Starting phenix.real_space_refine
on Sun Apr  5 03:41:11 2026 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/9rw7_54302/04_2026/9rw7_54302.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/9rw7_54302/04_2026/9rw7_54302.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.4
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    model {
      file = "/net/cci-nas-00/data/ceres_data/9rw7_54302/04_2026/9rw7_54302.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/9rw7_54302/04_2026/9rw7_54302.cif"
    real_map_files = "/net/cci-nas-00/data/ceres_data/9rw7_54302/04_2026/9rw7_54302.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/9rw7_54302/04_2026/9rw7_54302.map"
  }
  resolution = 3.4
  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=   0.054
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      98      5.49       5
     S      38      5.16       5
     C    4561      2.51       5
     N    1342      2.21       5
     O    1777      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 30 residue(s): 0.01s

  Monomer Library directory:
    "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.1rc1-6017/lib/python3.9/site-packages/chem_data/mon_lib"
  Total number of atoms: 7816
  Number of models: 1
  Model: ""
    Number of chains: 6
    Chain: "A"
      Number of atoms: 423
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 53, 423
          Classifications: {'peptide': 53}
          Incomplete info: {'truncation_to_alanine': 4}
          Link IDs: {'TRANS': 52}
          Unresolved non-hydrogen bonds: 19
          Unresolved non-hydrogen angles: 23
          Unresolved non-hydrogen dihedrals: 15
          Planarities with less than four sites: {'GLU:plan': 1, 'ASP:plan': 1, 'ARG:plan': 2}
          Unresolved non-hydrogen planarities: 17
    Chain: "B"
      Number of atoms: 423
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 53, 423
          Classifications: {'peptide': 53}
          Incomplete info: {'truncation_to_alanine': 4}
          Link IDs: {'TRANS': 52}
          Unresolved non-hydrogen bonds: 19
          Unresolved non-hydrogen angles: 23
          Unresolved non-hydrogen dihedrals: 15
          Planarities with less than four sites: {'GLU:plan': 1, 'ASP:plan': 1, 'ARG:plan': 2}
          Unresolved non-hydrogen planarities: 17
    Chain: "C"
      Number of atoms: 1249
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 154, 1249
          Classifications: {'peptide': 154}
          Link IDs: {'PTRANS': 4, 'TRANS': 149}
          Chain breaks: 1
    Chain: "D"
      Number of atoms: 3623
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 460, 3623
          Classifications: {'peptide': 460}
          Incomplete info: {'truncation_to_alanine': 21}
          Link IDs: {'PCIS': 1, 'PTRANS': 10, 'TRANS': 448}
          Chain breaks: 3
          Unresolved non-hydrogen bonds: 90
          Unresolved non-hydrogen angles: 108
          Unresolved non-hydrogen dihedrals: 77
          Planarities with less than four sites: {'ASP:plan': 4, 'PHE:plan': 1, 'ASN:plan1': 1, 'GLU:plan': 5, 'ARG:plan': 2, 'GLN:plan1': 1, 'TYR:plan': 1}
          Unresolved non-hydrogen planarities: 62
    Chain: "E"
      Number of atoms: 1049
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 50, 1049
          Classifications: {'RNA': 50}
          Modifications used: {'5*END': 1, 'rna2p_pur': 1, 'rna2p_pyr': 7, 'rna3p_pur': 21, 'rna3p_pyr': 21}
          Link IDs: {'rna2p': 8, 'rna3p': 41}
          Chain breaks: 1
    Chain: "F"
      Number of atoms: 1049
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 50, 1049
          Classifications: {'RNA': 50}
          Modifications used: {'5*END': 1, 'rna2p_pur': 1, 'rna2p_pyr': 7, 'rna3p_pur': 21, 'rna3p_pyr': 21}
          Link IDs: {'rna2p': 8, 'rna3p': 41}
          Chain breaks: 1
  Time building chain proxies: 1.93, per 1000 atoms: 0.25
  Number of scatterers: 7816
  At special positions: 0
  Unit cell: (90.015, 97.428, 150.378, 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      38     16.00
     P      98     15.00
     O    1777      8.00
     N    1342      7.00
     C    4561      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: 0.69
  Conformation dependent library (CDL) restraints added in 228.0 milliseconds
  

  1408 Ramachandran restraints generated.
    704 Oldfield, 0 Emsley, 704 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  1372

  Finding SS restraints...
    Secondary structure from input PDB file:
      41 helices and 5 sheets defined
      69.9% alpha, 7.5% beta
      42 base pairs and 46 stacking pairs defined.
    Time for finding SS restraints: 1.11
  Creating SS restraints...
    Processing helix  chain 'A' and resid 695 through 747
      removed outlier: 3.605A  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 'C' and resid 6 through 25
      removed outlier: 3.627A  pdb=" N   LYS C  24 " --> pdb=" O   ARG C  20 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 30 through 35
    Processing helix  chain 'C' and resid 36 through 39
    Processing helix  chain 'C' and resid 43 through 51
      removed outlier: 3.596A  pdb=" N   GLY C  51 " --> pdb=" O   ARG C  47 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 53 through 62
    Processing helix  chain 'C' and resid 95 through 110
    Processing helix  chain 'C' and resid 119 through 125
      removed outlier: 3.679A  pdb=" N   GLY C 124 " --> pdb=" O   ARG C 120 " (cutoff:3.500A)
      removed outlier: 3.854A  pdb=" N   HIS C 125 " --> pdb=" O   SER C 121 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 126 through 128
      No H-bonds generated for 'chain 'C' and resid 126 through 128'
    Processing helix  chain 'C' and resid 130 through 137
    Processing helix  chain 'C' and resid 140 through 150
    Processing helix  chain 'D' and resid 5 through 25
      removed outlier: 3.831A  pdb=" N   LYS D  24 " --> pdb=" O   ARG D  20 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 30 through 35
    Processing helix  chain 'D' and resid 36 through 39
    Processing helix  chain 'D' and resid 43 through 50
    Processing helix  chain 'D' and resid 53 through 62
    Processing helix  chain 'D' and resid 95 through 111
      removed outlier: 3.720A  pdb=" N   GLU D  99 " --> pdb=" O   ASP D  95 " (cutoff:3.500A)
      removed outlier: 3.586A  pdb=" N   TYR D 111 " --> pdb=" O   LYS D 107 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 119 through 123
    Processing helix  chain 'D' and resid 124 through 128
    Processing helix  chain 'D' and resid 130 through 137
      removed outlier: 3.505A  pdb=" N   ILE D 136 " --> pdb=" O   GLN D 132 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 140 through 152
      removed outlier: 3.787A  pdb=" N   HIS D 151 " --> pdb=" O   PHE D 147 " (cutoff:3.500A)
      removed outlier: 3.502A  pdb=" N   THR D 152 " --> pdb=" O   LEU D 148 " (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 594 through 600
      removed outlier: 4.136A  pdb=" N   THR D 598 " --> pdb=" O   PRO D 594 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 601 through 608
    Processing helix  chain 'D' and resid 617 through 630
      removed outlier: 4.380A  pdb=" N   ASP D 621 " --> pdb=" O   ASP D 617 " (cutoff:3.500A)
      removed outlier: 3.712A  pdb=" N   LEU D 625 " --> pdb=" O   ASP D 621 " (cutoff:3.500A)
      removed outlier: 3.524A  pdb=" N   TYR D 626 " --> pdb=" O   ALA D 622 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 639 through 652
    Processing helix  chain 'D' and resid 662 through 670
    Processing helix  chain 'D' and resid 675 through 680
      removed outlier: 3.881A  pdb=" N   LYS D 678 " --> pdb=" O   ASN D 675 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 681 through 688
    Processing helix  chain 'D' and resid 689 through 694
      removed outlier: 4.545A  pdb=" N   TRP D 692 " --> pdb=" O   GLN D 689 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 698 through 714
      removed outlier: 4.159A  pdb=" N   ASP D 708 " --> pdb=" O   TYR D 704 " (cutoff:3.500A)
      removed outlier: 4.819A  pdb=" N   VAL D 709 " --> pdb=" O   ALA D 705 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 717 through 725
    Processing helix  chain 'D' and resid 726 through 728
      No H-bonds generated for 'chain 'D' and resid 726 through 728'
    Processing helix  chain 'D' and resid 729 through 743
    Processing helix  chain 'D' and resid 746 through 773
      removed outlier: 3.524A  pdb=" N   SER D 764 " --> pdb=" O   SER D 760 " (cutoff:3.500A)
      removed outlier: 4.183A  pdb=" N   THR D 773 " --> pdb=" O   LYS D 769 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 780 through 787
      removed outlier: 3.510A  pdb=" N   ARG D 785 " --> pdb=" O   ASN D 781 " (cutoff:3.500A)
      removed outlier: 3.713A  pdb=" N   LEU D 787 " --> pdb=" O   GLU D 783 " (cutoff:3.500A)
    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 sheet with id=AA1, first strand: chain 'C' and resid 28 through 29
      removed outlier: 3.846A  pdb=" N   TYR C  74 " --> pdb=" O   ASP C  71 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'C' and resid 117 through 118
    Processing sheet with id=AA3, first strand: chain 'D' and resid 28 through 29
    Processing sheet with id=AA4, first strand: chain 'D' and resid 117 through 118
    Processing sheet with id=AA5, first strand: chain 'D' and resid 530 through 533
      removed outlier: 3.524A  pdb=" N   ILE D 576 " --> pdb=" O   PHE D 588 " (cutoff:3.500A)
      removed outlier: 5.332A  pdb=" N   ILE D 573 " --> pdb=" O   ILE D 565 " (cutoff:3.500A)
      removed outlier: 7.022A  pdb=" N   ILE D 565 " --> pdb=" O   ILE D 573 " (cutoff:3.500A)
      removed outlier: 3.539A  pdb=" N   LEU D 575 " --> pdb=" O   GLU D 563 " (cutoff:3.500A)
      removed outlier: 6.492A  pdb=" N   LYS D 613 " --> pdb=" O   PHE D 637 " (cutoff:3.500A)

