Starting phenix.real_space_refine
on Thu Jul  2 06:51:41 2026 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/9rw8_54303/07_2026/9rw8_54303.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/9rw8_54303/07_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_54303/07_2026/9rw8_54303.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/9rw8_54303/07_2026/9rw8_54303.cif"
    real_map_files = "/net/cci-nas-00/data/ceres_data/9rw8_54303/07_2026/9rw8_54303.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/9rw8_54303/07_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-dev-6108/lib/python3.11/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: 1.90, per 1000 atoms: 0.26
  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: 0.56
  Conformation dependent library (CDL) restraints added in 415.6 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: 0.56
  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: 1.30

  Time building geometry restraints manager: 0.75 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=" N9    A E   1 "
       pdb=" C4    A E   1 "
    ideal  model  delta    sigma   weight residual
    1.374  1.386 -0.012 6.00e-03 2.78e+04 3.93e+00
  bond pdb=" N1    G E  50 "
       pdb=" C2    G E  50 "
    ideal  model  delta    sigma   weight residual
    1.373  1.357  0.016 8.00e-03 1.56e+04 3.89e+00
  bond pdb=" N7    G F  18 "
       pdb=" C5    G F  18 "
    ideal  model  delta    sigma   weight residual
    1.388  1.377  0.011 6.00e-03 2.78e+04 3.53e+00
  bond pdb=" C2    G E  50 "
       pdb=" N3    G E  50 "
    ideal  model  delta    sigma   weight residual
    1.323  1.308  0.015 8.00e-03 1.56e+04 3.50e+00
  bond pdb=" N9    G F  18 "
       pdb=" C8    G F  18 "
    ideal  model  delta    sigma   weight residual
    1.374  1.361  0.013 7.00e-03 2.04e+04 3.46e+00
  ... (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=" 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 1.30e+00 5.92e-01 4.31e+01
  angle pdb=" N9    G E  50 "
        pdb=" C4    G E  50 "
        pdb=" C5    G E  50 "
      ideal   model   delta    sigma   weight residual
     105.40  107.98   -2.58 4.00e-01 6.25e+00 4.15e+01
  angle pdb=" O6    G E  50 "
        pdb=" C6    G E  50 "
        pdb=" N1    G E  50 "
      ideal   model   delta    sigma   weight residual
     119.90  116.05    3.85 6.00e-01 2.78e+00 4.12e+01
  angle pdb=" C1'   G F  18 "
        pdb=" N9    G F  18 "
        pdb=" C8    G F  18 "
      ideal   model   delta    sigma   weight residual
     127.00  119.18    7.82 1.30e+00 5.92e-01 3.62e+01
  angle pdb=" C1'   G E  18 "
        pdb=" N9    G E  18 "
        pdb=" C4    G E  18 "
      ideal   model   delta    sigma   weight residual
     126.50  134.08   -7.58 1.30e+00 5.92e-01 3.40e+01
  ... (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:             3.670
  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:          0.110
  Check model and map are aligned:         0.020
  Set scattering table:                    0.020
  Process input model:                     8.200
  Find NCS groups from input model:        0.100
  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:1.130
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   13.260
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7072
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= 0.194
  Angle     :  0.637   8.534  10702  Z= 0.540
  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/Z
  covalent geometry    : bond        0.00212 /  0.19 ( 7422)
  covalent geometry    : angle       0.63651 /  0.54 (10702)
  hydrogen bonds       : bond        0.23551 / 18.14 (  603)
  hydrogen bonds       : angle       8.03865 /  6.46 ( 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  : 0.225 
Fit side-chains
  outliers start: 0
  outliers final: 0
  residues processed: 31
  average time/residue: 0.0303
  time to fit residues: 2.0184
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  : 0.162 
-------------------------------------------------------------------------------
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:   10.0000
   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:    5.9990

