Starting phenix.real_space_refine
on Fri Aug  7 02:54:30 2026 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/9hm6_52287/08_2026/9hm6_52287_neut.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/9hm6_52287/08_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 {
    real_map_files = "/net/cci-nas-00/data/ceres_data/9hm6_52287/08_2026/9hm6_52287.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/9hm6_52287/08_2026/9hm6_52287.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/9hm6_52287/08_2026/9hm6_52287_neut.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/9hm6_52287/08_2026/9hm6_52287_neut.cif"
  }
  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-2.2rc3-6140/lib/python3.11/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: 3.11, per 1000 atoms: 0.17
  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: 1.55
  Conformation dependent library (CDL) restraints added in 568.5 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: 2.76
  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: 3.98

  Time building geometry restraints manager: 2.20 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: 24692
        2.55 -     5.11: 5914
        5.11 -     7.66: 2620
        7.66 -    10.22: 450
       10.22 -    12.77: 83
  Bond angle restraints: 33759
  Sorted by residual:
  angle pdb=" O4'   A B  38 "
        pdb=" C1'   A B  38 "
        pdb=" N9    A B  38 "
      ideal   model   delta    sigma   weight residual
     108.50  118.80  -10.30 7.00e-01 2.04e+00 2.17e+02
  angle pdb=" O4'   U C  30 "
        pdb=" C1'   U C  30 "
        pdb=" N1    U C  30 "
      ideal   model   delta    sigma   weight residual
     108.50  117.29   -8.79 7.00e-01 2.04e+00 1.58e+02
  angle pdb=" O4'   G B  40 "
        pdb=" C1'   G B  40 "
        pdb=" N9    G B  40 "
      ideal   model   delta    sigma   weight residual
     108.50  116.46   -7.96 7.00e-01 2.04e+00 1.29e+02
  angle pdb=" N6    A C  13 "
        pdb=" C6    A C  13 "
        pdb=" N1    A C  13 "
      ideal   model   delta    sigma   weight residual
     118.60  112.07    6.53 6.00e-01 2.78e+00 1.19e+02
  angle pdb=" N6    A B  38 "
        pdb=" C6    A B  38 "
        pdb=" N1    A B  38 "
      ideal   model   delta    sigma   weight residual
     118.60  112.33    6.27 6.00e-01 2.78e+00 1.09e+02
  ... (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: 984
       0.151 -    0.301: 55
       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:             1.080
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.000
  Construct map_model_manager:             0.110
  Extract box with map and model:          0.300
  Check model and map are aligned:         0.030
  Set scattering table:                    0.040
  Process input model:                     19.350
  Find NCS groups from input model:        0.060
  Set up NCS constraints:                  0.020
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.000
  Load rotamer database and sin/cos tables:0.970
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   21.960
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7550
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= 1.889
  Angle     :  2.707  12.040  13683  Z= 1.977
  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/Z
  covalent geometry    : bond        0.03578 /  1.89 ( 9891)
  covalent geometry    : angle       2.70685 /  1.98 (13683)
  hydrogen bonds       : bond        0.21964 / 14.18 (  456)
  hydrogen bonds       : angle       7.76064 /  5.38 ( 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  : 0.497 
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: 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 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: 0.2458
  time to fit residues: 34.1788
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  : 0.479 
-------------------------------------------------------------------------------
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:    5.9990
   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:    0.9990
   chunk 51 optimal weight:    5.9990
   chunk 100 optimal weight:    6.9990
   chunk 38 optimal weight:    5.9990
   chunk 61 optimal weight:    1.9990
   overall best weight:    3.1988

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
A 358 ASN
A 361 GLN
A 847 ASN
A1105 GLN

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3718 r_free = 0.3718 target = 0.080633 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 46)----------------|
| r_work = 0.3204 r_free = 0.3204 target = 0.059642 restraints weight = 132258.603|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 50)----------------|
| r_work = 0.3273 r_free = 0.3273 target = 0.062576 restraints weight = 58552.554|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 31)----------------|
| r_work = 0.3318 r_free = 0.3318 target = 0.064432 restraints weight = 36511.001|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 43)----------------|
| r_work = 0.3344 r_free = 0.3344 target = 0.065560 restraints weight = 27329.747|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 39)----------------|
| r_work = 0.3361 r_free = 0.3361 target = 0.066257 restraints weight = 22906.202|
|-----------------------------------------------------------------------------|
r_work (final): 0.3353
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7535
moved from start:          0.1407

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.049   9891  Z= 0.210
  Angle     :  0.749   9.073  13683  Z= 0.444
  Chirality :  0.049   0.373   1572
  Planarity :  0.005   0.049   1458
  Dihedral  : 21.653 178.588   2259
  Min Nonbonded Distance : 2.321