    362 hydrogen bonds defined for protein.
    1038 hydrogen bond angles defined for protein.
    Restraints generated for nucleic acids:
      96 hydrogen bonds
      176 hydrogen bond angles
      0 basepair planarities
      42 basepair parallelities
      46 stacking parallelities
  Total time for adding SS restraints: 1.45

  Time building geometry restraints manager: 0.93 seconds

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

  Histogram of bond lengths:
        1.18 -     1.31: 1105
        1.31 -     1.43: 2612
        1.43 -     1.56: 4162
        1.56 -     1.69: 196
        1.69 -     1.81: 63
  Bond restraints: 8138
  Sorted by residual:
  bond pdb=" CG  PRO D 696 "
       pdb=" CD  PRO D 696 "
    ideal  model  delta    sigma   weight residual
    1.512  1.180  0.332 2.70e-02 1.37e+03 1.52e+02
  bond pdb=" N   PRO D 696 "
       pdb=" CD  PRO D 696 "
    ideal  model  delta    sigma   weight residual
    1.474  1.562 -0.088 1.40e-02 5.10e+03 3.96e+01
  bond pdb=" N   PRO D 696 "
       pdb=" CA  PRO D 696 "
    ideal  model  delta    sigma   weight residual
    1.468  1.383  0.085 1.70e-02 3.46e+03 2.53e+01
  bond pdb=" C   HIS C  31 "
       pdb=" O   HIS C  31 "
    ideal  model  delta    sigma   weight residual
    1.237  1.186  0.051 1.17e-02 7.31e+03 1.88e+01
  bond pdb=" CB  PRO D 696 "
       pdb=" CG  PRO D 696 "
    ideal  model  delta    sigma   weight residual
    1.506  1.628 -0.122 3.90e-02 6.57e+02 9.74e+00
  ... (remaining 8133 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     3.55: 11388
        3.55 -     7.10: 32
        7.10 -    10.64: 6
       10.64 -    14.19: 2
       14.19 -    17.74: 2
  Bond angle restraints: 11430
  Sorted by residual:
  angle pdb=" N   PRO D 696 "
        pdb=" CD  PRO D 696 "
        pdb=" CG  PRO D 696 "
      ideal   model   delta    sigma   weight residual
     103.80   87.95   15.85 1.20e+00 6.94e-01 1.74e+02
  angle pdb=" CA  PRO D 696 "
        pdb=" N   PRO D 696 "
        pdb=" CD  PRO D 696 "
      ideal   model   delta    sigma   weight residual
     111.50   93.76   17.74 1.40e+00 5.10e-01 1.61e+02
  angle pdb=" C3'   C E  49 "
        pdb=" C2'   C E  49 "
        pdb=" O2'   C E  49 "
      ideal   model   delta    sigma   weight residual
     110.70  121.40  -10.70 1.50e+00 4.44e-01 5.09e+01
  angle pdb=" N   PRO D 696 "
        pdb=" CA  PRO D 696 "
        pdb=" CB  PRO D 696 "
      ideal   model   delta    sigma   weight residual
     102.60   96.63    5.97 1.10e+00 8.26e-01 2.95e+01
  angle pdb=" O3'   C E  49 "
        pdb=" C3'   C E  49 "
        pdb=" C2'   C E  49 "
      ideal   model   delta    sigma   weight residual
     113.70  121.37   -7.67 1.50e+00 4.44e-01 2.62e+01
  ... (remaining 11425 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    33.86: 4717
       33.86 -    67.72: 313
       67.72 -   101.58: 41
      101.58 -   135.44: 0
      135.44 -   169.30: 2
  Dihedral angle restraints: 5073
    sinusoidal: 2960
      harmonic: 2113
  Sorted by residual:
  dihedral pdb=" CA  ARG B 744 "
           pdb=" C   ARG B 744 "
           pdb=" N   GLU B 745 "
           pdb=" CA  GLU B 745 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  158.23   21.77     0      5.00e+00 4.00e-02 1.90e+01
  dihedral pdb=" C4'   C F  49 "
           pdb=" C3'   C F  49 "
           pdb=" O3'   C F  49 "
           pdb=" P     G F  50 "
      ideal   model   delta sinusoidal    sigma   weight residual
     220.00   50.70  169.30     1      3.50e+01 8.16e-04 1.55e+01
  dihedral pdb=" C4'   C E  49 "
           pdb=" C3'   C E  49 "
           pdb=" O3'   C E  49 "
           pdb=" P     G E  50 "
      ideal   model   delta sinusoidal    sigma   weight residual
     220.00   56.05  163.95     1      3.50e+01 8.16e-04 1.54e+01
  ... (remaining 5070 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.290: 1378
       0.290 -    0.581: 1
       0.581 -    0.871: 0
       0.871 -    1.161: 0
       1.161 -    1.452: 1
  Chirality restraints: 1380
  Sorted by residual:
  chirality pdb=" CB  VAL D 162 "
            pdb=" CA  VAL D 162 "
            pdb=" CG1 VAL D 162 "
            pdb=" CG2 VAL D 162 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.63   -1.18   -1.45 2.00e-01 2.50e+01 5.27e+01
  chirality pdb=" C3'   C E  49 "
            pdb=" C4'   C E  49 "
            pdb=" O3'   C E  49 "
            pdb=" C2'   C E  49 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.48   -2.14   -0.33 2.00e-01 2.50e+01 2.80e+00
  chirality pdb=" C2'   C E  49 "
            pdb=" C3'   C E  49 "
            pdb=" O2'   C E  49 "
            pdb=" C1'   C E  49 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.75   -2.47   -0.28 2.00e-01 2.50e+01 2.03e+00
  ... (remaining 1377 not shown)

