Starting phenix.real_space_refine
on Tue Aug  4 23:04:00 2026 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/9rw8_54303/08_2026/9rw8_54303.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/9rw8_54303/08_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 {
    real_map_files = "/net/cci-nas-00/data/ceres_data/9rw8_54303/08_2026/9rw8_54303.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/9rw8_54303/08_2026/9rw8_54303.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/9rw8_54303/08_2026/9rw8_54303.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/9rw8_54303/08_2026/9rw8_54303.cif"
  }
  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-2.2rc3-6140/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: 1.60, per 1000 atoms: 0.22
  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: 0.48
  Conformation dependent library (CDL) restraints added in 261.6 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: 0.73
  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: 1.14

  Time building geometry restraints manager: 0.61 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: 10223
        1.71 -     3.41: 445
        3.41 -     5.12: 23
        5.12 -     6.83: 7
        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=" 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 7.00e-01 2.04e+00 3.90e+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
  ... (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: 1225
       0.057 -    0.114: 221
       0.114 -    0.172: 33
       0.172 -    0.229: 0
       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=" 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
  chirality pdb=" C1'   G E  50 "
            pdb=" O4'   G E  50 "
            pdb=" C2'   G E  50 "
            pdb=" N9    G E  50 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.47    2.32    0.15 2.00e-01 2.50e+01 5.69e-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:             3.250
  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:             0.010
  Extract box with map and model:          0.130
  Check model and map are aligned:         0.020
  Set scattering table:                    0.020
  Process input model:                     7.350
  Find NCS groups from input model:        0.120
  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:1.150
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   12.060
-------------------------------------------------------------------------------
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= 0.210
  Angle     :  0.711   8.534  10702  Z= 0.619
  Chirality :  0.045   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        0.00228 /  0.21 ( 7422)
  covalent geometry    : angle       0.71138 /  0.62 (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  : 0.211 
Fit side-chains
  outliers start: 0
  outliers final: 0
  residues processed: 31
  average time/residue: 0.0244
  time to fit residues: 1.6070
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  : 0.129 
-------------------------------------------------------------------------------
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:   20.0000
   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 = 0.3668 r_free = 0.3668 target = 0.064303 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 51)----------------|
| r_work = 0.3182 r_free = 0.3182 target = 0.043154 restraints weight = 86622.476|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 30)----------------|
| r_work = 0.3199 r_free = 0.3199 target = 0.043775 restraints weight = 71160.191|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 32)----------------|
| r_work = 0.3211 r_free = 0.3211 target = 0.044196 restraints weight = 61752.662|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 29)----------------|
| r_work = 0.3220 r_free = 0.3220 target = 0.044511 restraints weight = 56100.593|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 22)----------------|
| r_work = 0.3224 r_free = 0.3224 target = 0.044647 restraints weight = 52258.462|
|-----------------------------------------------------------------------------|
r_work (final): 0.3113
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7309
moved from start:          0.2312

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.034   7422  Z= 0.358
  Angle     :  0.790  16.379  10702  Z= 0.487
  Chirality :  0.049   0.362   1480
  Planarity :  0.005   0.025   1118
  Dihedral  : 21.612 174.444   2524
  Min Nonbonded Distance : 2.103

Molprobity Statistics.
  All-atom Clashscore : 15.95
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.46 %
    Favored  : 95.54 %
  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: -1.02 (0.25), residues: 1008
  helix: -0.39 (0.18), residues: 652
  sheet: -2.08 (0.57), residues: 57
  loop : -0.62 (0.36), residues: 299

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        0.00464 /  0.36 ( 7422)
  covalent geometry    : angle       0.79038 /  0.49 (10702)
  hydrogen bonds       : bond        0.10077 /  7.51 (  603)
  hydrogen bonds       : angle       6.13903 /  4.90 ( 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  : 0.180 
Fit side-chains
  outliers start: 0
  outliers final: 0
  residues processed: 31
  average time/residue: 0.0318
  time to fit residues: 2.0662
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  : 0.231 
-------------------------------------------------------------------------------
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:   20.0000
   chunk 110 optimal weight:    9.9990
   chunk 68 optimal weight:    4.9990
   chunk 4 optimal weight:    9.9990
   chunk 73 optimal weight:    5.9990
   chunk 27 optimal weight:   40.0000
   chunk 21 optimal weight:    0.8980
   chunk 76 optimal weight:   50.0000
   chunk 22 optimal weight:    0.8980
   overall best weight:    3.5586

