Starting phenix.real_space_refine
on Wed Feb  4 14:32:06 2026 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/9qh5_53155/02_2026/9qh5_53155_neut.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/9qh5_53155/02_2026/9qh5_53155.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.09
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    model {
      file = "/net/cci-nas-00/data/ceres_data/9qh5_53155/02_2026/9qh5_53155_neut.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/9qh5_53155/02_2026/9qh5_53155_neut.cif"
    real_map_files = "/net/cci-nas-00/data/ceres_data/9qh5_53155/02_2026/9qh5_53155.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/9qh5_53155/02_2026/9qh5_53155.map"
  }
  resolution = 3.09
  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=   0.016
Set stop_for_unknowns flag
  Set to: True
Assert model is a single copy model
Assert all atoms have isotropic ADPs
Construct map_model_manager
Extract box with map and model
Check model and map are aligned
Set scattering table
  Set to: electron
  Number of scattering types: 5
    Type Number    sf(0)   Gaussians
     P       7      5.49       5
     S      51      5.16       5
     C    6892      2.51       5
     N    1835      2.21       5
     O    2061      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 59 residue(s): 0.01s

  Monomer Library directory:
    "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5952/lib/python3.9/site-packages/chem_data/mon_lib"
  Total number of atoms: 10846
  Number of models: 1
  Model: ""
    Number of chains: 6
    Chain: "A"
      Number of atoms: 2331
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 291, 2331
          Classifications: {'peptide': 291}
          Link IDs: {'PCIS': 1, 'PTRANS': 16, 'TRANS': 273}
    Chain: "B"
      Number of atoms: 7834
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 988, 7834
          Classifications: {'peptide': 988}
          Link IDs: {'CIS': 1, 'PCIS': 4, 'PTRANS': 47, 'TRANS': 935}
          Chain breaks: 1
    Chain: "C"
      Number of atoms: 20
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 3, 20
          Classifications: {'peptide': 3}
          Link IDs: {'TRANS': 2}
    Chain: "E"
      Number of atoms: 603
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 76, 603
          Classifications: {'peptide': 76}
          Modifications used: {'COO': 1}
          Link IDs: {'PTRANS': 3, 'TRANS': 72}
    Chain: "B"
      Number of atoms: 36
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 1, 36
          Unusual residues: {'IHP': 1}
          Classifications: {'undetermined': 1}
    Chain: "E"
      Number of atoms: 22
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 1, 22
          Unusual residues: {'AMP%rna2p': 1}
          Classifications: {'RNA_mixed': 1}
          Modifications used: {'rna2p': 1}
          Unresolved non-hydrogen bonds: 1
          Unresolved non-hydrogen angles: 3
          Unresolved non-hydrogen dihedrals: 1
  Time building chain proxies: 2.53, per 1000 atoms: 0.23
  Number of scatterers: 10846
  At special positions: 0
  Unit cell: (87.55, 100.3, 130.9, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 5
    Type Number    sf(0)
     S      51     16.00
     P       7     15.00
     O    2061      8.00
     N    1835      7.00
     C    6892      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=1, symmetry=0
  Number of additional bonds: simple=1, symmetry=0
  Coordination:
  Other bonds:
  Time building additional restraints: 0.77
  Conformation dependent library (CDL) restraints added in 536.3 milliseconds
  

  2696 Ramachandran restraints generated.
    1348 Oldfield, 0 Emsley, 1348 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  2578