  Planarity restraints: 1105
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   ARG D 695 "   -0.055 5.00e-02 4.00e+02   7.51e-02 9.01e+00
        pdb=" N   PRO D 696 "    0.129 5.00e-02 4.00e+02
        pdb=" CA  PRO D 696 "   -0.042 5.00e-02 4.00e+02
        pdb=" CD  PRO D 696 "   -0.032 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C1'   U E  19 "   -0.028 2.00e-02 2.50e+03   1.51e-02 5.15e+00
        pdb=" N1    U E  19 "    0.034 2.00e-02 2.50e+03
        pdb=" C2    U E  19 "    0.002 2.00e-02 2.50e+03
        pdb=" O2    U E  19 "    0.002 2.00e-02 2.50e+03
        pdb=" N3    U E  19 "   -0.002 2.00e-02 2.50e+03
        pdb=" C4    U E  19 "   -0.006 2.00e-02 2.50e+03
        pdb=" O4    U E  19 "   -0.006 2.00e-02 2.50e+03
        pdb=" C5    U E  19 "   -0.002 2.00e-02 2.50e+03
        pdb=" C6    U E  19 "    0.005 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C1'   C E  38 "   -0.024 2.00e-02 2.50e+03   1.28e-02 3.68e+00
        pdb=" N1    C E  38 "    0.028 2.00e-02 2.50e+03
        pdb=" C2    C E  38 "    0.004 2.00e-02 2.50e+03
        pdb=" O2    C E  38 "    0.001 2.00e-02 2.50e+03
        pdb=" N3    C E  38 "   -0.003 2.00e-02 2.50e+03
        pdb=" C4    C E  38 "   -0.003 2.00e-02 2.50e+03
        pdb=" N4    C E  38 "   -0.009 2.00e-02 2.50e+03
        pdb=" C5    C E  38 "    0.005 2.00e-02 2.50e+03
        pdb=" C6    C E  38 "    0.000 2.00e-02 2.50e+03
  ... (remaining 1102 not shown)

  Histogram of nonbonded interaction distances:
        1.99 -     2.57: 69
        2.57 -     3.15: 6671
        3.15 -     3.74: 13118
        3.74 -     4.32: 17203
        4.32 -     4.90: 26741
  Nonbonded interactions: 63802
  Sorted by model distance:
  nonbonded pdb=" O2'   U E  48 "
            pdb=" OP1   G E  50 "
     model   vdw
     1.988 3.040
  nonbonded pdb=" O2'   C F  49 "
            pdb=" OP1   G F  50 "
     model   vdw
     2.010 3.040
  nonbonded pdb=" O2'   U F  19 "
            pdb=" OP2   A F  20 "
     model   vdw
     2.018 3.040
  nonbonded pdb=" O2'   U E  19 "
            pdb=" OP2   A E  20 "
     model   vdw
     2.068 3.040
  nonbonded pdb=" O   LYS C 142 "
            pdb=" OG1 THR C 145 "
     model   vdw
     2.114 3.040
  ... (remaining 63797 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' and (resid 695 through 703 or (resid 704 and (name N or name CA or na \ 
me C or name O or name CB )) or resid 705 through 747))
  selection = (chain 'B' and (resid 695 through 702 or (resid 703 through 704 and (name N or n \ 
ame CA or name C or name O or name CB )) or resid 705 through 747))
}
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 individual isotropic
Make a string to write initial .geo file
Internal consistency checks
Time:
  Set random seed:                         0.000
  Set model cs if undefined:               0.000
  Decide on map wrapping:                  0.000
  Normalize map: mean=0, sd=1:             3.490
  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:             0.000
  Extract box with map and model:          0.140
  Check model and map are aligned:         0.030
  Set scattering table:                    0.020
  Process input model:                     9.540
  Find NCS groups from input model:        0.050
  Set up NCS constraints:                  0.010
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.000
  Load rotamer database and sin/cos tables:1.320
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   14.610
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6653
moved from start:          0.0000

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.332   8138  Z= 0.211
  Angle     :  0.657  17.738  11430  Z= 0.371
  Chirality :  0.052   1.452   1380
  Planarity :  0.004   0.075   1105
  Dihedral  : 20.201 169.297   3701
  Min Nonbonded Distance : 1.988

Molprobity Statistics.
  All-atom Clashscore : 5.42
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.56 %
    Favored  : 98.44 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  : 15.11 %
    Favored  : 84.89 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 6.67 %
    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:  1.39 (0.33), residues: 704
  helix:  1.48 (0.25), residues: 443
  sheet: -0.21 (0.95), residues: 31
  loop :  0.16 (0.43), residues: 230

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.008   0.001   ARG A 744 
 TYR   0.010   0.001   TYR D   6 
 PHE   0.012   0.001   PHE D  17 
 TRP   0.004   0.001   TRP D 522 
 HIS   0.010   0.001   HIS C  31 

Details of bonding type rmsd
  covalent geometry    : bond        0.00479 ( 8138)
  covalent geometry    : angle       0.65719 (11430)
  hydrogen bonds       : bond        0.17659 (  458)
  hydrogen bonds       : angle       6.48774 ( 1214)

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

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

  1408 Ramachandran restraints generated.
    704 Oldfield, 0 Emsley, 704 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1408 Ramachandran restraints generated.
    704 Oldfield, 0 Emsley, 704 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  124 residues out of total 638 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 124
  time to evaluate  : 0.240 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  731 LEU cc_start: 0.8649 (mt) cc_final: 0.8306 (mt)
REVERT: A  735 GLN cc_start: 0.8501 (tm-30) cc_final: 0.8279 (tm-30)
REVERT: C  106 ASN cc_start: 0.8491 (m-40) cc_final: 0.8167 (m-40)
REVERT: C  141 ILE cc_start: 0.7670 (tp) cc_final: 0.7456 (tp)
REVERT: D   19 GLU cc_start: 0.7074 (tt0) cc_final: 0.6690 (mt-10)
REVERT: D  632 LEU cc_start: 0.8062 (mt) cc_final: 0.7573 (mt)
REVERT: D  692 TRP cc_start: 0.6329 (m100) cc_final: 0.6030 (m100)
REVERT: D  735 GLU cc_start: 0.8313 (tp30) cc_final: 0.7699 (tt0)
REVERT: D  743 MET cc_start: 0.8018 (tpp) cc_final: 0.7608 (ttm)
REVERT: D  746 LYS cc_start: 0.6788 (mttt) cc_final: 0.6193 (mttt)
REVERT: D  811 GLU cc_start: 0.7974 (pt0) cc_final: 0.7550 (pp20)
  outliers start: 0
  outliers final: 0
  residues processed: 124
  average time/residue: 0.1090
  time to fit residues: 17.7021
Evaluate side-chains
  102 residues out of total 638 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 102
  time to evaluate  : 0.238 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 81
   random chunks:
   chunk 49 optimal weight:    3.9990
   chunk 53 optimal weight:    0.0770
   chunk 5 optimal weight:    0.0870
   chunk 33 optimal weight:    2.9990
   chunk 65 optimal weight:    0.7980
   chunk 62 optimal weight:    0.2980
   chunk 51 optimal weight:    0.1980
   chunk 38 optimal weight:    0.5980
   chunk 61 optimal weight:    4.9990
   chunk 45 optimal weight:    7.9990
   chunk 74 optimal weight:    2.9990
   overall best weight:    0.2516

