Starting phenix.real_space_refine
on Thu Jul 24 17:11:19 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/7s1z_24813/07_2025/7s1z_24813.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/7s1z_24813/07_2025/7s1z_24813.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.3
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/7s1z_24813/07_2025/7s1z_24813.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/7s1z_24813/07_2025/7s1z_24813.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/7s1z_24813/07_2025/7s1z_24813.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/7s1z_24813/07_2025/7s1z_24813.cif"
  }
  resolution = 3.3
  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=   0.010 sd=   0.150
Set stop_for_unknowns flag
  Set to: True
Assert model is a single copy model
Assert all atoms have isotropic ADPs
Construct map_model_manager
Extract box with map and model
Check model and map are aligned
Set scattering table
  Set to: electron
  Number of scattering types: 4
    Type Number    sf(0)   Gaussians
     S      34      5.16       5
     C    4224      2.51       5
     N    1034      2.21       5
     O    1124      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 13 residue(s): 0.02s

  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5711/modules/chem_data/mon_lib"
  Total number of atoms: 6416
  Number of models: 1
  Model: ""
    Number of chains: 2
    Chain: "A"
      Number of atoms: 3208
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 472, 3208
          Classifications: {'peptide': 472}
          Incomplete info: {'backbone_only': 21, 'truncation_to_alanine': 83}
          Link IDs: {'PTRANS': 15, 'TRANS': 456}
          Unresolved chain link angles: 1
          Unresolved non-hydrogen bonds: 392
          Unresolved non-hydrogen angles: 507
          Unresolved non-hydrogen dihedrals: 302
          Unresolved non-hydrogen chiralities: 52
          Planarities with less than four sites: {'GLN:plan1': 3, 'TYR:plan': 4, 'ASN:plan1': 10, 'ASP:plan': 8, 'PHE:plan': 6, 'GLU:plan': 12, 'ARG:plan': 5}
          Unresolved non-hydrogen planarities: 208
    Chain: "B"
      Number of atoms: 3208
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 472, 3208
          Classifications: {'peptide': 472}
          Incomplete info: {'backbone_only': 21, 'truncation_to_alanine': 83}
          Link IDs: {'PTRANS': 15, 'TRANS': 456}
          Unresolved chain link angles: 1
          Unresolved non-hydrogen bonds: 392
          Unresolved non-hydrogen angles: 507
          Unresolved non-hydrogen dihedrals: 302
          Unresolved non-hydrogen chiralities: 52
          Planarities with less than four sites: {'GLN:plan1': 3, 'TYR:plan': 4, 'ASN:plan1': 10, 'ASP:plan': 8, 'PHE:plan': 6, 'GLU:plan': 12, 'ARG:plan': 5}
          Unresolved non-hydrogen planarities: 208
  Time building chain proxies: 4.95, per 1000 atoms: 0.77
  Number of scatterers: 6416
  At special positions: 0
  Unit cell: (104.94, 83.74, 87.98, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 4
    Type Number    sf(0)
     S      34     16.00
     O    1124      8.00
     N    1034      7.00
     C    4224      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=2.03
    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=0, symmetry=0
  Time building additional restraints: 1.84
  Conformation dependent library (CDL) restraints added in 1.0 seconds
  

  1880 Ramachandran restraints generated.
    940 Oldfield, 0 Emsley, 940 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  1640

  Finding SS restraints...
    Secondary structure from input PDB file:
      42 helices and 0 sheets defined
      71.4% alpha, 0.0% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.59
  Creating SS restraints...
    Processing helix  chain 'A' and resid 288 through 300
    Processing helix  chain 'A' and resid 301 through 306
      removed outlier: 4.532A  pdb=" N   PHE A 305 " --> pdb=" O   GLY A 301 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 306 through 315
      removed outlier: 4.532A  pdb=" N   TRP A 310 " --> pdb=" O   ILE A 306 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 316 through 344
      removed outlier: 4.115A  pdb=" N   LEU A 322 " --> pdb=" O   GLY A 318 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 361 through 398
      removed outlier: 4.508A  pdb=" N   GLY A 365 " --> pdb=" O   GLY A 361 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 407 through 425
      removed outlier: 3.502A  pdb=" N   ILE A 411 " --> pdb=" O   ASN A 407 " (cutoff:3.500A)
      removed outlier: 3.910A  pdb=" N   VAL A 425 " --> pdb=" O   LEU A 421 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 428 through 454
      removed outlier: 3.650A  pdb=" N   ALA A 432 " --> pdb=" O   MET A 428 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 457 through 461
      removed outlier: 3.651A  pdb=" N   LYS A 460 " --> pdb=" O   LEU A 457 " (cutoff:3.500A)
      removed outlier: 3.631A  pdb=" N   LYS A 461 " --> pdb=" O   GLU A 458 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'A' and resid 457 through 461'
    Processing helix  chain 'A' and resid 469 through 477
    Processing helix  chain 'A' and resid 486 through 495
    Processing helix  chain 'A' and resid 496 through 499
    Processing helix  chain 'A' and resid 500 through 506
      removed outlier: 4.358A  pdb=" N   GLY A 504 " --> pdb=" O   GLY A 500 " (cutoff:3.500A)
      removed outlier: 3.536A  pdb=" N   ALA A 505 " --> pdb=" O   ILE A 501 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 507 through 511
    Processing helix  chain 'A' and resid 516 through 542
    Processing helix  chain 'A' and resid 565 through 570
      removed outlier: 3.599A  pdb=" N   CYS A 568 " --> pdb=" O   SER A 565 " (cutoff:3.500A)
      removed outlier: 3.759A  pdb=" N   LEU A 570 " --> pdb=" O   ALA A 567 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 591 through 597
      removed outlier: 3.562A  pdb=" N   SER A 597 " --> pdb=" O   MET A 593 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 599 through 630
      removed outlier: 3.647A  pdb=" N   ILE A 603 " --> pdb=" O   PHE A 599 " (cutoff:3.500A)
      Proline residue:  A 623  - end of helix
    Processing helix  chain 'A' and resid 654 through 667
      removed outlier: 4.131A  pdb=" N   THR A 658 " --> pdb=" O   GLY A 654 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 673 through 699
      removed outlier: 4.242A  pdb=" N   ILE A 677 " --> pdb=" O   VAL A 673 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 712 through 730
    Processing helix  chain 'A' and resid 731 through 753
    Processing helix  chain 'B' and resid 288 through 300
    Processing helix  chain 'B' and resid 301 through 306
      removed outlier: 4.441A  pdb=" N   PHE B 305 " --> pdb=" O   GLY B 301 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 306 through 315
      removed outlier: 4.511A  pdb=" N   TRP B 310 " --> pdb=" O   ILE B 306 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 316 through 344
      removed outlier: 4.170A  pdb=" N   LEU B 322 " --> pdb=" O   GLY B 318 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 361 through 398
      removed outlier: 4.482A  pdb=" N   GLY B 365 " --> pdb=" O   GLY B 361 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 407 through 425
      removed outlier: 3.654A  pdb=" N   ILE B 411 " --> pdb=" O   ASN B 407 " (cutoff:3.500A)
      removed outlier: 3.637A  pdb=" N   VAL B 425 " --> pdb=" O   LEU B 421 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 428 through 454
      removed outlier: 3.639A  pdb=" N   ALA B 432 " --> pdb=" O   MET B 428 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 457 through 461
      removed outlier: 3.646A  pdb=" N   LYS B 460 " --> pdb=" O   LEU B 457 " (cutoff:3.500A)
      removed outlier: 3.609A  pdb=" N   LYS B 461 " --> pdb=" O   GLU B 458 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'B' and resid 457 through 461'
    Processing helix  chain 'B' and resid 469 through 477
    Processing helix  chain 'B' and resid 486 through 495
    Processing helix  chain 'B' and resid 496 through 500
      removed outlier: 5.936A  pdb=" N   GLY B 500 " --> pdb=" O   ALA B 497 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 501 through 506
      removed outlier: 3.585A  pdb=" N   ALA B 505 " --> pdb=" O   ILE B 501 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 507 through 511
    Processing helix  chain 'B' and resid 516 through 542
    Processing helix  chain 'B' and resid 565 through 570
      removed outlier: 3.598A  pdb=" N   CYS B 568 " --> pdb=" O   SER B 565 " (cutoff:3.500A)
      removed outlier: 3.806A  pdb=" N   LEU B 570 " --> pdb=" O   ALA B 567 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 591 through 597
      removed outlier: 3.529A  pdb=" N   SER B 597 " --> pdb=" O   MET B 593 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 599 through 630
      removed outlier: 3.526A  pdb=" N   ILE B 603 " --> pdb=" O   PHE B 599 " (cutoff:3.500A)
      Proline residue:  B 623  - end of helix
    Processing helix  chain 'B' and resid 654 through 667
      removed outlier: 3.964A  pdb=" N   THR B 658 " --> pdb=" O   GLY B 654 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 673 through 699
      removed outlier: 3.924A  pdb=" N   ILE B 677 " --> pdb=" O   VAL B 673 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 712 through 730
      removed outlier: 3.505A  pdb=" N   SER B 716 " --> pdb=" O   ASN B 712 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 731 through 753