Molprobity Statistics.
  All-atom Clashscore : 12.43
  Ramachandran Plot:
    Outliers :  0.32 %
    Allowed  :  6.93 %
    Favored  : 92.75 %
  Rotamer:
    Outliers :  1.04 %
    Allowed  :  6.57 %
    Favored  : 92.39 %
  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: -1.08 (0.26), residues: 952
  helix: -0.16 (0.23), residues: 426
  sheet: -0.06 (0.50), residues: 113
  loop : -1.43 (0.30), residues: 413

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.001   ARG A 960 
 TYR   0.017   0.002   TYR A 783 
 PHE   0.017   0.002   PHE A1062 
 TRP   0.009   0.002   TRP A 897 
 HIS   0.007   0.002   HIS A 838 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00406 /  0.21 ( 9891)
  covalent geometry    : angle       0.74903 /  0.44 (13683)
  hydrogen bonds       : bond        0.07991 /  5.23 (  456)
  hydrogen bonds       : angle       5.81620 /  4.06 ( 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
  94 residues out of total 867 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 85
  time to evaluate  : 0.435 
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  294 GLN cc_start: 0.9149 (tp40) cc_final: 0.8605 (tm-30)
REVERT: A  298 ASN cc_start: 0.9487 (m110) cc_final: 0.8819 (m110)
REVERT: A  369 LYS cc_start: 0.9623 (OUTLIER) cc_final: 0.9279 (mttm)
REVERT: A  694 ASP cc_start: 0.9445 (t0) cc_final: 0.9070 (m-30)
REVERT: A 1055 GLU cc_start: 0.9112 (tm-30) cc_final: 0.8854 (tm-30)
  outliers start: 9
  outliers final: 6
  residues processed: 91
  average time/residue: 0.2484
  time to fit residues: 30.7269
Evaluate side-chains
  83 residues out of total 867 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 76
  time to evaluate  : 0.482 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  254 PHE
Chi-restraints excluded: chain A residue  363 LYS
Chi-restraints excluded: chain A residue  369 LYS
Chi-restraints excluded: chain A residue  566 ILE
Chi-restraints excluded: chain A residue  657 ASN
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:    0.0570
   chunk 85 optimal weight:    1.9990
   chunk 101 optimal weight:   20.0000
   chunk 8 optimal weight:    9.9990
   chunk 89 optimal weight:    4.9990
   chunk 7 optimal weight:   10.0000
   chunk 24 optimal weight:    7.9990
   chunk 3 optimal weight:    2.9990
   chunk 63 optimal weight:    3.9990
   chunk 76 optimal weight:    4.9990
   chunk 45 optimal weight:    3.9990
   overall best weight:    2.6106

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
** A 401 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
A 419 GLN
A 545 GLN
A 657 ASN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3724 r_free = 0.3724 target = 0.080598 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 45)----------------|
| r_work = 0.3217 r_free = 0.3217 target = 0.059804 restraints weight = 131977.777|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 49)----------------|
| r_work = 0.3286 r_free = 0.3286 target = 0.062710 restraints weight = 58196.662|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 36)----------------|
| r_work = 0.3330 r_free = 0.3330 target = 0.064543 restraints weight = 36123.504|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 37)----------------|
| r_work = 0.3359 r_free = 0.3359 target = 0.065746 restraints weight = 27091.320|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 39)----------------|
| r_work = 0.3376 r_free = 0.3376 target = 0.066461 restraints weight = 22471.090|
|-----------------------------------------------------------------------------|
r_work (final): 0.3363
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7534
moved from start:          0.1816

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.046   9891  Z= 0.175
  Angle     :  0.636   8.881  13683  Z= 0.381
  Chirality :  0.041   0.269   1572
  Planarity :  0.004   0.037   1458
  Dihedral  : 21.639 178.104   2259
  Min Nonbonded Distance : 2.353

Molprobity Statistics.
  All-atom Clashscore : 10.84
  Ramachandran Plot:
    Outliers :  0.32 %
    Allowed  :  6.72 %
    Favored  : 92.96 %
  Rotamer:
    Outliers :  1.61 %
    Allowed  :  8.42 %
    Favored  : 89.97 %
  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: -0.69 (0.26), residues: 952
  helix:  0.36 (0.24), residues: 426
  sheet: -0.08 (0.51), residues: 108
  loop : -1.40 (0.30), residues: 418