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

Flipped N/Q/H residues before XYZ refinement:
B 721 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4702 r_free = 0.4702 target = 0.240971 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.4300 r_free = 0.4300 target = 0.197108 restraints weight = 9811.101|
|-----------------------------------------------------------------------------|
r_work (start): 0.4305 rms_B_bonded: 2.92
r_work (final): 0.4305
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6560
moved from start:          0.2002

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.045   8138  Z= 0.127
  Angle     :  0.603   8.598  11430  Z= 0.300
  Chirality :  0.036   0.159   1380
  Planarity :  0.004   0.037   1105
  Dihedral  : 19.831 172.729   2282
  Min Nonbonded Distance : 2.254

Molprobity Statistics.
  All-atom Clashscore : 6.72
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.42 %
    Favored  : 98.58 %
  Rotamer:
    Outliers :  1.97 %
    Allowed  : 16.58 %
    Favored  : 81.44 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 6.67 %
    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:  1.86 (0.33), residues: 704
  helix:  1.85 (0.25), residues: 464
  sheet: -0.56 (0.82), residues: 25
  loop :  0.21 (0.46), residues: 215

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG A 744 
 TYR   0.022   0.002   TYR D 626 
 PHE   0.011   0.001   PHE D  17 
 TRP   0.006   0.001   TRP D 522 
 HIS   0.005   0.001   HIS C 135 

Details of bonding type rmsd
  covalent geometry    : bond        0.00266 ( 8138)
  covalent geometry    : angle       0.60339 (11430)
  hydrogen bonds       : bond        0.04892 (  458)
  hydrogen bonds       : angle       4.35666 ( 1214)

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

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

  1408 Ramachandran restraints generated.
    704 Oldfield, 0 Emsley, 704 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1408 Ramachandran restraints generated.
    704 Oldfield, 0 Emsley, 704 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  129 residues out of total 638 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 117
  time to evaluate  : 0.272 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  735 GLN cc_start: 0.8409 (tm-30) cc_final: 0.8196 (tm-30)
REVERT: A  740 MET cc_start: 0.6165 (ttp) cc_final: 0.5431 (ttp)
  outliers start: 12
  outliers final: 9
  residues processed: 124
  average time/residue: 0.0974
  time to fit residues: 16.1469
Evaluate side-chains
  100 residues out of total 638 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 91
  time to evaluate  : 0.236 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue  738 GLU
Chi-restraints excluded: chain B residue  744 ARG
Chi-restraints excluded: chain D residue   29 THR
Chi-restraints excluded: chain D residue   53 SER
Chi-restraints excluded: chain D residue   76 GLN
Chi-restraints excluded: chain D residue  163 MET
Chi-restraints excluded: chain D residue  708 ASP
Chi-restraints excluded: chain D residue  750 VAL
Chi-restraints excluded: chain D residue  764 SER
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 81
   random chunks:
   chunk 28 optimal weight:    0.4980
   chunk 45 optimal weight:    3.9990
   chunk 76 optimal weight:    3.9990
   chunk 13 optimal weight:    0.0270
   chunk 68 optimal weight:    0.8980
   chunk 50 optimal weight:    0.9990
   chunk 34 optimal weight:    0.7980
   chunk 80 optimal weight:    2.9990
   chunk 25 optimal weight:    0.8980
   chunk 23 optimal weight:    0.9990
   chunk 56 optimal weight:    2.9990
   overall best weight:    0.6238

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

Flipped N/Q/H residues before XYZ refinement:
** C 135 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 = 0.4671 r_free = 0.4671 target = 0.238154 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 32)----------------|
| r_work = 0.4267 r_free = 0.4267 target = 0.194117 restraints weight = 9717.234|
|-----------------------------------------------------------------------------|
r_work (start): 0.4267 rms_B_bonded: 3.24
r_work (final): 0.4267
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6626
moved from start:          0.2494

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.042   8138  Z= 0.162
  Angle     :  0.597   9.083  11430  Z= 0.296
  Chirality :  0.036   0.177   1380
  Planarity :  0.004   0.038   1105
  Dihedral  : 19.794 172.347   2282
  Min Nonbonded Distance : 2.365

Molprobity Statistics.
  All-atom Clashscore : 8.10
  Ramachandran Plot:
    Outliers :  0.14 %
    Allowed  :  1.28 %
    Favored  : 98.58 %
  Rotamer:
    Outliers :  3.28 %
    Allowed  : 18.72 %
    Favored  : 78.00 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 6.67 %
    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:  1.47 (0.32), residues: 704
  helix:  1.57 (0.24), residues: 465
  sheet: -0.84 (0.78), residues: 25
  loop :  0.01 (0.44), residues: 214

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.000   ARG A 744 
 TYR   0.021   0.002   TYR D 626 
 PHE   0.014   0.002   PHE D  17 
 TRP   0.011   0.002   TRP D 692 
 HIS   0.005   0.001   HIS D 616 

Details of bonding type rmsd
  covalent geometry    : bond        0.00371 ( 8138)
  covalent geometry    : angle       0.59707 (11430)
  hydrogen bonds       : bond        0.05100 (  458)
  hydrogen bonds       : angle       4.22863 ( 1214)

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

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

  1408 Ramachandran restraints generated.
    704 Oldfield, 0 Emsley, 704 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1408 Ramachandran restraints generated.
    704 Oldfield, 0 Emsley, 704 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  116 residues out of total 638 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 96
  time to evaluate  : 0.329 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  740 MET cc_start: 0.6117 (ttp) cc_final: 0.5240 (ttp)
  outliers start: 20
  outliers final: 16
  residues processed: 111
  average time/residue: 0.0974
  time to fit residues: 14.4133
Evaluate side-chains
  102 residues out of total 638 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 86
  time to evaluate  : 0.251 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue  702 VAL
Chi-restraints excluded: chain B residue  738 GLU
Chi-restraints excluded: chain B residue  744 ARG
Chi-restraints excluded: chain C residue   81 GLN
Chi-restraints excluded: chain C residue  159 ASP
Chi-restraints excluded: chain D residue   29 THR
Chi-restraints excluded: chain D residue   53 SER
Chi-restraints excluded: chain D residue   75 VAL
Chi-restraints excluded: chain D residue   76 GLN
Chi-restraints excluded: chain D residue  146 ASP
Chi-restraints excluded: chain D residue  163 MET
Chi-restraints excluded: chain D residue  557 VAL
Chi-restraints excluded: chain D residue  708 ASP
Chi-restraints excluded: chain D residue  750 VAL
Chi-restraints excluded: chain D residue  764 SER
Chi-restraints excluded: chain D residue  815 SER
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 81
   random chunks:
   chunk 35 optimal weight:    0.9980
   chunk 51 optimal weight:    5.9990
   chunk 68 optimal weight:    6.9990
   chunk 26 optimal weight:    0.0870
   chunk 54 optimal weight:    5.9990
   chunk 8 optimal weight:    0.6980
   chunk 40 optimal weight:    2.9990
   chunk 61 optimal weight:    0.9990
   chunk 71 optimal weight:    4.9990
   chunk 1 optimal weight:    0.6980
   chunk 50 optimal weight:    0.4980
   overall best weight:    0.5958

