: 10
  loop : -3.60 (0.29), residues: 401

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.034   0.002   TRP A 336 
 HIS   0.006   0.001   HIS B 615 
 PHE   0.039   0.002   PHE B 513 
 TYR   0.022   0.001   TYR A 215 
 ARG   0.003   0.000   ARG A 450 

*********************** 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  : 1.174 
Fit side-chains
REVERT: A  190 GLU cc_start: 0.8552 (pp20) cc_final: 0.8308 (pp20)
REVERT: A  353 ASN cc_start: 0.8624 (t0) cc_final: 0.8376 (m-40)
REVERT: A  378 MET cc_start: 0.4390 (tmm) cc_final: 0.3710 (tmm)
REVERT: A  425 PHE cc_start: 0.7473 (t80) cc_final: 0.7151 (t80)
REVERT: A  436 LEU cc_start: 0.8916 (mp) cc_final: 0.8499 (mt)
REVERT: A  437 SER cc_start: 0.9020 (m) cc_final: 0.8434 (p)
REVERT: B   72 ASP cc_start: 0.8442 (t0) cc_final: 0.8160 (t0)
REVERT: B  308 GLN cc_start: 0.7481 (mt0) cc_final: 0.6539 (mt0)
REVERT: B  369 PHE cc_start: 0.8301 (t80) cc_final: 0.8073 (t80)
REVERT: B  376 PHE cc_start: 0.8199 (t80) cc_final: 0.7909 (t80)
REVERT: B  416 PHE cc_start: 0.7699 (OUTLIER) cc_final: 0.7408 (t80)
REVERT: B  447 HIS cc_start: 0.8923 (m90) cc_final: 0.8580 (m170)
REVERT: B  618 GLN cc_start: 0.8372 (tm-30) cc_final: 0.7975 (tm-30)
  outliers start: 19
  outliers final: 9
  residues processed: 172
  average time/residue: 0.1661
  time to fit residues: 42.2445
Evaluate side-chains
  157 residues out of total 1064 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 147
  time to evaluate  : 0.987 
-------------------------------------------------------------------------------
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  559 VAL
Chi-restraints excluded: chain B residue  231 THR
Chi-restraints excluded: chain B residue  416 PHE
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 71 optimal weight:    0.9990
   chunk 81 optimal weight:    4.9990
   chunk 112 optimal weight:    0.9990
   chunk 80 optimal weight:    0.6980
   chunk 100 optimal weight:    0.9990
   chunk 43 optimal weight:    5.9990
   chunk 15 optimal weight:    1.9990
   chunk 68 optimal weight:    0.0980
   chunk 82 optimal weight:    4.9990
   chunk 5 optimal weight:    6.9990
   chunk 56 optimal weight:    0.6980
   overall best weight:    0.6984

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

Flipped N/Q/H residues before XYZ refinement:
B 208 GLN
** 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 = 0.3797 r_free = 0.3797 target = 0.147994 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 51)----------------|
| r_work = 0.3320 r_free = 0.3320 target = 0.112637 restraints weight = 15542.325|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 30)----------------|
| r_work = 0.3353 r_free = 0.3353 target = 0.115069 restraints weight = 9446.879|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 46)----------------|
| r_work = 0.3382 r_free = 0.3382 target = 0.116947 restraints weight = 7027.511|
|-----------------------------------------------------------------------------|
r_work (final): 0.3384
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7666
moved from start:          0.2626

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.065   8909  Z= 0.226
  Angle     :  0.751  13.300  12239  Z= 0.385
  Chirality :  0.043   0.202   1516
  Planarity :  0.006   0.104   1520
  Dihedral  :  6.504  68.384   1271
  Min Nonbonded Distance : 2.509

Molprobity Statistics.
  All-atom Clashscore : 10.89
  Ramachandran Plot:
    Outliers :  0.25 %
    Allowed  : 12.70 %
    Favored  : 87.05 %
  Rotamer:
    Outliers :  3.31 %
    Allowed  : 22.17 %
    Favored  : 74.52 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.09 %
    Twisted Proline : 3.57 %
    Twisted General : 0.43 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.92 (0.25), residues: 1205
  helix:  0.69 (0.19), residues: 801
  sheet: -0.00 (1.75), residues: 10
  loop : -3.50 (0.29), residues: 394

