Starting phenix.real_space_refine
on Wed Aug  5 01:08:07 2026 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/9rw4_54298/08_2026/9rw4_54298.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/9rw4_54298/08_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 {
    real_map_files = "/net/cci-nas-00/data/ceres_data/9rw4_54298/08_2026/9rw4_54298.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/9rw4_54298/08_2026/9rw4_54298.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/9rw4_54298/08_2026/9rw4_54298.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/9rw4_54298/08_2026/9rw4_54298.cif"
  }
  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-2.2rc3-6140/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: 2.12, per 1000 atoms: 0.27
  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: 0.73
  Conformation dependent library (CDL) restraints added in 455.2 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: 1.10
  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: 1.15

  Time building geometry restraints manager: 0.97 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: 10944
        1.65 -     3.30: 406
        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=" O5'   U E  35 "
        pdb=" C5'   U E  35 "
        pdb=" C4'   U E  35 "
      ideal   model   delta    sigma   weight residual
     109.40  112.49   -3.09 8.00e-01 1.56e+00 1.50e+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 -    0.030: 1022
       0.030 -    0.061: 214
       0.061 -    0.091: 95
       0.091 -    0.122: 141
       0.122 -    0.152: 3
  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      2.47    2.32    0.15 2.00e-01 2.50e+01 5.81e-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=" C2'   U E  39 "
            pdb=" C3'   U E  39 "
            pdb=" O2'   U E  39 "
            pdb=" C1'   U E  39 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.62   -2.74    0.12 2.00e-01 2.50e+01 3.86e-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:             1.060
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.010
  Construct map_model_manager:             0.010
  Extract box with map and model:          0.130
  Check model and map are aligned:         0.020
  Set scattering table:                    0.020
  Process input model:                     9.810
  Find NCS groups from input model:        0.160
  Set up NCS constraints:                  0.020
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.000
  Load rotamer database and sin/cos tables:1.240
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   12.480
-------------------------------------------------------------------------------
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= 0.166
  Angle     :  0.629   8.250  11390  Z= 0.497
  Chirality :  0.043   0.152   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        0.00249 /  0.17 ( 8033)
  covalent geometry    : angle       0.62852 /  0.50 (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  : 0.171 
Fit side-chains
   revert: symmetry clash
REVERT: A  713 GLU cc_start: 0.8813 (tm-30) cc_final: 0.8217 (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: 0.7257 (t0)
REVERT: D  106 ASN cc_start: 0.8051 (m-40) cc_final: 0.7727 (m110)
  outliers start: 0
  outliers final: 0
  residues processed: 105
  average time/residue: 0.1103
  time to fit residues: 15.1219
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  : 0.211 
-------------------------------------------------------------------------------
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:   20.0000
   chunk 38 optimal weight:   10.0000
   chunk 61 optimal weight:    0.0070
   overall best weight:    4.2006

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
** A 721 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
D 140 HIS
C  54 GLN
C 125 HIS
C 128 GLN
** C 151 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**

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 = 0.083424 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.3328 r_free = 0.3328 target = 0.066328 restraints weight = 39294.602|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 28)----------------|
| r_work = 0.3264 r_free = 0.3264 target = 0.064197 restraints weight = 37593.876|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 27)----------------|
| r_work = 0.3275 r_free = 0.3275 target = 0.064657 restraints weight = 36601.752|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 23)----------------|
| r_work = 0.3282 r_free = 0.3282 target = 0.064897 restraints weight = 29555.204|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 23)----------------|
| r_work = 0.3281 r_free = 0.3281 target = 0.064858 restraints weight = 25724.312|
|-----------------------------------------------------------------------------|
r_work (final): 0.3241
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8025
moved from start:          0.1652

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.044   8033  Z= 0.260
  Angle     :  0.620   9.198  11390  Z= 0.356
  Chirality :  0.042   0.218   1475
  Planarity :  0.005   0.056   1222
  Dihedral  : 18.566 108.013   2344
  Min Nonbonded Distance : 2.436

Molprobity Statistics.
  All-atom Clashscore : 8.37
  Ramachandran Plot:
    Outliers :  0.20 %
    Allowed  :  3.04 %
    Favored  : 96.75 %
  Rotamer:
    Outliers :  2.90 %
    Allowed  : 18.84 %
    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:  0.61 (0.26), residues: 986
  helix:  1.09 (0.19), residues: 639
  sheet: -1.60 (0.72), residues: 50
  loop : -0.59 (0.38), residues: 297

