Starting phenix.real_space_refine
on Wed Mar  4 09:11:32 2026 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/7mez_23808/03_2026/7mez_23808.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/7mez_23808/03_2026/7mez_23808.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=2.89
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    model {
      file = "/net/cci-nas-00/data/ceres_data/7mez_23808/03_2026/7mez_23808.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/7mez_23808/03_2026/7mez_23808.cif"
    real_map_files = "/net/cci-nas-00/data/ceres_data/7mez_23808/03_2026/7mez_23808.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/7mez_23808/03_2026/7mez_23808.map"
  }
  resolution = 2.89
  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=  -0.002 sd=   0.135
Set stop_for_unknowns flag
  Set to: True
Assert model is a single copy model
Assert all atoms have isotropic ADPs
Construct map_model_manager
Extract box with map and model
Check model and map are aligned
Set scattering table
  Set to: electron
  Number of scattering types: 4
    Type Number    sf(0)   Gaussians
     S      57      5.16       5
     C    7923      2.51       5
     N    2130      2.21       5
     O    2251      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 12 residue(s): 0.01s

  Monomer Library directory:
    "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/chem_data/mon_lib"
  Total number of atoms: 12361
  Number of models: 1
  Model: ""
    Number of chains: 2
    Chain: "A"
      Number of atoms: 8046
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 989, 8046
          Classifications: {'peptide': 989}
          Link IDs: {'PTRANS': 46, 'TRANS': 942}
          Chain breaks: 5
    Chain: "B"
      Number of atoms: 4315
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 547, 4315
          Classifications: {'peptide': 547}
          Link IDs: {'PTRANS': 27, 'TRANS': 519}
          Chain breaks: 5
  Time building chain proxies: 2.36, per 1000 atoms: 0.19
  Number of scatterers: 12361
  At special positions: 0
  Unit cell: (90.015, 108.018, 149.319, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 4
    Type Number    sf(0)
     S      57     16.00
     O    2251      8.00
     N    2130      7.00
     C    7923      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=0, symmetry=0

  Automatic linking
    Parameters for automatic linking
      Linking & cutoffs
        Metal                : Auto  - 3.00
        Amino acid           : True  - 1.90
        Carbohydrate         : True  - 1.99
        Ligands              : True  - 1.99
        Small molecules      : False - 1.98
        Amino acid - RNA/DNA : False
      
  Number of custom bonds: simple=0, symmetry=0
  Time building additional restraints: 1.01
  Conformation dependent library (CDL) restraints added in 567.0 milliseconds
  

  3024 Ramachandran restraints generated.
    1512 Oldfield, 0 Emsley, 1512 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  2920