    473 hydrogen bonds defined for protein.
    1395 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: 1.84

  Time building geometry restraints manager: 2.18 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: 2004
        1.34 -     1.46: 1560
        1.46 -     1.58: 2948
        1.58 -     1.70: 0
        1.70 -     1.81: 48
  Bond restraints: 6560
  Sorted by residual:
  bond pdb=" CG1 ILE B 747 "
       pdb=" CD1 ILE B 747 "
    ideal  model  delta    sigma   weight residual
    1.513  1.452  0.061 3.90e-02 6.57e+02 2.44e+00
  bond pdb=" CG1 ILE A 747 "
       pdb=" CD1 ILE A 747 "
    ideal  model  delta    sigma   weight residual
    1.513  1.455  0.058 3.90e-02 6.57e+02 2.22e+00
  bond pdb=" C   ALA B 675 "
       pdb=" N   PRO B 676 "
    ideal  model  delta    sigma   weight residual
    1.334  1.355 -0.021 1.51e-02 4.39e+03 1.91e+00
  bond pdb=" C   ALA A 675 "
       pdb=" N   PRO A 676 "
    ideal  model  delta    sigma   weight residual
    1.334  1.354 -0.020 1.51e-02 4.39e+03 1.76e+00
  bond pdb=" C   PHE A 495 "
       pdb=" N   PRO A 496 "
    ideal  model  delta    sigma   weight residual
    1.333  1.351 -0.018 1.44e-02 4.82e+03 1.59e+00
  ... (remaining 6555 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     1.45: 8568
        1.45 -     2.91: 318
        2.91 -     4.36: 68
        4.36 -     5.81: 16
        5.81 -     7.27: 10
  Bond angle restraints: 8980
  Sorted by residual:
  angle pdb=" N   ILE A 507 "
        pdb=" CA  ILE A 507 "
        pdb=" C   ILE A 507 "
      ideal   model   delta    sigma   weight residual
     112.80  106.16    6.64 1.15e+00 7.56e-01 3.33e+01
  angle pdb=" N   ILE B 507 "
        pdb=" CA  ILE B 507 "
        pdb=" C   ILE B 507 "
      ideal   model   delta    sigma   weight residual
     113.07  107.03    6.04 1.36e+00 5.41e-01 1.97e+01
  angle pdb=" N   ILE B 556 "
        pdb=" CA  ILE B 556 "
        pdb=" C   ILE B 556 "
      ideal   model   delta    sigma   weight residual
     111.91  108.72    3.19 8.90e-01 1.26e+00 1.28e+01
  angle pdb=" N   ILE A 556 "
        pdb=" CA  ILE A 556 "
        pdb=" C   ILE A 556 "
      ideal   model   delta    sigma   weight residual
     111.91  108.85    3.06 8.90e-01 1.26e+00 1.18e+01
  angle pdb=" N   SER A 516 "
        pdb=" CA  SER A 516 "
        pdb=" C   SER A 516 "
      ideal   model   delta    sigma   weight residual
     112.72  109.19    3.53 1.28e+00 6.10e-01 7.60e+00
  ... (remaining 8975 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    16.22: 3350
       16.22 -    32.45: 255
       32.45 -    48.67: 50
       48.67 -    64.89: 3
       64.89 -    81.12: 4
  Dihedral angle restraints: 3662
    sinusoidal: 1056
      harmonic: 2606
  Sorted by residual:
  dihedral pdb=" CB  CYS B 577 "
           pdb=" SG  CYS B 577 "
           pdb=" SG  CYS B 582 "
           pdb=" CB  CYS B 582 "
      ideal   model   delta sinusoidal    sigma   weight residual
      93.00   21.59   71.41     1      1.00e+01 1.00e-02 6.54e+01
  dihedral pdb=" CB  CYS A 577 "
           pdb=" SG  CYS A 577 "
           pdb=" SG  CYS A 582 "
           pdb=" CB  CYS A 582 "
      ideal   model   delta sinusoidal    sigma   weight residual
      93.00   21.64   71.36     1      1.00e+01 1.00e-02 6.53e+01
  dihedral pdb=" CA  GLY A 286 "
           pdb=" C   GLY A 286 "
           pdb=" N   TRP A 287 "
           pdb=" CA  TRP A 287 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  158.96   21.04     0      5.00e+00 4.00e-02 1.77e+01
  ... (remaining 3659 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.026: 555
       0.026 -    0.052: 309
       0.052 -    0.079: 162
       0.079 -    0.105: 58
       0.105 -    0.131: 10
  Chirality restraints: 1094
  Sorted by residual:
  chirality pdb=" CG  LEU B 743 "
            pdb=" CB  LEU B 743 "
            pdb=" CD1 LEU B 743 "
            pdb=" CD2 LEU B 743 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.59   -2.72    0.13 2.00e-01 2.50e+01 4.28e-01
  chirality pdb=" CG  LEU A 743 "
            pdb=" CB  LEU A 743 "
            pdb=" CD1 LEU A 743 "
            pdb=" CD2 LEU A 743 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.59   -2.72    0.13 2.00e-01 2.50e+01 4.12e-01
  chirality pdb=" CA  ILE B 507 "
            pdb=" N   ILE B 507 "
            pdb=" C   ILE B 507 "
            pdb=" CB  ILE B 507 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.43    2.56   -0.13 2.00e-01 2.50e+01 4.00e-01
  ... (remaining 1091 not shown)

