Starting phenix.real_space_refine
on Thu Feb  5 16:38:35 2026 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/9hm6_52287/02_2026/9hm6_52287_neut.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/9hm6_52287/02_2026/9hm6_52287.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=4.0
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    model {
      file = "/net/cci-nas-00/data/ceres_data/9hm6_52287/02_2026/9hm6_52287_neut.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/9hm6_52287/02_2026/9hm6_52287_neut.cif"
    real_map_files = "/net/cci-nas-00/data/ceres_data/9hm6_52287/02_2026/9hm6_52287.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/9hm6_52287/02_2026/9hm6_52287.map"
  }
  resolution = 4.0
  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=   0.012
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: 6
    Type Number    sf(0)   Gaussians
     P      80      5.49       5
     S      20      5.16       5
     C    5767      2.51       5
     N    1645      2.21       5
     O    2044      1.98       5
     H    8795      0.53       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 35 residue(s): 0.01s

  Monomer Library directory:
    "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5952/lib/python3.9/site-packages/chem_data/mon_lib"
  Total number of atoms: 18351
  Number of models: 1
  Model: ""
    Number of chains: 3
    Chain: "A"
      Number of atoms: 15793
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 960, 15793
          Classifications: {'peptide': 960}
          Modifications used: {'NH3': 1}
          Link IDs: {'PTRANS': 19, 'TRANS': 940}
          Chain breaks: 3
    Chain: "B"
      Number of atoms: 1506
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 47, 1506
          Classifications: {'RNA': 47}
          Modifications used: {'rna2p_pur': 1, 'rna2p_pyr': 3, 'rna3p_pur': 24, 'rna3p_pyr': 19}
          Link IDs: {'rna2p': 4, 'rna3p': 42}
    Chain: "C"
      Number of atoms: 1052
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 33, 1052
          Classifications: {'RNA': 33}
          Modifications used: {'rna3p_pur': 15, 'rna3p_pyr': 18}
          Link IDs: {'rna3p': 32}
  Time building chain proxies: 3.34, per 1000 atoms: 0.18
  Number of scatterers: 18351
  At special positions: 0
  Unit cell: (98.28, 107.38, 131.95, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 6
    Type Number    sf(0)
     S      20     16.00
     P      80     15.00
     O    2044      8.00
     N    1645      7.00
     C    5767      6.00
     H    8795      1.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=0, symmetry=0

  Automatic linking
    Parameters for automatic linking
      Linking & cutoffs
        Metal                : Auto  - 3.00
        Amino acid           : True  - 1.90
        Carbohydrate         : True  - 1.99
        Ligands              : True  - 1.99
        Small molecules      : False - 1.98
        Amino acid - RNA/DNA : False
      
  Number of custom bonds: simple=0, symmetry=0
  Time building additional restraints: 1.45
  Conformation dependent library (CDL) restraints added in 562.1 milliseconds
  

  1904 Ramachandran restraints generated.
    952 Oldfield, 0 Emsley, 952 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  1836

  Finding SS restraints...
    Secondary structure from input PDB file:
      45 helices and 7 sheets defined
      54.1% alpha, 12.0% beta
      28 base pairs and 40 stacking pairs defined.
    Time for finding SS restraints: 2.81
  Creating SS restraints...
    Processing helix  chain 'A' and resid 21 through 26
    Processing helix  chain 'A' and resid 219 through 223
      removed outlier: 3.559A  pdb=" N   LYS A 223 " --> pdb=" O   THR A 220 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 230 through 237
      removed outlier: 4.252A  pdb=" N   GLU A 234 " --> pdb=" O   ASN A 230 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 242 through 250
      removed outlier: 4.616A  pdb=" N   PHE A 247 " --> pdb=" O   ASP A 244 " (cutoff:3.500A)
      removed outlier: 3.963A  pdb=" N   THR A 250 " --> pdb=" O   PHE A 247 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 255 through 270
    Processing helix  chain 'A' and resid 292 through 314
    Processing helix  chain 'A' and resid 316 through 323
    Processing helix  chain 'A' and resid 332 through 355
      removed outlier: 3.762A  pdb=" N   PHE A 336 " --> pdb=" O   GLU A 332 " (cutoff:3.500A)
      removed outlier: 3.820A  pdb=" N   ASP A 337 " --> pdb=" O   GLN A 333 " (cutoff:3.500A)
      removed outlier: 3.801A  pdb=" N   ASN A 338 " --> pdb=" O   ARG A 334 " (cutoff:3.500A)
      removed outlier: 3.552A  pdb=" N   LYS A 352 " --> pdb=" O   LYS A 348 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 358 through 384
      removed outlier: 3.725A  pdb=" N   PHE A 384 " --> pdb=" O   MET A 380 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 384 through 415
      removed outlier: 4.277A  pdb=" N   GLN A 399 " --> pdb=" O   ARG A 395 " (cutoff:3.500A)
      removed outlier: 4.206A  pdb=" N   GLU A 400 " --> pdb=" O   THR A 396 " (cutoff:3.500A)
      removed outlier: 3.705A  pdb=" N   HIS A 401 " --> pdb=" O   ILE A 397 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 441 through 453
      removed outlier: 4.280A  pdb=" N   ALA A 445 " --> pdb=" O   ARG A 441 " (cutoff:3.500A)
      removed outlier: 5.188A  pdb=" N   SER A 446 " --> pdb=" O   GLU A 442 " (cutoff:3.500A)
      removed outlier: 3.721A  pdb=" N   SER A 453 " --> pdb=" O   GLN A 449 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 471 through 480
    Processing helix  chain 'A' and resid 481 through 486
      removed outlier: 3.794A  pdb=" N   GLU A 484 " --> pdb=" O   GLY A 481 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 488 through 493
      removed outlier: 4.124A  pdb=" N   LYS A 492 " --> pdb=" O   ASN A 488 " (cutoff:3.500A)
      removed outlier: 3.625A  pdb=" N   ASN A 493 " --> pdb=" O   LYS A 489 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'A' and resid 488 through 493'
    Processing helix  chain 'A' and resid 494 through 498
    Processing helix  chain 'A' and resid 509 through 513
    Processing helix  chain 'A' and resid 516 through 530
      removed outlier: 3.560A  pdb=" N   LYS A 520 " --> pdb=" O   ASP A 516 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 530 through 535
    Processing helix  chain 'A' and resid 540 through 548
    Processing helix  chain 'A' and resid 555 through 568
      removed outlier: 3.758A  pdb=" N   PHE A 559 " --> pdb=" O   SER A 555 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 577 through 587
      removed outlier: 3.689A  pdb=" N   LYS A 587 " --> pdb=" O   LEU A 583 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 607 through 618
      removed outlier: 3.640A  pdb=" N   GLN A 611 " --> pdb=" O   LYS A 607 " (cutoff:3.500A)
      removed outlier: 4.070A  pdb=" N   ILE A 612 " --> pdb=" O   SER A 608 " (cutoff:3.500A)
      removed outlier: 3.708A  pdb=" N   TRP A 613 " --> pdb=" O   HIS A 609 " (cutoff:3.500A)
      removed outlier: 4.128A  pdb=" N   TRP A 617 " --> pdb=" O   TRP A 613 " (cutoff:3.500A)
      removed outlier: 3.812A  pdb=" N   THR A 618 " --> pdb=" O   LYS A 614 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 618 through 624
      removed outlier: 3.785A  pdb=" N   LYS A 622 " --> pdb=" O   THR A 618 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 642 through 646
      removed outlier: 3.624A  pdb=" N   LYS A 645 " --> pdb=" O   LYS A 642 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 685 through 698
      removed outlier: 3.711A  pdb=" N   LYS A 690 " --> pdb=" O   ASP A 686 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 725 through 729
    Processing helix  chain 'A' and resid 732 through 741
    Processing helix  chain 'A' and resid 742 through 747
    Processing helix  chain 'A' and resid 773 through 778
      removed outlier: 3.539A  pdb=" N   TYR A 776 " --> pdb=" O   ASN A 773 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 779 through 788
    Processing helix  chain 'A' and resid 790 through 801
    Processing helix  chain 'A' and resid 827 through 848
      removed outlier: 4.539A  pdb=" N   LEU A 831 " --> pdb=" O   ASP A 827 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 866 through 875
    Processing helix  chain 'A' and resid 876 through 878
      No H-bonds generated for 'chain 'A' and resid 876 through 878'
    Processing helix  chain 'A' and resid 879 through 884
    Processing helix  chain 'A' and resid 887 through 900
    Processing helix  chain 'A' and resid 908 through 919
    Processing helix  chain 'A' and resid 952 through 956
    Processing helix  chain 'A' and resid 961 through 966
    Processing helix  chain 'A' and resid 968 through 982
      removed outlier: 3.872A  pdb=" N   TYR A 979 " --> pdb=" O   LEU A 975 " (cutoff:3.500A)
      removed outlier: 3.705A  pdb=" N   ASN A 980 " --> pdb=" O   ILE A 976 " (cutoff:3.500A)
      removed outlier: 3.908A  pdb=" N   THR A 981 " --> pdb=" O   ASP A 977 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 983 through 986
    Processing helix  chain 'A' and resid 989 through 1024
      removed outlier: 3.993A  pdb=" N   LEU A 995 " --> pdb=" O   GLU A 991 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1050 through 1064
      removed outlier: 3.651A  pdb=" N   ASN A1064 " --> pdb=" O   GLN A1060 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1073 through 1077
    Processing helix  chain 'A' and resid 1135 through 1155
      removed outlier: 4.216A  pdb=" N   ILE A1139 " --> pdb=" O   SER A1135 " (cutoff:3.500A)
      removed outlier: 3.968A  pdb=" N   ALA A1140 " --> pdb=" O   ASN A1136 " (cutoff:3.500A)
      removed outlier: 3.581A  pdb=" N   ALA A1145 " --> pdb=" O   SER A1141 " (cutoff:3.500A)
    Processing sheet with id=AA1, first strand: chain 'A' and resid 569 through 574
      removed outlier: 5.760A  pdb=" N   PHE A 467 " --> pdb=" O   ALA A 425 " (cutoff:3.500A)
      removed outlier: 8.518A  pdb=" N   ALA A 425 " --> pdb=" O   PHE A 467 " (cutoff:3.500A)
      removed outlier: 3.512A  pdb=" N   ILE A 437 " --> pdb=" O   LEU A 426 " (cutoff:3.500A)
      removed outlier: 5.541A  pdb=" N   HIS A 434 " --> pdb=" O   ILE A 593 " (cutoff:3.500A)
      removed outlier: 3.886A  pdb=" N   ILE A 593 " --> pdb=" O   HIS A 434 " (cutoff:3.500A)
      removed outlier: 6.730A  pdb=" N   ILE A 590 " --> pdb=" O   GLN A  17 " (cutoff:3.500A)
      removed outlier: 4.000A  pdb=" N   TYR A 664 " --> pdb=" O   LEU A  14 " (cutoff:3.500A)
      removed outlier: 4.623A  pdb=" N   THR A 669 " --> pdb=" O   GLU A 633 " (cutoff:3.500A)
      removed outlier: 6.419A  pdb=" N   GLU A 633 " --> pdb=" O   THR A 669 " (cutoff:3.500A)
      removed outlier: 8.168A  pdb=" N   SER A 671 " --> pdb=" O   ASN A 631 " (cutoff:3.500A)
      removed outlier: 7.539A  pdb=" N   ASN A 631 " --> pdb=" O   SER A 671 " (cutoff:3.500A)
      removed outlier: 3.524A  pdb=" N   ALA A 212 " --> pdb=" O   ILE A 636 " (cutoff:3.500A)
      removed outlier: 5.985A  pdb=" N   TYR A 638 " --> pdb=" O   PRO A 210 " (cutoff:3.500A)
      removed outlier: 9.657A  pdb=" N   TYR A 423 " --> pdb=" O   VAL A 211 " (cutoff:3.500A)
      removed outlier: 7.408A  pdb=" N   LYS A 213 " --> pdb=" O   TYR A 423 " (cutoff:3.500A)
      removed outlier: 7.885A  pdb=" N   ALA A 425 " --> pdb=" O   LYS A 213 " (cutoff:3.500A)
      removed outlier: 6.300A  pdb=" N   SER A 215 " --> pdb=" O   ALA A 425 " (cutoff:3.500A)
      removed outlier: 8.593A  pdb=" N   ILE A 427 " --> pdb=" O   SER A 215 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'A' and resid 275 through 277
    Processing sheet with id=AA3, first strand: chain 'A' and resid 809 through 810
      removed outlier: 3.584A  pdb=" N   LEU A 810 " --> pdb=" O   LEU A 721 " (cutoff:3.500A)
      removed outlier: 3.565A  pdb=" N   LEU A 721 " --> pdb=" O   LEU A 810 " (cutoff:3.500A)
      removed outlier: 3.959A  pdb=" N   ILE A1030 " --> pdb=" O   PHE A 709 " (cutoff:3.500A)
      removed outlier: 3.657A  pdb=" N   GLU A1032 " --> pdb=" O   ILE A 711 " (cutoff:3.500A)
      removed outlier: 3.649A  pdb=" N   ILE A1098 " --> pdb=" O   LYS A1031 " (cutoff:3.500A)
    Processing sheet with id=AA4, first strand: chain 'A' and resid 748 through 753
    Processing sheet with id=AA5, first strand: chain 'A' and resid 759 through 761
    Processing sheet with id=AA6, first strand: chain 'A' and resid 816 through 818
    Processing sheet with id=AA7, first strand: chain 'A' and resid 856 through 858