  Finding SS restraints...
    Secondary structure from input PDB file:
      61 helices and 10 sheets defined
      49.9% alpha, 12.8% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.46
  Creating SS restraints...
    Processing helix  chain 'A' and resid 4524 through 4533
    Processing helix  chain 'A' and resid 4559 through 4566
    Processing helix  chain 'A' and resid 4572 through 4586
      removed outlier: 3.784A  pdb=" N   VAL A4583 " --> pdb=" O   ALA A4579 " (cutoff:3.500A)
      removed outlier: 3.866A  pdb=" N   THR A4584 " --> pdb=" O   GLN A4580 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 4676 through 4680
      removed outlier: 4.046A  pdb=" N   LYS A4680 " --> pdb=" O   PRO A4677 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 4687 through 4699
    Processing helix  chain 'A' and resid 4703 through 4708
      removed outlier: 3.776A  pdb=" N   GLU A4708 " --> pdb=" O   TYR A4705 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 4711 through 4715
    Processing helix  chain 'A' and resid 4717 through 4739
    Processing helix  chain 'A' and resid 4740 through 4746
    Processing helix  chain 'A' and resid 4751 through 4762
      removed outlier: 3.631A  pdb=" N   LYS A4762 " --> pdb=" O   HIS A4758 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 4762 through 4778
      removed outlier: 3.601A  pdb=" N   GLN A4778 " --> pdb=" O   ILE A4774 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 4779 through 4781
      No H-bonds generated for 'chain 'A' and resid 4779 through 4781'
    Processing helix  chain 'A' and resid 4786 through 4810
      removed outlier: 3.634A  pdb=" N   GLN A4803 " --> pdb=" O   ARG A4799 " (cutoff:3.500A)
      removed outlier: 3.718A  pdb=" N   GLU A4806 " --> pdb=" O   ALA A4802 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 40 through 52
      removed outlier: 6.971A  pdb=" N   ARG B  46 " --> pdb=" O   ALA B  42 " (cutoff:3.500A)
      removed outlier: 5.932A  pdb=" N   GLN B  47 " --> pdb=" O   LEU B  43 " (cutoff:3.500A)
      removed outlier: 4.059A  pdb=" N   TYR B  49 " --> pdb=" O   SER B  45 " (cutoff:3.500A)
      removed outlier: 3.954A  pdb=" N   VAL B  50 " --> pdb=" O   ARG B  46 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 52 through 60
    Processing helix  chain 'B' and resid 70 through 84
    Processing helix  chain 'B' and resid 97 through 103
      removed outlier: 3.608A  pdb=" N   GLY B 102 " --> pdb=" O   TRP B  99 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 108 through 115
    Processing helix  chain 'B' and resid 117 through 128
      removed outlier: 3.610A  pdb=" N   VAL B 122 " --> pdb=" O   ARG B 118 " (cutoff:3.500A)
      removed outlier: 4.526A  pdb=" N   LYS B 124 " --> pdb=" O   GLU B 120 " (cutoff:3.500A)
      removed outlier: 5.403A  pdb=" N   HIS B 125 " --> pdb=" O   ALA B 121 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 147 through 154
      removed outlier: 4.380A  pdb=" N   PHE B 150 " --> pdb=" O   ASP B 147 " (cutoff:3.500A)
      removed outlier: 3.523A  pdb=" N   ASP B 152 " --> pdb=" O   SER B 149 " (cutoff:3.500A)
      removed outlier: 3.573A  pdb=" N   LYS B 153 " --> pdb=" O   PHE B 150 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 163 through 175
    Processing helix  chain 'B' and resid 253 through 257
    Processing helix  chain 'B' and resid 301 through 306
    Processing helix  chain 'B' and resid 320 through 340
      removed outlier: 3.637A  pdb=" N   GLU B 324 " --> pdb=" O   GLU B 320 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 347 through 365
      removed outlier: 3.682A  pdb=" N   GLU B 363 " --> pdb=" O   THR B 359 " (cutoff:3.500A)
      removed outlier: 4.006A  pdb=" N   THR B 364 " --> pdb=" O   SER B 360 " (cutoff:3.500A)
      removed outlier: 3.513A  pdb=" N   LEU B 365 " --> pdb=" O   ILE B 361 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 372 through 382
    Processing helix  chain 'B' and resid 387 through 408
    Processing helix  chain 'B' and resid 421 through 427
      removed outlier: 4.363A  pdb=" N   VAL B 425 " --> pdb=" O   ALA B 421 " (cutoff:3.500A)
      removed outlier: 4.052A  pdb=" N   SER B 427 " --> pdb=" O   ASP B 423 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 432 through 437
      removed outlier: 3.507A  pdb=" N   GLU B 435 " --> pdb=" O   GLU B 432 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 443 through 451
    Processing helix  chain 'B' and resid 451 through 460
      removed outlier: 3.688A  pdb=" N   ASN B 460 " --> pdb=" O   GLN B 456 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 469 through 483
      removed outlier: 3.690A  pdb=" N   GLU B 474 " --> pdb=" O   ALA B 470 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 502 through 508
      removed outlier: 3.633A  pdb=" N   ASN B 507 " --> pdb=" O   SER B 504 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 513 through 517
      removed outlier: 3.671A  pdb=" N   ILE B 517 " --> pdb=" O   PRO B 514 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 520 through 533
      removed outlier: 3.570A  pdb=" N   LYS B 531 " --> pdb=" O   ASP B 527 " (cutoff:3.500A)
      removed outlier: 3.728A  pdb=" N   ILE B 532 " --> pdb=" O   ALA B 528 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 546 through 552
      removed outlier: 4.566A  pdb=" N   THR B 551 " --> pdb=" O   THR B 548 " (cutoff:3.500A)
      removed outlier: 3.504A  pdb=" N   ILE B 552 " --> pdb=" O   THR B 549 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 554 through 561
    Processing helix  chain 'B' and resid 570 through 583
      removed outlier: 3.578A  pdb=" N   ARG B 574 " --> pdb=" O   ASN B 570 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 610 through 614
    Processing helix  chain 'B' and resid 623 through 629
    Processing helix  chain 'B' and resid 633 through 650
      removed outlier: 3.630A  pdb=" N   THR B 637 " --> pdb=" O   ALA B 633 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 650 through 663
    Processing helix  chain 'B' and resid 665 through 675
    Processing helix  chain 'B' and resid 681 through 691
    Processing helix  chain 'B' and resid 695 through 712
    Processing helix  chain 'B' and resid 712 through 722
      removed outlier: 3.504A  pdb=" N   LEU B 716 " --> pdb=" O   ASN B 712 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 751 through 770
    Processing helix  chain 'B' and resid 774 through 778
    Processing helix  chain 'B' and resid 779 through 788
    Processing helix  chain 'B' and resid 821 through 834
    Processing helix  chain 'B' and resid 838 through 842
    Processing helix  chain 'B' and resid 857 through 873
    Processing helix  chain 'B' and resid 879 through 889
    Processing helix  chain 'B' and resid 894 through 915
      removed outlier: 3.827A  pdb=" N   THR B 898 " --> pdb=" O   ILE B 894 " (cutoff:3.500A)
      removed outlier: 3.681A  pdb=" N   ILE B 910 " --> pdb=" O   ALA B 906 " (cutoff:3.500A)
      removed outlier: 3.785A  pdb=" N   LYS B 911 " --> pdb=" O   LEU B 907 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 917 through 921
      removed outlier: 3.655A  pdb=" N   TYR B 921 " --> pdb=" O   PHE B 918 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 967 through 980
    Processing helix  chain 'B' and resid 1001 through 1007
      removed outlier: 3.694A  pdb=" N   LEU B1005 " --> pdb=" O   ALA B1002 " (cutoff:3.500A)
      removed outlier: 3.540A  pdb=" N   LEU B1007 " --> pdb=" O   ARG B1004 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 1008 through 1014
    Processing helix  chain 'E' and resid 22 through 35
      removed outlier: 3.577A  pdb=" N   ILE E  30 " --> pdb=" O   VAL E  26 " (cutoff:3.500A)
      removed outlier: 3.720A  pdb=" N   GLN E  31 " --> pdb=" O   LYS E  27 " (cutoff:3.500A)
      removed outlier: 3.793A  pdb=" N   ASP E  32 " --> pdb=" O   ALA E  28 " (cutoff:3.500A)
      removed outlier: 4.097A  pdb=" N   LYS E  33 " --> pdb=" O   LYS E  29 " (cutoff:3.500A)
    Processing helix  chain 'E' and resid 37 through 41
      removed outlier: 3.552A  pdb=" N   GLN E  41 " --> pdb=" O   PRO E  38 " (cutoff:3.500A)
    Processing helix  chain 'E' and resid 55 through 60
      removed outlier: 3.735A  pdb=" N   TYR E  59 " --> pdb=" O   THR E  55 " (cutoff:3.500A)
    Processing sheet with id=AA1, first strand: chain 'A' and resid 4537 through 4540
      removed outlier: 3.632A  pdb=" N   ASP A4538 " --> pdb=" O   VAL A4599 " (cutoff:3.500A)
      removed outlier: 3.622A  pdb=" N   CYS A4601 " --> pdb=" O   ASP A4538 " (cutoff:3.500A)
      removed outlier: 3.639A  pdb=" N   ASP A4602 " --> pdb=" O   ILE A4608 " (cutoff:3.500A)
      removed outlier: 7.241A  pdb=" N   ILE A4608 " --> pdb=" O   ASP A4602 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'A' and resid 4543 through 4545
    Processing sheet with id=AA3, first strand: chain 'B' and resid 134 through 138
      removed outlier: 3.727A  pdb=" N   CYS B 156 " --> pdb=" O   HIS B  63 " (cutoff:3.500A)
    Processing sheet with id=AA4, first strand: chain 'B' and resid 202 through 205
    Processing sheet with id=AA5, first strand: chain 'B' and resid 260 through 262
      removed outlier: 4.693A  pdb=" N   PHE B 244 " --> pdb=" O   VAL B 291 " (cutoff:3.500A)
      removed outlier: 6.394A  pdb=" N   SER B 272 " --> pdb=" O   VAL B 265 " (cutoff:3.500A)
      removed outlier: 5.931A  pdb=" N   VAL B 265 " --> pdb=" O   SER B 272 " (cutoff:3.500A)
    Processing sheet with id=AA6, first strand: chain 'B' and resid 538 through 541
      removed outlier: 5.924A  pdb=" N   ILE B 493 " --> pdb=" O   ASP B 539 " (cutoff:3.500A)
      removed outlier: 7.354A  pdb=" N   HIS B 541 " --> pdb=" O   ILE B 493 " (cutoff:3.500A)
      removed outlier: 6.447A  pdb=" N   VAL B 495 " --> pdb=" O   HIS B 541 " (cutoff:3.500A)
      removed outlier: 3.533A  pdb=" N   THR B 496 " --> pdb=" O   LEU B 465 " (cutoff:3.500A)
      removed outlier: 3.648A  pdb=" N   VAL B 563 " --> pdb=" O   ASN B 462 " (cutoff:3.500A)
      removed outlier: 6.633A  pdb=" N   ILE B 564 " --> pdb=" O   LEU B 589 " (cutoff:3.500A)
      removed outlier: 8.441A  pdb=" N   SER B 591 " --> pdb=" O   ILE B 564 " (cutoff:3.500A)
      removed outlier: 6.859A  pdb=" N   THR B 566 " --> pdb=" O   SER B 591 " (cutoff:3.500A)
      removed outlier: 8.952A  pdb=" N   THR B 593 " --> pdb=" O   THR B 566 " (cutoff:3.500A)
      removed outlier: 3.669A  pdb=" N   CYS B 924 " --> pdb=" O   THR B 600 " (cutoff:3.500A)
    Processing sheet with id=AA7, first strand: chain 'B' and resid 944 through 945
    Processing sheet with id=AA8, first strand: chain 'B' and resid 958 through 961
      removed outlier: 6.471A  pdb=" N   TRP B 958 " --> pdb=" O   ARG B1044 " (cutoff:3.500A)
      removed outlier: 7.797A  pdb=" N   TYR B1046 " --> pdb=" O   TRP B 958 " (cutoff:3.500A)
      removed outlier: 6.821A  pdb=" N   VAL B 960 " --> pdb=" O   TYR B1046 " (cutoff:3.500A)
      removed outlier: 3.978A  pdb=" N   MET B 985 " --> pdb=" O   SER B1027 " (cutoff:3.500A)
      removed outlier: 6.611A  pdb=" N   VAL B 986 " --> pdb=" O   LEU B 993 " (cutoff:3.500A)
    Processing sheet with id=AA9, first strand: chain 'B' and resid 958 through 961
      removed outlier: 6.471A  pdb=" N   TRP B 958 " --> pdb=" O   ARG B1044 " (cutoff:3.500A)
      removed outlier: 7.797A  pdb=" N   TYR B1046 " --> pdb=" O   TRP B 958 " (cutoff:3.500A)
      removed outlier: 6.821A  pdb=" N   VAL B 960 " --> pdb=" O   TYR B1046 " (cutoff:3.500A)
    Processing sheet with id=AB1, first strand: chain 'E' and resid 12 through 16
      removed outlier: 4.259A  pdb=" N   SER E  65 " --> pdb=" O   GLN E   2 " (cutoff:3.500A)
      removed outlier: 4.020A  pdb=" N   ARG E  42 " --> pdb=" O   VAL E  70 " (cutoff:3.500A)

    519 hydrogen bonds defined for protein.
    1416 hydrogen bond angles defined for protein.
    Restraints generated for nucleic acids:
      0 hydrogen bonds
      0 hydrogen bond angles
      0 basepair planarities
      0 basepair parallelities
      0 stacking parallelities
  Total time for adding SS restraints: 1.92

