Starting phenix.real_space_refine
on Tue Mar  3 15:54:01 2026 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/7s1y_24812/03_2026/7s1y_24812.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/7s1y_24812/03_2026/7s1y_24812.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.6
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/7s1y_24812/03_2026/7s1y_24812.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/7s1y_24812/03_2026/7s1y_24812.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/7s1y_24812/03_2026/7s1y_24812.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/7s1y_24812/03_2026/7s1y_24812.cif"
  }
  resolution = 3.6
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }


Starting job
===============================================================================
-------------------------------------------------------------------------------
Citation:
*********
Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams
PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography.
Acta Cryst. D74:531-544.

Validating inputs
Origin is already at (0, 0, 0), no shifts will be applied
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=   0.008 sd=   0.074
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: 6
    Type Number    sf(0)   Gaussians
     K       2      8.98       5
     S      34      5.16       5
     Cl      2      4.86       5
     C    4338      2.51       5
     N    1054      2.21       5
     O    1150      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 8 residue(s): 0.00s

  Monomer Library directory:
    "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/chem_data/mon_lib"
  Total number of atoms: 6580
  Number of models: 1
  Model: ""
    Number of chains: 4
    Chain: "A"
      Number of atoms: 3263
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 474, 3263
          Classifications: {'peptide': 474}
          Incomplete info: {'backbone_only': 21, 'truncation_to_alanine': 78}
          Link IDs: {'PTRANS': 16, 'TRANS': 457}
          Unresolved non-hydrogen bonds: 348
          Unresolved non-hydrogen angles: 449
          Unresolved non-hydrogen dihedrals: 258
          Unresolved non-hydrogen chiralities: 55
          Planarities with less than four sites: {'ASN:plan1': 9, 'PHE:plan': 4, 'ARG:plan': 3, 'GLU:plan': 12, 'ASP:plan': 8, 'GLN:plan1': 3, 'TYR:plan': 1}
          Unresolved non-hydrogen planarities: 162
    Chain: "B"
      Number of atoms: 3263
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 474, 3263
          Classifications: {'peptide': 474}
          Incomplete info: {'backbone_only': 21, 'truncation_to_alanine': 78}
          Link IDs: {'PTRANS': 16, 'TRANS': 457}
          Unresolved non-hydrogen bonds: 348
          Unresolved non-hydrogen angles: 449
          Unresolved non-hydrogen dihedrals: 258
          Unresolved non-hydrogen chiralities: 55
          Planarities with less than four sites: {'ASN:plan1': 9, 'PHE:plan': 4, 'ARG:plan': 3, 'GLU:plan': 12, 'ASP:plan': 8, 'GLN:plan1': 3, 'TYR:plan': 1}
          Unresolved non-hydrogen planarities: 162
    Chain: "A"
      Number of atoms: 27
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 3, 27
          Unusual residues: {'  K': 1, ' CL': 1, '82U': 1}
          Classifications: {'undetermined': 3}
          Link IDs: {None: 2}
    Chain: "B"
      Number of atoms: 27
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 3, 27
          Unusual residues: {'  K': 1, ' CL': 1, '82U': 1}
          Classifications: {'undetermined': 3}
          Link IDs: {None: 2}
  Time building chain proxies: 1.54, per 1000 atoms: 0.23
  Number of scatterers: 6580
  At special positions: 0
  Unit cell: (107.06, 66.78, 86.92, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 6
    Type Number    sf(0)
     K       2     19.00
     Cl      2     17.00
     S      34     16.00
     O    1150      8.00
     N    1054      7.00
     C    4338      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=4, symmetry=0
    Simple disulfide: pdb=" SG  CYS A 563 " - pdb=" SG  CYS A 568 " distance=2.03
    Simple disulfide: pdb=" SG  CYS A 577 " - pdb=" SG  CYS A 582 " distance=2.03
    Simple disulfide: pdb=" SG  CYS B 563 " - pdb=" SG  CYS B 568 " distance=2.04
    Simple disulfide: pdb=" SG  CYS B 577 " - pdb=" SG  CYS B 582 " distance=2.03

  Automatic linking
    Parameters for automatic linking
      Linking & cutoffs
        Metal                : Auto  - 3.00
        Amino acid           : True  - 1.90
        Carbohydrate         : True  - 1.99
        Ligands              : True  - 1.99
        Small molecules      : False - 1.98
        Amino acid - RNA/DNA : False
      
  Number of custom bonds: simple=2, symmetry=0
  Number of additional bonds: simple=2, symmetry=0
  Coordination:
  Other bonds:
  Time building additional restraints: 0.67
  Conformation dependent library (CDL) restraints added in 343.9 milliseconds
  

  1888 Ramachandran restraints generated.
    944 Oldfield, 0 Emsley, 944 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
    Skipped
      Input volumes are d-peptide like
        pdb=" CB  82U A1303 "
        pdb=" CB  82U B1303 "
  Number of C-beta restraints generated:  1648

  Finding SS restraints...
    Secondary structure from input PDB file:
      40 helices and 0 sheets defined
      74.3% alpha, 0.0% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.18
  Creating SS restraints...
    Processing helix  chain 'A' and resid 286 through 300
      removed outlier: 3.742A  pdb=" N   GLY A 290 " --> pdb=" O   GLY A 286 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 306 through 315
      removed outlier: 4.033A  pdb=" N   TRP A 310 " --> pdb=" O   ILE A 306 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 316 through 343
      removed outlier: 4.321A  pdb=" N   LEU A 322 " --> pdb=" O   GLY A 318 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 351 through 361
      removed outlier: 3.760A  pdb=" N   LEU A 355 " --> pdb=" O   GLY A 351 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 361 through 399
      removed outlier: 3.743A  pdb=" N   ALA A 381 " --> pdb=" O   ALA A 377 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 404 through 425
      removed outlier: 4.241A  pdb=" N   ILE A 409 " --> pdb=" O   GLU A 405 " (cutoff:3.500A)
      removed outlier: 5.403A  pdb=" N   ARG A 410 " --> pdb=" O   ILE A 406 " (cutoff:3.500A)
      removed outlier: 3.852A  pdb=" N   ILE A 415 " --> pdb=" O   ILE A 411 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 426 through 455
      removed outlier: 4.320A  pdb=" N   TRP A 430 " --> pdb=" O   ALA A 426 " (cutoff:3.500A)
      removed outlier: 3.962A  pdb=" N   GLU A 431 " --> pdb=" O   GLY A 427 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 457 through 461
      removed outlier: 3.657A  pdb=" N   LYS A 460 " --> pdb=" O   LEU A 457 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 469 through 475
    Processing helix  chain 'A' and resid 486 through 499
      Proline residue:  A 496  - end of helix
    Processing helix  chain 'A' and resid 502 through 507
      removed outlier: 3.516A  pdb=" N   ILE A 507 " --> pdb=" O   ALA A 503 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 508 through 511
      removed outlier: 3.688A  pdb=" N   LEU A 511 " --> pdb=" O   SER A 508 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'A' and resid 508 through 511'
    Processing helix  chain 'A' and resid 516 through 544
      removed outlier: 4.436A  pdb=" N   LYS A 520 " --> pdb=" O   SER A 516 " (cutoff:3.500A)
      removed outlier: 3.672A  pdb=" N   LEU A 524 " --> pdb=" O   LYS A 520 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 565 through 571
      removed outlier: 4.530A  pdb=" N   LYS A 569 " --> pdb=" O   SER A 565 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 591 through 596
    Processing helix  chain 'A' and resid 599 through 632
      removed outlier: 3.512A  pdb=" N   ILE A 603 " --> pdb=" O   PHE A 599 " (cutoff:3.500A)
      Proline residue:  A 623  - end of helix
      removed outlier: 3.825A  pdb=" N   ASP A 632 " --> pdb=" O   ALA A 628 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 651 through 669
    Processing helix  chain 'A' and resid 674 through 699
      removed outlier: 4.476A  pdb=" N   ASN A 680 " --> pdb=" O   PRO A 676 " (cutoff:3.500A)
      removed outlier: 4.762A  pdb=" N   PHE A 681 " --> pdb=" O   ILE A 677 " (cutoff:3.500A)
      removed outlier: 4.066A  pdb=" N   PHE A 682 " --> pdb=" O   ILE A 678 " (cutoff:3.500A)
      removed outlier: 3.964A  pdb=" N   LEU A 683 " --> pdb=" O   SER A 679 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 713 through 730
      removed outlier: 3.831A  pdb=" N   LEU A 717 " --> pdb=" O   MET A 713 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 731 through 752
    Processing helix  chain 'B' and resid 286 through 300
      removed outlier: 3.680A  pdb=" N   GLY B 290 " --> pdb=" O   GLY B 286 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 306 through 315
      removed outlier: 4.056A  pdb=" N   TRP B 310 " --> pdb=" O   ILE B 306 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 316 through 343
      removed outlier: 4.364A  pdb=" N   LEU B 322 " --> pdb=" O   GLY B 318 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 351 through 361
      removed outlier: 3.752A  pdb=" N   LEU B 355 " --> pdb=" O   GLY B 351 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 361 through 399
      removed outlier: 3.631A  pdb=" N   ALA B 381 " --> pdb=" O   ALA B 377 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 404 through 425
      removed outlier: 4.173A  pdb=" N   ILE B 409 " --> pdb=" O   GLU B 405 " (cutoff:3.500A)
      removed outlier: 5.280A  pdb=" N   ARG B 410 " --> pdb=" O   ILE B 406 " (cutoff:3.500A)
      removed outlier: 3.898A  pdb=" N   ILE B 415 " --> pdb=" O   ILE B 411 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 426 through 455
      removed outlier: 4.324A  pdb=" N   TRP B 430 " --> pdb=" O   ALA B 426 " (cutoff:3.500A)
      removed outlier: 3.890A  pdb=" N   GLU B 431 " --> pdb=" O   GLY B 427 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 457 through 461
      removed outlier: 3.647A  pdb=" N   LYS B 460 " --> pdb=" O   LEU B 457 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 469 through 475
      removed outlier: 3.515A  pdb=" N   PHE B 473 " --> pdb=" O   LYS B 469 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 486 through 499
      Proline residue:  B 496  - end of helix
    Processing helix  chain 'B' and resid 502 through 507
    Processing helix  chain 'B' and resid 508 through 511
      removed outlier: 3.670A  pdb=" N   LEU B 511 " --> pdb=" O   SER B 508 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'B' and resid 508 through 511'
    Processing helix  chain 'B' and resid 516 through 544
      removed outlier: 4.373A  pdb=" N   LYS B 520 " --> pdb=" O   SER B 516 " (cutoff:3.500A)
      removed outlier: 3.704A  pdb=" N   LEU B 524 " --> pdb=" O   LYS B 520 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 565 through 571
      removed outlier: 4.120A  pdb=" N   LYS B 569 " --> pdb=" O   SER B 565 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 591 through 596
    Processing helix  chain 'B' and resid 599 through 632
      removed outlier: 3.612A  pdb=" N   ILE B 603 " --> pdb=" O   PHE B 599 " (cutoff:3.500A)
      Proline residue:  B 623  - end of helix
      removed outlier: 3.844A  pdb=" N   ASP B 632 " --> pdb=" O   ALA B 628 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 651 through 669
    Processing helix  chain 'B' and resid 674 through 699
      removed outlier: 4.145A  pdb=" N   ASN B 680 " --> pdb=" O   PRO B 676 " (cutoff:3.500A)
      removed outlier: 4.598A  pdb=" N   PHE B 681 " --> pdb=" O   ILE B 677 " (cutoff:3.500A)
      removed outlier: 4.112A  pdb=" N   PHE B 682 " --> pdb=" O   ILE B 678 " (cutoff:3.500A)
      removed outlier: 3.969A  pdb=" N   LEU B 683 " --> pdb=" O   SER B 679 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 713 through 730
      removed outlier: 4.036A  pdb=" N   LEU B 717 " --> pdb=" O   MET B 713 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 731 through 752