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.001   ARG C 126 
 TYR   0.014   0.002   TYR C 103 
 PHE   0.016   0.002   PHE C  60 
 TRP   0.000   0.000   TRP D 522 
 HIS   0.010   0.002   HIS D 151 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00513 /  0.26 ( 8033)
  covalent geometry    : angle       0.62000 /  0.36 (11390)
  hydrogen bonds       : bond        0.06902 /  4.82 (  572)
  hydrogen bonds       : angle       5.89520 /  4.56 ( 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
  101 residues out of total 890 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 93
  time to evaluate  : 0.270 
Fit side-chains
REVERT: A  713 GLU cc_start: 0.8628 (tm-30) cc_final: 0.8361 (tm-30)
REVERT: A  714 GLU cc_start: 0.8801 (mm-30) cc_final: 0.8291 (mm-30)
REVERT: B  722 LEU cc_start: 0.9111 (mt) cc_final: 0.8876 (mt)
REVERT: D  101 LYS cc_start: 0.9037 (ttpp) cc_final: 0.8762 (ttpp)
REVERT: D  126 ARG cc_start: 0.8827 (ttp80) cc_final: 0.8349 (ttp80)
REVERT: C   24 LYS cc_start: 0.8671 (tptt) cc_final: 0.8382 (tptm)
  outliers start: 8
  outliers final: 4
  residues processed: 99
  average time/residue: 0.1043
  time to fit residues: 13.5980
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  : 0.222 
-------------------------------------------------------------------------------
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:   10.0000
   chunk 78 optimal weight:   20.0000
   chunk 2 optimal weight:    0.9980
   chunk 84 optimal weight:   40.0000
   chunk 4 optimal weight:    9.9990
   chunk 14 optimal weight:    0.0970
   chunk 75 optimal weight:    0.0770
   chunk 76 optimal weight:   40.0000
   chunk 60 optimal weight:    0.8980
   chunk 56 optimal weight:    0.0570
   chunk 25 optimal weight:    0.0170
   overall best weight:    0.2292

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
D  48 GLN
D  98 GLN
** D 151 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
C 151 HIS

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3762 r_free = 0.3762 target = 0.083964 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 49)----------------|
| r_work = 0.3276 r_free = 0.3276 target = 0.063852 restraints weight = 36738.012|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 34)----------------|
| r_work = 0.3311 r_free = 0.3311 target = 0.065184 restraints weight = 22849.923|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 42)----------------|
| r_work = 0.3332 r_free = 0.3332 target = 0.066020 restraints weight = 17022.898|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 36)----------------|
| r_work = 0.3346 r_free = 0.3346 target = 0.066538 restraints weight = 14276.681|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 19)----------------|
| r_work = 0.3349 r_free = 0.3349 target = 0.066674 restraints weight = 12847.432|
|-----------------------------------------------------------------------------|
r_work (final): 0.3365
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7911
moved from start:          0.1998

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.039   8033  Z= 0.128
  Angle     :  0.503   8.436  11390  Z= 0.289
  Chirality :  0.036   0.156   1475
  Planarity :  0.003   0.046   1222
  Dihedral  : 18.444 106.917   2344
  Min Nonbonded Distance : 2.495

Molprobity Statistics.
  All-atom Clashscore : 5.01
  Ramachandran Plot:
    Outliers :  0.10 %
    Allowed  :  2.74 %
    Favored  : 97.16 %
  Rotamer:
    Outliers :  3.62 %
    Allowed  : 18.48 %
    Favored  : 77.90 %
  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:  1.69 (0.27), residues: 986
  helix:  2.01 (0.20), residues: 646
  sheet: -1.76 (0.67), residues: 56
  loop : -0.26 (0.39), residues: 284

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.001   ARG D  28 
 TYR   0.006   0.001   TYR D  64 
 PHE   0.012   0.001   PHE D  17 
 TRP   0.000   0.000   TRP D 522 
 HIS   0.005   0.002   HIS D 125 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00238 /  0.13 ( 8033)
  covalent geometry    : angle       0.50331 /  0.29 (11390)
  hydrogen bonds       : bond        0.05200 /  3.71 (  572)
  hydrogen bonds       : angle       4.89735 /  3.81 ( 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
  116 residues out of total 890 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 106
  time to evaluate  : 0.207 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  713 GLU cc_start: 0.8493 (tm-30) cc_final: 0.8143 (tm-30)
REVERT: A  714 GLU cc_start: 0.8812 (mm-30) cc_final: 0.8178 (mm-30)
REVERT: A  717 LYS cc_start: 0.9024 (tptt) cc_final: 0.8737 (tptp)
REVERT: A  721 GLN cc_start: 0.8524 (mt0) cc_final: 0.8115 (mt0)
REVERT: D  102 ASP cc_start: 0.6204 (t0) cc_final: 0.5952 (t0)
  outliers start: 10
  outliers final: 6
  residues processed: 114
  average time/residue: 0.1032
  time to fit residues: 15.5892
Evaluate side-chains
  99 residues out of total 890 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 93
  time to evaluate  : 0.248 
-------------------------------------------------------------------------------
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  110 GLN
Chi-restraints excluded: chain D residue  117 VAL
Chi-restraints excluded: chain C residue   46 MET
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:    0.4980
   chunk 21 optimal weight:    3.9990
   chunk 62 optimal weight:    2.9990
   chunk 69 optimal weight:    0.0570
   chunk 45 optimal weight:   50.0000
   chunk 9 optimal weight:   10.0000
   chunk 41 optimal weight:   50.0000
   chunk 97 optimal weight:    5.9990
   chunk 28 optimal weight:    1.9990
   chunk 4 optimal weight:    9.9990
   chunk 78 optimal weight:   50.0000
   overall best weight:    1.9104

