Starting phenix.real_space_refine
on Tue Mar 11 22:49:49 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/7s1y_24812/03_2025/7s1y_24812.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/7s1y_24812/03_2025/7s1y_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_2025/7s1y_24812.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/7s1y_24812/03_2025/7s1y_24812.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/7s1y_24812/03_2025/7s1y_24812.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/7s1y_24812/03_2025/7s1y_24812.cif"
  }
  resolution = 3.6
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }
  qi {
    qm_restraints {
      package {
        program = *test
      }
    }
  }


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

Validating inputs
Origin is already at (0, 0, 0), no shifts will be applied
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=   0.008 sd=   0.074
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): 0.02s

  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5624/modules/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: {'GLN:plan1': 3, 'TYR:plan': 1, 'ASN:plan1': 9, 'ASP:plan': 8, 'PHE:plan': 4, 'GLU:plan': 12, 'ARG:plan': 3}
          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: {'GLN:plan1': 3, 'TYR:plan': 1, 'ASN:plan1': 9, 'ASP:plan': 8, 'PHE:plan': 4, 'GLU:plan': 12, 'ARG:plan': 3}
          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: 4.76, per 1000 atoms: 0.72
  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: 1.89
  Conformation dependent library (CDL) restraints added in 1.0 seconds
  

  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: 0.57
  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: 1.91

  Time building geometry restraints manager: 2.11 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: 0.04
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:             1.210
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.000
  Construct map_model_manager:             0.010
  Extract box with map and model:          0.270
  Check model and map are aligned:         0.050
  Set scattering table:                    0.060
  Process input model:                     19.930
  Find NCS groups from input model:        0.230
  Set up NCS constraints:                  0.030
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.000
  Load rotamer database and sin/cos tables:2.910
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   24.700
-------------------------------------------------------------------------------
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   6736  Z= 0.323
  Angle     :  0.772  15.702   9222  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 : 12.97
  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 (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.33 (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
 TRP   0.017   0.001   TRP A 287 
 HIS   0.004   0.001   HIS A 398 
 PHE   0.025   0.001   PHE A 608 
 TYR   0.016   0.001   TYR B 739 
 ARG   0.001   0.000   ARG A 358 

*********************** 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  : 0.966 
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: 0.3591 (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: 0.3869 (p)
REVERT: B  677 ILE cc_start: 0.7566 (mm) cc_final: 0.7212 (mm)
  outliers start: 0
  outliers final: 0
  residues processed: 153
  average time/residue: 0.1207
  time to fit residues: 27.5095
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  : 0.737 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 94
   random chunks:
   chunk 79 optimal weight:    1.9990
   chunk 71 optimal weight:    0.9990
   chunk 39 optimal weight:    0.9990
   chunk 24 optimal weight:    0.5980
   chunk 48 optimal weight:    0.5980
   chunk 38 optimal weight:    0.5980
   chunk 73 optimal weight:    9.9990
   chunk 28 optimal weight:    6.9990
   chunk 44 optimal weight:    0.7980
   chunk 54 optimal weight:    0.9990
   chunk 85 optimal weight:    0.9990
   overall best weight:    0.7182

-------------------------------------------------------------------------------
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 = 0.4900 r_free = 0.4900 target = 0.255822 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 60)----------------|
| r_work = 0.4662 r_free = 0.4662 target = 0.225615 restraints weight = 7995.664|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 32)----------------|
| r_work = 0.4694 r_free = 0.4694 target = 0.230420 restraints weight = 4583.647|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 45)----------------|
| r_work = 0.4731 r_free = 0.4731 target = 0.234184 restraints weight = 3191.878|
|-----------------------------------------------------------------------------|
r_work (final): 0.4732
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6282
moved from start:          0.1784

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.050   6736  Z= 0.218
  Angle     :  0.646  10.505   9222  Z= 0.330
  Chirality :  0.043   0.307   1094
  Planarity :  0.005   0.083   1158
  Dihedral  :  6.044  38.573   1022
  Min Nonbonded Distance : 2.550

Molprobity Statistics.
  All-atom Clashscore : 12.42
  Ramachandran Plot:
    Outliers :  0.21 %
    Allowed  :  8.58 %
    Favored  : 91.21 %
  Rotamer:
    Outliers :  2.26 %
    Allowed  : 12.33 %
    Favored  : 85.42 %
  Cbeta Deviations :  0.24 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.31 (0.27), residues: 944
  helix:  0.88 (0.21), residues: 636
  sheet:  None (None), residues: 0
  loop : -2.58 (0.33), residues: 308