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG A 441 
 TYR   0.017   0.001   TYR A 783 
 PHE   0.011   0.001   PHE A 465 
 TRP   0.011   0.002   TRP A 897 
 HIS   0.006   0.001   HIS A 838 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00339 /  0.18 ( 9891)
  covalent geometry    : angle       0.63558 /  0.38 (13683)
  hydrogen bonds       : bond        0.06491 /  4.29 (  456)
  hydrogen bonds       : angle       5.30371 /  3.71 ( 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
  88 residues out of total 867 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 74
  time to evaluate  : 0.489 
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  294 GLN cc_start: 0.9114 (tp40) cc_final: 0.8551 (tm-30)
REVERT: A  298 ASN cc_start: 0.9453 (m110) cc_final: 0.8811 (m110)
REVERT: A  333 GLN cc_start: 0.9432 (tt0) cc_final: 0.9222 (tm-30)
REVERT: A  369 LYS cc_start: 0.9611 (OUTLIER) cc_final: 0.9247 (mttm)
REVERT: A  694 ASP cc_start: 0.9428 (t0) cc_final: 0.9081 (m-30)
REVERT: A 1055 GLU cc_start: 0.9101 (tm-30) cc_final: 0.8847 (tm-30)
  outliers start: 14
  outliers final: 12
  residues processed: 83
  average time/residue: 0.2130
  time to fit residues: 24.3836
Evaluate side-chains
  84 residues out of total 867 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 71
  time to evaluate  : 0.466 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   22 ILE
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  471 THR
Chi-restraints excluded: chain A residue  566 ILE
Chi-restraints excluded: chain A residue  657 ASN
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:   10.0000
   chunk 26 optimal weight:   10.0000
   chunk 29 optimal weight:    3.9990
   chunk 32 optimal weight:    9.9990
   chunk 36 optimal weight:   10.0000
   chunk 37 optimal weight:    0.8980
   chunk 44 optimal weight:    3.9990
   chunk 61 optimal weight:    4.9990
   chunk 90 optimal weight:    5.9990
   chunk 46 optimal weight:   10.0000
   overall best weight:    3.9788

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
A 222 ASN
A 344 ASN
** A 401 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
A 782 ASN
** A1117 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3704 r_free = 0.3704 target = 0.079754 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 47)----------------|
| r_work = 0.3189 r_free = 0.3189 target = 0.059000 restraints weight = 136298.069|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 43)----------------|
| r_work = 0.3259 r_free = 0.3259 target = 0.061849 restraints weight = 60081.915|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 49)----------------|
| r_work = 0.3302 r_free = 0.3302 target = 0.063654 restraints weight = 37679.302|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 34)----------------|
| r_work = 0.3329 r_free = 0.3329 target = 0.064736 restraints weight = 28419.696|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 37)----------------|
| r_work = 0.3346 r_free = 0.3346 target = 0.065433 restraints weight = 23995.347|
|-----------------------------------------------------------------------------|
r_work (final): 0.3332
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7583
moved from start:          0.2152

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.064   9891  Z= 0.216
  Angle     :  0.631   8.491  13683  Z= 0.374
  Chirality :  0.041   0.234   1572
  Planarity :  0.004   0.067   1458
  Dihedral  : 21.661 179.574   2259
  Min Nonbonded Distance : 2.333

Molprobity Statistics.
  All-atom Clashscore : 12.92
  Ramachandran Plot:
    Outliers :  0.42 %
    Allowed  :  7.14 %
    Favored  : 92.44 %
  Rotamer:
    Outliers :  1.73 %
    Allowed  :  8.77 %
    Favored  : 89.50 %
  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: -0.74 (0.27), residues: 952
  helix:  0.39 (0.24), residues: 431
  sheet: -0.10 (0.52), residues: 106
  loop : -1.52 (0.30), residues: 415

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.000   ARG A 441 
 TYR   0.017   0.001   TYR A 783 
 PHE   0.015   0.001   PHE A1062 
 TRP   0.012   0.002   TRP A 897 
 HIS   0.006   0.002   HIS A1117 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00423 /  0.22 ( 9891)
  covalent geometry    : angle       0.63106 /  0.37 (13683)
  hydrogen bonds       : bond        0.06148 /  4.05 (  456)
  hydrogen bonds       : angle       5.16478 /  3.59 ( 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
  90 residues out of total 867 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 75
  time to evaluate  : 0.478 
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  222 ASN cc_start: 0.7402 (OUTLIER) cc_final: 0.6996 (m-40)
REVERT: A  294 GLN cc_start: 0.9136 (tp40) cc_final: 0.8577 (tm-30)
REVERT: A  298 ASN cc_start: 0.9444 (m110) cc_final: 0.8815 (m110)
REVERT: A  369 LYS cc_start: 0.9606 (mtpm) cc_final: 0.9236 (mttm)
REVERT: A  450 TRP cc_start: 0.9405 (t60) cc_final: 0.9144 (t60)
REVERT: A  679 LYS cc_start: 0.9005 (mttp) cc_final: 0.8667 (mmtt)
REVERT: A  694 ASP cc_start: 0.9430 (t0) cc_final: 0.9103 (m-30)
  outliers start: 15
  outliers final: 14
  residues processed: 83
  average time/residue: 0.2360
  time to fit residues: 26.6607
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  : 0.456 
-------------------------------------------------------------------------------
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  347 GLU
Chi-restraints excluded: chain A residue  363 LYS
Chi-restraints excluded: chain A residue  383 ASN
Chi-restraints excluded: chain A residue  405 LEU
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  817 VAL
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:    3.9990
   chunk 47 optimal weight:    5.9990
   chunk 40 optimal weight:    6.9990
   chunk 75 optimal weight:    8.9990
   chunk 79 optimal weight:    9.9990
   chunk 22 optimal weight:    8.9990
   chunk 88 optimal weight:   10.0000
   chunk 10 optimal weight:    9.9990
   chunk 16 optimal weight:    6.9990
   chunk 100 optimal weight:   40.0000
   chunk 36 optimal weight:   10.0000
   overall best weight:    6.5990

