Starting phenix.real_space_refine
on Wed Aug  5 21:42:30 2026 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/9qhi_53170/08_2026/9qhi_53170_neut.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/9qhi_53170/08_2026/9qhi_53170.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=4.27
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    model {
      file = "/net/cci-nas-00/data/ceres_data/9qhi_53170/08_2026/9qhi_53170_neut.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/9qhi_53170/08_2026/9qhi_53170_neut.cif"
    real_map_files = "/net/cci-nas-00/data/ceres_data/9qhi_53170/08_2026/9qhi_53170.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/9qhi_53170/08_2026/9qhi_53170.map"
  }
  resolution = 4.27
  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=   0.015
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      52      5.16       5
     C    7252      2.51       5
     N    1933      2.21       5
     O    2175      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 61 residue(s): 0.01s

  Monomer Library directory:
    "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.2rc3-6140/lib/python3.11/site-packages/chem_data/mon_lib"
  Total number of atoms: 11419
  Number of models: 1
  Model: ""
    Number of chains: 6
    Chain: "A"
      Number of atoms: 2330
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 291, 2330
          Classifications: {'peptide': 291}
          Link IDs: {'PCIS': 1, 'PTRANS': 15, 'TRANS': 274}
    Chain: "B"
      Number of atoms: 7826
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 987, 7826
          Classifications: {'peptide': 987}
          Link IDs: {'CIS': 1, 'PCIS': 4, 'PTRANS': 47, 'TRANS': 934}
          Chain breaks: 1
    Chain: "C"
      Number of atoms: 602
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 76, 602
          Classifications: {'peptide': 76}
          Link IDs: {'PTRANS': 3, 'TRANS': 72}
    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: 2.35, per 1000 atoms: 0.21
  Number of scatterers: 11419
  At special positions: 0
  Unit cell: (90.1, 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      52     16.00
     P       7     15.00
     O    2175      8.00
     N    1933      7.00
     C    7252      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: 0.97
  Conformation dependent library (CDL) restraints added in 561.3 milliseconds
  

  2840 Ramachandran restraints generated.
    1420 Oldfield, 0 Emsley, 1420 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  2714

  Finding SS restraints...
    Secondary structure from input PDB file:
      61 helices and 11 sheets defined
      48.0% alpha, 12.6% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.34
  Creating SS restraints...
    Processing helix  chain 'A' and resid 4523 through 4535
      removed outlier: 3.813A  pdb=" N   LYS A4534 " --> pdb=" O   ALA A4530 " (cutoff:3.500A)
      removed outlier: 3.834A  pdb=" N   LEU A4535 " --> pdb=" O   VAL A4531 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 4559 through 4566
    Processing helix  chain 'A' and resid 4572 through 4588
      removed outlier: 3.807A  pdb=" N   VAL A4583 " --> pdb=" O   ALA A4579 " (cutoff:3.500A)
      removed outlier: 3.947A  pdb=" N   THR A4584 " --> pdb=" O   GLN A4580 " (cutoff:3.500A)
      removed outlier: 4.056A  pdb=" N   THR A4587 " --> pdb=" O   VAL A4583 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 4676 through 4680
      removed outlier: 3.554A  pdb=" N   LYS A4680 " --> pdb=" O   PRO A4677 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 4687 through 4700
      removed outlier: 3.576A  pdb=" N   VAL A4695 " --> pdb=" O   VAL A4691 " (cutoff:3.500A)
      removed outlier: 4.057A  pdb=" N   GLN A4696 " --> pdb=" O   LEU A4692 " (cutoff:3.500A)
      removed outlier: 4.641A  pdb=" N   SER A4697 " --> pdb=" O   VAL A4693 " (cutoff:3.500A)
      removed outlier: 3.666A  pdb=" N   LEU A4698 " --> pdb=" O   SER A4694 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 4703 through 4708
      removed outlier: 3.501A  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 4779
      removed outlier: 3.655A  pdb=" N   LEU A4761 " --> pdb=" O   LYS A4757 " (cutoff:3.500A)
      removed outlier: 5.699A  pdb=" N   VAL A4764 " --> pdb=" O   TYR A4760 " (cutoff:3.500A)
      removed outlier: 6.201A  pdb=" N   GLU A4765 " --> pdb=" O   LEU A4761 " (cutoff:3.500A)
      removed outlier: 3.591A  pdb=" N   GLN A4778 " --> pdb=" O   ILE A4774 " (cutoff:3.500A)
      removed outlier: 3.860A  pdb=" N   GLN A4779 " --> pdb=" O   ALA A4775 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 4786 through 4810
      removed outlier: 3.555A  pdb=" N   GLN A4803 " --> pdb=" O   ARG A4799 " (cutoff:3.500A)
      removed outlier: 3.797A  pdb=" N   GLU A4806 " --> pdb=" O   ALA A4802 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 41 through 52
      removed outlier: 7.237A  pdb=" N   ARG B  46 " --> pdb=" O   ALA B  42 " (cutoff:3.500A)
      removed outlier: 5.840A  pdb=" N   GLN B  47 " --> pdb=" O   LEU B  43 " (cutoff:3.500A)
      removed outlier: 3.698A  pdb=" N   TYR B  49 " --> pdb=" O   SER B  45 " (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
    Processing helix  chain 'B' and resid 108 through 115
    Processing helix  chain 'B' and resid 117 through 122
      removed outlier: 4.107A  pdb=" N   VAL B 122 " --> pdb=" O   ARG B 118 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 122 through 130
      removed outlier: 3.670A  pdb=" N   ALA B 127 " --> pdb=" O   LEU B 123 " (cutoff:3.500A)
      removed outlier: 3.584A  pdb=" N   GLU B 128 " --> pdb=" O   LYS B 124 " (cutoff:3.500A)
      removed outlier: 3.955A  pdb=" N   LEU B 129 " --> pdb=" O   HIS B 125 " (cutoff:3.500A)
      removed outlier: 4.226A  pdb=" N   ASN B 130 " --> pdb=" O   ILE B 126 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 148 through 154
    Processing helix  chain 'B' and resid 163 through 176
    Processing helix  chain 'B' and resid 253 through 257
    Processing helix  chain 'B' and resid 301 through 307
      removed outlier: 3.751A  pdb=" N   LYS B 307 " --> pdb=" O   GLU B 303 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 320 through 340
      removed outlier: 3.677A  pdb=" N   GLU B 324 " --> pdb=" O   GLU B 320 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 347 through 365
      removed outlier: 3.540A  pdb=" N   THR B 364 " --> pdb=" O   SER B 360 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 372 through 382
    Processing helix  chain 'B' and resid 387 through 408
      removed outlier: 3.601A  pdb=" N   ALA B 391 " --> pdb=" O   LEU B 387 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 422 through 427