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.009   0.001   TRP B 287 
 HIS   0.005   0.002   HIS B 398 
 PHE   0.023   0.002   PHE B 477 
 TYR   0.029   0.002   TYR A 739 
 ARG   0.004   0.000   ARG A 546 

*********************** 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
  135 residues out of total 772 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 122
  time to evaluate  : 0.761 
Fit side-chains
REVERT: A  437 VAL cc_start: 0.8372 (m) cc_final: 0.8063 (t)
REVERT: A  471 GLU cc_start: 0.8319 (tm-30) cc_final: 0.7876 (tt0)
REVERT: A  681 PHE cc_start: 0.5712 (m-80) cc_final: 0.5476 (m-80)
REVERT: B  713 MET cc_start: 0.5886 (tmm) cc_final: 0.5555 (tmm)
  outliers start: 13
  outliers final: 9
  residues processed: 133
  average time/residue: 0.1191
  time to fit residues: 23.9052
Evaluate side-chains
  115 residues out of total 772 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 106
  time to evaluate  : 0.655 
-------------------------------------------------------------------------------
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
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 94
   random chunks:
   chunk 57 optimal weight:    0.8980
   chunk 47 optimal weight:    9.9990
   chunk 91 optimal weight:    0.5980
   chunk 3 optimal weight:    3.9990
   chunk 15 optimal weight:    0.7980
   chunk 66 optimal weight:    2.9990
   chunk 29 optimal weight:   20.0000
   chunk 46 optimal weight:    0.6980
   chunk 58 optimal weight:    1.9990
   chunk 37 optimal weight:    2.9990
   chunk 55 optimal weight:    0.5980
   overall best weight:    0.7180

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

Flipped N/Q/H residues before XYZ refinement:
** B 314 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 435 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4883 r_free = 0.4883 target = 0.254245 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 55)----------------|
| r_work = 0.4637 r_free = 0.4637 target = 0.223549 restraints weight = 8127.357|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 46)----------------|
| r_work = 0.4677 r_free = 0.4677 target = 0.228532 restraints weight = 4750.203|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 33)----------------|
| r_work = 0.4697 r_free = 0.4697 target = 0.231473 restraints weight = 3330.677|
|-----------------------------------------------------------------------------|
r_work (final): 0.4691
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6347
moved from start:          0.2267

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.036   6736  Z= 0.209
  Angle     :  0.628  11.423   9222  Z= 0.318
  Chirality :  0.043   0.256   1094
  Planarity :  0.004   0.069   1158
  Dihedral  :  6.106  41.024   1022
  Min Nonbonded Distance : 2.585

Molprobity Statistics.
  All-atom Clashscore : 12.18
  Ramachandran Plot:
    Outliers :  0.21 %
    Allowed  :  7.84 %
    Favored  : 91.95 %
  Rotamer:
    Outliers :  2.78 %
    Allowed  : 17.88 %
    Favored  : 79.34 %
  Cbeta Deviations :  0.24 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.22 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.30 (0.27), residues: 944
  helix:  0.91 (0.21), residues: 636
  sheet:  None (None), residues: 0
  loop : -2.65 (0.32), residues: 308

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.016   0.001   TRP A 300 
 HIS   0.003   0.001   HIS B 398 
 PHE   0.021   0.002   PHE A 285 
 TYR   0.026   0.002   TYR A 739 
 ARG   0.004   0.000   ARG A 546 

*********************** 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
  133 residues out of total 772 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 117
  time to evaluate  : 0.724 
Fit side-chains
REVERT: A  296 MET cc_start: 0.7665 (mmp) cc_final: 0.6881 (mmt)
REVERT: A  437 VAL cc_start: 0.8334 (m) cc_final: 0.8030 (t)
REVERT: A  471 GLU cc_start: 0.8252 (tm-30) cc_final: 0.7937 (tt0)
REVERT: A  604 SER cc_start: 0.8279 (OUTLIER) cc_final: 0.7789 (t)
REVERT: A  728 PHE cc_start: 0.6392 (m-80) cc_final: 0.6104 (m-10)
REVERT: A  748 TYR cc_start: 0.5031 (t80) cc_final: 0.4540 (m-80)
REVERT: B  428 MET cc_start: 0.5344 (mmp) cc_final: 0.5047 (mtm)
REVERT: B  748 TYR cc_start: 0.5069 (t80) cc_final: 0.4654 (m-80)
  outliers start: 16
  outliers final: 8
  residues processed: 128
  average time/residue: 0.1178
  time to fit residues: 23.2766
Evaluate side-chains
  116 residues out of total 772 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 107
  time to evaluate  : 0.720 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  312 VAL
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  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 91 optimal weight:    0.4980
   chunk 23 optimal weight:    1.9990
   chunk 72 optimal weight:    2.9990
   chunk 16 optimal weight:    4.9990
   chunk 15 optimal weight:    3.9990
   chunk 53 optimal weight:    1.9990
   chunk 82 optimal weight:    4.9990
   chunk 31 optimal weight:    3.9990
   chunk 56 optimal weight:    0.9990
   chunk 65 optimal weight:    9.9990
   chunk 29 optimal weight:   50.0000
   overall best weight:    1.6988