  Planarity restraints: 1126
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   ARG B 705 "   -0.065 5.00e-02 4.00e+02   9.77e-02 1.53e+01
        pdb=" N   PRO B 706 "    0.169 5.00e-02 4.00e+02
        pdb=" CA  PRO B 706 "   -0.051 5.00e-02 4.00e+02
        pdb=" CD  PRO B 706 "   -0.053 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   ALA B 675 "    0.059 5.00e-02 4.00e+02   8.98e-02 1.29e+01
        pdb=" N   PRO B 676 "   -0.155 5.00e-02 4.00e+02
        pdb=" CA  PRO B 676 "    0.046 5.00e-02 4.00e+02
        pdb=" CD  PRO B 676 "    0.050 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   ALA A 675 "   -0.054 5.00e-02 4.00e+02   8.22e-02 1.08e+01
        pdb=" N   PRO A 676 "    0.142 5.00e-02 4.00e+02
        pdb=" CA  PRO A 676 "   -0.042 5.00e-02 4.00e+02
        pdb=" CD  PRO A 676 "   -0.046 5.00e-02 4.00e+02
  ... (remaining 1123 not shown)

  Histogram of nonbonded interaction distances:
        2.24 -     2.78: 1424
        2.78 -     3.31: 6932
        3.31 -     3.84: 10887
        3.84 -     4.37: 11091
        4.37 -     4.90: 19946
  Nonbonded interactions: 50280
  Sorted by model distance:
  nonbonded pdb=" OD1 ASN A 476 "
            pdb=" NH1 ARG A 546 "
     model   vdw
     2.245 3.120
  nonbonded pdb=" O   ILE B 356 "
            pdb=" OG  SER B 692 "
     model   vdw
     2.260 3.040
  nonbonded pdb=" O   ILE A 356 "
            pdb=" OG  SER A 692 "
     model   vdw
     2.274 3.040
  nonbonded pdb=" O   VAL B 450 "
            pdb=" OG1 THR B 453 "
     model   vdw
     2.299 3.040
  nonbonded pdb=" O   VAL A 450 "
            pdb=" OG1 THR A 453 "
     model   vdw
     2.305 3.040
  ... (remaining 50275 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 individual isotropic
Make a string to write initial .geo file
Internal consistency checks
Time:
  Set random seed:                         0.000
  Set model cs if undefined:               0.000
  Decide on map wrapping:                  0.000
  Normalize map: mean=0, sd=1:             0.840
  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:                    0.070
  Process input model:                     20.450
  Find NCS groups from input model:        0.220
  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:2.810
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   24.750
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.4670
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      :  0.003   0.061   6564  Z= 0.153
  Angle     :  0.702   7.266   8988  Z= 0.397
  Chirality :  0.041   0.131   1094
  Planarity :  0.007   0.098   1126
  Dihedral  : 12.332  81.117   2010
  Min Nonbonded Distance : 2.245

Molprobity Statistics.
  All-atom Clashscore : 12.11
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  9.36 %
    Favored  : 90.64 %
  Rotamer:
    Outliers :  0.18 %
    Allowed  :  0.18 %
    Favored  : 99.64 %
  Cbeta Deviations :  0.00 %
  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: -0.47 (0.27), residues: 940
  helix:  1.26 (0.21), residues: 592
  sheet:  None (None), residues: 0
  loop : -3.30 (0.30), residues: 348

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.011   0.001   TRP A 300 
 HIS   0.005   0.001   HIS B 695 
 PHE   0.021   0.001   PHE B 364 
 TYR   0.011   0.001   TYR A 533 
 ARG   0.008   0.001   ARG B 294 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.12045 (  473)
  hydrogen bonds       : angle       5.60206 ( 1395)
  SS BOND              : bond        0.00214 (    4)
  SS BOND              : angle       0.88471 (    8)
  covalent geometry    : bond        0.00329 ( 6560)
  covalent geometry    : angle       0.70213 ( 8980)

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

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

  1880 Ramachandran restraints generated.
    940 Oldfield, 0 Emsley, 940 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1880 Ramachandran restraints generated.
    940 Oldfield, 0 Emsley, 940 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  60 residues out of total 768 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 59
  time to evaluate  : 0.625 
Fit side-chains
REVERT: A  428 MET cc_start: 0.4302 (tpp) cc_final: 0.3394 (ttp)
REVERT: A  469 LYS cc_start: 0.6823 (mmmt) cc_final: 0.6396 (mmtt)
REVERT: A  713 MET cc_start: 0.5462 (ptp) cc_final: 0.5207 (ptm)
REVERT: B  428 MET cc_start: 0.4384 (tpp) cc_final: 0.3450 (ttp)
REVERT: B  469 LYS cc_start: 0.7017 (mmmt) cc_final: 0.6809 (mmtp)
  outliers start: 1
  outliers final: 0
  residues processed: 59
  average time/residue: 0.1358
  time to fit residues: 12.1436
Evaluate side-chains
  45 residues out of total 768 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 45
  time to evaluate  : 0.617 
-------------------------------------------------------------------------------
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:    0.6980
   chunk 71 optimal weight:    2.9990
   chunk 39 optimal weight:    2.9990
   chunk 24 optimal weight:    1.9990
   chunk 48 optimal weight:    0.5980
   chunk 38 optimal weight:    0.7980
   chunk 73 optimal weight:    6.9990
   chunk 28 optimal weight:    3.9990
   chunk 44 optimal weight:    0.9980
   chunk 54 optimal weight:    0.0060
   chunk 85 optimal weight:    0.8980
   overall best weight:    0.5996

-------------------------------------------------------------------------------
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 = 0.4377 r_free = 0.4377 target = 0.207091 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 52)----------------|
| r_work = 0.3995 r_free = 0.3995 target = 0.165732 restraints weight = 6966.196|
|-----------------------------------------------------------------------------|
r_work (start): 0.4016 rms_B_bonded: 2.54
r_work: 0.3842 rms_B_bonded: 3.96 restraints_weight: 0.5000
r_work (final): 0.3842
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6349
moved from start:          0.1328

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.042   6564  Z= 0.148
  Angle     :  0.605   5.369   8988  Z= 0.317
  Chirality :  0.042   0.132   1094
  Planarity :  0.006   0.076   1126
  Dihedral  :  4.544  23.220    974
  Min Nonbonded Distance : 2.510