    490 hydrogen bonds defined for protein.
    1464 hydrogen bond angles defined for protein.
    Restraints generated for nucleic acids:
      0 hydrogen bonds
      0 hydrogen bond angles
      0 basepair planarities
      0 basepair parallelities
      0 stacking parallelities
  Total time for adding SS restraints: 0.93

  Time building geometry restraints manager: 0.85 seconds

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

  Histogram of bond lengths:
        1.23 -     1.34: 2040
        1.34 -     1.46: 1702
        1.46 -     1.58: 2942
        1.58 -     1.70: 2
        1.70 -     1.81: 50
  Bond restraints: 6736
  Sorted by residual:
  bond pdb=" CG  PRO A 676 "
       pdb=" CD  PRO A 676 "
    ideal  model  delta    sigma   weight residual
    1.503  1.346  0.157 3.40e-02 8.65e+02 2.15e+01
  bond pdb=" N   82U A1303 "
       pdb=" CA  82U A1303 "
    ideal  model  delta    sigma   weight residual
    1.366  1.442 -0.076 2.00e-02 2.50e+03 1.44e+01
  bond pdb=" N   82U B1303 "
       pdb=" CA  82U B1303 "
    ideal  model  delta    sigma   weight residual
    1.366  1.439 -0.073 2.00e-02 2.50e+03 1.34e+01
  bond pdb=" CB  PRO A 676 "
       pdb=" CG  PRO A 676 "
    ideal  model  delta    sigma   weight residual
    1.492  1.658 -0.166 5.00e-02 4.00e+02 1.11e+01
  bond pdb=" N   PRO A 676 "
       pdb=" CD  PRO A 676 "
    ideal  model  delta    sigma   weight residual
    1.473  1.516 -0.043 1.40e-02 5.10e+03 9.51e+00
  ... (remaining 6731 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     3.14: 9126
        3.14 -     6.28: 84
        6.28 -     9.42: 10
        9.42 -    12.56: 1
       12.56 -    15.70: 1
  Bond angle restraints: 9222
  Sorted by residual:
  angle pdb=" CA  PRO A 676 "
        pdb=" N   PRO A 676 "
        pdb=" CD  PRO A 676 "
      ideal   model   delta    sigma   weight residual
     112.00   96.30   15.70 1.40e+00 5.10e-01 1.26e+02
  angle pdb=" N   PRO A 676 "
        pdb=" CD  PRO A 676 "
        pdb=" CG  PRO A 676 "
      ideal   model   delta    sigma   weight residual
     103.20   92.75   10.45 1.50e+00 4.44e-01 4.85e+01
  angle pdb=" CA  PRO A 636 "
        pdb=" N   PRO A 636 "
        pdb=" CD  PRO A 636 "
      ideal   model   delta    sigma   weight residual
     112.00  104.41    7.59 1.40e+00 5.10e-01 2.94e+01
  angle pdb=" CA  PRO A 676 "
        pdb=" CB  PRO A 676 "
        pdb=" CG  PRO A 676 "
      ideal   model   delta    sigma   weight residual
     104.50   97.20    7.30 1.90e+00 2.77e-01 1.48e+01
  angle pdb=" C   PRO A 676 "
        pdb=" CA  PRO A 676 "
        pdb=" CB  PRO A 676 "
      ideal   model   delta    sigma   weight residual
     110.88  115.84   -4.96 1.41e+00 5.03e-01 1.24e+01
  ... (remaining 9217 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    17.69: 3427
       17.69 -    35.39: 286
       35.39 -    53.08: 37
       53.08 -    70.77: 5
       70.77 -    88.47: 3
  Dihedral angle restraints: 3758
    sinusoidal: 1134
      harmonic: 2624
  Sorted by residual:
  dihedral pdb=" CB  CYS B 563 "
           pdb=" SG  CYS B 563 "
           pdb=" SG  CYS B 568 "
           pdb=" CB  CYS B 568 "
      ideal   model   delta sinusoidal    sigma   weight residual
      93.00  168.61  -75.61     1      1.00e+01 1.00e-02 7.21e+01
  dihedral pdb=" CB  CYS A 563 "
           pdb=" SG  CYS A 563 "
           pdb=" SG  CYS A 568 "
           pdb=" CB  CYS A 568 "
      ideal   model   delta sinusoidal    sigma   weight residual
      93.00  148.54  -55.54     1      1.00e+01 1.00e-02 4.17e+01
  dihedral pdb=" CA  TYR B 711 "
           pdb=" C   TYR B 711 "
           pdb=" N   ASN B 712 "
           pdb=" CA  ASN B 712 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  157.13   22.87     0      5.00e+00 4.00e-02 2.09e+01
  ... (remaining 3755 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.053: 862
       0.053 -    0.106: 214
       0.106 -    0.159: 15
       0.159 -    0.212: 0
       0.212 -    0.265: 3
  Chirality restraints: 1094
  Sorted by residual:
  chirality pdb=" CA  TYR A 711 "
            pdb=" N   TYR A 711 "
            pdb=" C   TYR A 711 "
            pdb=" CB  TYR A 711 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.25    0.27 2.00e-01 2.50e+01 1.76e+00
  chirality pdb=" CA  TYR B 711 "
            pdb=" N   TYR B 711 "
            pdb=" C   TYR B 711 "
            pdb=" CB  TYR B 711 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.25    0.26 2.00e-01 2.50e+01 1.73e+00
  chirality pdb=" CA  PRO A 676 "
            pdb=" N   PRO A 676 "
            pdb=" C   PRO A 676 "
            pdb=" CB  PRO A 676 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.72    2.48    0.24 2.00e-01 2.50e+01 1.47e+00
  ... (remaining 1091 not shown)