-------------------------------------------------------------------------------
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 = 0.4789 r_free = 0.4789 target = 0.243123 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 46)----------------|
| r_work = 0.4524 r_free = 0.4524 target = 0.210915 restraints weight = 8329.670|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 36)----------------|
| r_work = 0.4562 r_free = 0.4562 target = 0.215829 restraints weight = 4892.739|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 41)----------------|
| r_work = 0.4588 r_free = 0.4588 target = 0.219047 restraints weight = 3470.255|
|-----------------------------------------------------------------------------|
r_work (final): 0.4583
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6565
moved from start:          0.3294

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.043   6736  Z= 0.337
  Angle     :  0.727  11.842   9222  Z= 0.373
  Chirality :  0.047   0.282   1094
  Planarity :  0.005   0.065   1158
  Dihedral  :  7.085  48.190   1022
  Min Nonbonded Distance : 2.558

Molprobity Statistics.
  All-atom Clashscore : 14.32
  Ramachandran Plot:
    Outliers :  0.21 %
    Allowed  :  9.96 %
    Favored  : 89.83 %
  Rotamer:
    Outliers :  5.21 %
    Allowed  : 20.66 %
    Favored  : 74.13 %
  Cbeta Deviations :  0.24 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.22 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.94 (0.27), residues: 944
  helix:  0.36 (0.20), residues: 636
  sheet:  None (None), residues: 0
  loop : -2.72 (0.32), residues: 308

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.010   0.001   TRP A 287 
 HIS   0.003   0.001   HIS A 398 
 PHE   0.025   0.002   PHE A 608 
 TYR   0.020   0.002   TYR B 584 
 ARG   0.001   0.000   ARG B 294 

*********************** 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
  144 residues out of total 772 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 30
    poor density    : 114
  time to evaluate  : 0.650 
Fit side-chains
REVERT: A  296 MET cc_start: 0.7715 (mmp) cc_final: 0.7169 (mmt)
REVERT: A  604 SER cc_start: 0.8216 (OUTLIER) cc_final: 0.7967 (t)
REVERT: B  676 PRO cc_start: 0.8255 (Cg_endo) cc_final: 0.8051 (Cg_exo)
REVERT: B  748 TYR cc_start: 0.5448 (t80) cc_final: 0.5037 (m-80)
  outliers start: 30
  outliers final: 17
  residues processed: 137
  average time/residue: 0.1093
  time to fit residues: 22.8876
Evaluate side-chains
  120 residues out of total 772 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 102
  time to evaluate  : 0.638 
-------------------------------------------------------------------------------
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  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  292 LEU
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  674 ILE
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 86 optimal weight:    0.0010
   chunk 25 optimal weight:    1.9990
   chunk 85 optimal weight:    0.6980
   chunk 42 optimal weight:    0.1980
   chunk 65 optimal weight:    3.9990
   chunk 10 optimal weight:    0.7980
   chunk 12 optimal weight:    9.9990
   chunk 58 optimal weight:    4.9990
   chunk 46 optimal weight:    0.7980
   chunk 61 optimal weight:   10.0000
   chunk 29 optimal weight:    9.9990
   overall best weight:    0.4986

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

Flipped N/Q/H residues before XYZ refinement:
A 298 ASN
** B 314 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4847 r_free = 0.4847 target = 0.251116 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 59)----------------|
| r_work = 0.4602 r_free = 0.4602 target = 0.220429 restraints weight = 8084.003|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 47)----------------|
| r_work = 0.4640 r_free = 0.4640 target = 0.225283 restraints weight = 4800.176|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 49)----------------|
| r_work = 0.4666 r_free = 0.4666 target = 0.228683 restraints weight = 3409.971|
|-----------------------------------------------------------------------------|
r_work (final): 0.4661
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6402
moved from start:          0.3156

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.034   6736  Z= 0.197
  Angle     :  0.654  14.970   9222  Z= 0.330
  Chirality :  0.043   0.277   1094
  Planarity :  0.004   0.059   1158
  Dihedral  :  6.285  41.747   1022
  Min Nonbonded Distance : 2.601