Molprobity Statistics.
  All-atom Clashscore : 10.26
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  8.83 %
    Favored  : 91.17 %
  Rotamer:
    Outliers :  0.89 %
    Allowed  : 10.50 %
    Favored  : 88.61 %
  Cbeta Deviations :  0.00 %
  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: -0.27 (0.28), residues: 940
  helix:  1.32 (0.21), residues: 610
  sheet:  None (None), residues: 0
  loop : -3.26 (0.32), residues: 330

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.014   0.002   TRP A 732 
 HIS   0.002   0.001   HIS A 695 
 PHE   0.015   0.002   PHE B 681 
 TYR   0.006   0.001   TYR A 533 
 ARG   0.003   0.001   ARG B 294 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03861 (  473)
  hydrogen bonds       : angle       4.52792 ( 1395)
  SS BOND              : bond        0.00186 (    4)
  SS BOND              : angle       0.65920 (    8)
  covalent geometry    : bond        0.00338 ( 6560)
  covalent geometry    : angle       0.60463 ( 8980)

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

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

  1880 Ramachandran restraints generated.
    940 Oldfield, 0 Emsley, 940 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1880 Ramachandran restraints generated.
    940 Oldfield, 0 Emsley, 940 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  59 residues out of total 768 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 5
    poor density    : 54
  time to evaluate  : 0.621 
Fit side-chains
REVERT: A  428 MET cc_start: 0.4906 (tpp) cc_final: 0.3709 (ttp)
REVERT: A  469 LYS cc_start: 0.7434 (mmmt) cc_final: 0.7141 (mmtp)
REVERT: B  428 MET cc_start: 0.5269 (tpp) cc_final: 0.3974 (ttp)
  outliers start: 5
  outliers final: 1
  residues processed: 59
  average time/residue: 0.1264
  time to fit residues: 11.5265
Evaluate side-chains
  48 residues out of total 768 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 47
  time to evaluate  : 0.595 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  697 SER
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 94
   random chunks:
   chunk 47 optimal weight:    6.9990
   chunk 23 optimal weight:    2.9990
   chunk 48 optimal weight:    0.6980
   chunk 29 optimal weight:    7.9990
   chunk 19 optimal weight:    0.9990
   chunk 24 optimal weight:    0.9990
   chunk 22 optimal weight:    0.0970
   chunk 80 optimal weight:    0.9980
   chunk 36 optimal weight:    5.9990
   chunk 35 optimal weight:    0.3980
   chunk 30 optimal weight:    0.0370
   overall best weight:    0.4456

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

Flipped N/Q/H residues before XYZ refinement:
A 506 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4371 r_free = 0.4371 target = 0.207030 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 47)----------------|
| r_work = 0.3993 r_free = 0.3993 target = 0.165438 restraints weight = 6997.078|
|-----------------------------------------------------------------------------|
r_work (start): 0.4013 rms_B_bonded: 2.62
r_work: 0.3839 rms_B_bonded: 4.04 restraints_weight: 0.5000
r_work (final): 0.3839
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6318
moved from start:          0.1641

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.037   6564  Z= 0.125
  Angle     :  0.557   5.235   8988  Z= 0.290
  Chirality :  0.041   0.120   1094
  Planarity :  0.005   0.063   1126
  Dihedral  :  4.387  21.936    974
  Min Nonbonded Distance : 2.598

Molprobity Statistics.
  All-atom Clashscore : 9.21
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  8.19 %
    Favored  : 91.81 %
  Rotamer:
    Outliers :  2.14 %
    Allowed  : 14.23 %
    Favored  : 83.63 %
  Cbeta Deviations :  0.00 %
  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: -0.02 (0.28), residues: 940
  helix:  1.56 (0.21), residues: 610
  sheet:  None (None), residues: 0
  loop : -3.27 (0.32), residues: 330

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.009   0.001   TRP B 430 
 HIS   0.002   0.001   HIS A 695 
 PHE   0.011   0.001   PHE B 681 
 TYR   0.004   0.001   TYR B 655 
 ARG   0.002   0.001   ARG B 294 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03654 (  473)
  hydrogen bonds       : angle       4.32828 ( 1395)
  SS BOND              : bond        0.00175 (    4)
  SS BOND              : angle       0.45395 (    8)
  covalent geometry    : bond        0.00280 ( 6560)
  covalent geometry    : angle       0.55683 ( 8980)

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

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

  1880 Ramachandran restraints generated.
    940 Oldfield, 0 Emsley, 940 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1880 Ramachandran restraints generated.
    940 Oldfield, 0 Emsley, 940 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  55 residues out of total 768 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 43
  time to evaluate  : 0.647 
Fit side-chains
REVERT: A  428 MET cc_start: 0.5305 (tpp) cc_final: 0.4104 (ttp)
REVERT: A  492 GLU cc_start: 0.7932 (tt0) cc_final: 0.7707 (tt0)
REVERT: B  428 MET cc_start: 0.5444 (tpp) cc_final: 0.4220 (ttp)
REVERT: B  492 GLU cc_start: 0.7905 (tt0) cc_final: 0.7663 (tt0)
  outliers start: 12
  outliers final: 4
  residues processed: 55
  average time/residue: 0.1279
  time to fit residues: 11.1071
Evaluate side-chains
  46 residues out of total 768 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 4
    poor density    : 42
  time to evaluate  : 0.593 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  453 THR
Chi-restraints excluded: chain A residue  697 SER
Chi-restraints excluded: chain A residue  715 ILE
Chi-restraints excluded: chain B residue  697 SER
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 94
   random chunks:
   chunk 86 optimal weight:    0.8980
   chunk 7 optimal weight:    3.9990
   chunk 43 optimal weight:    0.6980
   chunk 89 optimal weight:    2.9990
   chunk 60 optimal weight:    0.8980
   chunk 9 optimal weight:    0.5980
   chunk 61 optimal weight:    0.7980
   chunk 52 optimal weight:    0.5980
   chunk 40 optimal weight:    0.6980
   chunk 68 optimal weight:    0.7980
   chunk 18 optimal weight:    3.9990
   overall best weight:    0.6780

-------------------------------------------------------------------------------
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 = 0.4325 r_free = 0.4325 target = 0.200478 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 53)----------------|
| r_work = 0.3934 r_free = 0.3934 target = 0.159142 restraints weight = 7151.849|
|-----------------------------------------------------------------------------|
r_work (start): 0.3963 rms_B_bonded: 2.57
r_work: 0.3784 rms_B_bonded: 3.89 restraints_weight: 0.5000
r_work (final): 0.3784
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6443
moved from start:          0.2223

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.043   6564  Z= 0.143
  Angle     :  0.565   5.197   8988  Z= 0.296
  Chirality :  0.041   0.120   1094
  Planarity :  0.005   0.060   1126
  Dihedral  :  4.384  21.027    974
  Min Nonbonded Distance : 2.576