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4672 r_free = 0.4672 target = 0.237766 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 30)----------------|
| r_work = 0.4275 r_free = 0.4275 target = 0.194735 restraints weight = 9851.236|
|-----------------------------------------------------------------------------|
r_work (start): 0.4277 rms_B_bonded: 3.02
r_work (final): 0.4277
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6608
moved from start:          0.2765

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.037   8138  Z= 0.156
  Angle     :  0.584   9.112  11430  Z= 0.289
  Chirality :  0.036   0.172   1380
  Planarity :  0.004   0.037   1105
  Dihedral  : 19.711 171.350   2282
  Min Nonbonded Distance : 2.350

Molprobity Statistics.
  All-atom Clashscore : 8.99
  Ramachandran Plot:
    Outliers :  0.14 %
    Allowed  :  1.85 %
    Favored  : 98.01 %
  Rotamer:
    Outliers :  3.45 %
    Allowed  : 19.70 %
    Favored  : 76.85 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 6.67 %
    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:  1.38 (0.32), residues: 704
  helix:  1.51 (0.24), residues: 465
  sheet: -0.75 (0.81), residues: 25
  loop : -0.04 (0.44), residues: 214

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG C  47 
 TYR   0.014   0.002   TYR D 626 
 PHE   0.015   0.002   PHE D  17 
 TRP   0.008   0.001   TRP D 692 
 HIS   0.004   0.001   HIS D 616 

Details of bonding type rmsd
  covalent geometry    : bond        0.00356 ( 8138)
  covalent geometry    : angle       0.58403 (11430)
  hydrogen bonds       : bond        0.04955 (  458)
  hydrogen bonds       : angle       4.22137 ( 1214)

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

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

  1408 Ramachandran restraints generated.
    704 Oldfield, 0 Emsley, 704 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1408 Ramachandran restraints generated.
    704 Oldfield, 0 Emsley, 704 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  112 residues out of total 638 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 91
  time to evaluate  : 0.266 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  740 MET cc_start: 0.6154 (ttp) cc_final: 0.5481 (ttp)
REVERT: C   81 GLN cc_start: 0.6745 (OUTLIER) cc_final: 0.6534 (mp10)
REVERT: D   48 GLN cc_start: 0.8505 (tm-30) cc_final: 0.7990 (tm-30)
  outliers start: 21
  outliers final: 15
  residues processed: 107
  average time/residue: 0.0919
  time to fit residues: 13.1792
Evaluate side-chains
  96 residues out of total 638 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 80
  time to evaluate  : 0.234 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue  738 GLU
Chi-restraints excluded: chain B residue  744 ARG
Chi-restraints excluded: chain C residue   81 GLN
Chi-restraints excluded: chain C residue  122 LEU
Chi-restraints excluded: chain C residue  159 ASP
Chi-restraints excluded: chain D residue   29 THR
Chi-restraints excluded: chain D residue   53 SER
Chi-restraints excluded: chain D residue   75 VAL
Chi-restraints excluded: chain D residue   76 GLN
Chi-restraints excluded: chain D residue  146 ASP
Chi-restraints excluded: chain D residue  557 VAL
Chi-restraints excluded: chain D residue  580 THR
Chi-restraints excluded: chain D residue  708 ASP
Chi-restraints excluded: chain D residue  750 VAL
Chi-restraints excluded: chain D residue  764 SER
Chi-restraints excluded: chain D residue  815 SER
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 81
   random chunks:
   chunk 28 optimal weight:    0.2980
   chunk 12 optimal weight:    0.4980
   chunk 21 optimal weight:    0.5980
   chunk 15 optimal weight:    0.0980
   chunk 57 optimal weight:    0.7980
   chunk 4 optimal weight:    0.8980
   chunk 80 optimal weight:    3.9990
   chunk 9 optimal weight:    0.9990
   chunk 47 optimal weight:   10.0000
   chunk 23 optimal weight:    0.8980
   chunk 32 optimal weight:    0.0870
   overall best weight:    0.3158

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4689 r_free = 0.4689 target = 0.239898 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 32)----------------|
| r_work = 0.4301 r_free = 0.4301 target = 0.197025 restraints weight = 9786.781|
|-----------------------------------------------------------------------------|
r_work (start): 0.4301 rms_B_bonded: 2.96
r_work (final): 0.4301
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6557
moved from start:          0.3139

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.030   8138  Z= 0.119
  Angle     :  0.562   8.949  11430  Z= 0.278
  Chirality :  0.034   0.165   1380
  Planarity :  0.003   0.036   1105
  Dihedral  : 19.671 170.347   2282
  Min Nonbonded Distance : 2.302

Molprobity Statistics.
  All-atom Clashscore : 8.44
  Ramachandran Plot:
    Outliers :  0.14 %
    Allowed  :  1.56 %
    Favored  : 98.30 %
  Rotamer:
    Outliers :  2.79 %
    Allowed  : 20.85 %
    Favored  : 76.35 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 6.67 %
    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:  1.55 (0.32), residues: 704
  helix:  1.66 (0.24), residues: 464
  sheet: -0.99 (0.78), residues: 25
  loop :  0.02 (0.43), residues: 215

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG D 757 
 TYR   0.016   0.001   TYR D 549 
 PHE   0.013   0.001   PHE D  17 
 TRP   0.005   0.001   TRP D 522 
 HIS   0.003   0.001   HIS D 616 

Details of bonding type rmsd
  covalent geometry    : bond        0.00256 ( 8138)
  covalent geometry    : angle       0.56246 (11430)
  hydrogen bonds       : bond        0.04499 (  458)
  hydrogen bonds       : angle       4.20413 ( 1214)

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

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

  1408 Ramachandran restraints generated.
    704 Oldfield, 0 Emsley, 704 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1408 Ramachandran restraints generated.
    704 Oldfield, 0 Emsley, 704 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  108 residues out of total 638 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 91
  time to evaluate  : 0.243 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  740 MET cc_start: 0.6039 (ttp) cc_final: 0.5265 (ttp)
REVERT: D   48 GLN cc_start: 0.8531 (tm-30) cc_final: 0.7940 (tm-30)
  outliers start: 17
  outliers final: 13
  residues processed: 106
  average time/residue: 0.0980
  time to fit residues: 13.7668
Evaluate side-chains
  95 residues out of total 638 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 82
  time to evaluate  : 0.242 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue  705 LEU
Chi-restraints excluded: chain B residue  738 GLU
Chi-restraints excluded: chain C residue  159 ASP
Chi-restraints excluded: chain D residue   29 THR
Chi-restraints excluded: chain D residue   75 VAL
Chi-restraints excluded: chain D residue   76 GLN
Chi-restraints excluded: chain D residue  146 ASP
Chi-restraints excluded: chain D residue  557 VAL
Chi-restraints excluded: chain D residue  580 THR
Chi-restraints excluded: chain D residue  655 VAL
Chi-restraints excluded: chain D residue  708 ASP
Chi-restraints excluded: chain D residue  750 VAL
Chi-restraints excluded: chain D residue  764 SER
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 81
   random chunks:
   chunk 3 optimal weight:    0.0980
   chunk 12 optimal weight:    0.7980
   chunk 21 optimal weight:    2.9990
   chunk 26 optimal weight:    0.1980
   chunk 16 optimal weight:    0.4980
   chunk 23 optimal weight:    0.7980
   chunk 4 optimal weight:    0.9980
   chunk 28 optimal weight:    0.3980
   chunk 6 optimal weight:    0.7980
   chunk 72 optimal weight:    1.9990
   chunk 11 optimal weight:    0.3980
   overall best weight:    0.3180

