Starting phenix.real_space_refine
on Sun Apr  5 02:14:23 2026 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/9rw8_54303/04_2026/9rw8_54303.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/9rw8_54303/04_2026/9rw8_54303.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=4.4
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    model {
      file = "/net/cci-nas-00/data/ceres_data/9rw8_54303/04_2026/9rw8_54303.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/9rw8_54303/04_2026/9rw8_54303.cif"
    real_map_files = "/net/cci-nas-00/data/ceres_data/9rw8_54303/04_2026/9rw8_54303.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/9rw8_54303/04_2026/9rw8_54303.map"
  }
  resolution = 4.4
  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=   0.025
Set stop_for_unknowns flag
  Set to: True
Assert model is a single copy model
Assert all atoms have isotropic ADPs
Construct map_model_manager
Extract box with map and model
Check model and map are aligned
Set scattering table
  Set to: electron
  Number of scattering types: 4
    Type Number    sf(0)   Gaussians
     P      98      5.49       5
     C    3982      2.51       5
     N    1378      2.21       5
     O    1734      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model
  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: 7192
  Number of models: 1
  Model: ""
    Number of chains: 6
    Chain: "A"
      Number of atoms: 265
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 53, 265
          Classifications: {'peptide': 53}
          Incomplete info: {'truncation_to_alanine': 49}
          Link IDs: {'TRANS': 52}
          Unresolved non-hydrogen bonds: 178
          Unresolved non-hydrogen angles: 222
          Unresolved non-hydrogen dihedrals: 137
          Unresolved non-hydrogen chiralities: 15
          Planarities with less than four sites: {'GLU:plan': 10, 'TYR:plan': 1, 'GLN:plan1': 6, 'ASP:plan': 3, 'ASN:plan1': 2, 'ARG:plan': 5}
          Unresolved non-hydrogen planarities: 111
    Chain: "B"
      Number of atoms: 265
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 53, 265
          Classifications: {'peptide': 53}
          Incomplete info: {'truncation_to_alanine': 49}
          Link IDs: {'TRANS': 52}
          Unresolved non-hydrogen bonds: 178
          Unresolved non-hydrogen angles: 222
          Unresolved non-hydrogen dihedrals: 137
          Unresolved non-hydrogen chiralities: 15
          Planarities with less than four sites: {'GLU:plan': 10, 'TYR:plan': 1, 'GLN:plan1': 6, 'ASP:plan': 3, 'ASN:plan1': 2, 'ARG:plan': 5}
          Unresolved non-hydrogen planarities: 111
    Chain: "C"
      Number of atoms: 2277
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 460, 2277
          Classifications: {'peptide': 460}
          Incomplete info: {'truncation_to_alanine': 407}
          Link IDs: {'PCIS': 1, 'PTRANS': 10, 'TRANS': 448}
          Chain breaks: 3
          Unresolved chain link angles: 11
          Unresolved non-hydrogen bonds: 1499
          Unresolved non-hydrogen angles: 1898
          Unresolved non-hydrogen dihedrals: 1241
          Unresolved non-hydrogen chiralities: 130
          Planarities with less than four sites: {'GLU:plan': 31, 'TYR:plan': 20, 'ARG:plan': 23, 'ASN:plan1': 21, 'PHE:plan': 18, 'ASP:plan': 26, 'HIS:plan': 10, 'GLN:plan1': 31, 'TRP:plan': 2}
          Unresolved non-hydrogen planarities: 820
    Chain: "D"
      Number of atoms: 2287
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 462, 2287
          Classifications: {'peptide': 462}
          Incomplete info: {'truncation_to_alanine': 409}
          Link IDs: {'PCIS': 1, 'PTRANS': 10, 'TRANS': 450}
          Chain breaks: 3
          Unresolved chain link angles: 11
          Unresolved non-hydrogen bonds: 1501
          Unresolved non-hydrogen angles: 1899
          Unresolved non-hydrogen dihedrals: 1242
          Unresolved non-hydrogen chiralities: 130
          Planarities with less than four sites: {'GLU:plan': 32, 'TYR:plan': 20, 'ARG:plan': 23, 'ASN:plan1': 21, 'PHE:plan': 18, 'ASP:plan': 26, 'HIS:plan': 9, 'GLN:plan1': 31, 'TRP:plan': 2}
          Unresolved non-hydrogen planarities: 819
    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': 8, 'rna3p_pur': 21, 'rna3p_pyr': 20}
          Link IDs: {'rna2p': 9, 'rna3p': 40}
          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: 2.13, per 1000 atoms: 0.30
  Number of scatterers: 7192
  At special positions: 0
  Unit cell: (86.838, 94.251, 174.735, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 4
    Type Number    sf(0)
     P      98     15.00
     O    1734      8.00
     N    1378      7.00
     C    3982      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 250.4 milliseconds
  

  2016 Ramachandran restraints generated.
    1008 Oldfield, 0 Emsley, 1008 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  1964