Molprobity Statistics.
  All-atom Clashscore : 9.53
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  9.04 %
    Favored  : 90.96 %
  Rotamer:
    Outliers :  2.49 %
    Allowed  : 16.01 %
    Favored  : 81.49 %
  Cbeta Deviations :  0.00 %
  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: -0.17 (0.28), residues: 940
  helix:  1.55 (0.21), residues: 592
  sheet:  None (None), residues: 0
  loop : -3.29 (0.30), residues: 348

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.011   0.001   TRP A 714 
 HIS   0.001   0.001   HIS B 695 
 PHE   0.014   0.002   PHE B 364 
 TYR   0.006   0.001   TYR A 655 
 ARG   0.002   0.000   ARG B 294 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03790 (  473)
  hydrogen bonds       : angle       4.31077 ( 1395)
  SS BOND              : bond        0.00236 (    4)
  SS BOND              : angle       0.68914 (    8)
  covalent geometry    : bond        0.00335 ( 6560)
  covalent geometry    : angle       0.56471 ( 8980)

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

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

  1880 Ramachandran restraints generated.
    940 Oldfield, 0 Emsley, 940 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1880 Ramachandran restraints generated.
    940 Oldfield, 0 Emsley, 940 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  59 residues out of total 768 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 45
  time to evaluate  : 0.646 
Fit side-chains
REVERT: A  428 MET cc_start: 0.5492 (tpp) cc_final: 0.4205 (ttp)
REVERT: A  468 TYR cc_start: 0.5261 (OUTLIER) cc_final: 0.4698 (m-80)
REVERT: B  360 LEU cc_start: 0.4755 (OUTLIER) cc_final: 0.4536 (pp)
REVERT: B  428 MET cc_start: 0.5543 (tpp) cc_final: 0.4242 (ttp)
  outliers start: 14
  outliers final: 6
  residues processed: 59
  average time/residue: 0.1154
  time to fit residues: 10.9225
Evaluate side-chains
  53 residues out of total 768 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 45
  time to evaluate  : 0.639 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  453 THR
Chi-restraints excluded: chain A residue  468 TYR
Chi-restraints excluded: chain A residue  697 SER
Chi-restraints excluded: chain A residue  715 ILE
Chi-restraints excluded: chain B residue  343 THR
Chi-restraints excluded: chain B residue  360 LEU
Chi-restraints excluded: chain B residue  697 SER
Chi-restraints excluded: chain B residue  747 ILE
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 94
   random chunks:
   chunk 15 optimal weight:    0.8980
   chunk 19 optimal weight:    0.6980
   chunk 8 optimal weight:    1.9990
   chunk 67 optimal weight:    2.9990
   chunk 70 optimal weight:    0.9980
   chunk 43 optimal weight:    0.8980
   chunk 9 optimal weight:    0.6980
   chunk 22 optimal weight:    0.7980
   chunk 34 optimal weight:    1.9990
   chunk 76 optimal weight:    8.9990
   chunk 36 optimal weight:    9.9990
   overall best weight:    0.7980

-------------------------------------------------------------------------------
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 = 0.4304 r_free = 0.4304 target = 0.197852 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 46)----------------|
| r_work = 0.3904 r_free = 0.3904 target = 0.156000 restraints weight = 7103.721|
|-----------------------------------------------------------------------------|
r_work (start): 0.3931 rms_B_bonded: 2.57
r_work: 0.3757 rms_B_bonded: 3.82 restraints_weight: 0.5000
r_work (final): 0.3757
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6492
moved from start:          0.2626

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.044   6564  Z= 0.153
  Angle     :  0.574   5.221   8988  Z= 0.300
  Chirality :  0.042   0.128   1094
  Planarity :  0.005   0.058   1126
  Dihedral  :  4.392  19.666    974
  Min Nonbonded Distance : 2.564

Molprobity Statistics.
  All-atom Clashscore : 9.61
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  8.83 %
    Favored  : 91.17 %
  Rotamer:
    Outliers :  2.31 %
    Allowed  : 17.79 %
    Favored  : 79.89 %
  Cbeta Deviations :  0.00 %
  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: -0.22 (0.28), residues: 940
  helix:  1.49 (0.21), residues: 594
  sheet:  None (None), residues: 0
  loop : -3.28 (0.31), residues: 346

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.012   0.001   TRP B 714 
 HIS   0.001   0.001   HIS B 695 
 PHE   0.011   0.001   PHE A 728 
 TYR   0.005   0.001   TYR B 584 
 ARG   0.002   0.001   ARG B 546 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03915 (  473)
  hydrogen bonds       : angle       4.34412 ( 1395)
  SS BOND              : bond        0.00572 (    4)
  SS BOND              : angle       0.65477 (    8)
  covalent geometry    : bond        0.00367 ( 6560)
  covalent geometry    : angle       0.57360 ( 8980)

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

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

  1880 Ramachandran restraints generated.
    940 Oldfield, 0 Emsley, 940 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1880 Ramachandran restraints generated.
    940 Oldfield, 0 Emsley, 940 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  63 residues out of total 768 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 50
  time to evaluate  : 0.622 
Fit side-chains
REVERT: A  727 MET cc_start: 0.8205 (ttm) cc_final: 0.7992 (ttp)
REVERT: B  428 MET cc_start: 0.5495 (tpp) cc_final: 0.4328 (ttm)
REVERT: B  468 TYR cc_start: 0.5141 (OUTLIER) cc_final: 0.4393 (m-10)
REVERT: B  499 THR cc_start: 0.8839 (p) cc_final: 0.8520 (p)
REVERT: B  722 LEU cc_start: 0.7252 (OUTLIER) cc_final: 0.6904 (tt)
  outliers start: 13
  outliers final: 5
  residues processed: 63
  average time/residue: 0.1238
  time to fit residues: 12.0236
Evaluate side-chains
  55 residues out of total 768 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 48
  time to evaluate  : 0.571 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  453 THR
Chi-restraints excluded: chain A residue  715 ILE
Chi-restraints excluded: chain B residue  343 THR
Chi-restraints excluded: chain B residue  468 TYR
Chi-restraints excluded: chain B residue  697 SER
Chi-restraints excluded: chain B residue  722 LEU
Chi-restraints excluded: chain B residue  747 ILE
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 94
   random chunks:
   chunk 73 optimal weight:    2.9990
   chunk 53 optimal weight:    5.9990
   chunk 88 optimal weight:    0.5980
   chunk 60 optimal weight:    0.9980
   chunk 77 optimal weight:    0.9990
   chunk 23 optimal weight:    3.9990
   chunk 71 optimal weight:    1.9990
   chunk 86 optimal weight:    0.9990
   chunk 8 optimal weight:    1.9990
   chunk 84 optimal weight:    2.9990
   chunk 62 optimal weight:    1.9990
   overall best weight:    1.1186