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.024   0.001   TRP A 336 
 HIS   0.006   0.001   HIS B 615 
 PHE   0.047   0.002   PHE B 513 
 TYR   0.021   0.001   TYR A 171 
 ARG   0.002   0.000   ARG B 661 

*********************** 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: 26
    poor density    : 157
  time to evaluate  : 1.007 
Fit side-chains
   revert: symmetry clash
REVERT: A  336 TRP cc_start: 0.7337 (m-10) cc_final: 0.6930 (m-10)
REVERT: A  353 ASN cc_start: 0.8586 (t0) cc_final: 0.8362 (m-40)
REVERT: A  378 MET cc_start: 0.4392 (OUTLIER) cc_final: 0.3931 (tmm)
REVERT: A  425 PHE cc_start: 0.7483 (t80) cc_final: 0.7185 (t80)
REVERT: A  436 LEU cc_start: 0.8938 (mp) cc_final: 0.8513 (mt)
REVERT: A  437 SER cc_start: 0.9012 (m) cc_final: 0.8426 (p)
REVERT: A  620 ILE cc_start: 0.7959 (tt) cc_final: 0.7539 (tp)
REVERT: B   72 ASP cc_start: 0.8431 (t0) cc_final: 0.8146 (t0)
REVERT: B  376 PHE cc_start: 0.8274 (t80) cc_final: 0.7936 (t80)
REVERT: B  416 PHE cc_start: 0.7683 (OUTLIER) cc_final: 0.7411 (t80)
REVERT: B  447 HIS cc_start: 0.8940 (m90) cc_final: 0.8594 (m170)
REVERT: B  618 GLN cc_start: 0.8361 (tm-30) cc_final: 0.7952 (tm-30)
  outliers start: 26
  outliers final: 16
  residues processed: 172
  average time/residue: 0.1790
  time to fit residues: 45.3103
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  : 1.006 
-------------------------------------------------------------------------------
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 B residue  212 ILE
Chi-restraints excluded: chain B residue  231 THR
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 33 optimal weight:   10.0000
   chunk 58 optimal weight:    0.7980
   chunk 54 optimal weight:    0.6980
   chunk 106 optimal weight:    7.9990
   chunk 21 optimal weight:    9.9990
   chunk 115 optimal weight:    0.6980
   chunk 55 optimal weight:    0.6980
   chunk 46 optimal weight:    7.9990
   chunk 24 optimal weight:    0.6980
   chunk 43 optimal weight:    0.7980
   chunk 94 optimal weight:    3.9990
   overall best weight:    0.7180

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

Flipped N/Q/H residues before XYZ refinement:
** B 353 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 = 0.3812 r_free = 0.3812 target = 0.149145 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 53)----------------|
| r_work = 0.3334 r_free = 0.3334 target = 0.113525 restraints weight = 15548.667|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 44)----------------|
| r_work = 0.3373 r_free = 0.3373 target = 0.116249 restraints weight = 9453.364|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 29)----------------|
| r_work = 0.3393 r_free = 0.3393 target = 0.117707 restraints weight = 6926.203|
|-----------------------------------------------------------------------------|
r_work (final): 0.3384
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7672
moved from start:          0.2804

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.055   8909  Z= 0.226
  Angle     :  0.751  13.215  12239  Z= 0.382
  Chirality :  0.043   0.189   1516
  Planarity :  0.006   0.104   1520
  Dihedral  :  6.367  67.762   1271
  Min Nonbonded Distance : 2.506

Molprobity Statistics.
  All-atom Clashscore : 10.71
  Ramachandran Plot:
    Outliers :  0.25 %
    Allowed  : 12.61 %
    Favored  : 87.14 %
  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 (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.82 (0.25), residues: 1205
  helix:  0.81 (0.19), residues: 795
  sheet: -1.69 (1.16), residues: 22
  loop : -3.49 (0.29), residues: 388

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.023   0.001   TRP A 336 
 HIS   0.004   0.001   HIS B 615 
 PHE   0.043   0.002   PHE B 513 
 TYR   0.018   0.001   TYR A 171 
 ARG   0.002   0.000   ARG B 661 