  Planarity restraints: 1158
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   TYR A 635 "    0.090 5.00e-02 4.00e+02   1.31e-01 2.76e+01
        pdb=" N   PRO A 636 "   -0.227 5.00e-02 4.00e+02
        pdb=" CA  PRO A 636 "    0.068 5.00e-02 4.00e+02
        pdb=" CD  PRO A 636 "    0.069 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   ALA A 675 "    0.084 5.00e-02 4.00e+02   1.14e-01 2.10e+01
        pdb=" N   PRO A 676 "   -0.197 5.00e-02 4.00e+02
        pdb=" CA  PRO A 676 "    0.051 5.00e-02 4.00e+02
        pdb=" CD  PRO A 676 "    0.063 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  ILE B 288 "   -0.009 2.00e-02 2.50e+03   1.78e-02 3.16e+00
        pdb=" C   ILE B 288 "    0.031 2.00e-02 2.50e+03
        pdb=" O   ILE B 288 "   -0.012 2.00e-02 2.50e+03
        pdb=" N   ASN B 289 "   -0.010 2.00e-02 2.50e+03
  ... (remaining 1155 not shown)

  Histogram of nonbonded interaction distances:
        1.57 -     2.28: 4
        2.28 -     3.00: 3840
        3.00 -     3.71: 12513
        3.71 -     4.43: 17616
        4.43 -     5.14: 28763
  Nonbonded interactions: 62736
  Sorted by model distance:
  nonbonded pdb=" K     K A1301 "
            pdb=" O5  82U A1303 "
     model   vdw
     1.566 2.850
  nonbonded pdb=" K     K B1301 "
            pdb=" O5  82U B1303 "
     model   vdw
     1.614 2.850
  nonbonded pdb=" OG  SER A 339 "
            pdb=" OH  TYR A 711 "
     model   vdw
     2.133 3.040
  nonbonded pdb=" OG  SER B 339 "
            pdb=" OH  TYR B 711 "
     model   vdw
     2.142 3.040
  nonbonded pdb=" OE1 GLU B 485 "
            pdb=" OG  SER B 489 "
     model   vdw
     2.313 3.040
  ... (remaining 62731 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: 0.01
Found NCS groups:
ncs_group {
  reference = chain 'A'
  selection = chain 'B'
}

Set up NCS constraints
  No NCS constraints will be used in refinement.
Set refine NCS operators
Adjust number of macro_cycles
  Number of macro_cycles: 10
Reset NCS operators
Extract rigid body selections
Check and reset occupancies
  Occupancies: min=1.00 max=1.00 mean=1.00
Load rotamer database and sin/cos tables
Set ADP refinement strategy
  ADPs will be refined as group one per residue
Make a string to write initial .geo file
Internal consistency checks
Time:
  Set random seed:                         0.000
  Set model cs if undefined:               0.000
  Decide on map wrapping:                  0.000
  Normalize map: mean=0, sd=1:             1.520
  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:          0.060
  Check model and map are aligned:         0.020
  Set scattering table:                    0.010
  Process input model:                     7.350
  Find NCS groups from input model:        0.100
  Set up NCS constraints:                  0.010
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.000
  Load rotamer database and sin/cos tables:1.350
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   10.420
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.5418
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      :  0.005   0.166   6742  Z= 0.198
  Angle     :  0.773  15.702   9230  Z= 0.417
  Chirality :  0.044   0.265   1094
  Planarity :  0.006   0.131   1158
  Dihedral  : 12.892  88.467   2098
  Min Nonbonded Distance : 1.566

Molprobity Statistics.
  All-atom Clashscore : 13.33
  Ramachandran Plot:
    Outliers :  0.21 %
    Allowed  :  7.20 %
    Favored  : 92.58 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.87 %
    Favored  : 99.13 %
  Cbeta Deviations :  0.24 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -0.33 (0.28), residues: 944
  helix:  0.96 (0.21), residues: 616
  sheet:  None (None), residues: 0
  loop : -2.61 (0.32), residues: 328

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.001   0.000   ARG A 358 
 TYR   0.016   0.001   TYR B 739 
 PHE   0.025   0.001   PHE A 608 
 TRP   0.017   0.001   TRP A 287 
 HIS   0.004   0.001   HIS A 398 

Details of bonding type rmsd
  covalent geometry    : bond        0.00468 ( 6736)
  covalent geometry    : angle       0.77208 ( 9222)
  SS BOND              : bond        0.00439 (    4)
  SS BOND              : angle       1.59179 (    8)
  hydrogen bonds       : bond        0.10765 (  490)
  hydrogen bonds       : angle       5.22050 ( 1464)
  Misc. bond           : bond        0.00079 (    2)

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

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

  1888 Ramachandran restraints generated.
    944 Oldfield, 0 Emsley, 944 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1888 Ramachandran restraints generated.
    944 Oldfield, 0 Emsley, 944 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  153 residues out of total 772 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 153
  time to evaluate  : 0.154 
Fit side-chains
REVERT: A  389 GLU cc_start: 0.7564 (mt-10) cc_final: 0.7227 (mt-10)
REVERT: A  465 PHE cc_start: 0.7882 (t80) cc_final: 0.7521 (t80)
REVERT: A  471 GLU cc_start: 0.8330 (tm-30) cc_final: 0.7788 (tt0)
REVERT: A  630 CYS cc_start: 0.3999 (m) cc_final: 0.3590 (p)
REVERT: A  676 PRO cc_start: 0.7727 (Cg_endo) cc_final: 0.7511 (Cg_exo)
REVERT: A  725 ILE cc_start: 0.8035 (mm) cc_final: 0.7791 (mt)
REVERT: B  630 CYS cc_start: 0.4421 (m) cc_final: 0.3868 (p)
REVERT: B  677 ILE cc_start: 0.7567 (mm) cc_final: 0.7212 (mm)
  outliers start: 0
  outliers final: 0
  residues processed: 153
  average time/residue: 0.0478
  time to fit residues: 11.2183
Evaluate side-chains
  112 residues out of total 772 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 112
  time to evaluate  : 0.220 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 94
   random chunks:
   chunk 49 optimal weight:    0.9990
   chunk 53 optimal weight:    1.9990
   chunk 5 optimal weight:    0.8980
   chunk 33 optimal weight:    0.9980
   chunk 65 optimal weight:    0.7980
   chunk 62 optimal weight:    0.9980
   chunk 51 optimal weight:    1.9990
   chunk 38 optimal weight:    0.6980
   chunk 61 optimal weight:    1.9990
   chunk 45 optimal weight:    2.9990
   chunk 74 optimal weight:   30.0000
   overall best weight:    0.8780

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

Flipped N/Q/H residues before XYZ refinement:
A 298 ASN
B 298 ASN
B 435 GLN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4885 r_free = 0.4885 target = 0.253544 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 54)----------------|
| r_work = 0.4641 r_free = 0.4641 target = 0.222968 restraints weight = 8077.984|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 36)----------------|
| r_work = 0.4680 r_free = 0.4680 target = 0.228140 restraints weight = 4603.520|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 44)----------------|
| r_work = 0.4712 r_free = 0.4712 target = 0.231708 restraints weight = 3149.660|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 33)----------------|
| r_work = 0.4726 r_free = 0.4726 target = 0.233833 restraints weight = 2435.157|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 46)----------------|
| r_work = 0.4744 r_free = 0.4744 target = 0.235705 restraints weight = 2050.792|
|-----------------------------------------------------------------------------|
r_work (final): 0.4748
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6267
moved from start:          0.1940

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.056   6742  Z= 0.155
  Angle     :  0.658  10.723   9230  Z= 0.336
  Chirality :  0.043   0.305   1094
  Planarity :  0.005   0.084   1158
  Dihedral  :  6.127  39.141   1022
  Min Nonbonded Distance : 2.543

Molprobity Statistics.
  All-atom Clashscore : 13.01
  Ramachandran Plot:
    Outliers :  0.21 %
    Allowed  :  8.79 %
    Favored  : 91.00 %
  Rotamer:
    Outliers :  2.43 %
    Allowed  : 12.85 %
    Favored  : 84.72 %
  Cbeta Deviations :  0.24 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.11 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -0.38 (0.27), residues: 944
  helix:  0.83 (0.21), residues: 634
  sheet:  None (None), residues: 0
  loop : -2.61 (0.33), residues: 310

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG A 546 
 TYR   0.028   0.002   TYR A 739 
 PHE   0.023   0.002   PHE B 477 
 TRP   0.009   0.001   TRP B 287 
 HIS   0.006   0.002   HIS B 398 

Details of bonding type rmsd
  covalent geometry    : bond        0.00353 ( 6736)
  covalent geometry    : angle       0.65711 ( 9222)
  SS BOND              : bond        0.00069 (    4)
  SS BOND              : angle       1.27837 (    8)
  hydrogen bonds       : bond        0.04309 (  490)
  hydrogen bonds       : angle       4.51406 ( 1464)
  Misc. bond           : bond        0.00084 (    2)

