Starting phenix.real_space_refine
on Sun Apr  5 02:13:51 2026 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/9rw9_54304/04_2026/9rw9_54304.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/9rw9_54304/04_2026/9rw9_54304.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=4.2
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    model {
      file = "/net/cci-nas-00/data/ceres_data/9rw9_54304/04_2026/9rw9_54304.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/9rw9_54304/04_2026/9rw9_54304.cif"
    real_map_files = "/net/cci-nas-00/data/ceres_data/9rw9_54304/04_2026/9rw9_54304.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/9rw9_54304/04_2026/9rw9_54304.map"
  }
  resolution = 4.2
  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=   0.001 sd=   0.039
Set stop_for_unknowns flag
  Set to: True
Assert model is a single copy model
Assert all atoms have isotropic ADPs
Construct map_model_manager
Extract box with map and model
Check model and map are aligned
Set scattering table
  Set to: electron
  Number of scattering types: 4
    Type Number    sf(0)   Gaussians
     P      98      5.49       5
     C    3982      2.51       5
     N    1378      2.21       5
     O    1734      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model
  Monomer Library directory:
    "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.1rc1-6017/lib/python3.9/site-packages/chem_data/mon_lib"
  Total number of atoms: 7192
  Number of models: 1
  Model: ""
    Number of chains: 6
    Chain: "A"
      Number of atoms: 265
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 53, 265
          Classifications: {'peptide': 53}
          Incomplete info: {'truncation_to_alanine': 49}
          Link IDs: {'TRANS': 52}
          Unresolved non-hydrogen bonds: 178
          Unresolved non-hydrogen angles: 222
          Unresolved non-hydrogen dihedrals: 137
          Unresolved non-hydrogen chiralities: 15
          Planarities with less than four sites: {'GLU:plan': 10, 'TYR:plan': 1, 'GLN:plan1': 6, 'ASP:plan': 3, 'ASN:plan1': 2, 'ARG:plan': 5}
          Unresolved non-hydrogen planarities: 111
    Chain: "B"
      Number of atoms: 265
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 53, 265
          Classifications: {'peptide': 53}
          Incomplete info: {'truncation_to_alanine': 49}
          Link IDs: {'TRANS': 52}
          Unresolved non-hydrogen bonds: 178
          Unresolved non-hydrogen angles: 222
          Unresolved non-hydrogen dihedrals: 137
          Unresolved non-hydrogen chiralities: 15
          Planarities with less than four sites: {'GLU:plan': 10, 'TYR:plan': 1, 'GLN:plan1': 6, 'ASP:plan': 3, 'ASN:plan1': 2, 'ARG:plan': 5}
          Unresolved non-hydrogen planarities: 111
    Chain: "C"
      Number of atoms: 2277
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 460, 2277
          Classifications: {'peptide': 460}
          Incomplete info: {'truncation_to_alanine': 407}
          Link IDs: {'PCIS': 1, 'PTRANS': 10, 'TRANS': 448}
          Chain breaks: 3
          Unresolved chain link angles: 11
          Unresolved non-hydrogen bonds: 1499
          Unresolved non-hydrogen angles: 1898
          Unresolved non-hydrogen dihedrals: 1241
          Unresolved non-hydrogen chiralities: 130
          Planarities with less than four sites: {'GLU:plan': 31, 'TYR:plan': 20, 'ARG:plan': 23, 'ASN:plan1': 21, 'PHE:plan': 18, 'ASP:plan': 26, 'HIS:plan': 10, 'GLN:plan1': 31, 'TRP:plan': 2}
          Unresolved non-hydrogen planarities: 820
    Chain: "D"
      Number of atoms: 2287
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 462, 2287
          Classifications: {'peptide': 462}
          Incomplete info: {'truncation_to_alanine': 409}
          Link IDs: {'PCIS': 1, 'PTRANS': 10, 'TRANS': 450}
          Chain breaks: 3
          Unresolved chain link angles: 11
          Unresolved non-hydrogen bonds: 1501
          Unresolved non-hydrogen angles: 1899
          Unresolved non-hydrogen dihedrals: 1242
          Unresolved non-hydrogen chiralities: 130
          Planarities with less than four sites: {'GLU:plan': 32, 'TYR:plan': 20, 'ARG:plan': 23, 'ASN:plan1': 21, 'PHE:plan': 18, 'ASP:plan': 26, 'HIS:plan': 9, 'GLN:plan1': 31, 'TRP:plan': 2}
          Unresolved non-hydrogen planarities: 819
    Chain: "E"
      Number of atoms: 1049
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 50, 1049
          Classifications: {'RNA': 50}
          Modifications used: {'5*END': 1, 'rna2p_pur': 1, 'rna2p_pyr': 7, 'rna3p_pur': 21, 'rna3p_pyr': 21}
          Link IDs: {'rna2p': 8, 'rna3p': 41}
          Chain breaks: 1
    Chain: "F"
      Number of atoms: 1049
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 50, 1049
          Classifications: {'RNA': 50}
          Modifications used: {'5*END': 1, 'rna2p_pur': 1, 'rna2p_pyr': 7, 'rna3p_pur': 21, 'rna3p_pyr': 21}
          Link IDs: {'rna2p': 8, 'rna3p': 41}
          Chain breaks: 1
  Time building chain proxies: 1.91, per 1000 atoms: 0.27
  Number of scatterers: 7192
  At special positions: 0
  Unit cell: (88.956, 95.31, 169.44, 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: 0.63
  Conformation dependent library (CDL) restraints added in 243.4 milliseconds
  