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
A 222 ASN
** A 401 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
A 675 ASN
A 772 GLN
** A1117 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3678 r_free = 0.3678 target = 0.077993 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 42)----------------|
| r_work = 0.3156 r_free = 0.3156 target = 0.057315 restraints weight = 135650.357|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 33)----------------|
| r_work = 0.3225 r_free = 0.3225 target = 0.060094 restraints weight = 61354.998|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 37)----------------|
| r_work = 0.3269 r_free = 0.3269 target = 0.061863 restraints weight = 38591.860|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 42)----------------|
| r_work = 0.3295 r_free = 0.3295 target = 0.062942 restraints weight = 29026.883|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 40)----------------|
| r_work = 0.3311 r_free = 0.3311 target = 0.063636 restraints weight = 24416.982|
|-----------------------------------------------------------------------------|
r_work (final): 0.3298
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7653
moved from start:          0.2479

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.006   0.080   9891  Z= 0.321
  Angle     :  0.708   7.474  13683  Z= 0.415
  Chirality :  0.042   0.260   1572
  Planarity :  0.005   0.069   1458
  Dihedral  : 21.835 178.864   2255
  Min Nonbonded Distance : 2.282

Molprobity Statistics.
  All-atom Clashscore : 17.44
  Ramachandran Plot:
    Outliers :  0.32 %
    Allowed  :  8.51 %
    Favored  : 91.18 %
  Rotamer:
    Outliers :  2.19 %
    Allowed  : 10.61 %
    Favored  : 87.20 %
  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: -1.19 (0.26), residues: 952
  helix:  0.11 (0.24), residues: 424
  sheet: -0.29 (0.53), residues: 99
  loop : -1.84 (0.28), residues: 429

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.001   ARG A 441 
 TYR   0.015   0.002   TYR A 783 
 PHE   0.018   0.002   PHE A1062 
 TRP   0.011   0.002   TRP A 897 
 HIS   0.006   0.002   HIS A1117 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00627 /  0.32 ( 9891)
  covalent geometry    : angle       0.70829 /  0.42 (13683)
  hydrogen bonds       : bond        0.06617 /  4.35 (  456)
  hydrogen bonds       : angle       5.39195 /  3.75 ( 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
  91 residues out of total 867 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 72
  time to evaluate  : 0.312 
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    1 MET cc_start: 0.8737 (mtm) cc_final: 0.8499 (ptt)
REVERT: A  369 LYS cc_start: 0.9616 (mtpm) cc_final: 0.9245 (mttm)
REVERT: A  679 LYS cc_start: 0.9087 (mttp) cc_final: 0.8819 (mmtt)
REVERT: A  694 ASP cc_start: 0.9456 (t0) cc_final: 0.9136 (m-30)
  outliers start: 19
  outliers final: 16
  residues processed: 83
  average time/residue: 0.2231
  time to fit residues: 25.4305
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  : 0.513 
-------------------------------------------------------------------------------
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  375 GLN
Chi-restraints excluded: chain A residue  383 ASN
Chi-restraints excluded: chain A residue  405 LEU
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  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  817 VAL
Chi-restraints excluded: chain A residue  828 VAL
Chi-restraints excluded: chain A residue  997 ILE
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:    9.9990
   chunk 88 optimal weight:    6.9990
   chunk 23 optimal weight:    7.9990
   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:   20.0000
   overall best weight:    4.3990

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
** A 401 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** A1117 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 = 0.3682 r_free = 0.3682 target = 0.078635 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 45)----------------|
| r_work = 0.3164 r_free = 0.3164 target = 0.057911 restraints weight = 134615.074|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 48)----------------|
| r_work = 0.3234 r_free = 0.3234 target = 0.060695 restraints weight = 60003.164|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 39)----------------|
| r_work = 0.3276 r_free = 0.3276 target = 0.062402 restraints weight = 37785.490|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 37)----------------|
| r_work = 0.3303 r_free = 0.3303 target = 0.063517 restraints weight = 28730.560|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 39)----------------|
| r_work = 0.3319 r_free = 0.3319 target = 0.064189 restraints weight = 24106.096|
|-----------------------------------------------------------------------------|
r_work (final): 0.3305
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7624
moved from start:          0.2665

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.037   9891  Z= 0.216
  Angle     :  0.625   7.420  13683  Z= 0.371
  Chirality :  0.040   0.241   1572
  Planarity :  0.004   0.060   1458
  Dihedral  : 21.791 177.109   2255
  Min Nonbonded Distance : 2.344