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

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

  1888 Ramachandran restraints generated.
    944 Oldfield, 0 Emsley, 944 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1888 Ramachandran restraints generated.
    944 Oldfield, 0 Emsley, 944 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  140 residues out of total 772 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 126
  time to evaluate  : 0.180 
Fit side-chains
REVERT: A  437 VAL cc_start: 0.8368 (m) cc_final: 0.8058 (t)
REVERT: A  471 GLU cc_start: 0.8326 (tm-30) cc_final: 0.7909 (tt0)
REVERT: A  604 SER cc_start: 0.8194 (OUTLIER) cc_final: 0.7748 (t)
REVERT: B  677 ILE cc_start: 0.7354 (mm) cc_final: 0.7095 (mm)
  outliers start: 14
  outliers final: 9
  residues processed: 137
  average time/residue: 0.0474
  time to fit residues: 9.9818
Evaluate side-chains
  116 residues out of total 772 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 106
  time to evaluate  : 0.214 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  312 VAL
Chi-restraints excluded: chain A residue  333 ILE
Chi-restraints excluded: chain A residue  444 LEU
Chi-restraints excluded: chain A residue  604 SER
Chi-restraints excluded: chain A residue  611 THR
Chi-restraints excluded: chain A residue  621 SER
Chi-restraints excluded: chain B residue  312 VAL
Chi-restraints excluded: chain B residue  611 THR
Chi-restraints excluded: chain B residue  621 SER
Chi-restraints excluded: chain B residue  740 VAL
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 94
   random chunks:
   chunk 27 optimal weight:   20.0000
   chunk 68 optimal weight:    1.9990
   chunk 32 optimal weight:    3.9990
   chunk 92 optimal weight:    0.6980
   chunk 45 optimal weight:    3.9990
   chunk 80 optimal weight:    1.9990
   chunk 64 optimal weight:    8.9990
   chunk 1 optimal weight:    0.5980
   chunk 66 optimal weight:    5.9990
   chunk 8 optimal weight:    0.5980
   chunk 84 optimal weight:    0.9990
   overall best weight:    0.9784

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

Flipped N/Q/H residues before XYZ refinement:
B 435 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4850 r_free = 0.4850 target = 0.249982 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 56)----------------|
| r_work = 0.4603 r_free = 0.4603 target = 0.219118 restraints weight = 8072.123|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 47)----------------|
| r_work = 0.4646 r_free = 0.4646 target = 0.224260 restraints weight = 4617.512|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 43)----------------|
| r_work = 0.4673 r_free = 0.4673 target = 0.227780 restraints weight = 3190.581|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 33)----------------|
| r_work = 0.4691 r_free = 0.4691 target = 0.230052 restraints weight = 2472.684|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 27)----------------|
| r_work = 0.4700 r_free = 0.4700 target = 0.231220 restraints weight = 2080.636|
|-----------------------------------------------------------------------------|
r_work (final): 0.4705
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6352
moved from start:          0.2490

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.030   6742  Z= 0.157
  Angle     :  0.661  12.434   9230  Z= 0.334
  Chirality :  0.044   0.268   1094
  Planarity :  0.004   0.070   1158
  Dihedral  :  6.300  42.095   1022
  Min Nonbonded Distance : 2.581

Molprobity Statistics.
  All-atom Clashscore : 13.56
  Ramachandran Plot:
    Outliers :  0.21 %
    Allowed  :  7.94 %
    Favored  : 91.84 %
  Rotamer:
    Outliers :  3.47 %
    Allowed  : 18.40 %
    Favored  : 78.12 %
  Cbeta Deviations :  0.24 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.22 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -0.47 (0.27), residues: 944
  helix:  0.76 (0.21), residues: 636
  sheet:  None (None), residues: 0
  loop : -2.66 (0.32), residues: 308

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG A 546 
 TYR   0.025   0.002   TYR A 739 
 PHE   0.027   0.002   PHE A 608 
 TRP   0.014   0.001   TRP A 300 
 HIS   0.003   0.001   HIS B 398 

Details of bonding type rmsd
  covalent geometry    : bond        0.00358 ( 6736)
  covalent geometry    : angle       0.66011 ( 9222)
  SS BOND              : bond        0.00105 (    4)
  SS BOND              : angle       1.05725 (    8)
  hydrogen bonds       : bond        0.04358 (  490)
  hydrogen bonds       : angle       4.53731 ( 1464)
  Misc. bond           : bond        0.00141 (    2)

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

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

  1888 Ramachandran restraints generated.
    944 Oldfield, 0 Emsley, 944 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1888 Ramachandran restraints generated.
    944 Oldfield, 0 Emsley, 944 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  136 residues out of total 772 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 116
  time to evaluate  : 0.214 
Fit side-chains
REVERT: A  296 MET cc_start: 0.7647 (mmp) cc_final: 0.6935 (mmt)
REVERT: A  437 VAL cc_start: 0.8278 (m) cc_final: 0.7991 (t)
REVERT: A  471 GLU cc_start: 0.8258 (tm-30) cc_final: 0.7954 (tt0)
REVERT: A  604 SER cc_start: 0.8192 (OUTLIER) cc_final: 0.7915 (t)
REVERT: A  681 PHE cc_start: 0.5954 (m-80) cc_final: 0.5712 (m-80)
REVERT: B  748 TYR cc_start: 0.5101 (t80) cc_final: 0.4805 (m-80)
  outliers start: 20
  outliers final: 10
  residues processed: 130
  average time/residue: 0.0420
  time to fit residues: 8.7316
Evaluate side-chains
  119 residues out of total 772 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 108
  time to evaluate  : 0.147 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  312 VAL
Chi-restraints excluded: chain A residue  333 ILE
Chi-restraints excluded: chain A residue  604 SER
Chi-restraints excluded: chain A residue  611 THR
Chi-restraints excluded: chain A residue  621 SER
Chi-restraints excluded: chain A residue  740 VAL
Chi-restraints excluded: chain B residue  312 VAL
Chi-restraints excluded: chain B residue  486 THR
Chi-restraints excluded: chain B residue  611 THR
Chi-restraints excluded: chain B residue  621 SER
Chi-restraints excluded: chain B residue  740 VAL
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 94
   random chunks:
   chunk 34 optimal weight:    2.9990
   chunk 55 optimal weight:    1.9990
   chunk 73 optimal weight:    9.9990
   chunk 61 optimal weight:    0.4980
   chunk 40 optimal weight:    3.9990
   chunk 18 optimal weight:    4.9990
   chunk 47 optimal weight:    7.9990
   chunk 13 optimal weight:    0.6980
   chunk 78 optimal weight:    7.9990
   chunk 65 optimal weight:    0.0060
   chunk 27 optimal weight:    0.9990
   overall best weight:    0.8400

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

Flipped N/Q/H residues before XYZ refinement:
B 314 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4852 r_free = 0.4852 target = 0.250586 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 56)----------------|
| r_work = 0.4608 r_free = 0.4608 target = 0.220076 restraints weight = 8135.083|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 42)----------------|
| r_work = 0.4646 r_free = 0.4646 target = 0.225010 restraints weight = 4723.668|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 37)----------------|
| r_work = 0.4665 r_free = 0.4665 target = 0.227973 restraints weight = 3300.826|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 51)----------------|
| r_work = 0.4692 r_free = 0.4692 target = 0.230569 restraints weight = 2621.624|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 29)----------------|
| r_work = 0.4700 r_free = 0.4700 target = 0.231795 restraints weight = 2203.329|
|-----------------------------------------------------------------------------|
r_work (final): 0.4694
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6359
moved from start:          0.2749

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.034   6742  Z= 0.145
  Angle     :  0.645  13.155   9230  Z= 0.326
  Chirality :  0.043   0.245   1094
  Planarity :  0.004   0.063   1158
  Dihedral  :  6.270  42.148   1022
  Min Nonbonded Distance : 2.597

Molprobity Statistics.
  All-atom Clashscore : 12.78
  Ramachandran Plot:
    Outliers :  0.21 %
    Allowed  :  8.16 %
    Favored  : 91.63 %
  Rotamer:
    Outliers :  4.51 %
    Allowed  : 19.97 %
    Favored  : 75.52 %
  Cbeta Deviations :  0.24 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.22 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -0.42 (0.27), residues: 944
  helix:  0.81 (0.21), residues: 636
  sheet:  None (None), residues: 0
  loop : -2.67 (0.32), residues: 308

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG A 546 
 TYR   0.025   0.002   TYR A 739 
 PHE   0.022   0.001   PHE A 608 
 TRP   0.006   0.001   TRP A 287 
 HIS   0.003   0.001   HIS B 398 

Details of bonding type rmsd
  covalent geometry    : bond        0.00328 ( 6736)
  covalent geometry    : angle       0.64455 ( 9222)
  SS BOND              : bond        0.00109 (    4)
  SS BOND              : angle       0.96756 (    8)
  hydrogen bonds       : bond        0.04214 (  490)
  hydrogen bonds       : angle       4.49270 ( 1464)
  Misc. bond           : bond        0.00137 (    2)