  Finding SS restraints...
    Secondary structure from input PDB file:
      67 helices and 12 sheets defined
      50.4% alpha, 15.0% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.49
  Creating SS restraints...
    Processing helix  chain 'A' and resid 69 through 82
    Processing helix  chain 'A' and resid 82 through 90
      removed outlier: 4.082A  pdb=" N   ARG A  90 " --> pdb=" O   ASP A  86 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 114 through 117
    Processing helix  chain 'A' and resid 118 through 129
      removed outlier: 3.654A  pdb=" N   LEU A 122 " --> pdb=" O   THR A 118 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 144 through 159
    Processing helix  chain 'A' and resid 171 through 180
    Processing helix  chain 'A' and resid 180 through 190
    Processing helix  chain 'A' and resid 192 through 199
    Processing helix  chain 'A' and resid 208 through 213
    Processing helix  chain 'A' and resid 240 through 251
    Processing helix  chain 'A' and resid 286 through 289
    Processing helix  chain 'A' and resid 290 through 299
    Processing helix  chain 'A' and resid 312 through 317
    Processing helix  chain 'A' and resid 335 through 340
    Processing helix  chain 'A' and resid 355 through 357
      No H-bonds generated for 'chain 'A' and resid 355 through 357'
    Processing helix  chain 'A' and resid 421 through 423
      No H-bonds generated for 'chain 'A' and resid 421 through 423'
    Processing helix  chain 'A' and resid 498 through 503
      removed outlier: 3.767A  pdb=" N   THR A 503 " --> pdb=" O   ASP A 500 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 548 through 561
    Processing helix  chain 'A' and resid 568 through 578
    Processing helix  chain 'A' and resid 578 through 583
    Processing helix  chain 'A' and resid 584 through 587
      removed outlier: 6.593A  pdb=" N   LYS A 587 " --> pdb=" O   LYS A 584 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'A' and resid 584 through 587'
    Processing helix  chain 'A' and resid 588 through 595
    Processing helix  chain 'A' and resid 600 through 613
      removed outlier: 3.815A  pdb=" N   ARG A 613 " --> pdb=" O   GLN A 609 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 623 through 631
    Processing helix  chain 'A' and resid 637 through 649
    Processing helix  chain 'A' and resid 652 through 667
      removed outlier: 5.294A  pdb=" N   LEU A 661 " --> pdb=" O   LEU A 657 " (cutoff:3.500A)
      removed outlier: 5.817A  pdb=" N   GLN A 662 " --> pdb=" O   HIS A 658 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 668 through 670
      No H-bonds generated for 'chain 'A' and resid 668 through 670'
    Processing helix  chain 'A' and resid 675 through 688
      removed outlier: 3.562A  pdb=" N   ASN A 688 " --> pdb=" O   ARG A 684 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 688 through 706
      removed outlier: 3.576A  pdb=" N   GLU A 702 " --> pdb=" O   PHE A 698 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 709 through 724
    Processing helix  chain 'A' and resid 725 through 752
      removed outlier: 3.800A  pdb=" N   LEU A 752 " --> pdb=" O   ASP A 748 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 766 through 776