Molprobity Statistics.
  All-atom Clashscore : 12.74
  Ramachandran Plot:
    Outliers :  0.21 %
    Allowed  :  8.37 %
    Favored  : 91.42 %
  Rotamer:
    Outliers :  3.65 %
    Allowed  : 24.13 %
    Favored  : 72.22 %
  Cbeta Deviations :  0.24 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.22 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.55 (0.27), residues: 944
  helix:  0.76 (0.21), residues: 630
  sheet:  None (None), residues: 0
  loop : -2.76 (0.31), residues: 314

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.009   0.001   TRP B 287 
 HIS   0.003   0.001   HIS B 398 
 PHE   0.023   0.002   PHE A 608 
 TYR   0.018   0.001   TYR A 739 
 ARG   0.003   0.000   ARG A 546 

*********************** 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
  142 residues out of total 772 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 121
  time to evaluate  : 0.661 
Fit side-chains
REVERT: A  296 MET cc_start: 0.7654 (mmp) cc_final: 0.7208 (mmt)
REVERT: A  681 PHE cc_start: 0.5987 (m-80) cc_final: 0.5616 (m-80)
REVERT: A  728 PHE cc_start: 0.6514 (m-80) cc_final: 0.6264 (m-10)
REVERT: B  285 PHE cc_start: 0.6675 (p90) cc_final: 0.6427 (p90)
REVERT: B  748 TYR cc_start: 0.5384 (t80) cc_final: 0.5057 (m-80)
  outliers start: 21
  outliers final: 12
  residues processed: 136
  average time/residue: 0.1135
  time to fit residues: 23.6277
Evaluate side-chains
  123 residues out of total 772 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 111
  time to evaluate  : 0.660 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  312 VAL
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 A residue  677 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  611 THR
Chi-restraints excluded: chain B residue  621 SER
Chi-restraints excluded: chain B residue  677 ILE
Chi-restraints excluded: chain B residue  717 LEU
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 94
   random chunks:
   chunk 68 optimal weight:    0.6980
   chunk 86 optimal weight:    0.5980
   chunk 91 optimal weight:    0.7980
   chunk 67 optimal weight:    0.9990
   chunk 43 optimal weight:    3.9990
   chunk 44 optimal weight:    0.7980
   chunk 31 optimal weight:    0.6980
   chunk 50 optimal weight:    0.5980
   chunk 60 optimal weight:    0.5980
   chunk 46 optimal weight:    0.8980
   chunk 89 optimal weight:    0.0770
   overall best weight:    0.5138

-------------------------------------------------------------------------------
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 = 0.251686 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 55)----------------|
| r_work = 0.4603 r_free = 0.4603 target = 0.221247 restraints weight = 8046.677|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 52)----------------|
| r_work = 0.4641 r_free = 0.4641 target = 0.226203 restraints weight = 4734.233|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 44)----------------|
| r_work = 0.4667 r_free = 0.4667 target = 0.229552 restraints weight = 3336.221|
|-----------------------------------------------------------------------------|
r_work (final): 0.4663
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6395
moved from start:          0.3229

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.044   6736  Z= 0.208
  Angle     :  0.668  14.311   9222  Z= 0.337
  Chirality :  0.046   0.325   1094
  Planarity :  0.004   0.058   1158
  Dihedral  :  6.257  41.969   1022
  Min Nonbonded Distance : 2.567

Molprobity Statistics.
  All-atom Clashscore : 13.53
  Ramachandran Plot:
    Outliers :  0.21 %
    Allowed  :  7.84 %
    Favored  : 91.95 %
  Rotamer:
    Outliers :  4.69 %
    Allowed  : 23.26 %
    Favored  : 72.05 %
  Cbeta Deviations :  0.24 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.22 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.49 (0.27), residues: 944
  helix:  0.78 (0.21), residues: 628
  sheet:  None (None), residues: 0
  loop : -2.66 (0.31), residues: 316

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.010   0.001   TRP B 287 
 HIS   0.003   0.001   HIS B 398 
 PHE   0.021   0.002   PHE A 608 
 TYR   0.018   0.001   TYR B 584 
 ARG   0.003   0.000   ARG A 546 