  Finding SS restraints...
    Secondary structure from input PDB file:
      55 helices and 7 sheets defined
      69.7% alpha, 6.8% beta
      42 base pairs and 46 stacking pairs defined.
    Time for finding SS restraints: 1.09
  Creating SS restraints...
    Processing helix  chain 'A' and resid 695 through 746
    Processing helix  chain 'B' and resid 696 through 747
      removed outlier: 3.664A  pdb=" N   ARG B 747 " --> pdb=" O   ASP B 743 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 6 through 25
    Processing helix  chain 'C' and resid 30 through 37
    Processing helix  chain 'C' and resid 43 through 51
    Processing helix  chain 'C' and resid 53 through 63
    Processing helix  chain 'C' and resid 95 through 111
      removed outlier: 4.329A  pdb=" N   GLU C  99 " --> pdb=" O   ASP C  95 " (cutoff:3.500A)
      removed outlier: 3.569A  pdb=" N   PHE C 104 " --> pdb=" O   ALA C 100 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 119 through 126
      removed outlier: 3.586A  pdb=" N   LEU C 123 " --> pdb=" O   VAL C 119 " (cutoff:3.500A)
      removed outlier: 3.806A  pdb=" N   GLY C 124 " --> pdb=" O   ARG C 120 " (cutoff:3.500A)
      removed outlier: 3.848A  pdb=" N   HIS C 125 " --> pdb=" O   SER C 121 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 130 through 138
    Processing helix  chain 'C' and resid 140 through 151
    Processing helix  chain 'C' and resid 521 through 529
    Processing helix  chain 'C' and resid 535 through 554
    Processing helix  chain 'C' and resid 595 through 600
    Processing helix  chain 'C' and resid 601 through 608
      removed outlier: 3.720A  pdb=" N   VAL C 605 " --> pdb=" O   GLY C 601 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 617 through 630
      removed outlier: 4.069A  pdb=" N   ALA C 623 " --> pdb=" O   ARG C 619 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 639 through 652
    Processing helix  chain 'C' and resid 662 through 670
      removed outlier: 3.593A  pdb=" N   TYR C 670 " --> pdb=" O   LEU C 666 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 676 through 681
      removed outlier: 4.040A  pdb=" N   GLN C 680 " --> pdb=" O   PRO C 676 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 681 through 688
    Processing helix  chain 'C' and resid 690 through 694
    Processing helix  chain 'C' and resid 698 through 705
    Processing helix  chain 'C' and resid 706 through 713
    Processing helix  chain 'C' and resid 717 through 725
    Processing helix  chain 'C' and resid 726 through 746
      removed outlier: 3.781A  pdb=" N   ARG C 730 " --> pdb=" O   LYS C 726 " (cutoff:3.500A)
      removed outlier: 3.877A  pdb=" N   ALA C 731 " --> pdb=" O   PRO C 727 " (cutoff:3.500A)
      removed outlier: 3.810A  pdb=" N   LEU C 732 " --> pdb=" O   GLU C 728 " (cutoff:3.500A)
      removed outlier: 3.928A  pdb=" N   GLU C 735 " --> pdb=" O   ALA C 731 " (cutoff:3.500A)
      removed outlier: 3.873A  pdb=" N   LEU C 742 " --> pdb=" O   THR C 738 " (cutoff:3.500A)
      removed outlier: 3.797A  pdb=" N   MET C 743 " --> pdb=" O   GLU C 739 " (cutoff:3.500A)
      removed outlier: 5.055A  pdb=" N   GLN C 744 " --> pdb=" O   GLN C 740 " (cutoff:3.500A)
      removed outlier: 4.134A  pdb=" N   ILE C 745 " --> pdb=" O   ILE C 741 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 746 through 773
      removed outlier: 4.197A  pdb=" N   THR C 773 " --> pdb=" O   LYS C 769 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 780 through 788
      removed outlier: 3.581A  pdb=" N   ARG C 785 " --> pdb=" O   ASN C 781 " (cutoff:3.500A)
      removed outlier: 3.682A  pdb=" N   LEU C 786 " --> pdb=" O   ARG C 782 " (cutoff:3.500A)
      removed outlier: 4.424A  pdb=" N   ARG C 788 " --> pdb=" O   ILE C 784 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 793 through 802
    Processing helix  chain 'C' and resid 803 through 814
    Processing helix  chain 'D' and resid 3 through 25
    Processing helix  chain 'D' and resid 29 through 37
      removed outlier: 3.561A  pdb=" N   PHE D  37 " --> pdb=" O   LEU D  33 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 43 through 50
    Processing helix  chain 'D' and resid 53 through 63
    Processing helix  chain 'D' and resid 95 through 110
    Processing helix  chain 'D' and resid 119 through 125
      removed outlier: 4.194A  pdb=" N   GLY D 124 " --> pdb=" O   ARG D 120 " (cutoff:3.500A)
      removed outlier: 4.044A  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 138
    Processing helix  chain 'D' and resid 140 through 152
      removed outlier: 3.769A  pdb=" N   HIS D 151 " --> pdb=" O   PHE D 147 " (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 593
    Processing helix  chain 'D' and resid 594 through 600
      removed outlier: 3.959A  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 618 through 630
    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 670
    Processing helix  chain 'D' and resid 676 through 688
      removed outlier: 4.212A  pdb=" N   GLN D 680 " --> pdb=" O   PRO D 676 " (cutoff:3.500A)
      removed outlier: 3.862A  pdb=" N   LEU D 681 " --> pdb=" O   ILE D 677 " (cutoff:3.500A)
      removed outlier: 3.983A  pdb=" N   GLN D 683 " --> pdb=" O   ASP D 679 " (cutoff:3.500A)
      removed outlier: 4.246A  pdb=" N   ILE D 684 " --> pdb=" O   GLN D 680 " (cutoff:3.500A)
      removed outlier: 3.790A  pdb=" N   ARG D 687 " --> pdb=" O   GLN D 683 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 689 through 694
      removed outlier: 4.336A  pdb=" N   TRP D 692 " --> pdb=" O   GLN D 689 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 698 through 714
      removed outlier: 3.967A  pdb=" N   VAL D 709 " --> pdb=" O   ALA D 705 " (cutoff:3.500A)
      removed outlier: 3.641A  pdb=" N   VAL D 711 " --> pdb=" O   GLY D 707 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 714 through 725
      removed outlier: 4.185A  pdb=" N   ASN D 720 " --> pdb=" O   GLN D 716 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 728 through 743
      removed outlier: 4.617A  pdb=" N   LEU D 732 " --> pdb=" O   GLU D 728 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 746 through 773
      removed outlier: 3.723A  pdb=" N   THR D 773 " --> pdb=" O   LYS D 769 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 780 through 790
      removed outlier: 3.641A  pdb=" N   LEU D 787 " --> pdb=" O   GLU D 783 " (cutoff:3.500A)
      removed outlier: 4.043A  pdb=" N   ARG D 788 " --> pdb=" O   ILE D 784 " (cutoff:3.500A)
      removed outlier: 4.305A  pdb=" N   TYR D 789 " --> pdb=" O   ARG D 785 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 793 through 802
    Processing helix  chain 'D' and resid 803 through 816
      removed outlier: 4.437A  pdb=" N   ALA D 807 " --> pdb=" O   TYR D 803 " (cutoff:3.500A)
    Processing sheet with id=AA1, first strand: chain 'C' and resid 28 through 29
    Processing sheet with id=AA2, first strand: chain 'C' and resid 117 through 118
    Processing sheet with id=AA3, first strand: chain 'C' and resid 530 through 533
      removed outlier: 6.491A  pdb=" N   THR C 531 " --> pdb=" O   LEU C 587 " (cutoff:3.500A)
      removed outlier: 3.962A  pdb=" N   ILE C 576 " --> pdb=" O   PHE C 588 " (cutoff:3.500A)
      removed outlier: 6.428A  pdb=" N   LYS C 613 " --> pdb=" O   PHE C 637 " (cutoff:3.500A)
    Processing sheet with id=AA4, first strand: chain 'D' and resid 68 through 71
    Processing sheet with id=AA5, first strand: chain 'D' and resid 117 through 118
    Processing sheet with id=AA6, first strand: chain 'D' and resid 530 through 533
      removed outlier: 6.440A  pdb=" N   THR D 531 " --> pdb=" O   LEU D 587 " (cutoff:3.500A)
      removed outlier: 6.515A  pdb=" N   LYS D 613 " --> pdb=" O   PHE D 637 " (cutoff:3.500A)
    Processing sheet with id=AA7, first strand: chain 'D' and resid 564 through 565