-------------------------------------------------------------------------------
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 = 0.3681 r_free = 0.3681 target = 0.064576 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 58)----------------|
| r_work = 0.3190 r_free = 0.3190 target = 0.043153 restraints weight = 85717.006|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 39)----------------|
| r_work = 0.3209 r_free = 0.3209 target = 0.043827 restraints weight = 69172.811|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 37)----------------|
| r_work = 0.3221 r_free = 0.3221 target = 0.044291 restraints weight = 59558.518|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 26)----------------|
| r_work = 0.3228 r_free = 0.3228 target = 0.044511 restraints weight = 53740.782|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 32)----------------|
| r_work = 0.3235 r_free = 0.3235 target = 0.044795 restraints weight = 50661.487|
|-----------------------------------------------------------------------------|
r_work (final): 0.3124
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7261
moved from start:          0.3261

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.024   7422  Z= 0.223
  Angle     :  0.628  11.972  10702  Z= 0.376
  Chirality :  0.043   0.410   1480
  Planarity :  0.003   0.021   1118
  Dihedral  : 21.358 176.078   2524
  Min Nonbonded Distance : 2.217

Molprobity Statistics.
  All-atom Clashscore : 11.20
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.08 %
    Favored  : 96.92 %
  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:  0.22 (0.26), residues: 1008
  helix:  0.67 (0.20), residues: 656
  sheet: -2.21 (0.55), residues: 60
  loop : -0.23 (0.39), residues: 292

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        0.00287 /  0.22 ( 7422)
  covalent geometry    : angle       0.62766 /  0.38 (10702)
  hydrogen bonds       : bond        0.07151 /  5.34 (  603)
  hydrogen bonds       : angle       4.98301 /  4.03 ( 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  : 0.191 
Fit side-chains
  outliers start: 0
  outliers final: 0
  residues processed: 31
  average time/residue: 0.0268
  time to fit residues: 1.7953
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  : 0.200 
-------------------------------------------------------------------------------
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:    0.0030
   chunk 67 optimal weight:   10.0000
   chunk 88 optimal weight:   40.0000
   chunk 68 optimal weight:    2.9990
   chunk 72 optimal weight:    0.9990
   chunk 105 optimal weight:    9.9990
   chunk 64 optimal weight:    0.8980
   chunk 100 optimal weight:    1.9990
   chunk 48 optimal weight:   10.0000
   chunk 18 optimal weight:    0.9980
   overall best weight:    0.9794

-------------------------------------------------------------------------------
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 = 0.3713 r_free = 0.3713 target = 0.066002 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 57)----------------|
| r_work = 0.3219 r_free = 0.3219 target = 0.044065 restraints weight = 85003.562|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 40)----------------|
| r_work = 0.3238 r_free = 0.3238 target = 0.044776 restraints weight = 67904.150|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 46)----------------|
| r_work = 0.3251 r_free = 0.3251 target = 0.045273 restraints weight = 58426.160|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 37)----------------|
| r_work = 0.3261 r_free = 0.3261 target = 0.045627 restraints weight = 52588.240|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 26)----------------|
| r_work = 0.3265 r_free = 0.3265 target = 0.045790 restraints weight = 48833.698|
|-----------------------------------------------------------------------------|
r_work (final): 0.3154
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7229
moved from start:          0.3418

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= 0.120
  Angle     :  0.465  10.026  10702  Z= 0.288
  Chirality :  0.037   0.280   1480
  Planarity :  0.002   0.022   1118
  Dihedral  : 20.783 179.190   2524
  Min Nonbonded Distance : 2.168

Molprobity Statistics.
  All-atom Clashscore : 7.69
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.28 %
    Favored  : 97.72 %
  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:  1.83 (0.28), residues: 1008
  helix:  2.06 (0.21), residues: 662
  sheet: -1.88 (0.63), residues: 54
  loop : -0.06 (0.40), residues: 292