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

  Finding SS restraints...
    Secondary structure from input PDB file:
      59 helices and 6 sheets defined
      69.6% alpha, 6.7% beta
      40 base pairs and 48 stacking pairs defined.
    Time for finding SS restraints: 0.98
  Creating SS restraints...
    Processing helix  chain 'A' and resid 695 through 746
    Processing helix  chain 'B' and resid 696 through 747
    Processing helix  chain 'C' and resid 6 through 25
      removed outlier: 3.940A  pdb=" N   LYS C  24 " --> pdb=" O   ARG C  20 " (cutoff:3.500A)
    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 112
      removed outlier: 3.786A  pdb=" N   TYR C 111 " --> pdb=" O   LYS C 107 " (cutoff:3.500A)
      removed outlier: 4.350A  pdb=" N   GLY C 112 " --> pdb=" O   MET C 108 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 119 through 126
      removed outlier: 3.847A  pdb=" N   LEU C 123 " --> pdb=" O   VAL C 119 " (cutoff:3.500A)
      removed outlier: 3.844A  pdb=" N   GLY C 124 " --> pdb=" O   ARG C 120 " (cutoff:3.500A)
      removed outlier: 3.646A  pdb=" N   HIS C 125 " --> pdb=" O   SER C 121 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 130 through 138
      removed outlier: 3.595A  pdb=" N   GLY C 138 " --> pdb=" O   ARG C 134 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 140 through 151
    Processing helix  chain 'C' and resid 521 through 525
    Processing helix  chain 'C' and resid 526 through 530
      removed outlier: 3.501A  pdb=" N   THR C 530 " --> pdb=" O   LEU C 527 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 535 through 554
    Processing helix  chain 'C' and resid 590 through 593
    Processing helix  chain 'C' and resid 594 through 599
      removed outlier: 3.625A  pdb=" N   THR C 598 " --> pdb=" O   PRO C 594 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 601 through 608
      removed outlier: 3.682A  pdb=" N   VAL C 605 " --> pdb=" O   GLY C 601 " (cutoff:3.500A)
      removed outlier: 3.855A  pdb=" N   LEU C 606 " --> pdb=" O   LEU C 602 " (cutoff:3.500A)
      removed outlier: 3.786A  pdb=" N   GLU C 607 " --> pdb=" O   LYS C 603 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 620 through 622
      No H-bonds generated for 'chain 'C' and resid 620 through 622'
    Processing helix  chain 'C' and resid 623 through 630
      removed outlier: 3.651A  pdb=" N   LEU C 627 " --> pdb=" O   ALA C 623 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 639 through 652
    Processing helix  chain 'C' and resid 662 through 670
      removed outlier: 3.545A  pdb=" N   CYS C 667 " --> pdb=" O   LEU C 663 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 675 through 680
      removed outlier: 3.550A  pdb=" N   GLN C 680 " --> pdb=" O   ILE C 677 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 681 through 686
    Processing helix  chain 'C' and resid 690 through 694
    Processing helix  chain 'C' and resid 698 through 713
      removed outlier: 4.038A  pdb=" N   TYR C 704 " --> pdb=" O   GLU C 700 " (cutoff:3.500A)
      removed outlier: 4.322A  pdb=" N   GLY C 707 " --> pdb=" O   LEU C 703 " (cutoff:3.500A)
      removed outlier: 3.589A  pdb=" N   ASP C 708 " --> pdb=" O   TYR C 704 " (cutoff:3.500A)
      removed outlier: 4.198A  pdb=" N   VAL C 709 " --> pdb=" O   ALA C 705 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 717 through 725
    Processing helix  chain 'C' and resid 726 through 728
      No H-bonds generated for 'chain 'C' and resid 726 through 728'
    Processing helix  chain 'C' and resid 729 through 746
      removed outlier: 5.041A  pdb=" N   GLN C 744 " --> pdb=" O   GLN C 740 " (cutoff:3.500A)
      removed outlier: 4.430A  pdb=" N   ILE C 745 " --> pdb=" O   ILE C 741 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 746 through 773
      removed outlier: 3.524A  pdb=" N   THR C 761 " --> pdb=" O   ARG C 757 " (cutoff:3.500A)
      removed outlier: 4.322A  pdb=" N   THR C 773 " --> pdb=" O   LYS C 769 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 782 through 789
      removed outlier: 3.826A  pdb=" N   LEU C 787 " --> pdb=" O   ILE C 784 " (cutoff:3.500A)
      removed outlier: 3.890A  pdb=" N   ARG C 788 " --> pdb=" O   ARG C 785 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 793 through 802
      removed outlier: 3.842A  pdb=" N   GLU C 798 " --> pdb=" O   GLU C 794 " (cutoff:3.500A)
      removed outlier: 4.562A  pdb=" N   ARG C 799 " --> pdb=" O   ASP C 795 " (cutoff:3.500A)
      removed outlier: 3.811A  pdb=" N   LEU C 800 " --> pdb=" O   GLU C 796 " (cutoff:3.500A)
      removed outlier: 3.593A  pdb=" N   GLY C 802 " --> pdb=" O   GLU C 798 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 803 through 816
      removed outlier: 4.115A  pdb=" N   ALA C 807 " --> pdb=" O   TYR C 803 " (cutoff:3.500A)
      removed outlier: 4.223A  pdb=" N   LYS C 808 " --> pdb=" O   TYR C 804 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 3 through 25
    Processing helix  chain 'D' and resid 30 through 36
    Processing helix  chain 'D' and resid 37 through 39
      No H-bonds generated for 'chain 'D' and resid 37 through 39'
    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 112
      removed outlier: 3.611A  pdb=" N   GLU D  99 " --> pdb=" O   ASP D  95 " (cutoff:3.500A)
      removed outlier: 3.570A  pdb=" N   LYS D 107 " --> pdb=" O   TYR D 103 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 119 through 123
      removed outlier: 3.670A  pdb=" N   LEU D 123 " --> pdb=" O   VAL D 119 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'D' and resid 119 through 123'
    Processing helix  chain 'D' and resid 124 through 129
      removed outlier: 3.610A  pdb=" N   GLN D 128 " --> pdb=" O   HIS D 125 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 130 through 138
    Processing helix  chain 'D' and resid 140 through 152
    Processing helix  chain 'D' and resid 521 through 529
      removed outlier: 3.511A  pdb=" N   GLN D 528 " --> pdb=" O   ILE D 524 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 535 through 554
    Processing helix  chain 'D' and resid 594 through 600
      removed outlier: 4.411A  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
      removed outlier: 3.560A  pdb=" N   ASN D 624 " --> pdb=" O   ASN D 620 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 639 through 652
    Processing helix  chain 'D' and resid 654 through 658
    Processing helix  chain 'D' and resid 662 through 670
    Processing helix  chain 'D' and resid 677 through 688
      removed outlier: 4.036A  pdb=" N   LEU D 681 " --> pdb=" O   ILE D 677 " (cutoff:3.500A)
      removed outlier: 3.611A  pdb=" N   GLN D 683 " --> pdb=" O   ASP D 679 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 690 through 694
    Processing helix  chain 'D' and resid 698 through 714
      removed outlier: 3.776A  pdb=" N   ASP D 708 " --> pdb=" O   TYR D 704 " (cutoff:3.500A)
      removed outlier: 3.908A  pdb=" N   VAL D 709 " --> pdb=" O   ALA D 705 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 717 through 725
    Processing helix  chain 'D' and resid 726 through 743
      removed outlier: 3.679A  pdb=" N   ARG D 730 " --> pdb=" O   LYS D 726 " (cutoff:3.500A)
      removed outlier: 4.308A  pdb=" N   ALA D 731 " --> pdb=" O   PRO D 727 " (cutoff:3.500A)
      removed outlier: 4.536A  pdb=" N   LEU D 732 " --> pdb=" O   GLU D 728 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 746 through 773
      removed outlier: 3.809A  pdb=" N   SER D 764 " --> pdb=" O   SER D 760 " (cutoff:3.500A)
      removed outlier: 4.140A  pdb=" N   THR D 773 " --> pdb=" O   LYS D 769 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 780 through 787
      removed outlier: 3.757A  pdb=" N   LEU D 787 " --> pdb=" O   GLU D 783 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 788 through 790
      No H-bonds generated for 'chain 'D' and resid 788 through 790'
    Processing helix  chain 'D' and resid 793 through 801
    Processing helix  chain 'D' and resid 803 through 816
      removed outlier: 3.714A  pdb=" N   LYS D 809 " --> pdb=" O   LYS D 805 " (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
      removed outlier: 3.882A  pdb=" N   VAL C 117 " --> pdb=" O   VAL C 162 " (cutoff:3.500A)
    Processing sheet with id=AA3, first strand: chain 'C' and resid 532 through 533
      removed outlier: 3.922A  pdb=" N   GLU C 584 " --> pdb=" O   THR C 580 " (cutoff:3.500A)
      removed outlier: 3.609A  pdb=" N   GLU C 572 " --> pdb=" O   ILE C 565 " (cutoff:3.500A)
      removed outlier: 6.817A  pdb=" N   GLU C 563 " --> pdb=" O   THR C 574 " (cutoff:3.500A)
      removed outlier: 4.847A  pdb=" N   ILE C 576 " --> pdb=" O   ASP C 561 " (cutoff:3.500A)
      removed outlier: 6.835A  pdb=" N   ASP C 561 " --> pdb=" O   ILE C 576 " (cutoff:3.500A)
      removed outlier: 4.378A  pdb=" N   ILE C 578 " --> pdb=" O   SER C 559 " (cutoff:3.500A)
      removed outlier: 6.525A  pdb=" N   SER C 559 " --> pdb=" O   ILE C 578 " (cutoff:3.500A)
      removed outlier: 6.460A  pdb=" N   LYS C 613 " --> pdb=" O   PHE C 637 " (cutoff:3.500A)
    Processing sheet with id=AA4, first strand: chain 'D' and resid 28 through 29
      removed outlier: 3.575A  pdb=" N   ARG D  28 " --> pdb=" O   VAL D  75 " (cutoff:3.500A)
    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: 6.540A  pdb=" N   LYS D 613 " --> pdb=" O   PHE D 637 " (cutoff:3.500A)