*********************** 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
  139 residues out of total 772 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 27
    poor density    : 112
  time to evaluate  : 0.703 
Fit side-chains
REVERT: A  296 MET cc_start: 0.7450 (mmp) cc_final: 0.7110 (mmt)
REVERT: A  604 SER cc_start: 0.8220 (OUTLIER) cc_final: 0.7958 (t)
REVERT: A  681 PHE cc_start: 0.5734 (m-80) cc_final: 0.5512 (m-80)
REVERT: A  712 ASN cc_start: 0.3468 (OUTLIER) cc_final: 0.3187 (t0)
REVERT: A  728 PHE cc_start: 0.6368 (m-80) cc_final: 0.6122 (m-10)
REVERT: B  748 TYR cc_start: 0.5374 (t80) cc_final: 0.5007 (m-80)
  outliers start: 27
  outliers final: 16
  residues processed: 132
  average time/residue: 0.1152
  time to fit residues: 23.3516
Evaluate side-chains
  128 residues out of total 772 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 110
  time to evaluate  : 0.653 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  312 VAL
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  604 SER
Chi-restraints excluded: chain A residue  611 THR
Chi-restraints excluded: chain A residue  621 SER
Chi-restraints excluded: chain A residue  677 ILE
Chi-restraints excluded: chain A residue  712 ASN
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  443 LEU
Chi-restraints excluded: chain B residue  611 THR
Chi-restraints excluded: chain B residue  621 SER
Chi-restraints excluded: chain B residue  677 ILE
Chi-restraints excluded: chain B residue  692 SER
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 74 optimal weight:    5.9990
   chunk 73 optimal weight:    7.9990
   chunk 51 optimal weight:    0.7980
   chunk 11 optimal weight:    1.9990
   chunk 2 optimal weight:    4.9990
   chunk 32 optimal weight:    0.9990
   chunk 36 optimal weight:    9.9990
   chunk 37 optimal weight:    0.9980
   chunk 66 optimal weight:    4.9990
   chunk 22 optimal weight:    0.0670
   chunk 25 optimal weight:    2.9990
   overall best weight:    0.9722

-------------------------------------------------------------------------------
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 = 0.4814 r_free = 0.4814 target = 0.247714 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 57)----------------|
| r_work = 0.4568 r_free = 0.4568 target = 0.216835 restraints weight = 7924.754|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 42)----------------|
| r_work = 0.4607 r_free = 0.4607 target = 0.221908 restraints weight = 4604.175|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 60)----------------|
| r_work = 0.4636 r_free = 0.4636 target = 0.225447 restraints weight = 3215.907|
|-----------------------------------------------------------------------------|
r_work (final): 0.4637
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6450
moved from start:          0.3417

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.051   6736  Z= 0.254
  Angle     :  0.697  15.345   9222  Z= 0.348
  Chirality :  0.048   0.375   1094
  Planarity :  0.004   0.056   1158
  Dihedral  :  6.487  45.211   1022
  Min Nonbonded Distance : 2.599

Molprobity Statistics.
  All-atom Clashscore : 13.53
  Ramachandran Plot:
    Outliers :  0.21 %
    Allowed  :  8.26 %
    Favored  : 91.53 %
  Rotamer:
    Outliers :  4.69 %
    Allowed  : 22.57 %
    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 (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.68 (0.27), residues: 944
  helix:  0.61 (0.20), residues: 636
  sheet:  None (None), residues: 0
  loop : -2.78 (0.31), residues: 308

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.009   0.001   TRP B 287 
 HIS   0.003   0.001   HIS B 398 
 PHE   0.019   0.002   PHE A 495 
 TYR   0.013   0.001   TYR A 711 
 ARG   0.003   0.000   ARG B 294 

*********************** 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
  137 residues out of total 772 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 27
    poor density    : 110
  time to evaluate  : 0.643 
Fit side-chains
REVERT: A  296 MET cc_start: 0.7497 (mmp) cc_final: 0.6960 (mmt)
REVERT: A  471 GLU cc_start: 0.8008 (tm-30) cc_final: 0.7742 (tt0)
REVERT: A  604 SER cc_start: 0.8237 (OUTLIER) cc_final: 0.7957 (t)
REVERT: A  728 PHE cc_start: 0.6721 (m-80) cc_final: 0.6508 (m-10)
REVERT: B  296 MET cc_start: 0.7516 (mmp) cc_final: 0.6993 (mmt)
REVERT: B  384 VAL cc_start: 0.6777 (OUTLIER) cc_final: 0.6507 (t)
REVERT: B  676 PRO cc_start: 0.8251 (Cg_endo) cc_final: 0.8047 (Cg_exo)
REVERT: B  748 TYR cc_start: 0.5421 (t80) cc_final: 0.4993 (m-80)
  outliers start: 27
  outliers final: 18
  residues processed: 131
  average time/residue: 0.1108
  time to fit residues: 22.5042
Evaluate side-chains
  130 residues out of total 772 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 110
  time to evaluate  : 0.649 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  312 VAL
Chi-restraints excluded: chain A residue  321 VAL
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  604 SER
Chi-restraints excluded: chain A residue  611 THR
Chi-restraints excluded: chain A residue  621 SER
Chi-restraints excluded: chain A residue  677 ILE
Chi-restraints excluded: chain A residue  740 VAL
Chi-restraints excluded: chain B residue  312 VAL
Chi-restraints excluded: chain B residue  384 VAL
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  677 ILE
Chi-restraints excluded: chain B residue  692 SER
Chi-restraints excluded: chain B residue  717 LEU
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 94
   random chunks:
   chunk 22 optimal weight:    0.9980
   chunk 71 optimal weight:    0.6980
   chunk 30 optimal weight:    0.0570
   chunk 55 optimal weight:    1.9990
   chunk 84 optimal weight:    0.0980
   chunk 17 optimal weight:    0.0170
   chunk 78 optimal weight:    0.1980
   chunk 6 optimal weight:    3.9990
   chunk 89 optimal weight:    0.2980
   chunk 35 optimal weight:    0.9980
   chunk 28 optimal weight:    0.0170
   overall best weight:    0.0774