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

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3654 r_free = 0.3654 target = 0.063728 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 58)----------------|
| r_work = 0.3161 r_free = 0.3161 target = 0.042583 restraints weight = 86619.898|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 40)----------------|
| r_work = 0.3177 r_free = 0.3177 target = 0.043167 restraints weight = 71463.610|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 26)----------------|
| r_work = 0.3185 r_free = 0.3185 target = 0.043460 restraints weight = 62594.965|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 44)----------------|
| r_work = 0.3195 r_free = 0.3195 target = 0.043816 restraints weight = 57644.209|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 39)----------------|
| r_work = 0.3201 r_free = 0.3201 target = 0.044045 restraints weight = 53815.833|
|-----------------------------------------------------------------------------|
r_work (final): 0.3096
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7326
moved from start:          0.2682

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.037   7422  Z= 0.351
  Angle     :  0.791   9.863  10702  Z= 0.505
  Chirality :  0.050   0.323   1480
  Planarity :  0.005   0.025   1118
  Dihedral  : 21.949 178.505   2524
  Min Nonbonded Distance : 2.072

Molprobity Statistics.
  All-atom Clashscore : 18.99
  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: -1.52 (0.24), residues: 1008
  helix: -0.83 (0.18), residues: 658
  sheet: -2.17 (0.58), residues: 57
  loop : -0.70 (0.37), residues: 293

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/Z
  covalent geometry    : bond        0.00481 /  0.35 ( 7422)
  covalent geometry    : angle       0.79061 /  0.50 (10702)
  hydrogen bonds       : bond        0.10629 /  7.91 (  603)
  hydrogen bonds       : angle       6.23732 /  4.96 ( 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  : 0.202 
Fit side-chains
  outliers start: 0
  outliers final: 0
  residues processed: 31
  average time/residue: 0.0295
  time to fit residues: 1.9543
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  : 0.226 
-------------------------------------------------------------------------------
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:    4.9990
   chunk 0 optimal weight:   40.0000
   chunk 111 optimal weight:   10.0000
   chunk 110 optimal weight:    9.9990
   chunk 68 optimal weight:    6.9990
   chunk 4 optimal weight:   10.0000
   chunk 73 optimal weight:    7.9990
   chunk 27 optimal weight:    5.9990
   chunk 21 optimal weight:    0.8980
   chunk 76 optimal weight:   50.0000
   chunk 22 optimal weight:    0.9980
   overall best weight:    3.9786

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

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3654 r_free = 0.3654 target = 0.063454 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 65)----------------|
| r_work = 0.3161 r_free = 0.3161 target = 0.042306 restraints weight = 86775.731|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 38)----------------|
| r_work = 0.3179 r_free = 0.3179 target = 0.042967 restraints weight = 69678.850|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 37)----------------|
| r_work = 0.3191 r_free = 0.3191 target = 0.043420 restraints weight = 60003.570|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 43)----------------|
| r_work = 0.3200 r_free = 0.3200 target = 0.043729 restraints weight = 54241.559|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 29)----------------|
| r_work = 0.3205 r_free = 0.3205 target = 0.043910 restraints weight = 50684.960|
|-----------------------------------------------------------------------------|
r_work (final): 0.3097
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7290
moved from start:          0.3367

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.029   7422  Z= 0.255
  Angle     :  0.615   9.394  10702  Z= 0.392
  Chirality :  0.043   0.314   1480
  Planarity :  0.003   0.023   1118
  Dihedral  : 21.799 177.876   2524
  Min Nonbonded Distance : 2.179