    507 hydrogen bonds defined for protein.
    1470 hydrogen bond angles defined for protein.
    Restraints generated for nucleic acids:
      96 hydrogen bonds
      180 hydrogen bond angles
      0 basepair planarities
      42 basepair parallelities
      46 stacking parallelities
  Total time for adding SS restraints: 1.39

  Time building geometry restraints manager: 0.95 seconds

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

  Histogram of bond lengths:
        1.22 -     1.30: 1140
        1.30 -     1.38: 1530
        1.38 -     1.45: 919
        1.45 -     1.53: 3461
        1.53 -     1.61: 372
  Bond restraints: 7422
  Sorted by residual:
  bond pdb=" C   ALA C 672 "
       pdb=" N   PRO C 673 "
    ideal  model  delta    sigma   weight residual
    1.330  1.343 -0.013 1.19e-02 7.06e+03 1.20e+00
  bond pdb=" CA  ASP C 160 "
       pdb=" C   ASP C 160 "
    ideal  model  delta    sigma   weight residual
    1.522  1.540 -0.018 1.72e-02 3.38e+03 1.11e+00
  bond pdb=" CA  PHE C 637 "
       pdb=" CB  PHE C 637 "
    ideal  model  delta    sigma   weight residual
    1.526  1.544 -0.017 1.70e-02 3.46e+03 1.06e+00
  bond pdb=" N   GLY C  25 "
       pdb=" CA  GLY C  25 "
    ideal  model  delta    sigma   weight residual
    1.449  1.463 -0.013 1.45e-02 4.76e+03 8.49e-01
  bond pdb=" C   VAL C 636 "
       pdb=" N   PHE C 637 "
    ideal  model  delta    sigma   weight residual
    1.332  1.344 -0.012 1.31e-02 5.83e+03 8.44e-01
  ... (remaining 7417 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     1.71: 10442
        1.71 -     3.41: 226
        3.41 -     5.12: 24
        5.12 -     6.83: 6
        6.83 -     8.53: 4
  Bond angle restraints: 10702
  Sorted by residual:
  angle pdb=" C3'   G F  18 "
        pdb=" O3'   G F  18 "
        pdb=" P     U F  19 "
      ideal   model   delta    sigma   weight residual
     120.20  124.97   -4.77 1.50e+00 4.44e-01 1.01e+01
  angle pdb=" O3'   C E  49 "
        pdb=" C3'   C E  49 "
        pdb=" C2'   C E  49 "
      ideal   model   delta    sigma   weight residual
     109.50  114.22   -4.72 1.50e+00 4.44e-01 9.92e+00
  angle pdb=" N   GLU C 390 "
        pdb=" CA  GLU C 390 "
        pdb=" C   GLU C 390 "
      ideal   model   delta    sigma   weight residual
     114.75  111.08    3.67 1.26e+00 6.30e-01 8.50e+00
  angle pdb=" O4'   G E  50 "
        pdb=" C1'   G E  50 "
        pdb=" N9    G E  50 "
      ideal   model   delta    sigma   weight residual
     108.50  112.87   -4.37 1.50e+00 4.44e-01 8.50e+00
  angle pdb=" C1'   G F  18 "
        pdb=" N9    G F  18 "
        pdb=" C4    G F  18 "
      ideal   model   delta    sigma   weight residual
     126.50  135.03   -8.53 3.00e+00 1.11e-01 8.09e+00
  ... (remaining 10697 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    33.34: 4175
       33.34 -    66.68: 271
       66.68 -   100.02: 35
      100.02 -   133.37: 4
      133.37 -   166.71: 3
  Dihedral angle restraints: 4488
    sinusoidal: 1506
      harmonic: 2982
  Sorted by residual:
  dihedral pdb=" C4'   C E  49 "
           pdb=" C3'   C E  49 "
           pdb=" C2'   C E  49 "
           pdb=" C1'   C E  49 "
      ideal   model   delta sinusoidal    sigma   weight residual
     -35.00   33.31  -68.31     1      8.00e+00 1.56e-02 9.46e+01
  dihedral pdb=" C5'   C E  49 "
           pdb=" C4'   C E  49 "
           pdb=" C3'   C E  49 "
           pdb=" O3'   C E  49 "
      ideal   model   delta sinusoidal    sigma   weight residual
     147.00   79.66   67.34     1      8.00e+00 1.56e-02 9.22e+01
  dihedral pdb=" O4'   U F  42 "
           pdb=" C1'   U F  42 "
           pdb=" N1    U F  42 "
           pdb=" C2    U F  42 "
      ideal   model   delta sinusoidal    sigma   weight residual
     200.00   40.57  159.43     1      1.50e+01 4.44e-03 8.26e+01
  ... (remaining 4485 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.057: 1324
       0.057 -    0.114: 135
       0.114 -    0.172: 19
       0.172 -    0.229: 1
       0.229 -    0.286: 1
  Chirality restraints: 1480
  Sorted by residual:
  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     -2.74   -2.46   -0.29 2.00e-01 2.50e+01 2.05e+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     -2.52   -2.71    0.20 2.00e-01 2.50e+01 9.51e-01
  chirality pdb=" C4'   C F  17 "
            pdb=" C5'   C F  17 "
            pdb=" O4'   C F  17 "
            pdb=" C3'   C F  17 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.50   -2.35   -0.15 2.00e-01 2.50e+01 5.95e-01
  ... (remaining 1477 not shown)

  Planarity restraints: 1118
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C1'   U F  19 "   -0.030 2.00e-02 2.50e+03   1.54e-02 5.36e+00
        pdb=" N1    U F  19 "    0.032 2.00e-02 2.50e+03
        pdb=" C2    U F  19 "    0.003 2.00e-02 2.50e+03
        pdb=" O2    U F  19 "    0.004 2.00e-02 2.50e+03
        pdb=" N3    U F  19 "   -0.003 2.00e-02 2.50e+03
        pdb=" C4    U F  19 "   -0.004 2.00e-02 2.50e+03
        pdb=" O4    U F  19 "   -0.008 2.00e-02 2.50e+03
        pdb=" C5    U F  19 "    0.000 2.00e-02 2.50e+03
        pdb=" C6    U F  19 "    0.007 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C1'   C F  38 "    0.019 2.00e-02 2.50e+03   9.52e-03 2.04e+00
        pdb=" N1    C F  38 "   -0.019 2.00e-02 2.50e+03
        pdb=" C2    C F  38 "    0.001 2.00e-02 2.50e+03
        pdb=" O2    C F  38 "   -0.004 2.00e-02 2.50e+03
        pdb=" N3    C F  38 "    0.002 2.00e-02 2.50e+03
        pdb=" C4    C F  38 "    0.003 2.00e-02 2.50e+03
        pdb=" N4    C F  38 "    0.006 2.00e-02 2.50e+03
        pdb=" C5    C F  38 "   -0.004 2.00e-02 2.50e+03
        pdb=" C6    C F  38 "   -0.002 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C1'   G F   5 "    0.018 2.00e-02 2.50e+03   7.84e-03 1.85e+00
        pdb=" N9    G F   5 "   -0.019 2.00e-02 2.50e+03
        pdb=" C8    G F   5 "   -0.004 2.00e-02 2.50e+03
        pdb=" N7    G F   5 "    0.001 2.00e-02 2.50e+03
        pdb=" C5    G F   5 "    0.001 2.00e-02 2.50e+03
        pdb=" C6    G F   5 "    0.001 2.00e-02 2.50e+03
        pdb=" O6    G F   5 "    0.005 2.00e-02 2.50e+03
        pdb=" N1    G F   5 "    0.002 2.00e-02 2.50e+03
        pdb=" C2    G F   5 "   -0.001 2.00e-02 2.50e+03
        pdb=" N2    G F   5 "   -0.002 2.00e-02 2.50e+03
        pdb=" N3    G F   5 "   -0.002 2.00e-02 2.50e+03
        pdb=" C4    G F   5 "   -0.002 2.00e-02 2.50e+03
  ... (remaining 1115 not shown)