    385 hydrogen bonds defined for protein.
    1044 hydrogen bond angles defined for protein.
    Restraints generated for nucleic acids:
      71 hydrogen bonds
      128 hydrogen bond angles
      0 basepair planarities
      28 basepair parallelities
      40 stacking parallelities
  Total time for adding SS restraints: 3.49

  Time building geometry restraints manager: 2.14 seconds

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

  Histogram of bond lengths:
        0.84 -     1.03: 4529
        1.03 -     1.23: 4474
        1.23 -     1.42: 4935
        1.42 -     1.62: 4718
        1.62 -     1.81: 30
  Bond restraints: 18686
  Sorted by residual:
  bond pdb=" CE1 HIS A 661 "
       pdb=" NE2 HIS A 661 "
    ideal  model  delta    sigma   weight residual
    1.321  1.232  0.089 1.00e-02 1.00e+04 7.88e+01
  bond pdb=" CE1 HIS A 401 "
       pdb=" NE2 HIS A 401 "
    ideal  model  delta    sigma   weight residual
    1.321  1.232  0.089 1.00e-02 1.00e+04 7.86e+01
  bond pdb=" CE1 HIS A 838 "
       pdb=" NE2 HIS A 838 "
    ideal  model  delta    sigma   weight residual
    1.321  1.232  0.089 1.00e-02 1.00e+04 7.84e+01
  bond pdb=" CE1 HIS A 673 "
       pdb=" NE2 HIS A 673 "
    ideal  model  delta    sigma   weight residual
    1.321  1.233  0.088 1.00e-02 1.00e+04 7.80e+01
  bond pdb=" ND1 HIS A 849 "
       pdb=" CE1 HIS A 849 "
    ideal  model  delta    sigma   weight residual
    1.321  1.233  0.088 1.00e-02 1.00e+04 7.74e+01
  ... (remaining 18681 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     2.55: 24715
        2.55 -     5.11: 5897
        5.11 -     7.66: 2613
        7.66 -    10.22: 451
       10.22 -    12.77: 83
  Bond angle restraints: 33759
  Sorted by residual:
  angle pdb=" C   GLN A 294 "
        pdb=" N   ILE A 295 "
        pdb=" CA  ILE A 295 "
      ideal   model   delta    sigma   weight residual
     120.60  130.94  -10.34 1.29e+00 6.01e-01 6.43e+01
  angle pdb=" CA  HIS A 838 "
        pdb=" CB  HIS A 838 "
        pdb=" CG  HIS A 838 "
      ideal   model   delta    sigma   weight residual
     113.80  121.28   -7.48 1.00e+00 1.00e+00 5.60e+01
  angle pdb=" CA  ASN A 788 "
        pdb=" CB  ASN A 788 "
        pdb=" CG  ASN A 788 "
      ideal   model   delta    sigma   weight residual
     112.60  120.00   -7.40 1.00e+00 1.00e+00 5.47e+01
  angle pdb=" CA  HIS A 401 "
        pdb=" CB  HIS A 401 "
        pdb=" CG  HIS A 401 "
      ideal   model   delta    sigma   weight residual
     113.80  121.18   -7.38 1.00e+00 1.00e+00 5.45e+01
  angle pdb=" CA  PHE A 591 "
        pdb=" CB  PHE A 591 "
        pdb=" CG  PHE A 591 "
      ideal   model   delta    sigma   weight residual
     113.80  121.15   -7.35 1.00e+00 1.00e+00 5.40e+01
  ... (remaining 33754 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    35.76: 8421
       35.76 -    71.51: 343
       71.51 -   107.27: 31
      107.27 -   143.02: 9
      143.02 -   178.78: 9
  Dihedral angle restraints: 8813
    sinusoidal: 5469
      harmonic: 3344
  Sorted by residual:
  dihedral pdb=" C5'   G B  37 "
           pdb=" C4'   G B  37 "
           pdb=" C3'   G B  37 "
           pdb=" O3'   G B  37 "
      ideal   model   delta sinusoidal    sigma   weight residual
     147.00   78.37   68.63     1      8.00e+00 1.56e-02 9.53e+01
  dihedral pdb=" C5'   U B  36 "
           pdb=" C4'   U B  36 "
           pdb=" C3'   U B  36 "
           pdb=" O3'   U B  36 "
      ideal   model   delta sinusoidal    sigma   weight residual
     147.00   79.45   67.55     1      8.00e+00 1.56e-02 9.27e+01
  dihedral pdb=" O4'   U C  30 "
           pdb=" C1'   U C  30 "
           pdb=" N1    U C  30 "
           pdb=" C2    U C  30 "
      ideal   model   delta sinusoidal    sigma   weight residual
     200.00   40.16  159.84     1      1.50e+01 4.44e-03 8.27e+01
  ... (remaining 8810 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.151: 977
       0.151 -    0.301: 62
       0.301 -    0.452: 95
       0.452 -    0.602: 330
       0.602 -    0.753: 108
  Chirality restraints: 1572
  Sorted by residual:
  chirality pdb=" CG  LEU A 310 "
            pdb=" CB  LEU A 310 "
            pdb=" CD1 LEU A 310 "
            pdb=" CD2 LEU A 310 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.59   -1.84   -0.75 2.00e-01 2.50e+01 1.42e+01
  chirality pdb=" CG  LEU A 998 "
            pdb=" CB  LEU A 998 "
            pdb=" CD1 LEU A 998 "
            pdb=" CD2 LEU A 998 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.59   -1.84   -0.75 2.00e-01 2.50e+01 1.41e+01
  chirality pdb=" CB  ILE A1029 "
            pdb=" CA  ILE A1029 "
            pdb=" CG1 ILE A1029 "
            pdb=" CG2 ILE A1029 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.64    1.91    0.74 2.00e-01 2.50e+01 1.35e+01
  ... (remaining 1569 not shown)