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
A 729 GLN
D  98 GLN
** D 151 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3741 r_free = 0.3741 target = 0.084365 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 64)----------------|
| r_work = 0.3231 r_free = 0.3231 target = 0.063641 restraints weight = 37934.030|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 40)----------------|
| r_work = 0.3257 r_free = 0.3257 target = 0.064669 restraints weight = 25712.296|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 42)----------------|
| r_work = 0.3275 r_free = 0.3275 target = 0.065381 restraints weight = 20339.065|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 25)----------------|
| r_work = 0.3284 r_free = 0.3284 target = 0.065708 restraints weight = 17562.774|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 25)----------------|
| r_work = 0.3286 r_free = 0.3286 target = 0.065766 restraints weight = 16234.189|
|-----------------------------------------------------------------------------|
r_work (final): 0.3237
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8030
moved from start:          0.2215

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.043   8033  Z= 0.150
  Angle     :  0.492   9.321  11390  Z= 0.277
  Chirality :  0.037   0.179   1475
  Planarity :  0.004   0.061   1222
  Dihedral  : 18.309 106.981   2344
  Min Nonbonded Distance : 2.502

Molprobity Statistics.
  All-atom Clashscore : 5.87
  Ramachandran Plot:
    Outliers :  0.10 %
    Allowed  :  2.84 %
    Favored  : 97.06 %
  Rotamer:
    Outliers :  5.07 %
    Allowed  : 19.20 %
    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:  1.77 (0.27), residues: 986
  helix:  2.09 (0.20), residues: 652
  sheet: -1.43 (0.69), residues: 50
  loop : -0.48 (0.37), residues: 284

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.008   0.001   ARG C  47 
 TYR   0.008   0.001   TYR D  64 
 PHE   0.009   0.001   PHE D  17 
 TRP   0.000   0.000   TRP D 522 
 HIS   0.016   0.002   HIS D 151 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00305 /  0.15 ( 8033)
  covalent geometry    : angle       0.49196 /  0.28 (11390)
  hydrogen bonds       : bond        0.05068 /  3.56 (  572)
  hydrogen bonds       : angle       4.69347 /  3.64 ( 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
  108 residues out of total 890 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 94
  time to evaluate  : 0.331 
Fit side-chains
   revert: symmetry clash
REVERT: A  713 GLU cc_start: 0.8599 (tm-30) cc_final: 0.8195 (tm-30)
REVERT: A  714 GLU cc_start: 0.8895 (mm-30) cc_final: 0.8184 (mm-30)
REVERT: A  717 LYS cc_start: 0.9073 (tptt) cc_final: 0.8670 (tptp)
REVERT: A  721 GLN cc_start: 0.8615 (mt0) cc_final: 0.8112 (mt0)
REVERT: D   22 LEU cc_start: 0.9558 (OUTLIER) cc_final: 0.9332 (mp)
  outliers start: 14
  outliers final: 10
  residues processed: 105
  average time/residue: 0.0936
  time to fit residues: 13.1605
Evaluate side-chains
  101 residues out of total 890 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 90
  time to evaluate  : 0.250 
-------------------------------------------------------------------------------
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   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   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=3.50
-------------------------------------------------------------------------------
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:   10.0000
   chunk 10 optimal weight:    0.8980
   chunk 105 optimal weight:   20.0000
   chunk 40 optimal weight:   40.0000
   chunk 26 optimal weight:   50.0000
   chunk 18 optimal weight:    1.9990
   chunk 57 optimal weight:    4.9990
   chunk 64 optimal weight:    3.9990
   chunk 67 optimal weight:    0.0970
   overall best weight:    2.3984