      removed outlier: 3.820A  pdb=" N   SER B 427 " --> pdb=" O   ASP B 423 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 432 through 437
    Processing helix  chain 'B' and resid 443 through 451
    Processing helix  chain 'B' and resid 451 through 459
    Processing helix  chain 'B' and resid 469 through 483
      removed outlier: 3.575A  pdb=" N   GLU B 474 " --> pdb=" O   ALA B 470 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 503 through 508
    Processing helix  chain 'B' and resid 513 through 517
      removed outlier: 3.547A  pdb=" N   ILE B 517 " --> pdb=" O   PRO B 514 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 520 through 533
    Processing helix  chain 'B' and resid 547 through 552
      removed outlier: 4.144A  pdb=" N   THR B 551 " --> pdb=" O   THR B 548 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 554 through 561
    Processing helix  chain 'B' and resid 570 through 583
      removed outlier: 3.680A  pdb=" N   ARG B 574 " --> pdb=" O   ASN B 570 " (cutoff:3.500A)
      removed outlier: 3.505A  pdb=" N   ALA B 583 " --> pdb=" O   SER B 579 " (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: 3.591A  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
    Processing helix  chain 'B' and resid 751 through 769
    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 857 through 873
    Processing helix  chain 'B' and resid 879 through 889
      removed outlier: 3.579A  pdb=" N   THR B 883 " --> pdb=" O   ASP B 879 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 894 through 914
      removed outlier: 3.639A  pdb=" N   THR B 898 " --> pdb=" O   ILE B 894 " (cutoff:3.500A)
      removed outlier: 3.752A  pdb=" N   ILE B 910 " --> pdb=" O   ALA B 906 " (cutoff:3.500A)
      removed outlier: 3.766A  pdb=" N   LYS B 911 " --> pdb=" O   LEU B 907 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 917 through 921
    Processing helix  chain 'B' and resid 967 through 979
    Processing helix  chain 'B' and resid 1001 through 1007
      removed outlier: 3.592A  pdb=" N   LEU B1007 " --> pdb=" O   ARG B1004 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 1008 through 1014
    Processing helix  chain 'C' and resid 22 through 30
      removed outlier: 3.590A  pdb=" N   VAL C  26 " --> pdb=" O   THR C  22 " (cutoff:3.500A)
      removed outlier: 3.683A  pdb=" N   ALA C  28 " --> pdb=" O   GLU C  24 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 30 through 35
      removed outlier: 4.158A  pdb=" N   GLU C  34 " --> pdb=" O   ILE C  30 " (cutoff:3.500A)
    Processing helix  chain 'E' and resid 22 through 35
      removed outlier: 4.050A  pdb=" N   ILE E  30 " --> pdb=" O   VAL E  26 " (cutoff:3.500A)
      removed outlier: 4.034A  pdb=" N   GLN E  31 " --> pdb=" O   LYS E  27 " (cutoff:3.500A)
      removed outlier: 3.991A  pdb=" N   ASP E  32 " --> pdb=" O   ALA E  28 " (cutoff:3.500A)
      removed outlier: 4.898A  pdb=" N   LYS E  33 " --> pdb=" O   LYS E  29 " (cutoff:3.500A)
    Processing helix  chain 'E' and resid 37 through 41
      removed outlier: 3.569A  pdb=" N   GLN E  41 " --> pdb=" O   PRO E  38 " (cutoff:3.500A)
    Processing helix  chain 'E' and resid 55 through 60
      removed outlier: 3.520A  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: 3.589A  pdb=" N   ASP A4538 " --> pdb=" O   VAL A4599 " (cutoff:3.500A)
      removed outlier: 4.129A  pdb=" N   ASP A4602 " --> pdb=" O   ILE A4608 " (cutoff:3.500A)
      removed outlier: 7.327A  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 136
      removed outlier: 6.161A  pdb=" N   VAL B  64 " --> pdb=" O   THR B  89 " (cutoff:3.500A)
      removed outlier: 4.158A  pdb=" N   CYS B 156 " --> pdb=" O   HIS B  63 " (cutoff:3.500A)
      removed outlier: 3.527A  pdb=" N   ALA B 186 " --> pdb=" O   LEU B 159 " (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: 3.555A  pdb=" N   LEU B 245 " --> pdb=" O   GLN B 261 " (cutoff:3.500A)
      removed outlier: 3.783A  pdb=" N   VAL B 229 " --> pdb=" O   PHE B 271 " (cutoff:3.500A)
      removed outlier: 5.822A  pdb=" N   SER B 272 " --> pdb=" O   VAL B 265 " (cutoff:3.500A)
      removed outlier: 5.424A  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: 6.253A  pdb=" N   ILE B 493 " --> pdb=" O   ASP B 539 " (cutoff:3.500A)
      removed outlier: 7.819A  pdb=" N   HIS B 541 " --> pdb=" O   ILE B 493 " (cutoff:3.500A)
      removed outlier: 6.482A  pdb=" N   VAL B 495 " --> pdb=" O   HIS B 541 " (cutoff:3.500A)
      removed outlier: 3.893A  pdb=" N   THR B 496 " --> pdb=" O   LEU B 465 " (cutoff:3.500A)
      removed outlier: 3.918A  pdb=" N   VAL B 563 " --> pdb=" O   ASN B 462 " (cutoff:3.500A)
      removed outlier: 6.735A  pdb=" N   ILE B 564 " --> pdb=" O   LEU B 589 " (cutoff:3.500A)
      removed outlier: 8.588A  pdb=" N   SER B 591 " --> pdb=" O   ILE B 564 " (cutoff:3.500A)
      removed outlier: 7.021A  pdb=" N   THR B 566 " --> pdb=" O   SER B 591 " (cutoff:3.500A)
      removed outlier: 8.928A  pdb=" N   THR B 593 " --> pdb=" O   THR B 566 " (cutoff:3.500A)
      removed outlier: 3.809A  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 947
      removed outlier: 6.601A  pdb=" N   ILE B 950 " --> pdb=" O   ILE B 946 " (cutoff:3.500A)
    Processing sheet with id=AA8, first strand: chain 'B' and resid 958 through 961
      removed outlier: 6.493A  pdb=" N   TRP B 958 " --> pdb=" O   ARG B1044 " (cutoff:3.500A)
      removed outlier: 7.695A  pdb=" N   TYR B1046 " --> pdb=" O   TRP B 958 " (cutoff:3.500A)
      removed outlier: 6.670A  pdb=" N   VAL B 960 " --> pdb=" O   TYR B1046 " (cutoff:3.500A)
      removed outlier: 3.737A  pdb=" N   MET B 985 " --> pdb=" O   SER B1027 " (cutoff:3.500A)
      removed outlier: 7.082A  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: 6.493A  pdb=" N   TRP B 958 " --> pdb=" O   ARG B1044 " (cutoff:3.500A)
      removed outlier: 7.695A  pdb=" N   TYR B1046 " --> pdb=" O   TRP B 958 " (cutoff:3.500A)
      removed outlier: 6.670A  pdb=" N   VAL B 960 " --> pdb=" O   TYR B1046 " (cutoff:3.500A)
    Processing sheet with id=AB1, first strand: chain 'C' and resid 12 through 16
      removed outlier: 3.592A  pdb=" N   LEU C  15 " --> pdb=" O   ILE C   3 " (cutoff:3.500A)
      removed outlier: 3.524A  pdb=" N   LEU C  67 " --> pdb=" O   PHE C   4 " (cutoff:3.500A)
      removed outlier: 3.572A  pdb=" N   ARG C  42 " --> pdb=" O   VAL C  70 " (cutoff:3.500A)
    Processing sheet with id=AB2, first strand: chain 'E' and resid 12 through 16
      removed outlier: 3.839A  pdb=" N   LEU E  69 " --> pdb=" O   LYS E   6 " (cutoff:3.500A)
      removed outlier: 3.671A  pdb=" N   ARG E  42 " --> pdb=" O   VAL E  70 " (cutoff:3.500A)