  Planarity restraints: 2454
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C1'   A C  37 "    0.431 2.00e-02 2.50e+03   1.62e-01 8.56e+02
        pdb=" N9    A C  37 "   -0.083 2.00e-02 2.50e+03
        pdb=" C8    A C  37 "   -0.096 2.00e-02 2.50e+03
        pdb=" N7    A C  37 "   -0.110 2.00e-02 2.50e+03
        pdb=" C5    A C  37 "   -0.090 2.00e-02 2.50e+03
        pdb=" C6    A C  37 "    0.041 2.00e-02 2.50e+03
        pdb=" N6    A C  37 "    0.273 2.00e-02 2.50e+03
        pdb=" N1    A C  37 "    0.037 2.00e-02 2.50e+03
        pdb=" C2    A C  37 "   -0.051 2.00e-02 2.50e+03
        pdb=" N3    A C  37 "   -0.127 2.00e-02 2.50e+03
        pdb=" C4    A C  37 "   -0.144 2.00e-02 2.50e+03
        pdb=" H8    A C  37 "   -0.043 2.00e-02 2.50e+03
        pdb=" H2    A C  37 "   -0.039 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C1'   C C  36 "    0.387 2.00e-02 2.50e+03   1.63e-01 7.28e+02
        pdb=" N1    C C  36 "   -0.030 2.00e-02 2.50e+03
        pdb=" C2    C C  36 "   -0.019 2.00e-02 2.50e+03
        pdb=" O2    C C  36 "   -0.268 2.00e-02 2.50e+03
        pdb=" N3    C C  36 "    0.035 2.00e-02 2.50e+03
        pdb=" C4    C C  36 "    0.087 2.00e-02 2.50e+03
        pdb=" N4    C C  36 "    0.137 2.00e-02 2.50e+03
        pdb=" C5    C C  36 "   -0.020 2.00e-02 2.50e+03
        pdb=" C6    C C  36 "   -0.098 2.00e-02 2.50e+03
        pdb=" H5    C C  36 "   -0.042 2.00e-02 2.50e+03
        pdb=" H6    C C  36 "   -0.170 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C1'   U B  45 "   -0.365 2.00e-02 2.50e+03   1.54e-01 7.07e+02
        pdb=" N1    U B  45 "   -0.026 2.00e-02 2.50e+03
        pdb=" C2    U B  45 "    0.054 2.00e-02 2.50e+03
        pdb=" O2    U B  45 "    0.218 2.00e-02 2.50e+03
        pdb=" N3    U B  45 "   -0.011 2.00e-02 2.50e+03
        pdb=" C4    U B  45 "   -0.087 2.00e-02 2.50e+03
        pdb=" O4    U B  45 "   -0.203 2.00e-02 2.50e+03
        pdb=" C5    U B  45 "    0.021 2.00e-02 2.50e+03
        pdb=" C6    U B  45 "    0.074 2.00e-02 2.50e+03
        pdb=" H5    U B  45 "    0.074 2.00e-02 2.50e+03
        pdb=" H3    U B  45 "    0.068 2.00e-02 2.50e+03
        pdb=" H6    U B  45 "    0.183 2.00e-02 2.50e+03
  ... (remaining 2451 not shown)

  Histogram of nonbonded interaction distances:
        1.47 -     2.10: 619
        2.10 -     2.72: 29261
        2.72 -     3.35: 51046
        3.35 -     3.97: 63520
        3.97 -     4.60: 96683
  Nonbonded interactions: 241129
  Sorted by model distance:
  nonbonded pdb=" O   PHE A1034 "
            pdb="HH12 ARG A1078 "
     model   vdw
     1.471 2.450
  nonbonded pdb=" H   THR A 968 "
            pdb=" OE1 GLU A 971 "
     model   vdw
     1.479 2.450
  nonbonded pdb=" OE1 GLN A 495 "
            pdb=" H   GLN A 495 "
     model   vdw
     1.533 2.450
  nonbonded pdb=" OE1 GLU A 969 "
            pdb=" H   GLU A 969 "
     model   vdw
     1.558 2.450
  nonbonded pdb="HD21 ASN A 358 "
            pdb=" OE1 GLN A 361 "
     model   vdw
     1.560 2.450
  ... (remaining 241124 not shown)

  NOTE: a complete listing of the restraints can be obtained by requesting
        output of .geo file.
Find NCS groups from input model
Time spend for trying shortcut: 0.00
========== WARNING! ============

  No NCS relation were found !!!

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

Found NCS groups:
  found none.
Set up NCS constraints
  No NCS constraints will be used in refinement.
Set refine NCS operators
Adjust number of macro_cycles
  Number of macro_cycles: 10
Reset NCS operators
Extract rigid body selections
Check and reset occupancies
  Occupancies: min=1.00 max=1.00 mean=1.00
Load rotamer database and sin/cos tables
Set ADP refinement strategy
  ADPs will be refined as 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:             1.120
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.010
  Construct map_model_manager:             0.100
  Extract box with map and model:          0.270
  Check model and map are aligned:         0.050
  Set scattering table:                    0.050
  Process input model:                     18.690
  Find NCS groups from input model:        0.040
  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:             0.010
  Load rotamer database and sin/cos tables:1.080
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   21.440
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7827
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      :  0.036   0.150   9891  Z= 1.805
  Angle     :  2.701  12.040  13683  Z= 1.720
  Chirality :  0.327   0.753   1572
  Planarity :  0.017   0.175   1458
  Dihedral  : 19.367 171.793   4292
  Min Nonbonded Distance : 1.915

Molprobity Statistics.
  All-atom Clashscore : 5.23
  Ramachandran Plot:
    Outliers :  0.42 %
    Allowed  :  7.14 %
    Favored  : 92.44 %
  Rotamer:
    Outliers :  0.23 %
    Allowed  :  4.96 %
    Favored  : 94.81 %
  Cbeta Deviations : 22.98 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -2.02 (0.25), residues: 952
  helix: -1.31 (0.23), residues: 420
  sheet: -0.06 (0.51), residues: 108
  loop : -1.61 (0.28), residues: 424

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.009   0.001   ARG A 785 
 TYR   0.109   0.010   TYR A 218 
 PHE   0.036   0.008   PHE A 787 
 TRP   0.033   0.008   TRP A 613 
 HIS   0.006   0.001   HIS A1117 

Details of bonding type rmsd
  covalent geometry    : bond        0.03578 ( 9891)
  covalent geometry    : angle       2.70084 (13683)
  hydrogen bonds       : bond        0.21964 (  456)
  hydrogen bonds       : angle       7.76064 ( 1172)