Molprobity Statistics.
  All-atom Clashscore : 13.24
  Ramachandran Plot:
    Outliers :  0.32 %
    Allowed  :  7.77 %
    Favored  : 91.91 %
  Rotamer:
    Outliers :  2.19 %
    Allowed  : 11.19 %
    Favored  : 86.62 %
  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: -0.99 (0.26), residues: 952
  helix:  0.34 (0.24), residues: 423
  sheet: -0.17 (0.56), residues: 93
  loop : -1.79 (0.28), residues: 436

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.001   ARG A 658 
 TYR   0.016   0.002   TYR A 783 
 PHE   0.014   0.002   PHE A 465 
 TRP   0.016   0.002   TRP A 450 
 HIS   0.006   0.001   HIS A1117 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00419 /  0.22 ( 9891)
  covalent geometry    : angle       0.62550 /  0.37 (13683)
  hydrogen bonds       : bond        0.05769 /  3.78 (  456)
  hydrogen bonds       : angle       5.07930 /  3.53 ( 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
  92 residues out of total 867 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 73
  time to evaluate  : 0.394 
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  369 LYS cc_start: 0.9599 (mtpm) cc_final: 0.9165 (mttm)
REVERT: A  679 LYS cc_start: 0.9071 (mttp) cc_final: 0.8799 (mmtt)
  outliers start: 19
  outliers final: 18
  residues processed: 82
  average time/residue: 0.2286
  time to fit residues: 26.0555
Evaluate side-chains
  89 residues out of total 867 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 71
  time to evaluate  : 0.472 
-------------------------------------------------------------------------------
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  375 GLN
Chi-restraints excluded: chain A residue  383 ASN
Chi-restraints excluded: chain A residue  394 TYR
Chi-restraints excluded: chain A residue  405 LEU
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  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  817 VAL
Chi-restraints excluded: chain A residue  828 VAL
Chi-restraints excluded: chain A residue  942 GLU
Chi-restraints excluded: chain A residue  997 ILE
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 103
   random chunks:
   chunk 55 optimal weight:    1.9990
   chunk 95 optimal weight:    5.9990
   chunk 93 optimal weight:    7.9990
   chunk 33 optimal weight:    3.9990
   chunk 15 optimal weight:    5.9990
   chunk 47 optimal weight:    5.9990
   chunk 77 optimal weight:    6.9990
   chunk 25 optimal weight:    6.9990
   chunk 60 optimal weight:    5.9990
   chunk 76 optimal weight:    5.9990
   chunk 50 optimal weight:    9.9990
   overall best weight:    4.7990

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
** A 401 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
A 697 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3670 r_free = 0.3670 target = 0.077846 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 47)----------------|
| r_work = 0.3151 r_free = 0.3151 target = 0.057275 restraints weight = 135803.147|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 37)----------------|
| r_work = 0.3221 r_free = 0.3221 target = 0.060017 restraints weight = 60761.788|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 39)----------------|
| r_work = 0.3265 r_free = 0.3265 target = 0.061752 restraints weight = 38176.965|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 48)----------------|
| r_work = 0.3291 r_free = 0.3291 target = 0.062828 restraints weight = 28859.567|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 40)----------------|
| r_work = 0.3307 r_free = 0.3307 target = 0.063472 restraints weight = 24265.955|
|-----------------------------------------------------------------------------|
r_work (final): 0.3291
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7653
moved from start:          0.2942

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.042   9891  Z= 0.258
  Angle     :  0.657   7.485  13683  Z= 0.385
  Chirality :  0.040   0.245   1572
  Planarity :  0.004   0.053   1458
  Dihedral  : 21.845 175.374   2255
  Min Nonbonded Distance : 2.352

Molprobity Statistics.
  All-atom Clashscore : 14.77
  Ramachandran Plot:
    Outliers :  0.32 %
    Allowed  :  8.82 %
    Favored  : 90.86 %
  Rotamer:
    Outliers :  2.19 %
    Allowed  : 11.65 %
    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: -1.12 (0.26), residues: 952
  helix:  0.25 (0.24), residues: 425
  sheet: -0.17 (0.53), residues: 95
  loop : -1.92 (0.28), residues: 432