    488 hydrogen bonds defined for protein.
    1395 hydrogen bond angles defined for protein.
    Restraints generated for nucleic acids:
      92 hydrogen bonds
      176 hydrogen bond angles
      0 basepair planarities
      40 basepair parallelities
      48 stacking parallelities
  Total time for adding SS restraints: 1.24

  Time building geometry restraints manager: 0.83 seconds

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

  Histogram of bond lengths:
        1.21 -     1.29: 1139
        1.29 -     1.37: 1516
        1.37 -     1.45: 879
        1.45 -     1.53: 3501
        1.53 -     1.61: 387
  Bond restraints: 7422
  Sorted by residual:
  bond pdb=" C4'   G F  18 "
       pdb=" C3'   G F  18 "
    ideal  model  delta    sigma   weight residual
    1.521  1.538 -0.017 1.50e-02 4.44e+03 1.23e+00
  bond pdb=" O4'   G F  18 "
       pdb=" C1'   G F  18 "
    ideal  model  delta    sigma   weight residual
    1.412  1.395  0.017 1.50e-02 4.44e+03 1.21e+00
  bond pdb=" C2'   G F  18 "
       pdb=" C1'   G F  18 "
    ideal  model  delta    sigma   weight residual
    1.529  1.513  0.016 1.50e-02 4.44e+03 1.12e+00
  bond pdb=" P     U F  19 "
       pdb=" OP2   U F  19 "
    ideal  model  delta    sigma   weight residual
    1.485  1.466  0.019 2.00e-02 2.50e+03 9.25e-01
  bond pdb=" N   ASN D 671 "
       pdb=" CA  ASN D 671 "
    ideal  model  delta    sigma   weight residual
    1.457  1.469 -0.011 1.29e-02 6.01e+03 7.43e-01
  ... (remaining 7417 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     1.66: 10444
        1.66 -     3.32: 223
        3.32 -     4.98: 26
        4.98 -     6.64: 4
        6.64 -     8.30: 5
  Bond angle restraints: 10702
  Sorted by residual:
  angle pdb=" C   GLN B 729 "
        pdb=" CA  GLN B 729 "
        pdb=" CB  GLN B 729 "
      ideal   model   delta    sigma   weight residual
     109.72  116.51   -6.79 1.92e+00 2.71e-01 1.25e+01
  angle pdb=" CA  GLY C 138 "
        pdb=" C   GLY C 138 "
        pdb=" N   GLN C 139 "
      ideal   model   delta    sigma   weight residual
     114.23  117.22   -2.99 8.80e-01 1.29e+00 1.16e+01
  angle pdb=" N   GLU C  19 "
        pdb=" CA  GLU C  19 "
        pdb=" CB  GLU C  19 "
      ideal   model   delta    sigma   weight residual
     110.12  114.56   -4.44 1.47e+00 4.63e-01 9.13e+00
  angle pdb=" O4'   G E  50 "
        pdb=" C1'   G E  50 "
        pdb=" N9    G E  50 "
      ideal   model   delta    sigma   weight residual
     108.50  113.01   -4.51 1.50e+00 4.44e-01 9.03e+00
  angle pdb=" C   ARG C 782 "
        pdb=" CA  ARG C 782 "
        pdb=" CB  ARG C 782 "
      ideal   model   delta    sigma   weight residual
     110.96  106.46    4.50 1.54e+00 4.22e-01 8.55e+00
  ... (remaining 10697 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    32.65: 4217
       32.65 -    65.30: 231
       65.30 -    97.96: 36
       97.96 -   130.61: 1
      130.61 -   163.26: 3
  Dihedral angle restraints: 4488
    sinusoidal: 1506
      harmonic: 2982
  Sorted by residual:
  dihedral pdb=" CA  GLN C  76 "
           pdb=" C   GLN C  76 "
           pdb=" N   VAL C  77 "
           pdb=" CA  VAL C  77 "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00 -153.67  -26.33     0      5.00e+00 4.00e-02 2.77e+01
  dihedral pdb=" CA  GLN B 729 "
           pdb=" C   GLN B 729 "
           pdb=" N   LYS B 730 "
           pdb=" CA  LYS B 730 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  158.79   21.21     0      5.00e+00 4.00e-02 1.80e+01
  dihedral pdb=" CA  ARG C 782 "
           pdb=" C   ARG C 782 "
           pdb=" N   GLU C 783 "
           pdb=" CA  GLU C 783 "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00 -160.24  -19.76     0      5.00e+00 4.00e-02 1.56e+01
  ... (remaining 4485 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.042: 1177
       0.042 -    0.084: 216
       0.084 -    0.126: 81
       0.126 -    0.169: 5
       0.169 -    0.211: 1
  Chirality restraints: 1480
  Sorted by residual:
  chirality pdb=" CA  GLN B 729 "
            pdb=" N   GLN B 729 "
            pdb=" C   GLN B 729 "
            pdb=" CB  GLN B 729 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.30    0.21 2.00e-01 2.50e+01 1.11e+00
  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      2.46    2.30    0.16 2.00e-01 2.50e+01 6.33e-01
  chirality pdb=" C1'   G F  50 "
            pdb=" O4'   G F  50 "
            pdb=" C2'   G F  50 "
            pdb=" N9    G F  50 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.46    2.30    0.15 2.00e-01 2.50e+01 5.93e-01
  ... (remaining 1477 not shown)