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        0.00152 /  0.12 ( 7422)
  covalent geometry    : angle       0.46477 /  0.29 (10702)
  hydrogen bonds       : bond        0.05831 /  4.35 (  603)
  hydrogen bonds       : angle       4.34845 /  3.51 ( 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  : 0.213 
Fit side-chains
  outliers start: 0
  outliers final: 0
  residues processed: 31
  average time/residue: 0.0282
  time to fit residues: 1.8773
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  : 0.216 
-------------------------------------------------------------------------------
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:    9.9990
   chunk 88 optimal weight:   40.0000
   chunk 28 optimal weight:   40.0000
   chunk 16 optimal weight:   10.0000
   chunk 76 optimal weight:   40.0000
   chunk 50 optimal weight:   10.0000
   chunk 37 optimal weight:    5.9990
   chunk 87 optimal weight:    0.4980
   chunk 41 optimal weight:   30.0000
   chunk 81 optimal weight:    1.9990
   overall best weight:    5.6988

-------------------------------------------------------------------------------
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 = 0.3617 r_free = 0.3617 target = 0.061851 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 53)----------------|
| r_work = 0.3116 r_free = 0.3116 target = 0.041034 restraints weight = 89210.234|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 37)----------------|
| r_work = 0.3135 r_free = 0.3135 target = 0.041660 restraints weight = 71942.458|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 36)----------------|
| r_work = 0.3147 r_free = 0.3147 target = 0.042091 restraints weight = 62007.482|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 31)----------------|
| r_work = 0.3156 r_free = 0.3156 target = 0.042372 restraints weight = 56010.463|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 28)----------------|
| r_work = 0.3161 r_free = 0.3161 target = 0.042552 restraints weight = 52373.865|
|-----------------------------------------------------------------------------|
r_work (final): 0.3053
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7330
moved from start:          0.4268

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.033   7422  Z= 0.294
  Angle     :  0.704   9.436  10702  Z= 0.429
  Chirality :  0.046   0.390   1480
  Planarity :  0.004   0.022   1118
  Dihedral  : 21.382 179.100   2524
  Min Nonbonded Distance : 2.087

Molprobity Statistics.
  All-atom Clashscore : 16.61
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.37 %
    Favored  : 95.63 %
  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: -0.21 (0.26), residues: 1008
  helix:  0.36 (0.19), residues: 656
  sheet: -2.09 (0.63), residues: 52
  loop : -0.61 (0.38), 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        0.00380 /  0.29 ( 7422)
  covalent geometry    : angle       0.70436 /  0.43 (10702)
  hydrogen bonds       : bond        0.09218 /  6.90 (  603)
  hydrogen bonds       : angle       5.33130 /  4.32 ( 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  : 0.206 
Fit side-chains
  outliers start: 0
  outliers final: 0
  residues processed: 31
  average time/residue: 0.0259
  time to fit residues: 1.7370
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  : 0.210 
-------------------------------------------------------------------------------
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:    0.9980
   chunk 50 optimal weight:    9.9990
   chunk 51 optimal weight:    9.9990
   chunk 49 optimal weight:    0.8980
   chunk 105 optimal weight:    9.9990
   chunk 72 optimal weight:    2.9990
   chunk 29 optimal weight:   40.0000
   chunk 13 optimal weight:    6.9990
   chunk 84 optimal weight:    2.9990
   chunk 44 optimal weight:    3.9990
   chunk 106 optimal weight:   20.0000
   overall best weight:    2.3786

-------------------------------------------------------------------------------
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 = 0.3653 r_free = 0.3653 target = 0.063296 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 52)----------------|
| r_work = 0.3152 r_free = 0.3152 target = 0.042000 restraints weight = 86795.831|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 42)----------------|
| r_work = 0.3172 r_free = 0.3172 target = 0.042689 restraints weight = 68891.744|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 39)----------------|
| r_work = 0.3186 r_free = 0.3186 target = 0.043164 restraints weight = 58938.000|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 32)----------------|
| r_work = 0.3195 r_free = 0.3195 target = 0.043485 restraints weight = 53028.802|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 29)----------------|
| r_work = 0.3201 r_free = 0.3201 target = 0.043683 restraints weight = 49357.451|
|-----------------------------------------------------------------------------|
r_work (final): 0.3082
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7289
moved from start:          0.4351

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.022   7422  Z= 0.168
  Angle     :  0.504   6.234  10702  Z= 0.317
  Chirality :  0.039   0.266   1480
  Planarity :  0.003   0.021   1118
  Dihedral  : 21.165 178.327   2524
  Min Nonbonded Distance : 2.189

