Starting phenix.real_space_refine
on Thu Jul  2 08:43:30 2026 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/9rw4_54298/07_2026/9rw4_54298.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/9rw4_54298/07_2026/9rw4_54298.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.9
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    model {
      file = "/net/cci-nas-00/data/ceres_data/9rw4_54298/07_2026/9rw4_54298.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/9rw4_54298/07_2026/9rw4_54298.cif"
    real_map_files = "/net/cci-nas-00/data/ceres_data/9rw4_54298/07_2026/9rw4_54298.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/9rw4_54298/07_2026/9rw4_54298.map"
  }
  resolution = 3.9
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }


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

Validating inputs
Origin is already at (0, 0, 0), no shifts will be applied
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=  -0.000 sd=   0.001
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: 5
    Type Number    sf(0)   Gaussians
     P      84      5.49       5
     S      12      5.16       5
     C    4491      2.51       5
     N    1433      2.21       5
     O    1761      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 6 residue(s): 0.00s

  Monomer Library directory:
    "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/chem_data/mon_lib"
  Total number of atoms: 7781
  Number of models: 1
  Model: ""
    Number of chains: 6
    Chain: "A"
      Number of atoms: 334
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 53, 334
          Classifications: {'peptide': 53}
          Incomplete info: {'truncation_to_alanine': 29}
          Link IDs: {'TRANS': 52}
          Unresolved non-hydrogen bonds: 109
          Unresolved non-hydrogen angles: 136
          Unresolved non-hydrogen dihedrals: 85
          Unresolved non-hydrogen chiralities: 6
          Planarities with less than four sites: {'GLU:plan': 7, 'TYR:plan': 1, 'GLN:plan1': 3, 'ASP:plan': 3, 'ASN:plan1': 1, 'ARG:plan': 4}
          Unresolved non-hydrogen planarities: 79
    Chain: "B"
      Number of atoms: 334
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 53, 334
          Classifications: {'peptide': 53}
          Incomplete info: {'truncation_to_alanine': 29}
          Link IDs: {'TRANS': 52}
          Unresolved non-hydrogen bonds: 109
          Unresolved non-hydrogen angles: 136
          Unresolved non-hydrogen dihedrals: 85
          Unresolved non-hydrogen chiralities: 6
          Planarities with less than four sites: {'GLU:plan': 7, 'TYR:plan': 1, 'GLN:plan1': 3, 'ASP:plan': 3, 'ASN:plan1': 1, 'ARG:plan': 4}
          Unresolved non-hydrogen planarities: 79
    Chain: "D"
      Number of atoms: 2670
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 447, 2670
          Classifications: {'peptide': 447}
          Incomplete info: {'truncation_to_alanine': 271}
          Link IDs: {'PCIS': 1, 'PTRANS': 9, 'TRANS': 436}
          Chain breaks: 2
          Unresolved chain link angles: 6
          Unresolved non-hydrogen bonds: 967
          Unresolved non-hydrogen angles: 1219
          Unresolved non-hydrogen dihedrals: 792
          Unresolved non-hydrogen chiralities: 93
          Planarities with less than four sites: {'ASP:plan': 17, 'TRP:plan': 2, 'GLN:plan1': 20, 'ASN:plan1': 14, 'PHE:plan': 8, 'TYR:plan': 11, 'GLU:plan': 20, 'ARG:plan': 15, 'HIS:plan': 4}
          Unresolved non-hydrogen planarities: 491
    Chain: "C"
      Number of atoms: 2635
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 449, 2635
          Classifications: {'peptide': 449}
          Incomplete info: {'truncation_to_alanine': 285}
          Link IDs: {'PCIS': 1, 'PTRANS': 9, 'TRANS': 438}
          Chain breaks: 2
          Unresolved chain link angles: 6
          Unresolved non-hydrogen bonds: 1024
          Unresolved non-hydrogen angles: 1288
          Unresolved non-hydrogen dihedrals: 839
          Unresolved non-hydrogen chiralities: 94
          Planarities with less than four sites: {'GLU:plan': 23, 'ASP:plan': 21, 'HIS:plan': 5, 'ARG:plan': 16, 'GLN:plan1': 21, 'TRP:plan': 2, 'ASN:plan1': 14, 'PHE:plan': 8, 'TYR:plan': 11}
          Unresolved non-hydrogen planarities: 529
    Chain: "E"
      Number of atoms: 904
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 43, 904
          Classifications: {'RNA': 43}
          Modifications used: {'5*END': 1, 'rna2p_pyr': 2, 'rna3p_pur': 19, 'rna3p_pyr': 22}
          Link IDs: {'rna2p': 2, 'rna3p': 40}
          Chain breaks: 1
    Chain: "F"
      Number of atoms: 904
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 43, 904
          Classifications: {'RNA': 43}
          Modifications used: {'5*END': 1, 'rna2p_pyr': 3, 'rna3p_pur': 19, 'rna3p_pyr': 21}
          Link IDs: {'rna2p': 3, 'rna3p': 39}
          Chain breaks: 1
  Time building chain proxies: 1.49, per 1000 atoms: 0.19
  Number of scatterers: 7781
  At special positions: 0
  Unit cell: (84.8, 109.18, 169.6, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 5
    Type Number    sf(0)
     S      12     16.00
     P      84     15.00
     O    1761      8.00
     N    1433      7.00
     C    4491      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=0, symmetry=0

  Automatic linking
    Parameters for automatic linking
      Linking & cutoffs
        Metal                : Auto  - 3.00
        Amino acid           : True  - 1.90
        Carbohydrate         : True  - 1.99
        Ligands              : True  - 1.99
        Small molecules      : False - 1.98
        Amino acid - RNA/DNA : False
      
  Number of custom bonds: simple=0, symmetry=0
  Time building additional restraints: 0.44
  Conformation dependent library (CDL) restraints added in 346.0 milliseconds
  

  1972 Ramachandran restraints generated.
    986 Oldfield, 0 Emsley, 986 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  1916