  Histogram of nonbonded interaction distances:
        1.92 -     2.52: 38
        2.52 -     3.11: 6073
        3.11 -     3.71: 12508
        3.71 -     4.30: 14667
        4.30 -     4.90: 21096
  Nonbonded interactions: 54382
  Sorted by model distance:
  nonbonded pdb=" O2'   U E  48 "
            pdb=" OP1   G E  50 "
     model   vdw
     1.920 3.040
  nonbonded pdb=" O2'   C F  49 "
            pdb=" OP1   G F  50 "
     model   vdw
     2.013 3.040
  nonbonded pdb=" O2'   U F  41 "
            pdb=" O5'   U F  42 "
     model   vdw
     2.035 3.040
  nonbonded pdb=" O2'   U F  41 "
            pdb=" O4'   U F  42 "
     model   vdw
     2.134 3.040
  nonbonded pdb=" O2    U E   8 "
            pdb=" N2    G E  50 "
     model   vdw
     2.145 3.120
  ... (remaining 54377 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 81 or resid 92 through 816))
  selection = (chain 'D' and resid 5 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:             4.180
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.000
  Construct map_model_manager:             0.000
  Extract box with map and model:          0.100
  Check model and map are aligned:         0.010
  Set scattering table:                    0.020
  Process input model:                     9.550
  Find NCS groups from input model:        0.110
  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:             0.010
  Load rotamer database and sin/cos tables:1.440
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   15.430
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6990
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   0.018   7422  Z= 0.141
  Angle     :  0.636   8.534  10702  Z= 0.374
  Chirality :  0.038   0.286   1480
  Planarity :  0.002   0.015   1118
  Dihedral  : 21.883 166.708   2524
  Min Nonbonded Distance : 1.920

Molprobity Statistics.
  All-atom Clashscore : 9.49
  Ramachandran Plot:
    Outliers :  0.10 %
    Allowed  :  4.17 %
    Favored  : 95.73 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.00 %
    Favored  :  0.00 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 9.09 %
    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: -0.40 (0.26), residues: 1008
  helix:  0.10 (0.20), residues: 590
  sheet: -1.25 (0.63), residues: 56
  loop : -0.47 (0.34), residues: 362

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TYR   0.000   0.000   TYR A 698 
 PHE   0.000   0.000   PHE C  16 
 TRP   0.000   0.000   TRP C 522 

Details of bonding type rmsd
  covalent geometry    : bond        0.00211 ( 7422)
  covalent geometry    : angle       0.63642 (10702)
  hydrogen bonds       : bond        0.23551 (  603)
  hydrogen bonds       : angle       8.03865 ( 1650)

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

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

  2016 Ramachandran restraints generated.
    1008 Oldfield, 0 Emsley, 1008 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2016 Ramachandran restraints generated.
    1008 Oldfield, 0 Emsley, 1008 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  31 residues out of total 914 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 31
  time to evaluate  : 0.212 
Fit side-chains
  outliers start: 0
  outliers final: 0
  residues processed: 31
  average time/residue: 0.0317
  time to fit residues: 2.0923
Evaluate side-chains
  31 residues out of total 914 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 31
  time to evaluate  : 0.188 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 112
   random chunks:
   chunk 108 optimal weight:    7.9990
   chunk 49 optimal weight:    5.9990
   chunk 97 optimal weight:   10.0000
   chunk 53 optimal weight:    5.9990
   chunk 5 optimal weight:   30.0000
   chunk 33 optimal weight:   50.0000
   chunk 65 optimal weight:    2.9990
   chunk 62 optimal weight:    5.9990
   chunk 51 optimal weight:    8.9990
   chunk 100 optimal weight:    8.9990
   chunk 106 optimal weight:    9.9990
   overall best weight:    5.7990

-------------------------------------------------------------------------------
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 = 0.3590 r_free = 0.3590 target = 0.060974 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 58)----------------|
| r_work = 0.3087 r_free = 0.3087 target = 0.040403 restraints weight = 90459.777|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 31)----------------|
| r_work = 0.3104 r_free = 0.3104 target = 0.040967 restraints weight = 73688.767|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 28)----------------|
| r_work = 0.3116 r_free = 0.3116 target = 0.041371 restraints weight = 64273.520|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 28)----------------|
| r_work = 0.3124 r_free = 0.3124 target = 0.041611 restraints weight = 58323.481|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 37)----------------|
| r_work = 0.3130 r_free = 0.3130 target = 0.041825 restraints weight = 54745.586|
|-----------------------------------------------------------------------------|
r_work (final): 0.3023
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7363
moved from start:          0.4607

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.006   0.045   7422  Z= 0.410
  Angle     :  0.967  11.395  10702  Z= 0.522
  Chirality :  0.050   0.316   1480
  Planarity :  0.005   0.026   1118
  Dihedral  : 22.353 176.790   2524
  Min Nonbonded Distance : 2.062

Molprobity Statistics.
  All-atom Clashscore : 20.69
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.66 %
    Favored  : 95.34 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.00 %
    Favored  :  0.00 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 9.09 %
    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: -1.21 (0.25), residues: 1008
  helix: -0.49 (0.18), residues: 664
  sheet: -1.96 (0.60), residues: 54
  loop : -0.92 (0.38), residues: 290

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TYR   0.000   0.000   TYR A 698 
 PHE   0.000   0.000   PHE C  16 
 TRP   0.000   0.000   TRP C 522 

Details of bonding type rmsd
  covalent geometry    : bond        0.00643 ( 7422)
  covalent geometry    : angle       0.96729 (10702)
  hydrogen bonds       : bond        0.09972 (  603)
  hydrogen bonds       : angle       5.89088 ( 1650)