Molprobity Statistics.
  All-atom Clashscore : 11.11
  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:  0.73 (0.27), residues: 1008
  helix:  1.21 (0.20), residues: 662
  sheet: -2.14 (0.63), residues: 54
  loop : -0.51 (0.40), residues: 292

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        0.00215 /  0.17 ( 7422)
  covalent geometry    : angle       0.50439 /  0.32 (10702)
  hydrogen bonds       : bond        0.06391 /  4.77 (  603)
  hydrogen bonds       : angle       4.68571 /  3.80 ( 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  : 0.158 
Fit side-chains
  outliers start: 0
  outliers final: 0
  residues processed: 31
  average time/residue: 0.0245
  time to fit residues: 1.5855
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  : 0.206 
-------------------------------------------------------------------------------
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:   30.0000
   chunk 63 optimal weight:   20.0000
   chunk 71 optimal weight:   20.0000
   chunk 28 optimal weight:    5.9990
   chunk 25 optimal weight:   20.0000
   chunk 32 optimal weight:   30.0000
   chunk 21 optimal weight:    2.9990
   chunk 6 optimal weight:    0.6980
   chunk 109 optimal weight:   10.0000
   chunk 35 optimal weight:    8.9990
   chunk 88 optimal weight:   40.0000
   overall best weight:    5.7390

-------------------------------------------------------------------------------
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 = 0.3578 r_free = 0.3578 target = 0.060367 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 57)----------------|
| r_work = 0.3076 r_free = 0.3076 target = 0.039918 restraints weight = 91593.499|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 37)----------------|
| r_work = 0.3093 r_free = 0.3093 target = 0.040470 restraints weight = 74644.885|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 40)----------------|
| r_work = 0.3104 r_free = 0.3104 target = 0.040846 restraints weight = 65067.832|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 44)----------------|
| r_work = 0.3111 r_free = 0.3111 target = 0.041113 restraints weight = 59298.386|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 25)----------------|
| r_work = 0.3114 r_free = 0.3114 target = 0.041220 restraints weight = 55580.136|
|-----------------------------------------------------------------------------|
r_work (final): 0.3018
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7347
moved from start:          0.5269

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.031   7422  Z= 0.330
  Angle     :  0.744   9.531  10702  Z= 0.455
  Chirality :  0.049   0.391   1480
  Planarity :  0.004   0.021   1118
  Dihedral  : 21.668 177.480   2524
  Min Nonbonded Distance : 1.990

Molprobity Statistics.
  All-atom Clashscore : 19.56
  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: -1.07 (0.26), residues: 1008
  helix: -0.22 (0.19), residues: 660
  sheet: -2.24 (0.66), residues: 52
  loop : -1.23 (0.39), residues: 296

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        0.00425 /  0.33 ( 7422)
  covalent geometry    : angle       0.74428 /  0.46 (10702)
  hydrogen bonds       : bond        0.10147 /  7.60 (  603)
  hydrogen bonds       : angle       5.63586 /  4.56 ( 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  : 0.194 
Fit side-chains
  outliers start: 0
  outliers final: 0
  residues processed: 31
  average time/residue: 0.0295
  time to fit residues: 1.9788
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 
-------------------------------------------------------------------------------
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:    2.9990
   chunk 108 optimal weight:   10.0000
   chunk 61 optimal weight:    0.9980
   chunk 78 optimal weight:   40.0000
   chunk 44 optimal weight:    0.6980
   chunk 37 optimal weight:   20.0000
   chunk 49 optimal weight:    0.7980
   chunk 27 optimal weight:    7.9990
   chunk 99 optimal weight:    7.9990
   chunk 51 optimal weight:   10.0000
   chunk 102 optimal weight:   10.0000
   overall best weight:    2.6984

-------------------------------------------------------------------------------
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 = 0.3605 r_free = 0.3605 target = 0.061441 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 55)----------------|
| r_work = 0.3115 r_free = 0.3115 target = 0.040645 restraints weight = 91475.558|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 33)----------------|
| r_work = 0.3132 r_free = 0.3132 target = 0.041231 restraints weight = 74118.035|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 34)----------------|
| r_work = 0.3144 r_free = 0.3144 target = 0.041646 restraints weight = 64432.678|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 26)----------------|
| r_work = 0.3151 r_free = 0.3151 target = 0.041884 restraints weight = 58456.018|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 30)----------------|
| r_work = 0.3157 r_free = 0.3157 target = 0.042103 restraints weight = 54907.490|
|-----------------------------------------------------------------------------|
r_work (final): 0.3027
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7214
moved from start:          0.5271