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

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

  1888 Ramachandran restraints generated.
    944 Oldfield, 0 Emsley, 944 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1888 Ramachandran restraints generated.
    944 Oldfield, 0 Emsley, 944 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  143 residues out of total 772 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 26
    poor density    : 117
  time to evaluate  : 0.211 
Fit side-chains
REVERT: A  296 MET cc_start: 0.7735 (mmp) cc_final: 0.7081 (mmt)
REVERT: A  437 VAL cc_start: 0.8352 (m) cc_final: 0.8035 (t)
REVERT: A  713 MET cc_start: 0.6510 (tmm) cc_final: 0.6257 (tmm)
REVERT: B  748 TYR cc_start: 0.5145 (t80) cc_final: 0.4872 (m-80)
  outliers start: 26
  outliers final: 15
  residues processed: 134
  average time/residue: 0.0456
  time to fit residues: 9.6720
Evaluate side-chains
  126 residues out of total 772 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 111
  time to evaluate  : 0.231 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  312 VAL
Chi-restraints excluded: chain A residue  333 ILE
Chi-restraints excluded: chain A residue  415 ILE
Chi-restraints excluded: chain A residue  611 THR
Chi-restraints excluded: chain A residue  621 SER
Chi-restraints excluded: chain B residue  288 ILE
Chi-restraints excluded: chain B residue  312 VAL
Chi-restraints excluded: chain B residue  364 PHE
Chi-restraints excluded: chain B residue  415 ILE
Chi-restraints excluded: chain B residue  486 THR
Chi-restraints excluded: chain B residue  532 VAL
Chi-restraints excluded: chain B residue  611 THR
Chi-restraints excluded: chain B residue  621 SER
Chi-restraints excluded: chain B residue  722 LEU
Chi-restraints excluded: chain B residue  740 VAL
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 94
   random chunks:
   chunk 52 optimal weight:    0.5980
   chunk 73 optimal weight:    7.9990
   chunk 6 optimal weight:    2.9990
   chunk 49 optimal weight:    4.9990
   chunk 81 optimal weight:    0.9980
   chunk 44 optimal weight:    0.7980
   chunk 8 optimal weight:    0.9980
   chunk 45 optimal weight:    1.9990
   chunk 71 optimal weight:    0.6980
   chunk 27 optimal weight:    7.9990
   chunk 70 optimal weight:    2.9990
   overall best weight:    0.8180

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

Flipped N/Q/H residues before XYZ refinement:
A 298 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4841 r_free = 0.4841 target = 0.249577 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 54)----------------|
| r_work = 0.4592 r_free = 0.4592 target = 0.218635 restraints weight = 8191.516|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 42)----------------|
| r_work = 0.4632 r_free = 0.4632 target = 0.223693 restraints weight = 4696.658|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 36)----------------|
| r_work = 0.4654 r_free = 0.4654 target = 0.227026 restraints weight = 3249.730|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 45)----------------|
| r_work = 0.4679 r_free = 0.4679 target = 0.229451 restraints weight = 2532.282|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 28)----------------|
| r_work = 0.4687 r_free = 0.4687 target = 0.230668 restraints weight = 2138.479|
|-----------------------------------------------------------------------------|
r_work (final): 0.4692
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6367
moved from start:          0.2946

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.031   6742  Z= 0.145
  Angle     :  0.654  13.796   9230  Z= 0.328
  Chirality :  0.043   0.275   1094
  Planarity :  0.004   0.060   1158
  Dihedral  :  6.291  42.924   1022
  Min Nonbonded Distance : 2.603

Molprobity Statistics.
  All-atom Clashscore : 13.96
  Ramachandran Plot:
    Outliers :  0.21 %
    Allowed  :  8.05 %
    Favored  : 91.74 %
  Rotamer:
    Outliers :  5.38 %
    Allowed  : 21.18 %
    Favored  : 73.44 %
  Cbeta Deviations :  0.24 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.22 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -0.46 (0.27), residues: 944
  helix:  0.79 (0.21), residues: 636
  sheet:  None (None), residues: 0
  loop : -2.71 (0.32), residues: 308

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG A 546 
 TYR   0.026   0.002   TYR A 739 
 PHE   0.021   0.002   PHE A 495 
 TRP   0.007   0.001   TRP A 287 
 HIS   0.003   0.001   HIS A 398 

Details of bonding type rmsd
  covalent geometry    : bond        0.00326 ( 6736)
  covalent geometry    : angle       0.65394 ( 9222)
  SS BOND              : bond        0.00094 (    4)
  SS BOND              : angle       0.92118 (    8)
  hydrogen bonds       : bond        0.04246 (  490)
  hydrogen bonds       : angle       4.46044 ( 1464)
  Misc. bond           : bond        0.00134 (    2)

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

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

  1888 Ramachandran restraints generated.
    944 Oldfield, 0 Emsley, 944 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1888 Ramachandran restraints generated.
    944 Oldfield, 0 Emsley, 944 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  144 residues out of total 772 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 31
    poor density    : 113
  time to evaluate  : 0.249 
Fit side-chains
REVERT: A  296 MET cc_start: 0.7821 (mmp) cc_final: 0.7438 (mmt)
REVERT: A  437 VAL cc_start: 0.8306 (m) cc_final: 0.8015 (t)
REVERT: A  604 SER cc_start: 0.8178 (OUTLIER) cc_final: 0.7924 (t)
REVERT: A  713 MET cc_start: 0.6424 (tmm) cc_final: 0.6180 (tmm)
REVERT: B  748 TYR cc_start: 0.5260 (t80) cc_final: 0.5013 (m-80)
  outliers start: 31
  outliers final: 19
  residues processed: 135
  average time/residue: 0.0421
  time to fit residues: 9.1272
Evaluate side-chains
  133 residues out of total 772 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 113
  time to evaluate  : 0.229 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  312 VAL
Chi-restraints excluded: chain A residue  344 ASN
Chi-restraints excluded: chain A residue  415 ILE
Chi-restraints excluded: chain A residue  444 LEU
Chi-restraints excluded: chain A residue  486 THR
Chi-restraints excluded: chain A residue  604 SER
Chi-restraints excluded: chain A residue  611 THR
Chi-restraints excluded: chain A residue  621 SER
Chi-restraints excluded: chain A residue  740 VAL
Chi-restraints excluded: chain B residue  288 ILE
Chi-restraints excluded: chain B residue  312 VAL
Chi-restraints excluded: chain B residue  364 PHE
Chi-restraints excluded: chain B residue  415 ILE
Chi-restraints excluded: chain B residue  486 THR
Chi-restraints excluded: chain B residue  532 VAL
Chi-restraints excluded: chain B residue  533 TYR
Chi-restraints excluded: chain B residue  611 THR
Chi-restraints excluded: chain B residue  621 SER
Chi-restraints excluded: chain B residue  717 LEU
Chi-restraints excluded: chain B residue  740 VAL
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 94
   random chunks:
   chunk 57 optimal weight:    0.9990
   chunk 58 optimal weight:    2.9990
   chunk 47 optimal weight:    9.9990
   chunk 72 optimal weight:    0.7980
   chunk 18 optimal weight:   10.0000
   chunk 38 optimal weight:    0.8980
   chunk 67 optimal weight:    1.9990
   chunk 34 optimal weight:    0.9990
   chunk 49 optimal weight:    0.6980
   chunk 60 optimal weight:    2.9990
   chunk 2 optimal weight:    3.9990
   overall best weight:    0.8784

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

Flipped N/Q/H residues before XYZ refinement:
A 298 ASN
A 435 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4831 r_free = 0.4831 target = 0.249000 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.4582 r_free = 0.4582 target = 0.218203 restraints weight = 8125.212|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 48)----------------|
| r_work = 0.4626 r_free = 0.4626 target = 0.223335 restraints weight = 4653.510|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 44)----------------|
| r_work = 0.4652 r_free = 0.4652 target = 0.226747 restraints weight = 3220.550|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 34)----------------|
| r_work = 0.4667 r_free = 0.4667 target = 0.228865 restraints weight = 2512.179|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 53)----------------|
| r_work = 0.4684 r_free = 0.4684 target = 0.230592 restraints weight = 2115.240|
|-----------------------------------------------------------------------------|
r_work (final): 0.4688
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6364
moved from start:          0.3123

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.045   6742  Z= 0.153
  Angle     :  0.673  14.402   9230  Z= 0.337
  Chirality :  0.045   0.326   1094
  Planarity :  0.004   0.057   1158
  Dihedral  :  6.369  44.108   1022
  Min Nonbonded Distance : 2.548

Molprobity Statistics.
  All-atom Clashscore : 14.35
  Ramachandran Plot:
    Outliers :  0.21 %
    Allowed  :  7.73 %
    Favored  : 92.06 %
  Rotamer:
    Outliers :  5.21 %
    Allowed  : 22.05 %
    Favored  : 72.74 %
  Cbeta Deviations :  0.24 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.22 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -0.58 (0.27), residues: 944
  helix:  0.70 (0.20), residues: 636
  sheet:  None (None), residues: 0
  loop : -2.76 (0.31), residues: 308