  Time building geometry restraints manager: 1.05 seconds

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

  Histogram of bond lengths:
        1.22 -     1.34: 3523
        1.34 -     1.46: 1581
        1.46 -     1.57: 5902
        1.57 -     1.69: 7
        1.69 -     1.81: 75
  Bond restraints: 11088
  Sorted by residual:
  bond pdb=" CA  SER E  20 "
       pdb=" CB  SER E  20 "
    ideal  model  delta    sigma   weight residual
    1.539  1.498  0.041 1.20e-02 6.94e+03 1.15e+01
  bond pdb=" CZ  ARG C  74 "
       pdb=" NH2 ARG C  74 "
    ideal  model  delta    sigma   weight residual
    1.330  1.298  0.032 1.30e-02 5.92e+03 5.95e+00
  bond pdb=" N   SER E  20 "
       pdb=" CA  SER E  20 "
    ideal  model  delta    sigma   weight residual
    1.460  1.488 -0.029 1.28e-02 6.10e+03 5.05e+00
  bond pdb=" N   GLU E  18 "
       pdb=" CA  GLU E  18 "
    ideal  model  delta    sigma   weight residual
    1.453  1.479 -0.026 1.18e-02 7.18e+03 4.91e+00
  bond pdb=" N   ASP E  21 "
       pdb=" CA  ASP E  21 "
    ideal  model  delta    sigma   weight residual
    1.454  1.482 -0.029 1.34e-02 5.57e+03 4.68e+00
  ... (remaining 11083 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     1.84: 14848
        1.84 -     3.67: 164
        3.67 -     5.51: 19
        5.51 -     7.35: 2
        7.35 -     9.19: 2
  Bond angle restraints: 15035
  Sorted by residual:
  angle pdb=" N   CYS A4666 "
        pdb=" CA  CYS A4666 "
        pdb=" CB  CYS A4666 "
      ideal   model   delta    sigma   weight residual
     110.55  103.39    7.16 1.57e+00 4.06e-01 2.08e+01
  angle pdb=" CA  THR E  22 "
        pdb=" CB  THR E  22 "
        pdb=" OG1 THR E  22 "
      ideal   model   delta    sigma   weight residual
     109.60  103.45    6.15 1.50e+00 4.44e-01 1.68e+01
  angle pdb=" CA  PRO E  19 "
        pdb=" C   PRO E  19 "
        pdb=" O   PRO E  19 "
      ideal   model   delta    sigma   weight residual
     121.95  117.30    4.65 1.25e+00 6.40e-01 1.38e+01
  angle pdb=" CA  VAL E  17 "
        pdb=" C   VAL E  17 "
        pdb=" O   VAL E  17 "
      ideal   model   delta    sigma   weight residual
     121.64  118.24    3.40 9.80e-01 1.04e+00 1.20e+01
  angle pdb=" N   PRO E  19 "
        pdb=" CA  PRO E  19 "
        pdb=" C   PRO E  19 "
      ideal   model   delta    sigma   weight residual
     111.34  106.02    5.32 1.55e+00 4.16e-01 1.18e+01
  ... (remaining 15030 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    17.25: 6367
       17.25 -    34.50: 302
       34.50 -    51.75: 62
       51.75 -    69.00: 9
       69.00 -    86.25: 5
  Dihedral angle restraints: 6745
    sinusoidal: 2776
      harmonic: 3969
  Sorted by residual:
  dihedral pdb=" N   LEU E  15 "
           pdb=" CA  LEU E  15 "
           pdb=" CB  LEU E  15 "
           pdb=" CG  LEU E  15 "
      ideal   model   delta sinusoidal    sigma   weight residual
     -60.00 -113.82   53.82     3      1.50e+01 4.44e-03 9.24e+00
  dihedral pdb=" N   MET A4560 "
           pdb=" CA  MET A4560 "
           pdb=" CB  MET A4560 "
           pdb=" CG  MET A4560 "
      ideal   model   delta sinusoidal    sigma   weight residual
     -60.00 -113.75   53.75     3      1.50e+01 4.44e-03 9.23e+00
  dihedral pdb=" CA  MET E   1 "
           pdb=" CB  MET E   1 "
           pdb=" CG  MET E   1 "
           pdb=" SD  MET E   1 "
      ideal   model   delta sinusoidal    sigma   weight residual
    -180.00 -127.81  -52.19     3      1.50e+01 4.44e-03 9.09e+00
  ... (remaining 6742 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.043: 1281
       0.043 -    0.086: 294
       0.086 -    0.129: 109
       0.129 -    0.172: 1
       0.172 -    0.215: 2
  Chirality restraints: 1687
  Sorted by residual:
  chirality pdb=" C3' AMP E 101 "
            pdb=" C2' AMP E 101 "
            pdb=" C4' AMP E 101 "
            pdb=" O3' AMP E 101 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.51   -2.73    0.21 2.00e-01 2.50e+01 1.15e+00
  chirality pdb=" CA  VAL E  17 "
            pdb=" N   VAL E  17 "
            pdb=" C   VAL E  17 "
            pdb=" CB  VAL E  17 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.44    2.62   -0.18 2.00e-01 2.50e+01 8.22e-01
  chirality pdb=" CA  GLU E  18 "
            pdb=" N   GLU E  18 "
            pdb=" C   GLU E  18 "
            pdb=" CB  GLU E  18 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.66   -0.15 2.00e-01 2.50e+01 5.61e-01
  ... (remaining 1684 not shown)

  Planarity restraints: 1928
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   ASN A4656 "   -0.029 5.00e-02 4.00e+02   4.34e-02 3.01e+00
        pdb=" N   PRO A4657 "    0.075 5.00e-02 4.00e+02
        pdb=" CA  PRO A4657 "   -0.022 5.00e-02 4.00e+02
        pdb=" CD  PRO A4657 "   -0.024 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   ARG A4676 "   -0.022 5.00e-02 4.00e+02   3.30e-02 1.74e+00
        pdb=" N   PRO A4677 "    0.057 5.00e-02 4.00e+02
        pdb=" CA  PRO A4677 "   -0.017 5.00e-02 4.00e+02
        pdb=" CD  PRO A4677 "   -0.018 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   CYS B 546 "   -0.021 5.00e-02 4.00e+02   3.21e-02 1.65e+00
        pdb=" N   PRO B 547 "    0.055 5.00e-02 4.00e+02
        pdb=" CA  PRO B 547 "   -0.016 5.00e-02 4.00e+02
        pdb=" CD  PRO B 547 "   -0.018 5.00e-02 4.00e+02
  ... (remaining 1925 not shown)

  Histogram of nonbonded interaction distances:
        1.33 -     2.04: 2
        2.04 -     2.76: 1565
        2.76 -     3.47: 14562
        3.47 -     4.19: 23035
        4.19 -     4.90: 43214
  Nonbonded interactions: 82378
  Sorted by model distance:
  nonbonded pdb=" OG  SER B 625 "
            pdb=" C   ALA C  76 "
     model   vdw
     1.329 3.270
  nonbonded pdb=" SG  CYS A4666 "
            pdb=" CB  ALA C  76 "
     model   vdw
     1.816 3.820
  nonbonded pdb=" CG  GLU E  24 "
            pdb=" OD1 ASP E  52 "
     model   vdw
     2.089 3.440
  nonbonded pdb=" O   LEU B 568 "
            pdb=" CB  ALA E  76 "
     model   vdw
     2.101 3.460
  nonbonded pdb=" OG  SER B 625 "
            pdb=" O   ALA C  76 "
     model   vdw
     2.229 3.040
  ... (remaining 82373 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
========== WARNING! ============

  No NCS relation were found !!!

================================

Found NCS groups:
  found none.
Set up NCS constraints
  No NCS constraints will be used in refinement.
Set refine NCS operators
Adjust number of macro_cycles
  Number of macro_cycles: 10
Reset NCS operators
Extract rigid body selections
Check and reset occupancies
  Occupancies: min=1.00 max=1.00 mean=1.00
Load rotamer database and sin/cos tables
Set ADP refinement strategy
  ADPs will be refined as individual isotropic
Make a string to write initial .geo file
Internal consistency checks
Time:
  Set random seed:                         0.000
  Set model cs if undefined:               0.000
  Decide on map wrapping:                  0.000
  Normalize map: mean=0, sd=1:             2.520
  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:             0.030
  Extract box with map and model:          0.170
  Check model and map are aligned:         0.020
  Set scattering table:                    0.020
  Process input model:                     11.240
  Find NCS groups from input model:        0.030
  Set up NCS constraints:                  0.020
  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:1.140
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   15.190
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8319
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      :  0.004   0.041  11089  Z= 0.180
  Angle     :  0.501   9.186  15035  Z= 0.277
  Chirality :  0.041   0.215   1687
  Planarity :  0.003   0.043   1928
  Dihedral  : 10.737  86.251   4167
  Min Nonbonded Distance : 1.329