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.024   7422  Z= 0.198
  Angle     :  0.530   6.085  10702  Z= 0.334
  Chirality :  0.040   0.248   1480
  Planarity :  0.003   0.019   1118
  Dihedral  : 21.433 174.972   2524
  Min Nonbonded Distance : 2.133

Molprobity Statistics.
  All-atom Clashscore : 12.63
  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:  0.05 (0.27), residues: 1008
  helix:  0.74 (0.20), residues: 661
  sheet: -2.30 (0.65), residues: 54
  loop : -0.94 (0.41), 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        0.00255 /  0.20 ( 7422)
  covalent geometry    : angle       0.53033 /  0.33 (10702)
  hydrogen bonds       : bond        0.06867 /  5.13 (  603)
  hydrogen bonds       : angle       4.91396 /  4.00 ( 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  : 0.133 
Fit side-chains
  outliers start: 0
  outliers final: 0
  residues processed: 31
  average time/residue: 0.0243
  time to fit residues: 1.6223
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  : 0.130 
-------------------------------------------------------------------------------
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:   40.0000
   chunk 11 optimal weight:    5.9990
   chunk 48 optimal weight:    0.7980
   chunk 31 optimal weight:   30.0000
   chunk 15 optimal weight:    9.9990
   chunk 17 optimal weight:    0.8980
   chunk 19 optimal weight:    3.9990
   chunk 51 optimal weight:    9.9990
   chunk 65 optimal weight:    1.9990
   chunk 2 optimal weight:   10.0000
   chunk 86 optimal weight:    0.9980
   overall best weight:    1.7384

-------------------------------------------------------------------------------
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 = 0.3690 r_free = 0.3690 target = 0.063290 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 48)----------------|
| r_work = 0.3180 r_free = 0.3180 target = 0.043608 restraints weight = 79437.173|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 40)----------------|
| r_work = 0.3214 r_free = 0.3214 target = 0.044688 restraints weight = 56167.813|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 28)----------------|
| r_work = 0.3232 r_free = 0.3232 target = 0.045276 restraints weight = 44943.850|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 46)----------------|
| r_work = 0.3245 r_free = 0.3245 target = 0.045727 restraints weight = 39143.150|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 32)----------------|
| r_work = 0.3252 r_free = 0.3252 target = 0.045979 restraints weight = 35711.532|
|-----------------------------------------------------------------------------|
r_work (final): 0.3176
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7804
moved from start:          0.5362

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= 0.133
  Angle     :  0.431   5.750  10702  Z= 0.272
  Chirality :  0.036   0.145   1480
  Planarity :  0.002   0.018   1118
  Dihedral  : 21.093 172.647   2524
  Min Nonbonded Distance : 2.207

Molprobity Statistics.
  All-atom Clashscore : 9.40
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.46 %
    Favored  : 95.54 %
  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:  1.44 (0.28), residues: 1008
  helix:  1.91 (0.20), residues: 659
  sheet: -2.29 (0.64), residues: 54
  loop : -0.54 (0.42), 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        0.00170 /  0.13 ( 7422)
  covalent geometry    : angle       0.43078 /  0.27 (10702)
  hydrogen bonds       : bond        0.05733 /  4.27 (  603)
  hydrogen bonds       : angle       4.39826 /  3.59 ( 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  : 0.145 
Fit side-chains
  outliers start: 0
  outliers final: 0
  residues processed: 31
  average time/residue: 0.0268
  time to fit residues: 1.7604
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 
-------------------------------------------------------------------------------
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:    0.2980
   chunk 91 optimal weight:   30.0000
   chunk 36 optimal weight:   40.0000
   chunk 76 optimal weight:   30.0000
   chunk 82 optimal weight:    6.9990
   chunk 67 optimal weight:    0.0020
   chunk 71 optimal weight:   10.0000
   chunk 102 optimal weight:    9.9990
   chunk 80 optimal weight:   10.0000
   chunk 57 optimal weight:    7.9990
   chunk 97 optimal weight:    7.9990
   overall best weight:    4.6594