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

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

  2016 Ramachandran restraints generated.
    1008 Oldfield, 0 Emsley, 1008 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2016 Ramachandran restraints generated.
    1008 Oldfield, 0 Emsley, 1008 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  31 residues out of total 914 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 31
  time to evaluate  : 0.212 
Fit side-chains
  outliers start: 0
  outliers final: 0
  residues processed: 31
  average time/residue: 0.0316
  time to fit residues: 2.0605
Evaluate side-chains
  31 residues out of total 914 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 31
  time to evaluate  : 0.136 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 112
   random chunks:
   chunk 49 optimal weight:    6.9990
   chunk 0 optimal weight:   40.0000
   chunk 111 optimal weight:    6.9990
   chunk 110 optimal weight:    4.9990
   chunk 68 optimal weight:    3.9990
   chunk 4 optimal weight:   20.0000
   chunk 73 optimal weight:    6.9990
   chunk 27 optimal weight:   40.0000
   chunk 21 optimal weight:    8.9990
   chunk 76 optimal weight:   50.0000
   chunk 22 optimal weight:    2.9990
   overall best weight:    5.1990

-------------------------------------------------------------------------------
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 = 0.3535 r_free = 0.3535 target = 0.058801 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 53)----------------|
| r_work = 0.3050 r_free = 0.3050 target = 0.038936 restraints weight = 93707.049|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 36)----------------|
| r_work = 0.3066 r_free = 0.3066 target = 0.039466 restraints weight = 76763.446|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 18)----------------|
| r_work = 0.3076 r_free = 0.3076 target = 0.039783 restraints weight = 67148.162|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 34)----------------|
| r_work = 0.3083 r_free = 0.3083 target = 0.040059 restraints weight = 61529.175|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 27)----------------|
| r_work = 0.3088 r_free = 0.3088 target = 0.040226 restraints weight = 57733.527|
|-----------------------------------------------------------------------------|
r_work (final): 0.2963
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7204
moved from start:          0.6545

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.031   7422  Z= 0.342
  Angle     :  0.804   8.717  10702  Z= 0.441
  Chirality :  0.044   0.256   1480
  Planarity :  0.004   0.017   1118
  Dihedral  : 22.587 178.941   2524
  Min Nonbonded Distance : 2.096

Molprobity Statistics.
  All-atom Clashscore : 18.99
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.35 %
    Favored  : 93.65 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.00 %
    Favored  :  0.00 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 9.09 %
    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: -1.36 (0.25), residues: 1008
  helix: -0.49 (0.19), residues: 663
  sheet: -2.14 (0.64), residues: 51
  loop : -1.29 (0.39), residues: 294

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TYR   0.000   0.000   TYR A 698 
 PHE   0.000   0.000   PHE C  16 
 TRP   0.000   0.000   TRP C 522 

Details of bonding type rmsd
  covalent geometry    : bond        0.00528 ( 7422)
  covalent geometry    : angle       0.80364 (10702)
  hydrogen bonds       : bond        0.08883 (  603)
  hydrogen bonds       : angle       5.71872 ( 1650)

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

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

  2016 Ramachandran restraints generated.
    1008 Oldfield, 0 Emsley, 1008 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2016 Ramachandran restraints generated.
    1008 Oldfield, 0 Emsley, 1008 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  31 residues out of total 914 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 31
  time to evaluate  : 0.239 
Fit side-chains
  outliers start: 0
  outliers final: 0
  residues processed: 31
  average time/residue: 0.0266
  time to fit residues: 1.7938
Evaluate side-chains
  31 residues out of total 914 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 31
  time to evaluate  : 0.158 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 112
   random chunks:
   chunk 103 optimal weight:    4.9990
   chunk 77 optimal weight:   20.0000
   chunk 67 optimal weight:    0.4980
   chunk 88 optimal weight:   30.0000
   chunk 68 optimal weight:    0.9990
   chunk 72 optimal weight:    2.9990
   chunk 105 optimal weight:    5.9990
   chunk 64 optimal weight:    0.8980
   chunk 100 optimal weight:   30.0000
   chunk 48 optimal weight:    0.9980
   chunk 18 optimal weight:   20.0000
   overall best weight:    1.2784

-------------------------------------------------------------------------------
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 = 0.3686 r_free = 0.3686 target = 0.063005 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 81)----------------|
| r_work = 0.3182 r_free = 0.3182 target = 0.043428 restraints weight = 80464.594|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 39)----------------|
| r_work = 0.3211 r_free = 0.3211 target = 0.044424 restraints weight = 56706.467|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 29)----------------|
| r_work = 0.3230 r_free = 0.3230 target = 0.045079 restraints weight = 45661.892|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 27)----------------|
| r_work = 0.3240 r_free = 0.3240 target = 0.045411 restraints weight = 39801.685|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 37)----------------|
| r_work = 0.3250 r_free = 0.3250 target = 0.045768 restraints weight = 36677.404|
|-----------------------------------------------------------------------------|
r_work (final): 0.3179
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7771
moved from start:          0.6276

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.014   7422  Z= 0.127
  Angle     :  0.526   7.060  10702  Z= 0.278
  Chirality :  0.036   0.212   1480
  Planarity :  0.002   0.014   1118
  Dihedral  : 21.481 171.985   2524
  Min Nonbonded Distance : 2.255

Molprobity Statistics.
  All-atom Clashscore : 7.88
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.88 %
    Favored  : 97.12 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.00 %
    Favored  :  0.00 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 9.09 %
    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:  0.86 (0.27), residues: 1008
  helix:  1.37 (0.20), residues: 669
  sheet: -2.24 (0.61), residues: 54
  loop : -0.66 (0.41), residues: 285

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TYR   0.000   0.000   TYR A 698 
 PHE   0.000   0.000   PHE C  16 
 TRP   0.000   0.000   TRP C 522 

Details of bonding type rmsd
  covalent geometry    : bond        0.00197 ( 7422)
  covalent geometry    : angle       0.52645 (10702)
  hydrogen bonds       : bond        0.05021 (  603)
  hydrogen bonds       : angle       4.30934 ( 1650)

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

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

  2016 Ramachandran restraints generated.
    1008 Oldfield, 0 Emsley, 1008 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2016 Ramachandran restraints generated.
    1008 Oldfield, 0 Emsley, 1008 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  31 residues out of total 914 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 31
  time to evaluate  : 0.156 
Fit side-chains
  outliers start: 0
  outliers final: 0
  residues processed: 31
  average time/residue: 0.0283
  time to fit residues: 1.8362
Evaluate side-chains
  31 residues out of total 914 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 31
  time to evaluate  : 0.202 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 112
   random chunks:
   chunk 90 optimal weight:   20.0000
   chunk 75 optimal weight:   10.0000
   chunk 88 optimal weight:   40.0000
   chunk 28 optimal weight:   40.0000
   chunk 16 optimal weight:    9.9990
   chunk 76 optimal weight:    9.9990
   chunk 50 optimal weight:    8.9990
   chunk 37 optimal weight:   10.0000
   chunk 87 optimal weight:    9.9990
   chunk 41 optimal weight:   30.0000
   chunk 81 optimal weight:   30.0000
   overall best weight:    9.7992