  Finding SS restraints...
    Secondary structure from input PDB file:
      55 helices and 10 sheets defined
      71.0% alpha, 5.9% beta
      35 base pairs and 41 stacking pairs defined.
    Time for finding SS restraints: 0.97
  Creating SS restraints...
    Processing helix  chain 'A' and resid 695 through 747
      removed outlier: 3.842A  pdb=" N   VAL A 699 " --> pdb=" O   CYS A 695 " (cutoff:3.500A)
      removed outlier: 3.689A  pdb=" N   ARG A 747 " --> pdb=" O   ASP A 743 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 696 through 747
    Processing helix  chain 'D' and resid 6 through 25
      removed outlier: 3.899A  pdb=" N   LYS D  24 " --> pdb=" O   ARG D  20 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 30 through 37
    Processing helix  chain 'D' and resid 43 through 50
    Processing helix  chain 'D' and resid 53 through 63
    Processing helix  chain 'D' and resid 96 through 111
      removed outlier: 3.775A  pdb=" N   PHE D 104 " --> pdb=" O   ALA D 100 " (cutoff:3.500A)
      removed outlier: 3.857A  pdb=" N   TYR D 111 " --> pdb=" O   LYS D 107 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 119 through 125
      removed outlier: 3.702A  pdb=" N   GLY D 124 " --> pdb=" O   ARG D 120 " (cutoff:3.500A)
      removed outlier: 3.943A  pdb=" N   HIS D 125 " --> pdb=" O   SER D 121 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 126 through 128
      No H-bonds generated for 'chain 'D' and resid 126 through 128'
    Processing helix  chain 'D' and resid 130 through 137
      removed outlier: 3.687A  pdb=" N   SER D 137 " --> pdb=" O   VAL D 133 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 140 through 152
      removed outlier: 3.592A  pdb=" N   PHE D 147 " --> pdb=" O   GLU D 143 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 521 through 529
    Processing helix  chain 'D' and resid 535 through 554
    Processing helix  chain 'D' and resid 590 through 592
      No H-bonds generated for 'chain 'D' and resid 590 through 592'
    Processing helix  chain 'D' and resid 593 through 600
      removed outlier: 4.138A  pdb=" N   VAL D 597 " --> pdb=" O   CYS D 593 " (cutoff:3.500A)
      removed outlier: 3.875A  pdb=" N   THR D 598 " --> pdb=" O   PRO D 594 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 601 through 608
      removed outlier: 3.556A  pdb=" N   VAL D 605 " --> pdb=" O   GLY D 601 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 617 through 629
      removed outlier: 4.508A  pdb=" N   ASP D 621 " --> pdb=" O   ASP D 617 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 639 through 652
    Processing helix  chain 'D' and resid 654 through 658
    Processing helix  chain 'D' and resid 662 through 671
    Processing helix  chain 'D' and resid 676 through 688
      removed outlier: 3.602A  pdb=" N   GLN D 680 " --> pdb=" O   PRO D 676 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 690 through 694
    Processing helix  chain 'D' and resid 698 through 714
      removed outlier: 4.317A  pdb=" N   ASP D 708 " --> pdb=" O   TYR D 704 " (cutoff:3.500A)
      removed outlier: 3.995A  pdb=" N   VAL D 709 " --> pdb=" O   ALA D 705 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 714 through 723
      removed outlier: 3.509A  pdb=" N   ASN D 720 " --> pdb=" O   GLN D 716 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 726 through 742
    Processing helix  chain 'D' and resid 746 through 773
      removed outlier: 3.864A  pdb=" N   SER D 764 " --> pdb=" O   SER D 760 " (cutoff:3.500A)
      removed outlier: 3.741A  pdb=" N   ASP D 765 " --> pdb=" O   THR D 761 " (cutoff:3.500A)
      removed outlier: 3.547A  pdb=" N   LEU D 766 " --> pdb=" O   GLU D 762 " (cutoff:3.500A)
      removed outlier: 3.887A  pdb=" N   LYS D 767 " --> pdb=" O   VAL D 763 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 780 through 787
    Processing helix  chain 'D' and resid 788 through 790
      No H-bonds generated for 'chain 'D' and resid 788 through 790'
    Processing helix  chain 'D' and resid 793 through 801
    Processing helix  chain 'D' and resid 803 through 816
    Processing helix  chain 'C' and resid 6 through 25
    Processing helix  chain 'C' and resid 30 through 36
    Processing helix  chain 'C' and resid 43 through 50
    Processing helix  chain 'C' and resid 53 through 63
      removed outlier: 3.670A  pdb=" N   GLN C  63 " --> pdb=" O   LYS C  59 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 95 through 111
      removed outlier: 4.166A  pdb=" N   GLU C  99 " --> pdb=" O   ASP C  95 " (cutoff:3.500A)
      removed outlier: 3.777A  pdb=" N   MET C 108 " --> pdb=" O   PHE C 104 " (cutoff:3.500A)
      removed outlier: 3.706A  pdb=" N   GLN C 110 " --> pdb=" O   ASN C 106 " (cutoff:3.500A)
      removed outlier: 3.880A  pdb=" N   TYR C 111 " --> pdb=" O   LYS C 107 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 121 through 127
    Processing helix  chain 'C' and resid 130 through 137
      removed outlier: 3.569A  pdb=" N   ILE C 136 " --> pdb=" O   GLN C 132 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 140 through 152
    Processing helix  chain 'C' and resid 521 through 530
    Processing helix  chain 'C' and resid 535 through 554
      removed outlier: 3.595A  pdb=" N   ASN C 553 " --> pdb=" O   TYR C 549 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 595 through 600
    Processing helix  chain 'C' and resid 601 through 608
      removed outlier: 3.503A  pdb=" N   VAL C 605 " --> pdb=" O   GLY C 601 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 618 through 630
      removed outlier: 3.531A  pdb=" N   ALA C 623 " --> pdb=" O   ARG C 619 " (cutoff:3.500A)
      removed outlier: 3.604A  pdb=" N   ASN C 624 " --> pdb=" O   ASN C 620 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 639 through 652
    Processing helix  chain 'C' and resid 654 through 658
    Processing helix  chain 'C' and resid 662 through 670
    Processing helix  chain 'C' and resid 675 through 688
      removed outlier: 4.078A  pdb=" N   ASP C 679 " --> pdb=" O   ASN C 675 " (cutoff:3.500A)
      removed outlier: 3.736A  pdb=" N   GLN C 680 " --> pdb=" O   PRO C 676 " (cutoff:3.500A)
      removed outlier: 3.754A  pdb=" N   GLN C 683 " --> pdb=" O   ASP C 679 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 689 through 694
      removed outlier: 3.843A  pdb=" N   TRP C 692 " --> pdb=" O   GLN C 689 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 698 through 714
      removed outlier: 3.704A  pdb=" N   ASP C 708 " --> pdb=" O   TYR C 704 " (cutoff:3.500A)
      removed outlier: 3.703A  pdb=" N   VAL C 709 " --> pdb=" O   ALA C 705 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 714 through 723
    Processing helix  chain 'C' and resid 726 through 742
    Processing helix  chain 'C' and resid 746 through 772
    Processing helix  chain 'C' and resid 780 through 786
    Processing helix  chain 'C' and resid 793 through 802
    Processing helix  chain 'C' and resid 803 through 816
      removed outlier: 3.839A  pdb=" N   LYS C 808 " --> pdb=" O   TYR C 804 " (cutoff:3.500A)
      removed outlier: 3.544A  pdb=" N   GLU C 814 " --> pdb=" O   LEU C 810 " (cutoff:3.500A)
    Processing sheet with id=AA1, first strand: chain 'D' and resid 28 through 29
    Processing sheet with id=AA2, first strand: chain 'D' and resid 155 through 158
      removed outlier: 3.603A  pdb=" N   MET D 163 " --> pdb=" O   LYS D 156 " (cutoff:3.500A)
    Processing sheet with id=AA3, first strand: chain 'D' and resid 530 through 533
      removed outlier: 7.195A  pdb=" N   THR D 531 " --> pdb=" O   LEU D 587 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AA3
    Processing sheet with id=AA4, first strand: chain 'D' and resid 577 through 579
      removed outlier: 5.712A  pdb=" N   ILE D 556 " --> pdb=" O   ILE D 612 " (cutoff:3.500A)
      removed outlier: 6.960A  pdb=" N   VAL D 614 " --> pdb=" O   ILE D 556 " (cutoff:3.500A)
      removed outlier: 6.709A  pdb=" N   VAL D 558 " --> pdb=" O   VAL D 614 " (cutoff:3.500A)
    Processing sheet with id=AA5, first strand: chain 'D' and resid 564 through 565
    Processing sheet with id=AA6, first strand: chain 'C' and resid 28 through 29
      removed outlier: 3.563A  pdb=" N   ARG C  28 " --> pdb=" O   VAL C  75 " (cutoff:3.500A)
      removed outlier: 3.548A  pdb=" N   GLN C  76 " --> pdb=" O   LEU C  69 " (cutoff:3.500A)
    Processing sheet with id=AA7, first strand: chain 'C' and resid 155 through 158
    Processing sheet with id=AA8, first strand: chain 'C' and resid 531 through 533
    Processing sheet with id=AA9, first strand: chain 'C' and resid 556 through 559
      removed outlier: 6.195A  pdb=" N   ILE C 556 " --> pdb=" O   ILE C 612 " (cutoff:3.500A)
      removed outlier: 7.236A  pdb=" N   VAL C 614 " --> pdb=" O   ILE C 556 " (cutoff:3.500A)
      removed outlier: 6.599A  pdb=" N   VAL C 558 " --> pdb=" O   VAL C 614 " (cutoff:3.500A)
      removed outlier: 7.590A  pdb=" N   PHE C 637 " --> pdb=" O   VAL C 611 " (cutoff:3.500A)
      removed outlier: 6.240A  pdb=" N   LYS C 613 " --> pdb=" O   PHE C 637 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AA9
    Processing sheet with id=AB1, first strand: chain 'C' and resid 564 through 565
      removed outlier: 3.655A  pdb=" N   GLU C 572 " --> pdb=" O   ILE C 565 " (cutoff:3.500A)

    488 hydrogen bonds defined for protein.
    1404 hydrogen bond angles defined for protein.
    Restraints generated for nucleic acids:
      84 hydrogen bonds
      160 hydrogen bond angles
      0 basepair planarities
      35 basepair parallelities
      41 stacking parallelities
  Total time for adding SS restraints: 1.28