*********************** 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
  179 residues out of total 1064 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 24
    poor density    : 155
  time to evaluate  : 0.964 
Fit side-chains
   revert: symmetry clash
REVERT: A  336 TRP cc_start: 0.7430 (m-10) cc_final: 0.6970 (m-10)
REVERT: A  378 MET cc_start: 0.4429 (OUTLIER) cc_final: 0.3754 (tmm)
REVERT: A  436 LEU cc_start: 0.8944 (mp) cc_final: 0.8519 (mt)
REVERT: A  437 SER cc_start: 0.9010 (m) cc_final: 0.8432 (p)
REVERT: A  572 TYR cc_start: 0.8530 (m-10) cc_final: 0.8232 (m-10)
REVERT: B   72 ASP cc_start: 0.8428 (t0) cc_final: 0.8139 (t0)
REVERT: B  447 HIS cc_start: 0.8939 (m90) cc_final: 0.8599 (m170)
REVERT: B  618 GLN cc_start: 0.8426 (tm-30) cc_final: 0.8063 (tm-30)
REVERT: B  661 ARG cc_start: 0.7356 (tpt170) cc_final: 0.6924 (tpt170)
  outliers start: 24
  outliers final: 16
  residues processed: 169
  average time/residue: 0.1702
  time to fit residues: 42.1846
Evaluate side-chains
  164 residues out of total 1064 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 147
  time to evaluate  : 0.926 
-------------------------------------------------------------------------------
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 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 97 optimal weight:    2.9990
   chunk 121 optimal weight:    0.9990
   chunk 86 optimal weight:    1.9990
   chunk 65 optimal weight:    0.0040
   chunk 89 optimal weight:    0.0470
   chunk 20 optimal weight:   10.0000
   chunk 114 optimal weight:    0.6980
   chunk 21 optimal weight:    5.9990
   chunk 74 optimal weight:    0.6980
   chunk 115 optimal weight:    0.6980
   chunk 107 optimal weight:    3.9990
   overall best weight:    0.4290

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

Flipped N/Q/H residues before XYZ refinement:
** A 308 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 353 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 = 0.3832 r_free = 0.3832 target = 0.150628 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.3361 r_free = 0.3361 target = 0.115456 restraints weight = 15494.232|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 45)----------------|
| r_work = 0.3399 r_free = 0.3399 target = 0.118092 restraints weight = 9336.449|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 31)----------------|
| r_work = 0.3423 r_free = 0.3423 target = 0.119801 restraints weight = 6818.919|
|-----------------------------------------------------------------------------|
r_work (final): 0.3419
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7624
moved from start:          0.3081

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= 0.209
  Angle     :  0.745  13.739  12239  Z= 0.378
  Chirality :  0.042   0.228   1516
  Planarity :  0.006   0.106   1520
  Dihedral  :  6.247  67.143   1271
  Min Nonbonded Distance : 2.506

Molprobity Statistics.
  All-atom Clashscore : 10.83
  Ramachandran Plot:
    Outliers :  0.25 %
    Allowed  : 12.20 %
    Favored  : 87.55 %
  Rotamer:
    Outliers :  3.06 %
    Allowed  : 24.46 %
    Favored  : 72.48 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.09 %
    Twisted Proline : 3.57 %
    Twisted General : 0.43 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.74 (0.25), residues: 1205
  helix:  0.87 (0.19), residues: 796
  sheet: -1.69 (1.17), residues: 22
  loop : -3.46 (0.29), residues: 387

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.024   0.001   TRP A 336 
 HIS   0.004   0.001   HIS B 615 
 PHE   0.043   0.001   PHE B 513 
 TYR   0.018   0.001   TYR A 364 
 ARG   0.002   0.000   ARG A 450 