-------------------------------------------------------------------------------
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 = 0.4887 r_free = 0.4887 target = 0.256692 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 44)----------------|
| r_work = 0.4656 r_free = 0.4656 target = 0.227508 restraints weight = 7969.987|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 45)----------------|
| r_work = 0.4699 r_free = 0.4699 target = 0.232667 restraints weight = 4625.634|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 33)----------------|
| r_work = 0.4720 r_free = 0.4720 target = 0.235915 restraints weight = 3181.338|
|-----------------------------------------------------------------------------|
r_work (final): 0.4733
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6267
moved from start:          0.3316

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.049   6736  Z= 0.187
  Angle     :  0.683  14.991   9222  Z= 0.339
  Chirality :  0.047   0.362   1094
  Planarity :  0.004   0.054   1158
  Dihedral  :  5.895  38.092   1022
  Min Nonbonded Distance : 2.613

Molprobity Statistics.
  All-atom Clashscore : 13.29
  Ramachandran Plot:
    Outliers :  0.21 %
    Allowed  :  6.89 %
    Favored  : 92.90 %
  Rotamer:
    Outliers :  3.65 %
    Allowed  : 24.48 %
    Favored  : 71.88 %
  Cbeta Deviations :  0.24 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.31 (0.27), residues: 944
  helix:  0.92 (0.21), residues: 632
  sheet:  None (None), residues: 0
  loop : -2.64 (0.31), residues: 312

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.011   0.001   TRP B 287 
 HIS   0.003   0.001   HIS A 398 
 PHE   0.027   0.002   PHE A 681 
 TYR   0.021   0.001   TYR A 739 
 ARG   0.004   0.001   ARG B 294 

*********************** 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
  141 residues out of total 772 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 120
  time to evaluate  : 0.699 
Fit side-chains
REVERT: A  604 SER cc_start: 0.8199 (OUTLIER) cc_final: 0.7881 (t)
REVERT: A  713 MET cc_start: 0.6334 (tmm) cc_final: 0.5954 (tmm)
REVERT: A  748 TYR cc_start: 0.5317 (t80) cc_final: 0.4871 (m-80)
REVERT: B  681 PHE cc_start: 0.5449 (m-80) cc_final: 0.5104 (m-80)
REVERT: B  748 TYR cc_start: 0.5206 (t80) cc_final: 0.4928 (m-80)
  outliers start: 21
  outliers final: 14
  residues processed: 138
  average time/residue: 0.1214
  time to fit residues: 24.9685
Evaluate side-chains
  121 residues out of total 772 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 106
  time to evaluate  : 0.695 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  312 VAL
Chi-restraints excluded: chain A residue  364 PHE
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  677 ILE
Chi-restraints excluded: chain B residue  364 PHE
Chi-restraints excluded: chain B residue  395 LEU
Chi-restraints excluded: chain B residue  415 ILE
Chi-restraints excluded: chain B residue  611 THR
Chi-restraints excluded: chain B residue  621 SER
Chi-restraints excluded: chain B residue  677 ILE
Chi-restraints excluded: chain B residue  692 SER
Chi-restraints excluded: chain B residue  717 LEU
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 94
   random chunks:
   chunk 12 optimal weight:    9.9990
   chunk 84 optimal weight:    0.7980
   chunk 0 optimal weight:   10.0000
   chunk 68 optimal weight:    0.3980
   chunk 40 optimal weight:    2.9990
   chunk 85 optimal weight:    0.7980
   chunk 67 optimal weight:    1.9990
   chunk 69 optimal weight:    0.3980
   chunk 13 optimal weight:    0.8980
   chunk 26 optimal weight:    9.9990
   chunk 25 optimal weight:    0.5980
   overall best weight:    0.5980