  Planarity restraints: 1118
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C1'   C E  39 "    0.044 2.00e-02 2.50e+03   2.28e-02 1.17e+01
        pdb=" N1    C E  39 "   -0.049 2.00e-02 2.50e+03
        pdb=" C2    C E  39 "   -0.009 2.00e-02 2.50e+03
        pdb=" O2    C E  39 "   -0.004 2.00e-02 2.50e+03
        pdb=" N3    C E  39 "    0.005 2.00e-02 2.50e+03
        pdb=" C4    C E  39 "    0.006 2.00e-02 2.50e+03
        pdb=" N4    C E  39 "    0.012 2.00e-02 2.50e+03
        pdb=" C5    C E  39 "    0.001 2.00e-02 2.50e+03
        pdb=" C6    C E  39 "   -0.007 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  GLN B 729 "    0.014 2.00e-02 2.50e+03   2.81e-02 7.90e+00
        pdb=" C   GLN B 729 "   -0.049 2.00e-02 2.50e+03
        pdb=" O   GLN B 729 "    0.018 2.00e-02 2.50e+03
        pdb=" N   LYS B 730 "    0.016 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C1'   C F  38 "    0.026 2.00e-02 2.50e+03   1.35e-02 4.07e+00
        pdb=" N1    C F  38 "   -0.028 2.00e-02 2.50e+03
        pdb=" C2    C F  38 "   -0.001 2.00e-02 2.50e+03
        pdb=" O2    C F  38 "   -0.005 2.00e-02 2.50e+03
        pdb=" N3    C F  38 "    0.003 2.00e-02 2.50e+03
        pdb=" C4    C F  38 "    0.002 2.00e-02 2.50e+03
        pdb=" N4    C F  38 "    0.009 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
  ... (remaining 1115 not shown)

  Histogram of nonbonded interaction distances:
        1.96 -     2.55: 50
        2.55 -     3.14: 6330
        3.14 -     3.73: 12394
        3.73 -     4.31: 14116
        4.31 -     4.90: 20826
  Nonbonded interactions: 53716
  Sorted by model distance:
  nonbonded pdb=" O2'   C F  49 "
            pdb=" OP1   G F  50 "
     model   vdw
     1.963 3.040
  nonbonded pdb=" O2'   G F  50 "
            pdb=" O4'   A F  51 "
     model   vdw
     1.982 3.040
  nonbonded pdb=" O2'   U F  19 "
            pdb=" OP2   A F  20 "
     model   vdw
     1.988 3.040
  nonbonded pdb=" O2'   C E  49 "
            pdb=" OP1   G E  50 "
     model   vdw
     2.028 3.040
  nonbonded pdb=" O2'   U F  48 "
            pdb=" OP1   G F  50 "
     model   vdw
     2.034 3.040
  ... (remaining 53711 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:             2.980
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.000
  Construct map_model_manager:             0.000
  Extract box with map and model:          0.100
  Check model and map are aligned:         0.020
  Set scattering table:                    0.010
  Process input model:                     8.760
  Find NCS groups from input model:        0.110
  Set up NCS constraints:                  0.010
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.000
  Load rotamer database and sin/cos tables:1.260
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   13.250
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6397
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   0.019   7422  Z= 0.151
  Angle     :  0.643   8.302  10702  Z= 0.387
  Chirality :  0.038   0.211   1480
  Planarity :  0.002   0.028   1118
  Dihedral  : 20.686 163.261   2524
  Min Nonbonded Distance : 1.963

Molprobity Statistics.
  All-atom Clashscore : 7.78
  Ramachandran Plot:
    Outliers :  0.10 %
    Allowed  :  4.07 %
    Favored  : 95.83 %
  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: -0.73 (0.25), residues: 1008
  helix: -0.28 (0.20), residues: 575
  sheet: -1.29 (0.59), residues: 61
  loop : -0.38 (0.33), residues: 372