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

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

  1904 Ramachandran restraints generated.
    952 Oldfield, 0 Emsley, 952 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1904 Ramachandran restraints generated.
    952 Oldfield, 0 Emsley, 952 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  105 residues out of total 867 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 2
    poor density    : 103
  time to evaluate  : 0.483 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  294 GLN cc_start: 0.9253 (tp40) cc_final: 0.8693 (tm-30)
REVERT: A  298 ASN cc_start: 0.9484 (m110) cc_final: 0.8766 (m110)
REVERT: A  679 LYS cc_start: 0.8975 (mttp) cc_final: 0.8526 (mmtt)
REVERT: A 1055 GLU cc_start: 0.9040 (tm-30) cc_final: 0.8799 (tm-30)
REVERT: A 1072 LYS cc_start: 0.8441 (mmtt) cc_final: 0.8221 (mmtt)
REVERT: A 1137 ASP cc_start: 0.8255 (m-30) cc_final: 0.7631 (p0)
  outliers start: 2
  outliers final: 1
  residues processed: 104
  average time/residue: 0.2416
  time to fit residues: 32.8453
Evaluate side-chains
  84 residues out of total 867 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 83
  time to evaluate  : 0.402 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  369 LYS
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 103
   random chunks:
   chunk 49 optimal weight:    5.9990
   chunk 97 optimal weight:    1.9990
   chunk 53 optimal weight:    0.9980
   chunk 5 optimal weight:    5.9990
   chunk 33 optimal weight:    5.9990
   chunk 65 optimal weight:    5.9990
   chunk 62 optimal weight:    1.9990
   chunk 51 optimal weight:    5.9990
   chunk 100 optimal weight:    5.9990
   chunk 38 optimal weight:    5.9990
   chunk 61 optimal weight:    1.9990
   overall best weight:    2.5988

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

Flipped N/Q/H residues before XYZ refinement:
A 419 GLN
A 847 ASN
A1105 GLN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3728 r_free = 0.3728 target = 0.080867 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 43)----------------|
| r_work = 0.3220 r_free = 0.3220 target = 0.059944 restraints weight = 131258.377|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 39)----------------|
| r_work = 0.3290 r_free = 0.3290 target = 0.062897 restraints weight = 58330.951|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 41)----------------|
| r_work = 0.3334 r_free = 0.3334 target = 0.064726 restraints weight = 36044.027|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 37)----------------|
| r_work = 0.3362 r_free = 0.3362 target = 0.065875 restraints weight = 26995.078|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 43)----------------|
| r_work = 0.3379 r_free = 0.3379 target = 0.066590 restraints weight = 22557.676|
|-----------------------------------------------------------------------------|
r_work (final): 0.3367
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7800
moved from start:          0.1851

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.042   9891  Z= 0.180
  Angle     :  0.698   7.228  13683  Z= 0.380
  Chirality :  0.041   0.348   1572
  Planarity :  0.004   0.035   1458
  Dihedral  : 21.477 178.970   2259
  Min Nonbonded Distance : 2.350

Molprobity Statistics.
  All-atom Clashscore : 10.63
  Ramachandran Plot:
    Outliers :  0.32 %
    Allowed  :  6.51 %
    Favored  : 93.17 %
  Rotamer:
    Outliers :  1.04 %
    Allowed  :  7.50 %
    Favored  : 91.46 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -0.52 (0.27), residues: 952
  helix:  0.46 (0.25), residues: 420
  sheet:  0.11 (0.51), residues: 108
  loop : -1.27 (0.29), residues: 424

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.001   ARG A1078 
 TYR   0.014   0.002   TYR A 783 
 PHE   0.014   0.001   PHE A 951 
 TRP   0.010   0.001   TRP A 897 
 HIS   0.007   0.001   HIS A 838 

Details of bonding type rmsd
  covalent geometry    : bond        0.00360 ( 9891)
  covalent geometry    : angle       0.69780 (13683)
  hydrogen bonds       : bond        0.05903 (  456)
  hydrogen bonds       : angle       5.22727 ( 1172)

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

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

  1904 Ramachandran restraints generated.
    952 Oldfield, 0 Emsley, 952 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1904 Ramachandran restraints generated.
    952 Oldfield, 0 Emsley, 952 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  95 residues out of total 867 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 86
  time to evaluate  : 0.357 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  294 GLN cc_start: 0.9163 (tp40) cc_final: 0.8647 (tm-30)
REVERT: A  298 ASN cc_start: 0.9476 (m110) cc_final: 0.8820 (m110)
REVERT: A  369 LYS cc_start: 0.9618 (OUTLIER) cc_final: 0.9248 (mttm)
REVERT: A  477 LYS cc_start: 0.9195 (tttt) cc_final: 0.8964 (tttt)
REVERT: A  694 ASP cc_start: 0.9428 (t0) cc_final: 0.9024 (m-30)
  outliers start: 9
  outliers final: 7
  residues processed: 93
  average time/residue: 0.2184
  time to fit residues: 27.4559
Evaluate side-chains
  81 residues out of total 867 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 73
  time to evaluate  : 0.406 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  254 PHE
Chi-restraints excluded: chain A residue  347 GLU
Chi-restraints excluded: chain A residue  363 LYS
Chi-restraints excluded: chain A residue  369 LYS
Chi-restraints excluded: chain A residue  383 ASN
Chi-restraints excluded: chain A residue  566 ILE
Chi-restraints excluded: chain A residue  689 PHE
Chi-restraints excluded: chain A residue  997 ILE
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 103
   random chunks:
   chunk 27 optimal weight:    0.4980
   chunk 85 optimal weight:    2.9990
   chunk 101 optimal weight:    9.9990
   chunk 8 optimal weight:    0.4980
   chunk 89 optimal weight:    4.9990
   chunk 7 optimal weight:   10.0000
   chunk 24 optimal weight:   10.0000
   chunk 3 optimal weight:    0.8980
   chunk 63 optimal weight:    4.9990
   chunk 76 optimal weight:    3.9990
   chunk 45 optimal weight:    7.9990
   overall best weight:    1.7784

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

Flipped N/Q/H residues before XYZ refinement:
A 222 ASN
A 772 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3732 r_free = 0.3732 target = 0.081448 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 53)----------------|
| r_work = 0.3231 r_free = 0.3231 target = 0.060766 restraints weight = 132417.844|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 43)----------------|
| r_work = 0.3300 r_free = 0.3300 target = 0.063729 restraints weight = 57840.225|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 36)----------------|
| r_work = 0.3344 r_free = 0.3344 target = 0.065573 restraints weight = 35909.395|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 35)----------------|
| r_work = 0.3372 r_free = 0.3372 target = 0.066747 restraints weight = 26870.062|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 31)----------------|
| r_work = 0.3388 r_free = 0.3388 target = 0.067455 restraints weight = 22314.599|
|-----------------------------------------------------------------------------|
r_work (final): 0.3374
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7779
moved from start:          0.2331

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.037   9891  Z= 0.135
  Angle     :  0.596   7.088  13683  Z= 0.328
  Chirality :  0.038   0.359   1572
  Planarity :  0.003   0.031   1458
  Dihedral  : 21.360 176.198   2259
  Min Nonbonded Distance : 2.390

Molprobity Statistics.
  All-atom Clashscore : 7.14
  Ramachandran Plot:
    Outliers :  0.32 %
    Allowed  :  6.51 %
    Favored  : 93.17 %
  Rotamer:
    Outliers :  1.50 %
    Allowed  :  8.65 %
    Favored  : 89.85 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -0.01 (0.27), residues: 952
  helix:  1.11 (0.25), residues: 423
  sheet:  0.13 (0.52), residues: 101
  loop : -1.17 (0.30), residues: 428

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.010   0.001   ARG A 441 
 TYR   0.014   0.001   TYR A 783 
 PHE   0.009   0.001   PHE A 787 
 TRP   0.009   0.001   TRP A 897 
 HIS   0.007   0.001   HIS A 838 

Details of bonding type rmsd
  covalent geometry    : bond        0.00273 ( 9891)
  covalent geometry    : angle       0.59611 (13683)
  hydrogen bonds       : bond        0.04748 (  456)
  hydrogen bonds       : angle       4.66345 ( 1172)