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG B 294 
 TYR   0.026   0.002   TYR A 739 
 PHE   0.021   0.002   PHE A 495 
 TRP   0.007   0.001   TRP A 287 
 HIS   0.003   0.001   HIS B 398 

Details of bonding type rmsd
  covalent geometry    : bond        0.00352 ( 6736)
  covalent geometry    : angle       0.67287 ( 9222)
  SS BOND              : bond        0.00112 (    4)
  SS BOND              : angle       0.88111 (    8)
  hydrogen bonds       : bond        0.04368 (  490)
  hydrogen bonds       : angle       4.46075 ( 1464)
  Misc. bond           : bond        0.00145 (    2)

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

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

  1888 Ramachandran restraints generated.
    944 Oldfield, 0 Emsley, 944 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1888 Ramachandran restraints generated.
    944 Oldfield, 0 Emsley, 944 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  146 residues out of total 772 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 30
    poor density    : 116
  time to evaluate  : 0.255 
Fit side-chains
REVERT: A  296 MET cc_start: 0.7602 (mmp) cc_final: 0.7164 (mmt)
REVERT: A  437 VAL cc_start: 0.8361 (m) cc_final: 0.8091 (t)
REVERT: A  439 LEU cc_start: 0.9076 (tt) cc_final: 0.8786 (tp)
REVERT: A  604 SER cc_start: 0.8191 (OUTLIER) cc_final: 0.7923 (t)
REVERT: A  713 MET cc_start: 0.6390 (tmm) cc_final: 0.6152 (tmm)
REVERT: B  296 MET cc_start: 0.7553 (mmp) cc_final: 0.6978 (mmt)
REVERT: B  676 PRO cc_start: 0.8242 (Cg_endo) cc_final: 0.7990 (Cg_exo)
REVERT: B  681 PHE cc_start: 0.5803 (m-80) cc_final: 0.5441 (m-80)
REVERT: B  748 TYR cc_start: 0.5338 (t80) cc_final: 0.5022 (m-80)
  outliers start: 30
  outliers final: 21
  residues processed: 139
  average time/residue: 0.0484
  time to fit residues: 10.4888
Evaluate side-chains
  131 residues out of total 772 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 22
    poor density    : 109
  time to evaluate  : 0.237 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  312 VAL
Chi-restraints excluded: chain A residue  344 ASN
Chi-restraints excluded: chain A residue  364 PHE
Chi-restraints excluded: chain A residue  415 ILE
Chi-restraints excluded: chain A residue  444 LEU
Chi-restraints excluded: chain A residue  486 THR
Chi-restraints excluded: chain A residue  531 LEU
Chi-restraints excluded: chain A residue  604 SER
Chi-restraints excluded: chain A residue  611 THR
Chi-restraints excluded: chain A residue  621 SER
Chi-restraints excluded: chain A residue  740 VAL
Chi-restraints excluded: chain B residue  288 ILE
Chi-restraints excluded: chain B residue  312 VAL
Chi-restraints excluded: chain B residue  364 PHE
Chi-restraints excluded: chain B residue  415 ILE
Chi-restraints excluded: chain B residue  486 THR
Chi-restraints excluded: chain B residue  532 VAL
Chi-restraints excluded: chain B residue  533 TYR
Chi-restraints excluded: chain B residue  611 THR
Chi-restraints excluded: chain B residue  621 SER
Chi-restraints excluded: chain B residue  715 ILE
Chi-restraints excluded: chain B residue  717 LEU
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 94
   random chunks:
   chunk 60 optimal weight:    0.5980
   chunk 45 optimal weight:    0.9990
   chunk 7 optimal weight:    4.9990
   chunk 21 optimal weight:    0.8980
   chunk 1 optimal weight:    0.9980
   chunk 54 optimal weight:    0.6980
   chunk 46 optimal weight:    1.9990
   chunk 27 optimal weight:    0.3980
   chunk 85 optimal weight:    0.9980
   chunk 92 optimal weight:    0.7980
   chunk 2 optimal weight:    0.7980
   overall best weight:    0.6580

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

Flipped N/Q/H residues before XYZ refinement:
A 298 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4847 r_free = 0.4847 target = 0.251225 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 56)----------------|
| r_work = 0.4599 r_free = 0.4599 target = 0.220518 restraints weight = 8107.343|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 34)----------------|
| r_work = 0.4637 r_free = 0.4637 target = 0.225469 restraints weight = 4771.634|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 23)----------------|
| r_work = 0.4656 r_free = 0.4656 target = 0.228221 restraints weight = 3360.525|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 45)----------------|
| r_work = 0.4683 r_free = 0.4683 target = 0.230921 restraints weight = 2707.409|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 17)----------------|
| r_work = 0.4689 r_free = 0.4689 target = 0.231772 restraints weight = 2291.673|
|-----------------------------------------------------------------------------|
r_work (final): 0.4689
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6365
moved from start:          0.3222

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.038   6742  Z= 0.142
  Angle     :  0.674  15.279   9230  Z= 0.337
  Chirality :  0.045   0.346   1094
  Planarity :  0.004   0.056   1158
  Dihedral  :  6.283  43.100   1022
  Min Nonbonded Distance : 2.473

Molprobity Statistics.
  All-atom Clashscore : 14.12
  Ramachandran Plot:
    Outliers :  0.21 %
    Allowed  :  7.42 %
    Favored  : 92.37 %
  Rotamer:
    Outliers :  5.03 %
    Allowed  : 21.88 %
    Favored  : 73.09 %
  Cbeta Deviations :  0.24 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.22 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -0.54 (0.27), residues: 944
  helix:  0.73 (0.20), residues: 636
  sheet:  None (None), residues: 0
  loop : -2.73 (0.31), residues: 308

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG B 294 
 TYR   0.028   0.002   TYR A 739 
 PHE   0.020   0.002   PHE A 495 
 TRP   0.007   0.001   TRP A 287 
 HIS   0.003   0.001   HIS A 398 

Details of bonding type rmsd
  covalent geometry    : bond        0.00318 ( 6736)
  covalent geometry    : angle       0.67405 ( 9222)
  SS BOND              : bond        0.00118 (    4)
  SS BOND              : angle       0.86322 (    8)
  hydrogen bonds       : bond        0.04259 (  490)
  hydrogen bonds       : angle       4.46615 ( 1464)
  Misc. bond           : bond        0.00136 (    2)

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

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

  1888 Ramachandran restraints generated.
    944 Oldfield, 0 Emsley, 944 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1888 Ramachandran restraints generated.
    944 Oldfield, 0 Emsley, 944 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  146 residues out of total 772 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 29
    poor density    : 117
  time to evaluate  : 0.166 
Fit side-chains
REVERT: A  439 LEU cc_start: 0.9044 (tt) cc_final: 0.8815 (tp)
REVERT: A  604 SER cc_start: 0.8251 (OUTLIER) cc_final: 0.7926 (t)
REVERT: A  713 MET cc_start: 0.6281 (tmm) cc_final: 0.6055 (tmm)
REVERT: B  681 PHE cc_start: 0.5857 (m-80) cc_final: 0.5572 (m-80)
REVERT: B  748 TYR cc_start: 0.5286 (t80) cc_final: 0.4928 (m-80)
  outliers start: 29
  outliers final: 21
  residues processed: 137
  average time/residue: 0.0522
  time to fit residues: 10.9108
Evaluate side-chains
  134 residues out of total 772 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 22
    poor density    : 112
  time to evaluate  : 0.224 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  312 VAL
Chi-restraints excluded: chain A residue  344 ASN
Chi-restraints excluded: chain A residue  364 PHE
Chi-restraints excluded: chain A residue  415 ILE
Chi-restraints excluded: chain A residue  444 LEU
Chi-restraints excluded: chain A residue  486 THR
Chi-restraints excluded: chain A residue  531 LEU
Chi-restraints excluded: chain A residue  604 SER
Chi-restraints excluded: chain A residue  611 THR
Chi-restraints excluded: chain A residue  621 SER
Chi-restraints excluded: chain A residue  740 VAL
Chi-restraints excluded: chain B residue  288 ILE
Chi-restraints excluded: chain B residue  312 VAL
Chi-restraints excluded: chain B residue  364 PHE
Chi-restraints excluded: chain B residue  415 ILE
Chi-restraints excluded: chain B residue  533 TYR
Chi-restraints excluded: chain B residue  611 THR
Chi-restraints excluded: chain B residue  621 SER
Chi-restraints excluded: chain B residue  692 SER
Chi-restraints excluded: chain B residue  715 ILE
Chi-restraints excluded: chain B residue  717 LEU
Chi-restraints excluded: chain B residue  740 VAL
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 94
   random chunks:
   chunk 76 optimal weight:    8.9990
   chunk 1 optimal weight:    0.8980
   chunk 44 optimal weight:    0.8980
   chunk 71 optimal weight:    0.9990
   chunk 38 optimal weight:    0.9990
   chunk 77 optimal weight:    0.0000
   chunk 17 optimal weight:    1.9990
   chunk 10 optimal weight:    1.9990
   chunk 24 optimal weight:    0.5980
   chunk 40 optimal weight:    0.7980
   chunk 81 optimal weight:    0.7980
   overall best weight:    0.6184