Molprobity Statistics.
  All-atom Clashscore : 2.36
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.78 %
    Favored  : 98.22 %
  Rotamer:
    Outliers :  1.00 %
    Allowed  :  3.67 %
    Favored  : 95.33 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 7.04 %
    Cis-general     : 0.08 %
    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:  1.93 (0.24), residues: 1348
  helix:  2.50 (0.23), residues: 538
  sheet:  0.96 (0.36), residues: 215
  loop :  0.35 (0.27), residues: 595

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG A4799 
 TYR   0.014   0.001   TYR A4660 
 PHE   0.009   0.001   PHE A4628 
 TRP   0.011   0.001   TRP A4673 
 HIS   0.003   0.000   HIS B 326 

Details of bonding type rmsd
  covalent geometry    : bond        0.00383 (11088)
  covalent geometry    : angle       0.50146 (15035)
  hydrogen bonds       : bond        0.19104 (  515)
  hydrogen bonds       : angle       6.12007 ( 1416)
  Misc. bond           : bond        0.00051 (    1)

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

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

  2696 Ramachandran restraints generated.
    1348 Oldfield, 0 Emsley, 1348 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2696 Ramachandran restraints generated.
    1348 Oldfield, 0 Emsley, 1348 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  71 residues out of total 1199 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 59
  time to evaluate  : 0.301 
Fit side-chains
   revert: symmetry clash
REVERT: A 4644 ASN cc_start: 0.8809 (OUTLIER) cc_final: 0.8606 (t0)
REVERT: A 4673 TRP cc_start: 0.7157 (p-90) cc_final: 0.5955 (p-90)
REVERT: B  619 GLU cc_start: 0.9402 (mp0) cc_final: 0.8591 (tp30)
REVERT: B  621 GLU cc_start: 0.9447 (mm-30) cc_final: 0.8758 (pp20)
REVERT: E   22 THR cc_start: 0.8935 (OUTLIER) cc_final: 0.5919 (t)
REVERT: E   58 ASP cc_start: 0.8925 (m-30) cc_final: 0.8615 (m-30)
  outliers start: 12
  outliers final: 5
  residues processed: 68
  average time/residue: 0.1141
  time to fit residues: 11.2377
Evaluate side-chains
  61 residues out of total 1199 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 54
  time to evaluate  : 0.455 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue 4644 ASN
Chi-restraints excluded: chain B residue  345 VAL
Chi-restraints excluded: chain B residue  495 VAL
Chi-restraints excluded: chain B residue  551 THR
Chi-restraints excluded: chain B residue  936 THR
Chi-restraints excluded: chain B residue  946 ILE
Chi-restraints excluded: chain E residue   22 THR
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 134
   random chunks:
   chunk 98 optimal weight:    3.9990
   chunk 107 optimal weight:    2.9990
   chunk 10 optimal weight:    0.7980
   chunk 66 optimal weight:    0.9990
   chunk 130 optimal weight:    4.9990
   chunk 124 optimal weight:    0.1980
   chunk 103 optimal weight:    7.9990
   chunk 77 optimal weight:    8.9990
   chunk 122 optimal weight:    6.9990
   chunk 91 optimal weight:    2.9990
   chunk 55 optimal weight:    2.9990
   overall best weight:    1.5986

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

Flipped N/Q/H residues before XYZ refinement:
B  47 GLN
B 505 ASN
B 858 HIS

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3088 r_free = 0.3088 target = 0.056753 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 42)----------------|
| r_work = 0.2608 r_free = 0.2608 target = 0.038602 restraints weight = 35748.849|
|-----------------------------------------------------------------------------|
r_work (start): 0.2621 rms_B_bonded: 4.44
r_work: 0.2434 rms_B_bonded: 4.73 restraints_weight: 0.5000
r_work (final): 0.2434
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8441
moved from start:          0.0732

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.026  11089  Z= 0.147
  Angle     :  0.483   6.522  15035  Z= 0.253
  Chirality :  0.041   0.142   1687
  Planarity :  0.004   0.045   1928
  Dihedral  :  4.838  58.598   1508
  Min Nonbonded Distance : 2.491

Molprobity Statistics.
  All-atom Clashscore : 2.22
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.85 %
    Favored  : 98.15 %
  Rotamer:
    Outliers :  1.00 %
    Allowed  :  4.67 %
    Favored  : 94.33 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 7.04 %
    Cis-general     : 0.08 %
    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:  1.98 (0.24), residues: 1348
  helix:  2.56 (0.23), residues: 545
  sheet:  0.72 (0.36), residues: 212
  loop :  0.44 (0.27), residues: 591

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG E  54 
 TYR   0.014   0.001   TYR B 611 
 PHE   0.009   0.001   PHE B 624 
 TRP   0.005   0.001   TRP B 378 
 HIS   0.002   0.001   HIS B 326 

Details of bonding type rmsd
  covalent geometry    : bond        0.00341 (11088)
  covalent geometry    : angle       0.48287 (15035)
  hydrogen bonds       : bond        0.04496 (  515)
  hydrogen bonds       : angle       4.74257 ( 1416)
  Misc. bond           : bond        0.00106 (    1)

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

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

  2696 Ramachandran restraints generated.
    1348 Oldfield, 0 Emsley, 1348 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2696 Ramachandran restraints generated.
    1348 Oldfield, 0 Emsley, 1348 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  66 residues out of total 1199 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 54
  time to evaluate  : 0.439 
Fit side-chains
REVERT: A 4644 ASN cc_start: 0.8809 (OUTLIER) cc_final: 0.8598 (t0)
REVERT: A 4673 TRP cc_start: 0.7008 (p-90) cc_final: 0.6363 (p-90)
REVERT: B  162 MET cc_start: 0.9350 (mmm) cc_final: 0.9042 (mmm)
REVERT: B  619 GLU cc_start: 0.9394 (mp0) cc_final: 0.8587 (tp30)
REVERT: B  621 GLU cc_start: 0.9422 (mm-30) cc_final: 0.8781 (pp20)
REVERT: E   31 GLN cc_start: 0.9358 (tt0) cc_final: 0.9102 (tt0)
REVERT: E   34 GLU cc_start: 0.9201 (mm-30) cc_final: 0.8982 (mm-30)
REVERT: E   58 ASP cc_start: 0.9015 (m-30) cc_final: 0.8766 (m-30)
  outliers start: 12
  outliers final: 8
  residues processed: 65
  average time/residue: 0.0927
  time to fit residues: 9.0606
Evaluate side-chains
  59 residues out of total 1199 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 50
  time to evaluate  : 0.421 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue 4644 ASN
Chi-restraints excluded: chain B residue  289 VAL
Chi-restraints excluded: chain B residue  345 VAL
Chi-restraints excluded: chain B residue  495 VAL
Chi-restraints excluded: chain B residue  551 THR
Chi-restraints excluded: chain B residue  855 HIS
Chi-restraints excluded: chain B residue  936 THR
Chi-restraints excluded: chain E residue   15 LEU
Chi-restraints excluded: chain E residue   69 LEU
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 134
   random chunks:
   chunk 104 optimal weight:    0.0870
   chunk 106 optimal weight:    5.9990
   chunk 64 optimal weight:    0.9990
   chunk 26 optimal weight:    7.9990
   chunk 38 optimal weight:    0.0570
   chunk 107 optimal weight:    6.9990
   chunk 4 optimal weight:    6.9990
   chunk 81 optimal weight:    0.0770
   chunk 46 optimal weight:    7.9990
   chunk 102 optimal weight:    0.8980
   chunk 76 optimal weight:    6.9990
   overall best weight:    0.4236

-------------------------------------------------------------------------------
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 = 0.3137 r_free = 0.3137 target = 0.058815 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.2678 r_free = 0.2678 target = 0.040900 restraints weight = 35669.609|
|-----------------------------------------------------------------------------|
r_work (start): 0.2679 rms_B_bonded: 4.42
r_work: 0.2498 rms_B_bonded: 4.71 restraints_weight: 0.5000
r_work (final): 0.2498
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8392
moved from start:          0.1119

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.021  11089  Z= 0.077
  Angle     :  0.419   5.774  15035  Z= 0.218
  Chirality :  0.039   0.138   1687
  Planarity :  0.003   0.044   1928
  Dihedral  :  4.410  58.357   1505
  Min Nonbonded Distance : 2.506

Molprobity Statistics.
  All-atom Clashscore : 2.08
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.04 %
    Favored  : 98.96 %
  Rotamer:
    Outliers :  0.83 %
    Allowed  :  5.42 %
    Favored  : 93.74 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 7.04 %
    Cis-general     : 0.08 %
    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:  2.09 (0.24), residues: 1348
  helix:  2.60 (0.23), residues: 552
  sheet:  0.90 (0.36), residues: 213
  loop :  0.47 (0.27), residues: 583