*********************** 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
  192 residues out of total 1064 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 24
    poor density    : 168
  time to evaluate  : 1.019 
Fit side-chains
   revert: symmetry clash
REVERT: A  308 GLN cc_start: 0.8386 (mm-40) cc_final: 0.8158 (mm-40)
REVERT: A  336 TRP cc_start: 0.7277 (m-10) cc_final: 0.6952 (m-10)
REVERT: A  353 ASN cc_start: 0.8583 (t0) cc_final: 0.8053 (m-40)
REVERT: A  378 MET cc_start: 0.4396 (OUTLIER) cc_final: 0.3798 (tmm)
REVERT: A  436 LEU cc_start: 0.8877 (mp) cc_final: 0.8454 (mt)
REVERT: A  437 SER cc_start: 0.8959 (m) cc_final: 0.8362 (p)
REVERT: A  572 TYR cc_start: 0.8506 (m-10) cc_final: 0.8229 (m-10)
REVERT: A  620 ILE cc_start: 0.7979 (tt) cc_final: 0.7454 (tp)
REVERT: B   72 ASP cc_start: 0.8401 (t0) cc_final: 0.8104 (t0)
REVERT: B  231 THR cc_start: 0.7609 (OUTLIER) cc_final: 0.7338 (p)
REVERT: B  351 ASN cc_start: 0.8972 (OUTLIER) cc_final: 0.8403 (t0)
REVERT: B  447 HIS cc_start: 0.8909 (m90) cc_final: 0.8590 (m170)
REVERT: B  618 GLN cc_start: 0.8239 (tm-30) cc_final: 0.7963 (tm-30)
REVERT: B  661 ARG cc_start: 0.7366 (tpt170) cc_final: 0.7025 (tpt170)
  outliers start: 24
  outliers final: 18
  residues processed: 181
  average time/residue: 0.1695
  time to fit residues: 45.2595
Evaluate side-chains
  178 residues out of total 1064 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 157
  time to evaluate  : 0.999 
-------------------------------------------------------------------------------
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 B residue  212 ILE
Chi-restraints excluded: chain B residue  231 THR
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  601 VAL
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 122
   random chunks:
   chunk 8 optimal weight:    0.7980
   chunk 20 optimal weight:    3.9990
   chunk 99 optimal weight:    2.9990
   chunk 114 optimal weight:    0.5980
   chunk 41 optimal weight:    6.9990
   chunk 52 optimal weight:    2.9990
   chunk 90 optimal weight:    0.0970
   chunk 115 optimal weight:    0.6980
   chunk 62 optimal weight:   20.0000
   chunk 85 optimal weight:    3.9990
   chunk 95 optimal weight:    0.6980
   overall best weight:    0.5778

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

Flipped N/Q/H residues before XYZ refinement:
** A 308 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 392 ASN
B 208 GLN
** B 353 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3839 r_free = 0.3839 target = 0.151126 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 49)----------------|
| r_work = 0.3369 r_free = 0.3369 target = 0.115764 restraints weight = 15518.146|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 34)----------------|
| r_work = 0.3407 r_free = 0.3407 target = 0.118469 restraints weight = 9321.990|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 26)----------------|
| r_work = 0.3424 r_free = 0.3424 target = 0.119682 restraints weight = 6809.926|
|-----------------------------------------------------------------------------|
r_work (final): 0.3420
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7629
moved from start:          0.3264

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.044   8909  Z= 0.215
  Angle     :  0.766  17.489  12239  Z= 0.380
  Chirality :  0.043   0.261   1516
  Planarity :  0.006   0.106   1520
  Dihedral  :  6.105  65.225   1271
  Min Nonbonded Distance : 2.382

Molprobity Statistics.
  All-atom Clashscore : 10.53
  Ramachandran Plot:
    Outliers :  0.25 %
    Allowed  : 12.12 %
    Favored  : 87.63 %
  Rotamer:
    Outliers :  3.31 %
    Allowed  : 25.10 %
    Favored  : 71.59 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.09 %
    Twisted Proline : 3.57 %
    Twisted General : 0.43 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.64 (0.25), residues: 1205
  helix:  0.95 (0.19), residues: 796
  sheet: -1.74 (1.16), residues: 22
  loop : -3.44 (0.29), residues: 387

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.025   0.001   TRP B 548 
 HIS   0.005   0.001   HIS B 615 
 PHE   0.045   0.001   PHE B 513 
 TYR   0.018   0.001   TYR A 364 
 ARG   0.001   0.000   ARG A 450 