-------------------------------------------------------------------------------
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 = 0.4852 r_free = 0.4852 target = 0.251914 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 45)----------------|
| r_work = 0.4604 r_free = 0.4604 target = 0.221135 restraints weight = 8207.213|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 37)----------------|
| r_work = 0.4646 r_free = 0.4646 target = 0.226135 restraints weight = 4855.591|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 40)----------------|
| r_work = 0.4670 r_free = 0.4670 target = 0.229440 restraints weight = 3412.580|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 28)----------------|
| r_work = 0.4682 r_free = 0.4682 target = 0.231184 restraints weight = 2699.663|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 48)----------------|
| r_work = 0.4701 r_free = 0.4701 target = 0.233076 restraints weight = 2330.718|
|-----------------------------------------------------------------------------|
r_work (final): 0.4705
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6345
moved from start:          0.3302

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.055   6742  Z= 0.144
  Angle     :  0.686  15.708   9230  Z= 0.342
  Chirality :  0.045   0.383   1094
  Planarity :  0.004   0.055   1158
  Dihedral  :  6.235  42.859   1022
  Min Nonbonded Distance : 2.606

Molprobity Statistics.
  All-atom Clashscore : 14.59
  Ramachandran Plot:
    Outliers :  0.21 %
    Allowed  :  7.52 %
    Favored  : 92.27 %
  Rotamer:
    Outliers :  4.17 %
    Allowed  : 23.26 %
    Favored  : 72.57 %
  Cbeta Deviations :  0.24 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.22 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -0.51 (0.27), residues: 944
  helix:  0.74 (0.20), residues: 634
  sheet:  None (None), residues: 0
  loop : -2.69 (0.31), residues: 310

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.001   ARG A 546 
 TYR   0.029   0.001   TYR A 739 
 PHE   0.020   0.002   PHE B 495 
 TRP   0.007   0.001   TRP A 287 
 HIS   0.003   0.001   HIS A 398 

Details of bonding type rmsd
  covalent geometry    : bond        0.00330 ( 6736)
  covalent geometry    : angle       0.68555 ( 9222)
  SS BOND              : bond        0.00121 (    4)
  SS BOND              : angle       0.87438 (    8)
  hydrogen bonds       : bond        0.04244 (  490)
  hydrogen bonds       : angle       4.48463 ( 1464)
  Misc. bond           : bond        0.00129 (    2)

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

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

  1888 Ramachandran restraints generated.
    944 Oldfield, 0 Emsley, 944 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1888 Ramachandran restraints generated.
    944 Oldfield, 0 Emsley, 944 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  139 residues out of total 772 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 24
    poor density    : 115
  time to evaluate  : 0.180 
Fit side-chains
REVERT: A  439 LEU cc_start: 0.9053 (tt) cc_final: 0.8823 (tp)
REVERT: A  604 SER cc_start: 0.8291 (OUTLIER) cc_final: 0.7986 (t)
REVERT: B  296 MET cc_start: 0.7349 (mmt) cc_final: 0.6901 (mmt)
REVERT: B  681 PHE cc_start: 0.5859 (m-80) cc_final: 0.5631 (m-80)
REVERT: B  748 TYR cc_start: 0.5299 (t80) cc_final: 0.4912 (m-80)
  outliers start: 24
  outliers final: 19
  residues processed: 131
  average time/residue: 0.0448
  time to fit residues: 9.2863
Evaluate side-chains
  128 residues out of total 772 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 108
  time to evaluate  : 0.148 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  312 VAL
Chi-restraints excluded: chain A residue  344 ASN
Chi-restraints excluded: chain A residue  364 PHE
Chi-restraints excluded: chain A residue  415 ILE
Chi-restraints excluded: chain A residue  444 LEU
Chi-restraints excluded: chain A residue  531 LEU
Chi-restraints excluded: chain A residue  604 SER
Chi-restraints excluded: chain A residue  611 THR
Chi-restraints excluded: chain A residue  621 SER
Chi-restraints excluded: chain B residue  312 VAL
Chi-restraints excluded: chain B residue  364 PHE
Chi-restraints excluded: chain B residue  415 ILE
Chi-restraints excluded: chain B residue  532 VAL
Chi-restraints excluded: chain B residue  533 TYR
Chi-restraints excluded: chain B residue  611 THR
Chi-restraints excluded: chain B residue  621 SER
Chi-restraints excluded: chain B residue  692 SER
Chi-restraints excluded: chain B residue  715 ILE
Chi-restraints excluded: chain B residue  717 LEU
Chi-restraints excluded: chain B residue  740 VAL
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 94
   random chunks:
   chunk 85 optimal weight:    0.7980
   chunk 2 optimal weight:    0.6980
   chunk 50 optimal weight:    0.7980
   chunk 73 optimal weight:    7.9990
   chunk 5 optimal weight:    0.5980
   chunk 18 optimal weight:    2.9990
   chunk 42 optimal weight:    0.9990
   chunk 79 optimal weight:    1.9990
   chunk 43 optimal weight:    6.9990
   chunk 65 optimal weight:    1.9990
   chunk 19 optimal weight:    0.0670
   overall best weight:    0.5918

-------------------------------------------------------------------------------
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 = 0.4849 r_free = 0.4849 target = 0.251848 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 57)----------------|
| r_work = 0.4603 r_free = 0.4603 target = 0.220755 restraints weight = 8094.561|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 45)----------------|
| r_work = 0.4643 r_free = 0.4643 target = 0.225870 restraints weight = 4706.167|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 40)----------------|
| r_work = 0.4673 r_free = 0.4673 target = 0.229486 restraints weight = 3278.754|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 32)----------------|
| r_work = 0.4685 r_free = 0.4685 target = 0.231332 restraints weight = 2557.416|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 37)----------------|
| r_work = 0.4695 r_free = 0.4695 target = 0.232802 restraints weight = 2190.481|
|-----------------------------------------------------------------------------|
r_work (final): 0.4709
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6343
moved from start:          0.3389

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.056   6742  Z= 0.144
  Angle     :  0.700  15.833   9230  Z= 0.347
  Chirality :  0.045   0.328   1094
  Planarity :  0.004   0.054   1158
  Dihedral  :  6.188  42.773   1022
  Min Nonbonded Distance : 2.580

Molprobity Statistics.
  All-atom Clashscore : 14.51
  Ramachandran Plot:
    Outliers :  0.21 %
    Allowed  :  7.20 %
    Favored  : 92.58 %
  Rotamer:
    Outliers :  3.99 %
    Allowed  : 24.65 %
    Favored  : 71.35 %
  Cbeta Deviations :  0.24 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.22 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -0.53 (0.27), residues: 944
  helix:  0.75 (0.20), residues: 638
  sheet:  None (None), residues: 0
  loop : -2.80 (0.30), residues: 306

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.001   ARG B 294 
 TYR   0.030   0.001   TYR A 739 
 PHE   0.020   0.001   PHE B 495 
 TRP   0.009   0.001   TRP A 287 
 HIS   0.003   0.001   HIS A 398 

Details of bonding type rmsd
  covalent geometry    : bond        0.00333 ( 6736)
  covalent geometry    : angle       0.69965 ( 9222)
  SS BOND              : bond        0.00142 (    4)
  SS BOND              : angle       0.91059 (    8)
  hydrogen bonds       : bond        0.04253 (  490)
  hydrogen bonds       : angle       4.53043 ( 1464)
  Misc. bond           : bond        0.00131 (    2)