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
** D 151 HIS ** 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 = 0.3734 r_free = 0.3734 target = 0.084090 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 60)----------------|
| r_work = 0.3223 r_free = 0.3223 target = 0.063300 restraints weight = 37852.068|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 47)----------------|
| r_work = 0.3252 r_free = 0.3252 target = 0.064375 restraints weight = 25760.838|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 27)----------------|
| r_work = 0.3268 r_free = 0.3268 target = 0.064967 restraints weight = 20223.806|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 35)----------------|
| r_work = 0.3279 r_free = 0.3279 target = 0.065402 restraints weight = 17627.916|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 24)----------------|
| r_work = 0.3280 r_free = 0.3280 target = 0.065444 restraints weight = 16208.031|
|-----------------------------------------------------------------------------|
r_work (final): 0.3233
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8039
moved from start:          0.2358

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.040   8033  Z= 0.162
  Angle     :  0.504   9.838  11390  Z= 0.281
  Chirality :  0.038   0.238   1475
  Planarity :  0.003   0.047   1222
  Dihedral  : 18.298 106.804   2344
  Min Nonbonded Distance : 2.497

Molprobity Statistics.
  All-atom Clashscore : 6.88
  Ramachandran Plot:
    Outliers :  0.20 %
    Allowed  :  2.94 %
    Favored  : 96.86 %
  Rotamer:
    Outliers :  5.43 %
    Allowed  : 19.93 %
    Favored  : 74.64 %
  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:  1.92 (0.27), residues: 986
  helix:  2.21 (0.20), residues: 646
  sheet: -1.39 (0.70), residues: 50
  loop : -0.35 (0.37), residues: 290

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.008   0.001   ARG C  47 
 TYR   0.010   0.001   TYR D  64 
 PHE   0.011   0.001   PHE D  17 
 TRP   0.000   0.000   TRP D 522 
 HIS   0.007   0.001   HIS D 151 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00338 /  0.16 ( 8033)
  covalent geometry    : angle       0.50425 /  0.28 (11390)
  hydrogen bonds       : bond        0.04907 /  3.45 (  572)
  hydrogen bonds       : angle       4.58012 /  3.57 ( 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
  109 residues out of total 890 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 94
  time to evaluate  : 0.253 
Fit side-chains
   revert: symmetry clash
REVERT: A  713 GLU cc_start: 0.8634 (tm-30) cc_final: 0.8165 (tm-30)
REVERT: A  714 GLU cc_start: 0.8886 (mm-30) cc_final: 0.8171 (mm-30)
REVERT: A  717 LYS cc_start: 0.9077 (tptt) cc_final: 0.8361 (tptp)
REVERT: A  721 GLN cc_start: 0.8601 (mt0) cc_final: 0.7852 (mt0)
REVERT: B  714 GLU cc_start: 0.7807 (mm-30) cc_final: 0.6735 (mm-30)
REVERT: C  107 LYS cc_start: 0.8690 (mmtt) cc_final: 0.8390 (mmmm)
  outliers start: 15
  outliers final: 12
  residues processed: 104
  average time/residue: 0.0875
  time to fit residues: 11.9883
Evaluate side-chains
  102 residues out of total 890 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 90
  time to evaluate  : 0.252 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  725 LEU
Chi-restraints excluded: chain B residue  716 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 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=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 106
   random chunks:
   chunk 45 optimal weight:   50.0000
   chunk 9 optimal weight:    0.9990
   chunk 1 optimal weight:    9.9990
   chunk 19 optimal weight:    6.9990
   chunk 20 optimal weight:    0.8980
   chunk 90 optimal weight:   20.0000
   chunk 59 optimal weight:    1.9990
   chunk 91 optimal weight:    9.9990
   chunk 71 optimal weight:   50.0000
   chunk 47 optimal weight:   20.0000
   chunk 35 optimal weight:   20.0000
   overall best weight:    4.1788

-------------------------------------------------------------------------------
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 = 0.3730 r_free = 0.3730 target = 0.083470 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 66)----------------|
| r_work = 0.3197 r_free = 0.3197 target = 0.062014 restraints weight = 38952.607|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 34)----------------|
| r_work = 0.3224 r_free = 0.3224 target = 0.063010 restraints weight = 26545.383|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 54)----------------|
| r_work = 0.3245 r_free = 0.3245 target = 0.063808 restraints weight = 20939.814|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 28)----------------|
| r_work = 0.3253 r_free = 0.3253 target = 0.064142 restraints weight = 18074.835|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 31)----------------|
| r_work = 0.3260 r_free = 0.3260 target = 0.064408 restraints weight = 16737.227|
|-----------------------------------------------------------------------------|
r_work (final): 0.3232
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8103
moved from start:          0.2510