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.008   0.001   ARG A 441 
 TYR   0.019   0.002   TYR A 783 
 PHE   0.018   0.002   PHE A1062 
 TRP   0.017   0.002   TRP A 450 
 HIS   0.007   0.002   HIS A1117 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00507 /  0.26 ( 9891)
  covalent geometry    : angle       0.65713 /  0.39 (13683)
  hydrogen bonds       : bond        0.05731 /  3.73 (  456)
  hydrogen bonds       : angle       5.08317 /  3.53 ( 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
  92 residues out of total 867 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 73
  time to evaluate  : 0.334 
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: A  369 LYS cc_start: 0.9603 (mtpm) cc_final: 0.9154 (mttm)
REVERT: A  679 LYS cc_start: 0.9081 (mttp) cc_final: 0.8809 (mmtt)
REVERT: A  694 ASP cc_start: 0.9462 (t0) cc_final: 0.9180 (m-30)
  outliers start: 19
  outliers final: 19
  residues processed: 81
  average time/residue: 0.2090
  time to fit residues: 23.3130
Evaluate side-chains
  90 residues out of total 867 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 71
  time to evaluate  : 0.400 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   22 ILE
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  375 GLN
Chi-restraints excluded: chain A residue  383 ASN
Chi-restraints excluded: chain A residue  394 TYR
Chi-restraints excluded: chain A residue  405 LEU
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  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  817 VAL
Chi-restraints excluded: chain A residue  828 VAL
Chi-restraints excluded: chain A residue  942 GLU
Chi-restraints excluded: chain A residue  997 ILE
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 103
   random chunks:
   chunk 90 optimal weight:    0.9990
   chunk 0 optimal weight:    7.9990
   chunk 83 optimal weight:    9.9990
   chunk 74 optimal weight:    7.9990
   chunk 71 optimal weight:    9.9990
   chunk 19 optimal weight:    6.9990
   chunk 63 optimal weight:    2.9990
   chunk 65 optimal weight:    7.9990
   chunk 82 optimal weight:    0.7980
   chunk 3 optimal weight:    6.9990
   chunk 77 optimal weight:    0.8980
   overall best weight:    2.5386

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
** 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 = 0.3692 r_free = 0.3692 target = 0.079230 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 44)----------------|
| r_work = 0.3178 r_free = 0.3178 target = 0.058383 restraints weight = 133325.777|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 30)----------------|
| r_work = 0.3249 r_free = 0.3249 target = 0.061268 restraints weight = 58923.902|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 37)----------------|
| r_work = 0.3293 r_free = 0.3293 target = 0.063030 restraints weight = 36639.246|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 37)----------------|
| r_work = 0.3320 r_free = 0.3320 target = 0.064140 restraints weight = 27642.467|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 48)----------------|
| r_work = 0.3336 r_free = 0.3336 target = 0.064797 restraints weight = 23150.972|
|-----------------------------------------------------------------------------|
r_work (final): 0.3320
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7600
moved from start:          0.3007

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.038   9891  Z= 0.151
  Angle     :  0.590   7.574  13683  Z= 0.346
  Chirality :  0.039   0.226   1572
  Planarity :  0.004   0.049   1458
  Dihedral  : 21.755 173.501   2255
  Min Nonbonded Distance : 2.374

Molprobity Statistics.
  All-atom Clashscore : 11.44
  Ramachandran Plot:
    Outliers :  0.32 %
    Allowed  :  7.25 %
    Favored  : 92.44 %
  Rotamer:
    Outliers :  2.31 %
    Allowed  : 12.00 %
    Favored  : 85.70 %
  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: -0.74 (0.27), residues: 952
  helix:  0.61 (0.25), residues: 426
  sheet:  0.07 (0.56), residues: 92
  loop : -1.78 (0.28), residues: 434

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.001   ARG A 658 
 TYR   0.018   0.001   TYR A 783 
 PHE   0.012   0.001   PHE A 465 
 TRP   0.018   0.002   TRP A 450 
 HIS   0.006   0.001   HIS A1117 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00296 /  0.15 ( 9891)
  covalent geometry    : angle       0.58957 /  0.35 (13683)
  hydrogen bonds       : bond        0.05120 /  3.33 (  456)
  hydrogen bonds       : angle       4.75187 /  3.30 ( 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
  93 residues out of total 867 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 73
  time to evaluate  : 0.338 
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: 0.8950 (OUTLIER) cc_final: 0.8571 (p90)
REVERT: A  369 LYS cc_start: 0.9584 (mtpm) cc_final: 0.9109 (mttm)
REVERT: A  679 LYS cc_start: 0.9066 (mttp) cc_final: 0.8792 (mmtt)
REVERT: A  694 ASP cc_start: 0.9453 (t0) cc_final: 0.9164 (m-30)
  outliers start: 20
  outliers final: 17
  residues processed: 82
  average time/residue: 0.2251
  time to fit residues: 25.3186
Evaluate side-chains
  89 residues out of total 867 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 71
  time to evaluate  : 0.371 
-------------------------------------------------------------------------------
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  394 TYR
Chi-restraints excluded: chain A residue  405 LEU
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  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  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=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 103
   random chunks:
   chunk 53 optimal weight:    5.9990
   chunk 29 optimal weight:    4.9990
   chunk 41 optimal weight:    2.9990
   chunk 42 optimal weight:    4.9990
   chunk 58 optimal weight:    2.9990
   chunk 86 optimal weight:    1.9990
   chunk 26 optimal weight:    7.9990
   chunk 93 optimal weight:    0.8980
   chunk 98 optimal weight:   10.0000
   chunk 40 optimal weight:    0.8980
   chunk 2 optimal weight:    0.9980
   overall best weight:    1.5584