-------------------------------------------------------------------------------
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 = 0.4262 r_free = 0.4262 target = 0.192788 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 45)----------------|
| r_work = 0.3852 r_free = 0.3852 target = 0.151075 restraints weight = 7050.529|
|-----------------------------------------------------------------------------|
r_work (start): 0.3877 rms_B_bonded: 2.55
r_work: 0.3705 rms_B_bonded: 3.72 restraints_weight: 0.5000
r_work (final): 0.3705
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6580
moved from start:          0.3153

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.049   6564  Z= 0.190
  Angle     :  0.618   5.376   8988  Z= 0.325
  Chirality :  0.043   0.148   1094
  Planarity :  0.005   0.059   1126
  Dihedral  :  4.572  17.827    974
  Min Nonbonded Distance : 2.535

Molprobity Statistics.
  All-atom Clashscore : 10.58
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  9.15 %
    Favored  : 90.85 %
  Rotamer:
    Outliers :  3.91 %
    Allowed  : 17.44 %
    Favored  : 78.65 %
  Cbeta Deviations :  0.00 %
  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: -0.51 (0.28), residues: 940
  helix:  1.17 (0.21), residues: 606
  sheet:  None (None), residues: 0
  loop : -3.38 (0.31), residues: 334

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.013   0.002   TRP B 714 
 HIS   0.001   0.001   HIS B 695 
 PHE   0.013   0.002   PHE B 728 
 TYR   0.009   0.001   TYR A 584 
 ARG   0.002   0.001   ARG B 546 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04374 (  473)
  hydrogen bonds       : angle       4.52814 ( 1395)
  SS BOND              : bond        0.00143 (    4)
  SS BOND              : angle       0.79106 (    8)
  covalent geometry    : bond        0.00467 ( 6560)
  covalent geometry    : angle       0.61776 ( 8980)

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

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

  1880 Ramachandran restraints generated.
    940 Oldfield, 0 Emsley, 940 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1880 Ramachandran restraints generated.
    940 Oldfield, 0 Emsley, 940 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  69 residues out of total 768 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 22
    poor density    : 47
  time to evaluate  : 0.584 
Fit side-chains
REVERT: B  360 LEU cc_start: 0.6164 (OUTLIER) cc_final: 0.5866 (pp)
REVERT: B  499 THR cc_start: 0.8759 (p) cc_final: 0.8430 (p)
  outliers start: 22
  outliers final: 11
  residues processed: 69
  average time/residue: 0.1179
  time to fit residues: 12.6580
Evaluate side-chains
  58 residues out of total 768 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 46
  time to evaluate  : 0.629 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  392 VAL
Chi-restraints excluded: chain A residue  453 THR
Chi-restraints excluded: chain A residue  490 VAL
Chi-restraints excluded: chain A residue  715 ILE
Chi-restraints excluded: chain A residue  722 LEU
Chi-restraints excluded: chain B residue  343 THR
Chi-restraints excluded: chain B residue  360 LEU
Chi-restraints excluded: chain B residue  384 VAL
Chi-restraints excluded: chain B residue  392 VAL
Chi-restraints excluded: chain B residue  697 SER
Chi-restraints excluded: chain B residue  722 LEU
Chi-restraints excluded: chain B residue  747 ILE
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 94
   random chunks:
   chunk 18 optimal weight:    0.9980
   chunk 28 optimal weight:    6.9990
   chunk 64 optimal weight:    0.0030
   chunk 13 optimal weight:    0.6980
   chunk 86 optimal weight:    0.7980
   chunk 23 optimal weight:    0.3980
   chunk 4 optimal weight:    0.5980
   chunk 82 optimal weight:   30.0000
   chunk 44 optimal weight:    0.9990
   chunk 80 optimal weight:    1.9990
   chunk 45 optimal weight:    0.7980
   overall best weight:    0.4990

-------------------------------------------------------------------------------
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 = 0.4313 r_free = 0.4313 target = 0.198385 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 47)----------------|
| r_work = 0.3914 r_free = 0.3914 target = 0.156498 restraints weight = 6916.100|
|-----------------------------------------------------------------------------|
r_work (start): 0.3936 rms_B_bonded: 2.56
r_work: 0.3766 rms_B_bonded: 3.73 restraints_weight: 0.5000
r_work (final): 0.3766
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6462
moved from start:          0.3108

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.037   6564  Z= 0.130
  Angle     :  0.569   5.504   8988  Z= 0.293
  Chirality :  0.041   0.150   1094
  Planarity :  0.004   0.055   1126
  Dihedral  :  4.327  17.690    974
  Min Nonbonded Distance : 2.588

Molprobity Statistics.
  All-atom Clashscore : 9.61
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  8.51 %
    Favored  : 91.49 %
  Rotamer:
    Outliers :  2.67 %
    Allowed  : 19.75 %
    Favored  : 77.58 %
  Cbeta Deviations :  0.00 %
  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: -0.26 (0.28), residues: 940
  helix:  1.41 (0.21), residues: 606
  sheet:  None (None), residues: 0
  loop : -3.39 (0.31), residues: 334

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.008   0.001   TRP B 430 
 HIS   0.001   0.000   HIS B 695 
 PHE   0.011   0.001   PHE A 488 
 TYR   0.008   0.001   TYR B 711 
 ARG   0.002   0.001   ARG B 294 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03828 (  473)
  hydrogen bonds       : angle       4.29001 ( 1395)
  SS BOND              : bond        0.00114 (    4)
  SS BOND              : angle       0.68013 (    8)
  covalent geometry    : bond        0.00294 ( 6560)
  covalent geometry    : angle       0.56853 ( 8980)

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

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

  1880 Ramachandran restraints generated.
    940 Oldfield, 0 Emsley, 940 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1880 Ramachandran restraints generated.
    940 Oldfield, 0 Emsley, 940 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  57 residues out of total 768 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 42
  time to evaluate  : 0.668 
Fit side-chains
REVERT: B  360 LEU cc_start: 0.6187 (OUTLIER) cc_final: 0.5895 (pp)
REVERT: B  454 PHE cc_start: 0.7485 (OUTLIER) cc_final: 0.7230 (t80)
REVERT: B  499 THR cc_start: 0.8745 (p) cc_final: 0.8402 (p)
REVERT: B  722 LEU cc_start: 0.7128 (OUTLIER) cc_final: 0.6862 (tt)
  outliers start: 15
  outliers final: 8
  residues processed: 57
  average time/residue: 0.1329
  time to fit residues: 11.6265
Evaluate side-chains
  53 residues out of total 768 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 42
  time to evaluate  : 0.655 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  392 VAL
Chi-restraints excluded: chain A residue  453 THR
Chi-restraints excluded: chain A residue  468 TYR
Chi-restraints excluded: chain A residue  490 VAL
Chi-restraints excluded: chain A residue  715 ILE
Chi-restraints excluded: chain B residue  360 LEU
Chi-restraints excluded: chain B residue  384 VAL
Chi-restraints excluded: chain B residue  392 VAL
Chi-restraints excluded: chain B residue  454 PHE
Chi-restraints excluded: chain B residue  722 LEU
Chi-restraints excluded: chain B residue  747 ILE
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 94
   random chunks:
   chunk 5 optimal weight:    0.8980
   chunk 61 optimal weight:   10.0000
   chunk 7 optimal weight:    1.9990
   chunk 36 optimal weight:    9.9990
   chunk 79 optimal weight:    1.9990
   chunk 56 optimal weight:    0.5980
   chunk 19 optimal weight:    0.5980
   chunk 2 optimal weight:    0.6980
   chunk 18 optimal weight:    5.9990
   chunk 25 optimal weight:    0.6980
   chunk 32 optimal weight:    0.0000
   overall best weight:    0.5184