    519 hydrogen bonds defined for protein.
    1407 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: 2.10

  Time building geometry restraints manager: 1.29 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: 3719
        1.34 -     1.46: 2374
        1.46 -     1.58: 5490
        1.58 -     1.70: 7
        1.70 -     1.82: 77
  Bond restraints: 11667
  Sorted by residual:
  bond pdb=" N   GLY C  75 "
       pdb=" CA  GLY C  75 "
    ideal  model  delta    sigma   weight residual
    1.446  1.474 -0.028 1.06e-02 8.90e+03 7.04e+00
  bond pdb=" CZ  ARG C  74 "
       pdb=" NH2 ARG C  74 "
    ideal  model  delta    sigma   weight residual
    1.330  1.296  0.034 1.30e-02 5.92e+03 6.72e+00
  bond pdb=" CA  ILE B 622 "
       pdb=" C   ILE B 622 "
    ideal  model  delta    sigma   weight residual
    1.524  1.544 -0.020 9.30e-03 1.16e+04 4.56e+00
  bond pdb=" CZ2 TRP A4673 "
       pdb=" CH2 TRP A4673 "
    ideal  model  delta    sigma   weight residual
    1.368  1.404 -0.036 1.90e-02 2.77e+03 3.61e+00
  bond pdb=" CG  TRP A4673 "
       pdb=" CD2 TRP A4673 "
    ideal  model  delta    sigma   weight residual
    1.433  1.467 -0.034 1.80e-02 3.09e+03 3.54e+00
  ... (remaining 11662 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     2.07: 15578
        2.07 -     4.14: 214
        4.14 -     6.21: 20
        6.21 -     8.28: 2
        8.28 -    10.35: 1
  Bond angle restraints: 15815
  Sorted by residual:
  angle pdb=" CA  ASN A4671 "
        pdb=" CB  ASN A4671 "
        pdb=" CG  ASN A4671 "
      ideal   model   delta    sigma   weight residual
     112.60  117.65   -5.05 1.00e+00 1.00e+00 2.55e+01
  angle pdb=" C   PHE B 624 "
        pdb=" N   SER B 625 "
        pdb=" CA  SER B 625 "
      ideal   model   delta    sigma   weight residual
     120.38  125.46   -5.08 1.37e+00 5.33e-01 1.38e+01
  angle pdb=" CB  MET B 844 "
        pdb=" CG  MET B 844 "
        pdb=" SD  MET B 844 "
      ideal   model   delta    sigma   weight residual
     112.70  102.35   10.35 3.00e+00 1.11e-01 1.19e+01
  angle pdb=" N   PRO B 623 "
        pdb=" CA  PRO B 623 "
        pdb=" CB  PRO B 623 "
      ideal   model   delta    sigma   weight residual
     103.25  106.22   -2.97 8.80e-01 1.29e+00 1.14e+01
  angle pdb=" C   GLY C  75 "
        pdb=" N   ALA C  76 "
        pdb=" CA  ALA C  76 "
      ideal   model   delta    sigma   weight residual
     121.70  127.73   -6.03 1.80e+00 3.09e-01 1.12e+01
  ... (remaining 15810 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    16.96: 6591
       16.96 -    33.93: 422
       33.93 -    50.89: 72
       50.89 -    67.86: 18
       67.86 -    84.82: 6
  Dihedral angle restraints: 7109
    sinusoidal: 2931
      harmonic: 4178
  Sorted by residual:
  dihedral pdb=" CA  ILE C  44 "
           pdb=" C   ILE C  44 "
           pdb=" N   PHE C  45 "
           pdb=" CA  PHE C  45 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  160.73   19.27     0      5.00e+00 4.00e-02 1.49e+01
  dihedral pdb=" CA  MET B  69 "
           pdb=" C   MET B  69 "
           pdb=" N   GLY B  70 "
           pdb=" CA  GLY B  70 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  163.67   16.33     0      5.00e+00 4.00e-02 1.07e+01
  dihedral pdb=" CA  VAL A4695 "
           pdb=" C   VAL A4695 "
           pdb=" N   GLN A4696 "
           pdb=" CA  GLN A4696 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00 -164.23  -15.77     0      5.00e+00 4.00e-02 9.94e+00
  ... (remaining 7106 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.051: 1459
       0.051 -    0.102: 262
       0.102 -    0.153: 53
       0.153 -    0.204: 6
       0.204 -    0.254: 1
  Chirality restraints: 1781
  Sorted by residual:
  chirality pdb=" CA  ILE B 622 "
            pdb=" N   ILE B 622 "
            pdb=" C   ILE B 622 "
            pdb=" CB  ILE B 622 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.43    2.69   -0.25 2.00e-01 2.50e+01 1.62e+00
  chirality pdb=" CA  PRO B 623 "
            pdb=" N   PRO B 623 "
            pdb=" C   PRO B 623 "
            pdb=" CB  PRO B 623 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.72    2.54    0.18 2.00e-01 2.50e+01 7.74e-01
  chirality pdb=" CG  LEU C  50 "
            pdb=" CB  LEU C  50 "
            pdb=" CD1 LEU C  50 "
            pdb=" CD2 LEU C  50 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.59   -2.42   -0.17 2.00e-01 2.50e+01 7.01e-01
  ... (remaining 1778 not shown)

  Planarity restraints: 2028
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CB  TRP A4673 "    0.081 2.00e-02 2.50e+03   4.08e-02 4.17e+01
        pdb=" CG  TRP A4673 "   -0.025 2.00e-02 2.50e+03
        pdb=" CD1 TRP A4673 "   -0.008 2.00e-02 2.50e+03
        pdb=" CD2 TRP A4673 "   -0.047 2.00e-02 2.50e+03
        pdb=" NE1 TRP A4673 "   -0.021 2.00e-02 2.50e+03
        pdb=" CE2 TRP A4673 "   -0.005 2.00e-02 2.50e+03
        pdb=" CE3 TRP A4673 "   -0.056 2.00e-02 2.50e+03
        pdb=" CZ2 TRP A4673 "    0.038 2.00e-02 2.50e+03
        pdb=" CZ3 TRP A4673 "   -0.005 2.00e-02 2.50e+03
        pdb=" CH2 TRP A4673 "    0.047 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CB  TYR A4660 "   -0.059 2.00e-02 2.50e+03   3.40e-02 2.31e+01
        pdb=" CG  TYR A4660 "    0.010 2.00e-02 2.50e+03
        pdb=" CD1 TYR A4660 "    0.034 2.00e-02 2.50e+03
        pdb=" CD2 TYR A4660 "    0.026 2.00e-02 2.50e+03
        pdb=" CE1 TYR A4660 "    0.018 2.00e-02 2.50e+03
        pdb=" CE2 TYR A4660 "    0.026 2.00e-02 2.50e+03
        pdb=" CZ  TYR A4660 "   -0.001 2.00e-02 2.50e+03
        pdb=" OH  TYR A4660 "   -0.053 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  SER B 625 "    0.009 2.00e-02 2.50e+03   1.72e-02 2.95e+00
        pdb=" C   SER B 625 "   -0.030 2.00e-02 2.50e+03
        pdb=" O   SER B 625 "    0.011 2.00e-02 2.50e+03
        pdb=" N   THR B 626 "    0.010 2.00e-02 2.50e+03
  ... (remaining 2025 not shown)

  Histogram of nonbonded interaction distances:
        1.33 -     2.04: 4
        2.04 -     2.76: 1638
        2.76 -     3.47: 17387
        3.47 -     4.19: 26896
        4.19 -     4.90: 47296
  Nonbonded interactions: 93221
  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
     1.821 3.820
  nonbonded pdb=" CH2 TRP A4673 "
            pdb=" N   GLY A4675 "
     model   vdw
     1.956 3.420
  nonbonded pdb=" CZ3 TRP A4673 "
            pdb=" N   GLY A4675 "
     model   vdw
     1.992 3.420
  nonbonded pdb=" CZ2 TRP A4673 "
            pdb=" CA  GLY A4675 "
     model   vdw
     2.125 3.740
  ... (remaining 93216 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 'C'
  selection = (chain 'E' and (resid 1 through 75 or (resid 76 and (name N or name CA or name C \ 
 or name O or name CB ))))
}

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:             2.370
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.000
  Construct map_model_manager:             0.010
  Extract box with map and model:          0.180
  Check model and map are aligned:         0.020
  Set scattering table:                    0.030
  Process input model:                     11.460
  Find NCS groups from input model:        0.050
  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:1.290
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   15.430
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8511
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      :  0.003   0.048  11668  Z= 0.161
  Angle     :  0.576  10.355  15815  Z= 0.314
  Chirality :  0.042   0.254   1781
  Planarity :  0.004   0.041   2028
  Dihedral  : 12.009  84.822   4395
  Min Nonbonded Distance : 1.329

Molprobity Statistics.
  All-atom Clashscore : 12.06
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.76 %
    Favored  : 98.24 %
  Rotamer:
    Outliers :  0.08 %
    Allowed  :  0.63 %
    Favored  : 99.29 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 6.85 %
    Cis-general     : 0.07 %
    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:  1.24 (0.23), residues: 1420
  helix:  1.74 (0.22), residues: 575
  sheet:  0.10 (0.37), residues: 205
  loop :  0.35 (0.26), residues: 640

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.000   ARG C  54 
 TYR   0.059   0.002   TYR A4660 
 PHE   0.018   0.002   PHE B 630 
 TRP   0.081   0.003   TRP A4673 
 HIS   0.016   0.001   HIS A4800 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00324 /  0.16 (11667)
  covalent geometry    : angle       0.57604 /  0.31 (15815)
  hydrogen bonds       : bond        0.17533 / 11.15 (  515)
  hydrogen bonds       : angle       6.65327 /  4.72 ( 1407)
  Misc. bond           : bond        0.00067 /  0.04 (    1)