  Time building geometry restraints manager: 0.62 seconds

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

  Histogram of bond lengths:
        1.22 -     1.34: 2428
        1.34 -     1.46: 1511
        1.46 -     1.58: 3908
        1.58 -     1.70: 166
        1.70 -     1.82: 20
  Bond restraints: 8033
  Sorted by residual:
  bond pdb=" N9    A E   3 "
       pdb=" C4    A E   3 "
    ideal  model  delta    sigma   weight residual
    1.374  1.385 -0.011 6.00e-03 2.78e+04 3.29e+00
  bond pdb=" N   CYS A 695 "
       pdb=" CA  CYS A 695 "
    ideal  model  delta    sigma   weight residual
    1.458  1.491 -0.033 1.90e-02 2.77e+03 3.00e+00
  bond pdb=" N   CYS B 695 "
       pdb=" CA  CYS B 695 "
    ideal  model  delta    sigma   weight residual
    1.458  1.490 -0.032 1.90e-02 2.77e+03 2.86e+00
  bond pdb=" N1    U E  39 "
       pdb=" C2    U E  39 "
    ideal  model  delta    sigma   weight residual
    1.381  1.396 -0.015 9.00e-03 1.23e+04 2.65e+00
  bond pdb=" C2    U F  41 "
       pdb=" N3    U F  41 "
    ideal  model  delta    sigma   weight residual
    1.373  1.363  0.010 7.00e-03 2.04e+04 2.23e+00
  ... (remaining 8028 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     1.65: 11166
        1.65 -     3.30: 184
        3.30 -     4.95: 34
        4.95 -     6.60: 4
        6.60 -     8.25: 2
  Bond angle restraints: 11390
  Sorted by residual:
  angle pdb=" C1'   U E  39 "
        pdb=" N1    U E  39 "
        pdb=" C2    U E  39 "
      ideal   model   delta    sigma   weight residual
     117.70  125.95   -8.25 1.20e+00 6.94e-01 4.73e+01
  angle pdb=" N1    U E  39 "
        pdb=" C2    U E  39 "
        pdb=" O2    U E  39 "
      ideal   model   delta    sigma   weight residual
     122.80  126.20   -3.40 7.00e-01 2.04e+00 2.36e+01
  angle pdb=" C1'   U E  39 "
        pdb=" N1    U E  39 "
        pdb=" C6    U E  39 "
      ideal   model   delta    sigma   weight residual
     121.20  114.73    6.47 1.40e+00 5.10e-01 2.14e+01
  angle pdb=" O2    U E  39 "
        pdb=" C2    U E  39 "
        pdb=" N3    U E  39 "
      ideal   model   delta    sigma   weight residual
     122.20  119.00    3.20 7.00e-01 2.04e+00 2.09e+01
  angle pdb=" N1    U E  39 "
        pdb=" C6    U E  39 "
        pdb=" C5    U E  39 "
      ideal   model   delta    sigma   weight residual
     122.70  124.50   -1.80 5.00e-01 4.00e+00 1.30e+01
  ... (remaining 11385 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    22.01: 4413
       22.01 -    44.03: 292
       44.03 -    66.04: 148
       66.04 -    88.06: 33
       88.06 -   110.07: 6
  Dihedral angle restraints: 4892
    sinusoidal: 1966
      harmonic: 2926
  Sorted by residual:
  dihedral pdb=" O4'   U E  39 "
           pdb=" C1'   U E  39 "
           pdb=" N1    U E  39 "
           pdb=" C2    U E  39 "
      ideal   model   delta sinusoidal    sigma   weight residual
     200.00  122.43   77.57     1      1.50e+01 4.44e-03 3.35e+01
  dihedral pdb=" N   LEU C  14 "
           pdb=" CA  LEU C  14 "
           pdb=" CB  LEU C  14 "
           pdb=" CG  LEU C  14 "
      ideal   model   delta sinusoidal    sigma   weight residual
     -60.00 -119.40   59.40     3      1.50e+01 4.44e-03 9.48e+00
  dihedral pdb=" O5'   U F  35 "
           pdb=" C5'   U F  35 "
           pdb=" C4'   U F  35 "
           pdb=" C3'   U F  35 "
      ideal   model   delta sinusoidal    sigma   weight residual
     -65.00   -6.95  -58.05     3      1.50e+01 4.44e-03 9.46e+00
  ... (remaining 4889 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.028: 990
       0.028 -    0.056: 321
       0.056 -    0.083: 94
       0.083 -    0.111: 52
       0.111 -    0.139: 18
  Chirality restraints: 1475
  Sorted by residual:
  chirality pdb=" C1'   A F   3 "
            pdb=" O4'   A F   3 "
            pdb=" C2'   A F   3 "
            pdb=" N9    A F   3 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.46    2.32    0.14 2.00e-01 2.50e+01 4.84e-01
  chirality pdb=" CA  ILE C 578 "
            pdb=" N   ILE C 578 "
            pdb=" C   ILE C 578 "
            pdb=" CB  ILE C 578 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.43    2.56   -0.13 2.00e-01 2.50e+01 3.94e-01
  chirality pdb=" CA  ILE C 631 "
            pdb=" N   ILE C 631 "
            pdb=" C   ILE C 631 "
            pdb=" CB  ILE C 631 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.43    2.55   -0.12 2.00e-01 2.50e+01 3.64e-01
  ... (remaining 1472 not shown)

  Planarity restraints: 1222
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C1'   A F   3 "    0.028 2.00e-02 2.50e+03   1.35e-02 5.00e+00
        pdb=" N9    A F   3 "   -0.033 2.00e-02 2.50e+03
        pdb=" C8    A F   3 "   -0.003 2.00e-02 2.50e+03
        pdb=" N7    A F   3 "    0.001 2.00e-02 2.50e+03
        pdb=" C5    A F   3 "    0.001 2.00e-02 2.50e+03
        pdb=" C6    A F   3 "    0.004 2.00e-02 2.50e+03
        pdb=" N6    A F   3 "    0.008 2.00e-02 2.50e+03
        pdb=" N1    A F   3 "   -0.001 2.00e-02 2.50e+03
        pdb=" C2    A F   3 "   -0.001 2.00e-02 2.50e+03
        pdb=" N3    A F   3 "   -0.003 2.00e-02 2.50e+03
        pdb=" C4    A F   3 "   -0.002 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   VAL D 117 "   -0.030 5.00e-02 4.00e+02   4.58e-02 3.35e+00
        pdb=" N   PRO D 118 "    0.079 5.00e-02 4.00e+02
        pdb=" CA  PRO D 118 "   -0.024 5.00e-02 4.00e+02
        pdb=" CD  PRO D 118 "   -0.025 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  ARG D 120 "    0.008 2.00e-02 2.50e+03   1.56e-02 2.44e+00
        pdb=" C   ARG D 120 "   -0.027 2.00e-02 2.50e+03
        pdb=" O   ARG D 120 "    0.010 2.00e-02 2.50e+03
        pdb=" N   SER D 121 "    0.009 2.00e-02 2.50e+03
  ... (remaining 1219 not shown)

  Histogram of nonbonded interaction distances:
        2.03 -     2.60: 97
        2.60 -     3.18: 7380
        3.18 -     3.75: 13318
        3.75 -     4.33: 16163
        4.33 -     4.90: 24720
  Nonbonded interactions: 61678
  Sorted by model distance:
  nonbonded pdb=" O2'   C F  38 "
            pdb=" OP1   U F  40 "
     model   vdw
     2.030 3.040
  nonbonded pdb=" O   PRO C 118 "
            pdb=" N   ARG C 120 "
     model   vdw
     2.208 3.120
  nonbonded pdb=" O2'   C E  38 "
            pdb=" OP1   U E  40 "
     model   vdw
     2.232 3.040
  nonbonded pdb=" O   THR C 154 "
            pdb=" N   VAL C 165 "
     model   vdw
     2.242 3.120
  nonbonded pdb=" O2'   G F  45 "
            pdb=" O4'   U F  46 "
     model   vdw
     2.281 3.040
  ... (remaining 61673 not shown)

  NOTE: a complete listing of the restraints can be obtained by requesting
        output of .geo file.
Find NCS groups from input model
Time spend for trying shortcut: 0.00
Found NCS groups:
ncs_group {
  reference = chain 'A'
  selection = chain 'B'
}
ncs_group {
  reference = (chain 'C' and (resid 5 through 31 or (resid 32 and (name N or name CA or name C \ 
 or name O or name CB )) or resid 33 or (resid 34 and (name N or name CA or name \ 
 C or name O or name CB )) or resid 35 through 81 or resid 95 through 107 or (re \ 
sid 108 and (name N or name CA or name C or name O or name CB )) or resid 109 th \ 
rough 816))
  selection = (chain 'D' and (resid 5 through 43 or (resid 44 through 45 and (name N or name C \ 
A or name C or name O or name CB )) or resid 46 through 72 or (resid 73 and (nam \ 
e N or name CA or name C or name O or name CB )) or resid 74 through 100 or (res \ 
id 101 and (name N or name CA or name C or name O or name CB )) or resid 102 thr \ 
ough 115 or (resid 116 and (name N or name CA or name C or name O or name CB ))  \ 
or resid 117 through 119 or (resid 120 and (name N or name CA or name C or name  \ 
O or name CB )) or resid 121 through 138 or (resid 139 and (name N or name CA or \ 
 name C or name O or name CB )) or resid 140 through 141 or (resid 142 through 1 \ 
43 and (name N or name CA or name C or name O or name CB )) or resid 144 through \ 
 145 or (resid 146 and (name N or name CA or name C or name O or name CB )) or r \ 
esid 147 through 148 or (resid 149 and (name N or name CA or name C or name O or \ 
 name CB )) or resid 150 through 152 or (resid 153 and (name N or name CA or nam \ 
e C or name O or name CB )) or resid 154 through 155 or (resid 156 and (name N o \ 
r name CA or name C or name O or name CB )) or resid 157 or (resid 158 through 1 \ 
60 and (name N or name CA or name C or name O or name CB )) or resid 161 through \ 
 816))
}
ncs_group {
  reference = chain 'E'
  selection = chain 'F'
}

Set up NCS constraints
  No NCS constraints will be used in refinement.
Set refine NCS operators
Adjust number of macro_cycles
  Number of macro_cycles: 10
Reset NCS operators
Extract rigid body selections
Check and reset occupancies
  Occupancies: min=1.00 max=1.00 mean=1.00
Load rotamer database and sin/cos tables
Set ADP refinement strategy
  ADPs will be refined as group one per residue
Make a string to write initial .geo file
Internal consistency checks
Time:
  Set random seed:                         0.000
  Set model cs if undefined:               0.000
  Decide on map wrapping:                  0.000
  Normalize map: mean=0, sd=1:             0.760
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.000
  Construct map_model_manager:             0.000
  Extract box with map and model:          0.100
  Check model and map are aligned:         0.010
  Set scattering table:                    0.020
  Process input model:                     7.820
  Find NCS groups from input model:        0.130
  Set up NCS constraints:                  0.010
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.000
  Load rotamer database and sin/cos tables:0.940
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:    9.790
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7845
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      :  0.002   0.043   8033  Z= 0.155
  Angle     :  0.552   8.250  11390  Z= 0.411
  Chirality :  0.035   0.139   1475
  Planarity :  0.003   0.046   1222
  Dihedral  : 19.428 110.074   2976
  Min Nonbonded Distance : 2.030