Molprobity Statistics.
  All-atom Clashscore : 12.44
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.17 %
    Favored  : 96.83 %
  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 (0.26), residues: 1008
  helix:  0.03 (0.19), residues: 657
  sheet: -2.13 (0.61), residues: 54
  loop : -0.45 (0.39), 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/Z
  covalent geometry    : bond        0.00346 /  0.26 ( 7422)
  covalent geometry    : angle       0.61474 /  0.39 (10702)
  hydrogen bonds       : bond        0.07730 /  5.79 (  603)
  hydrogen bonds       : angle       5.26279 /  4.25 ( 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  : 0.188 
Fit side-chains
  outliers start: 0
  outliers final: 0
  residues processed: 31
  average time/residue: 0.0290
  time to fit residues: 1.9110
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  : 0.233 
-------------------------------------------------------------------------------
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:   10.0000
   chunk 77 optimal weight:   30.0000
   chunk 67 optimal weight:    9.9990
   chunk 88 optimal weight:   40.0000
   chunk 68 optimal weight:    4.9990
   chunk 72 optimal weight:    0.9990
   chunk 105 optimal weight:    9.9990
   chunk 64 optimal weight:    0.1980
   chunk 100 optimal weight:    5.9990
   chunk 48 optimal weight:    9.9990
   chunk 18 optimal weight:    0.9980
   overall best weight:    2.6386

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

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3660 r_free = 0.3660 target = 0.063686 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 52)----------------|
| r_work = 0.3160 r_free = 0.3160 target = 0.042273 restraints weight = 87261.334|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 38)----------------|
| r_work = 0.3180 r_free = 0.3180 target = 0.042956 restraints weight = 69701.188|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 35)----------------|
| r_work = 0.3193 r_free = 0.3193 target = 0.043415 restraints weight = 59840.671|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 36)----------------|
| r_work = 0.3202 r_free = 0.3202 target = 0.043739 restraints weight = 53999.213|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 34)----------------|
| r_work = 0.3207 r_free = 0.3207 target = 0.043914 restraints weight = 50334.392|
|-----------------------------------------------------------------------------|
r_work (final): 0.3100
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7949
moved from start:          0.3838

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.022   7422  Z= 0.191
  Angle     :  0.504   6.814  10702  Z= 0.330
  Chirality :  0.040   0.344   1480
  Planarity :  0.003   0.019   1118
  Dihedral  : 21.402 179.402   2524
  Min Nonbonded Distance : 2.149

Molprobity Statistics.
  All-atom Clashscore : 10.73
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.37 %
    Favored  : 96.63 %
  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:  0.64 (0.27), residues: 1008
  helix:  1.11 (0.20), residues: 661
  sheet: -2.22 (0.60), residues: 54
  loop : -0.45 (0.39), residues: 293

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/Z
  covalent geometry    : bond        0.00260 /  0.19 ( 7422)
  covalent geometry    : angle       0.50447 /  0.33 (10702)
  hydrogen bonds       : bond        0.06863 /  5.12 (  603)
  hydrogen bonds       : angle       4.76641 /  3.85 ( 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  : 0.212 
Fit side-chains
  outliers start: 0
  outliers final: 0
  residues processed: 31
  average time/residue: 0.0312
  time to fit residues: 2.0859
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  : 0.140 
-------------------------------------------------------------------------------
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:    9.9990
   chunk 75 optimal weight:    8.9990
   chunk 88 optimal weight:   40.0000
   chunk 28 optimal weight:    6.9990
   chunk 16 optimal weight:   10.0000
   chunk 76 optimal weight:   50.0000
   chunk 50 optimal weight:    9.9990
   chunk 37 optimal weight:   30.0000
   chunk 87 optimal weight:   20.0000
   chunk 41 optimal weight:   20.0000
   chunk 81 optimal weight:    1.9990
   overall best weight:    7.5990

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

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3544 r_free = 0.3544 target = 0.058983 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 55)----------------|
| r_work = 0.3045 r_free = 0.3045 target = 0.039005 restraints weight = 92994.881|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 39)----------------|
| r_work = 0.3062 r_free = 0.3062 target = 0.039542 restraints weight = 75822.096|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 39)----------------|
| r_work = 0.3073 r_free = 0.3073 target = 0.039910 restraints weight = 65985.536|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 25)----------------|
| r_work = 0.3078 r_free = 0.3078 target = 0.040086 restraints weight = 60080.029|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 41)----------------|
| r_work = 0.3084 r_free = 0.3084 target = 0.040305 restraints weight = 56873.406|
|-----------------------------------------------------------------------------|
r_work (final): 0.2986
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7349
moved from start:          0.5382