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

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

  1888 Ramachandran restraints generated.
    944 Oldfield, 0 Emsley, 944 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1888 Ramachandran restraints generated.
    944 Oldfield, 0 Emsley, 944 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  129 residues out of total 772 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 23
    poor density    : 106
  time to evaluate  : 0.182 
Fit side-chains
REVERT: A  439 LEU cc_start: 0.9065 (tt) cc_final: 0.8813 (tp)
REVERT: B  296 MET cc_start: 0.7448 (mmt) cc_final: 0.7029 (mmt)
REVERT: B  384 VAL cc_start: 0.6579 (OUTLIER) cc_final: 0.6319 (t)
REVERT: B  748 TYR cc_start: 0.5351 (t80) cc_final: 0.4935 (m-80)
  outliers start: 23
  outliers final: 19
  residues processed: 123
  average time/residue: 0.0482
  time to fit residues: 9.3530
Evaluate side-chains
  125 residues out of total 772 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 105
  time to evaluate  : 0.193 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  312 VAL
Chi-restraints excluded: chain A residue  344 ASN
Chi-restraints excluded: chain A residue  364 PHE
Chi-restraints excluded: chain A residue  415 ILE
Chi-restraints excluded: chain A residue  486 THR
Chi-restraints excluded: chain A residue  531 LEU
Chi-restraints excluded: chain A residue  611 THR
Chi-restraints excluded: chain A residue  621 SER
Chi-restraints excluded: chain B residue  312 VAL
Chi-restraints excluded: chain B residue  364 PHE
Chi-restraints excluded: chain B residue  384 VAL
Chi-restraints excluded: chain B residue  415 ILE
Chi-restraints excluded: chain B residue  531 LEU
Chi-restraints excluded: chain B residue  532 VAL
Chi-restraints excluded: chain B residue  533 TYR
Chi-restraints excluded: chain B residue  611 THR
Chi-restraints excluded: chain B residue  621 SER
Chi-restraints excluded: chain B residue  692 SER
Chi-restraints excluded: chain B residue  715 ILE
Chi-restraints excluded: chain B residue  717 LEU
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 94
   random chunks:
   chunk 55 optimal weight:    0.8980
   chunk 61 optimal weight:   10.0000
   chunk 64 optimal weight:    2.9990
   chunk 23 optimal weight:    0.5980
   chunk 83 optimal weight:   10.0000
   chunk 11 optimal weight:    0.9990
   chunk 63 optimal weight:    0.5980
   chunk 7 optimal weight:    0.9990
   chunk 85 optimal weight:    0.7980
   chunk 90 optimal weight:    0.8980
   chunk 40 optimal weight:    0.5980
   overall best weight:    0.6980

-------------------------------------------------------------------------------
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 = 0.4850 r_free = 0.4850 target = 0.252015 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 47)----------------|
| r_work = 0.4602 r_free = 0.4602 target = 0.221255 restraints weight = 8135.627|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 43)----------------|
| r_work = 0.4643 r_free = 0.4643 target = 0.226204 restraints weight = 4830.272|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 40)----------------|
| r_work = 0.4667 r_free = 0.4667 target = 0.229438 restraints weight = 3407.086|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 35)----------------|
| r_work = 0.4681 r_free = 0.4681 target = 0.231476 restraints weight = 2700.844|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 40)----------------|
| r_work = 0.4698 r_free = 0.4698 target = 0.233129 restraints weight = 2298.701|
|-----------------------------------------------------------------------------|
r_work (final): 0.4700
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6357
moved from start:          0.3504

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.059   6742  Z= 0.149
  Angle     :  0.713  16.068   9230  Z= 0.353
  Chirality :  0.046   0.301   1094
  Planarity :  0.004   0.054   1158
  Dihedral  :  6.254  43.901   1022
  Min Nonbonded Distance : 2.566

Molprobity Statistics.
  All-atom Clashscore : 14.59
  Ramachandran Plot:
    Outliers :  0.21 %
    Allowed  :  7.42 %
    Favored  : 92.37 %
  Rotamer:
    Outliers :  3.82 %
    Allowed  : 25.00 %
    Favored  : 71.18 %
  Cbeta Deviations :  0.24 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.22 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -0.55 (0.27), residues: 944
  helix:  0.72 (0.20), residues: 640
  sheet:  None (None), residues: 0
  loop : -2.76 (0.31), residues: 304

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.001   ARG B 294 
 TYR   0.030   0.001   TYR A 739 
 PHE   0.021   0.002   PHE B 495 
 TRP   0.010   0.001   TRP B 732 
 HIS   0.003   0.001   HIS A 398 

Details of bonding type rmsd
  covalent geometry    : bond        0.00349 ( 6736)
  covalent geometry    : angle       0.71320 ( 9222)
  SS BOND              : bond        0.00143 (    4)
  SS BOND              : angle       0.86282 (    8)
  hydrogen bonds       : bond        0.04298 (  490)
  hydrogen bonds       : angle       4.54020 ( 1464)
  Misc. bond           : bond        0.00140 (    2)

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

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

  1888 Ramachandran restraints generated.
    944 Oldfield, 0 Emsley, 944 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1888 Ramachandran restraints generated.
    944 Oldfield, 0 Emsley, 944 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  125 residues out of total 772 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 22
    poor density    : 103
  time to evaluate  : 0.152 
Fit side-chains
REVERT: A  439 LEU cc_start: 0.9053 (tt) cc_final: 0.8841 (tp)
REVERT: A  681 PHE cc_start: 0.5641 (m-80) cc_final: 0.5390 (t80)
REVERT: B  296 MET cc_start: 0.7435 (mmt) cc_final: 0.6995 (mmt)
REVERT: B  384 VAL cc_start: 0.6535 (OUTLIER) cc_final: 0.6287 (t)
REVERT: B  748 TYR cc_start: 0.5398 (t80) cc_final: 0.4951 (m-80)
  outliers start: 22
  outliers final: 19
  residues processed: 120
  average time/residue: 0.0461
  time to fit residues: 8.7896
Evaluate side-chains
  122 residues out of total 772 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 102
  time to evaluate  : 0.225 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  312 VAL
Chi-restraints excluded: chain A residue  344 ASN
Chi-restraints excluded: chain A residue  364 PHE
Chi-restraints excluded: chain A residue  415 ILE
Chi-restraints excluded: chain A residue  531 LEU
Chi-restraints excluded: chain A residue  611 THR
Chi-restraints excluded: chain A residue  621 SER
Chi-restraints excluded: chain B residue  312 VAL
Chi-restraints excluded: chain B residue  364 PHE
Chi-restraints excluded: chain B residue  384 VAL
Chi-restraints excluded: chain B residue  415 ILE
Chi-restraints excluded: chain B residue  531 LEU
Chi-restraints excluded: chain B residue  532 VAL
Chi-restraints excluded: chain B residue  533 TYR
Chi-restraints excluded: chain B residue  611 THR
Chi-restraints excluded: chain B residue  621 SER
Chi-restraints excluded: chain B residue  692 SER
Chi-restraints excluded: chain B residue  715 ILE
Chi-restraints excluded: chain B residue  717 LEU
Chi-restraints excluded: chain B residue  740 VAL
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 94
   random chunks:
   chunk 14 optimal weight:    8.9990
   chunk 55 optimal weight:    0.9980
   chunk 65 optimal weight:    5.9990
   chunk 0 optimal weight:    8.9990
   chunk 86 optimal weight:    0.7980
   chunk 5 optimal weight:    0.5980
   chunk 68 optimal weight:    0.8980
   chunk 63 optimal weight:    0.6980
   chunk 76 optimal weight:   20.0000
   chunk 90 optimal weight:    0.0670
   chunk 82 optimal weight:    6.9990
   overall best weight:    0.6118

-------------------------------------------------------------------------------
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 = 0.4856 r_free = 0.4856 target = 0.252768 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 54)----------------|
| r_work = 0.4611 r_free = 0.4611 target = 0.221434 restraints weight = 7932.330|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 44)----------------|
| r_work = 0.4651 r_free = 0.4651 target = 0.226527 restraints weight = 4720.187|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 45)----------------|
| r_work = 0.4678 r_free = 0.4678 target = 0.230007 restraints weight = 3332.311|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 38)----------------|
| r_work = 0.4689 r_free = 0.4689 target = 0.231852 restraints weight = 2628.614|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 32)----------------|
| r_work = 0.4706 r_free = 0.4706 target = 0.233661 restraints weight = 2258.847|
|-----------------------------------------------------------------------------|
r_work (final): 0.4709
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6339
moved from start:          0.3542

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.059   6742  Z= 0.147
  Angle     :  0.718  16.079   9230  Z= 0.354
  Chirality :  0.046   0.292   1094
  Planarity :  0.004   0.053   1158
  Dihedral  :  6.228  43.392   1022
  Min Nonbonded Distance : 2.578

Molprobity Statistics.
  All-atom Clashscore : 14.59
  Ramachandran Plot:
    Outliers :  0.21 %
    Allowed  :  7.20 %
    Favored  : 92.58 %
  Rotamer:
    Outliers :  3.99 %
    Allowed  : 25.35 %
    Favored  : 70.66 %
  Cbeta Deviations :  0.24 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.11 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -0.49 (0.27), residues: 944
  helix:  0.76 (0.20), residues: 640
  sheet:  None (None), residues: 0
  loop : -2.75 (0.31), residues: 304

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.001   ARG B 294 
 TYR   0.037   0.001   TYR A 739 
 PHE   0.026   0.002   PHE B 466 
 TRP   0.009   0.001   TRP B 732 
 HIS   0.003   0.001   HIS A 398 

Details of bonding type rmsd
  covalent geometry    : bond        0.00339 ( 6736)
  covalent geometry    : angle       0.71734 ( 9222)
  SS BOND              : bond        0.00534 (    4)
  SS BOND              : angle       1.02007 (    8)
  hydrogen bonds       : bond        0.04272 (  490)
  hydrogen bonds       : angle       4.53503 ( 1464)
  Misc. bond           : bond        0.00138 (    2)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 1066.99 seconds
wall clock time: 19 minutes 4.53 seconds (1144.53 seconds total)