Molprobity Statistics.
  All-atom Clashscore : 9.23
  Ramachandran Plot:
    Outliers :  0.30 %
    Allowed  :  3.35 %
    Favored  : 96.35 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  : 23.91 %
    Favored  : 76.09 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 10.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  0.52 (0.27), residues: 986
  helix:  1.14 (0.21), residues: 595
  sheet: -1.35 (0.73), residues: 48
  loop : -0.72 (0.35), residues: 343

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.012   0.001   ARG D 120 
 TYR   0.012   0.001   TYR D  64 
 PHE   0.008   0.001   PHE C  68 
 TRP   0.000   0.000   TRP D 522 
 HIS   0.006   0.001   HIS C 151 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00238 /  0.15 ( 8033)
  covalent geometry    : angle       0.55178 /  0.41 (11390)
  hydrogen bonds       : bond        0.22490 / 15.62 (  572)
  hydrogen bonds       : angle       7.80938 /  5.97 ( 1564)

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

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

  1972 Ramachandran restraints generated.
    986 Oldfield, 0 Emsley, 986 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1972 Ramachandran restraints generated.
    986 Oldfield, 0 Emsley, 986 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  105 residues out of total 890 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 105
  time to evaluate  : 0.216 
Fit side-chains
REVERT: A  713 GLU cc_start: 0.8813 (tm-30) cc_final: 0.8216 (tm-30)
REVERT: A  717 LYS cc_start: 0.9161 (tptt) cc_final: 0.8615 (tppt)
REVERT: D  102 ASP cc_start: 0.7789 (m-30) cc_final: 0.7250 (t0)
REVERT: D  106 ASN cc_start: 0.8051 (m-40) cc_final: 0.7736 (m110)
  outliers start: 0
  outliers final: 0
  residues processed: 105
  average time/residue: 0.0851
  time to fit residues: 11.6536
Evaluate side-chains
  87 residues out of total 890 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 87
  time to evaluate  : 0.153 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 106
   random chunks:
   chunk 49 optimal weight:    6.9990
   chunk 97 optimal weight:    5.9990
   chunk 53 optimal weight:    4.9990
   chunk 5 optimal weight:   40.0000
   chunk 33 optimal weight:   50.0000
   chunk 65 optimal weight:    8.9990
   chunk 62 optimal weight:    2.9990
   chunk 51 optimal weight:   10.0000
   chunk 100 optimal weight:   10.0000
   chunk 38 optimal weight:   10.0000
   chunk 61 optimal weight:    0.0980
   overall best weight:    4.2188

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
D 140 HIS
C  54 GLN
C 125 HIS
C 128 GLN

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3732 r_free = 0.3732 target = 0.083448 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 44)----------------|
| r_work = 0.3281 r_free = 0.3281 target = 0.064541 restraints weight = 39362.294|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 28)----------------|
| r_work = 0.3240 r_free = 0.3240 target = 0.063354 restraints weight = 35229.870|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 25)----------------|
| r_work = 0.3254 r_free = 0.3254 target = 0.063805 restraints weight = 32392.548|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 30)----------------|
| r_work = 0.3263 r_free = 0.3263 target = 0.064181 restraints weight = 25775.577|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 25)----------------|
| r_work = 0.3263 r_free = 0.3263 target = 0.064154 restraints weight = 23843.009|
|-----------------------------------------------------------------------------|
r_work (final): 0.3219
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8058
moved from start:          0.1477

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.048   8033  Z= 0.270
  Angle     :  0.593   9.306  11390  Z= 0.346
  Chirality :  0.041   0.170   1475
  Planarity :  0.005   0.052   1222
  Dihedral  : 18.597 106.219   2344
  Min Nonbonded Distance : 2.452

Molprobity Statistics.
  All-atom Clashscore : 7.67
  Ramachandran Plot:
    Outliers :  0.20 %
    Allowed  :  3.04 %
    Favored  : 96.75 %
  Rotamer:
    Outliers :  2.54 %
    Allowed  : 18.84 %
    Favored  : 78.62 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 10.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  0.70 (0.26), residues: 986
  helix:  1.16 (0.19), residues: 639
  sheet: -1.60 (0.72), residues: 50
  loop : -0.55 (0.38), residues: 297

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.001   ARG C 126 
 TYR   0.012   0.002   TYR C 103 
 PHE   0.016   0.002   PHE C  60 
 TRP   0.000   0.000   TRP D 522 
 HIS   0.009   0.002   HIS D 151 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00533 /  0.27 ( 8033)
  covalent geometry    : angle       0.59313 /  0.35 (11390)
  hydrogen bonds       : bond        0.07145 /  5.00 (  572)
  hydrogen bonds       : angle       5.96938 /  4.63 ( 1564)

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

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

  1972 Ramachandran restraints generated.
    986 Oldfield, 0 Emsley, 986 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1972 Ramachandran restraints generated.
    986 Oldfield, 0 Emsley, 986 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  100 residues out of total 890 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 93
  time to evaluate  : 0.196 
Fit side-chains
REVERT: A  713 GLU cc_start: 0.8591 (tm-30) cc_final: 0.8322 (tm-30)
REVERT: A  714 GLU cc_start: 0.8793 (mm-30) cc_final: 0.8296 (mm-30)
REVERT: B  722 LEU cc_start: 0.9098 (mt) cc_final: 0.8890 (mt)
REVERT: D  102 ASP cc_start: 0.7121 (m-30) cc_final: 0.6776 (t0)
REVERT: D  106 ASN cc_start: 0.7295 (m-40) cc_final: 0.7091 (m110)
REVERT: D  126 ARG cc_start: 0.8842 (ttp80) cc_final: 0.8295 (ttp80)
REVERT: C   24 LYS cc_start: 0.8593 (tptt) cc_final: 0.8320 (tptm)
  outliers start: 7
  outliers final: 4
  residues processed: 98
  average time/residue: 0.0720
  time to fit residues: 9.3468
Evaluate side-chains
  84 residues out of total 890 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 4
    poor density    : 80
  time to evaluate  : 0.171 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  725 LEU
Chi-restraints excluded: chain D residue  117 VAL
Chi-restraints excluded: chain C residue   13 THR
Chi-restraints excluded: chain C residue  152 THR
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 106
   random chunks:
   chunk 42 optimal weight:   20.0000
   chunk 78 optimal weight:   30.0000
   chunk 2 optimal weight:    0.9980
   chunk 84 optimal weight:    6.9990
   chunk 4 optimal weight:    0.7980
   chunk 14 optimal weight:    0.7980
   chunk 75 optimal weight:   20.0000
   chunk 76 optimal weight:   40.0000
   chunk 60 optimal weight:    0.8980
   chunk 56 optimal weight:    0.0270
   chunk 25 optimal weight:    0.9990
   overall best weight:    0.7038

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
D  48 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3778 r_free = 0.3778 target = 0.085528 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 42)----------------|
| r_work = 0.3351 r_free = 0.3351 target = 0.067118 restraints weight = 38952.699|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 31)----------------|
| r_work = 0.3306 r_free = 0.3306 target = 0.065825 restraints weight = 34120.488|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 29)----------------|
| r_work = 0.3325 r_free = 0.3325 target = 0.066503 restraints weight = 29705.767|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 28)----------------|
| r_work = 0.3332 r_free = 0.3332 target = 0.066764 restraints weight = 23808.135|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 28)----------------|
| r_work = 0.3332 r_free = 0.3332 target = 0.066743 restraints weight = 21411.950|
|-----------------------------------------------------------------------------|
r_work (final): 0.3317
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7959
moved from start:          0.1817

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.036   8033  Z= 0.139
  Angle     :  0.491   8.494  11390  Z= 0.289
  Chirality :  0.037   0.136   1475
  Planarity :  0.003   0.048   1222
  Dihedral  : 18.495 106.940   2344
  Min Nonbonded Distance : 2.534

Molprobity Statistics.
  All-atom Clashscore : 5.24
  Ramachandran Plot:
    Outliers :  0.10 %
    Allowed  :  2.94 %
    Favored  : 96.96 %
  Rotamer:
    Outliers :  3.62 %
    Allowed  : 18.12 %
    Favored  : 78.26 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 10.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  1.54 (0.27), residues: 986
  helix:  1.85 (0.20), residues: 646
  sheet: -1.48 (0.72), residues: 50
  loop : -0.34 (0.38), residues: 290

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.001   ARG D  28 
 TYR   0.008   0.001   TYR D 161 
 PHE   0.011   0.001   PHE D  17 
 TRP   0.000   0.000   TRP D 522 
 HIS   0.006   0.002   HIS D 151 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00258 /  0.14 ( 8033)
  covalent geometry    : angle       0.49137 /  0.29 (11390)
  hydrogen bonds       : bond        0.05332 /  3.79 (  572)
  hydrogen bonds       : angle       5.08662 /  3.95 ( 1564)