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
** 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 = 0.3709 r_free = 0.3709 target = 0.080025 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 43)----------------|
| r_work = 0.3203 r_free = 0.3203 target = 0.059344 restraints weight = 132762.180|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 48)----------------|
| r_work = 0.3274 r_free = 0.3274 target = 0.062239 restraints weight = 58493.958|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 42)----------------|
| r_work = 0.3318 r_free = 0.3318 target = 0.064048 restraints weight = 36290.512|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 38)----------------|
| r_work = 0.3346 r_free = 0.3346 target = 0.065166 restraints weight = 27246.401|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 49)----------------|
| r_work = 0.3362 r_free = 0.3362 target = 0.065862 restraints weight = 22771.185|
|-----------------------------------------------------------------------------|
r_work (final): 0.3347
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7568
moved from start:          0.3111

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.037   9891  Z= 0.124
  Angle     :  0.565   7.821  13683  Z= 0.330
  Chirality :  0.039   0.223   1572
  Planarity :  0.004   0.066   1458
  Dihedral  : 21.667 171.432   2255
  Min Nonbonded Distance : 2.384

Molprobity Statistics.
  All-atom Clashscore : 9.10
  Ramachandran Plot:
    Outliers :  0.32 %
    Allowed  :  6.62 %
    Favored  : 93.07 %
  Rotamer:
    Outliers :  1.96 %
    Allowed  : 12.23 %
    Favored  : 85.81 %
  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 (0.27), residues: 952
  helix:  0.97 (0.25), residues: 425
  sheet:  0.13 (0.53), residues: 98
  loop : -1.62 (0.29), residues: 429

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.001   ARG A 569 
 TYR   0.021   0.001   TYR A 783 
 PHE   0.026   0.001   PHE A 247 
 TRP   0.022   0.002   TRP A 450 
 HIS   0.005   0.001   HIS A1117 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00244 /  0.12 ( 9891)
  covalent geometry    : angle       0.56479 /  0.33 (13683)
  hydrogen bonds       : bond        0.04684 /  3.07 (  456)
  hydrogen bonds       : angle       4.51091 /  3.13 ( 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
  89 residues out of total 867 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 72
  time to evaluate  : 0.355 
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  336 PHE cc_start: 0.8964 (OUTLIER) cc_final: 0.8591 (p90)
REVERT: A  679 LYS cc_start: 0.9014 (mttp) cc_final: 0.8727 (mmtt)
REVERT: A  694 ASP cc_start: 0.9435 (t0) cc_final: 0.9112 (m-30)
  outliers start: 17
  outliers final: 15
  residues processed: 79
  average time/residue: 0.2183
  time to fit residues: 23.9748
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  : 0.329 
-------------------------------------------------------------------------------
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  363 LYS
Chi-restraints excluded: chain A residue  375 GLN
Chi-restraints excluded: chain A residue  394 TYR
Chi-restraints excluded: chain A residue  405 LEU
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  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
Chi-restraints excluded: chain A residue 1058 LEU
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 103
   random chunks:
   chunk 23 optimal weight:    7.9990
   chunk 22 optimal weight:    9.9990
   chunk 40 optimal weight:    4.9990
   chunk 24 optimal weight:    0.9990
   chunk 76 optimal weight:    4.9990
   chunk 43 optimal weight:    7.9990
   chunk 68 optimal weight:    2.9990
   chunk 96 optimal weight:    9.9990
   chunk 59 optimal weight:    4.9990
   chunk 94 optimal weight:    5.9990
   chunk 63 optimal weight:    3.9990
   overall best weight:    3.5990

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
** 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 = 0.3689 r_free = 0.3689 target = 0.078931 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 43)----------------|
| r_work = 0.3179 r_free = 0.3179 target = 0.058359 restraints weight = 132631.667|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 49)----------------|
| r_work = 0.3250 r_free = 0.3250 target = 0.061204 restraints weight = 58568.408|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 46)----------------|
| r_work = 0.3294 r_free = 0.3294 target = 0.062992 restraints weight = 36237.962|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 40)----------------|
| r_work = 0.3321 r_free = 0.3321 target = 0.064099 restraints weight = 27071.067|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 21)----------------|
| r_work = 0.3333 r_free = 0.3333 target = 0.064640 restraints weight = 22573.280|
|-----------------------------------------------------------------------------|
r_work (final): 0.3318
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7609
moved from start:          0.3237

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.035   9891  Z= 0.190
  Angle     :  0.585   7.839  13683  Z= 0.342
  Chirality :  0.038   0.226   1572
  Planarity :  0.004   0.039   1458
  Dihedral  : 21.704 171.826   2255
  Min Nonbonded Distance : 2.384