-------------------------------------------------------------------------------
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 = 0.4314 r_free = 0.4314 target = 0.198526 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 45)----------------|
| r_work = 0.3917 r_free = 0.3917 target = 0.156614 restraints weight = 7025.547|
|-----------------------------------------------------------------------------|
r_work (start): 0.3939 rms_B_bonded: 2.58
r_work: 0.3769 rms_B_bonded: 3.76 restraints_weight: 0.5000
r_work (final): 0.3769
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6468
moved from start:          0.3171

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.036   6564  Z= 0.130
  Angle     :  0.564   5.669   8988  Z= 0.289
  Chirality :  0.041   0.127   1094
  Planarity :  0.004   0.054   1126
  Dihedral  :  4.226  16.733    974
  Min Nonbonded Distance : 2.575

Molprobity Statistics.
  All-atom Clashscore : 8.80
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  9.36 %
    Favored  : 90.64 %
  Rotamer:
    Outliers :  2.31 %
    Allowed  : 19.75 %
    Favored  : 77.94 %
  Cbeta Deviations :  0.00 %
  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: -0.13 (0.28), residues: 940
  helix:  1.59 (0.21), residues: 594
  sheet:  None (None), residues: 0
  loop : -3.32 (0.30), residues: 346

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.008   0.001   TRP A 733 
 HIS   0.001   0.000   HIS B 695 
 PHE   0.010   0.001   PHE A 488 
 TYR   0.005   0.001   TYR B 711 
 ARG   0.001   0.000   ARG B 546 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03770 (  473)
  hydrogen bonds       : angle       4.24008 ( 1395)
  SS BOND              : bond        0.00151 (    4)
  SS BOND              : angle       0.71361 (    8)
  covalent geometry    : bond        0.00296 ( 6560)
  covalent geometry    : angle       0.56361 ( 8980)

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

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

  1880 Ramachandran restraints generated.
    940 Oldfield, 0 Emsley, 940 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1880 Ramachandran restraints generated.
    940 Oldfield, 0 Emsley, 940 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  56 residues out of total 768 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 43
  time to evaluate  : 0.591 
Fit side-chains
REVERT: B  360 LEU cc_start: 0.6322 (OUTLIER) cc_final: 0.6047 (pp)
REVERT: B  454 PHE cc_start: 0.7529 (OUTLIER) cc_final: 0.7309 (t80)
REVERT: B  499 THR cc_start: 0.8826 (p) cc_final: 0.8471 (p)
REVERT: B  722 LEU cc_start: 0.7151 (OUTLIER) cc_final: 0.6883 (tt)
  outliers start: 13
  outliers final: 9
  residues processed: 55
  average time/residue: 0.1250
  time to fit residues: 10.6155
Evaluate side-chains
  54 residues out of total 768 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 42
  time to evaluate  : 0.588 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  392 VAL
Chi-restraints excluded: chain A residue  453 THR
Chi-restraints excluded: chain A residue  468 TYR
Chi-restraints excluded: chain A residue  490 VAL
Chi-restraints excluded: chain A residue  715 ILE
Chi-restraints excluded: chain B residue  360 LEU
Chi-restraints excluded: chain B residue  384 VAL
Chi-restraints excluded: chain B residue  392 VAL
Chi-restraints excluded: chain B residue  454 PHE
Chi-restraints excluded: chain B residue  577 CYS
Chi-restraints excluded: chain B residue  722 LEU
Chi-restraints excluded: chain B residue  747 ILE
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 94
   random chunks:
   chunk 78 optimal weight:    5.9990
   chunk 87 optimal weight:    0.7980
   chunk 45 optimal weight:    0.9990
   chunk 7 optimal weight:    1.9990
   chunk 74 optimal weight:    9.9990
   chunk 19 optimal weight:    0.8980
   chunk 38 optimal weight:    0.2980
   chunk 46 optimal weight:    0.5980
   chunk 85 optimal weight:    1.9990
   chunk 30 optimal weight:    0.3980
   chunk 67 optimal weight:    0.9980
   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 = 0.4310 r_free = 0.4310 target = 0.198115 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 58)----------------|
| r_work = 0.3913 r_free = 0.3913 target = 0.156298 restraints weight = 6987.922|
|-----------------------------------------------------------------------------|
r_work (start): 0.3936 rms_B_bonded: 2.56
r_work: 0.3766 rms_B_bonded: 3.73 restraints_weight: 0.5000
r_work (final): 0.3766
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6466
moved from start:          0.3244

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.036   6564  Z= 0.135
  Angle     :  0.567   5.636   8988  Z= 0.291
  Chirality :  0.041   0.127   1094
  Planarity :  0.004   0.055   1126
  Dihedral  :  4.230  16.453    974
  Min Nonbonded Distance : 2.563

Molprobity Statistics.
  All-atom Clashscore : 8.80
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  8.51 %
    Favored  : 91.49 %
  Rotamer:
    Outliers :  2.85 %
    Allowed  : 19.75 %
    Favored  : 77.40 %
  Cbeta Deviations :  0.00 %
  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: -0.13 (0.28), residues: 940
  helix:  1.59 (0.21), residues: 594
  sheet:  None (None), residues: 0
  loop : -3.33 (0.30), residues: 346

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.009   0.001   TRP A 733 
 HIS   0.001   0.000   HIS B 695 
 PHE   0.010   0.001   PHE A 488 
 TYR   0.015   0.001   TYR A 739 
 ARG   0.002   0.000   ARG B 546 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03805 (  473)
  hydrogen bonds       : angle       4.23832 ( 1395)
  SS BOND              : bond        0.00157 (    4)
  SS BOND              : angle       0.70600 (    8)
  covalent geometry    : bond        0.00313 ( 6560)
  covalent geometry    : angle       0.56673 ( 8980)