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.052   8033  Z= 0.255
  Angle     :  0.589  10.175  11390  Z= 0.324
  Chirality :  0.041   0.184   1475
  Planarity :  0.004   0.053   1222
  Dihedral  : 18.334 108.027   2344
  Min Nonbonded Distance : 2.478

Molprobity Statistics.
  All-atom Clashscore : 9.39
  Ramachandran Plot:
    Outliers :  0.20 %
    Allowed  :  4.16 %
    Favored  : 95.64 %
  Rotamer:
    Outliers :  6.88 %
    Allowed  : 19.93 %
    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:  1.68 (0.27), residues: 986
  helix:  2.00 (0.20), residues: 646
  sheet: -1.47 (0.69), residues: 50
  loop : -0.39 (0.38), residues: 290

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.008   0.001   ARG C  47 
 TYR   0.010   0.002   TYR D 111 
 PHE   0.015   0.002   PHE C  60 
 TRP   0.000   0.000   TRP D 522 
 HIS   0.009   0.002   HIS C 125 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00532 /  0.25 ( 8033)
  covalent geometry    : angle       0.58876 /  0.32 (11390)
  hydrogen bonds       : bond        0.05617 /  3.86 (  572)
  hydrogen bonds       : angle       4.75168 /  3.70 ( 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
  108 residues out of total 890 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 89
  time to evaluate  : 0.309 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  713 GLU cc_start: 0.8485 (tm-30) cc_final: 0.8080 (tm-30)
REVERT: A  714 GLU cc_start: 0.8775 (mm-30) cc_final: 0.8079 (mm-30)
REVERT: B  714 GLU cc_start: 0.7502 (mm-30) cc_final: 0.6694 (mm-30)
REVERT: C  126 ARG cc_start: 0.8533 (OUTLIER) cc_final: 0.7960 (ptt180)
  outliers start: 19
  outliers final: 11
  residues processed: 100
  average time/residue: 0.1126
  time to fit residues: 14.6481
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  : 0.352 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  725 LEU
Chi-restraints excluded: chain B residue  716 LYS
Chi-restraints excluded: chain D residue   29 THR
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  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=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 106
   random chunks:
   chunk 79 optimal weight:    8.9990
   chunk 85 optimal weight:    8.9990
   chunk 86 optimal weight:   30.0000
   chunk 48 optimal weight:   20.0000
   chunk 93 optimal weight:   20.0000
   chunk 98 optimal weight:   10.0000
   chunk 84 optimal weight:    8.9990
   chunk 9 optimal weight:   10.0000
   chunk 51 optimal weight:   20.0000
   chunk 37 optimal weight:   20.0000
   chunk 72 optimal weight:   30.0000
   overall best weight:    9.3994

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
** D 128 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** C 151 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3669 r_free = 0.3669 target = 0.080679 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.3223 r_free = 0.3223 target = 0.062411 restraints weight = 39353.603|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 34)----------------|
| r_work = 0.3139 r_free = 0.3139 target = 0.059880 restraints weight = 39000.262|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 27)----------------|
| r_work = 0.3162 r_free = 0.3162 target = 0.060707 restraints weight = 32966.993|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 29)----------------|
| r_work = 0.3172 r_free = 0.3172 target = 0.061070 restraints weight = 25790.758|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 28)----------------|
| r_work = 0.3169 r_free = 0.3169 target = 0.060954 restraints weight = 26497.271|
|-----------------------------------------------------------------------------|
r_work (final): 0.3150
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8170
moved from start:          0.2781

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.011   0.103   8033  Z= 0.524
  Angle     :  0.877  14.391  11390  Z= 0.465
  Chirality :  0.051   0.226   1475
  Planarity :  0.005   0.064   1222
  Dihedral  : 18.642 110.987   2344
  Min Nonbonded Distance : 2.443

Molprobity Statistics.
  All-atom Clashscore : 13.69
  Ramachandran Plot:
    Outliers :  0.20 %
    Allowed  :  4.87 %
    Favored  : 94.93 %
  Rotamer:
    Outliers :  7.61 %
    Allowed  : 21.38 %
    Favored  : 71.01 %
  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:  0.36 (0.26), residues: 986
  helix:  0.93 (0.19), residues: 645
  sheet: -1.75 (0.68), residues: 50
  loop : -0.80 (0.39), residues: 291