-------------------------------------------------------------------------------
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 = 0.3619 r_free = 0.3619 target = 0.060715 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 63)----------------|
| r_work = 0.3099 r_free = 0.3099 target = 0.041389 restraints weight = 82520.196|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 33)----------------|
| r_work = 0.3127 r_free = 0.3127 target = 0.042311 restraints weight = 59197.552|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 34)----------------|
| r_work = 0.3145 r_free = 0.3145 target = 0.042918 restraints weight = 48294.402|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 23)----------------|
| r_work = 0.3155 r_free = 0.3155 target = 0.043216 restraints weight = 42129.106|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 32)----------------|
| r_work = 0.3163 r_free = 0.3163 target = 0.043469 restraints weight = 38879.004|
|-----------------------------------------------------------------------------|
r_work (final): 0.3093
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7914
moved from start:          0.5907

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.028   7422  Z= 0.257
  Angle     :  0.614   7.572  10702  Z= 0.379
  Chirality :  0.043   0.286   1480
  Planarity :  0.004   0.018   1118
  Dihedral  : 21.593 174.715   2524
  Min Nonbonded Distance : 2.055

Molprobity Statistics.
  All-atom Clashscore : 17.28
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.85 %
    Favored  : 94.15 %
  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: -0.16 (0.27), residues: 1008
  helix:  0.62 (0.20), residues: 663
  sheet: -2.88 (0.63), residues: 50
  loop : -1.08 (0.40), 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        0.00332 /  0.26 ( 7422)
  covalent geometry    : angle       0.61428 /  0.38 (10702)
  hydrogen bonds       : bond        0.08575 /  6.41 (  603)
  hydrogen bonds       : angle       5.12939 /  4.18 ( 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  : 0.143 
Fit side-chains
  outliers start: 0
  outliers final: 0
  residues processed: 31
  average time/residue: 0.0278
  time to fit residues: 1.8304
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  : 0.153 
-------------------------------------------------------------------------------
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:   10.0000
   chunk 47 optimal weight:    6.9990
   chunk 79 optimal weight:   30.0000
   chunk 61 optimal weight:    0.4980
   chunk 25 optimal weight:   20.0000
   chunk 37 optimal weight:   30.0000
   chunk 52 optimal weight:    3.9990
   chunk 72 optimal weight:    3.9990
   chunk 62 optimal weight:    3.9990
   chunk 92 optimal weight:    5.9990
   chunk 28 optimal weight:    5.9990
   overall best weight:    3.6988

-------------------------------------------------------------------------------
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 = 0.3633 r_free = 0.3633 target = 0.061147 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 62)----------------|
| r_work = 0.3113 r_free = 0.3113 target = 0.041733 restraints weight = 82676.106|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 51)----------------|
| r_work = 0.3143 r_free = 0.3143 target = 0.042737 restraints weight = 58466.531|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 34)----------------|
| r_work = 0.3161 r_free = 0.3161 target = 0.043338 restraints weight = 46905.516|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 32)----------------|
| r_work = 0.3172 r_free = 0.3172 target = 0.043687 restraints weight = 40937.518|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 36)----------------|
| r_work = 0.3181 r_free = 0.3181 target = 0.043979 restraints weight = 37620.205|
|-----------------------------------------------------------------------------|
r_work (final): 0.3112
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7893
moved from start:          0.6153

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.023   7422  Z= 0.210
  Angle     :  0.539   6.366  10702  Z= 0.338
  Chirality :  0.040   0.208   1480
  Planarity :  0.003   0.017   1118
  Dihedral  : 21.638 172.682   2524
  Min Nonbonded Distance : 2.096

Molprobity Statistics.
  All-atom Clashscore : 14.33
  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:  0.09 (0.27), residues: 1008
  helix:  0.84 (0.20), residues: 668
  sheet: -2.90 (0.63), residues: 50
  loop : -1.07 (0.41), 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/Z
  covalent geometry    : bond        0.00271 /  0.21 ( 7422)
  covalent geometry    : angle       0.53923 /  0.34 (10702)
  hydrogen bonds       : bond        0.07170 /  5.35 (  603)
  hydrogen bonds       : angle       4.89198 /  3.99 ( 1650)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 1439.36 seconds
wall clock time: 25 minutes 9.61 seconds (1509.61 seconds total)