    Processing helix  chain 'A' and resid 798 through 801
    Processing helix  chain 'A' and resid 838 through 858
    Processing helix  chain 'A' and resid 888 through 896
      removed outlier: 4.142A  pdb=" N   THR A 895 " --> pdb=" O   ILE A 891 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 905 through 914
    Processing helix  chain 'A' and resid 917 through 943
    Processing helix  chain 'A' and resid 948 through 950
      No H-bonds generated for 'chain 'A' and resid 948 through 950'
    Processing helix  chain 'A' and resid 964 through 976
      removed outlier: 3.906A  pdb=" N   ILE A 968 " --> pdb=" O   ASP A 964 " (cutoff:3.500A)
      removed outlier: 3.579A  pdb=" N   GLY A 970 " --> pdb=" O   GLY A 966 " (cutoff:3.500A)
      removed outlier: 3.917A  pdb=" N   ASN A 971 " --> pdb=" O   HIS A 967 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 988 through 996
    Processing helix  chain 'A' and resid 1003 through 1023
      removed outlier: 3.643A  pdb=" N   HIS A1023 " --> pdb=" O   ALA A1019 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1023 through 1039
      removed outlier: 3.929A  pdb=" N   MET A1039 " --> pdb=" O   LEU A1035 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1049 through 1055
    Processing helix  chain 'A' and resid 1060 through 1078
    Processing helix  chain 'A' and resid 1080 through 1091
    Processing helix  chain 'B' and resid 12 through 22
    Processing helix  chain 'B' and resid 42 through 49
      removed outlier: 4.037A  pdb=" N   SER B  49 " --> pdb=" O   GLN B  45 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 51 through 73
      removed outlier: 3.803A  pdb=" N   PHE B  55 " --> pdb=" O   ASP B  51 " (cutoff:3.500A)
      removed outlier: 3.982A  pdb=" N   LEU B  56 " --> pdb=" O   PRO B  52 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 77 through 92
    Processing helix  chain 'B' and resid 100 through 111
    Processing helix  chain 'B' and resid 112 through 115
    Processing helix  chain 'B' and resid 116 through 136
      removed outlier: 3.993A  pdb=" N   ILE B 122 " --> pdb=" O   PRO B 118 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 138 through 150
    Processing helix  chain 'B' and resid 172 through 184
    Processing helix  chain 'B' and resid 188 through 205
      removed outlier: 3.845A  pdb=" N   THR B 204 " --> pdb=" O   ALA B 200 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 210 through 220
      removed outlier: 3.953A  pdb=" N   SER B 220 " --> pdb=" O   ARG B 216 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 222 through 241
    Processing helix  chain 'B' and resid 245 through 265
    Processing helix  chain 'B' and resid 299 through 310
      removed outlier: 3.772A  pdb=" N   GLU B 303 " --> pdb=" O   ASP B 299 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 522 through 524
      No H-bonds generated for 'chain 'B' and resid 522 through 524'
    Processing helix  chain 'B' and resid 525 through 540
    Processing helix  chain 'B' and resid 543 through 548
      removed outlier: 3.675A  pdb=" N   THR B 547 " --> pdb=" O   ARG B 543 " (cutoff:3.500A)