-------------------------------------------------------------------------------
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 = 0.3444 r_free = 0.3444 target = 0.055717 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 58)----------------|
| r_work = 0.2976 r_free = 0.2976 target = 0.037382 restraints weight = 98280.526|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 37)----------------|
| r_work = 0.2988 r_free = 0.2988 target = 0.037779 restraints weight = 83468.095|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 36)----------------|
| r_work = 0.2996 r_free = 0.2996 target = 0.038041 restraints weight = 74730.959|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 29)----------------|
| r_work = 0.3001 r_free = 0.3001 target = 0.038201 restraints weight = 69263.525|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 27)----------------|
| r_work = 0.3005 r_free = 0.3005 target = 0.038343 restraints weight = 65987.083|
|-----------------------------------------------------------------------------|
r_work (final): 0.2875
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7498
moved from start:          0.8438

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.010   0.057   7422  Z= 0.615
  Angle     :  1.168  12.293  10702  Z= 0.649
  Chirality :  0.057   0.408   1480
  Planarity :  0.006   0.024   1118
  Dihedral  : 23.773 174.724   2524
  Min Nonbonded Distance : 2.006

Molprobity Statistics.
  All-atom Clashscore : 36.26
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  : 11.11 %
    Favored  : 88.89 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.00 %
    Favored  :  0.00 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 9.09 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.10 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -2.53 (0.25), residues: 1008
  helix: -1.53 (0.18), residues: 629
  sheet: -2.92 (0.62), residues: 46
  loop : -1.40 (0.38), residues: 333

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TYR   0.000   0.000   TYR A 698 
 PHE   0.000   0.000   PHE C  16 
 TRP   0.000   0.000   TRP C 522 

Details of bonding type rmsd
  covalent geometry    : bond        0.00966 ( 7422)
  covalent geometry    : angle       1.16784 (10702)
  hydrogen bonds       : bond        0.13274 (  603)
  hydrogen bonds       : angle       7.21014 ( 1650)

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

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

  2016 Ramachandran restraints generated.
    1008 Oldfield, 0 Emsley, 1008 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2016 Ramachandran restraints generated.
    1008 Oldfield, 0 Emsley, 1008 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  31 residues out of total 914 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 31
  time to evaluate  : 0.202 
Fit side-chains
  outliers start: 0
  outliers final: 0
  residues processed: 31
  average time/residue: 0.0310
  time to fit residues: 2.0731
Evaluate side-chains
  31 residues out of total 914 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 31
  time to evaluate  : 0.191 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 112
   random chunks:
   chunk 60 optimal weight:    9.9990
   chunk 50 optimal weight:    2.9990
   chunk 51 optimal weight:    6.9990
   chunk 49 optimal weight:    0.8980
   chunk 105 optimal weight:    0.7980
   chunk 72 optimal weight:    1.9990
   chunk 29 optimal weight:    8.9990
   chunk 13 optimal weight:    0.8980
   chunk 84 optimal weight:    0.9990
   chunk 44 optimal weight:    7.9990
   chunk 106 optimal weight:    4.9990
   overall best weight:    1.1184

-------------------------------------------------------------------------------
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 = 0.3591 r_free = 0.3591 target = 0.060964 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 48)----------------|
| r_work = 0.3107 r_free = 0.3107 target = 0.040360 restraints weight = 90154.832|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 36)----------------|
| r_work = 0.3126 r_free = 0.3126 target = 0.041022 restraints weight = 71170.302|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 34)----------------|
| r_work = 0.3139 r_free = 0.3139 target = 0.041460 restraints weight = 60847.513|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 31)----------------|
| r_work = 0.3148 r_free = 0.3148 target = 0.041764 restraints weight = 54886.452|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 26)----------------|
| r_work = 0.3152 r_free = 0.3152 target = 0.041909 restraints weight = 51115.094|
|-----------------------------------------------------------------------------|
r_work (final): 0.3025
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7106
moved from start:          0.7567

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.014   7422  Z= 0.135
  Angle     :  0.557   6.798  10702  Z= 0.293
  Chirality :  0.036   0.203   1480
  Planarity :  0.003   0.014   1118
  Dihedral  : 21.994 168.862   2524
  Min Nonbonded Distance : 2.283

Molprobity Statistics.
  All-atom Clashscore : 7.69
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.26 %
    Favored  : 94.74 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.00 %
    Favored  :  0.00 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 9.09 %
    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: -0.24 (0.27), residues: 1008
  helix:  0.54 (0.19), residues: 671
  sheet: -2.81 (0.60), residues: 49
  loop : -1.13 (0.41), residues: 288

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TYR   0.000   0.000   TYR A 698 
 PHE   0.000   0.000   PHE C  16 
 TRP   0.000   0.000   TRP C 522 

Details of bonding type rmsd
  covalent geometry    : bond        0.00209 ( 7422)
  covalent geometry    : angle       0.55710 (10702)
  hydrogen bonds       : bond        0.05673 (  603)
  hydrogen bonds       : angle       4.71321 ( 1650)

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

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

  2016 Ramachandran restraints generated.
    1008 Oldfield, 0 Emsley, 1008 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2016 Ramachandran restraints generated.
    1008 Oldfield, 0 Emsley, 1008 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  31 residues out of total 914 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 31
  time to evaluate  : 0.121 
Fit side-chains
  outliers start: 0
  outliers final: 0
  residues processed: 31
  average time/residue: 0.0304
  time to fit residues: 2.0060
Evaluate side-chains
  31 residues out of total 914 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 31
  time to evaluate  : 0.119 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 112
   random chunks:
   chunk 54 optimal weight:   20.0000
   chunk 63 optimal weight:   20.0000
   chunk 71 optimal weight:    9.9990
   chunk 28 optimal weight:    6.9990
   chunk 25 optimal weight:   20.0000
   chunk 32 optimal weight:    8.9990
   chunk 21 optimal weight:    9.9990
   chunk 6 optimal weight:    0.8980
   chunk 109 optimal weight:    8.9990
   chunk 35 optimal weight:   20.0000
   chunk 88 optimal weight:   40.0000
   overall best weight:    7.1788

-------------------------------------------------------------------------------
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 = 0.3457 r_free = 0.3457 target = 0.056329 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 53)----------------|
| r_work = 0.2965 r_free = 0.2965 target = 0.037133 restraints weight = 97096.120|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 37)----------------|
| r_work = 0.2980 r_free = 0.2980 target = 0.037626 restraints weight = 79084.639|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 39)----------------|
| r_work = 0.2991 r_free = 0.2991 target = 0.037950 restraints weight = 68831.511|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 24)----------------|
| r_work = 0.2997 r_free = 0.2997 target = 0.038143 restraints weight = 62776.989|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 36)----------------|
| r_work = 0.3003 r_free = 0.3003 target = 0.038332 restraints weight = 59150.709|
|-----------------------------------------------------------------------------|
r_work (final): 0.2891
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7273
moved from start:          0.8658