Molprobity Statistics.
  All-atom Clashscore : 11.93
  Ramachandran Plot:
    Outliers :  0.32 %
    Allowed  :  7.25 %
    Favored  : 92.44 %
  Rotamer:
    Outliers :  1.96 %
    Allowed  : 12.46 %
    Favored  : 85.58 %
  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: -0.54 (0.27), residues: 952
  helix:  0.83 (0.25), residues: 427
  sheet: -0.01 (0.52), residues: 98
  loop : -1.71 (0.29), residues: 427

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.001   ARG A 441 
 TYR   0.019   0.001   TYR A 783 
 PHE   0.019   0.001   PHE A 247 
 TRP   0.022   0.002   TRP A 450 
 HIS   0.006   0.001   HIS A1117 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00372 /  0.19 ( 9891)
  covalent geometry    : angle       0.58508 /  0.34 (13683)
  hydrogen bonds       : bond        0.04927 /  3.19 (  456)
  hydrogen bonds       : angle       4.64690 /  3.22 ( 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: 17
    poor density    : 67
  time to evaluate  : 0.414 
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: A  336 PHE cc_start: 0.8955 (OUTLIER) cc_final: 0.8536 (p90)
REVERT: A  369 LYS cc_start: 0.9588 (mtpm) cc_final: 0.9201 (mtpp)
REVERT: A  679 LYS cc_start: 0.9035 (mttp) cc_final: 0.8788 (mmtt)
REVERT: A  694 ASP cc_start: 0.9454 (t0) cc_final: 0.9171 (m-30)
  outliers start: 17
  outliers final: 14
  residues processed: 75
  average time/residue: 0.2196
  time to fit residues: 22.3489
Evaluate side-chains
  81 residues out of total 867 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 66
  time to evaluate  : 0.454 
-------------------------------------------------------------------------------
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  363 LYS
Chi-restraints excluded: chain A residue  375 GLN
Chi-restraints excluded: chain A residue  394 TYR
Chi-restraints excluded: chain A residue  405 LEU
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  669 THR
Chi-restraints excluded: chain A residue  684 MET
Chi-restraints excluded: chain A residue  689 PHE
Chi-restraints excluded: chain A residue  828 VAL
Chi-restraints excluded: chain A residue  942 GLU
Chi-restraints excluded: chain A residue  997 ILE
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 103
   random chunks:
   chunk 55 optimal weight:    0.9980
   chunk 16 optimal weight:    7.9990
   chunk 24 optimal weight:    3.9990
   chunk 39 optimal weight:    8.9990
   chunk 5 optimal weight:    0.9980
   chunk 94 optimal weight:    3.9990
   chunk 13 optimal weight:    2.9990
   chunk 14 optimal weight:    3.9990
   chunk 48 optimal weight:    7.9990
   chunk 6 optimal weight:    5.9990
   chunk 25 optimal weight:    3.9990
   overall best weight:    2.5986

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
** 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 = 0.3699 r_free = 0.3699 target = 0.079425 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 42)----------------|
| r_work = 0.3190 r_free = 0.3190 target = 0.058811 restraints weight = 131302.010|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 42)----------------|
| r_work = 0.3262 r_free = 0.3262 target = 0.061677 restraints weight = 57993.414|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 42)----------------|
| r_work = 0.3306 r_free = 0.3306 target = 0.063474 restraints weight = 35920.614|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 33)----------------|
| r_work = 0.3331 r_free = 0.3331 target = 0.064553 restraints weight = 26789.388|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 34)----------------|
| r_work = 0.3349 r_free = 0.3349 target = 0.065265 restraints weight = 22479.338|
|-----------------------------------------------------------------------------|
r_work (final): 0.3334
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7589
moved from start:          0.3283

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.041   9891  Z= 0.147
  Angle     :  0.569   7.821  13683  Z= 0.332
  Chirality :  0.038   0.217   1572
  Planarity :  0.004   0.041   1458
  Dihedral  : 21.690 171.059   2255
  Min Nonbonded Distance : 2.388

Molprobity Statistics.
  All-atom Clashscore : 9.97
  Ramachandran Plot:
    Outliers :  0.21 %
    Allowed  :  7.14 %
    Favored  : 92.65 %
  Rotamer:
    Outliers :  1.73 %
    Allowed  : 13.03 %
    Favored  : 85.24 %
  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: -0.46 (0.27), residues: 952
  helix:  0.89 (0.25), residues: 426
  sheet:  0.09 (0.52), residues: 98
  loop : -1.69 (0.29), residues: 428

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.001   ARG A 658 
 TYR   0.020   0.001   TYR A 783 
 PHE   0.017   0.001   PHE A 247 
 TRP   0.023   0.002   TRP A 450 
 HIS   0.006   0.001   HIS A1117 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00291 /  0.15 ( 9891)
  covalent geometry    : angle       0.56933 /  0.33 (13683)
  hydrogen bonds       : bond        0.04697 /  3.04 (  456)
  hydrogen bonds       : angle       4.53320 /  3.15 ( 1172)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 2787.46 seconds
wall clock time: 48 minutes 25.57 seconds (2905.57 seconds total)