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

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

  2840 Ramachandran restraints generated.
    1420 Oldfield, 0 Emsley, 1420 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2840 Ramachandran restraints generated.
    1420 Oldfield, 0 Emsley, 1420 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  71 residues out of total 1265 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 70
  time to evaluate  : 0.453 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A 4542 MET cc_start: 0.9147 (mpp) cc_final: 0.8853 (mpp)
REVERT: A 4627 GLU cc_start: 0.8835 (tt0) cc_final: 0.8419 (tp30)
REVERT: A 4790 MET cc_start: 0.9625 (mmt) cc_final: 0.9109 (tpp)
REVERT: B   69 MET cc_start: 0.9136 (mpp) cc_final: 0.8549 (mpp)
REVERT: B  256 LEU cc_start: 0.8744 (tp) cc_final: 0.8348 (tp)
REVERT: B  329 MET cc_start: 0.9059 (tpt) cc_final: 0.8798 (tpp)
REVERT: B  475 MET cc_start: 0.9633 (mmp) cc_final: 0.9364 (mmm)
REVERT: B  594 MET cc_start: 0.9473 (tmm) cc_final: 0.8595 (tmm)
REVERT: B  616 ASP cc_start: 0.9659 (p0) cc_final: 0.9442 (t0)
REVERT: B  872 MET cc_start: 0.9155 (mmp) cc_final: 0.8919 (tpp)
REVERT: B  985 MET cc_start: 0.8805 (tmm) cc_final: 0.8571 (tmm)
REVERT: B 1009 MET cc_start: 0.9384 (mmp) cc_final: 0.9169 (mmm)
REVERT: C    1 MET cc_start: 0.7754 (ptm) cc_final: 0.7387 (ptm)
REVERT: E    1 MET cc_start: 0.8692 (ttt) cc_final: 0.7791 (tpp)
REVERT: E    6 LYS cc_start: 0.9740 (mtpp) cc_final: 0.9474 (mmtm)
  outliers start: 1
  outliers final: 1
  residues processed: 71
  average time/residue: 0.1030
  time to fit residues: 11.1793
Evaluate side-chains
  59 residues out of total 1265 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 58
  time to evaluate  : 0.463 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 141
   random chunks:
   chunk 98 optimal weight:   10.0000
   chunk 107 optimal weight:    4.9990
   chunk 10 optimal weight:   10.0000
   chunk 66 optimal weight:    4.9990
   chunk 130 optimal weight:    3.9990
   chunk 124 optimal weight:    0.8980
   chunk 103 optimal weight:    0.3980
   chunk 77 optimal weight:   20.0000
   chunk 122 optimal weight:    7.9990
   chunk 91 optimal weight:    6.9990
   chunk 55 optimal weight:    6.9990
   overall best weight:    3.0586

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
A4769 GLN
B 171 ASN
B 234 ASN
** C  68 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.2781 r_free = 0.2781 target = 0.030432 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.2540 r_free = 0.2540 target = 0.023581 restraints weight = 135757.610|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 26)----------------|
| r_work = 0.2564 r_free = 0.2564 target = 0.024179 restraints weight = 100059.655|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 21)----------------|
| r_work = 0.2580 r_free = 0.2580 target = 0.024562 restraints weight = 79450.700|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 31)----------------|
| r_work = 0.2595 r_free = 0.2595 target = 0.024940 restraints weight = 68211.092|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 27)----------------|
| r_work = 0.2604 r_free = 0.2604 target = 0.025198 restraints weight = 59297.206|
|-----------------------------------------------------------------------------|
r_work (final): 0.2609
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8514
moved from start:          0.0919

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.035  11668  Z= 0.152
  Angle     :  0.538   5.824  15815  Z= 0.283
  Chirality :  0.040   0.154   1781
  Planarity :  0.004   0.035   2028
  Dihedral  :  5.387  64.842   1575
  Min Nonbonded Distance : 2.565

Molprobity Statistics.
  All-atom Clashscore : 11.62
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.04 %
    Favored  : 97.96 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  3.64 %
    Favored  : 96.36 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 6.85 %
    Cis-general     : 0.07 %
    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:  1.30 (0.23), residues: 1420
  helix:  1.80 (0.22), residues: 589
  sheet:  0.13 (0.37), residues: 201
  loop :  0.33 (0.26), residues: 630

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG A4600 
 TYR   0.011   0.001   TYR B 611 
 PHE   0.020   0.001   PHE A4688 
 TRP   0.025   0.001   TRP A4673 
 HIS   0.005   0.001   HIS C  68 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00315 /  0.15 (11667)
  covalent geometry    : angle       0.53782 /  0.28 (15815)
  hydrogen bonds       : bond        0.03820 /  2.49 (  515)
  hydrogen bonds       : angle       5.19814 /  3.61 ( 1407)
  Misc. bond           : bond        0.00051 /  0.03 (    1)

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

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

  2840 Ramachandran restraints generated.
    1420 Oldfield, 0 Emsley, 1420 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2840 Ramachandran restraints generated.
    1420 Oldfield, 0 Emsley, 1420 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  67 residues out of total 1265 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 67
  time to evaluate  : 0.277 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A 4542 MET cc_start: 0.9264 (mpp) cc_final: 0.8901 (mpp)
REVERT: A 4627 GLU cc_start: 0.8763 (tt0) cc_final: 0.8524 (tp30)
REVERT: A 4790 MET cc_start: 0.9586 (mmt) cc_final: 0.9087 (tpp)
REVERT: B   69 MET cc_start: 0.9163 (mpp) cc_final: 0.8553 (mpp)
REVERT: B  256 LEU cc_start: 0.8729 (tp) cc_final: 0.8340 (tp)
REVERT: B  329 MET cc_start: 0.9049 (tpt) cc_final: 0.8775 (tpp)
REVERT: B  401 GLU cc_start: 0.9510 (mm-30) cc_final: 0.9303 (mm-30)
REVERT: B  475 MET cc_start: 0.9646 (mmp) cc_final: 0.9377 (mmm)
REVERT: B  594 MET cc_start: 0.9416 (tmm) cc_final: 0.8526 (tmm)
REVERT: B  985 MET cc_start: 0.8834 (tmm) cc_final: 0.8633 (tmm)
REVERT: E    1 MET cc_start: 0.8634 (ttt) cc_final: 0.7709 (tpp)
REVERT: E    6 LYS cc_start: 0.9753 (mtpp) cc_final: 0.9489 (mmtm)
  outliers start: 0
  outliers final: 0
  residues processed: 67
  average time/residue: 0.0887
  time to fit residues: 9.1927
Evaluate side-chains
  57 residues out of total 1265 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 57
  time to evaluate  : 0.458 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 141
   random chunks:
   chunk 49 optimal weight:    9.9990
   chunk 93 optimal weight:    6.9990
   chunk 76 optimal weight:    5.9990
   chunk 75 optimal weight:    2.9990
   chunk 117 optimal weight:    9.9990
   chunk 125 optimal weight:   10.0000
   chunk 128 optimal weight:    7.9990
   chunk 10 optimal weight:    7.9990
   chunk 87 optimal weight:   10.0000
   chunk 71 optimal weight:   10.0000
   chunk 110 optimal weight:    5.9990
   overall best weight:    5.9990

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
** A4558 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** A4769 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 171 ASN
B 234 ASN
** B 415 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 599 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** C  68 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.2738 r_free = 0.2738 target = 0.029989 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 24)----------------|
| r_work = 0.2529 r_free = 0.2529 target = 0.023779 restraints weight = 140936.724|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 32)----------------|
| r_work = 0.2552 r_free = 0.2552 target = 0.024345 restraints weight = 102840.351|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 28)----------------|
| r_work = 0.2566 r_free = 0.2566 target = 0.024710 restraints weight = 81366.559|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 24)----------------|
| r_work = 0.2580 r_free = 0.2580 target = 0.025076 restraints weight = 68612.653|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 18)----------------|
| r_work = 0.2588 r_free = 0.2588 target = 0.025310 restraints weight = 59811.310|
|-----------------------------------------------------------------------------|
r_work (final): 0.2574
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8607
moved from start:          0.1952

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.006   0.057  11668  Z= 0.276
  Angle     :  0.694   7.785  15815  Z= 0.363
  Chirality :  0.042   0.198   1781
  Planarity :  0.004   0.045   2028
  Dihedral  :  5.988  77.885   1575
  Min Nonbonded Distance : 2.531

Molprobity Statistics.
  All-atom Clashscore : 18.82
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.52 %
    Favored  : 96.48 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  5.22 %
    Favored  : 94.78 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 6.85 %
    Cis-general     : 0.07 %
    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:  0.75 (0.23), residues: 1420
  helix:  1.34 (0.21), residues: 582
  sheet: -0.20 (0.36), residues: 193
  loop :  0.07 (0.26), residues: 645

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.001   ARG C  42 
 TYR   0.018   0.002   TYR B  49 
 PHE   0.024   0.002   PHE A4598 
 TRP   0.017   0.002   TRP B 660 
 HIS   0.006   0.001   HIS C  68 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00562 /  0.28 (11667)
  covalent geometry    : angle       0.69405 /  0.36 (15815)
  hydrogen bonds       : bond        0.04117 /  2.72 (  515)
  hydrogen bonds       : angle       5.51542 /  3.81 ( 1407)
  Misc. bond           : bond        0.00040 /  0.02 (    1)