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG E  54 
 TYR   0.008   0.001   TYR B 979 
 PHE   0.009   0.001   PHE B 656 
 TRP   0.008   0.001   TRP A4673 
 HIS   0.002   0.000   HIS A4674 

Details of bonding type rmsd
  covalent geometry    : bond        0.00161 (11088)
  covalent geometry    : angle       0.41898 (15035)
  hydrogen bonds       : bond        0.03014 (  515)
  hydrogen bonds       : angle       4.23950 ( 1416)
  Misc. bond           : bond        0.00047 (    1)

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

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

  2696 Ramachandran restraints generated.
    1348 Oldfield, 0 Emsley, 1348 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2696 Ramachandran restraints generated.
    1348 Oldfield, 0 Emsley, 1348 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  66 residues out of total 1199 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 56
  time to evaluate  : 0.418 
Fit side-chains
   revert: symmetry clash
REVERT: A 4644 ASN cc_start: 0.8832 (OUTLIER) cc_final: 0.8578 (t0)
REVERT: A 4674 HIS cc_start: 0.7123 (t70) cc_final: 0.6661 (t70)
REVERT: B  162 MET cc_start: 0.9354 (mmm) cc_final: 0.9060 (mmm)
REVERT: B  619 GLU cc_start: 0.9419 (mp0) cc_final: 0.8610 (tp30)
REVERT: B  621 GLU cc_start: 0.9411 (mm-30) cc_final: 0.8768 (pp20)
REVERT: E   31 GLN cc_start: 0.9380 (tt0) cc_final: 0.9141 (tt0)
REVERT: E   58 ASP cc_start: 0.9089 (m-30) cc_final: 0.8847 (m-30)
  outliers start: 10
  outliers final: 7
  residues processed: 65
  average time/residue: 0.0910
  time to fit residues: 8.8553
Evaluate side-chains
  58 residues out of total 1199 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 50
  time to evaluate  : 0.448 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue 4644 ASN
Chi-restraints excluded: chain A residue 4744 ILE
Chi-restraints excluded: chain B residue  289 VAL
Chi-restraints excluded: chain B residue  551 THR
Chi-restraints excluded: chain B residue  552 ILE
Chi-restraints excluded: chain B residue  855 HIS
Chi-restraints excluded: chain E residue   15 LEU
Chi-restraints excluded: chain E residue   69 LEU
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 134
   random chunks:
   chunk 42 optimal weight:    4.9990
   chunk 71 optimal weight:    3.9990
   chunk 58 optimal weight:    3.9990
   chunk 84 optimal weight:    0.2980
   chunk 128 optimal weight:    3.9990
   chunk 79 optimal weight:    2.9990
   chunk 18 optimal weight:    1.9990
   chunk 114 optimal weight:    0.0570
   chunk 7 optimal weight:    5.9990
   chunk 57 optimal weight:    5.9990
   chunk 119 optimal weight:    1.9990
   overall best weight:    1.4704

-------------------------------------------------------------------------------
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 = 0.3101 r_free = 0.3101 target = 0.057332 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 43)----------------|
| r_work = 0.2628 r_free = 0.2628 target = 0.039232 restraints weight = 36082.641|
|-----------------------------------------------------------------------------|
r_work (start): 0.2635 rms_B_bonded: 4.45
r_work: 0.2446 rms_B_bonded: 4.76 restraints_weight: 0.5000
r_work (final): 0.2446
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8429
moved from start:          0.1089

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.024  11089  Z= 0.131
  Angle     :  0.446   9.674  15035  Z= 0.229
  Chirality :  0.040   0.133   1687
  Planarity :  0.003   0.045   1928
  Dihedral  :  4.304  54.949   1502
  Min Nonbonded Distance : 2.480

Molprobity Statistics.
  All-atom Clashscore : 1.94
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.93 %
    Favored  : 98.07 %
  Rotamer:
    Outliers :  1.08 %
    Allowed  :  6.01 %
    Favored  : 92.91 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 7.04 %
    Cis-general     : 0.08 %
    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:  2.14 (0.24), residues: 1348
  helix:  2.69 (0.23), residues: 552
  sheet:  0.86 (0.36), residues: 213
  loop :  0.47 (0.27), residues: 583

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG E  54 
 TYR   0.008   0.001   TYR B 611 
 PHE   0.009   0.001   PHE B 656 
 TRP   0.005   0.001   TRP B 660 
 HIS   0.003   0.000   HIS B 326 

Details of bonding type rmsd
  covalent geometry    : bond        0.00307 (11088)
  covalent geometry    : angle       0.44631 (15035)
  hydrogen bonds       : bond        0.03686 (  515)
  hydrogen bonds       : angle       4.27644 ( 1416)
  Misc. bond           : bond        0.00039 (    1)

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

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

  2696 Ramachandran restraints generated.
    1348 Oldfield, 0 Emsley, 1348 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2696 Ramachandran restraints generated.
    1348 Oldfield, 0 Emsley, 1348 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  65 residues out of total 1199 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 52
  time to evaluate  : 0.343 
Fit side-chains
REVERT: B  162 MET cc_start: 0.9393 (mmm) cc_final: 0.9083 (mmm)
REVERT: B  619 GLU cc_start: 0.9432 (mp0) cc_final: 0.8631 (tp30)
REVERT: B  621 GLU cc_start: 0.9420 (mm-30) cc_final: 0.8798 (pp20)
REVERT: B  677 HIS cc_start: 0.8382 (t-170) cc_final: 0.8161 (t-170)
REVERT: E   31 GLN cc_start: 0.9383 (tt0) cc_final: 0.9144 (tt0)
REVERT: E   58 ASP cc_start: 0.9066 (m-30) cc_final: 0.8819 (m-30)
  outliers start: 13
  outliers final: 10
  residues processed: 64
  average time/residue: 0.0952
  time to fit residues: 9.0298
Evaluate side-chains
  60 residues out of total 1199 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 50
  time to evaluate  : 0.415 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue  289 VAL
Chi-restraints excluded: chain B residue  345 VAL
Chi-restraints excluded: chain B residue  449 CYS
Chi-restraints excluded: chain B residue  495 VAL
Chi-restraints excluded: chain B residue  551 THR
Chi-restraints excluded: chain B residue  552 ILE
Chi-restraints excluded: chain B residue  936 THR
Chi-restraints excluded: chain E residue   15 LEU
Chi-restraints excluded: chain E residue   43 LEU
Chi-restraints excluded: chain E residue   69 LEU
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 134
   random chunks:
   chunk 80 optimal weight:    0.2980
   chunk 2 optimal weight:    0.9980
   chunk 59 optimal weight:    0.9990
   chunk 108 optimal weight:    8.9990
   chunk 115 optimal weight:    3.9990
   chunk 117 optimal weight:    0.9980
   chunk 19 optimal weight:    6.9990
   chunk 54 optimal weight:    3.9990
   chunk 25 optimal weight:    0.7980
   chunk 36 optimal weight:    6.9990
   chunk 89 optimal weight:    0.9980
   overall best weight:    0.8180

-------------------------------------------------------------------------------
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 = 0.3119 r_free = 0.3119 target = 0.058074 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.2653 r_free = 0.2653 target = 0.040029 restraints weight = 35585.531|
|-----------------------------------------------------------------------------|
r_work (start): 0.2660 rms_B_bonded: 4.43
r_work: 0.2474 rms_B_bonded: 4.75 restraints_weight: 0.5000
r_work (final): 0.2474
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8397
moved from start:          0.1221

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.022  11089  Z= 0.089
  Angle     :  0.423   8.190  15035  Z= 0.217
  Chirality :  0.039   0.133   1687
  Planarity :  0.003   0.044   1928
  Dihedral  :  4.144  53.386   1500
  Min Nonbonded Distance : 2.491

Molprobity Statistics.
  All-atom Clashscore : 1.90
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.19 %
    Favored  : 98.81 %
  Rotamer:
    Outliers :  1.17 %
    Allowed  :  6.17 %
    Favored  : 92.66 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 7.04 %
    Cis-general     : 0.08 %
    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:  2.17 (0.24), residues: 1348
  helix:  2.72 (0.23), residues: 552
  sheet:  0.89 (0.36), residues: 213
  loop :  0.48 (0.27), residues: 583

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG E  54 
 TYR   0.007   0.001   TYR B 611 
 PHE   0.008   0.001   PHE B 656 
 TRP   0.039   0.001   TRP A4673 
 HIS   0.002   0.000   HIS B 326 

Details of bonding type rmsd
  covalent geometry    : bond        0.00201 (11088)
  covalent geometry    : angle       0.42329 (15035)
  hydrogen bonds       : bond        0.03137 (  515)
  hydrogen bonds       : angle       4.13683 ( 1416)
  Misc. bond           : bond        0.00037 (    1)