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.006   0.042   7422  Z= 0.451
  Angle     :  0.884  10.125  10702  Z= 0.568
  Chirality :  0.054   0.339   1480
  Planarity :  0.006   0.026   1118
  Dihedral  : 22.369 178.863   2524
  Min Nonbonded Distance : 1.901

Molprobity Statistics.
  All-atom Clashscore : 28.95
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  8.43 %
    Favored  : 91.57 %
  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: -2.38 (0.24), residues: 1008
  helix: -1.29 (0.18), residues: 645
  sheet: -2.40 (0.63), residues: 52
  loop : -1.65 (0.36), residues: 311

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/Z
  covalent geometry    : bond        0.00621 /  0.45 ( 7422)
  covalent geometry    : angle       0.88447 /  0.57 (10702)
  hydrogen bonds       : bond        0.12564 /  9.42 (  603)
  hydrogen bonds       : angle       6.45994 /  5.20 ( 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  : 0.227 
Fit side-chains
  outliers start: 0
  outliers final: 0
  residues processed: 31
  average time/residue: 0.0290
  time to fit residues: 1.8913
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  : 0.228 
-------------------------------------------------------------------------------
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:    5.9990
   chunk 50 optimal weight:    8.9990
   chunk 51 optimal weight:    9.9990
   chunk 49 optimal weight:    2.9990
   chunk 105 optimal weight:   10.0000
   chunk 72 optimal weight:    6.9990
   chunk 29 optimal weight:   20.0000
   chunk 13 optimal weight:    4.9990
   chunk 84 optimal weight:    0.9980
   chunk 44 optimal weight:    6.9990
   chunk 106 optimal weight:   10.0000
   overall best weight:    4.3988

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

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3589 r_free = 0.3589 target = 0.060543 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 57)----------------|
| r_work = 0.3091 r_free = 0.3091 target = 0.040131 restraints weight = 90727.228|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 36)----------------|
| r_work = 0.3109 r_free = 0.3109 target = 0.040727 restraints weight = 73048.707|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 38)----------------|
| r_work = 0.3121 r_free = 0.3121 target = 0.041135 restraints weight = 62993.426|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 30)----------------|
| r_work = 0.3128 r_free = 0.3128 target = 0.041392 restraints weight = 57044.116|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 37)----------------|
| r_work = 0.3134 r_free = 0.3134 target = 0.041600 restraints weight = 53421.947|
|-----------------------------------------------------------------------------|
r_work (final): 0.3029
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8055
moved from start:          0.5442

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.030   7422  Z= 0.286
  Angle     :  0.610   6.622  10702  Z= 0.404
  Chirality :  0.044   0.310   1480
  Planarity :  0.003   0.019   1118
  Dihedral  : 22.090 176.055   2524
  Min Nonbonded Distance : 2.101

Molprobity Statistics.
  All-atom Clashscore : 16.33
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.75 %
    Favored  : 94.25 %
  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 (0.26), residues: 1008
  helix: -0.46 (0.19), residues: 655
  sheet: -2.34 (0.65), residues: 52
  loop : -1.28 (0.39), residues: 301

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/Z
  covalent geometry    : bond        0.00389 /  0.29 ( 7422)
  covalent geometry    : angle       0.61039 /  0.40 (10702)
  hydrogen bonds       : bond        0.08278 /  6.21 (  603)
  hydrogen bonds       : angle       5.55108 /  4.50 ( 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  : 0.221 
Fit side-chains
  outliers start: 0
  outliers final: 0
  residues processed: 31
  average time/residue: 0.0278
  time to fit residues: 1.8496
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  : 0.223 
-------------------------------------------------------------------------------
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:    9.9990
   chunk 63 optimal weight:    0.9990
   chunk 71 optimal weight:    9.9990
   chunk 28 optimal weight:    9.9990
   chunk 25 optimal weight:   10.0000
   chunk 32 optimal weight:   30.0000
   chunk 21 optimal weight:    1.9990
   chunk 6 optimal weight:   20.0000
   chunk 109 optimal weight:   10.0000
   chunk 35 optimal weight:    6.9990
   chunk 88 optimal weight:   40.0000
   overall best weight:    5.9990