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

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

  2840 Ramachandran restraints generated.
    1420 Oldfield, 0 Emsley, 1420 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2840 Ramachandran restraints generated.
    1420 Oldfield, 0 Emsley, 1420 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  59 residues out of total 1265 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 59
  time to evaluate  : 0.302 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A 4542 MET cc_start: 0.9256 (mpp) cc_final: 0.8896 (mpp)
REVERT: A 4560 MET cc_start: 0.8960 (mtm) cc_final: 0.8594 (mtt)
REVERT: A 4627 GLU cc_start: 0.8870 (tt0) cc_final: 0.8526 (tp30)
REVERT: A 4790 MET cc_start: 0.9558 (mmt) cc_final: 0.9186 (mmp)
REVERT: B   69 MET cc_start: 0.9306 (mpp) cc_final: 0.8472 (mpp)
REVERT: B  329 MET cc_start: 0.9068 (tpt) cc_final: 0.8748 (tpp)
REVERT: B  475 MET cc_start: 0.9670 (mmp) cc_final: 0.9441 (mmm)
REVERT: B  594 MET cc_start: 0.9436 (tmm) cc_final: 0.9013 (tmm)
REVERT: E    1 MET cc_start: 0.8595 (ttt) cc_final: 0.7935 (tpp)
REVERT: E    6 LYS cc_start: 0.9757 (mtpp) cc_final: 0.9461 (mmtp)
  outliers start: 0
  outliers final: 0
  residues processed: 59
  average time/residue: 0.0818
  time to fit residues: 7.6234
Evaluate side-chains
  52 residues out of total 1265 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 52
  time to evaluate  : 0.358 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 141
   random chunks:
   chunk 12 optimal weight:    6.9990
   chunk 48 optimal weight:    9.9990
   chunk 102 optimal weight:   10.0000
   chunk 107 optimal weight:    8.9990
   chunk 23 optimal weight:    7.9990
   chunk 138 optimal weight:    6.9990
   chunk 65 optimal weight:    3.9990
   chunk 10 optimal weight:    3.9990
   chunk 4 optimal weight:    9.9990
   chunk 109 optimal weight:    5.9990
   chunk 42 optimal weight:    6.9990
   overall best weight:    5.5990

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
A4558 HIS
A4769 GLN
B 171 ASN
** B 415 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 713 HIS
** C  68 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.2732 r_free = 0.2732 target = 0.029101 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 31)----------------|
| r_work = 0.2489 r_free = 0.2489 target = 0.022621 restraints weight = 146192.261|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 27)----------------|
| r_work = 0.2514 r_free = 0.2514 target = 0.023205 restraints weight = 105641.612|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 28)----------------|
| r_work = 0.2532 r_free = 0.2532 target = 0.023647 restraints weight = 83430.867|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 26)----------------|
| r_work = 0.2545 r_free = 0.2545 target = 0.023971 restraints weight = 69321.454|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 20)----------------|
| r_work = 0.2552 r_free = 0.2552 target = 0.024139 restraints weight = 60210.616|
|-----------------------------------------------------------------------------|
r_work (final): 0.2533
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8615
moved from start:          0.2611

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.043  11668  Z= 0.249
  Angle     :  0.637   8.131  15815  Z= 0.337
  Chirality :  0.042   0.212   1781
  Planarity :  0.004   0.045   2028
  Dihedral  :  6.193  80.763   1575
  Min Nonbonded Distance : 2.490

Molprobity Statistics.
  All-atom Clashscore : 16.63
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.66 %
    Favored  : 96.34 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  4.03 %
    Favored  : 95.97 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 6.85 %
    Cis-general     : 0.07 %
    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:  0.55 (0.23), residues: 1420
  helix:  1.17 (0.22), residues: 581
  sheet: -0.38 (0.36), residues: 205
  loop : -0.01 (0.26), residues: 634

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.001   ARG C  54 
 TYR   0.017   0.002   TYR A4559 
 PHE   0.024   0.002   PHE A4688 
 TRP   0.062   0.003   TRP A4773 
 HIS   0.005   0.001   HIS A4800 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00503 /  0.25 (11667)
  covalent geometry    : angle       0.63746 /  0.34 (15815)
  hydrogen bonds       : bond        0.03671 /  2.45 (  515)
  hydrogen bonds       : angle       5.36672 /  3.69 ( 1407)
  Misc. bond           : bond        0.00060 /  0.03 (    1)

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

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

  2840 Ramachandran restraints generated.
    1420 Oldfield, 0 Emsley, 1420 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2840 Ramachandran restraints generated.
    1420 Oldfield, 0 Emsley, 1420 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  62 residues out of total 1265 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 62
  time to evaluate  : 0.456 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A 4542 MET cc_start: 0.9180 (mpp) cc_final: 0.8852 (mpp)
REVERT: A 4627 GLU cc_start: 0.8598 (tt0) cc_final: 0.8322 (tp30)
REVERT: A 4790 MET cc_start: 0.9632 (mmt) cc_final: 0.9245 (mmp)
REVERT: B   69 MET cc_start: 0.9181 (mpp) cc_final: 0.8756 (mpp)
REVERT: B  256 LEU cc_start: 0.8751 (tp) cc_final: 0.8535 (tp)
REVERT: B  329 MET cc_start: 0.9073 (tpt) cc_final: 0.8756 (tpp)
REVERT: B  475 MET cc_start: 0.9649 (mmp) cc_final: 0.9428 (mmm)
REVERT: B  594 MET cc_start: 0.9450 (tmm) cc_final: 0.8975 (tmm)
REVERT: C   71 LEU cc_start: 0.9520 (pp) cc_final: 0.9297 (pp)
REVERT: E    1 MET cc_start: 0.8683 (ttt) cc_final: 0.8062 (tpp)
REVERT: E    6 LYS cc_start: 0.9762 (mtpp) cc_final: 0.9540 (mptt)
  outliers start: 0
  outliers final: 0
  residues processed: 62
  average time/residue: 0.0966
  time to fit residues: 9.3856
Evaluate side-chains
  51 residues out of total 1265 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 51
  time to evaluate  : 0.448 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 141
   random chunks:
   chunk 43 optimal weight:    8.9990
   chunk 124 optimal weight:   10.0000
   chunk 109 optimal weight:    1.9990
   chunk 18 optimal weight:    8.9990
   chunk 32 optimal weight:    0.9990
   chunk 15 optimal weight:    8.9990
   chunk 47 optimal weight:   10.0000
   chunk 97 optimal weight:    5.9990
   chunk 51 optimal weight:    5.9990
   chunk 33 optimal weight:    6.9990
   chunk 129 optimal weight:    0.0020
   overall best weight:    2.9996

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
A4769 GLN
B 171 ASN
B 606 HIS
** C  68 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.2754 r_free = 0.2754 target = 0.030258 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 33)----------------|
| r_work = 0.2537 r_free = 0.2537 target = 0.023962 restraints weight = 135645.648|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 25)----------------|
| r_work = 0.2563 r_free = 0.2563 target = 0.024565 restraints weight = 97627.184|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 22)----------------|
| r_work = 0.2580 r_free = 0.2580 target = 0.025016 restraints weight = 76695.774|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 20)----------------|
| r_work = 0.2593 r_free = 0.2593 target = 0.025356 restraints weight = 63411.855|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 21)----------------|
| r_work = 0.2602 r_free = 0.2602 target = 0.025603 restraints weight = 54734.623|
|-----------------------------------------------------------------------------|
r_work (final): 0.2578
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8577
moved from start:          0.2765

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.046  11668  Z= 0.143
  Angle     :  0.539   7.573  15815  Z= 0.279
  Chirality :  0.041   0.207   1781
  Planarity :  0.004   0.046   2028
  Dihedral  :  5.854  79.741   1575
  Min Nonbonded Distance : 2.560

Molprobity Statistics.
  All-atom Clashscore : 12.50
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.61 %
    Favored  : 97.39 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  3.16 %
    Favored  : 96.84 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 6.85 %
    Cis-general     : 0.07 %
    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:  0.99 (0.23), residues: 1420
  helix:  1.61 (0.22), residues: 584
  sheet: -0.13 (0.37), residues: 194
  loop :  0.13 (0.26), residues: 642

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.000   ARG B 304 
 TYR   0.016   0.001   TYR A4621 
 PHE   0.013   0.001   PHE B 881 
 TRP   0.022   0.001   TRP A4773 
 HIS   0.004   0.001   HIS C  68 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00300 /  0.14 (11667)
  covalent geometry    : angle       0.53933 /  0.28 (15815)
  hydrogen bonds       : bond        0.03139 /  2.11 (  515)
  hydrogen bonds       : angle       5.00127 /  3.44 ( 1407)
  Misc. bond           : bond        0.00048 /  0.03 (    1)