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

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

  2696 Ramachandran restraints generated.
    1348 Oldfield, 0 Emsley, 1348 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2696 Ramachandran restraints generated.
    1348 Oldfield, 0 Emsley, 1348 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  67 residues out of total 1199 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 53
  time to evaluate  : 0.468 
Fit side-chains
REVERT: A 4674 HIS cc_start: 0.6989 (t70) cc_final: 0.6585 (t-170)
REVERT: B   66 LEU cc_start: 0.8547 (OUTLIER) cc_final: 0.8183 (tt)
REVERT: B  162 MET cc_start: 0.9346 (mmm) cc_final: 0.9031 (mmm)
REVERT: B  619 GLU cc_start: 0.9429 (mp0) cc_final: 0.8643 (tp30)
REVERT: B  621 GLU cc_start: 0.9402 (mm-30) cc_final: 0.8760 (pp20)
REVERT: B  677 HIS cc_start: 0.8371 (t-170) cc_final: 0.8137 (t-170)
REVERT: B  841 ASP cc_start: 0.8860 (OUTLIER) cc_final: 0.8569 (m-30)
REVERT: E   31 GLN cc_start: 0.9392 (tt0) cc_final: 0.9153 (tt0)
REVERT: E   58 ASP cc_start: 0.9083 (m-30) cc_final: 0.8839 (m-30)
REVERT: E   63 LYS cc_start: 0.9697 (OUTLIER) cc_final: 0.9480 (ptpp)
REVERT: E   64 GLU cc_start: 0.9460 (mp0) cc_final: 0.9236 (pm20)
  outliers start: 14
  outliers final: 8
  residues processed: 65
  average time/residue: 0.1085
  time to fit residues: 10.5671
Evaluate side-chains
  61 residues out of total 1199 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 50
  time to evaluate  : 0.377 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue   66 LEU
Chi-restraints excluded: chain B residue  289 VAL
Chi-restraints excluded: chain B residue  345 VAL
Chi-restraints excluded: chain B residue  449 CYS
Chi-restraints excluded: chain B residue  551 THR
Chi-restraints excluded: chain B residue  552 ILE
Chi-restraints excluded: chain B residue  841 ASP
Chi-restraints excluded: chain B residue  936 THR
Chi-restraints excluded: chain E residue   15 LEU
Chi-restraints excluded: chain E residue   63 LYS
Chi-restraints excluded: chain E residue   69 LEU
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 134
   random chunks:
   chunk 29 optimal weight:    0.5980
   chunk 101 optimal weight:    3.9990
   chunk 39 optimal weight:    2.9990
   chunk 4 optimal weight:    6.9990
   chunk 60 optimal weight:    5.9990
   chunk 110 optimal weight:    0.8980
   chunk 132 optimal weight:    5.9990
   chunk 98 optimal weight:    3.9990
   chunk 86 optimal weight:    0.9990
   chunk 133 optimal weight:    7.9990
   chunk 61 optimal weight:    0.8980
   overall best weight:    1.2784

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3108 r_free = 0.3108 target = 0.057588 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 43)----------------|
| r_work = 0.2636 r_free = 0.2636 target = 0.039512 restraints weight = 35746.504|
|-----------------------------------------------------------------------------|
r_work (start): 0.2584 rms_B_bonded: 4.44
r_work: 0.2399 rms_B_bonded: 4.76 restraints_weight: 0.5000
r_work (final): 0.2399
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8301
moved from start:          0.1234

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.024  11089  Z= 0.117
  Angle     :  0.432   7.489  15035  Z= 0.222
  Chirality :  0.040   0.130   1687
  Planarity :  0.003   0.044   1928
  Dihedral  :  4.135  50.560   1500
  Min Nonbonded Distance : 2.481

Molprobity Statistics.
  All-atom Clashscore : 1.99
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.85 %
    Favored  : 98.15 %
  Rotamer:
    Outliers :  1.25 %
    Allowed  :  6.34 %
    Favored  : 92.41 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 7.04 %
    Cis-general     : 0.08 %
    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:  2.20 (0.24), residues: 1348
  helix:  2.74 (0.23), residues: 553
  sheet:  0.85 (0.36), residues: 213
  loop :  0.53 (0.27), residues: 582

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.001   0.000   ARG E  54 
 TYR   0.007   0.001   TYR B 611 
 PHE   0.009   0.001   PHE B 656 
 TRP   0.029   0.001   TRP A4673 
 HIS   0.003   0.000   HIS B 326 

Details of bonding type rmsd
  covalent geometry    : bond        0.00274 (11088)
  covalent geometry    : angle       0.43187 (15035)
  hydrogen bonds       : bond        0.03403 (  515)
  hydrogen bonds       : angle       4.15039 ( 1416)
  Misc. bond           : bond        0.00037 (    1)

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

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

  2696 Ramachandran restraints generated.
    1348 Oldfield, 0 Emsley, 1348 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2696 Ramachandran restraints generated.
    1348 Oldfield, 0 Emsley, 1348 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  64 residues out of total 1199 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 49
  time to evaluate  : 0.466 
Fit side-chains
REVERT: B   66 LEU cc_start: 0.8511 (OUTLIER) cc_final: 0.8119 (tt)
REVERT: B  162 MET cc_start: 0.9337 (mmm) cc_final: 0.9004 (mmm)
REVERT: B  619 GLU cc_start: 0.9409 (mp0) cc_final: 0.8634 (tp30)
REVERT: B  621 GLU cc_start: 0.9413 (mm-30) cc_final: 0.8722 (pp20)
REVERT: B  677 HIS cc_start: 0.8358 (t-170) cc_final: 0.8122 (t-170)
REVERT: B  841 ASP cc_start: 0.8846 (OUTLIER) cc_final: 0.8554 (m-30)
REVERT: E   58 ASP cc_start: 0.9048 (m-30) cc_final: 0.8800 (m-30)
  outliers start: 15
  outliers final: 9
  residues processed: 62
  average time/residue: 0.1155
  time to fit residues: 10.5256
Evaluate side-chains
  59 residues out of total 1199 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 48
  time to evaluate  : 0.421 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue   66 LEU
Chi-restraints excluded: chain B residue  289 VAL
Chi-restraints excluded: chain B residue  345 VAL
Chi-restraints excluded: chain B residue  449 CYS
Chi-restraints excluded: chain B residue  495 VAL
Chi-restraints excluded: chain B residue  551 THR
Chi-restraints excluded: chain B residue  552 ILE
Chi-restraints excluded: chain B residue  791 LYS
Chi-restraints excluded: chain B residue  841 ASP
Chi-restraints excluded: chain B residue  936 THR
Chi-restraints excluded: chain E residue   69 LEU
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 134
   random chunks:
   chunk 63 optimal weight:    2.9990
   chunk 47 optimal weight:    4.9990
   chunk 77 optimal weight:    0.8980
   chunk 11 optimal weight:    0.0170
   chunk 20 optimal weight:    3.9990
   chunk 113 optimal weight:    1.9990
   chunk 56 optimal weight:    0.7980
   chunk 41 optimal weight:    3.9990
   chunk 15 optimal weight:    6.9990
   chunk 94 optimal weight:    3.9990
   chunk 99 optimal weight:    0.0020
   overall best weight:    0.7428

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

Flipped N/Q/H residues before XYZ refinement:
A4778 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3154 r_free = 0.3154 target = 0.058864 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.2707 r_free = 0.2707 target = 0.041324 restraints weight = 34961.192|
|-----------------------------------------------------------------------------|
r_work (start): 0.2669 rms_B_bonded: 4.32
r_work: 0.2485 rms_B_bonded: 4.66 restraints_weight: 0.5000
r_work (final): 0.2485
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8416
moved from start:          0.1353

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.043  11089  Z= 0.086
  Angle     :  0.427   7.310  15035  Z= 0.218
  Chirality :  0.039   0.147   1687
  Planarity :  0.003   0.044   1928
  Dihedral  :  4.083  50.194   1500
  Min Nonbonded Distance : 2.492

Molprobity Statistics.
  All-atom Clashscore : 1.94
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.19 %
    Favored  : 98.81 %
  Rotamer:
    Outliers :  1.25 %
    Allowed  :  6.34 %
    Favored  : 92.41 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 7.04 %
    Cis-general     : 0.08 %
    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:  2.23 (0.24), residues: 1348
  helix:  2.76 (0.23), residues: 552
  sheet:  0.86 (0.36), residues: 213
  loop :  0.54 (0.27), residues: 583

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.001   0.000   ARG E  54 
 TYR   0.007   0.001   TYR B 611 
 PHE   0.009   0.001   PHE B 656 
 TRP   0.023   0.001   TRP A4673 
 HIS   0.002   0.000   HIS B 326 