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

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

  1972 Ramachandran restraints generated.
    986 Oldfield, 0 Emsley, 986 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1972 Ramachandran restraints generated.
    986 Oldfield, 0 Emsley, 986 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  109 residues out of total 890 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 99
  time to evaluate  : 0.241 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  713 GLU cc_start: 0.8432 (tm-30) cc_final: 0.8115 (tm-30)
REVERT: A  714 GLU cc_start: 0.8676 (mm-30) cc_final: 0.8001 (mm-30)
REVERT: A  717 LYS cc_start: 0.8963 (tptt) cc_final: 0.8643 (tptp)
REVERT: D  106 ASN cc_start: 0.6849 (m-40) cc_final: 0.6642 (m110)
REVERT: D  126 ARG cc_start: 0.8555 (ttp80) cc_final: 0.8299 (ttp80)
  outliers start: 10
  outliers final: 8
  residues processed: 107
  average time/residue: 0.0807
  time to fit residues: 11.4815
Evaluate side-chains
  95 residues out of total 890 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 87
  time to evaluate  : 0.216 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue  716 LYS
Chi-restraints excluded: chain D residue   15 LEU
Chi-restraints excluded: chain D residue   40 LYS
Chi-restraints excluded: chain D residue  110 GLN
Chi-restraints excluded: chain D residue  117 VAL
Chi-restraints excluded: chain C residue   46 MET
Chi-restraints excluded: chain C residue  119 VAL
Chi-restraints excluded: chain C residue  152 THR
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 106
   random chunks:
   chunk 3 optimal weight:    0.6980
   chunk 21 optimal weight:    4.9990
   chunk 62 optimal weight:    3.9990
   chunk 69 optimal weight:    0.0000
   chunk 45 optimal weight:   50.0000
   chunk 9 optimal weight:    9.9990
   chunk 41 optimal weight:   40.0000
   chunk 97 optimal weight:   40.0000
   chunk 28 optimal weight:    8.9990
   chunk 4 optimal weight:    7.9990
   chunk 78 optimal weight:   50.0000
   overall best weight:    3.5390

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
A 729 GLN
** D 151 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
C 151 HIS

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3714 r_free = 0.3714 target = 0.083182 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 57)----------------|
| r_work = 0.3188 r_free = 0.3188 target = 0.062143 restraints weight = 38225.674|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 44)----------------|
| r_work = 0.3215 r_free = 0.3215 target = 0.063153 restraints weight = 26456.179|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 28)----------------|
| r_work = 0.3230 r_free = 0.3230 target = 0.063695 restraints weight = 21059.882|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 34)----------------|
| r_work = 0.3241 r_free = 0.3241 target = 0.064119 restraints weight = 18568.116|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 28)----------------|
| r_work = 0.3246 r_free = 0.3246 target = 0.064309 restraints weight = 17138.308|
|-----------------------------------------------------------------------------|
r_work (final): 0.3199
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8083
moved from start:          0.2059

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.042   8033  Z= 0.224
  Angle     :  0.522   9.861  11390  Z= 0.300
  Chirality :  0.038   0.146   1475
  Planarity :  0.004   0.053   1222
  Dihedral  : 18.429 107.791   2344
  Min Nonbonded Distance : 2.514

Molprobity Statistics.
  All-atom Clashscore : 7.51
  Ramachandran Plot:
    Outliers :  0.10 %
    Allowed  :  3.35 %
    Favored  : 96.55 %
  Rotamer:
    Outliers :  6.16 %
    Allowed  : 18.12 %
    Favored  : 75.72 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 10.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  1.53 (0.27), residues: 986
  helix:  1.89 (0.20), residues: 646
  sheet: -1.49 (0.70), residues: 50
  loop : -0.47 (0.38), residues: 290

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.001   ARG C  47 
 TYR   0.010   0.001   TYR D  64 
 PHE   0.013   0.002   PHE C  60 
 TRP   0.000   0.000   TRP D 522 
 HIS   0.013   0.002   HIS D 151 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00454 /  0.22 ( 8033)
  covalent geometry    : angle       0.52165 /  0.30 (11390)
  hydrogen bonds       : bond        0.05517 /  3.84 (  572)
  hydrogen bonds       : angle       4.96810 /  3.86 ( 1564)

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

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

  1972 Ramachandran restraints generated.
    986 Oldfield, 0 Emsley, 986 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1972 Ramachandran restraints generated.
    986 Oldfield, 0 Emsley, 986 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  105 residues out of total 890 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 88
  time to evaluate  : 0.222 
Fit side-chains
   revert: symmetry clash
REVERT: A  713 GLU cc_start: 0.8641 (tm-30) cc_final: 0.8174 (tm-30)
REVERT: A  714 GLU cc_start: 0.8904 (mm-30) cc_final: 0.8120 (mm-30)
REVERT: A  717 LYS cc_start: 0.9082 (tptt) cc_final: 0.8674 (tptp)
REVERT: B  722 LEU cc_start: 0.9141 (mt) cc_final: 0.8902 (mt)
REVERT: D   22 LEU cc_start: 0.9562 (OUTLIER) cc_final: 0.9340 (mp)
REVERT: D  101 LYS cc_start: 0.8869 (ttpp) cc_final: 0.8633 (ttpp)
REVERT: D  126 ARG cc_start: 0.8824 (ttp80) cc_final: 0.8615 (ttp-170)
REVERT: C  108 MET cc_start: 0.7126 (ttm) cc_final: 0.6205 (tmm)
  outliers start: 17
  outliers final: 13
  residues processed: 99
  average time/residue: 0.0881
  time to fit residues: 11.6417
Evaluate side-chains
  97 residues out of total 890 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 83
  time to evaluate  : 0.298 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  725 LEU
Chi-restraints excluded: chain B residue  716 LYS
Chi-restraints excluded: chain B residue  717 LYS
Chi-restraints excluded: chain D residue   22 LEU
Chi-restraints excluded: chain D residue   29 THR
Chi-restraints excluded: chain D residue   40 LYS
Chi-restraints excluded: chain D residue   70 VAL
Chi-restraints excluded: chain D residue  110 GLN
Chi-restraints excluded: chain D residue  117 VAL
Chi-restraints excluded: chain C residue   13 THR
Chi-restraints excluded: chain C residue   46 MET
Chi-restraints excluded: chain C residue  119 VAL
Chi-restraints excluded: chain C residue  152 THR
Chi-restraints excluded: chain C residue  165 VAL
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 106
   random chunks:
   chunk 45 optimal weight:   50.0000
   chunk 35 optimal weight:   30.0000
   chunk 88 optimal weight:    5.9990
   chunk 10 optimal weight:    0.0170
   chunk 105 optimal weight:   20.0000
   chunk 40 optimal weight:   50.0000
   chunk 26 optimal weight:    8.9990
   chunk 18 optimal weight:    0.7980
   chunk 57 optimal weight:    1.9990
   chunk 64 optimal weight:    2.9990
   chunk 67 optimal weight:    5.9990
   overall best weight:    2.3624

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
D  98 GLN
** D 151 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
C 151 HIS

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3725 r_free = 0.3725 target = 0.083752 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 66)----------------|
| r_work = 0.3215 r_free = 0.3215 target = 0.063049 restraints weight = 38027.482|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 45)----------------|
| r_work = 0.3240 r_free = 0.3240 target = 0.064006 restraints weight = 26914.015|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 43)----------------|
| r_work = 0.3256 r_free = 0.3256 target = 0.064611 restraints weight = 21677.059|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 25)----------------|
| r_work = 0.3260 r_free = 0.3260 target = 0.064780 restraints weight = 19039.717|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 33)----------------|
| r_work = 0.3270 r_free = 0.3270 target = 0.065120 restraints weight = 17946.603|
|-----------------------------------------------------------------------------|
r_work (final): 0.3221
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8054
moved from start:          0.2280

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.035   8033  Z= 0.165
  Angle     :  0.497   9.898  11390  Z= 0.284
  Chirality :  0.038   0.239   1475
  Planarity :  0.003   0.051   1222
  Dihedral  : 18.422 107.779   2344
  Min Nonbonded Distance : 2.516

Molprobity Statistics.
  All-atom Clashscore : 6.80
  Ramachandran Plot:
    Outliers :  0.10 %
    Allowed  :  2.94 %
    Favored  : 96.96 %
  Rotamer:
    Outliers :  4.71 %
    Allowed  : 22.10 %
    Favored  : 73.19 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 10.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  1.71 (0.27), residues: 986
  helix:  2.07 (0.20), residues: 646
  sheet: -1.50 (0.69), residues: 50
  loop : -0.48 (0.37), residues: 290

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.001   ARG C  47 
 TYR   0.010   0.001   TYR D  64 
 PHE   0.012   0.001   PHE D  17 
 TRP   0.000   0.000   TRP D 522 
 HIS   0.011   0.002   HIS D 151 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00336 /  0.16 ( 8033)
  covalent geometry    : angle       0.49661 /  0.28 (11390)
  hydrogen bonds       : bond        0.04955 /  3.49 (  572)
  hydrogen bonds       : angle       4.74041 /  3.69 ( 1564)