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

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

  1904 Ramachandran restraints generated.
    952 Oldfield, 0 Emsley, 952 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1904 Ramachandran restraints generated.
    952 Oldfield, 0 Emsley, 952 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  95 residues out of total 867 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 82
  time to evaluate  : 0.445 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  222 ASN cc_start: 0.7278 (OUTLIER) cc_final: 0.6858 (m-40)
REVERT: A  294 GLN cc_start: 0.9159 (tp40) cc_final: 0.8631 (tm-30)
REVERT: A  298 ASN cc_start: 0.9443 (m110) cc_final: 0.8890 (m110)
REVERT: A  369 LYS cc_start: 0.9602 (mtpm) cc_final: 0.9187 (mttm)
REVERT: A  450 TRP cc_start: 0.9384 (t60) cc_final: 0.9055 (t60)
REVERT: A  477 LYS cc_start: 0.9084 (tttt) cc_final: 0.8862 (tttt)
REVERT: A  679 LYS cc_start: 0.8966 (mttp) cc_final: 0.8584 (mmtt)
REVERT: A  694 ASP cc_start: 0.9415 (t0) cc_final: 0.9054 (m-30)
  outliers start: 13
  outliers final: 10
  residues processed: 91
  average time/residue: 0.2150
  time to fit residues: 26.9557
Evaluate side-chains
  88 residues out of total 867 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 77
  time to evaluate  : 0.470 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   22 ILE
Chi-restraints excluded: chain A residue  222 ASN
Chi-restraints excluded: chain A residue  254 PHE
Chi-restraints excluded: chain A residue  363 LYS
Chi-restraints excluded: chain A residue  375 GLN
Chi-restraints excluded: chain A residue  471 THR
Chi-restraints excluded: chain A residue  635 THR
Chi-restraints excluded: chain A residue  669 THR
Chi-restraints excluded: chain A residue  684 MET
Chi-restraints excluded: chain A residue  689 PHE
Chi-restraints excluded: chain A residue  997 ILE
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 103
   random chunks:
   chunk 53 optimal weight:    5.9990
   chunk 19 optimal weight:    0.5980
   chunk 26 optimal weight:    5.9990
   chunk 29 optimal weight:    3.9990
   chunk 32 optimal weight:    9.9990
   chunk 36 optimal weight:    9.9990
   chunk 37 optimal weight:    0.9980
   chunk 44 optimal weight:    4.9990
   chunk 61 optimal weight:    6.9990
   chunk 90 optimal weight:    6.9990
   chunk 46 optimal weight:    8.9990
   overall best weight:    3.3186

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

Flipped N/Q/H residues before XYZ refinement:
A 344 ASN
** A 401 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 764 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 782 ASN
** A1117 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 = 0.3696 r_free = 0.3696 target = 0.079716 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 46)----------------|
| r_work = 0.3186 r_free = 0.3186 target = 0.059100 restraints weight = 133391.887|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 40)----------------|
| r_work = 0.3256 r_free = 0.3256 target = 0.061998 restraints weight = 58456.506|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 46)----------------|
| r_work = 0.3301 r_free = 0.3301 target = 0.063823 restraints weight = 35981.344|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 44)----------------|
| r_work = 0.3328 r_free = 0.3328 target = 0.064945 restraints weight = 26737.530|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 43)----------------|
| r_work = 0.3346 r_free = 0.3346 target = 0.065672 restraints weight = 22252.724|
|-----------------------------------------------------------------------------|
r_work (final): 0.3330
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7831
moved from start:          0.2725

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.039   9891  Z= 0.193
  Angle     :  0.612   6.703  13683  Z= 0.338
  Chirality :  0.038   0.337   1572
  Planarity :  0.003   0.035   1458
  Dihedral  : 21.449 178.053   2255
  Min Nonbonded Distance : 2.396

Molprobity Statistics.
  All-atom Clashscore : 9.97
  Ramachandran Plot:
    Outliers :  0.32 %
    Allowed  :  7.25 %
    Favored  : 92.44 %
  Rotamer:
    Outliers :  2.08 %
    Allowed  :  9.92 %
    Favored  : 88.00 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -0.22 (0.27), residues: 952
  helix:  0.96 (0.25), residues: 426
  sheet:  0.13 (0.53), residues: 102
  loop : -1.37 (0.29), residues: 424

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG A1078 
 TYR   0.013   0.001   TYR A 783 
 PHE   0.012   0.001   PHE A1127 
 TRP   0.010   0.002   TRP A 897 
 HIS   0.007   0.002   HIS A 838 

Details of bonding type rmsd
  covalent geometry    : bond        0.00388 ( 9891)
  covalent geometry    : angle       0.61155 (13683)
  hydrogen bonds       : bond        0.04671 (  456)
  hydrogen bonds       : angle       4.65346 ( 1172)

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

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

  1904 Ramachandran restraints generated.
    952 Oldfield, 0 Emsley, 952 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1904 Ramachandran restraints generated.
    952 Oldfield, 0 Emsley, 952 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  95 residues out of total 867 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 77
  time to evaluate  : 0.377 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  294 GLN cc_start: 0.9118 (tp40) cc_final: 0.8582 (tm-30)
REVERT: A  298 ASN cc_start: 0.9388 (m110) cc_final: 0.8811 (m110)
REVERT: A  336 PHE cc_start: 0.8970 (OUTLIER) cc_final: 0.8554 (p90)
REVERT: A  477 LYS cc_start: 0.9071 (tttt) cc_final: 0.8800 (tttt)
REVERT: A  679 LYS cc_start: 0.9011 (mttp) cc_final: 0.8702 (mmtt)
REVERT: A  687 ASP cc_start: 0.9022 (OUTLIER) cc_final: 0.8666 (p0)
  outliers start: 18
  outliers final: 13
  residues processed: 88
  average time/residue: 0.2161
  time to fit residues: 26.0686
Evaluate side-chains
  88 residues out of total 867 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 73
  time to evaluate  : 0.430 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  254 PHE
Chi-restraints excluded: chain A residue  336 PHE
Chi-restraints excluded: chain A residue  347 GLU
Chi-restraints excluded: chain A residue  363 LYS
Chi-restraints excluded: chain A residue  375 GLN
Chi-restraints excluded: chain A residue  471 THR
Chi-restraints excluded: chain A residue  630 LEU
Chi-restraints excluded: chain A residue  635 THR
Chi-restraints excluded: chain A residue  668 THR
Chi-restraints excluded: chain A residue  669 THR
Chi-restraints excluded: chain A residue  684 MET
Chi-restraints excluded: chain A residue  687 ASP
Chi-restraints excluded: chain A residue  689 PHE
Chi-restraints excluded: chain A residue  828 VAL
Chi-restraints excluded: chain A residue  997 ILE
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 103
   random chunks:
   chunk 83 optimal weight:   10.0000
   chunk 47 optimal weight:    6.9990
   chunk 40 optimal weight:    0.9980
   chunk 75 optimal weight:    8.9990
   chunk 79 optimal weight:   10.0000
   chunk 22 optimal weight:   10.0000
   chunk 88 optimal weight:    6.9990
   chunk 10 optimal weight:    2.9990
   chunk 16 optimal weight:    5.9990
   chunk 100 optimal weight:   20.0000
   chunk 36 optimal weight:    5.9990
   overall best weight:    4.5988

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

Flipped N/Q/H residues before XYZ refinement:
A 312 GLN
A 338 ASN
A 368 ASN
** A 401 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
A 631 ASN
A 675 ASN
A 697 ASN
** A1117 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 6

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3658 r_free = 0.3658 target = 0.077654 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 44)----------------|
| r_work = 0.3136 r_free = 0.3136 target = 0.057117 restraints weight = 136991.862|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 29)----------------|
| r_work = 0.3206 r_free = 0.3206 target = 0.059882 restraints weight = 60569.838|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 30)----------------|
| r_work = 0.3250 r_free = 0.3250 target = 0.061626 restraints weight = 38219.590|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 43)----------------|
| r_work = 0.3277 r_free = 0.3277 target = 0.062697 restraints weight = 28894.159|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 40)----------------|
| r_work = 0.3294 r_free = 0.3294 target = 0.063384 restraints weight = 24286.877|
|-----------------------------------------------------------------------------|
r_work (final): 0.3281
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7907
moved from start:          0.3337

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.033   9891  Z= 0.252
  Angle     :  0.668   6.522  13683  Z= 0.371
  Chirality :  0.040   0.340   1572
  Planarity :  0.004   0.058   1458
  Dihedral  : 21.660 179.435   2255
  Min Nonbonded Distance : 2.361

Molprobity Statistics.
  All-atom Clashscore : 12.97
  Ramachandran Plot:
    Outliers :  0.32 %
    Allowed  :  7.46 %
    Favored  : 92.23 %
  Rotamer:
    Outliers :  2.08 %
    Allowed  : 11.76 %
    Favored  : 86.16 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -0.61 (0.26), residues: 952
  helix:  0.59 (0.25), residues: 426
  sheet:  0.29 (0.53), residues: 98
  loop : -1.62 (0.28), residues: 428

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.011   0.001   ARG A 441 
 TYR   0.016   0.002   TYR A 472 
 PHE   0.017   0.002   PHE A 467 
 TRP   0.021   0.002   TRP A 450 
 HIS   0.007   0.002   HIS A 838 

Details of bonding type rmsd
  covalent geometry    : bond        0.00501 ( 9891)
  covalent geometry    : angle       0.66770 (13683)
  hydrogen bonds       : bond        0.04875 (  456)
  hydrogen bonds       : angle       4.80268 ( 1172)