      removed outlier: 3.665A  pdb=" N   ARG B 548 " --> pdb=" O   PRO B 544 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'B' and resid 543 through 548'
    Processing helix  chain 'B' and resid 605 through 613
    Processing helix  chain 'B' and resid 613 through 620
    Processing helix  chain 'B' and resid 652 through 663
    Processing helix  chain 'B' and resid 696 through 707
    Processing helix  chain 'B' and resid 757 through 763
      removed outlier: 3.753A  pdb=" N   GLN B 760 " --> pdb=" O   CYS B 757 " (cutoff:3.500A)
      removed outlier: 5.675A  pdb=" N   GLU B 761 " --> pdb=" O   ARG B 758 " (cutoff:3.500A)
      removed outlier: 3.552A  pdb=" N   GLU B 762 " --> pdb=" O   GLN B 759 " (cutoff:3.500A)
    Processing sheet with id=AA1, first strand: chain 'A' and resid 55 through 58
      removed outlier: 4.248A  pdb=" N   GLU A  55 " --> pdb=" O   LEU A  44 " (cutoff:3.500A)
      removed outlier: 6.634A  pdb=" N   GLU A  41 " --> pdb=" O   ILE A 135 " (cutoff:3.500A)
      removed outlier: 7.521A  pdb=" N   LEU A 137 " --> pdb=" O   GLU A  41 " (cutoff:3.500A)
      removed outlier: 6.457A  pdb=" N   VAL A  43 " --> pdb=" O   LEU A 137 " (cutoff:3.500A)
      removed outlier: 8.279A  pdb=" N   GLN A 139 " --> pdb=" O   VAL A  43 " (cutoff:3.500A)
      removed outlier: 8.458A  pdb=" N   GLN A 134 " --> pdb=" O   GLN A 101 " (cutoff:3.500A)
      removed outlier: 5.451A  pdb=" N   GLN A 101 " --> pdb=" O   GLN A 134 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'A' and resid 229 through 235
      removed outlier: 4.390A  pdb=" N   ILE A 303 " --> pdb=" O   PHE A 221 " (cutoff:3.500A)
      removed outlier: 4.458A  pdb=" N   LEU A 272 " --> pdb=" O   LEU A 281 " (cutoff:3.500A)
    Processing sheet with id=AA3, first strand: chain 'A' and resid 352 through 353
      removed outlier: 6.112A  pdb=" N   VAL A 352 " --> pdb=" O   ALA A 528 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AA3
    Processing sheet with id=AA4, first strand: chain 'A' and resid 407 through 419
      removed outlier: 7.547A  pdb=" N   VAL A 408 " --> pdb=" O   ASP A 369 " (cutoff:3.500A)
      removed outlier: 5.499A  pdb=" N   ASP A 369 " --> pdb=" O   VAL A 408 " (cutoff:3.500A)
      removed outlier: 6.666A  pdb=" N   TRP A 410 " --> pdb=" O   GLY A 367 " (cutoff:3.500A)
      removed outlier: 7.007A  pdb=" N   GLY A 367 " --> pdb=" O   TRP A 410 " (cutoff:3.500A)
      removed outlier: 4.339A  pdb=" N   PHE A 361 " --> pdb=" O   PHE A 416 " (cutoff:3.500A)
      removed outlier: 6.705A  pdb=" N   SER A 517 " --> pdb=" O   ARG A 366 " (cutoff:3.500A)
      removed outlier: 4.512A  pdb=" N   ILE A 368 " --> pdb=" O   SER A 515 " (cutoff:3.500A)
      removed outlier: 6.747A  pdb=" N   SER A 515 " --> pdb=" O   ILE A 368 " (cutoff:3.500A)
    Processing sheet with id=AA5, first strand: chain 'A' and resid 393 through 398
      removed outlier: 6.501A  pdb=" N   LEU A 429 " --> pdb=" O   ASN A 465 " (cutoff:3.500A)
      removed outlier: 4.345A  pdb=" N   ASN A 465 " --> pdb=" O   LEU A 429 " (cutoff:3.500A)
      removed outlier: 6.773A  pdb=" N   LEU A 431 " --> pdb=" O   TYR A 463 " (cutoff:3.500A)