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

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

  1972 Ramachandran restraints generated.
    986 Oldfield, 0 Emsley, 986 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1972 Ramachandran restraints generated.
    986 Oldfield, 0 Emsley, 986 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  103 residues out of total 890 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 90
  time to evaluate  : 0.260 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  713 GLU cc_start: 0.8692 (tm-30) cc_final: 0.8197 (tm-30)
REVERT: A  714 GLU cc_start: 0.8956 (mm-30) cc_final: 0.8236 (mm-30)
REVERT: A  717 LYS cc_start: 0.9086 (tptt) cc_final: 0.8682 (tptp)
REVERT: A  721 GLN cc_start: 0.8644 (mt0) cc_final: 0.8120 (mt0)
REVERT: D   22 LEU cc_start: 0.9565 (OUTLIER) cc_final: 0.9356 (mp)
REVERT: D  142 LYS cc_start: 0.8853 (ptmt) cc_final: 0.8570 (ptmm)
  outliers start: 13
  outliers final: 9
  residues processed: 100
  average time/residue: 0.0994
  time to fit residues: 13.1296
Evaluate side-chains
  95 residues out of total 890 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 85
  time to evaluate  : 0.244 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue  716 LYS
Chi-restraints excluded: chain D residue   22 LEU
Chi-restraints excluded: chain D residue   40 LYS
Chi-restraints excluded: chain D residue   70 VAL
Chi-restraints excluded: chain D residue  110 GLN
Chi-restraints excluded: chain D residue  117 VAL
Chi-restraints excluded: chain C residue   46 MET
Chi-restraints excluded: chain C residue  119 VAL
Chi-restraints excluded: chain C residue  152 THR
Chi-restraints excluded: chain C residue  162 VAL
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 106
   random chunks:
   chunk 45 optimal weight:   50.0000
   chunk 9 optimal weight:    0.6980
   chunk 1 optimal weight:   10.0000
   chunk 19 optimal weight:    5.9990
   chunk 20 optimal weight:    0.7980
   chunk 90 optimal weight:   20.0000
   chunk 59 optimal weight:    1.9990
   chunk 91 optimal weight:   20.0000
   chunk 71 optimal weight:   50.0000
   chunk 47 optimal weight:   20.0000
   chunk 35 optimal weight:   20.0000
   overall best weight:    3.8988

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
C 151 HIS

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3734 r_free = 0.3734 target = 0.083674 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 75)----------------|
| r_work = 0.3205 r_free = 0.3205 target = 0.062355 restraints weight = 39033.889|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 37)----------------|
| r_work = 0.3230 r_free = 0.3230 target = 0.063303 restraints weight = 27303.344|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 47)----------------|
| r_work = 0.3247 r_free = 0.3247 target = 0.063988 restraints weight = 21986.804|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 28)----------------|
| r_work = 0.3257 r_free = 0.3257 target = 0.064344 restraints weight = 19271.207|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 40)----------------|
| r_work = 0.3264 r_free = 0.3264 target = 0.064612 restraints weight = 17824.547|
|-----------------------------------------------------------------------------|
r_work (final): 0.3234
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8103
moved from start:          0.2442

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.067   8033  Z= 0.245
  Angle     :  0.536  10.150  11390  Z= 0.305
  Chirality :  0.039   0.143   1475
  Planarity :  0.004   0.054   1222
  Dihedral  : 18.420 108.349   2344
  Min Nonbonded Distance : 2.476

Molprobity Statistics.
  All-atom Clashscore : 8.68
  Ramachandran Plot:
    Outliers :  0.20 %
    Allowed  :  3.75 %
    Favored  : 96.04 %
  Rotamer:
    Outliers :  7.61 %
    Allowed  : 20.65 %
    Favored  : 71.74 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 10.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  1.58 (0.27), residues: 986
  helix:  1.99 (0.20), residues: 647
  sheet: -1.59 (0.68), residues: 50
  loop : -0.61 (0.37), residues: 289

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.001   ARG C  47 
 TYR   0.011   0.001   TYR D  64 
 PHE   0.013   0.002   PHE C  60 
 TRP   0.000   0.000   TRP D 522 
 HIS   0.008   0.001   HIS C 125 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00510 /  0.25 ( 8033)
  covalent geometry    : angle       0.53555 /  0.31 (11390)
  hydrogen bonds       : bond        0.05350 /  3.71 (  572)
  hydrogen bonds       : angle       4.78919 /  3.73 ( 1564)

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

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

  1972 Ramachandran restraints generated.
    986 Oldfield, 0 Emsley, 986 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1972 Ramachandran restraints generated.
    986 Oldfield, 0 Emsley, 986 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  107 residues out of total 890 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 86
  time to evaluate  : 0.269 
Fit side-chains
   revert: symmetry clash
REVERT: A  713 GLU cc_start: 0.8496 (tm-30) cc_final: 0.8101 (tm-30)
REVERT: A  714 GLU cc_start: 0.8759 (mm-30) cc_final: 0.8039 (mm-30)
REVERT: A  717 LYS cc_start: 0.9025 (tptt) cc_final: 0.8620 (tptp)
REVERT: B  714 GLU cc_start: 0.7698 (mm-30) cc_final: 0.7490 (mm-30)
REVERT: C  105 LYS cc_start: 0.8499 (tppt) cc_final: 0.7843 (tppt)
  outliers start: 21
  outliers final: 15
  residues processed: 99
  average time/residue: 0.1132
  time to fit residues: 14.6189
Evaluate side-chains
  97 residues out of total 890 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 82
  time to evaluate  : 0.272 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  718 THR
Chi-restraints excluded: chain A residue  725 LEU
Chi-restraints excluded: chain B residue  716 LYS
Chi-restraints excluded: chain B residue  717 LYS
Chi-restraints excluded: chain D residue   29 THR
Chi-restraints excluded: chain D residue   40 LYS
Chi-restraints excluded: chain D residue   70 VAL
Chi-restraints excluded: chain D residue  110 GLN
Chi-restraints excluded: chain D residue  117 VAL
Chi-restraints excluded: chain D residue  151 HIS
Chi-restraints excluded: chain C residue   46 MET
Chi-restraints excluded: chain C residue  119 VAL
Chi-restraints excluded: chain C residue  152 THR
Chi-restraints excluded: chain C residue  162 VAL
Chi-restraints excluded: chain C residue  165 VAL
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 106
   random chunks:
   chunk 79 optimal weight:    9.9990
   chunk 85 optimal weight:    5.9990
   chunk 86 optimal weight:    0.8980
   chunk 48 optimal weight:   20.0000
   chunk 93 optimal weight:   20.0000
   chunk 98 optimal weight:   10.0000
   chunk 84 optimal weight:   10.0000
   chunk 9 optimal weight:    0.7980
   chunk 51 optimal weight:   20.0000
   chunk 37 optimal weight:   20.0000
   chunk 72 optimal weight:   30.0000
   overall best weight:    5.5388

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
** D  98 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
C 151 HIS

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3710 r_free = 0.3710 target = 0.082481 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.3224 r_free = 0.3224 target = 0.062914 restraints weight = 38647.861|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 31)----------------|
| r_work = 0.3181 r_free = 0.3181 target = 0.061280 restraints weight = 29694.100|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 33)----------------|
| r_work = 0.3198 r_free = 0.3198 target = 0.062073 restraints weight = 28166.501|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 29)----------------|
| r_work = 0.3204 r_free = 0.3204 target = 0.062244 restraints weight = 23071.824|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 28)----------------|
| r_work = 0.3208 r_free = 0.3208 target = 0.062379 restraints weight = 21937.785|
|-----------------------------------------------------------------------------|
r_work (final): 0.3181
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8146
moved from start:          0.2617

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.007   0.073   8033  Z= 0.331
  Angle     :  0.642  10.811  11390  Z= 0.356
  Chirality :  0.042   0.212   1475
  Planarity :  0.004   0.060   1222
  Dihedral  : 18.519 109.442   2344
  Min Nonbonded Distance : 2.472

Molprobity Statistics.
  All-atom Clashscore : 10.32
  Ramachandran Plot:
    Outliers :  0.20 %
    Allowed  :  4.16 %
    Favored  : 95.64 %
  Rotamer:
    Outliers :  7.61 %
    Allowed  : 22.10 %
    Favored  : 70.29 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 10.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  1.23 (0.27), residues: 986
  helix:  1.70 (0.20), residues: 646
  sheet: -1.71 (0.67), residues: 50
  loop : -0.67 (0.38), residues: 290

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.008   0.001   ARG C 126 
 TYR   0.012   0.002   TYR D 111 
 PHE   0.017   0.002   PHE C  60 
 TRP   0.000   0.000   TRP D 522 
 HIS   0.010   0.002   HIS C 125 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00685 /  0.33 ( 8033)
  covalent geometry    : angle       0.64209 /  0.36 (11390)
  hydrogen bonds       : bond        0.05953 /  4.09 (  572)
  hydrogen bonds       : angle       5.00435 /  3.89 ( 1564)