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

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

  2840 Ramachandran restraints generated.
    1420 Oldfield, 0 Emsley, 1420 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2840 Ramachandran restraints generated.
    1420 Oldfield, 0 Emsley, 1420 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  62 residues out of total 1265 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 62
  time to evaluate  : 0.475 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A 4542 MET cc_start: 0.9364 (mpp) cc_final: 0.8957 (mpp)
REVERT: A 4627 GLU cc_start: 0.8736 (tt0) cc_final: 0.8334 (tp30)
REVERT: A 4790 MET cc_start: 0.9592 (mmt) cc_final: 0.9181 (mmp)
REVERT: B   69 MET cc_start: 0.9290 (mpp) cc_final: 0.8828 (mpp)
REVERT: B  329 MET cc_start: 0.9039 (tpt) cc_final: 0.8745 (tpp)
REVERT: B  475 MET cc_start: 0.9676 (mmp) cc_final: 0.9457 (mmm)
REVERT: B  594 MET cc_start: 0.9430 (tmm) cc_final: 0.9001 (tmm)
REVERT: B  616 ASP cc_start: 0.9476 (p0) cc_final: 0.9174 (t0)
REVERT: B  844 MET cc_start: 0.8961 (tpt) cc_final: 0.8690 (tpp)
REVERT: E    1 MET cc_start: 0.8620 (ttt) cc_final: 0.7884 (tpp)
REVERT: E    6 LYS cc_start: 0.9761 (mtpp) cc_final: 0.9551 (mptt)
  outliers start: 0
  outliers final: 0
  residues processed: 62
  average time/residue: 0.0983
  time to fit residues: 9.5601
Evaluate side-chains
  52 residues out of total 1265 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 52
  time to evaluate  : 0.464 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 141
   random chunks:
   chunk 51 optimal weight:   10.0000
   chunk 136 optimal weight:    7.9990
   chunk 38 optimal weight:    6.9990
   chunk 3 optimal weight:    6.9990
   chunk 85 optimal weight:    0.8980
   chunk 80 optimal weight:    0.0980
   chunk 10 optimal weight:    9.9990
   chunk 117 optimal weight:   20.0000
   chunk 64 optimal weight:    1.9990
   chunk 40 optimal weight:    4.9990
   chunk 59 optimal weight:    0.4980
   overall best weight:    1.6984

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
A4769 GLN
B 171 ASN
** C  68 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.2771 r_free = 0.2771 target = 0.030906 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 29)----------------|
| r_work = 0.2556 r_free = 0.2556 target = 0.024493 restraints weight = 132794.744|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 25)----------------|
| r_work = 0.2582 r_free = 0.2582 target = 0.025116 restraints weight = 95189.285|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 22)----------------|
| r_work = 0.2598 r_free = 0.2598 target = 0.025526 restraints weight = 74515.716|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 27)----------------|
| r_work = 0.2610 r_free = 0.2610 target = 0.025876 restraints weight = 61312.851|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 28)----------------|
| r_work = 0.2622 r_free = 0.2622 target = 0.026186 restraints weight = 53706.276|
|-----------------------------------------------------------------------------|
r_work (final): 0.2598
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8548
moved from start:          0.2874

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.031  11668  Z= 0.104
  Angle     :  0.509   6.360  15815  Z= 0.261
  Chirality :  0.040   0.185   1781
  Planarity :  0.003   0.046   2028
  Dihedral  :  5.635  79.023   1575
  Min Nonbonded Distance : 2.611

Molprobity Statistics.
  All-atom Clashscore : 10.09
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.32 %
    Favored  : 97.68 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  1.74 %
    Favored  : 98.26 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 6.85 %
    Cis-general     : 0.07 %
    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:  1.23 (0.23), residues: 1420
  helix:  1.85 (0.22), residues: 584
  sheet:  0.06 (0.37), residues: 192
  loop :  0.19 (0.26), residues: 644

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.000   ARG B 304 
 TYR   0.015   0.001   TYR A4621 
 PHE   0.011   0.001   PHE B 881 
 TRP   0.021   0.001   TRP A4773 
 HIS   0.003   0.001   HIS B  91 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00222 /  0.10 (11667)
  covalent geometry    : angle       0.50902 /  0.26 (15815)
  hydrogen bonds       : bond        0.02888 /  1.96 (  515)
  hydrogen bonds       : angle       4.76372 /  3.29 ( 1407)
  Misc. bond           : bond        0.00043 /  0.02 (    1)

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

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

  2840 Ramachandran restraints generated.
    1420 Oldfield, 0 Emsley, 1420 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2840 Ramachandran restraints generated.
    1420 Oldfield, 0 Emsley, 1420 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  67 residues out of total 1265 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 67
  time to evaluate  : 0.481 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A 4542 MET cc_start: 0.9343 (mpp) cc_final: 0.8884 (mpp)
REVERT: A 4790 MET cc_start: 0.9602 (mmt) cc_final: 0.9198 (mmp)
REVERT: B   69 MET cc_start: 0.9209 (mpp) cc_final: 0.8774 (mpp)
REVERT: B  253 MET cc_start: 0.8718 (mmt) cc_final: 0.8480 (mmm)
REVERT: B  329 MET cc_start: 0.9018 (tpt) cc_final: 0.8743 (tpp)
REVERT: B  475 MET cc_start: 0.9674 (mmp) cc_final: 0.9438 (mmm)
REVERT: B  594 MET cc_start: 0.9407 (tmm) cc_final: 0.9023 (tmm)
REVERT: B  616 ASP cc_start: 0.9507 (p0) cc_final: 0.9174 (t0)
REVERT: E    1 MET cc_start: 0.8681 (ttt) cc_final: 0.7495 (tpp)
REVERT: E    6 LYS cc_start: 0.9752 (mtpp) cc_final: 0.9496 (mmtm)
  outliers start: 0
  outliers final: 0
  residues processed: 67
  average time/residue: 0.0956
  time to fit residues: 10.0905
Evaluate side-chains
  51 residues out of total 1265 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 51
  time to evaluate  : 0.460 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 141
   random chunks:
   chunk 3 optimal weight:    9.9990
   chunk 67 optimal weight:    9.9990
   chunk 44 optimal weight:    9.9990
   chunk 40 optimal weight:    0.9990
   chunk 96 optimal weight:    8.9990
   chunk 135 optimal weight:    7.9990
   chunk 123 optimal weight:    5.9990
   chunk 42 optimal weight:    8.9990
   chunk 72 optimal weight:    0.9990
   chunk 45 optimal weight:    1.9990
   chunk 69 optimal weight:    8.9990
   overall best weight:    3.5990

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
A4769 GLN
B 171 ASN
** B 415 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** C  68 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.2749 r_free = 0.2749 target = 0.030148 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.2537 r_free = 0.2537 target = 0.024001 restraints weight = 137837.535|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 28)----------------|
| r_work = 0.2562 r_free = 0.2562 target = 0.024589 restraints weight = 99105.393|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 23)----------------|
| r_work = 0.2580 r_free = 0.2580 target = 0.025037 restraints weight = 78178.557|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 41)----------------|
| r_work = 0.2593 r_free = 0.2593 target = 0.025384 restraints weight = 64538.438|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 16)----------------|
| r_work = 0.2601 r_free = 0.2601 target = 0.025583 restraints weight = 55907.849|
|-----------------------------------------------------------------------------|
r_work (final): 0.2590
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8591
moved from start:          0.3135

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.035  11668  Z= 0.172
  Angle     :  0.562   8.608  15815  Z= 0.291
  Chirality :  0.040   0.179   1781
  Planarity :  0.004   0.044   2028
  Dihedral  :  5.751  82.265   1575
  Min Nonbonded Distance : 2.582

Molprobity Statistics.
  All-atom Clashscore : 13.91
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.10 %
    Favored  : 96.90 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  1.26 %
    Favored  : 98.74 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 6.85 %
    Cis-general     : 0.07 %
    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:  1.12 (0.23), residues: 1420
  helix:  1.79 (0.22), residues: 584
  sheet: -0.12 (0.37), residues: 192
  loop :  0.15 (0.26), residues: 644

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.000   ARG B 304 
 TYR   0.020   0.002   TYR B 154 
 PHE   0.017   0.002   PHE B 649 
 TRP   0.011   0.001   TRP A4773 
 HIS   0.005   0.001   HIS B  63 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00357 /  0.17 (11667)
  covalent geometry    : angle       0.56199 /  0.29 (15815)
  hydrogen bonds       : bond        0.03028 /  2.04 (  515)
  hydrogen bonds       : angle       4.85854 /  3.34 ( 1407)
  Misc. bond           : bond        0.00050 /  0.03 (    1)