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

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

  1904 Ramachandran restraints generated.
    952 Oldfield, 0 Emsley, 952 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1904 Ramachandran restraints generated.
    952 Oldfield, 0 Emsley, 952 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  90 residues out of total 867 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 72
  time to evaluate  : 0.366 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  336 PHE cc_start: 0.9033 (OUTLIER) cc_final: 0.8578 (p90)
REVERT: A  369 LYS cc_start: 0.9579 (mtpm) cc_final: 0.9187 (mtpp)
REVERT: A  455 ASN cc_start: 0.8549 (m-40) cc_final: 0.7943 (p0)
REVERT: A  477 LYS cc_start: 0.8932 (tttt) cc_final: 0.8700 (tttt)
REVERT: A  679 LYS cc_start: 0.9063 (mttp) cc_final: 0.8831 (mmtt)
REVERT: A  687 ASP cc_start: 0.9012 (t70) cc_final: 0.8663 (p0)
REVERT: A  694 ASP cc_start: 0.9437 (t0) cc_final: 0.9182 (m-30)
REVERT: A 1013 ASP cc_start: 0.9621 (OUTLIER) cc_final: 0.9378 (t0)
  outliers start: 18
  outliers final: 13
  residues processed: 83
  average time/residue: 0.2202
  time to fit residues: 24.7184
Evaluate side-chains
  85 residues out of total 867 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 70
  time to evaluate  : 0.316 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   22 ILE
Chi-restraints excluded: chain A residue  336 PHE
Chi-restraints excluded: chain A residue  347 GLU
Chi-restraints excluded: chain A residue  363 LYS
Chi-restraints excluded: chain A residue  383 ASN
Chi-restraints excluded: chain A residue  394 TYR
Chi-restraints excluded: chain A residue  471 THR
Chi-restraints excluded: chain A residue  630 LEU
Chi-restraints excluded: chain A residue  635 THR
Chi-restraints excluded: chain A residue  668 THR
Chi-restraints excluded: chain A residue  817 VAL
Chi-restraints excluded: chain A residue  828 VAL
Chi-restraints excluded: chain A residue  997 ILE
Chi-restraints excluded: chain A residue 1013 ASP
Chi-restraints excluded: chain A residue 1058 LEU
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 103
   random chunks:
   chunk 86 optimal weight:    2.9990
   chunk 92 optimal weight:    7.9990
   chunk 88 optimal weight:   10.0000
   chunk 23 optimal weight:    8.9990
   chunk 13 optimal weight:    5.9990
   chunk 44 optimal weight:    4.9990
   chunk 71 optimal weight:   10.0000
   chunk 94 optimal weight:    4.9990
   chunk 36 optimal weight:    9.9990
   chunk 55 optimal weight:    2.9990
   chunk 101 optimal weight:   10.0000
   overall best weight:    4.3990

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

Flipped N/Q/H residues before XYZ refinement:
** A 401 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3668 r_free = 0.3668 target = 0.078062 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 45)----------------|
| r_work = 0.3152 r_free = 0.3152 target = 0.057597 restraints weight = 133626.198|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 39)----------------|
| r_work = 0.3224 r_free = 0.3224 target = 0.060393 restraints weight = 59321.458|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 36)----------------|
| r_work = 0.3267 r_free = 0.3267 target = 0.062091 restraints weight = 37109.729|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 43)----------------|
| r_work = 0.3294 r_free = 0.3294 target = 0.063156 restraints weight = 28162.800|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 43)----------------|
| r_work = 0.3311 r_free = 0.3311 target = 0.063828 restraints weight = 23617.443|
|-----------------------------------------------------------------------------|
r_work (final): 0.3294
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7913
moved from start:          0.3634

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.032   9891  Z= 0.232
  Angle     :  0.635   6.423  13683  Z= 0.352
  Chirality :  0.039   0.333   1572
  Planarity :  0.004   0.047   1458
  Dihedral  : 21.657 176.752   2255
  Min Nonbonded Distance : 2.303

Molprobity Statistics.
  All-atom Clashscore : 12.53
  Ramachandran Plot:
    Outliers :  0.32 %
    Allowed  :  7.56 %
    Favored  : 92.12 %
  Rotamer:
    Outliers :  1.85 %
    Allowed  : 13.26 %
    Favored  : 84.89 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -0.70 (0.26), residues: 952
  helix:  0.56 (0.25), residues: 427
  sheet:  0.17 (0.55), residues: 92
  loop : -1.69 (0.28), residues: 433

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.001   ARG A 441 
 TYR   0.014   0.002   TYR A 783 
 PHE   0.014   0.002   PHE A 465 
 TRP   0.013   0.002   TRP A 450 
 HIS   0.006   0.001   HIS A1117 

Details of bonding type rmsd
  covalent geometry    : bond        0.00461 ( 9891)
  covalent geometry    : angle       0.63452 (13683)
  hydrogen bonds       : bond        0.04576 (  456)
  hydrogen bonds       : angle       4.73756 ( 1172)

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

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

  1904 Ramachandran restraints generated.
    952 Oldfield, 0 Emsley, 952 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1904 Ramachandran restraints generated.
    952 Oldfield, 0 Emsley, 952 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  86 residues out of total 867 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 70
  time to evaluate  : 0.482 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  336 PHE cc_start: 0.9034 (OUTLIER) cc_final: 0.8584 (p90)
REVERT: A  369 LYS cc_start: 0.9575 (mtpm) cc_final: 0.9173 (mtpp)
REVERT: A  455 ASN cc_start: 0.8581 (m-40) cc_final: 0.7956 (p0)
REVERT: A  687 ASP cc_start: 0.9019 (t70) cc_final: 0.8688 (p0)
REVERT: A  689 PHE cc_start: 0.8661 (OUTLIER) cc_final: 0.8338 (p90)
  outliers start: 16
  outliers final: 13
  residues processed: 78
  average time/residue: 0.2367
  time to fit residues: 24.8712
Evaluate side-chains
  85 residues out of total 867 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 70
  time to evaluate  : 0.357 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   22 ILE
Chi-restraints excluded: chain A residue  336 PHE
Chi-restraints excluded: chain A residue  347 GLU
Chi-restraints excluded: chain A residue  375 GLN
Chi-restraints excluded: chain A residue  383 ASN
Chi-restraints excluded: chain A residue  394 TYR
Chi-restraints excluded: chain A residue  471 THR
Chi-restraints excluded: chain A residue  630 LEU
Chi-restraints excluded: chain A residue  635 THR
Chi-restraints excluded: chain A residue  668 THR
Chi-restraints excluded: chain A residue  689 PHE
Chi-restraints excluded: chain A residue  817 VAL
Chi-restraints excluded: chain A residue  828 VAL
Chi-restraints excluded: chain A residue  997 ILE
Chi-restraints excluded: chain A residue 1058 LEU
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 103
   random chunks:
   chunk 55 optimal weight:    5.9990
   chunk 95 optimal weight:    0.9990
   chunk 93 optimal weight:    7.9990
   chunk 33 optimal weight:    0.8980
   chunk 15 optimal weight:    9.9990
   chunk 47 optimal weight:    4.9990
   chunk 77 optimal weight:    0.0050
   chunk 25 optimal weight:    0.9980
   chunk 60 optimal weight:    7.9990
   chunk 76 optimal weight:    3.9990
   chunk 50 optimal weight:    6.9990
   overall best weight:    1.3798

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

Flipped N/Q/H residues before XYZ refinement:
** A 401 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3700 r_free = 0.3700 target = 0.080305 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.3197 r_free = 0.3197 target = 0.060080 restraints weight = 131996.827|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 30)----------------|
| r_work = 0.3270 r_free = 0.3270 target = 0.063006 restraints weight = 58514.227|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 47)----------------|
| r_work = 0.3317 r_free = 0.3317 target = 0.064886 restraints weight = 36315.693|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 45)----------------|
| r_work = 0.3347 r_free = 0.3347 target = 0.066055 restraints weight = 26918.882|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 27)----------------|
| r_work = 0.3360 r_free = 0.3360 target = 0.066659 restraints weight = 22253.441|
|-----------------------------------------------------------------------------|
r_work (final): 0.3349
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7829
moved from start:          0.3756

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.032   9891  Z= 0.123
  Angle     :  0.559   6.543  13683  Z= 0.306
  Chirality :  0.036   0.287   1572
  Planarity :  0.003   0.031   1458
  Dihedral  : 21.490 175.252   2255
  Min Nonbonded Distance : 2.381

Molprobity Statistics.
  All-atom Clashscore : 7.63
  Ramachandran Plot:
    Outliers :  0.32 %
    Allowed  :  6.41 %
    Favored  : 93.28 %
  Rotamer:
    Outliers :  1.38 %
    Allowed  : 13.96 %
    Favored  : 84.66 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -0.11 (0.28), residues: 952
  helix:  1.07 (0.25), residues: 434
  sheet:  0.26 (0.52), residues: 100
  loop : -1.40 (0.30), residues: 418