Details of bonding type rmsd
  covalent geometry    : bond        0.00193 (11088)
  covalent geometry    : angle       0.42669 (15035)
  hydrogen bonds       : bond        0.02976 (  515)
  hydrogen bonds       : angle       4.05582 ( 1416)
  Misc. bond           : bond        0.00034 (    1)

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

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

  2696 Ramachandran restraints generated.
    1348 Oldfield, 0 Emsley, 1348 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2696 Ramachandran restraints generated.
    1348 Oldfield, 0 Emsley, 1348 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  65 residues out of total 1199 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 50
  time to evaluate  : 0.440 
Fit side-chains
   revert: symmetry clash
REVERT: A 4674 HIS cc_start: 0.6689 (t70) cc_final: 0.6084 (t70)
REVERT: B  142 PHE cc_start: 0.9350 (OUTLIER) cc_final: 0.9081 (m-80)
REVERT: B  162 MET cc_start: 0.9367 (mmm) cc_final: 0.9063 (mmm)
REVERT: B  619 GLU cc_start: 0.9407 (mp0) cc_final: 0.8646 (tp30)
REVERT: B  621 GLU cc_start: 0.9382 (mm-30) cc_final: 0.8722 (pp20)
REVERT: B  677 HIS cc_start: 0.8331 (t-170) cc_final: 0.8077 (t-170)
REVERT: B  841 ASP cc_start: 0.8863 (OUTLIER) cc_final: 0.8562 (m-30)
REVERT: E   58 ASP cc_start: 0.9093 (m-30) cc_final: 0.8847 (m-30)
  outliers start: 15
  outliers final: 8
  residues processed: 65
  average time/residue: 0.1008
  time to fit residues: 9.9710
Evaluate side-chains
  59 residues out of total 1199 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 49
  time to evaluate  : 0.466 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue  142 PHE
Chi-restraints excluded: chain B residue  289 VAL
Chi-restraints excluded: chain B residue  345 VAL
Chi-restraints excluded: chain B residue  449 CYS
Chi-restraints excluded: chain B residue  495 VAL
Chi-restraints excluded: chain B residue  551 THR
Chi-restraints excluded: chain B residue  552 ILE
Chi-restraints excluded: chain B residue  841 ASP
Chi-restraints excluded: chain B residue  936 THR
Chi-restraints excluded: chain E residue   69 LEU
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 134
   random chunks:
   chunk 62 optimal weight:    5.9990
   chunk 75 optimal weight:    2.9990
   chunk 19 optimal weight:    7.9990
   chunk 9 optimal weight:    3.9990
   chunk 51 optimal weight:   10.0000
   chunk 105 optimal weight:    0.5980
   chunk 33 optimal weight:    4.9990
   chunk 21 optimal weight:    4.9990
   chunk 84 optimal weight:    3.9990
   chunk 89 optimal weight:    1.9990
   chunk 57 optimal weight:    2.9990
   overall best weight:    2.5188

-------------------------------------------------------------------------------
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 = 0.3107 r_free = 0.3107 target = 0.056838 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.2636 r_free = 0.2636 target = 0.038931 restraints weight = 35522.138|
|-----------------------------------------------------------------------------|
r_work (start): 0.2562 rms_B_bonded: 4.35
r_work: 0.2373 rms_B_bonded: 4.70 restraints_weight: 0.5000
r_work (final): 0.2373
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8386
moved from start:          0.1256

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.029  11089  Z= 0.207
  Angle     :  0.500   7.011  15035  Z= 0.257
  Chirality :  0.041   0.129   1687
  Planarity :  0.003   0.044   1928
  Dihedral  :  4.283  45.509   1500
  Min Nonbonded Distance : 2.447

Molprobity Statistics.
  All-atom Clashscore : 2.17
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.30 %
    Favored  : 97.70 %
  Rotamer:
    Outliers :  1.00 %
    Allowed  :  6.76 %
    Favored  : 92.24 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 7.04 %
    Cis-general     : 0.08 %
    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:  2.11 (0.24), residues: 1348
  helix:  2.75 (0.23), residues: 551
  sheet:  0.61 (0.35), residues: 218
  loop :  0.47 (0.27), residues: 579

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG E  72 
 TYR   0.008   0.001   TYR A4621 
 PHE   0.011   0.001   PHE A4628 
 TRP   0.017   0.001   TRP A4673 
 HIS   0.004   0.001   HIS B 326 

Details of bonding type rmsd
  covalent geometry    : bond        0.00486 (11088)
  covalent geometry    : angle       0.50027 (15035)
  hydrogen bonds       : bond        0.04348 (  515)
  hydrogen bonds       : angle       4.32769 ( 1416)
  Misc. bond           : bond        0.00048 (    1)

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

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

  2696 Ramachandran restraints generated.
    1348 Oldfield, 0 Emsley, 1348 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2696 Ramachandran restraints generated.
    1348 Oldfield, 0 Emsley, 1348 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  62 residues out of total 1199 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 50
  time to evaluate  : 0.432 
Fit side-chains
REVERT: B  142 PHE cc_start: 0.9373 (OUTLIER) cc_final: 0.9149 (m-80)
REVERT: B  162 MET cc_start: 0.9395 (mmm) cc_final: 0.9054 (mmm)
REVERT: B  619 GLU cc_start: 0.9394 (mp0) cc_final: 0.8626 (tp30)
REVERT: B  621 GLU cc_start: 0.9377 (mm-30) cc_final: 0.8755 (pp20)
REVERT: B  841 ASP cc_start: 0.8864 (OUTLIER) cc_final: 0.8557 (m-30)
REVERT: E   58 ASP cc_start: 0.9010 (m-30) cc_final: 0.8755 (m-30)
  outliers start: 12
  outliers final: 9
  residues processed: 62
  average time/residue: 0.1164
  time to fit residues: 10.6011
Evaluate side-chains
  60 residues out of total 1199 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 49
  time to evaluate  : 0.454 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue  142 PHE
Chi-restraints excluded: chain B residue  289 VAL
Chi-restraints excluded: chain B residue  345 VAL
Chi-restraints excluded: chain B residue  449 CYS
Chi-restraints excluded: chain B residue  495 VAL
Chi-restraints excluded: chain B residue  551 THR
Chi-restraints excluded: chain B residue  552 ILE
Chi-restraints excluded: chain B residue  791 LYS
Chi-restraints excluded: chain B residue  841 ASP
Chi-restraints excluded: chain B residue  936 THR
Chi-restraints excluded: chain E residue   69 LEU
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 134
   random chunks:
   chunk 53 optimal weight:    4.9990
   chunk 75 optimal weight:    0.4980
   chunk 17 optimal weight:    0.9990
   chunk 65 optimal weight:    3.9990
   chunk 56 optimal weight:    0.5980
   chunk 127 optimal weight:    2.9990
   chunk 4 optimal weight:    5.9990
   chunk 5 optimal weight:    2.9990
   chunk 112 optimal weight:    1.9990
   chunk 22 optimal weight:    3.9990
   chunk 79 optimal weight:    2.9990
   overall best weight:    1.4186

-------------------------------------------------------------------------------
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 = 0.3096 r_free = 0.3096 target = 0.057074 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.2620 r_free = 0.2620 target = 0.038972 restraints weight = 35432.090|
|-----------------------------------------------------------------------------|
r_work (start): 0.2633 rms_B_bonded: 4.40
r_work: 0.2445 rms_B_bonded: 4.72 restraints_weight: 0.5000
r_work (final): 0.2445
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8461
moved from start:          0.1304

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.026  11089  Z= 0.128
  Angle     :  0.460   7.336  15035  Z= 0.236
  Chirality :  0.040   0.138   1687
  Planarity :  0.003   0.046   1928
  Dihedral  :  4.209  45.987   1500
  Min Nonbonded Distance : 2.479

Molprobity Statistics.
  All-atom Clashscore : 2.36
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.41 %
    Favored  : 98.59 %
  Rotamer:
    Outliers :  1.00 %
    Allowed  :  6.84 %
    Favored  : 92.16 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 7.04 %
    Cis-general     : 0.08 %
    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:  2.15 (0.24), residues: 1348
  helix:  2.74 (0.23), residues: 553
  sheet:  0.69 (0.36), residues: 213
  loop :  0.49 (0.27), residues: 582

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG E  72 
 TYR   0.006   0.001   TYR A4621 
 PHE   0.008   0.001   PHE B 656 
 TRP   0.018   0.001   TRP A4673 
 HIS   0.003   0.000   HIS B 326 

Details of bonding type rmsd
  covalent geometry    : bond        0.00300 (11088)
  covalent geometry    : angle       0.45999 (15035)
  hydrogen bonds       : bond        0.03576 (  515)
  hydrogen bonds       : angle       4.17185 ( 1416)
  Misc. bond           : bond        0.00040 (    1)