-------------------------------------------------------------------------------
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 = 0.4866 r_free = 0.4866 target = 0.254136 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 56)----------------|
| r_work = 0.4622 r_free = 0.4622 target = 0.223261 restraints weight = 8269.529|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 44)----------------|
| r_work = 0.4661 r_free = 0.4661 target = 0.228388 restraints weight = 4863.934|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 38)----------------|
| r_work = 0.4684 r_free = 0.4684 target = 0.231694 restraints weight = 3408.284|
|-----------------------------------------------------------------------------|
r_work (final): 0.4698
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6366
moved from start:          0.3408

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.058   6736  Z= 0.222
  Angle     :  0.710  16.019   9222  Z= 0.348
  Chirality :  0.047   0.331   1094
  Planarity :  0.004   0.053   1158
  Dihedral  :  6.002  40.171   1022
  Min Nonbonded Distance : 2.550

Molprobity Statistics.
  All-atom Clashscore : 14.08
  Ramachandran Plot:
    Outliers :  0.21 %
    Allowed  :  6.89 %
    Favored  : 92.90 %
  Rotamer:
    Outliers :  3.12 %
    Allowed  : 26.39 %
    Favored  : 70.49 %
  Cbeta Deviations :  0.24 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.11 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.33 (0.27), residues: 944
  helix:  0.89 (0.20), residues: 636
  sheet:  None (None), residues: 0
  loop : -2.68 (0.31), residues: 308

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.008   0.001   TRP B 287 
 HIS   0.003   0.001   HIS A 398 
 PHE   0.021   0.002   PHE A 495 
 TYR   0.019   0.001   TYR A 739 
 ARG   0.004   0.001   ARG B 294 

*********************** 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
  124 residues out of total 772 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 106
  time to evaluate  : 0.723 
Fit side-chains
REVERT: A  471 GLU cc_start: 0.7919 (tm-30) cc_final: 0.7674 (tt0)
REVERT: A  604 SER cc_start: 0.8222 (OUTLIER) cc_final: 0.7906 (t)
REVERT: A  713 MET cc_start: 0.6378 (tmm) cc_final: 0.5962 (tmm)
REVERT: B  681 PHE cc_start: 0.5681 (m-80) cc_final: 0.5363 (m-80)
REVERT: B  748 TYR cc_start: 0.5251 (t80) cc_final: 0.4876 (m-80)
  outliers start: 18
  outliers final: 14
  residues processed: 122
  average time/residue: 0.1226
  time to fit residues: 23.0789
Evaluate side-chains
  120 residues out of total 772 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 105
  time to evaluate  : 0.738 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  312 VAL
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  604 SER
Chi-restraints excluded: chain A residue  611 THR
Chi-restraints excluded: chain A residue  621 SER
Chi-restraints excluded: chain A residue  677 ILE
Chi-restraints excluded: chain B residue  364 PHE
Chi-restraints excluded: chain B residue  415 ILE
Chi-restraints excluded: chain B residue  531 LEU
Chi-restraints excluded: chain B residue  611 THR
Chi-restraints excluded: chain B residue  621 SER
Chi-restraints excluded: chain B residue  677 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 34 optimal weight:    0.8980
   chunk 93 optimal weight:    0.9980
   chunk 79 optimal weight:    0.7980
   chunk 70 optimal weight:    0.7980
   chunk 8 optimal weight:    0.7980
   chunk 81 optimal weight:    0.6980
   chunk 30 optimal weight:    0.3980
   chunk 7 optimal weight:    1.9990
   chunk 41 optimal weight:    0.9980
   chunk 0 optimal weight:    9.9990
   chunk 75 optimal weight:    0.0060
   overall best weight:    0.5396

-------------------------------------------------------------------------------
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 = 0.4869 r_free = 0.4869 target = 0.253819 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 45)----------------|
| r_work = 0.4627 r_free = 0.4627 target = 0.223636 restraints weight = 8171.284|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 38)----------------|
| r_work = 0.4664 r_free = 0.4664 target = 0.228589 restraints weight = 4854.785|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 44)----------------|
| r_work = 0.4693 r_free = 0.4693 target = 0.231945 restraints weight = 3424.606|
|-----------------------------------------------------------------------------|
r_work (final): 0.4703
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6354
moved from start:          0.3488

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.060   6736  Z= 0.219
  Angle     :  0.714  15.853   9222  Z= 0.348
  Chirality :  0.045   0.303   1094
  Planarity :  0.004   0.053   1158
  Dihedral  :  6.013  40.866   1022
  Min Nonbonded Distance : 2.566