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG A 658 
 TYR   0.015   0.001   TYR A 783 
 PHE   0.011   0.001   PHE A 951 
 TRP   0.020   0.002   TRP A 450 
 HIS   0.006   0.001   HIS A1117 

Details of bonding type rmsd
  covalent geometry    : bond        0.00249 ( 9891)
  covalent geometry    : angle       0.55875 (13683)
  hydrogen bonds       : bond        0.03762 (  456)
  hydrogen bonds       : angle       4.27521 ( 1172)

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

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

  1904 Ramachandran restraints generated.
    952 Oldfield, 0 Emsley, 952 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1904 Ramachandran restraints generated.
    952 Oldfield, 0 Emsley, 952 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  87 residues out of total 867 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 75
  time to evaluate  : 0.365 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  336 PHE cc_start: 0.9004 (OUTLIER) cc_final: 0.8549 (p90)
REVERT: A  369 LYS cc_start: 0.9554 (mtpm) cc_final: 0.9124 (mtpp)
REVERT: A  687 ASP cc_start: 0.9050 (t70) cc_final: 0.8719 (p0)
REVERT: A  689 PHE cc_start: 0.8621 (OUTLIER) cc_final: 0.8365 (p90)
REVERT: A  694 ASP cc_start: 0.9443 (t0) cc_final: 0.9201 (m-30)
  outliers start: 12
  outliers final: 10
  residues processed: 80
  average time/residue: 0.2325
  time to fit residues: 25.3195
Evaluate side-chains
  86 residues out of total 867 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 74
  time to evaluate  : 0.461 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  336 PHE
Chi-restraints excluded: chain A residue  347 GLU
Chi-restraints excluded: chain A residue  375 GLN
Chi-restraints excluded: chain A residue  394 TYR
Chi-restraints excluded: chain A residue  471 THR
Chi-restraints excluded: chain A residue  630 LEU
Chi-restraints excluded: chain A residue  635 THR
Chi-restraints excluded: chain A residue  668 THR
Chi-restraints excluded: chain A residue  689 PHE
Chi-restraints excluded: chain A residue  828 VAL
Chi-restraints excluded: chain A residue  997 ILE
Chi-restraints excluded: chain A residue 1058 LEU
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 103
   random chunks:
   chunk 90 optimal weight:    0.0970
   chunk 0 optimal weight:    7.9990
   chunk 83 optimal weight:    9.9990
   chunk 74 optimal weight:    0.8980
   chunk 71 optimal weight:   10.0000
   chunk 19 optimal weight:    5.9990
   chunk 63 optimal weight:    4.9990
   chunk 65 optimal weight:    6.9990
   chunk 82 optimal weight:    0.5980
   chunk 3 optimal weight:    0.9980
   chunk 77 optimal weight:    0.9990
   overall best weight:    0.7180

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

Flipped N/Q/H residues before XYZ refinement:
** A 401 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3731 r_free = 0.3731 target = 0.081307 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 49)----------------|
| r_work = 0.3242 r_free = 0.3242 target = 0.060920 restraints weight = 129172.361|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 40)----------------|
| r_work = 0.3313 r_free = 0.3313 target = 0.063894 restraints weight = 55682.449|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 44)----------------|
| r_work = 0.3357 r_free = 0.3357 target = 0.065769 restraints weight = 34166.572|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 45)----------------|
| r_work = 0.3385 r_free = 0.3385 target = 0.066929 restraints weight = 25310.313|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 32)----------------|
| r_work = 0.3401 r_free = 0.3401 target = 0.067653 restraints weight = 20942.377|
|-----------------------------------------------------------------------------|
r_work (final): 0.3387
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7761
moved from start:          0.3940

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.031   9891  Z= 0.101
  Angle     :  0.533   6.854  13683  Z= 0.287
  Chirality :  0.036   0.255   1572
  Planarity :  0.003   0.033   1458
  Dihedral  : 21.294 175.105   2255
  Min Nonbonded Distance : 2.390

Molprobity Statistics.
  All-atom Clashscore : 5.99
  Ramachandran Plot:
    Outliers :  0.32 %
    Allowed  :  5.57 %
    Favored  : 94.12 %
  Rotamer:
    Outliers :  1.04 %
    Allowed  : 14.42 %
    Favored  : 84.54 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  0.37 (0.28), residues: 952
  helix:  1.61 (0.25), residues: 425
  sheet:  0.40 (0.51), residues: 100
  loop : -1.24 (0.30), residues: 427

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG A1147 
 TYR   0.013   0.001   TYR A 783 
 PHE   0.019   0.001   PHE A 480 
 TRP   0.025   0.002   TRP A 450 
 HIS   0.005   0.001   HIS A1117 

Details of bonding type rmsd
  covalent geometry    : bond        0.00209 ( 9891)
  covalent geometry    : angle       0.53290 (13683)
  hydrogen bonds       : bond        0.03448 (  456)
  hydrogen bonds       : angle       3.99404 ( 1172)

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

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

  1904 Ramachandran restraints generated.
    952 Oldfield, 0 Emsley, 952 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1904 Ramachandran restraints generated.
    952 Oldfield, 0 Emsley, 952 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  86 residues out of total 867 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 77
  time to evaluate  : 0.378 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  336 PHE cc_start: 0.9034 (OUTLIER) cc_final: 0.8591 (p90)
REVERT: A  369 LYS cc_start: 0.9568 (mtpm) cc_final: 0.9121 (mtpp)
REVERT: A  687 ASP cc_start: 0.9056 (t70) cc_final: 0.8726 (p0)
REVERT: A  694 ASP cc_start: 0.9410 (t0) cc_final: 0.9164 (m-30)
  outliers start: 9
  outliers final: 7
  residues processed: 81
  average time/residue: 0.2616
  time to fit residues: 28.1822
Evaluate side-chains
  81 residues out of total 867 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 73
  time to evaluate  : 0.381 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  336 PHE
Chi-restraints excluded: chain A residue  375 GLN
Chi-restraints excluded: chain A residue  394 TYR
Chi-restraints excluded: chain A residue  471 THR
Chi-restraints excluded: chain A residue  569 ARG
Chi-restraints excluded: chain A residue  630 LEU
Chi-restraints excluded: chain A residue  668 THR
Chi-restraints excluded: chain A residue  684 MET
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 103
   random chunks:
   chunk 53 optimal weight:    2.9990
   chunk 29 optimal weight:    1.9990
   chunk 41 optimal weight:    2.9990
   chunk 42 optimal weight:    3.9990
   chunk 58 optimal weight:    3.9990
   chunk 86 optimal weight:    4.9990
   chunk 26 optimal weight:    6.9990
   chunk 93 optimal weight:   10.0000
   chunk 98 optimal weight:    9.9990
   chunk 40 optimal weight:    0.9990
   chunk 2 optimal weight:    0.7980
   overall best weight:    1.9588

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

Flipped N/Q/H residues before XYZ refinement:
** A 401 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3712 r_free = 0.3712 target = 0.080810 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 46)----------------|
| r_work = 0.3214 r_free = 0.3214 target = 0.060773 restraints weight = 129449.696|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 31)----------------|
| r_work = 0.3288 r_free = 0.3288 target = 0.063726 restraints weight = 56535.068|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 46)----------------|
| r_work = 0.3336 r_free = 0.3336 target = 0.065622 restraints weight = 34695.959|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 39)----------------|
| r_work = 0.3365 r_free = 0.3365 target = 0.066818 restraints weight = 25501.500|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 30)----------------|
| r_work = 0.3380 r_free = 0.3380 target = 0.067510 restraints weight = 20947.107|
|-----------------------------------------------------------------------------|
r_work (final): 0.3379
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7802
moved from start:          0.4072

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.035   9891  Z= 0.128
  Angle     :  0.540   6.570  13683  Z= 0.295
  Chirality :  0.036   0.268   1572
  Planarity :  0.003   0.032   1458
  Dihedral  : 21.362 177.876   2255
  Min Nonbonded Distance : 2.395

Molprobity Statistics.
  All-atom Clashscore : 7.90
  Ramachandran Plot:
    Outliers :  0.32 %
    Allowed  :  5.99 %
    Favored  : 93.70 %
  Rotamer:
    Outliers :  1.04 %
    Allowed  : 14.88 %
    Favored  : 84.08 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  0.35 (0.28), residues: 952
  helix:  1.58 (0.26), residues: 427
  sheet:  0.25 (0.50), residues: 100
  loop : -1.20 (0.30), residues: 425

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG A1147 
 TYR   0.015   0.001   TYR A1051 
 PHE   0.019   0.001   PHE A 591 
 TRP   0.019   0.002   TRP A 450 
 HIS   0.006   0.001   HIS A1117 

Details of bonding type rmsd
  covalent geometry    : bond        0.00261 ( 9891)
  covalent geometry    : angle       0.54037 (13683)
  hydrogen bonds       : bond        0.03609 (  456)
  hydrogen bonds       : angle       4.09065 ( 1172)