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

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

  1972 Ramachandran restraints generated.
    986 Oldfield, 0 Emsley, 986 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1972 Ramachandran restraints generated.
    986 Oldfield, 0 Emsley, 986 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  107 residues out of total 890 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 86
  time to evaluate  : 0.266 
Fit side-chains
   revert: symmetry clash
REVERT: A  713 GLU cc_start: 0.8498 (tm-30) cc_final: 0.8154 (tm-30)
REVERT: A  714 GLU cc_start: 0.8762 (mm-30) cc_final: 0.8061 (mm-30)
REVERT: A  717 LYS cc_start: 0.8971 (tptt) cc_final: 0.8546 (tptp)
REVERT: C  126 ARG cc_start: 0.8496 (OUTLIER) cc_final: 0.7906 (ptt180)
  outliers start: 21
  outliers final: 17
  residues processed: 100
  average time/residue: 0.1086
  time to fit residues: 14.1862
Evaluate side-chains
  98 residues out of total 890 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 80
  time to evaluate  : 0.316 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  718 THR
Chi-restraints excluded: chain A residue  725 LEU
Chi-restraints excluded: chain B residue  716 LYS
Chi-restraints excluded: chain B residue  717 LYS
Chi-restraints excluded: chain D residue   13 THR
Chi-restraints excluded: chain D residue   29 THR
Chi-restraints excluded: chain D residue   40 LYS
Chi-restraints excluded: chain D residue   70 VAL
Chi-restraints excluded: chain D residue  110 GLN
Chi-restraints excluded: chain D residue  117 VAL
Chi-restraints excluded: chain D residue  151 HIS
Chi-restraints excluded: chain C residue   13 THR
Chi-restraints excluded: chain C residue   46 MET
Chi-restraints excluded: chain C residue  119 VAL
Chi-restraints excluded: chain C residue  126 ARG
Chi-restraints excluded: chain C residue  152 THR
Chi-restraints excluded: chain C residue  162 VAL
Chi-restraints excluded: chain C residue  165 VAL
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 106
   random chunks:
   chunk 12 optimal weight:    0.8980
   chunk 91 optimal weight:    0.0570
   chunk 39 optimal weight:   30.0000
   chunk 103 optimal weight:   10.0000
   chunk 92 optimal weight:   10.0000
   chunk 61 optimal weight:    0.7980
   chunk 50 optimal weight:    9.9990
   chunk 63 optimal weight:    2.9990
   chunk 5 optimal weight:   30.0000
   chunk 55 optimal weight:    0.8980
   chunk 60 optimal weight:    0.8980
   overall best weight:    0.7098

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
D  48 GLN
D  98 GLN
C 151 HIS

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3771 r_free = 0.3771 target = 0.085270 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 55)----------------|
| r_work = 0.3255 r_free = 0.3255 target = 0.064117 restraints weight = 38439.084|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 45)----------------|
| r_work = 0.3287 r_free = 0.3287 target = 0.065305 restraints weight = 24965.095|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 38)----------------|
| r_work = 0.3305 r_free = 0.3305 target = 0.065984 restraints weight = 19304.184|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 42)----------------|
| r_work = 0.3317 r_free = 0.3317 target = 0.066450 restraints weight = 16684.609|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 22)----------------|
| r_work = 0.3317 r_free = 0.3317 target = 0.066453 restraints weight = 15246.678|
|-----------------------------------------------------------------------------|
r_work (final): 0.3289
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8029
moved from start:          0.2685

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.047   8033  Z= 0.122
  Angle     :  0.518   9.889  11390  Z= 0.291
  Chirality :  0.037   0.169   1475
  Planarity :  0.004   0.051   1222
  Dihedral  : 18.496 108.629   2344
  Min Nonbonded Distance : 2.473

Molprobity Statistics.
  All-atom Clashscore : 7.82
  Ramachandran Plot:
    Outliers :  0.20 %
    Allowed  :  3.04 %
    Favored  : 96.75 %
  Rotamer:
    Outliers :  4.35 %
    Allowed  : 26.45 %
    Favored  : 69.20 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 10.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  1.88 (0.28), residues: 986
  helix:  2.20 (0.20), residues: 647
  sheet: -1.58 (0.68), residues: 50
  loop : -0.40 (0.39), residues: 289

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.009   0.001   ARG D 126 
 TYR   0.011   0.001   TYR D  64 
 PHE   0.009   0.001   PHE D  17 
 TRP   0.000   0.000   TRP D 522 
 HIS   0.004   0.001   HIS D 140 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00246 /  0.12 ( 8033)
  covalent geometry    : angle       0.51800 /  0.29 (11390)
  hydrogen bonds       : bond        0.04616 /  3.27 (  572)
  hydrogen bonds       : angle       4.46805 /  3.49 ( 1564)

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

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

  1972 Ramachandran restraints generated.
    986 Oldfield, 0 Emsley, 986 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1972 Ramachandran restraints generated.
    986 Oldfield, 0 Emsley, 986 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  106 residues out of total 890 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 94
  time to evaluate  : 0.262 
Fit side-chains
   revert: symmetry clash
REVERT: A  713 GLU cc_start: 0.8376 (tm-30) cc_final: 0.8050 (tm-30)
REVERT: A  714 GLU cc_start: 0.8645 (mm-30) cc_final: 0.8080 (mm-30)
REVERT: A  717 LYS cc_start: 0.8975 (tptt) cc_final: 0.8642 (tptp)
REVERT: A  721 GLN cc_start: 0.8445 (mt0) cc_final: 0.7996 (mt0)
REVERT: D  101 LYS cc_start: 0.9050 (ttpp) cc_final: 0.8571 (ttpp)
REVERT: D  126 ARG cc_start: 0.8725 (ttp80) cc_final: 0.8447 (ttp80)
REVERT: D  142 LYS cc_start: 0.8333 (ptmt) cc_final: 0.8099 (ptmm)
REVERT: C  105 LYS cc_start: 0.8352 (tppt) cc_final: 0.8075 (tppt)
  outliers start: 12
  outliers final: 10
  residues processed: 102
  average time/residue: 0.1078
  time to fit residues: 14.3976
Evaluate side-chains
  99 residues out of total 890 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 89
  time to evaluate  : 0.263 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue  716 LYS
Chi-restraints excluded: chain D residue   40 LYS
Chi-restraints excluded: chain D residue   70 VAL
Chi-restraints excluded: chain D residue  110 GLN
Chi-restraints excluded: chain D residue  117 VAL
Chi-restraints excluded: chain D residue  151 HIS
Chi-restraints excluded: chain C residue   46 MET
Chi-restraints excluded: chain C residue  109 LEU
Chi-restraints excluded: chain C residue  119 VAL
Chi-restraints excluded: chain C residue  152 THR
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 106
   random chunks:
   chunk 99 optimal weight:   10.0000
   chunk 52 optimal weight:   40.0000
   chunk 75 optimal weight:    8.9990
   chunk 83 optimal weight:    0.9980
   chunk 3 optimal weight:    0.9980
   chunk 37 optimal weight:    0.8980
   chunk 35 optimal weight:   50.0000
   chunk 73 optimal weight:   50.0000
   chunk 48 optimal weight:   20.0000
   chunk 68 optimal weight:    7.9990
   chunk 49 optimal weight:    9.9990
   overall best weight:    3.9784

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
C 151 HIS

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3729 r_free = 0.3729 target = 0.083420 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 50)----------------|
| r_work = 0.3266 r_free = 0.3266 target = 0.064439 restraints weight = 39242.110|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 36)----------------|
| r_work = 0.3213 r_free = 0.3213 target = 0.062643 restraints weight = 35987.199|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 33)----------------|
| r_work = 0.3222 r_free = 0.3222 target = 0.063017 restraints weight = 32014.451|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 32)----------------|
| r_work = 0.3227 r_free = 0.3227 target = 0.063227 restraints weight = 27943.595|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 30)----------------|
| r_work = 0.3232 r_free = 0.3232 target = 0.063372 restraints weight = 26218.746|
|-----------------------------------------------------------------------------|
r_work (final): 0.3202
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8132
moved from start:          0.2765

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.062   8033  Z= 0.245
  Angle     :  0.561  10.312  11390  Z= 0.315
  Chirality :  0.039   0.147   1475
  Planarity :  0.004   0.052   1222
  Dihedral  : 18.399 108.524   2344
  Min Nonbonded Distance : 2.458

Molprobity Statistics.
  All-atom Clashscore : 10.01
  Ramachandran Plot:
    Outliers :  0.20 %
    Allowed  :  3.75 %
    Favored  : 96.04 %
  Rotamer:
    Outliers :  5.07 %
    Allowed  : 25.00 %
    Favored  : 69.93 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 10.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  1.67 (0.28), residues: 986
  helix:  2.04 (0.20), residues: 654
  sheet: -1.58 (0.68), residues: 50
  loop : -0.58 (0.39), residues: 282

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.009   0.001   ARG D 126 
 TYR   0.012   0.001   TYR D  64 
 PHE   0.014   0.002   PHE C  60 
 TRP   0.000   0.000   TRP D 522 
 HIS   0.008   0.001   HIS C 125 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00512 /  0.24 ( 8033)
  covalent geometry    : angle       0.56118 /  0.32 (11390)
  hydrogen bonds       : bond        0.05202 /  3.62 (  572)
  hydrogen bonds       : angle       4.63124 /  3.61 ( 1564)