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

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3518 r_free = 0.3518 target = 0.058139 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 53)----------------|
| r_work = 0.3027 r_free = 0.3027 target = 0.038403 restraints weight = 96186.611|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 39)----------------|
| r_work = 0.3043 r_free = 0.3043 target = 0.038907 restraints weight = 78921.480|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 29)----------------|
| r_work = 0.3052 r_free = 0.3052 target = 0.039190 restraints weight = 69101.744|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 37)----------------|
| r_work = 0.3060 r_free = 0.3060 target = 0.039468 restraints weight = 63577.668|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 32)----------------|
| r_work = 0.3064 r_free = 0.3064 target = 0.039607 restraints weight = 59614.225|
|-----------------------------------------------------------------------------|
r_work (final): 0.2943
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7262
moved from start:          0.6412

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.032   7422  Z= 0.352
  Angle     :  0.750   7.933  10702  Z= 0.482
  Chirality :  0.050   0.335   1480
  Planarity :  0.005   0.021   1118
  Dihedral  : 22.575 175.801   2524
  Min Nonbonded Distance : 1.926

Molprobity Statistics.
  All-atom Clashscore : 23.73
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  : 10.22 %
    Favored  : 89.78 %
  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: -2.13 (0.25), residues: 1008
  helix: -1.09 (0.18), residues: 651
  sheet: -2.83 (0.68), residues: 47
  loop : -1.50 (0.39), residues: 310

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/Z
  covalent geometry    : bond        0.00483 /  0.35 ( 7422)
  covalent geometry    : angle       0.74985 /  0.48 (10702)
  hydrogen bonds       : bond        0.11191 /  8.41 (  603)
  hydrogen bonds       : angle       6.13003 /  4.96 ( 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  : 0.275 
Fit side-chains
  outliers start: 0
  outliers final: 0
  residues processed: 31
  average time/residue: 0.0315
  time to fit residues: 2.1223
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  : 0.227 
-------------------------------------------------------------------------------
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:    9.9990
   chunk 108 optimal weight:   10.0000
   chunk 61 optimal weight:    5.9990
   chunk 78 optimal weight:    7.9990
   chunk 44 optimal weight:    7.9990
   chunk 37 optimal weight:   20.0000
   chunk 49 optimal weight:    0.9990
   chunk 27 optimal weight:   30.0000
   chunk 99 optimal weight:    3.9990
   chunk 51 optimal weight:    4.9990
   chunk 102 optimal weight:    9.9990
   overall best weight:    4.7990

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

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3535 r_free = 0.3535 target = 0.058758 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 55)----------------|
| r_work = 0.3045 r_free = 0.3045 target = 0.038827 restraints weight = 94540.480|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 29)----------------|
| r_work = 0.3061 r_free = 0.3061 target = 0.039360 restraints weight = 77461.452|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 27)----------------|
| r_work = 0.3071 r_free = 0.3071 target = 0.039684 restraints weight = 67589.486|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 41)----------------|
| r_work = 0.3079 r_free = 0.3079 target = 0.039954 restraints weight = 61885.188|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 28)----------------|
| r_work = 0.3084 r_free = 0.3084 target = 0.040117 restraints weight = 58046.142|
|-----------------------------------------------------------------------------|
r_work (final): 0.2959
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7230
moved from start:          0.6523

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.029   7422  Z= 0.282
  Angle     :  0.613   6.177  10702  Z= 0.405
  Chirality :  0.044   0.266   1480
  Planarity :  0.004   0.017   1118
  Dihedral  : 22.432 173.723   2524
  Min Nonbonded Distance : 2.055