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.002   ARG C 126 
 TYR   0.016   0.003   TYR D 111 
 PHE   0.024   0.004   PHE D  37 
 TRP   0.000   0.000   TRP D 522 
 HIS   0.013   0.002   HIS C 125 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.01081 /  0.52 ( 8033)
  covalent geometry    : angle       0.87707 /  0.47 (11390)
  hydrogen bonds       : bond        0.07613 /  5.19 (  572)
  hydrogen bonds       : angle       5.55312 /  4.29 ( 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
  98 residues out of total 890 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 77
  time to evaluate  : 0.259 
Fit side-chains
REVERT: A  713 GLU cc_start: 0.8479 (tm-30) cc_final: 0.8135 (tm-30)
REVERT: A  714 GLU cc_start: 0.8705 (mm-30) cc_final: 0.8072 (mm-30)
REVERT: B  714 GLU cc_start: 0.7446 (mm-30) cc_final: 0.6831 (mm-30)
REVERT: B  717 LYS cc_start: 0.8570 (OUTLIER) cc_final: 0.7874 (ptpp)
REVERT: D    7 GLU cc_start: 0.7505 (pm20) cc_final: 0.7221 (pm20)
REVERT: D  142 LYS cc_start: 0.8580 (ptmt) cc_final: 0.8315 (ptmm)
REVERT: C  126 ARG cc_start: 0.8668 (OUTLIER) cc_final: 0.8169 (ptt180)
  outliers start: 21
  outliers final: 17
  residues processed: 93
  average time/residue: 0.1038
  time to fit residues: 12.6899
Evaluate side-chains
  94 residues out of total 890 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 75
  time to evaluate  : 0.257 
-------------------------------------------------------------------------------
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  717 LYS
Chi-restraints excluded: chain D residue   13 THR
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  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   41 GLU
Chi-restraints excluded: chain C residue   46 MET
Chi-restraints excluded: chain C residue   70 VAL
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:    0.9990
   chunk 91 optimal weight:    5.9990
   chunk 39 optimal weight:   10.0000
   chunk 103 optimal weight:   20.0000
   chunk 92 optimal weight:   10.0000
   chunk 61 optimal weight:    2.9990
   chunk 50 optimal weight:   30.0000
   chunk 63 optimal weight:    0.9990
   chunk 5 optimal weight:   30.0000
   chunk 55 optimal weight:    0.9990
   chunk 60 optimal weight:    0.4980
   overall best weight:    1.2988

-------------------------------------------------------------------------------
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 = 0.3742 r_free = 0.3742 target = 0.084000 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 65)----------------|
| r_work = 0.3222 r_free = 0.3222 target = 0.062814 restraints weight = 38801.982|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 33)----------------|
| r_work = 0.3250 r_free = 0.3250 target = 0.063856 restraints weight = 25853.280|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 41)----------------|
| r_work = 0.3269 r_free = 0.3269 target = 0.064601 restraints weight = 20306.324|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 40)----------------|
| r_work = 0.3281 r_free = 0.3281 target = 0.065031 restraints weight = 17599.954|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 39)----------------|
| r_work = 0.3287 r_free = 0.3287 target = 0.065272 restraints weight = 16156.234|
|-----------------------------------------------------------------------------|
r_work (final): 0.3259
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8070
moved from start:          0.2730

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= 0.147
  Angle     :  0.548  10.253  11390  Z= 0.309
  Chirality :  0.038   0.183   1475
  Planarity :  0.004   0.055   1222
  Dihedral  : 18.513 109.939   2344
  Min Nonbonded Distance : 2.461

Molprobity Statistics.
  All-atom Clashscore : 7.82
  Ramachandran Plot:
    Outliers :  0.20 %
    Allowed  :  3.55 %
    Favored  : 96.25 %
  Rotamer:
    Outliers :  4.71 %
    Allowed  : 24.64 %
    Favored  : 70.65 %
  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:  1.43 (0.27), residues: 986
  helix:  1.84 (0.20), residues: 653
  sheet: -1.77 (0.67), residues: 50
  loop : -0.59 (0.39), residues: 283