*********************** 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
  191 residues out of total 1064 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 26
    poor density    : 165
  time to evaluate  : 1.022 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  336 TRP cc_start: 0.7430 (m-10) cc_final: 0.6860 (m-10)
REVERT: A  378 MET cc_start: 0.4403 (OUTLIER) cc_final: 0.3805 (tmm)
REVERT: A  436 LEU cc_start: 0.8910 (mp) cc_final: 0.8477 (mt)
REVERT: A  437 SER cc_start: 0.8970 (m) cc_final: 0.8382 (p)
REVERT: A  572 TYR cc_start: 0.8598 (m-10) cc_final: 0.8346 (m-10)
REVERT: A  620 ILE cc_start: 0.7993 (tt) cc_final: 0.7435 (tp)
REVERT: B   72 ASP cc_start: 0.8387 (t0) cc_final: 0.8112 (t0)
REVERT: B  351 ASN cc_start: 0.8980 (OUTLIER) cc_final: 0.8242 (t0)
REVERT: B  447 HIS cc_start: 0.8905 (m90) cc_final: 0.8602 (m170)
REVERT: B  570 PHE cc_start: 0.8458 (OUTLIER) cc_final: 0.7071 (t80)
REVERT: B  618 GLN cc_start: 0.8333 (tm-30) cc_final: 0.7971 (tm-30)
REVERT: B  661 ARG cc_start: 0.7226 (tpt170) cc_final: 0.6939 (tpt170)
  outliers start: 26
  outliers final: 18
  residues processed: 177
  average time/residue: 0.1677
  time to fit residues: 43.8798
Evaluate side-chains
  176 residues out of total 1064 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 155
  time to evaluate  : 1.001 
-------------------------------------------------------------------------------
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  392 ASN
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  589 LEU
Chi-restraints excluded: chain B residue  212 ILE
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  416 PHE
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  589 LEU
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 41 optimal weight:    4.9990
   chunk 98 optimal weight:    4.9990
   chunk 105 optimal weight:    5.9990
   chunk 4 optimal weight:    0.3980
   chunk 120 optimal weight:    2.9990
   chunk 73 optimal weight:    0.7980
   chunk 47 optimal weight:    0.8980
   chunk 11 optimal weight:    0.0470
   chunk 79 optimal weight:    5.9990
   chunk 97 optimal weight:    4.9990
   chunk 50 optimal weight:    1.9990
   overall best weight:    0.8280

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

Flipped N/Q/H residues before XYZ refinement:
A 392 ASN
** 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 = 0.3842 r_free = 0.3842 target = 0.150160 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 42)----------------|
| r_work = 0.3353 r_free = 0.3353 target = 0.113857 restraints weight = 15830.148|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 36)----------------|
| r_work = 0.3395 r_free = 0.3395 target = 0.116698 restraints weight = 9245.627|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 30)----------------|
| r_work = 0.3416 r_free = 0.3416 target = 0.118277 restraints weight = 6618.221|
|-----------------------------------------------------------------------------|
r_work (final): 0.3414
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7725
moved from start:          0.3277

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.043   8909  Z= 0.230
  Angle     :  0.763  13.348  12239  Z= 0.384
  Chirality :  0.044   0.256   1516
  Planarity :  0.006   0.106   1520
  Dihedral  :  6.122  64.982   1271
  Min Nonbonded Distance : 2.360

Molprobity Statistics.
  All-atom Clashscore : 11.25
  Ramachandran Plot:
    Outliers :  0.25 %
    Allowed  : 12.28 %
    Favored  : 87.47 %
  Rotamer:
    Outliers :  2.93 %
    Allowed  : 25.48 %
    Favored  : 71.59 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.09 %
    Twisted Proline : 3.57 %
    Twisted General : 0.43 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.61 (0.25), residues: 1205
  helix:  0.99 (0.19), residues: 795
  sheet: -1.79 (1.15), residues: 22
  loop : -3.44 (0.29), residues: 388

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.026   0.001   TRP B 548 
 HIS   0.004   0.001   HIS B 615 
 PHE   0.043   0.001   PHE B 513 
 TYR   0.019   0.001   TYR A 364 
 ARG   0.002   0.000   ARG A 450 