Molprobity Statistics.
  All-atom Clashscore : 18.99
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  8.33 %
    Favored  : 91.67 %
  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: -1.78 (0.26), residues: 1008
  helix: -0.72 (0.19), residues: 656
  sheet: -3.15 (0.63), residues: 49
  loop : -1.52 (0.39), 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/Z
  covalent geometry    : bond        0.00385 /  0.28 ( 7422)
  covalent geometry    : angle       0.61273 /  0.41 (10702)
  hydrogen bonds       : bond        0.08862 /  6.65 (  603)
  hydrogen bonds       : angle       5.72337 /  4.66 ( 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  : 0.221 
Fit side-chains
  outliers start: 0
  outliers final: 0
  residues processed: 31
  average time/residue: 0.0312
  time to fit residues: 2.0955
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  : 0.224 
-------------------------------------------------------------------------------
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:   20.0000
   chunk 11 optimal weight:    8.9990
   chunk 48 optimal weight:   10.0000
   chunk 31 optimal weight:   30.0000
   chunk 15 optimal weight:    0.3980
   chunk 17 optimal weight:    7.9990
   chunk 19 optimal weight:    0.6980
   chunk 51 optimal weight:    9.9990
   chunk 65 optimal weight:    0.3980
   chunk 2 optimal weight:   10.0000
   chunk 86 optimal weight:   20.0000
   overall best weight:    3.6984

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

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3553 r_free = 0.3553 target = 0.059240 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 47)----------------|
| r_work = 0.3062 r_free = 0.3062 target = 0.039214 restraints weight = 92651.401|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 31)----------------|
| r_work = 0.3079 r_free = 0.3079 target = 0.039769 restraints weight = 75374.773|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 32)----------------|
| r_work = 0.3090 r_free = 0.3090 target = 0.040154 restraints weight = 65615.107|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 36)----------------|
| r_work = 0.3098 r_free = 0.3098 target = 0.040421 restraints weight = 59544.991|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 31)----------------|
| r_work = 0.3103 r_free = 0.3103 target = 0.040580 restraints weight = 55739.635|
|-----------------------------------------------------------------------------|
r_work (final): 0.2980
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7217
moved from start:          0.6698

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.022   7422  Z= 0.240
  Angle     :  0.544   6.034  10702  Z= 0.357
  Chirality :  0.041   0.252   1480
  Planarity :  0.003   0.016   1118
  Dihedral  : 22.213 171.365   2524
  Min Nonbonded Distance : 2.100

Molprobity Statistics.
  All-atom Clashscore : 15.00
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  8.23 %
    Favored  : 91.77 %
  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: -0.94 (0.27), residues: 1008
  helix: -0.00 (0.20), residues: 659
  sheet: -3.08 (0.63), residues: 48
  loop : -1.34 (0.41), residues: 301

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/Z
  covalent geometry    : bond        0.00328 /  0.24 ( 7422)
  covalent geometry    : angle       0.54391 /  0.36 (10702)
  hydrogen bonds       : bond        0.07642 /  5.72 (  603)
  hydrogen bonds       : angle       5.23399 /  4.28 ( 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  : 0.164 
Fit side-chains
  outliers start: 0
  outliers final: 0
  residues processed: 31
  average time/residue: 0.0321
  time to fit residues: 2.0464
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 
-------------------------------------------------------------------------------
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:   10.0000
   chunk 91 optimal weight:    5.9990
   chunk 36 optimal weight:    0.7980
   chunk 76 optimal weight:   40.0000
   chunk 82 optimal weight:   30.0000
   chunk 67 optimal weight:    0.0870
   chunk 71 optimal weight:    8.9990
   chunk 102 optimal weight:   10.0000
   chunk 80 optimal weight:    0.9980
   chunk 57 optimal weight:    7.9990
   chunk 97 optimal weight:    6.9990
   overall best weight:    2.9762