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4692 r_free = 0.4692 target = 0.239979 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.4285 r_free = 0.4285 target = 0.195054 restraints weight = 9700.782|
|-----------------------------------------------------------------------------|
r_work (start): 0.4280 rms_B_bonded: 2.65
r_work (final): 0.4280
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6581
moved from start:          0.3441

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.033   8138  Z= 0.118
  Angle     :  0.555   8.889  11430  Z= 0.275
  Chirality :  0.034   0.161   1380
  Planarity :  0.003   0.035   1105
  Dihedral  : 19.607 168.243   2282
  Min Nonbonded Distance : 2.339

Molprobity Statistics.
  All-atom Clashscore : 9.06
  Ramachandran Plot:
    Outliers :  0.14 %
    Allowed  :  1.85 %
    Favored  : 98.01 %
  Rotamer:
    Outliers :  2.46 %
    Allowed  : 21.18 %
    Favored  : 76.35 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 6.67 %
    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:  1.59 (0.32), residues: 704
  helix:  1.67 (0.24), residues: 463
  sheet: -0.76 (0.84), residues: 25
  loop :  0.05 (0.43), residues: 216

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG D 757 
 TYR   0.015   0.001   TYR D 549 
 PHE   0.012   0.001   PHE D  17 
 TRP   0.005   0.001   TRP D 522 
 HIS   0.003   0.001   HIS D 616 

Details of bonding type rmsd
  covalent geometry    : bond        0.00257 ( 8138)
  covalent geometry    : angle       0.55455 (11430)
  hydrogen bonds       : bond        0.04388 (  458)
  hydrogen bonds       : angle       4.05460 ( 1214)

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

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

  1408 Ramachandran restraints generated.
    704 Oldfield, 0 Emsley, 704 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1408 Ramachandran restraints generated.
    704 Oldfield, 0 Emsley, 704 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  103 residues out of total 638 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 88
  time to evaluate  : 0.237 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  740 MET cc_start: 0.5782 (ttp) cc_final: 0.5077 (ttp)
REVERT: A  745 GLU cc_start: 0.3662 (mm-30) cc_final: 0.3331 (tp30)
REVERT: D   48 GLN cc_start: 0.8499 (tm-30) cc_final: 0.7912 (tm-30)
  outliers start: 15
  outliers final: 13
  residues processed: 100
  average time/residue: 0.0979
  time to fit residues: 12.9793
Evaluate side-chains
  95 residues out of total 638 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 82
  time to evaluate  : 0.173 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue  705 LEU
Chi-restraints excluded: chain B residue  738 GLU
Chi-restraints excluded: chain C residue  159 ASP
Chi-restraints excluded: chain D residue   29 THR
Chi-restraints excluded: chain D residue   53 SER
Chi-restraints excluded: chain D residue   75 VAL
Chi-restraints excluded: chain D residue   76 GLN
Chi-restraints excluded: chain D residue  557 VAL
Chi-restraints excluded: chain D residue  614 VAL
Chi-restraints excluded: chain D residue  655 VAL
Chi-restraints excluded: chain D residue  708 ASP
Chi-restraints excluded: chain D residue  750 VAL
Chi-restraints excluded: chain D residue  815 SER
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 81
   random chunks:
   chunk 16 optimal weight:    0.9990
   chunk 34 optimal weight:    0.6980
   chunk 71 optimal weight:    4.9990
   chunk 74 optimal weight:    2.9990
   chunk 6 optimal weight:    0.7980
   chunk 2 optimal weight:    0.2980
   chunk 59 optimal weight:    3.9990
   chunk 73 optimal weight:    1.9990
   chunk 66 optimal weight:    0.9980
   chunk 54 optimal weight:    0.6980
   chunk 42 optimal weight:    0.6980
   overall best weight:    0.6380

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

Flipped N/Q/H residues before XYZ refinement:
D 151 HIS
D 756 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4668 r_free = 0.4668 target = 0.237475 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.4264 r_free = 0.4264 target = 0.193125 restraints weight = 9742.892|
|-----------------------------------------------------------------------------|
r_work (start): 0.4262 rms_B_bonded: 2.75
r_work (final): 0.4262
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6620
moved from start:          0.3526

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.034   8138  Z= 0.162
  Angle     :  0.602   9.163  11430  Z= 0.296
  Chirality :  0.035   0.169   1380
  Planarity :  0.004   0.041   1105
  Dihedral  : 19.644 167.322   2282
  Min Nonbonded Distance : 2.461

Molprobity Statistics.
  All-atom Clashscore : 9.61
  Ramachandran Plot:
    Outliers :  0.14 %
    Allowed  :  2.13 %
    Favored  : 97.73 %
  Rotamer:
    Outliers :  2.96 %
    Allowed  : 20.36 %
    Favored  : 76.68 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 6.67 %
    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 (0.32), residues: 704
  helix:  1.44 (0.24), residues: 463
  sheet: -0.86 (0.83), residues: 25
  loop : -0.06 (0.43), residues: 216

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.000   ARG D 757 
 TYR   0.014   0.001   TYR D  64 
 PHE   0.015   0.002   PHE D  17 
 TRP   0.005   0.001   TRP D 522 
 HIS   0.004   0.001   HIS D  31 

Details of bonding type rmsd
  covalent geometry    : bond        0.00368 ( 8138)
  covalent geometry    : angle       0.60168 (11430)
  hydrogen bonds       : bond        0.04984 (  458)
  hydrogen bonds       : angle       4.13699 ( 1214)

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

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

  1408 Ramachandran restraints generated.
    704 Oldfield, 0 Emsley, 704 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1408 Ramachandran restraints generated.
    704 Oldfield, 0 Emsley, 704 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  101 residues out of total 638 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 83
  time to evaluate  : 0.270 
Fit side-chains
   revert: symmetry clash
REVERT: A  740 MET cc_start: 0.5956 (ttp) cc_final: 0.5238 (ttp)
REVERT: C  108 MET cc_start: 0.7557 (tmm) cc_final: 0.7186 (tmm)
REVERT: D   48 GLN cc_start: 0.8511 (tm-30) cc_final: 0.8060 (tm-30)
REVERT: D  692 TRP cc_start: 0.4944 (m100) cc_final: 0.4582 (m100)
  outliers start: 18
  outliers final: 16
  residues processed: 97
  average time/residue: 0.1049
  time to fit residues: 13.5504
Evaluate side-chains
  96 residues out of total 638 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 80
  time to evaluate  : 0.265 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue  705 LEU
Chi-restraints excluded: chain B residue  738 GLU
Chi-restraints excluded: chain C residue  122 LEU
Chi-restraints excluded: chain C residue  159 ASP
Chi-restraints excluded: chain D residue   29 THR
Chi-restraints excluded: chain D residue   53 SER
Chi-restraints excluded: chain D residue   75 VAL
Chi-restraints excluded: chain D residue   76 GLN
Chi-restraints excluded: chain D residue  146 ASP
Chi-restraints excluded: chain D residue  557 VAL
Chi-restraints excluded: chain D residue  580 THR
Chi-restraints excluded: chain D residue  608 HIS
Chi-restraints excluded: chain D residue  614 VAL
Chi-restraints excluded: chain D residue  655 VAL
Chi-restraints excluded: chain D residue  708 ASP
Chi-restraints excluded: chain D residue  750 VAL
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 81
   random chunks:
   chunk 1 optimal weight:    0.7980
   chunk 73 optimal weight:    2.9990
   chunk 36 optimal weight:    0.5980
   chunk 69 optimal weight:    2.9990
   chunk 6 optimal weight:    1.9990
   chunk 56 optimal weight:    9.9990
   chunk 45 optimal weight:    6.9990
   chunk 16 optimal weight:    0.9990
   chunk 72 optimal weight:    1.9990
   chunk 8 optimal weight:    0.9990
   chunk 55 optimal weight:    0.7980
   overall best weight:    0.8384