*********************** 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
  179 residues out of total 1064 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 23
    poor density    : 156
  time to evaluate  : 1.022 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  336 TRP cc_start: 0.7399 (m-10) cc_final: 0.7038 (m-10)
REVERT: A  378 MET cc_start: 0.4370 (OUTLIER) cc_final: 0.3779 (tmm)
REVERT: A  437 SER cc_start: 0.9021 (m) cc_final: 0.8458 (p)
REVERT: A  572 TYR cc_start: 0.8618 (m-10) cc_final: 0.8385 (m-10)
REVERT: A  620 ILE cc_start: 0.8161 (tt) cc_final: 0.7577 (tp)
REVERT: B   72 ASP cc_start: 0.8229 (t0) cc_final: 0.7957 (t0)
REVERT: B  351 ASN cc_start: 0.8891 (OUTLIER) cc_final: 0.8252 (t0)
REVERT: B  376 PHE cc_start: 0.8366 (t80) cc_final: 0.8027 (t80)
REVERT: B  381 ILE cc_start: 0.8001 (mm) cc_final: 0.7747 (mm)
REVERT: B  447 HIS cc_start: 0.8875 (m90) cc_final: 0.8574 (m170)
REVERT: B  563 MET cc_start: 0.8889 (ttt) cc_final: 0.8682 (ttt)
REVERT: B  618 GLN cc_start: 0.8387 (tm-30) cc_final: 0.8020 (tm-30)
REVERT: B  661 ARG cc_start: 0.7328 (tpt170) cc_final: 0.7051 (tpt170)
  outliers start: 23
  outliers final: 20
  residues processed: 166
  average time/residue: 0.1650
  time to fit residues: 41.0063
Evaluate side-chains
  177 residues out of total 1064 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 22
    poor density    : 155
  time to evaluate  : 1.043 
-------------------------------------------------------------------------------
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  392 ASN
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 A residue  589 LEU
Chi-restraints excluded: chain B residue  212 ILE
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  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=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 122
   random chunks:
   chunk 92 optimal weight:    0.2980
   chunk 40 optimal weight:    1.9990
   chunk 66 optimal weight:    3.9990
   chunk 23 optimal weight:    2.9990
   chunk 110 optimal weight:    0.9990
   chunk 10 optimal weight:    0.0370
   chunk 81 optimal weight:    0.0000
   chunk 46 optimal weight:    0.0470
   chunk 24 optimal weight:    2.9990
   chunk 99 optimal weight:    0.7980
   chunk 97 optimal weight:    3.9990
   overall best weight:    0.2360

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

Flipped N/Q/H residues before XYZ refinement:
** B 353 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 = 0.3874 r_free = 0.3874 target = 0.152640 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 42)----------------|
| r_work = 0.3394 r_free = 0.3394 target = 0.116689 restraints weight = 15601.900|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 38)----------------|
| r_work = 0.3437 r_free = 0.3437 target = 0.119632 restraints weight = 9034.705|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 26)----------------|
| r_work = 0.3455 r_free = 0.3455 target = 0.121000 restraints weight = 6434.911|
|-----------------------------------------------------------------------------|
r_work (final): 0.3453
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7680
moved from start:          0.3478

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.041   8909  Z= 0.202
  Angle     :  0.756  13.769  12239  Z= 0.378
  Chirality :  0.043   0.235   1516
  Planarity :  0.006   0.106   1520
  Dihedral  :  6.067  63.586   1271
  Min Nonbonded Distance : 2.441

Molprobity Statistics.
  All-atom Clashscore : 10.41
  Ramachandran Plot:
    Outliers :  0.25 %
    Allowed  : 11.87 %
    Favored  : 87.88 %
  Rotamer:
    Outliers :  2.80 %
    Allowed  : 25.86 %
    Favored  : 71.34 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.09 %
    Twisted Proline : 3.57 %
    Twisted General : 0.43 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.56 (0.25), residues: 1205
  helix:  1.01 (0.19), residues: 796
  sheet: -1.75 (1.16), residues: 22
  loop : -3.39 (0.29), residues: 387

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.023   0.001   TRP B 548 
 HIS   0.005   0.001   HIS B 615 
 PHE   0.042   0.001   PHE B 513 
 TYR   0.018   0.001   TYR A 364 
 ARG   0.001   0.000   ARG A 450 