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

Details of bonding type rmsd
  covalent geometry    : bond        0.00229 ( 7422)
  covalent geometry    : angle       0.64339 (10702)
  hydrogen bonds       : bond        0.21050 (  580)
  hydrogen bonds       : angle       7.62260 ( 1571)

*********************** 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  : 0.169 
Fit side-chains
  outliers start: 0
  outliers final: 0
  residues processed: 31
  average time/residue: 0.0273
  time to fit residues: 1.8038
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=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 112
   random chunks:
   chunk 108 optimal weight:    9.9990
   chunk 49 optimal weight:    9.9990
   chunk 97 optimal weight:   10.0000
   chunk 53 optimal weight:   40.0000
   chunk 5 optimal weight:   50.0000
   chunk 33 optimal weight:   20.0000
   chunk 65 optimal weight:   20.0000
   chunk 62 optimal weight:    6.9990
   chunk 51 optimal weight:    0.2980
   chunk 100 optimal weight:   50.0000
   chunk 106 optimal weight:   10.0000
   overall best weight:    7.4590

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3912 r_free = 0.3912 target = 0.078086 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 68)----------------|
| r_work = 0.3439 r_free = 0.3439 target = 0.057669 restraints weight = 60117.694|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 67)----------------|
| r_work = 0.3473 r_free = 0.3473 target = 0.058996 restraints weight = 40878.387|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 45)----------------|
| r_work = 0.3492 r_free = 0.3492 target = 0.059731 restraints weight = 30632.074|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 59)----------------|
| r_work = 0.3508 r_free = 0.3508 target = 0.060380 restraints weight = 25020.755|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 32)----------------|
| r_work = 0.3515 r_free = 0.3515 target = 0.060663 restraints weight = 21904.279|
|-----------------------------------------------------------------------------|
r_work (final): 0.3465
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7098
moved from start:          0.4112

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.006   0.041   7422  Z= 0.381
  Angle     :  0.913   8.764  10702  Z= 0.501
  Chirality :  0.052   0.322   1480
  Planarity :  0.005   0.021   1118
  Dihedral  : 21.483 176.876   2524
  Min Nonbonded Distance : 2.060

Molprobity Statistics.
  All-atom Clashscore : 14.81
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.46 %
    Favored  : 94.54 %
  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: -0.77 (0.25), residues: 1008
  helix: -0.02 (0.19), residues: 637
  sheet: -1.98 (0.61), residues: 47
  loop : -1.03 (0.35), residues: 324

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

Details of bonding type rmsd
  covalent geometry    : bond        0.00610 ( 7422)
  covalent geometry    : angle       0.91309 (10702)
  hydrogen bonds       : bond        0.07402 (  580)
  hydrogen bonds       : angle       6.14020 ( 1571)

*********************** 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  : 0.192 
Fit side-chains
  outliers start: 0
  outliers final: 0
  residues processed: 31
  average time/residue: 0.0316
  time to fit residues: 2.0450
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  : 0.205 
-------------------------------------------------------------------------------
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:   10.0000
   chunk 0 optimal weight:   40.0000
   chunk 111 optimal weight:    9.9990
   chunk 110 optimal weight:    7.9990
   chunk 68 optimal weight:    1.9990
   chunk 4 optimal weight:    7.9990
   chunk 73 optimal weight:   10.0000
   chunk 27 optimal weight:    1.9990
   chunk 21 optimal weight:    8.9990
   chunk 76 optimal weight:   50.0000
   chunk 22 optimal weight:    6.9990
   overall best weight:    5.3990

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3927 r_free = 0.3927 target = 0.078371 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 69)----------------|
| r_work = 0.3458 r_free = 0.3458 target = 0.058230 restraints weight = 59328.441|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 57)----------------|
| r_work = 0.3494 r_free = 0.3494 target = 0.059537 restraints weight = 39856.922|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 30)----------------|
| r_work = 0.3510 r_free = 0.3510 target = 0.060124 restraints weight = 30191.781|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 38)----------------|
| r_work = 0.3525 r_free = 0.3525 target = 0.060740 restraints weight = 25172.276|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 27)----------------|
| r_work = 0.3533 r_free = 0.3533 target = 0.061033 restraints weight = 22257.216|
|-----------------------------------------------------------------------------|
r_work (final): 0.3482
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7083
moved from start:          0.4886

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.028   7422  Z= 0.271
  Angle     :  0.705   8.136  10702  Z= 0.386
  Chirality :  0.044   0.280   1480
  Planarity :  0.003   0.016   1118
  Dihedral  : 21.367 176.455   2524
  Min Nonbonded Distance : 2.090

Molprobity Statistics.
  All-atom Clashscore : 10.92
  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: -0.23 (0.26), residues: 1008
  helix:  0.45 (0.20), residues: 629
  sheet: -2.10 (0.62), residues: 47
  loop : -0.82 (0.36), residues: 332

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

Details of bonding type rmsd
  covalent geometry    : bond        0.00430 ( 7422)
  covalent geometry    : angle       0.70507 (10702)
  hydrogen bonds       : bond        0.05927 (  580)
  hydrogen bonds       : angle       5.58180 ( 1571)

*********************** 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  : 0.211 
Fit side-chains
  outliers start: 0
  outliers final: 0
  residues processed: 31
  average time/residue: 0.0295
  time to fit residues: 1.9921
Evaluate side-chains
  31 residues out of total 914 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 31
  time to evaluate  : 0.191 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 112
   random chunks:
   chunk 103 optimal weight:    5.9990
   chunk 77 optimal weight:   20.0000
   chunk 67 optimal weight:    9.9990
   chunk 88 optimal weight:   30.0000
   chunk 68 optimal weight:    3.9990
   chunk 72 optimal weight:   30.0000
   chunk 105 optimal weight:    6.9990
   chunk 64 optimal weight:   20.0000
   chunk 100 optimal weight:   40.0000
   chunk 48 optimal weight:   30.0000
   chunk 18 optimal weight:    2.9990
   overall best weight:    5.9990