      removed outlier: 4.333A  pdb=" N   TYR A 463 " --> pdb=" O   LEU A 431 " (cutoff:3.500A)
      removed outlier: 6.352A  pdb=" N   ILE A 433 " --> pdb=" O   LEU A 461 " (cutoff:3.500A)
    Processing sheet with id=AA6, first strand: chain 'A' and resid 783 through 785
      removed outlier: 5.804A  pdb=" N   LEU A 791 " --> pdb=" O   VAL A 785 " (cutoff:3.500A)
      removed outlier: 5.037A  pdb=" N   LYS A 816 " --> pdb=" O   GLY A 794 " (cutoff:3.500A)
      removed outlier: 5.194A  pdb=" N   LEU A 796 " --> pdb=" O   GLU A 814 " (cutoff:3.500A)
      removed outlier: 7.339A  pdb=" N   GLU A 814 " --> pdb=" O   LEU A 796 " (cutoff:3.500A)
    Processing sheet with id=AA7, first strand: chain 'A' and resid 783 through 785
      removed outlier: 5.804A  pdb=" N   LEU A 791 " --> pdb=" O   VAL A 785 " (cutoff:3.500A)
      removed outlier: 5.037A  pdb=" N   LYS A 816 " --> pdb=" O   GLY A 794 " (cutoff:3.500A)
      removed outlier: 5.194A  pdb=" N   LEU A 796 " --> pdb=" O   GLU A 814 " (cutoff:3.500A)
      removed outlier: 7.339A  pdb=" N   GLU A 814 " --> pdb=" O   LEU A 796 " (cutoff:3.500A)
      removed outlier: 6.653A  pdb=" N   ILE A 876 " --> pdb=" O   THR A 872 " (cutoff:3.500A)
    Processing sheet with id=AA8, first strand: chain 'A' and resid 885 through 887
    Processing sheet with id=AA9, first strand: chain 'B' and resid 288 through 290
      removed outlier: 8.400A  pdb=" N   TYR B 289 " --> pdb=" O   VAL B 161 " (cutoff:3.500A)
      removed outlier: 6.340A  pdb=" N   VAL B 163 " --> pdb=" O   TYR B 289 " (cutoff:3.500A)
      removed outlier: 6.539A  pdb=" N   THR B 162 " --> pdb=" O   ARG B 516 " (cutoff:3.500A)
      removed outlier: 7.572A  pdb=" N   VAL B 518 " --> pdb=" O   THR B 162 " (cutoff:3.500A)
      removed outlier: 6.606A  pdb=" N   LEU B 164 " --> pdb=" O   VAL B 518 " (cutoff:3.500A)
      removed outlier: 7.495A  pdb=" N   PHE B 520 " --> pdb=" O   LEU B 164 " (cutoff:3.500A)
      removed outlier: 6.818A  pdb=" N   LEU B 166 " --> pdb=" O   PHE B 520 " (cutoff:3.500A)
    Processing sheet with id=AB1, first strand: chain 'B' and resid 665 through 668
    Processing sheet with id=AB2, first strand: chain 'B' and resid 683 through 689
      removed outlier: 6.190A  pdb=" N   THR B 674 " --> pdb=" O   GLU B 686 " (cutoff:3.500A)
      removed outlier: 4.126A  pdb=" N   PHE B 688 " --> pdb=" O   TYR B 672 " (cutoff:3.500A)
      removed outlier: 6.695A  pdb=" N   TYR B 672 " --> pdb=" O   PHE B 688 " (cutoff:3.500A)
      removed outlier: 6.612A  pdb=" N   GLN B 673 " --> pdb=" O   VAL B 832 " (cutoff:3.500A)
      removed outlier: 4.349A  pdb=" N   VAL B 832 " --> pdb=" O   GLN B 673 " (cutoff:3.500A)
      removed outlier: 6.595A  pdb=" N   GLU B 675 " --> pdb=" O   CYS B 830 " (cutoff:3.500A)
      removed outlier: 4.452A  pdb=" N   CYS B 830 " --> pdb=" O   GLU B 675 " (cutoff:3.500A)
      removed outlier: 6.292A  pdb=" N   THR B 677 " --> pdb=" O   ILE B 828 " (cutoff:3.500A)
      removed outlier: 4.006A  pdb=" N   LYS B 801 " --> pdb=" O   SER B 731 " (cutoff:3.500A)
    Processing sheet with id=AB3, first strand: chain 'B' and resid 795 through 799