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.008   0.001   ARG C 126 
 TYR   0.014   0.001   TYR C  80 
 PHE   0.011   0.001   PHE D  17 
 TRP   0.000   0.000   TRP D 522 
 HIS   0.003   0.001   HIS C 151 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00313 /  0.15 ( 8033)
  covalent geometry    : angle       0.54813 /  0.31 (11390)
  hydrogen bonds       : bond        0.05231 /  3.66 (  572)
  hydrogen bonds       : angle       4.66019 /  3.63 ( 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
  105 residues out of total 890 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 92
  time to evaluate  : 0.254 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  713 GLU cc_start: 0.8389 (tm-30) cc_final: 0.8073 (tm-30)
REVERT: A  714 GLU cc_start: 0.8726 (mm-30) cc_final: 0.8211 (mm-30)
REVERT: D  142 LYS cc_start: 0.8347 (ptmt) cc_final: 0.7805 (ptmm)
  outliers start: 13
  outliers final: 10
  residues processed: 101
  average time/residue: 0.1008
  time to fit residues: 13.5094
Evaluate side-chains
  93 residues out of total 890 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 83
  time to evaluate  : 0.258 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
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 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=1.50
-------------------------------------------------------------------------------
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:    9.9990
   chunk 83 optimal weight:    0.8980
   chunk 3 optimal weight:    1.9990
   chunk 37 optimal weight:   20.0000
   chunk 35 optimal weight:   40.0000
   chunk 73 optimal weight:   50.0000
   chunk 48 optimal weight:   20.0000
   chunk 68 optimal weight:    1.9990
   chunk 49 optimal weight:    8.9990
   overall best weight:    4.7788

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
A 729 GLN
C 151 HIS

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3711 r_free = 0.3711 target = 0.082523 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.3243 r_free = 0.3243 target = 0.063601 restraints weight = 39190.875|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 29)----------------|
| r_work = 0.3192 r_free = 0.3192 target = 0.061673 restraints weight = 32292.362|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 30)----------------|
| r_work = 0.3203 r_free = 0.3203 target = 0.062254 restraints weight = 31547.641|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 29)----------------|
| r_work = 0.3212 r_free = 0.3212 target = 0.062622 restraints weight = 25776.301|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 25)----------------|
| r_work = 0.3213 r_free = 0.3213 target = 0.062614 restraints weight = 23252.466|
|-----------------------------------------------------------------------------|
r_work (final): 0.3189
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8133
moved from start:          0.2817

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.006   0.050   8033  Z= 0.285
  Angle     :  0.636  10.506  11390  Z= 0.350
  Chirality :  0.042   0.195   1475
  Planarity :  0.004   0.055   1222
  Dihedral  : 18.448 109.514   2344
  Min Nonbonded Distance : 2.442

Molprobity Statistics.
  All-atom Clashscore : 10.72
  Ramachandran Plot:
    Outliers :  0.20 %
    Allowed  :  4.56 %
    Favored  : 95.23 %
  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:  1.29 (0.27), residues: 986
  helix:  1.73 (0.20), residues: 654
  sheet: -1.83 (0.67), residues: 50
  loop : -0.66 (0.39), residues: 282

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.009   0.001   ARG C 126 
 TYR   0.015   0.002   TYR D  96 
 PHE   0.016   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        0.00593 /  0.28 ( 8033)
  covalent geometry    : angle       0.63589 /  0.35 (11390)
  hydrogen bonds       : bond        0.05900 /  4.06 (  572)
  hydrogen bonds       : angle       4.87248 /  3.79 ( 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
  93 residues out of total 890 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 82
  time to evaluate  : 0.257 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  713 GLU cc_start: 0.8459 (tm-30) cc_final: 0.8151 (tm-30)
REVERT: A  714 GLU cc_start: 0.8820 (mm-30) cc_final: 0.8218 (mm-30)
REVERT: D  142 LYS cc_start: 0.8305 (ptmt) cc_final: 0.8093 (ptmm)
REVERT: C  126 ARG cc_start: 0.8576 (OUTLIER) cc_final: 0.8105 (ptt180)
  outliers start: 11
  outliers final: 9
  residues processed: 90
  average time/residue: 0.1055
  time to fit residues: 12.4596
Evaluate side-chains
  88 residues out of total 890 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 78
  time to evaluate  : 0.253 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain D residue   22 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 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  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:    0.9980
   chunk 61 optimal weight:    1.9990
   chunk 3 optimal weight:    0.7980
   chunk 24 optimal weight:    3.9990
   chunk 62 optimal weight:    2.9990
   chunk 74 optimal weight:   30.0000
   chunk 21 optimal weight:    0.8980
   chunk 13 optimal weight:    0.7980
   chunk 36 optimal weight:   30.0000
   chunk 30 optimal weight:    9.9990
   overall best weight:    1.0982

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
A 729 GLN
C 151 HIS

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3750 r_free = 0.3750 target = 0.084299 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 54)----------------|
| r_work = 0.3233 r_free = 0.3233 target = 0.063204 restraints weight = 38512.093|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 41)----------------|
| r_work = 0.3262 r_free = 0.3262 target = 0.064309 restraints weight = 25803.464|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 45)----------------|
| r_work = 0.3281 r_free = 0.3281 target = 0.065045 restraints weight = 20270.050|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 33)----------------|
| r_work = 0.3293 r_free = 0.3293 target = 0.065493 restraints weight = 17464.002|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 28)----------------|
| r_work = 0.3297 r_free = 0.3297 target = 0.065665 restraints weight = 15984.171|
|-----------------------------------------------------------------------------|
r_work (final): 0.3270
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8055
moved from start:          0.2901