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3896 r_free = 0.3896 target = 0.076684 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 71)----------------|
| r_work = 0.3418 r_free = 0.3418 target = 0.056472 restraints weight = 60677.944|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 57)----------------|
| r_work = 0.3451 r_free = 0.3451 target = 0.057748 restraints weight = 42188.464|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 37)----------------|
| r_work = 0.3470 r_free = 0.3470 target = 0.058503 restraints weight = 31212.153|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 48)----------------|
| r_work = 0.3486 r_free = 0.3486 target = 0.059149 restraints weight = 25690.483|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 32)----------------|
| r_work = 0.3493 r_free = 0.3493 target = 0.059410 restraints weight = 22318.993|
|-----------------------------------------------------------------------------|
r_work (final): 0.3446
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7147
moved from start:          0.6281

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= 0.316
  Angle     :  0.813  10.831  10702  Z= 0.443
  Chirality :  0.048   0.272   1480
  Planarity :  0.004   0.017   1118
  Dihedral  : 21.931 178.160   2524
  Min Nonbonded Distance : 2.049

Molprobity Statistics.
  All-atom Clashscore : 14.14
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.25 %
    Favored  : 93.75 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.00 %
    Favored  :  0.00 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 9.09 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -0.81 (0.25), residues: 1008
  helix:  0.14 (0.19), residues: 638
  sheet: -2.53 (0.59), residues: 47
  loop : -1.41 (0.35), residues: 323

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

Details of bonding type rmsd
  covalent geometry    : bond        0.00507 ( 7422)
  covalent geometry    : angle       0.81286 (10702)
  hydrogen bonds       : bond        0.06811 (  580)
  hydrogen bonds       : angle       6.05212 ( 1571)

*********************** 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  : 0.192 
Fit side-chains
  outliers start: 0
  outliers final: 0
  residues processed: 31
  average time/residue: 0.0245
  time to fit residues: 1.6299
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  : 0.195 
-------------------------------------------------------------------------------
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:   10.0000
   chunk 75 optimal weight:   10.0000
   chunk 88 optimal weight:   30.0000
   chunk 28 optimal weight:   60.0000
   chunk 16 optimal weight:    8.9990
   chunk 76 optimal weight:   50.0000
   chunk 50 optimal weight:   10.0000
   chunk 37 optimal weight:   40.0000
   chunk 87 optimal weight:   30.0000
   chunk 41 optimal weight:   40.0000
   chunk 81 optimal weight:    7.9990
   overall best weight:    9.3996

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3854 r_free = 0.3854 target = 0.074812 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 56)----------------|
| r_work = 0.3376 r_free = 0.3376 target = 0.055145 restraints weight = 61549.080|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 55)----------------|
| r_work = 0.3405 r_free = 0.3405 target = 0.056190 restraints weight = 43278.242|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 66)----------------|
| r_work = 0.3424 r_free = 0.3424 target = 0.056909 restraints weight = 33661.687|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 33)----------------|
| r_work = 0.3433 r_free = 0.3433 target = 0.057253 restraints weight = 28306.427|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 36)----------------|
| r_work = 0.3442 r_free = 0.3442 target = 0.057586 restraints weight = 25241.426|
|-----------------------------------------------------------------------------|
r_work (final): 0.3393
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7227
moved from start:          0.7395

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.007   0.045   7422  Z= 0.455
  Angle     :  1.002  13.046  10702  Z= 0.542
  Chirality :  0.055   0.324   1480
  Planarity :  0.005   0.021   1118
  Dihedral  : 22.613 176.767   2524
  Min Nonbonded Distance : 2.013

Molprobity Statistics.
  All-atom Clashscore : 19.18
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  9.13 %
    Favored  : 90.87 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.00 %
    Favored  :  0.00 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 9.09 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.10 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -2.33 (0.24), residues: 1008
  helix: -1.11 (0.18), residues: 641
  sheet: -2.62 (0.63), residues: 44
  loop : -2.00 (0.35), residues: 323

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

Details of bonding type rmsd
  covalent geometry    : bond        0.00732 ( 7422)
  covalent geometry    : angle       1.00162 (10702)
  hydrogen bonds       : bond        0.08463 (  580)
  hydrogen bonds       : angle       7.05913 ( 1571)

*********************** 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  : 0.187 
Fit side-chains
  outliers start: 0
  outliers final: 0
  residues processed: 31
  average time/residue: 0.0289
  time to fit residues: 1.8972
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=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 112
   random chunks:
   chunk 60 optimal weight:   10.0000
   chunk 50 optimal weight:   10.0000
   chunk 51 optimal weight:    5.9990
   chunk 49 optimal weight:   10.0000
   chunk 105 optimal weight:    0.7980
   chunk 72 optimal weight:   30.0000
   chunk 29 optimal weight:   50.0000
   chunk 13 optimal weight:    3.9990
   chunk 84 optimal weight:   20.0000
   chunk 44 optimal weight:    9.9990
   chunk 106 optimal weight:    6.9990
   overall best weight:    5.5588

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3890 r_free = 0.3890 target = 0.076209 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.3460 r_free = 0.3460 target = 0.058066 restraints weight = 61148.867|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 36)----------------|
| r_work = 0.3457 r_free = 0.3457 target = 0.057861 restraints weight = 43042.878|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 30)----------------|
| r_work = 0.3471 r_free = 0.3471 target = 0.058353 restraints weight = 36667.577|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 26)----------------|
| r_work = 0.3476 r_free = 0.3476 target = 0.058576 restraints weight = 30007.522|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 24)----------------|
| r_work = 0.3480 r_free = 0.3480 target = 0.058743 restraints weight = 29126.433|
|-----------------------------------------------------------------------------|
r_work (final): 0.3423
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7171
moved from start:          0.7336

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.029   7422  Z= 0.285
  Angle     :  0.758   8.842  10702  Z= 0.411
  Chirality :  0.046   0.312   1480
  Planarity :  0.003   0.016   1118
  Dihedral  : 22.072 171.921   2524
  Min Nonbonded Distance : 2.045

Molprobity Statistics.
  All-atom Clashscore : 11.96
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  7.14 %
    Favored  : 92.86 %
  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 (0.25), residues: 1008
  helix: -0.41 (0.19), residues: 624
  sheet: -2.42 (0.66), residues: 44
  loop : -1.55 (0.35), residues: 340

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

Details of bonding type rmsd
  covalent geometry    : bond        0.00457 ( 7422)
  covalent geometry    : angle       0.75772 (10702)
  hydrogen bonds       : bond        0.06319 (  580)
  hydrogen bonds       : angle       6.04751 ( 1571)