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

Flipped N/Q/H residues before XYZ refinement:
D 756 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4654 r_free = 0.4654 target = 0.235813 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 30)----------------|
| r_work = 0.4245 r_free = 0.4245 target = 0.191931 restraints weight = 9831.757|
|-----------------------------------------------------------------------------|
r_work (start): 0.4250 rms_B_bonded: 2.96
r_work (final): 0.4250
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6645
moved from start:          0.3634

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.042   8138  Z= 0.193
  Angle     :  0.631  10.833  11430  Z= 0.309
  Chirality :  0.037   0.170   1380
  Planarity :  0.004   0.041   1105
  Dihedral  : 19.718 167.020   2282
  Min Nonbonded Distance : 2.420

Molprobity Statistics.
  All-atom Clashscore : 10.09
  Ramachandran Plot:
    Outliers :  0.14 %
    Allowed  :  2.41 %
    Favored  : 97.44 %
  Rotamer:
    Outliers :  2.79 %
    Allowed  : 22.33 %
    Favored  : 74.88 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 6.67 %
    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:  0.98 (0.31), residues: 704
  helix:  1.20 (0.24), residues: 463
  sheet: -0.80 (0.86), residues: 25
  loop : -0.21 (0.43), residues: 216

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG B 744 
 TYR   0.023   0.002   TYR D 549 
 PHE   0.016   0.002   PHE D  17 
 TRP   0.009   0.002   TRP D 692 
 HIS   0.004   0.001   HIS C  31 

Details of bonding type rmsd
  covalent geometry    : bond        0.00446 ( 8138)
  covalent geometry    : angle       0.63146 (11430)
  hydrogen bonds       : bond        0.05349 (  458)
  hydrogen bonds       : angle       4.17157 ( 1214)

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

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

  1408 Ramachandran restraints generated.
    704 Oldfield, 0 Emsley, 704 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1408 Ramachandran restraints generated.
    704 Oldfield, 0 Emsley, 704 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  95 residues out of total 638 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 78
  time to evaluate  : 0.151 
Fit side-chains
   revert: symmetry clash
REVERT: C  108 MET cc_start: 0.7695 (tmm) cc_final: 0.7255 (tmm)
REVERT: D   48 GLN cc_start: 0.8519 (tm-30) cc_final: 0.8136 (tm-30)
  outliers start: 17
  outliers final: 17
  residues processed: 91
  average time/residue: 0.1002
  time to fit residues: 12.1359
Evaluate side-chains
  94 residues out of total 638 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 77
  time to evaluate  : 0.232 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue  705 LEU
Chi-restraints excluded: chain B residue  738 GLU
Chi-restraints excluded: chain C residue  122 LEU
Chi-restraints excluded: chain C residue  159 ASP
Chi-restraints excluded: chain D residue   29 THR
Chi-restraints excluded: chain D residue   53 SER
Chi-restraints excluded: chain D residue   75 VAL
Chi-restraints excluded: chain D residue   76 GLN
Chi-restraints excluded: chain D residue  146 ASP
Chi-restraints excluded: chain D residue  557 VAL
Chi-restraints excluded: chain D residue  580 THR
Chi-restraints excluded: chain D residue  608 HIS
Chi-restraints excluded: chain D residue  614 VAL
Chi-restraints excluded: chain D residue  655 VAL
Chi-restraints excluded: chain D residue  708 ASP
Chi-restraints excluded: chain D residue  750 VAL
Chi-restraints excluded: chain D residue  815 SER
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 81
   random chunks:
   chunk 7 optimal weight:    0.2980
   chunk 1 optimal weight:    0.7980
   chunk 80 optimal weight:    3.9990
   chunk 65 optimal weight:    0.9990
   chunk 53 optimal weight:    0.8980
   chunk 47 optimal weight:    6.9990
   chunk 10 optimal weight:    0.1980
   chunk 5 optimal weight:    6.9990
   chunk 32 optimal weight:    0.7980
   chunk 56 optimal weight:    0.9980
   chunk 79 optimal weight:    3.9990
   overall best weight:    0.5980

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4665 r_free = 0.4665 target = 0.237220 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.4244 r_free = 0.4244 target = 0.191731 restraints weight = 9768.115|
|-----------------------------------------------------------------------------|
r_work (start): 0.4244 rms_B_bonded: 2.98
r_work (final): 0.4244
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6657
moved from start:          0.3717

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.035   8138  Z= 0.157
  Angle     :  0.625  11.459  11430  Z= 0.306
  Chirality :  0.036   0.169   1380
  Planarity :  0.004   0.035   1105
  Dihedral  : 19.701 167.416   2282
  Min Nonbonded Distance : 2.468

Molprobity Statistics.
  All-atom Clashscore : 9.61
  Ramachandran Plot:
    Outliers :  0.14 %
    Allowed  :  2.27 %
    Favored  : 97.59 %
  Rotamer:
    Outliers :  2.63 %
    Allowed  : 22.50 %
    Favored  : 74.88 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 6.67 %
    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:  0.96 (0.32), residues: 704
  helix:  1.15 (0.24), residues: 462
  sheet: -0.83 (0.86), residues: 25
  loop : -0.13 (0.43), residues: 217

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG D 757 
 TYR   0.022   0.001   TYR D 549 
 PHE   0.015   0.002   PHE D  17 
 TRP   0.004   0.001   TRP D 522 
 HIS   0.003   0.001   HIS D 616 

Details of bonding type rmsd
  covalent geometry    : bond        0.00359 ( 8138)
  covalent geometry    : angle       0.62458 (11430)
  hydrogen bonds       : bond        0.04986 (  458)
  hydrogen bonds       : angle       4.17566 ( 1214)