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.007   0.043   7422  Z= 0.466
  Angle     :  0.932   8.490  10702  Z= 0.516
  Chirality :  0.049   0.324   1480
  Planarity :  0.005   0.021   1118
  Dihedral  : 23.252 178.380   2524
  Min Nonbonded Distance : 2.048

Molprobity Statistics.
  All-atom Clashscore : 26.49
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  : 11.31 %
    Favored  : 88.69 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.00 %
    Favored  :  0.00 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 9.09 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -2.03 (0.26), residues: 1008
  helix: -0.93 (0.19), residues: 637
  sheet: -2.82 (0.59), residues: 53
  loop : -1.61 (0.39), residues: 318

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TYR   0.000   0.000   TYR A 698 
 PHE   0.000   0.000   PHE C  16 
 TRP   0.000   0.000   TRP C 522 

Details of bonding type rmsd
  covalent geometry    : bond        0.00731 ( 7422)
  covalent geometry    : angle       0.93237 (10702)
  hydrogen bonds       : bond        0.10644 (  603)
  hydrogen bonds       : angle       6.30016 ( 1650)

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

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

  2016 Ramachandran restraints generated.
    1008 Oldfield, 0 Emsley, 1008 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2016 Ramachandran restraints generated.
    1008 Oldfield, 0 Emsley, 1008 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  31 residues out of total 914 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 31
  time to evaluate  : 0.193 
Fit side-chains
  outliers start: 0
  outliers final: 0
  residues processed: 31
  average time/residue: 0.0265
  time to fit residues: 1.6960
Evaluate side-chains
  31 residues out of total 914 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 31
  time to evaluate  : 0.184 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 112
   random chunks:
   chunk 68 optimal weight:    4.9990
   chunk 108 optimal weight:    2.9990
   chunk 61 optimal weight:    0.8980
   chunk 78 optimal weight:   20.0000
   chunk 44 optimal weight:   10.0000
   chunk 37 optimal weight:   30.0000
   chunk 49 optimal weight:    0.5980
   chunk 27 optimal weight:   30.0000
   chunk 99 optimal weight:    0.8980
   chunk 51 optimal weight:    6.9990
   chunk 102 optimal weight:    6.9990
   overall best weight:    2.0784

-------------------------------------------------------------------------------
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 = 0.3548 r_free = 0.3548 target = 0.059396 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 61)----------------|
| r_work = 0.3064 r_free = 0.3064 target = 0.039303 restraints weight = 93090.654|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 38)----------------|
| r_work = 0.3081 r_free = 0.3081 target = 0.039879 restraints weight = 74945.225|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 27)----------------|
| r_work = 0.3094 r_free = 0.3094 target = 0.040279 restraints weight = 64855.028|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 38)----------------|
| r_work = 0.3102 r_free = 0.3102 target = 0.040556 restraints weight = 58688.793|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 29)----------------|
| r_work = 0.3107 r_free = 0.3107 target = 0.040717 restraints weight = 54790.773|
|-----------------------------------------------------------------------------|
r_work (final): 0.2984
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7172
moved from start:          0.8263

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.018   7422  Z= 0.175
  Angle     :  0.578   6.516  10702  Z= 0.307
  Chirality :  0.037   0.202   1480
  Planarity :  0.003   0.014   1118
  Dihedral  : 22.392 176.485   2524
  Min Nonbonded Distance : 2.212

Molprobity Statistics.
  All-atom Clashscore : 10.54
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.95 %
    Favored  : 94.05 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.00 %
    Favored  :  0.00 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 9.09 %
    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: -0.51 (0.27), residues: 1008
  helix:  0.41 (0.20), residues: 664
  sheet: -2.87 (0.60), residues: 47
  loop : -1.44 (0.41), residues: 297

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TYR   0.000   0.000   TYR A 698 
 PHE   0.000   0.000   PHE C  16 
 TRP   0.000   0.000   TRP C 522 

Details of bonding type rmsd
  covalent geometry    : bond        0.00270 ( 7422)
  covalent geometry    : angle       0.57775 (10702)
  hydrogen bonds       : bond        0.06152 (  603)
  hydrogen bonds       : angle       4.86679 ( 1650)

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

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

  2016 Ramachandran restraints generated.
    1008 Oldfield, 0 Emsley, 1008 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2016 Ramachandran restraints generated.
    1008 Oldfield, 0 Emsley, 1008 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  31 residues out of total 914 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 31
  time to evaluate  : 0.127 
Fit side-chains
  outliers start: 0
  outliers final: 0
  residues processed: 31
  average time/residue: 0.0284
  time to fit residues: 1.8080
Evaluate side-chains
  31 residues out of total 914 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 31
  time to evaluate  : 0.183 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 112
   random chunks:
   chunk 29 optimal weight:    0.0770
   chunk 11 optimal weight:    8.9990
   chunk 48 optimal weight:   20.0000
   chunk 31 optimal weight:    0.9980
   chunk 15 optimal weight:    3.9990
   chunk 17 optimal weight:    2.9990
   chunk 19 optimal weight:    4.9990
   chunk 51 optimal weight:    3.9990
   chunk 65 optimal weight:    0.4980
   chunk 2 optimal weight:   10.0000
   chunk 86 optimal weight:   20.0000
   overall best weight:    1.7142

-------------------------------------------------------------------------------
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 = 0.3633 r_free = 0.3633 target = 0.061116 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 63)----------------|
| r_work = 0.3131 r_free = 0.3131 target = 0.041997 restraints weight = 81225.017|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 55)----------------|
| r_work = 0.3159 r_free = 0.3159 target = 0.042937 restraints weight = 57909.263|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 29)----------------|
| r_work = 0.3176 r_free = 0.3176 target = 0.043497 restraints weight = 47006.140|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 40)----------------|
| r_work = 0.3189 r_free = 0.3189 target = 0.043909 restraints weight = 41210.490|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 26)----------------|
| r_work = 0.3193 r_free = 0.3193 target = 0.044043 restraints weight = 37876.280|
|-----------------------------------------------------------------------------|
r_work (final): 0.3127
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7852
moved from start:          0.8264

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.017   7422  Z= 0.145
  Angle     :  0.525   6.571  10702  Z= 0.273
  Chirality :  0.036   0.213   1480
  Planarity :  0.002   0.014   1118
  Dihedral  : 21.919 176.839   2524
  Min Nonbonded Distance : 2.233