*********************** 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  : 0.150 
Fit side-chains
  outliers start: 0
  outliers final: 0
  residues processed: 31
  average time/residue: 0.0295
  time to fit residues: 1.9549
Evaluate side-chains
  31 residues out of total 914 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 31
  time to evaluate  : 0.196 
-------------------------------------------------------------------------------
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:    0.9990
   chunk 71 optimal weight:   20.0000
   chunk 28 optimal weight:   30.0000
   chunk 25 optimal weight:   30.0000
   chunk 32 optimal weight:   30.0000
   chunk 21 optimal weight:    5.9990
   chunk 6 optimal weight:    0.8980
   chunk 109 optimal weight:    9.9990
   chunk 35 optimal weight:   40.0000
   chunk 88 optimal weight:   40.0000
   overall best weight:    7.5790

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3859 r_free = 0.3859 target = 0.074884 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 47)----------------|
| r_work = 0.3419 r_free = 0.3419 target = 0.056698 restraints weight = 61977.245|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 37)----------------|
| r_work = 0.3409 r_free = 0.3409 target = 0.056139 restraints weight = 46288.794|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 30)----------------|
| r_work = 0.3412 r_free = 0.3412 target = 0.056348 restraints weight = 43065.850|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 26)----------------|
| r_work = 0.3422 r_free = 0.3422 target = 0.056707 restraints weight = 34951.919|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 26)----------------|
| r_work = 0.3421 r_free = 0.3421 target = 0.056687 restraints weight = 33845.919|
|-----------------------------------------------------------------------------|
r_work (final): 0.3360
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7277
moved from start:          0.8030

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.006   0.037   7422  Z= 0.374
  Angle     :  0.899   9.127  10702  Z= 0.486
  Chirality :  0.052   0.337   1480
  Planarity :  0.004   0.019   1118
  Dihedral  : 22.558 177.046   2524
  Min Nonbonded Distance : 2.025

Molprobity Statistics.
  All-atom Clashscore : 16.90
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  : 10.71 %
    Favored  : 89.29 %
  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: -2.02 (0.25), residues: 1008
  helix: -0.85 (0.19), residues: 632
  sheet: -2.62 (0.68), residues: 43
  loop : -1.85 (0.35), residues: 333

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

Details of bonding type rmsd
  covalent geometry    : bond        0.00602 ( 7422)
  covalent geometry    : angle       0.89859 (10702)
  hydrogen bonds       : bond        0.07653 (  580)
  hydrogen bonds       : angle       6.72743 ( 1571)

*********************** 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  : 0.198 
Fit side-chains
  outliers start: 0
  outliers final: 0
  residues processed: 31
  average time/residue: 0.0285
  time to fit residues: 1.8340
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  : 0.190 
-------------------------------------------------------------------------------
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:   20.0000
   chunk 108 optimal weight:    6.9990
   chunk 61 optimal weight:    9.9990
   chunk 78 optimal weight:   30.0000
   chunk 44 optimal weight:   50.0000
   chunk 37 optimal weight:   40.0000
   chunk 49 optimal weight:    9.9990
   chunk 27 optimal weight:   20.0000
   chunk 99 optimal weight:    4.9990
   chunk 51 optimal weight:    7.9990
   chunk 102 optimal weight:    8.9990
   overall best weight:    7.7990

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3863 r_free = 0.3863 target = 0.074855 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 47)----------------|
| r_work = 0.3426 r_free = 0.3426 target = 0.056930 restraints weight = 61866.524|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 36)----------------|
| r_work = 0.3420 r_free = 0.3420 target = 0.056760 restraints weight = 44421.774|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 31)----------------|
| r_work = 0.3422 r_free = 0.3422 target = 0.056792 restraints weight = 38982.918|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 26)----------------|
| r_work = 0.3433 r_free = 0.3433 target = 0.057199 restraints weight = 32603.270|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 28)----------------|
| r_work = 0.3433 r_free = 0.3433 target = 0.057179 restraints weight = 31373.513|
|-----------------------------------------------------------------------------|
r_work (final): 0.3369
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7204
moved from start:          0.8497

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.006   0.036   7422  Z= 0.370
  Angle     :  0.858   8.227  10702  Z= 0.467
  Chirality :  0.050   0.346   1480
  Planarity :  0.004   0.018   1118
  Dihedral  : 22.665 179.536   2524
  Min Nonbonded Distance : 2.048

Molprobity Statistics.
  All-atom Clashscore : 16.80
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  9.13 %
    Favored  : 90.87 %
  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: -2.24 (0.25), residues: 1008
  helix: -0.94 (0.19), residues: 632
  sheet: -2.88 (0.66), residues: 43
  loop : -2.14 (0.35), residues: 333

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

Details of bonding type rmsd
  covalent geometry    : bond        0.00593 ( 7422)
  covalent geometry    : angle       0.85839 (10702)
  hydrogen bonds       : bond        0.07331 (  580)
  hydrogen bonds       : angle       6.55688 ( 1571)

*********************** 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  : 0.156 
Fit side-chains
  outliers start: 0
  outliers final: 0
  residues processed: 31
  average time/residue: 0.0294
  time to fit residues: 1.9194
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  : 0.185 
-------------------------------------------------------------------------------
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:   50.0000
   chunk 11 optimal weight:    6.9990
   chunk 48 optimal weight:   20.0000
   chunk 31 optimal weight:   50.0000
   chunk 15 optimal weight:    0.2980
   chunk 17 optimal weight:   20.0000
   chunk 19 optimal weight:   30.0000
   chunk 51 optimal weight:    5.9990
   chunk 65 optimal weight:   20.0000
   chunk 2 optimal weight:   20.0000
   chunk 86 optimal weight:   20.0000
   overall best weight:   10.6592

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3827 r_free = 0.3827 target = 0.073458 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 54)----------------|
| r_work = 0.3332 r_free = 0.3332 target = 0.053631 restraints weight = 61848.101|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 59)----------------|
| r_work = 0.3359 r_free = 0.3359 target = 0.054661 restraints weight = 44154.159|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 41)----------------|
| r_work = 0.3374 r_free = 0.3374 target = 0.055219 restraints weight = 35136.277|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 58)----------------|
| r_work = 0.3386 r_free = 0.3386 target = 0.055694 restraints weight = 30220.431|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 24)----------------|
| r_work = 0.3391 r_free = 0.3391 target = 0.055859 restraints weight = 27132.561|
|-----------------------------------------------------------------------------|
r_work (final): 0.3346
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7275
moved from start:          0.9159