********************** 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
  181 residues out of total 1064 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 22
    poor density    : 159
  time to evaluate  : 0.918 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  308 GLN cc_start: 0.8203 (mm-40) cc_final: 0.7883 (mm110)
REVERT: A  336 TRP cc_start: 0.7260 (m-10) cc_final: 0.6960 (m-10)
REVERT: A  369 PHE cc_start: 0.8806 (t80) cc_final: 0.8547 (t80)
REVERT: A  378 MET cc_start: 0.4353 (OUTLIER) cc_final: 0.3779 (tmm)
REVERT: A  436 LEU cc_start: 0.8880 (mp) cc_final: 0.8431 (mt)
REVERT: A  437 SER cc_start: 0.8967 (m) cc_final: 0.8388 (p)
REVERT: A  572 TYR cc_start: 0.8635 (m-10) cc_final: 0.8433 (m-10)
REVERT: A  620 ILE cc_start: 0.8177 (tt) cc_final: 0.7677 (tp)
REVERT: B   72 ASP cc_start: 0.8187 (t0) cc_final: 0.7917 (t0)
REVERT: B  351 ASN cc_start: 0.8870 (OUTLIER) cc_final: 0.8305 (t0)
REVERT: B  376 PHE cc_start: 0.8353 (t80) cc_final: 0.8016 (t80)
REVERT: B  570 PHE cc_start: 0.8475 (OUTLIER) cc_final: 0.7169 (t80)
REVERT: B  618 GLN cc_start: 0.8325 (tm-30) cc_final: 0.7970 (tm-30)
REVERT: B  661 ARG cc_start: 0.7317 (tpt170) cc_final: 0.7073 (tpt170)
  outliers start: 22
  outliers final: 17
  residues processed: 170
  average time/residue: 0.1599
  time to fit residues: 41.4257
Evaluate side-chains
  174 residues out of total 1064 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 154
  time to evaluate  : 0.980 
-------------------------------------------------------------------------------
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  212 ILE
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  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  570 PHE
Chi-restraints excluded: chain B residue  589 LEU
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 18 optimal weight:    0.0970
   chunk 94 optimal weight:    5.9990
   chunk 32 optimal weight:    3.9990
   chunk 54 optimal weight:    0.9980
   chunk 64 optimal weight:    1.9990
   chunk 55 optimal weight:    0.9980
   chunk 29 optimal weight:    4.9990
   chunk 30 optimal weight:    4.9990
   chunk 40 optimal weight:    3.9990
   chunk 119 optimal weight:    0.2980
   chunk 89 optimal weight:    0.7980
   overall best weight:    0.6378

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

Flipped N/Q/H residues before XYZ refinement:
** B 353 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 = 0.3860 r_free = 0.3860 target = 0.151674 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 56)----------------|
| r_work = 0.3374 r_free = 0.3374 target = 0.115196 restraints weight = 15738.677|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 32)----------------|
| r_work = 0.3412 r_free = 0.3412 target = 0.117953 restraints weight = 9242.552|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 42)----------------|
| r_work = 0.3441 r_free = 0.3441 target = 0.119868 restraints weight = 6717.834|
|-----------------------------------------------------------------------------|
r_work (final): 0.3438
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7699
moved from start:          0.3508

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.039   8909  Z= 0.219
  Angle     :  0.764  14.076  12239  Z= 0.381
  Chirality :  0.043   0.225   1516
  Planarity :  0.006   0.106   1520
  Dihedral  :  5.982  62.470   1271
  Min Nonbonded Distance : 2.454

Molprobity Statistics.
  All-atom Clashscore : 10.53
  Ramachandran Plot:
    Outliers :  0.25 %
    Allowed  : 12.03 %
    Favored  : 87.72 %
  Rotamer:
    Outliers :  2.80 %
    Allowed  : 26.24 %
    Favored  : 70.96 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.09 %
    Twisted Proline : 3.57 %
    Twisted General : 0.43 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.47 (0.26), residues: 1205
  helix:  1.16 (0.20), residues: 780
  sheet: -1.81 (1.12), residues: 22
  loop : -3.34 (0.28), residues: 403

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.024   0.001   TRP B 548 
 HIS   0.006   0.001   HIS B 615 
 PHE   0.041   0.001   PHE B 513 
 TYR   0.017   0.001   TYR A 364 
 ARG   0.002   0.000   ARG A 450 
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 2499.78 seconds
wall clock time: 45 minutes 49.31 seconds (2749.31 seconds total)