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

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

  1408 Ramachandran restraints generated.
    704 Oldfield, 0 Emsley, 704 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1408 Ramachandran restraints generated.
    704 Oldfield, 0 Emsley, 704 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  94 residues out of total 638 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 78
  time to evaluate  : 0.265 
Fit side-chains
   revert: symmetry clash
REVERT: C  143 GLU cc_start: 0.6499 (mp0) cc_final: 0.6226 (mp0)
REVERT: D   48 GLN cc_start: 0.8545 (tm-30) cc_final: 0.8101 (tm-30)
REVERT: D  692 TRP cc_start: 0.5194 (m100) cc_final: 0.4842 (m100)
  outliers start: 16
  outliers final: 15
  residues processed: 91
  average time/residue: 0.0993
  time to fit residues: 12.0670
Evaluate side-chains
  89 residues out of total 638 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 74
  time to evaluate  : 0.235 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue  705 LEU
Chi-restraints excluded: chain B residue  738 GLU
Chi-restraints excluded: chain C residue  122 LEU
Chi-restraints excluded: chain C residue  159 ASP
Chi-restraints excluded: chain D residue   29 THR
Chi-restraints excluded: chain D residue   53 SER
Chi-restraints excluded: chain D residue   75 VAL
Chi-restraints excluded: chain D residue   76 GLN
Chi-restraints excluded: chain D residue  146 ASP
Chi-restraints excluded: chain D residue  557 VAL
Chi-restraints excluded: chain D residue  608 HIS
Chi-restraints excluded: chain D residue  614 VAL
Chi-restraints excluded: chain D residue  655 VAL
Chi-restraints excluded: chain D residue  708 ASP
Chi-restraints excluded: chain D residue  815 SER
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 81
   random chunks:
   chunk 75 optimal weight:    3.9990
   chunk 7 optimal weight:    0.2980
   chunk 72 optimal weight:    1.9990
   chunk 10 optimal weight:    0.3980
   chunk 11 optimal weight:    0.2980
   chunk 48 optimal weight:   10.0000
   chunk 22 optimal weight:    0.7980
   chunk 69 optimal weight:    0.8980
   chunk 1 optimal weight:    0.8980
   chunk 79 optimal weight:    3.9990
   chunk 19 optimal weight:    0.9980
   overall best weight:    0.5380

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4665 r_free = 0.4665 target = 0.237371 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 32)----------------|
| r_work = 0.4252 r_free = 0.4252 target = 0.192724 restraints weight = 9732.866|
|-----------------------------------------------------------------------------|
r_work (start): 0.4257 rms_B_bonded: 2.98
r_work (final): 0.4257
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6628
moved from start:          0.3865

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.042   8138  Z= 0.151
  Angle     :  0.618  11.741  11430  Z= 0.310
  Chirality :  0.035   0.168   1380
  Planarity :  0.004   0.035   1105
  Dihedral  : 19.692 166.682   2282
  Min Nonbonded Distance : 2.277

Molprobity Statistics.
  All-atom Clashscore : 9.68
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.41 %
    Favored  : 97.59 %
  Rotamer:
    Outliers :  2.63 %
    Allowed  : 22.99 %
    Favored  : 74.38 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 6.67 %
    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:  0.98 (0.32), residues: 704
  helix:  1.16 (0.24), residues: 462
  sheet: -0.81 (0.87), residues: 25
  loop : -0.09 (0.44), residues: 217

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.000   ARG D 757 
 TYR   0.041   0.002   TYR D 549 
 PHE   0.015   0.002   PHE D  17 
 TRP   0.004   0.001   TRP D 522 
 HIS   0.003   0.001   HIS D 616 

Details of bonding type rmsd
  covalent geometry    : bond        0.00339 ( 8138)
  covalent geometry    : angle       0.61806 (11430)
  hydrogen bonds       : bond        0.04870 (  458)
  hydrogen bonds       : angle       4.13703 ( 1214)

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

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

  1408 Ramachandran restraints generated.
    704 Oldfield, 0 Emsley, 704 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1408 Ramachandran restraints generated.
    704 Oldfield, 0 Emsley, 704 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  94 residues out of total 638 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 78
  time to evaluate  : 0.257 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  740 MET cc_start: 0.6342 (ttp) cc_final: 0.5524 (ttp)
REVERT: B  746 MET cc_start: 0.4812 (ptt) cc_final: 0.4611 (mmp)
REVERT: C  143 GLU cc_start: 0.6419 (mp0) cc_final: 0.6153 (mp0)
REVERT: D   48 GLN cc_start: 0.8534 (tm-30) cc_final: 0.8095 (tm-30)
REVERT: D  692 TRP cc_start: 0.5157 (m100) cc_final: 0.4819 (m100)
  outliers start: 16
  outliers final: 15
  residues processed: 90
  average time/residue: 0.1052
  time to fit residues: 12.5609
Evaluate side-chains
  91 residues out of total 638 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 76
  time to evaluate  : 0.233 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue  705 LEU
Chi-restraints excluded: chain B residue  738 GLU
Chi-restraints excluded: chain C residue  122 LEU
Chi-restraints excluded: chain C residue  159 ASP
Chi-restraints excluded: chain D residue   29 THR
Chi-restraints excluded: chain D residue   53 SER
Chi-restraints excluded: chain D residue   75 VAL
Chi-restraints excluded: chain D residue   76 GLN
Chi-restraints excluded: chain D residue  146 ASP
Chi-restraints excluded: chain D residue  557 VAL
Chi-restraints excluded: chain D residue  608 HIS
Chi-restraints excluded: chain D residue  614 VAL
Chi-restraints excluded: chain D residue  655 VAL
Chi-restraints excluded: chain D residue  708 ASP
Chi-restraints excluded: chain D residue  815 SER
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 81
   random chunks:
   chunk 47 optimal weight:    3.9990
   chunk 19 optimal weight:    1.9990
   chunk 66 optimal weight:    0.0980
   chunk 11 optimal weight:    0.4980
   chunk 74 optimal weight:    2.9990
   chunk 39 optimal weight:    0.9980
   chunk 24 optimal weight:    2.9990
   chunk 73 optimal weight:    2.9990
   chunk 57 optimal weight:    0.9980
   chunk 77 optimal weight:    2.9990
   chunk 58 optimal weight:    0.5980
   overall best weight:    0.6380

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

Flipped N/Q/H residues before XYZ refinement:
C 128 GLN
D 610 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4662 r_free = 0.4662 target = 0.236862 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.4250 r_free = 0.4250 target = 0.192178 restraints weight = 9758.095|
|-----------------------------------------------------------------------------|
r_work (start): 0.4253 rms_B_bonded: 2.75
r_work (final): 0.4253
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6639
moved from start:          0.3945

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.042   8138  Z= 0.166
  Angle     :  0.635  12.102  11430  Z= 0.317
  Chirality :  0.036   0.169   1380
  Planarity :  0.004   0.035   1105
  Dihedral  : 19.708 166.204   2282
  Min Nonbonded Distance : 2.289

Molprobity Statistics.
  All-atom Clashscore : 9.06
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.41 %
    Favored  : 97.59 %
  Rotamer:
    Outliers :  2.63 %
    Allowed  : 23.65 %
    Favored  : 73.73 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 6.67 %
    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:  0.84 (0.32), residues: 704
  helix:  1.06 (0.24), residues: 462
  sheet: -0.84 (0.87), residues: 25
  loop : -0.17 (0.43), residues: 217

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG D 757 
 TYR   0.038   0.002   TYR D 549 
 PHE   0.015   0.002   PHE D  17 
 TRP   0.004   0.001   TRP D 692 
 HIS   0.003   0.001   HIS D  31 

Details of bonding type rmsd
  covalent geometry    : bond        0.00379 ( 8138)
  covalent geometry    : angle       0.63505 (11430)
  hydrogen bonds       : bond        0.05077 (  458)
  hydrogen bonds       : angle       4.16288 ( 1214)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 1477.94 seconds
wall clock time: 26 minutes 14.70 seconds (1574.70 seconds total)