Molprobity Statistics.
  All-atom Clashscore : 13.29
  Ramachandran Plot:
    Outliers :  0.21 %
    Allowed  :  7.31 %
    Favored  : 92.48 %
  Rotamer:
    Outliers :  2.78 %
    Allowed  : 26.22 %
    Favored  : 71.01 %
  Cbeta Deviations :  0.24 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.11 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.31 (0.27), residues: 944
  helix:  0.88 (0.20), residues: 640
  sheet:  None (None), residues: 0
  loop : -2.63 (0.32), residues: 304

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.013   0.001   TRP B 732 
 HIS   0.002   0.001   HIS A 398 
 PHE   0.021   0.002   PHE A 495 
 TYR   0.019   0.001   TYR A 739 
 ARG   0.004   0.001   ARG B 294 

********************** 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: 16
    poor density    : 109
  time to evaluate  : 0.687 
Fit side-chains
REVERT: A  471 GLU cc_start: 0.7973 (tm-30) cc_final: 0.7721 (tt0)
REVERT: A  713 MET cc_start: 0.6373 (tmm) cc_final: 0.5935 (tmm)
REVERT: B  681 PHE cc_start: 0.5745 (m-80) cc_final: 0.5475 (m-80)
REVERT: B  748 TYR cc_start: 0.5247 (t80) cc_final: 0.4866 (m-80)
  outliers start: 16
  outliers final: 13
  residues processed: 121
  average time/residue: 0.1210
  time to fit residues: 22.4077
Evaluate side-chains
  121 residues out of total 772 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 108
  time to evaluate  : 0.710 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  312 VAL
Chi-restraints excluded: chain A residue  364 PHE
Chi-restraints excluded: chain A residue  611 THR
Chi-restraints excluded: chain A residue  621 SER
Chi-restraints excluded: chain A residue  677 ILE
Chi-restraints excluded: chain B residue  353 TYR
Chi-restraints excluded: chain B residue  364 PHE
Chi-restraints excluded: chain B residue  415 ILE
Chi-restraints excluded: chain B residue  531 LEU
Chi-restraints excluded: chain B residue  611 THR
Chi-restraints excluded: chain B residue  621 SER
Chi-restraints excluded: chain B residue  677 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 9 optimal weight:    0.5980
   chunk 19 optimal weight:    3.9990
   chunk 25 optimal weight:    0.6980
   chunk 55 optimal weight:    0.9980
   chunk 12 optimal weight:    9.9990
   chunk 24 optimal weight:    0.8980
   chunk 64 optimal weight:    0.4980
   chunk 71 optimal weight:    0.9980
   chunk 89 optimal weight:    0.3980
   chunk 93 optimal weight:    0.4980
   chunk 16 optimal weight:    0.2980
   overall best weight:    0.4580

-------------------------------------------------------------------------------
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 = 0.4878 r_free = 0.4878 target = 0.255005 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 55)----------------|
| r_work = 0.4642 r_free = 0.4642 target = 0.224758 restraints weight = 8237.181|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 42)----------------|
| r_work = 0.4682 r_free = 0.4682 target = 0.229803 restraints weight = 4855.452|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 46)----------------|
| r_work = 0.4709 r_free = 0.4709 target = 0.233218 restraints weight = 3406.883|
|-----------------------------------------------------------------------------|
r_work (final): 0.4712
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6342
moved from start:          0.3573

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.061   6736  Z= 0.216
  Angle     :  0.720  16.196   9222  Z= 0.351
  Chirality :  0.045   0.282   1094
  Planarity :  0.004   0.053   1158
  Dihedral  :  5.998  40.447   1022
  Min Nonbonded Distance : 2.576

Molprobity Statistics.
  All-atom Clashscore : 13.21
  Ramachandran Plot:
    Outliers :  0.21 %
    Allowed  :  7.20 %
    Favored  : 92.58 %
  Rotamer:
    Outliers :  2.95 %
    Allowed  : 26.91 %
    Favored  : 70.14 %
  Cbeta Deviations :  0.24 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.11 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.28 (0.27), residues: 944
  helix:  0.90 (0.20), residues: 640
  sheet:  None (None), residues: 0
  loop : -2.61 (0.32), residues: 304

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.009   0.001   TRP B 732 
 HIS   0.003   0.001   HIS A 398 
 PHE   0.026   0.002   PHE B 466 
 TYR   0.021   0.001   TYR A 739 
 ARG   0.004   0.001   ARG B 294 
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 2058.94 seconds
wall clock time: 36 minutes 40.50 seconds (2200.50 seconds total)