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

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

  2840 Ramachandran restraints generated.
    1420 Oldfield, 0 Emsley, 1420 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2840 Ramachandran restraints generated.
    1420 Oldfield, 0 Emsley, 1420 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  65 residues out of total 1265 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 65
  time to evaluate  : 0.458 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A 4542 MET cc_start: 0.9341 (mpp) cc_final: 0.8819 (mpp)
REVERT: A 4578 LEU cc_start: 0.9690 (mt) cc_final: 0.9468 (pp)
REVERT: A 4627 GLU cc_start: 0.8736 (tt0) cc_final: 0.8308 (tp30)
REVERT: A 4790 MET cc_start: 0.9613 (mmt) cc_final: 0.9209 (mmp)
REVERT: B   69 MET cc_start: 0.9183 (mpp) cc_final: 0.8788 (mpp)
REVERT: B  253 MET cc_start: 0.8773 (mmt) cc_final: 0.8439 (mmm)
REVERT: B  329 MET cc_start: 0.9041 (tpt) cc_final: 0.8739 (tpp)
REVERT: B  475 MET cc_start: 0.9672 (mmp) cc_final: 0.9463 (mmm)
REVERT: B  594 MET cc_start: 0.9426 (tmm) cc_final: 0.8988 (tmm)
REVERT: B  616 ASP cc_start: 0.9556 (p0) cc_final: 0.9220 (t0)
REVERT: E    1 MET cc_start: 0.8655 (ttt) cc_final: 0.7938 (tpp)
REVERT: E    6 LYS cc_start: 0.9762 (mtpp) cc_final: 0.9497 (mmtm)
  outliers start: 0
  outliers final: 0
  residues processed: 65
  average time/residue: 0.1076
  time to fit residues: 10.4422
Evaluate side-chains
  54 residues out of total 1265 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 54
  time to evaluate  : 0.462 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 141
   random chunks:
   chunk 125 optimal weight:    6.9990
   chunk 88 optimal weight:    0.9990
   chunk 44 optimal weight:   20.0000
   chunk 96 optimal weight:    8.9990
   chunk 20 optimal weight:    6.9990
   chunk 28 optimal weight:   10.0000
   chunk 127 optimal weight:    0.9990
   chunk 40 optimal weight:    6.9990
   chunk 68 optimal weight:    3.9990
   chunk 76 optimal weight:    0.8980
   chunk 101 optimal weight:    6.9990
   overall best weight:    2.7788

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
A4769 GLN
B 171 ASN
** C  68 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.2760 r_free = 0.2760 target = 0.030651 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 33)----------------|
| r_work = 0.2548 r_free = 0.2548 target = 0.024393 restraints weight = 133861.978|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 34)----------------|
| r_work = 0.2571 r_free = 0.2571 target = 0.024988 restraints weight = 96955.004|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 32)----------------|
| r_work = 0.2588 r_free = 0.2588 target = 0.025436 restraints weight = 76106.727|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 24)----------------|
| r_work = 0.2600 r_free = 0.2600 target = 0.025752 restraints weight = 63440.790|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 20)----------------|
| r_work = 0.2608 r_free = 0.2608 target = 0.025940 restraints weight = 55477.979|
|-----------------------------------------------------------------------------|
r_work (final): 0.2596
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8571
moved from start:          0.3328

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.026  11668  Z= 0.132
  Angle     :  0.530   8.970  15815  Z= 0.272
  Chirality :  0.040   0.166   1781
  Planarity :  0.003   0.042   2028
  Dihedral  :  5.657  82.594   1575
  Min Nonbonded Distance : 2.592

Molprobity Statistics.
  All-atom Clashscore : 12.06
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.46 %
    Favored  : 97.54 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  1.42 %
    Favored  : 98.58 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 6.85 %
    Cis-general     : 0.07 %
    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:  1.18 (0.23), residues: 1420
  helix:  1.83 (0.22), residues: 586
  sheet: -0.15 (0.37), residues: 194
  loop :  0.21 (0.27), residues: 640

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.000   ARG B 304 
 TYR   0.018   0.001   TYR B  49 
 PHE   0.017   0.001   PHE B 649 
 TRP   0.014   0.001   TRP A4773 
 HIS   0.005   0.001   HIS B 858 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00279 /  0.13 (11667)
  covalent geometry    : angle       0.52982 /  0.27 (15815)
  hydrogen bonds       : bond        0.02885 /  1.95 (  515)
  hydrogen bonds       : angle       4.73535 /  3.25 ( 1407)
  Misc. bond           : bond        0.00053 /  0.03 (    1)

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

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

  2840 Ramachandran restraints generated.
    1420 Oldfield, 0 Emsley, 1420 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2840 Ramachandran restraints generated.
    1420 Oldfield, 0 Emsley, 1420 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  64 residues out of total 1265 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 64
  time to evaluate  : 0.581 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A 4542 MET cc_start: 0.9149 (mpp) cc_final: 0.8603 (mpp)
REVERT: A 4578 LEU cc_start: 0.9695 (mt) cc_final: 0.9475 (pp)
REVERT: A 4790 MET cc_start: 0.9613 (mmt) cc_final: 0.9225 (mmp)
REVERT: B  253 MET cc_start: 0.8809 (mmt) cc_final: 0.8481 (mmm)
REVERT: B  329 MET cc_start: 0.9034 (tpt) cc_final: 0.8752 (tpp)
REVERT: B  475 MET cc_start: 0.9579 (mmm) cc_final: 0.9315 (mmm)
REVERT: B  594 MET cc_start: 0.9406 (tmm) cc_final: 0.8998 (tmm)
REVERT: B  616 ASP cc_start: 0.9560 (p0) cc_final: 0.9221 (t0)
REVERT: E    1 MET cc_start: 0.8721 (ttt) cc_final: 0.8025 (tpp)
REVERT: E    6 LYS cc_start: 0.9761 (mtpp) cc_final: 0.9495 (mmtm)
  outliers start: 0
  outliers final: 0
  residues processed: 64
  average time/residue: 0.0931
  time to fit residues: 9.4860
Evaluate side-chains
  52 residues out of total 1265 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 52
  time to evaluate  : 0.448 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 141
   random chunks:
   chunk 11 optimal weight:    0.0980
   chunk 59 optimal weight:    0.9980
   chunk 9 optimal weight:    5.9990
   chunk 27 optimal weight:    9.9990
   chunk 92 optimal weight:    9.9990
   chunk 98 optimal weight:    8.9990
   chunk 106 optimal weight:    6.9990
   chunk 16 optimal weight:    2.9990
   chunk 64 optimal weight:    2.9990
   chunk 45 optimal weight:    3.9990
   chunk 41 optimal weight:    3.9990
   overall best weight:    2.2186

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
A4769 GLN
B 171 ASN
** C  68 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.2762 r_free = 0.2762 target = 0.030578 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 24)----------------|
| r_work = 0.2514 r_free = 0.2514 target = 0.023670 restraints weight = 135516.018|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 20)----------------|
| r_work = 0.2539 r_free = 0.2539 target = 0.024267 restraints weight = 98266.817|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 26)----------------|
| r_work = 0.2556 r_free = 0.2556 target = 0.024706 restraints weight = 77023.373|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 26)----------------|
| r_work = 0.2569 r_free = 0.2569 target = 0.025044 restraints weight = 65360.934|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 21)----------------|
| r_work = 0.2579 r_free = 0.2579 target = 0.025314 restraints weight = 57140.246|
|-----------------------------------------------------------------------------|
r_work (final): 0.2572
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8558
moved from start:          0.3464

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.048  11668  Z= 0.121
  Angle     :  0.538  10.921  15815  Z= 0.271
  Chirality :  0.041   0.327   1781
  Planarity :  0.003   0.042   2028
  Dihedral  :  5.589  83.036   1575
  Min Nonbonded Distance : 2.599

Molprobity Statistics.
  All-atom Clashscore : 11.67
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.75 %
    Favored  : 97.25 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.55 %
    Favored  : 99.45 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 6.85 %
    Cis-general     : 0.07 %
    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:  1.22 (0.24), residues: 1420
  helix:  1.89 (0.22), residues: 586
  sheet: -0.32 (0.37), residues: 199
  loop :  0.28 (0.27), residues: 635

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG B 304 
 TYR   0.015   0.001   TYR B  49 
 PHE   0.015   0.001   PHE B 649 
 TRP   0.014   0.001   TRP A4773 
 HIS   0.004   0.001   HIS B 858 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00264 /  0.12 (11667)
  covalent geometry    : angle       0.53756 /  0.27 (15815)
  hydrogen bonds       : bond        0.02875 /  1.95 (  515)
  hydrogen bonds       : angle       4.67767 /  3.20 ( 1407)
  Misc. bond           : bond        0.00045 /  0.02 (    1)