Molprobity Statistics.
  All-atom Clashscore : 9.49
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.25 %
    Favored  : 93.75 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.00 %
    Favored  :  0.00 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 9.09 %
    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:  0.92 (0.29), residues: 1008
  helix:  1.69 (0.21), residues: 656
  sheet: -2.60 (0.64), residues: 49
  loop : -1.21 (0.42), residues: 303

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TYR   0.000   0.000   TYR A 698 
 PHE   0.000   0.000   PHE C  16 
 TRP   0.000   0.000   TRP C 522 

Details of bonding type rmsd
  covalent geometry    : bond        0.00227 ( 7422)
  covalent geometry    : angle       0.52522 (10702)
  hydrogen bonds       : bond        0.05207 (  603)
  hydrogen bonds       : angle       4.32085 ( 1650)

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

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

  2016 Ramachandran restraints generated.
    1008 Oldfield, 0 Emsley, 1008 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2016 Ramachandran restraints generated.
    1008 Oldfield, 0 Emsley, 1008 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  31 residues out of total 914 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 31
  time to evaluate  : 0.199 
Fit side-chains
  outliers start: 0
  outliers final: 0
  residues processed: 31
  average time/residue: 0.0289
  time to fit residues: 1.9145
Evaluate side-chains
  31 residues out of total 914 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 31
  time to evaluate  : 0.169 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 112
   random chunks:
   chunk 16 optimal weight:    8.9990
   chunk 91 optimal weight:   30.0000
   chunk 36 optimal weight:   30.0000
   chunk 76 optimal weight:   30.0000
   chunk 82 optimal weight:   40.0000
   chunk 67 optimal weight:   10.0000
   chunk 71 optimal weight:    7.9990
   chunk 102 optimal weight:    8.9990
   chunk 80 optimal weight:   10.0000
   chunk 57 optimal weight:    6.9990
   chunk 97 optimal weight:    7.9990
   overall best weight:    8.1990

-------------------------------------------------------------------------------
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 = 0.3456 r_free = 0.3456 target = 0.055986 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 59)----------------|
| r_work = 0.2997 r_free = 0.2997 target = 0.037853 restraints weight = 97101.715|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 33)----------------|
| r_work = 0.3010 r_free = 0.3010 target = 0.038263 restraints weight = 82176.223|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 31)----------------|
| r_work = 0.3017 r_free = 0.3017 target = 0.038509 restraints weight = 73223.331|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 37)----------------|
| r_work = 0.3023 r_free = 0.3023 target = 0.038701 restraints weight = 68195.030|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 28)----------------|
| r_work = 0.3027 r_free = 0.3027 target = 0.038811 restraints weight = 64764.644|
|-----------------------------------------------------------------------------|
r_work (final): 0.2882
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7716
moved from start:          0.9484

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.008   0.054   7422  Z= 0.526
  Angle     :  1.018   8.836  10702  Z= 0.564
  Chirality :  0.051   0.334   1480
  Planarity :  0.005   0.023   1118
  Dihedral  : 23.434 177.482   2524
  Min Nonbonded Distance : 2.032

Molprobity Statistics.
  All-atom Clashscore : 31.71
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  : 12.60 %
    Favored  : 87.40 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.00 %
    Favored  :  0.00 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 9.09 %
    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: -1.99 (0.26), residues: 1008
  helix: -0.78 (0.19), residues: 632
  sheet: -2.70 (0.63), residues: 53
  loop : -1.90 (0.39), residues: 323

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TYR   0.000   0.000   TYR A 698 
 PHE   0.000   0.000   PHE C  16 
 TRP   0.000   0.000   TRP C 522 

Details of bonding type rmsd
  covalent geometry    : bond        0.00823 ( 7422)
  covalent geometry    : angle       1.01829 (10702)
  hydrogen bonds       : bond        0.11501 (  603)
  hydrogen bonds       : angle       6.60474 ( 1650)

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

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

  2016 Ramachandran restraints generated.
    1008 Oldfield, 0 Emsley, 1008 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2016 Ramachandran restraints generated.
    1008 Oldfield, 0 Emsley, 1008 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  31 residues out of total 914 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 31
  time to evaluate  : 0.196 
Fit side-chains
  outliers start: 0
  outliers final: 0
  residues processed: 31
  average time/residue: 0.0294
  time to fit residues: 1.9261
Evaluate side-chains
  31 residues out of total 914 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 31
  time to evaluate  : 0.186 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 112
   random chunks:
   chunk 96 optimal weight:    3.9990
   chunk 47 optimal weight:   10.0000
   chunk 79 optimal weight:    8.9990
   chunk 61 optimal weight:    1.9990
   chunk 25 optimal weight:   30.0000
   chunk 37 optimal weight:   30.0000
   chunk 52 optimal weight:    5.9990
   chunk 72 optimal weight:    7.9990
   chunk 62 optimal weight:    9.9990
   chunk 92 optimal weight:    5.9990
   chunk 28 optimal weight:    9.9990
   overall best weight:    5.1990

-------------------------------------------------------------------------------
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 = 0.3487 r_free = 0.3487 target = 0.056962 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 53)----------------|
| r_work = 0.3016 r_free = 0.3016 target = 0.038236 restraints weight = 95302.092|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 32)----------------|
| r_work = 0.3030 r_free = 0.3030 target = 0.038680 restraints weight = 80028.909|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 29)----------------|
| r_work = 0.3039 r_free = 0.3039 target = 0.038958 restraints weight = 70995.889|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 25)----------------|
| r_work = 0.3045 r_free = 0.3045 target = 0.039180 restraints weight = 65493.008|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 33)----------------|
| r_work = 0.3050 r_free = 0.3050 target = 0.039323 restraints weight = 61981.589|
|-----------------------------------------------------------------------------|
r_work (final): 0.2911
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7624
moved from start:          0.9481

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.006   0.032   7422  Z= 0.357
  Angle     :  0.790   8.068  10702  Z= 0.434
  Chirality :  0.044   0.253   1480
  Planarity :  0.004   0.018   1118
  Dihedral  : 23.070 178.659   2524
  Min Nonbonded Distance : 2.121

Molprobity Statistics.
  All-atom Clashscore : 20.22
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  : 11.81 %
    Favored  : 88.19 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.00 %
    Favored  :  0.00 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 9.09 %
    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: -1.90 (0.26), residues: 1008
  helix: -0.66 (0.19), residues: 636
  sheet: -2.90 (0.60), residues: 54
  loop : -1.94 (0.39), residues: 318

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TYR   0.000   0.000   TYR A 698 
 PHE   0.000   0.000   PHE C  16 
 TRP   0.000   0.000   TRP C 522 

Details of bonding type rmsd
  covalent geometry    : bond        0.00555 ( 7422)
  covalent geometry    : angle       0.79000 (10702)
  hydrogen bonds       : bond        0.08958 (  603)
  hydrogen bonds       : angle       5.92469 ( 1650)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 1652.88 seconds
wall clock time: 28 minutes 51.60 seconds (1731.60 seconds total)