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

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

  1904 Ramachandran restraints generated.
    952 Oldfield, 0 Emsley, 952 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1904 Ramachandran restraints generated.
    952 Oldfield, 0 Emsley, 952 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  83 residues out of total 867 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 74
  time to evaluate  : 0.465 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  336 PHE cc_start: 0.9048 (OUTLIER) cc_final: 0.8622 (p90)
REVERT: A  369 LYS cc_start: 0.9565 (mtpm) cc_final: 0.9116 (mtpp)
REVERT: A  455 ASN cc_start: 0.8612 (m-40) cc_final: 0.7986 (p0)
REVERT: A  687 ASP cc_start: 0.9031 (t70) cc_final: 0.8701 (p0)
REVERT: A  694 ASP cc_start: 0.9423 (t0) cc_final: 0.9181 (m-30)
REVERT: A 1013 ASP cc_start: 0.9557 (OUTLIER) cc_final: 0.9343 (t0)
  outliers start: 9
  outliers final: 6
  residues processed: 79
  average time/residue: 0.2551
  time to fit residues: 26.7773
Evaluate side-chains
  81 residues out of total 867 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 73
  time to evaluate  : 0.493 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  336 PHE
Chi-restraints excluded: chain A residue  375 GLN
Chi-restraints excluded: chain A residue  394 TYR
Chi-restraints excluded: chain A residue  471 THR
Chi-restraints excluded: chain A residue  630 LEU
Chi-restraints excluded: chain A residue  668 THR
Chi-restraints excluded: chain A residue  689 PHE
Chi-restraints excluded: chain A residue 1013 ASP
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 103
   random chunks:
   chunk 23 optimal weight:   10.0000
   chunk 22 optimal weight:    1.9990
   chunk 40 optimal weight:    5.9990
   chunk 24 optimal weight:    6.9990
   chunk 76 optimal weight:    0.0980
   chunk 43 optimal weight:    6.9990
   chunk 68 optimal weight:    0.9980
   chunk 96 optimal weight:    7.9990
   chunk 59 optimal weight:    4.9990
   chunk 94 optimal weight:    5.9990
   chunk 63 optimal weight:    4.9990
   overall best weight:    2.6186

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

Flipped N/Q/H residues before XYZ refinement:
** A 401 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3695 r_free = 0.3695 target = 0.079710 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 42)----------------|
| r_work = 0.3185 r_free = 0.3185 target = 0.059548 restraints weight = 132064.773|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 36)----------------|
| r_work = 0.3257 r_free = 0.3257 target = 0.062403 restraints weight = 58291.765|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 50)----------------|
| r_work = 0.3304 r_free = 0.3304 target = 0.064218 restraints weight = 36228.325|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 29)----------------|
| r_work = 0.3328 r_free = 0.3328 target = 0.065292 restraints weight = 26887.512|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 35)----------------|
| r_work = 0.3351 r_free = 0.3351 target = 0.066095 restraints weight = 22481.739|
|-----------------------------------------------------------------------------|
r_work (final): 0.3338
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7836
moved from start:          0.4201

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.036   9891  Z= 0.152
  Angle     :  0.563   7.179  13683  Z= 0.307
  Chirality :  0.036   0.270   1572
  Planarity :  0.004   0.096   1458
  Dihedral  : 21.465 178.810   2255
  Min Nonbonded Distance : 2.396

Molprobity Statistics.
  All-atom Clashscore : 9.16
  Ramachandran Plot:
    Outliers :  0.32 %
    Allowed  :  6.41 %
    Favored  : 93.28 %
  Rotamer:
    Outliers :  1.15 %
    Allowed  : 14.88 %
    Favored  : 83.97 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  0.17 (0.28), residues: 952
  helix:  1.44 (0.25), residues: 432
  sheet:  0.12 (0.50), residues: 100
  loop : -1.33 (0.30), residues: 420

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.015   0.001   ARG A1056 
 TYR   0.012   0.001   TYR A 783 
 PHE   0.014   0.001   PHE A 591 
 TRP   0.022   0.002   TRP A 450 
 HIS   0.006   0.001   HIS A1117 

Details of bonding type rmsd
  covalent geometry    : bond        0.00307 ( 9891)
  covalent geometry    : angle       0.56256 (13683)
  hydrogen bonds       : bond        0.03750 (  456)
  hydrogen bonds       : angle       4.16656 ( 1172)

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

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

  1904 Ramachandran restraints generated.
    952 Oldfield, 0 Emsley, 952 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1904 Ramachandran restraints generated.
    952 Oldfield, 0 Emsley, 952 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  84 residues out of total 867 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 74
  time to evaluate  : 0.480 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  336 PHE cc_start: 0.9042 (OUTLIER) cc_final: 0.8593 (p90)
REVERT: A  369 LYS cc_start: 0.9567 (mtpm) cc_final: 0.9121 (mtpp)
REVERT: A  455 ASN cc_start: 0.8582 (m-40) cc_final: 0.7946 (p0)
REVERT: A  687 ASP cc_start: 0.9014 (t70) cc_final: 0.8719 (p0)
REVERT: A  694 ASP cc_start: 0.9431 (t0) cc_final: 0.9213 (m-30)
  outliers start: 10
  outliers final: 8
  residues processed: 79
  average time/residue: 0.2110
  time to fit residues: 22.7534
Evaluate side-chains
  83 residues out of total 867 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 74
  time to evaluate  : 0.400 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  336 PHE
Chi-restraints excluded: chain A residue  347 GLU
Chi-restraints excluded: chain A residue  375 GLN
Chi-restraints excluded: chain A residue  394 TYR
Chi-restraints excluded: chain A residue  471 THR
Chi-restraints excluded: chain A residue  630 LEU
Chi-restraints excluded: chain A residue  668 THR
Chi-restraints excluded: chain A residue  684 MET
Chi-restraints excluded: chain A residue  689 PHE
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 103
   random chunks:
   chunk 55 optimal weight:    3.9990
   chunk 16 optimal weight:    8.9990
   chunk 24 optimal weight:    4.9990
   chunk 39 optimal weight:    7.9990
   chunk 5 optimal weight:   10.0000
   chunk 94 optimal weight:    0.3980
   chunk 13 optimal weight:    3.9990
   chunk 14 optimal weight:    1.9990
   chunk 48 optimal weight:    6.9990
   chunk 6 optimal weight:    8.9990
   chunk 25 optimal weight:    1.9990
   overall best weight:    2.4788

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

Flipped N/Q/H residues before XYZ refinement:
** A 401 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3696 r_free = 0.3696 target = 0.079713 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 44)----------------|
| r_work = 0.3197 r_free = 0.3197 target = 0.059801 restraints weight = 130035.022|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 32)----------------|
| r_work = 0.3270 r_free = 0.3270 target = 0.062700 restraints weight = 57418.656|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 47)----------------|
| r_work = 0.3316 r_free = 0.3316 target = 0.064501 restraints weight = 35347.293|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 33)----------------|
| r_work = 0.3343 r_free = 0.3343 target = 0.065636 restraints weight = 26171.871|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 42)----------------|
| r_work = 0.3364 r_free = 0.3364 target = 0.066396 restraints weight = 21734.940|
|-----------------------------------------------------------------------------|
r_work (final): 0.3346
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7835
moved from start:          0.4340

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.032   9891  Z= 0.145
  Angle     :  0.557   6.457  13683  Z= 0.305
  Chirality :  0.036   0.262   1572
  Planarity :  0.004   0.075   1458
  Dihedral  : 21.483 179.865   2255
  Min Nonbonded Distance : 2.394

Molprobity Statistics.
  All-atom Clashscore : 8.94
  Ramachandran Plot:
    Outliers :  0.32 %
    Allowed  :  6.62 %
    Favored  : 93.07 %
  Rotamer:
    Outliers :  1.15 %
    Allowed  : 14.99 %
    Favored  : 83.85 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  0.17 (0.27), residues: 952
  helix:  1.43 (0.25), residues: 433
  sheet:  0.06 (0.50), residues: 100
  loop : -1.31 (0.30), residues: 419

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.013   0.001   ARG A1056 
 TYR   0.012   0.001   TYR A 783 
 PHE   0.016   0.001   PHE A 591 
 TRP   0.021   0.002   TRP A 450 
 HIS   0.006   0.001   HIS A1117 

Details of bonding type rmsd
  covalent geometry    : bond        0.00292 ( 9891)
  covalent geometry    : angle       0.55686 (13683)
  hydrogen bonds       : bond        0.03691 (  456)
  hydrogen bonds       : angle       4.15777 ( 1172)
Origin is already at (0, 0, 0), no shifts will be applied

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Job complete
usr+sys time: 2865.62 seconds
wall clock time: 49 minutes 39.79 seconds (2979.79 seconds total)