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

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

  2840 Ramachandran restraints generated.
    1420 Oldfield, 0 Emsley, 1420 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2840 Ramachandran restraints generated.
    1420 Oldfield, 0 Emsley, 1420 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  63 residues out of total 1265 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 63
  time to evaluate  : 0.444 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A 4542 MET cc_start: 0.9117 (mpp) cc_final: 0.8549 (mpp)
REVERT: A 4578 LEU cc_start: 0.9679 (mt) cc_final: 0.9455 (pp)
REVERT: A 4790 MET cc_start: 0.9662 (mmt) cc_final: 0.9272 (mmp)
REVERT: B   69 MET cc_start: 0.9092 (mpp) cc_final: 0.8731 (mpp)
REVERT: B  253 MET cc_start: 0.8890 (mmt) cc_final: 0.8543 (mmm)
REVERT: B  329 MET cc_start: 0.9006 (tpt) cc_final: 0.8724 (tpp)
REVERT: B  475 MET cc_start: 0.9515 (mmm) cc_final: 0.9280 (mmm)
REVERT: B  594 MET cc_start: 0.9447 (tmm) cc_final: 0.9031 (tmm)
REVERT: B  616 ASP cc_start: 0.9507 (p0) cc_final: 0.9182 (t0)
REVERT: B  844 MET cc_start: 0.8962 (tpt) cc_final: 0.8737 (tpp)
REVERT: E    1 MET cc_start: 0.8758 (ttt) cc_final: 0.8163 (tpp)
REVERT: E    6 LYS cc_start: 0.9760 (mtpp) cc_final: 0.9487 (mmtm)
  outliers start: 0
  outliers final: 0
  residues processed: 63
  average time/residue: 0.0861
  time to fit residues: 8.8439
Evaluate side-chains
  53 residues out of total 1265 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 53
  time to evaluate  : 0.368 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 141
   random chunks:
   chunk 121 optimal weight:   10.0000
   chunk 29 optimal weight:    0.0770
   chunk 104 optimal weight:    3.9990
   chunk 110 optimal weight:   10.0000
   chunk 129 optimal weight:    0.2980
   chunk 100 optimal weight:    0.7980
   chunk 3 optimal weight:   10.0000
   chunk 87 optimal weight:    1.9990
   chunk 8 optimal weight:    0.9980
   chunk 19 optimal weight:    5.9990
   chunk 28 optimal weight:    0.9980
   overall best weight:    0.6338

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
A4769 GLN
B 171 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.2774 r_free = 0.2774 target = 0.030685 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.2538 r_free = 0.2538 target = 0.024162 restraints weight = 137009.309|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 29)----------------|
| r_work = 0.2565 r_free = 0.2565 target = 0.024808 restraints weight = 98192.251|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 29)----------------|
| r_work = 0.2583 r_free = 0.2583 target = 0.025287 restraints weight = 76706.907|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 38)----------------|
| r_work = 0.2598 r_free = 0.2598 target = 0.025650 restraints weight = 63430.132|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 25)----------------|
| r_work = 0.2608 r_free = 0.2608 target = 0.025927 restraints weight = 54584.956|
|-----------------------------------------------------------------------------|
r_work (final): 0.2606
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8513
moved from start:          0.3564

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.041  11668  Z= 0.089
  Angle     :  0.523   9.949  15815  Z= 0.259
  Chirality :  0.041   0.216   1781
  Planarity :  0.003   0.041   2028
  Dihedral  :  5.343  80.699   1575
  Min Nonbonded Distance : 2.617

Molprobity Statistics.
  All-atom Clashscore : 8.60
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.04 %
    Favored  : 97.96 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.32 %
    Favored  : 99.68 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 6.85 %
    Cis-general     : 0.07 %
    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:  1.40 (0.24), residues: 1420
  helix:  2.00 (0.22), residues: 587
  sheet: -0.21 (0.36), residues: 207
  loop :  0.42 (0.27), residues: 626

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG B 885 
 TYR   0.010   0.001   TYR B 154 
 PHE   0.015   0.001   PHE B 656 
 TRP   0.019   0.001   TRP A4773 
 HIS   0.004   0.001   HIS B 858 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00193 /  0.09 (11667)
  covalent geometry    : angle       0.52306 /  0.26 (15815)
  hydrogen bonds       : bond        0.02650 /  1.80 (  515)
  hydrogen bonds       : angle       4.46646 /  3.06 ( 1407)
  Misc. bond           : bond        0.00032 /  0.02 (    1)

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

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

  2840 Ramachandran restraints generated.
    1420 Oldfield, 0 Emsley, 1420 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2840 Ramachandran restraints generated.
    1420 Oldfield, 0 Emsley, 1420 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  70 residues out of total 1265 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 70
  time to evaluate  : 0.297 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A 4542 MET cc_start: 0.9099 (mpp) cc_final: 0.8681 (mpp)
REVERT: A 4790 MET cc_start: 0.9628 (mmt) cc_final: 0.9213 (mmp)
REVERT: B  253 MET cc_start: 0.8688 (mmt) cc_final: 0.8395 (mmm)
REVERT: B  329 MET cc_start: 0.8949 (tpt) cc_final: 0.8702 (tpp)
REVERT: B  475 MET cc_start: 0.9501 (mmm) cc_final: 0.9259 (mmm)
REVERT: B  594 MET cc_start: 0.9412 (tmm) cc_final: 0.9077 (tmm)
REVERT: B  616 ASP cc_start: 0.9432 (p0) cc_final: 0.9114 (t0)
REVERT: B  844 MET cc_start: 0.8936 (tpt) cc_final: 0.8622 (tpp)
REVERT: E    1 MET cc_start: 0.8598 (ttt) cc_final: 0.7495 (tpp)
REVERT: E    6 LYS cc_start: 0.9755 (mtpp) cc_final: 0.9499 (mmtm)
  outliers start: 0
  outliers final: 0
  residues processed: 70
  average time/residue: 0.0813
  time to fit residues: 9.0135
Evaluate side-chains
  55 residues out of total 1265 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 55
  time to evaluate  : 0.340 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 141
   random chunks:
   chunk 47 optimal weight:    9.9990
   chunk 113 optimal weight:    1.9990
   chunk 112 optimal weight:    3.9990
   chunk 56 optimal weight:    0.9990
   chunk 59 optimal weight:    0.9990
   chunk 71 optimal weight:    9.9990
   chunk 121 optimal weight:    7.9990
   chunk 55 optimal weight:    0.5980
   chunk 2 optimal weight:    6.9990
   chunk 6 optimal weight:    5.9990
   chunk 129 optimal weight:    1.9990
   overall best weight:    1.3188

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
A4769 GLN
B 171 ASN
** B 415 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.2773 r_free = 0.2773 target = 0.030053 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.2528 r_free = 0.2528 target = 0.023448 restraints weight = 140180.654|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 30)----------------|
| r_work = 0.2555 r_free = 0.2555 target = 0.024098 restraints weight = 99741.730|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 20)----------------|
| r_work = 0.2573 r_free = 0.2573 target = 0.024549 restraints weight = 77718.208|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 17)----------------|
| r_work = 0.2586 r_free = 0.2586 target = 0.024874 restraints weight = 64561.845|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 31)----------------|
| r_work = 0.2598 r_free = 0.2598 target = 0.025182 restraints weight = 56540.941|
|-----------------------------------------------------------------------------|
r_work (final): 0.2596
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8533
moved from start:          0.3637

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.039  11668  Z= 0.094
  Angle     :  0.512   9.196  15815  Z= 0.255
  Chirality :  0.040   0.245   1781
  Planarity :  0.003   0.042   2028
  Dihedral  :  5.285  81.148   1575
  Min Nonbonded Distance : 2.602

Molprobity Statistics.
  All-atom Clashscore : 9.21
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.90 %
    Favored  : 98.10 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.24 %
    Favored  : 99.76 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 6.85 %
    Cis-general     : 0.07 %
    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:  1.47 (0.24), residues: 1420
  helix:  2.06 (0.22), residues: 587
  sheet: -0.16 (0.37), residues: 207
  loop :  0.45 (0.27), residues: 626

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG C  54 
 TYR   0.011   0.001   TYR A4621 
 PHE   0.014   0.001   PHE B 656 
 TRP   0.015   0.001   TRP A4773 
 HIS   0.004   0.001   HIS B 858 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00208 /  0.09 (11667)
  covalent geometry    : angle       0.51238 /  0.26 (15815)
  hydrogen bonds       : bond        0.02690 /  1.83 (  515)
  hydrogen bonds       : angle       4.43157 /  3.03 ( 1407)
  Misc. bond           : bond        0.00027 /  0.01 (    1)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 1593.61 seconds
wall clock time: 28 minutes 38.31 seconds (1718.31 seconds total)