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.008   0.048   7422  Z= 0.511
  Angle     :  1.068   9.739  10702  Z= 0.583
  Chirality :  0.057   0.383   1480
  Planarity :  0.005   0.022   1118
  Dihedral  : 23.356 176.311   2524
  Min Nonbonded Distance : 1.987

Molprobity Statistics.
  All-atom Clashscore : 24.59
  Ramachandran Plot:
    Outliers :  0.20 %
    Allowed  : 13.29 %
    Favored  : 86.51 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.00 %
    Favored  :  0.00 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 9.09 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.10 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -3.18 (0.24), residues: 1008
  helix: -1.71 (0.18), residues: 622
  sheet: -2.72 (0.80), residues: 31
  loop : -2.55 (0.33), residues: 355

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

Details of bonding type rmsd
  covalent geometry    : bond        0.00822 ( 7422)
  covalent geometry    : angle       1.06778 (10702)
  hydrogen bonds       : bond        0.09436 (  580)
  hydrogen bonds       : angle       7.57406 ( 1571)

*********************** 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  : 0.120 
Fit side-chains
  outliers start: 0
  outliers final: 0
  residues processed: 31
  average time/residue: 0.0275
  time to fit residues: 1.8452
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  : 0.179 
-------------------------------------------------------------------------------
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:    3.9990
   chunk 91 optimal weight:    3.9990
   chunk 36 optimal weight:   20.0000
   chunk 76 optimal weight:   50.0000
   chunk 82 optimal weight:   10.0000
   chunk 67 optimal weight:    7.9990
   chunk 71 optimal weight:   20.0000
   chunk 102 optimal weight:    4.9990
   chunk 80 optimal weight:    2.9990
   chunk 57 optimal weight:    7.9990
   chunk 97 optimal weight:   20.0000
   overall best weight:    4.7990

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3878 r_free = 0.3878 target = 0.075498 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 46)----------------|
| r_work = 0.3442 r_free = 0.3442 target = 0.057610 restraints weight = 61050.194|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 31)----------------|
| r_work = 0.3438 r_free = 0.3438 target = 0.057346 restraints weight = 43899.442|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 25)----------------|
| r_work = 0.3435 r_free = 0.3435 target = 0.057289 restraints weight = 39275.942|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 28)----------------|
| r_work = 0.3447 r_free = 0.3447 target = 0.057708 restraints weight = 34791.182|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 26)----------------|
| r_work = 0.3451 r_free = 0.3451 target = 0.057839 restraints weight = 30121.140|
|-----------------------------------------------------------------------------|
r_work (final): 0.3397
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7183
moved from start:          0.8830

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.024   7422  Z= 0.255
  Angle     :  0.745   7.495  10702  Z= 0.402
  Chirality :  0.045   0.339   1480
  Planarity :  0.003   0.016   1118
  Dihedral  : 22.645 178.987   2524
  Min Nonbonded Distance : 2.080

Molprobity Statistics.
  All-atom Clashscore : 13.48
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  7.74 %
    Favored  : 92.26 %
  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: -2.12 (0.25), residues: 1008
  helix: -0.77 (0.19), residues: 635
  sheet: -2.49 (0.82), residues: 31
  loop : -2.35 (0.34), residues: 342

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

Details of bonding type rmsd
  covalent geometry    : bond        0.00407 ( 7422)
  covalent geometry    : angle       0.74489 (10702)
  hydrogen bonds       : bond        0.06247 (  580)
  hydrogen bonds       : angle       6.11074 ( 1571)

********************** 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  : 0.153 
Fit side-chains
  outliers start: 0
  outliers final: 0
  residues processed: 31
  average time/residue: 0.0278
  time to fit residues: 1.8382
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 
-------------------------------------------------------------------------------
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:   30.0000
   chunk 79 optimal weight:   30.0000
   chunk 61 optimal weight:    0.9990
   chunk 25 optimal weight:   40.0000
   chunk 37 optimal weight:    8.9990
   chunk 52 optimal weight:   20.0000
   chunk 72 optimal weight:   40.0000
   chunk 62 optimal weight:    6.9990
   chunk 92 optimal weight:   20.0000
   chunk 28 optimal weight:   50.0000
   overall best weight:    9.3994

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3833 r_free = 0.3833 target = 0.073778 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 56)----------------|
| r_work = 0.3402 r_free = 0.3402 target = 0.056026 restraints weight = 62068.723|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 35)----------------|
| r_work = 0.3388 r_free = 0.3388 target = 0.055538 restraints weight = 43074.285|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 30)----------------|
| r_work = 0.3387 r_free = 0.3387 target = 0.055585 restraints weight = 42646.591|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 28)----------------|
| r_work = 0.3396 r_free = 0.3396 target = 0.055884 restraints weight = 36993.462|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 27)----------------|
| r_work = 0.3401 r_free = 0.3401 target = 0.056015 restraints weight = 33184.086|
|-----------------------------------------------------------------------------|
r_work (final): 0.3346
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7266
moved from start:          0.9299

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.007   0.044   7422  Z= 0.455
  Angle     :  0.982   9.176  10702  Z= 0.537
  Chirality :  0.055   0.368   1480
  Planarity :  0.005   0.020   1118
  Dihedral  : 23.246 176.983   2524
  Min Nonbonded Distance : 2.014

Molprobity Statistics.
  All-atom Clashscore : 21.45
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  : 12.60 %
    Favored  : 87.40 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.00 %
    Favored  :  0.00 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 9.09 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.10 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -2.72 (0.24), residues: 1008
  helix: -1.25 (0.19), residues: 619
  sheet: -3.26 (0.75), residues: 29
  loop : -2.49 (0.33), residues: 360

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

Details of bonding type rmsd
  covalent geometry    : bond        0.00733 ( 7422)
  covalent geometry    : angle       0.98162 (10702)
  hydrogen bonds       : bond        0.08638 (  580)
  hydrogen bonds       : angle       7.13259 ( 1571)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 1544.96 seconds
wall clock time: 27 minutes 0.66 seconds (1620.66 seconds total)