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

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3570 r_free = 0.3570 target = 0.059865 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 50)----------------|
| r_work = 0.3081 r_free = 0.3081 target = 0.039630 restraints weight = 92259.142|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 36)----------------|
| r_work = 0.3099 r_free = 0.3099 target = 0.040223 restraints weight = 74444.806|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 30)----------------|
| r_work = 0.3110 r_free = 0.3110 target = 0.040581 restraints weight = 64225.392|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 38)----------------|
| r_work = 0.3119 r_free = 0.3119 target = 0.040890 restraints weight = 58460.613|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 15)----------------|
| r_work = 0.3122 r_free = 0.3122 target = 0.041011 restraints weight = 54507.650|
|-----------------------------------------------------------------------------|
r_work (final): 0.2996
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7197
moved from start:          0.6833

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.021   7422  Z= 0.202
  Angle     :  0.493   5.888  10702  Z= 0.324
  Chirality :  0.039   0.235   1480
  Planarity :  0.003   0.016   1118
  Dihedral  : 22.046 170.030   2524
  Min Nonbonded Distance : 2.134

Molprobity Statistics.
  All-atom Clashscore : 13.20
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.36 %
    Favored  : 94.64 %
  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: -0.30 (0.27), residues: 1008
  helix:  0.59 (0.20), residues: 665
  sheet: -3.14 (0.62), residues: 48
  loop : -1.32 (0.41), residues: 295

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/Z
  covalent geometry    : bond        0.00275 /  0.20 ( 7422)
  covalent geometry    : angle       0.49265 /  0.32 (10702)
  hydrogen bonds       : bond        0.06870 /  5.14 (  603)
  hydrogen bonds       : angle       4.93251 /  4.05 ( 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  : 0.222 
Fit side-chains
  outliers start: 0
  outliers final: 0
  residues processed: 31
  average time/residue: 0.0284
  time to fit residues: 1.9004
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  : 0.147 
-------------------------------------------------------------------------------
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:    9.9990
   chunk 47 optimal weight:    7.9990
   chunk 79 optimal weight:   20.0000
   chunk 61 optimal weight:    0.7980
   chunk 25 optimal weight:   20.0000
   chunk 37 optimal weight:   40.0000
   chunk 52 optimal weight:    5.9990
   chunk 72 optimal weight:    3.9990
   chunk 62 optimal weight:    6.9990
   chunk 92 optimal weight:   20.0000
   chunk 28 optimal weight:    5.9990
   overall best weight:    4.7588

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

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3590 r_free = 0.3590 target = 0.059214 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 65)----------------|
| r_work = 0.3067 r_free = 0.3067 target = 0.040274 restraints weight = 84696.986|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 46)----------------|
| r_work = 0.3095 r_free = 0.3095 target = 0.041161 restraints weight = 61290.204|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 31)----------------|
| r_work = 0.3111 r_free = 0.3111 target = 0.041637 restraints weight = 49979.605|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 29)----------------|
| r_work = 0.3124 r_free = 0.3124 target = 0.042051 restraints weight = 43956.106|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 22)----------------|
| r_work = 0.3124 r_free = 0.3124 target = 0.042056 restraints weight = 40423.240|
|-----------------------------------------------------------------------------|
r_work (final): 0.3055
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7968
moved from start:          0.7164

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.027   7422  Z= 0.286
  Angle     :  0.595   6.766  10702  Z= 0.387
  Chirality :  0.043   0.257   1480
  Planarity :  0.003   0.017   1118
  Dihedral  : 22.293 170.931   2524
  Min Nonbonded Distance : 2.048

Molprobity Statistics.
  All-atom Clashscore : 18.13
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  9.92 %
    Favored  : 90.08 %
  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: -0.93 (0.27), residues: 1008
  helix:  0.05 (0.20), residues: 659
  sheet: -3.11 (0.63), residues: 49
  loop : -1.44 (0.41), residues: 300

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/Z
  covalent geometry    : bond        0.00391 /  0.29 ( 7422)
  covalent geometry    : angle       0.59456 /  0.39 (10702)
  hydrogen bonds       : bond        0.08535 /  6.39 (  603)
  hydrogen bonds       : angle       5.29976 /  4.34 ( 1650)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 1553.27 seconds
wall clock time: 27 minutes 11.12 seconds (1631.12 seconds total)