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

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

  1880 Ramachandran restraints generated.
    940 Oldfield, 0 Emsley, 940 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1880 Ramachandran restraints generated.
    940 Oldfield, 0 Emsley, 940 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  60 residues out of total 768 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 44
  time to evaluate  : 0.583 
Fit side-chains
REVERT: B  360 LEU cc_start: 0.6359 (OUTLIER) cc_final: 0.6065 (pp)
REVERT: B  499 THR cc_start: 0.8830 (p) cc_final: 0.8478 (p)
REVERT: B  722 LEU cc_start: 0.7145 (OUTLIER) cc_final: 0.6858 (tt)
  outliers start: 16
  outliers final: 9
  residues processed: 58
  average time/residue: 0.1222
  time to fit residues: 10.8964
Evaluate side-chains
  55 residues out of total 768 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 44
  time to evaluate  : 0.574 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  392 VAL
Chi-restraints excluded: chain A residue  453 THR
Chi-restraints excluded: chain A residue  468 TYR
Chi-restraints excluded: chain A residue  490 VAL
Chi-restraints excluded: chain A residue  577 CYS
Chi-restraints excluded: chain A residue  715 ILE
Chi-restraints excluded: chain B residue  360 LEU
Chi-restraints excluded: chain B residue  384 VAL
Chi-restraints excluded: chain B residue  392 VAL
Chi-restraints excluded: chain B residue  577 CYS
Chi-restraints excluded: chain B residue  722 LEU
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 94
   random chunks:
   chunk 40 optimal weight:    2.9990
   chunk 8 optimal weight:    1.9990
   chunk 87 optimal weight:    0.9980
   chunk 23 optimal weight:    0.5980
   chunk 22 optimal weight:    0.0770
   chunk 28 optimal weight:    4.9990
   chunk 91 optimal weight:    0.1980
   chunk 73 optimal weight:    7.9990
   chunk 7 optimal weight:    0.0870
   chunk 86 optimal weight:    0.0770
   chunk 2 optimal weight:    1.9990
   overall best weight:    0.2074

-------------------------------------------------------------------------------
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 = 0.4372 r_free = 0.4372 target = 0.205119 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.3985 r_free = 0.3985 target = 0.163221 restraints weight = 6934.817|
|-----------------------------------------------------------------------------|
r_work (start): 0.4010 rms_B_bonded: 2.61
r_work: 0.3840 rms_B_bonded: 3.81 restraints_weight: 0.5000
r_work (final): 0.3840
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6366
moved from start:          0.3225

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.029   6564  Z= 0.108
  Angle     :  0.543   6.371   8988  Z= 0.274
  Chirality :  0.040   0.116   1094
  Planarity :  0.004   0.053   1126
  Dihedral  :  3.990  15.849    974
  Min Nonbonded Distance : 2.602

Molprobity Statistics.
  All-atom Clashscore : 9.45
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  8.30 %
    Favored  : 91.70 %
  Rotamer:
    Outliers :  2.14 %
    Allowed  : 20.82 %
    Favored  : 77.05 %
  Cbeta Deviations :  0.00 %
  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:  0.18 (0.28), residues: 940
  helix:  1.72 (0.21), residues: 612
  sheet:  None (None), residues: 0
  loop : -3.22 (0.32), residues: 328

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.007   0.001   TRP B 430 
 HIS   0.000   0.000   HIS B 695 
 PHE   0.008   0.001   PHE A 488 
 TYR   0.005   0.000   TYR B 711 
 ARG   0.002   0.001   ARG B 705 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03406 (  473)
  hydrogen bonds       : angle       4.05005 ( 1395)
  SS BOND              : bond        0.00121 (    4)
  SS BOND              : angle       0.82315 (    8)
  covalent geometry    : bond        0.00225 ( 6560)
  covalent geometry    : angle       0.54249 ( 8980)

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

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

  1880 Ramachandran restraints generated.
    940 Oldfield, 0 Emsley, 940 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1880 Ramachandran restraints generated.
    940 Oldfield, 0 Emsley, 940 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  54 residues out of total 768 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 42
  time to evaluate  : 0.585 
Fit side-chains
REVERT: B  296 MET cc_start: 0.5924 (ttm) cc_final: 0.5685 (ttp)
REVERT: B  360 LEU cc_start: 0.6238 (OUTLIER) cc_final: 0.6007 (pp)
REVERT: B  499 THR cc_start: 0.8891 (p) cc_final: 0.8561 (p)
  outliers start: 12
  outliers final: 9
  residues processed: 52
  average time/residue: 0.1281
  time to fit residues: 10.2842
Evaluate side-chains
  52 residues out of total 768 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 42
  time to evaluate  : 0.587 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  392 VAL
Chi-restraints excluded: chain A residue  453 THR
Chi-restraints excluded: chain A residue  490 VAL
Chi-restraints excluded: chain A residue  577 CYS
Chi-restraints excluded: chain A residue  715 ILE
Chi-restraints excluded: chain B residue  356 ILE
Chi-restraints excluded: chain B residue  360 LEU
Chi-restraints excluded: chain B residue  384 VAL
Chi-restraints excluded: chain B residue  392 VAL
Chi-restraints excluded: chain B residue  577 CYS
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 94
   random chunks:
   chunk 30 optimal weight:    2.9990
   chunk 80 optimal weight:    2.9990
   chunk 88 optimal weight:    1.9990
   chunk 23 optimal weight:    0.6980
   chunk 65 optimal weight:    0.6980
   chunk 74 optimal weight:   10.0000
   chunk 29 optimal weight:    8.9990
   chunk 90 optimal weight:    1.9990
   chunk 63 optimal weight:    0.9990
   chunk 10 optimal weight:    0.7980
   chunk 82 optimal weight:    9.9990
   overall best weight:    1.0384

-------------------------------------------------------------------------------
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 = 0.4615 r_free = 0.4615 target = 0.229111 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 53)----------------|
| r_work = 0.4212 r_free = 0.4212 target = 0.187446 restraints weight = 7302.575|
|-----------------------------------------------------------------------------|
r_work (start): 0.4274 rms_B_bonded: 2.55
r_work: 0.4054 rms_B_bonded: 4.06 restraints_weight: 0.5000
r_work (final): 0.4054
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6640
moved from start:          0.3486

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.048   6564  Z= 0.180
  Angle     :  0.609   5.897   8988  Z= 0.314
  Chirality :  0.043   0.136   1094
  Planarity :  0.005   0.056   1126
  Dihedral  :  4.283  15.386    974
  Min Nonbonded Distance : 2.545

Molprobity Statistics.
  All-atom Clashscore : 9.69
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  8.72 %
    Favored  : 91.28 %
  Rotamer:
    Outliers :  1.96 %
    Allowed  : 21.17 %
    Favored  : 76.87 %
  Cbeta Deviations :  0.00 %
  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: -0.15 (0.28), residues: 940
  helix:  1.55 (0.21), residues: 594
  sheet:  None (None), residues: 0
  loop : -3.29 (0.30), residues: 346

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.012   0.001   TRP A 714 
 HIS   0.001   0.001   HIS B 695 
 PHE   0.013   0.002   PHE A 488 
 TYR   0.008   0.001   TYR B 584 
 ARG   0.002   0.000   ARG B 546 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04104 (  473)
  hydrogen bonds       : angle       4.33032 ( 1395)
  SS BOND              : bond        0.00174 (    4)
  SS BOND              : angle       0.71029 (    8)
  covalent geometry    : bond        0.00443 ( 6560)
  covalent geometry    : angle       0.60900 ( 8980)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 3088.22 seconds
wall clock time: 54 minutes 11.34 seconds (3251.34 seconds total)