    621 hydrogen bonds defined for protein.
    1779 hydrogen bond angles defined for protein.
    Restraints generated for nucleic acids:
      0 hydrogen bonds
      0 hydrogen bond angles
      0 basepair planarities
      0 basepair parallelities
      0 stacking parallelities
  Total time for adding SS restraints: 2.17

  Time building geometry restraints manager: 1.40 seconds

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

  Histogram of bond lengths:
        1.22 -     1.34: 3968
        1.34 -     1.46: 1699
        1.46 -     1.57: 6891
        1.57 -     1.69: 0
        1.69 -     1.81: 81
  Bond restraints: 12639
  Sorted by residual:
  bond pdb=" N   ASP A 111 "
       pdb=" CA  ASP A 111 "
    ideal  model  delta    sigma   weight residual
    1.457  1.502 -0.044 1.29e-02 6.01e+03 1.17e+01
  bond pdb=" N   ARG A 472 "
       pdb=" CA  ARG A 472 "
    ideal  model  delta    sigma   weight residual
    1.456  1.481 -0.025 1.18e-02 7.18e+03 4.64e+00
  bond pdb=" N   LEU B 305 "
       pdb=" CA  LEU B 305 "
    ideal  model  delta    sigma   weight residual
    1.459  1.480 -0.020 1.19e-02 7.06e+03 2.88e+00
  bond pdb=" C   ARG A 472 "
       pdb=" O   ARG A 472 "
    ideal  model  delta    sigma   weight residual
    1.236  1.218  0.018 1.28e-02 6.10e+03 1.90e+00
  bond pdb=" C   ILE B 304 "
       pdb=" N   LEU B 305 "
    ideal  model  delta    sigma   weight residual
    1.334  1.350 -0.015 1.27e-02 6.20e+03 1.44e+00
  ... (remaining 12634 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     2.14: 16905
        2.14 -     4.27: 198
        4.27 -     6.41: 18
        6.41 -     8.55: 4
        8.55 -    10.69: 2
  Bond angle restraints: 17127
  Sorted by residual:
  angle pdb=" N   VAL B 269 "
        pdb=" CA  VAL B 269 "
        pdb=" C   VAL B 269 "
      ideal   model   delta    sigma   weight residual
     113.47  108.17    5.30 1.01e+00 9.80e-01 2.76e+01
  angle pdb=" N   LYS A 112 "
        pdb=" CA  LYS A 112 "
        pdb=" CB  LYS A 112 "
      ideal   model   delta    sigma   weight residual
     110.92  103.75    7.17 1.60e+00 3.91e-01 2.01e+01
  angle pdb=" N   GLY A 723 "
        pdb=" CA  GLY A 723 "
        pdb=" C   GLY A 723 "
      ideal   model   delta    sigma   weight residual
     112.49  116.42   -3.93 1.21e+00 6.83e-01 1.05e+01
  angle pdb=" N   GLU A 772 "
        pdb=" CA  GLU A 772 "
        pdb=" CB  GLU A 772 "
      ideal   model   delta    sigma   weight residual
     110.28  115.10   -4.82 1.55e+00 4.16e-01 9.67e+00
  angle pdb=" CA  LEU A 699 "
        pdb=" CB  LEU A 699 "
        pdb=" CG  LEU A 699 "
      ideal   model   delta    sigma   weight residual
     116.30  126.99  -10.69 3.50e+00 8.16e-02 9.32e+00
  ... (remaining 17122 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    17.65: 6933
       17.65 -    35.30: 579
       35.30 -    52.95: 81
       52.95 -    70.60: 16
       70.60 -    88.25: 10
  Dihedral angle restraints: 7619
    sinusoidal: 3128
      harmonic: 4491
  Sorted by residual:
  dihedral pdb=" CA  GLU A  68 "
           pdb=" C   GLU A  68 "
           pdb=" N   GLN A  69 "
           pdb=" CA  GLN A  69 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  150.75   29.25     0      5.00e+00 4.00e-02 3.42e+01
  dihedral pdb=" CA  HIS B  94 "
           pdb=" C   HIS B  94 "
           pdb=" N   PHE B  95 "
           pdb=" CA  PHE B  95 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  161.25   18.75     0      5.00e+00 4.00e-02 1.41e+01
  dihedral pdb=" CA  VAL A  67 "
           pdb=" C   VAL A  67 "
           pdb=" N   GLU A  68 "
           pdb=" CA  GLU A  68 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  162.26   17.74     0      5.00e+00 4.00e-02 1.26e+01
  ... (remaining 7616 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.039: 1366
       0.039 -    0.078: 403
       0.078 -    0.116: 141
       0.116 -    0.155: 20
       0.155 -    0.194: 2
  Chirality restraints: 1932
  Sorted by residual:
  chirality pdb=" CB  ILE A 368 "
            pdb=" CA  ILE A 368 "
            pdb=" CG1 ILE A 368 "
            pdb=" CG2 ILE A 368 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.64    2.45    0.19 2.00e-01 2.50e+01 9.42e-01
  chirality pdb=" CA  ILE B 729 "
            pdb=" N   ILE B 729 "
            pdb=" C   ILE B 729 "
            pdb=" CB  ILE B 729 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.43    2.61   -0.18 2.00e-01 2.50e+01 7.77e-01
  chirality pdb=" CA  THR A 182 "
            pdb=" N   THR A 182 "
            pdb=" C   THR A 182 "
            pdb=" CB  THR A 182 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.53    2.37    0.15 2.00e-01 2.50e+01 5.86e-01
  ... (remaining 1929 not shown)