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

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

  1972 Ramachandran restraints generated.
    986 Oldfield, 0 Emsley, 986 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1972 Ramachandran restraints generated.
    986 Oldfield, 0 Emsley, 986 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  100 residues out of total 890 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 86
  time to evaluate  : 0.272 
Fit side-chains
   revert: symmetry clash
REVERT: A  713 GLU cc_start: 0.8496 (tm-30) cc_final: 0.8088 (tm-30)
REVERT: A  714 GLU cc_start: 0.8784 (mm-30) cc_final: 0.8184 (mm-30)
REVERT: A  717 LYS cc_start: 0.9006 (tptt) cc_final: 0.8589 (tptp)
REVERT: A  721 GLN cc_start: 0.8521 (mt0) cc_final: 0.7993 (mt0)
REVERT: D  101 LYS cc_start: 0.9108 (ttpp) cc_final: 0.8649 (ttpp)
REVERT: D  126 ARG cc_start: 0.8901 (ttp80) cc_final: 0.8648 (ttp80)
REVERT: D  142 LYS cc_start: 0.8462 (ptmt) cc_final: 0.8250 (ptmm)
REVERT: C  108 MET cc_start: 0.7392 (tmm) cc_final: 0.7018 (tmm)
REVERT: C  126 ARG cc_start: 0.8430 (OUTLIER) cc_final: 0.7941 (ptt180)
  outliers start: 14
  outliers final: 11
  residues processed: 96
  average time/residue: 0.1125
  time to fit residues: 14.0657
Evaluate side-chains
  96 residues out of total 890 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 84
  time to evaluate  : 0.267 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue  716 LYS
Chi-restraints excluded: chain D residue   40 LYS
Chi-restraints excluded: chain D residue   70 VAL
Chi-restraints excluded: chain D residue  110 GLN
Chi-restraints excluded: chain D residue  117 VAL
Chi-restraints excluded: chain D residue  151 HIS
Chi-restraints excluded: chain C residue   46 MET
Chi-restraints excluded: chain C residue  109 LEU
Chi-restraints excluded: chain C residue  119 VAL
Chi-restraints excluded: chain C residue  126 ARG
Chi-restraints excluded: chain C residue  152 THR
Chi-restraints excluded: chain C residue  165 VAL
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 106
   random chunks:
   chunk 39 optimal weight:   30.0000
   chunk 19 optimal weight:    4.9990
   chunk 61 optimal weight:    3.9990
   chunk 3 optimal weight:    0.7980
   chunk 24 optimal weight:    8.9990
   chunk 62 optimal weight:    3.9990
   chunk 74 optimal weight:   40.0000
   chunk 21 optimal weight:    2.9990
   chunk 13 optimal weight:    1.9990
   chunk 36 optimal weight:   40.0000
   chunk 30 optimal weight:    0.0980
   overall best weight:    1.9786

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
C 151 HIS

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3752 r_free = 0.3752 target = 0.084472 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 71)----------------|
| r_work = 0.3238 r_free = 0.3238 target = 0.063490 restraints weight = 38661.477|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 35)----------------|
| r_work = 0.3263 r_free = 0.3263 target = 0.064484 restraints weight = 26902.423|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 43)----------------|
| r_work = 0.3281 r_free = 0.3281 target = 0.065169 restraints weight = 21578.899|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 45)----------------|
| r_work = 0.3292 r_free = 0.3292 target = 0.065593 restraints weight = 18786.832|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 21)----------------|
| r_work = 0.3294 r_free = 0.3294 target = 0.065655 restraints weight = 17291.231|
|-----------------------------------------------------------------------------|
r_work (final): 0.3264
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8069
moved from start:          0.2818

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.042   8033  Z= 0.153
  Angle     :  0.519  10.240  11390  Z= 0.291
  Chirality :  0.037   0.159   1475
  Planarity :  0.004   0.050   1222
  Dihedral  : 18.412 108.225   2344
  Min Nonbonded Distance : 2.538

Molprobity Statistics.
  All-atom Clashscore : 8.60
  Ramachandran Plot:
    Outliers :  0.20 %
    Allowed  :  3.14 %
    Favored  : 96.65 %
  Rotamer:
    Outliers :  5.07 %
    Allowed  : 26.09 %
    Favored  : 68.84 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 10.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  1.87 (0.28), residues: 986
  helix:  2.21 (0.20), residues: 652
  sheet: -1.49 (0.68), residues: 50
  loop : -0.53 (0.38), residues: 284

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.008   0.001   ARG C 126 
 TYR   0.012   0.001   TYR D  64 
 PHE   0.012   0.001   PHE D  17 
 TRP   0.000   0.000   TRP D 522 
 HIS   0.004   0.001   HIS D 151 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00324 /  0.15 ( 8033)
  covalent geometry    : angle       0.51904 /  0.29 (11390)
  hydrogen bonds       : bond        0.04717 /  3.31 (  572)
  hydrogen bonds       : angle       4.46647 /  3.49 ( 1564)

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

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

  1972 Ramachandran restraints generated.
    986 Oldfield, 0 Emsley, 986 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1972 Ramachandran restraints generated.
    986 Oldfield, 0 Emsley, 986 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  104 residues out of total 890 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 90
  time to evaluate  : 0.273 
Fit side-chains
   revert: symmetry clash
REVERT: A  713 GLU cc_start: 0.8425 (tm-30) cc_final: 0.8105 (tm-30)
REVERT: A  714 GLU cc_start: 0.8672 (mm-30) cc_final: 0.8088 (mm-30)
REVERT: A  717 LYS cc_start: 0.8998 (tptt) cc_final: 0.8578 (tptp)
REVERT: A  721 GLN cc_start: 0.8484 (mt0) cc_final: 0.7941 (mt0)
REVERT: D  101 LYS cc_start: 0.9084 (ttpp) cc_final: 0.8630 (ttpp)
REVERT: D  126 ARG cc_start: 0.8814 (ttp80) cc_final: 0.8453 (ttt180)
REVERT: D  142 LYS cc_start: 0.8442 (ptmt) cc_final: 0.8190 (ptmm)
REVERT: C  108 MET cc_start: 0.7188 (tmm) cc_final: 0.6836 (tmm)
  outliers start: 14
  outliers final: 10
  residues processed: 99
  average time/residue: 0.1047
  time to fit residues: 13.5817
Evaluate side-chains
  98 residues out of total 890 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 88
  time to evaluate  : 0.228 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue  716 LYS
Chi-restraints excluded: chain D residue   40 LYS
Chi-restraints excluded: chain D residue   70 VAL
Chi-restraints excluded: chain D residue  110 GLN
Chi-restraints excluded: chain D residue  117 VAL
Chi-restraints excluded: chain D residue  151 HIS
Chi-restraints excluded: chain C residue   46 MET
Chi-restraints excluded: chain C residue  119 VAL
Chi-restraints excluded: chain C residue  152 THR
Chi-restraints excluded: chain C residue  165 VAL
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 106
   random chunks:
   chunk 102 optimal weight:   10.0000
   chunk 58 optimal weight:    0.9980
   chunk 2 optimal weight:    0.9990
   chunk 22 optimal weight:    0.0870
   chunk 9 optimal weight:   20.0000
   chunk 39 optimal weight:   30.0000
   chunk 80 optimal weight:   40.0000
   chunk 65 optimal weight:    0.5980
   chunk 72 optimal weight:    0.9990
   chunk 31 optimal weight:   50.0000
   chunk 42 optimal weight:    0.0050
   overall best weight:    0.5374

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
** D  48 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
C 151 HIS

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3781 r_free = 0.3781 target = 0.085802 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.3287 r_free = 0.3287 target = 0.065457 restraints weight = 39180.917|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 26)----------------|
| r_work = 0.3302 r_free = 0.3302 target = 0.066123 restraints weight = 29794.447|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 31)----------------|
| r_work = 0.3306 r_free = 0.3306 target = 0.066178 restraints weight = 25249.258|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 27)----------------|
| r_work = 0.3308 r_free = 0.3308 target = 0.066221 restraints weight = 24614.223|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 31)----------------|
| r_work = 0.3311 r_free = 0.3311 target = 0.066345 restraints weight = 22156.756|
|-----------------------------------------------------------------------------|
r_work (final): 0.3270
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8071
moved from start:          0.3035

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.044   8033  Z= 0.116
  Angle     :  0.543  16.522  11390  Z= 0.293
  Chirality :  0.037   0.161   1475
  Planarity :  0.003   0.043   1222
  Dihedral  : 18.352 106.980   2344
  Min Nonbonded Distance : 2.552

Molprobity Statistics.
  All-atom Clashscore : 6.80
  Ramachandran Plot:
    Outliers :  0.20 %
    Allowed  :  3.14 %
    Favored  : 96.65 %
  Rotamer:
    Outliers :  3.99 %
    Allowed  : 26.09 %
    Favored  : 69.93 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 10.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  2.17 (0.28), residues: 986
  helix:  2.37 (0.21), residues: 651
  sheet: -1.26 (0.69), residues: 50
  loop : -0.23 (0.39), residues: 285

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.001   ARG C 126 
 TYR   0.018   0.001   TYR C 103 
 PHE   0.013   0.001   PHE D 155 
 TRP   0.000   0.000   TRP D 522 
 HIS   0.004   0.001   HIS D 125 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00241 /  0.12 ( 8033)
  covalent geometry    : angle       0.54265 /  0.29 (11390)
  hydrogen bonds       : bond        0.04046 /  2.89 (  572)
  hydrogen bonds       : angle       4.16750 /  3.26 ( 1564)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 1322.35 seconds
wall clock time: 23 minutes 32.31 seconds (1412.31 seconds total)