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

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

  2696 Ramachandran restraints generated.
    1348 Oldfield, 0 Emsley, 1348 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2696 Ramachandran restraints generated.
    1348 Oldfield, 0 Emsley, 1348 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  62 residues out of total 1199 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 50
  time to evaluate  : 0.466 
Fit side-chains
REVERT: A 4674 HIS cc_start: 0.6702 (t70) cc_final: 0.6383 (t70)
REVERT: B  142 PHE cc_start: 0.9404 (OUTLIER) cc_final: 0.9162 (m-80)
REVERT: B  162 MET cc_start: 0.9419 (mmm) cc_final: 0.9096 (mmm)
REVERT: B  619 GLU cc_start: 0.9388 (mp0) cc_final: 0.8631 (tp30)
REVERT: B  621 GLU cc_start: 0.9366 (mm-30) cc_final: 0.8761 (pp20)
REVERT: B  841 ASP cc_start: 0.8901 (OUTLIER) cc_final: 0.8591 (m-30)
REVERT: E   58 ASP cc_start: 0.9063 (m-30) cc_final: 0.8807 (m-30)
  outliers start: 12
  outliers final: 9
  residues processed: 62
  average time/residue: 0.1044
  time to fit residues: 9.6537
Evaluate side-chains
  61 residues out of total 1199 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 50
  time to evaluate  : 0.419 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue  142 PHE
Chi-restraints excluded: chain B residue  289 VAL
Chi-restraints excluded: chain B residue  345 VAL
Chi-restraints excluded: chain B residue  449 CYS
Chi-restraints excluded: chain B residue  495 VAL
Chi-restraints excluded: chain B residue  551 THR
Chi-restraints excluded: chain B residue  552 ILE
Chi-restraints excluded: chain B residue  791 LYS
Chi-restraints excluded: chain B residue  841 ASP
Chi-restraints excluded: chain B residue  936 THR
Chi-restraints excluded: chain E residue   69 LEU
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 134
   random chunks:
   chunk 66 optimal weight:    0.7980
   chunk 29 optimal weight:    5.9990
   chunk 116 optimal weight:    1.9990
   chunk 3 optimal weight:    3.9990
   chunk 23 optimal weight:    2.9990
   chunk 127 optimal weight:    5.9990
   chunk 11 optimal weight:    0.1980
   chunk 109 optimal weight:    2.9990
   chunk 69 optimal weight:    0.9980
   chunk 7 optimal weight:    0.7980
   chunk 87 optimal weight:    0.9980
   overall best weight:    0.7580

-------------------------------------------------------------------------------
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 = 0.3152 r_free = 0.3152 target = 0.058797 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.2702 r_free = 0.2702 target = 0.041119 restraints weight = 34757.062|
|-----------------------------------------------------------------------------|
r_work (start): 0.2666 rms_B_bonded: 4.32
r_work: 0.2482 rms_B_bonded: 4.67 restraints_weight: 0.5000
r_work (final): 0.2482
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8413
moved from start:          0.1443

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.029  11089  Z= 0.088
  Angle     :  0.433   7.712  15035  Z= 0.221
  Chirality :  0.039   0.135   1687
  Planarity :  0.003   0.047   1928
  Dihedral  :  4.040  47.642   1500
  Min Nonbonded Distance : 2.491

Molprobity Statistics.
  All-atom Clashscore : 2.03
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.93 %
    Favored  : 98.07 %
  Rotamer:
    Outliers :  0.83 %
    Allowed  :  6.92 %
    Favored  : 92.24 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 7.04 %
    Cis-general     : 0.08 %
    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 (0.24), residues: 1348
  helix:  2.78 (0.23), residues: 554
  sheet:  0.79 (0.36), residues: 213
  loop :  0.56 (0.27), residues: 581

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.001   0.000   ARG E  54 
 TYR   0.007   0.001   TYR B 611 
 PHE   0.008   0.001   PHE B 656 
 TRP   0.019   0.001   TRP A4673 
 HIS   0.002   0.000   HIS B 326 

Details of bonding type rmsd
  covalent geometry    : bond        0.00200 (11088)
  covalent geometry    : angle       0.43340 (15035)
  hydrogen bonds       : bond        0.02897 (  515)
  hydrogen bonds       : angle       4.00707 ( 1416)
  Misc. bond           : bond        0.00041 (    1)

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

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

  2696 Ramachandran restraints generated.
    1348 Oldfield, 0 Emsley, 1348 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2696 Ramachandran restraints generated.
    1348 Oldfield, 0 Emsley, 1348 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  57 residues out of total 1199 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 47
  time to evaluate  : 0.315 
Fit side-chains
   revert: symmetry clash
REVERT: A 4674 HIS cc_start: 0.6660 (t70) cc_final: 0.6337 (t70)
REVERT: B  142 PHE cc_start: 0.9351 (OUTLIER) cc_final: 0.9082 (m-80)
REVERT: B  162 MET cc_start: 0.9398 (mmm) cc_final: 0.9114 (mmm)
REVERT: B  621 GLU cc_start: 0.9342 (mm-30) cc_final: 0.8640 (pp20)
REVERT: B  841 ASP cc_start: 0.8895 (OUTLIER) cc_final: 0.8576 (m-30)
REVERT: B  985 MET cc_start: 0.8323 (tmm) cc_final: 0.8090 (tmm)
REVERT: E   58 ASP cc_start: 0.9066 (m-30) cc_final: 0.8805 (m-30)
  outliers start: 10
  outliers final: 8
  residues processed: 57
  average time/residue: 0.0871
  time to fit residues: 7.6025
Evaluate side-chains
  57 residues out of total 1199 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 47
  time to evaluate  : 0.435 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue  142 PHE
Chi-restraints excluded: chain B residue  289 VAL
Chi-restraints excluded: chain B residue  345 VAL
Chi-restraints excluded: chain B residue  449 CYS
Chi-restraints excluded: chain B residue  495 VAL
Chi-restraints excluded: chain B residue  551 THR
Chi-restraints excluded: chain B residue  552 ILE
Chi-restraints excluded: chain B residue  841 ASP
Chi-restraints excluded: chain B residue  936 THR
Chi-restraints excluded: chain E residue   69 LEU
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 134
   random chunks:
   chunk 18 optimal weight:    0.0870
   chunk 93 optimal weight:    3.9990
   chunk 114 optimal weight:    0.6980
   chunk 24 optimal weight:    4.9990
   chunk 74 optimal weight:    6.9990
   chunk 130 optimal weight:    0.4980
   chunk 46 optimal weight:    4.9990
   chunk 44 optimal weight:    0.7980
   chunk 10 optimal weight:    4.9990
   chunk 27 optimal weight:    1.9990
   chunk 26 optimal weight:    0.0670
   overall best weight:    0.4296

-------------------------------------------------------------------------------
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 = 0.3174 r_free = 0.3174 target = 0.060577 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.2719 r_free = 0.2719 target = 0.042596 restraints weight = 34836.188|
|-----------------------------------------------------------------------------|
r_work (start): 0.2700 rms_B_bonded: 4.44
r_work: 0.2514 rms_B_bonded: 4.75 restraints_weight: 0.5000
r_work (final): 0.2514
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8375
moved from start:          0.1597

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.045  11089  Z= 0.076
  Angle     :  0.427   7.947  15035  Z= 0.217
  Chirality :  0.039   0.130   1687
  Planarity :  0.003   0.045   1928
  Dihedral  :  3.904  48.637   1500
  Min Nonbonded Distance : 2.494

Molprobity Statistics.
  All-atom Clashscore : 2.31
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.26 %
    Favored  : 98.74 %
  Rotamer:
    Outliers :  0.92 %
    Allowed  :  6.92 %
    Favored  : 92.16 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 7.04 %
    Cis-general     : 0.08 %
    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:  2.32 (0.24), residues: 1348
  helix:  2.83 (0.22), residues: 555
  sheet:  0.89 (0.36), residues: 213
  loop :  0.60 (0.28), residues: 580

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.001   0.000   ARG E  54 
 TYR   0.006   0.001   TYR B 979 
 PHE   0.009   0.001   PHE B 656 
 TRP   0.019   0.001   TRP A4673 
 HIS   0.002   0.000   HIS B 677 

Details of bonding type rmsd
  covalent geometry    : bond        0.00167 (11088)
  covalent geometry    : angle       0.42659 (15035)
  hydrogen bonds       : bond        0.02525 (  515)
  hydrogen bonds       : angle       3.88856 ( 1416)
  Misc. bond           : bond        0.00034 (    1)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 2388.38 seconds
wall clock time: 41 minutes 45.66 seconds (2505.66 seconds total)