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.034   8033  Z= 0.135
  Angle     :  0.535   9.562  11390  Z= 0.303
  Chirality :  0.037   0.175   1475
  Planarity :  0.004   0.049   1222
  Dihedral  : 18.408 108.324   2344
  Min Nonbonded Distance : 2.444

Molprobity Statistics.
  All-atom Clashscore : 8.45
  Ramachandran Plot:
    Outliers :  0.20 %
    Allowed  :  3.25 %
    Favored  : 96.55 %
  Rotamer:
    Outliers :  4.71 %
    Allowed  : 25.36 %
    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:  1.74 (0.28), residues: 986
  helix:  2.08 (0.20), residues: 654
  sheet: -1.72 (0.68), residues: 50
  loop : -0.46 (0.39), residues: 282

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.009   0.001   ARG C 126 
 TYR   0.010   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 151 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00283 /  0.14 ( 8033)
  covalent geometry    : angle       0.53531 /  0.30 (11390)
  hydrogen bonds       : bond        0.04917 /  3.45 (  572)
  hydrogen bonds       : angle       4.47042 /  3.50 ( 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
  99 residues out of total 890 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 86
  time to evaluate  : 0.265 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  713 GLU cc_start: 0.8351 (tm-30) cc_final: 0.8065 (tm-30)
REVERT: A  714 GLU cc_start: 0.8746 (mm-30) cc_final: 0.8157 (mm-30)
  outliers start: 13
  outliers final: 11
  residues processed: 93
  average time/residue: 0.0954
  time to fit residues: 11.8074
Evaluate side-chains
  94 residues out of total 890 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 83
  time to evaluate  : 0.189 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  725 LEU
Chi-restraints excluded: chain B residue  722 LEU
Chi-restraints excluded: chain D residue   22 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 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:    0.9990
   chunk 2 optimal weight:    0.8980
   chunk 22 optimal weight:    2.9990
   chunk 9 optimal weight:   20.0000
   chunk 39 optimal weight:   30.0000
   chunk 80 optimal weight:   40.0000
   chunk 65 optimal weight:    0.8980
   chunk 72 optimal weight:   30.0000
   chunk 31 optimal weight:   50.0000
   chunk 42 optimal weight:    3.9990
   overall best weight:    1.9586

-------------------------------------------------------------------------------
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 = 0.3749 r_free = 0.3749 target = 0.084209 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 63)----------------|
| r_work = 0.3228 r_free = 0.3228 target = 0.063157 restraints weight = 38934.675|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 48)----------------|
| r_work = 0.3257 r_free = 0.3257 target = 0.064265 restraints weight = 25945.557|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 37)----------------|
| r_work = 0.3275 r_free = 0.3275 target = 0.064928 restraints weight = 20399.757|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 29)----------------|
| r_work = 0.3282 r_free = 0.3282 target = 0.065226 restraints weight = 17668.419|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 42)----------------|
| r_work = 0.3293 r_free = 0.3293 target = 0.065639 restraints weight = 16380.318|
|-----------------------------------------------------------------------------|
r_work (final): 0.3266
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8067
moved from start:          0.2965

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.038   8033  Z= 0.156
  Angle     :  0.532  10.140  11390  Z= 0.299
  Chirality :  0.038   0.173   1475
  Planarity :  0.003   0.048   1222
  Dihedral  : 18.325 107.529   2344
  Min Nonbonded Distance : 2.439

Molprobity Statistics.
  All-atom Clashscore : 7.90
  Ramachandran Plot:
    Outliers :  0.20 %
    Allowed  :  3.65 %
    Favored  : 96.15 %
  Rotamer:
    Outliers :  4.71 %
    Allowed  : 25.72 %
    Favored  : 69.57 %
  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:  1.83 (0.28), residues: 986
  helix:  2.12 (0.20), residues: 656
  sheet: -1.64 (0.68), residues: 50
  loop : -0.37 (0.40), residues: 280

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.010   0.001   ARG C 126 
 TYR   0.012   0.001   TYR D  64 
 PHE   0.014   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        0.00329 /  0.16 ( 8033)
  covalent geometry    : angle       0.53174 /  0.30 (11390)
  hydrogen bonds       : bond        0.04915 /  3.42 (  572)
  hydrogen bonds       : angle       4.40544 /  3.44 ( 1564)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 1346.43 seconds
wall clock time: 23 minutes 54.95 seconds (1434.95 seconds total)