  Planarity restraints: 2179
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  ILE B 304 "    0.020 2.00e-02 2.50e+03   3.85e-02 1.48e+01
        pdb=" C   ILE B 304 "   -0.067 2.00e-02 2.50e+03
        pdb=" O   ILE B 304 "    0.025 2.00e-02 2.50e+03
        pdb=" N   LEU B 305 "    0.022 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   THR A 988 "   -0.039 5.00e-02 4.00e+02   5.83e-02 5.43e+00
        pdb=" N   PRO A 989 "    0.101 5.00e-02 4.00e+02
        pdb=" CA  PRO A 989 "   -0.030 5.00e-02 4.00e+02
        pdb=" CD  PRO A 989 "   -0.032 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   LYS B 274 "   -0.032 5.00e-02 4.00e+02   4.81e-02 3.71e+00
        pdb=" N   PRO B 275 "    0.083 5.00e-02 4.00e+02
        pdb=" CA  PRO B 275 "   -0.025 5.00e-02 4.00e+02
        pdb=" CD  PRO B 275 "   -0.027 5.00e-02 4.00e+02
  ... (remaining 2176 not shown)

  Histogram of nonbonded interaction distances:
        2.19 -     2.73: 612
        2.73 -     3.27: 12420
        3.27 -     3.81: 20558
        3.81 -     4.36: 24737
        4.36 -     4.90: 42796
  Nonbonded interactions: 101123
  Sorted by model distance:
  nonbonded pdb=" OG  SER B 754 "
            pdb=" OG1 THR B 771 "
     model   vdw
     2.187 3.040
  nonbonded pdb=" OG  SER B 691 "
            pdb=" OD1 ASP B 817 "
     model   vdw
     2.201 3.040
  nonbonded pdb=" OG1 THR A 333 "
            pdb=" O   LEU A 529 "
     model   vdw
     2.224 3.040
  nonbonded pdb=" NH1 ARG B 537 "
            pdb=" O   LEU B 865 "
     model   vdw
     2.239 3.120
  nonbonded pdb=" NH1 ARG B 531 "
            pdb=" O   PHE B 688 "
     model   vdw
     2.240 3.120
  ... (remaining 101118 not shown)

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

  No NCS relation were found !!!

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

Found NCS groups:
  found none.
Set up NCS constraints
  No NCS constraints will be used in refinement.
Set refine NCS operators
Adjust number of macro_cycles
  Number of macro_cycles: 10
Reset NCS operators
Extract rigid body selections
Check and reset occupancies
  Occupancies: min=1.00 max=1.00 mean=1.00
Load rotamer database and sin/cos tables
Set ADP refinement strategy
  ADPs will be refined as individual isotropic
Make a string to write initial .geo file
Internal consistency checks
Time:
  Set random seed:                         0.000
  Set model cs if undefined:               0.000
  Decide on map wrapping:                  0.000
  Normalize map: mean=0, sd=1:             2.310
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.000
  Construct map_model_manager:             0.000
  Extract box with map and model:          0.200
  Check model and map are aligned:         0.030
  Set scattering table:                    0.030
  Process input model:                     12.110
  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:6.750
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   21.510
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7880
moved from start:          0.0000

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.044  12639  Z= 0.147
  Angle     :  0.564  10.685  17127  Z= 0.297
  Chirality :  0.042   0.194   1932
  Planarity :  0.004   0.058   2179
  Dihedral  : 13.142  88.251   4699
  Min Nonbonded Distance : 2.187

Molprobity Statistics.
  All-atom Clashscore : 8.96
  Ramachandran Plot:
    Outliers :  0.20 %
    Allowed  :  3.31 %
    Favored  : 96.49 %
  Rotamer:
    Outliers :  0.07 %
    Allowed  :  0.00 %
    Favored  : 99.93 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  0.61 (0.22), residues: 1512
  helix:  1.47 (0.20), residues: 687
  sheet: -0.35 (0.33), residues: 234
  loop : -0.46 (0.27), residues: 591

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.000   ARG A 123 
 TYR   0.017   0.001   TYR B 730 
 PHE   0.015   0.001   PHE B 298 
 TRP   0.017   0.001   TRP A 812 
 HIS   0.010   0.001   HIS A 346 

Details of bonding type rmsd
  covalent geometry    : bond        0.00326 (12639)
  covalent geometry    : angle       0.56365 (17127)
  hydrogen bonds       : bond        0.11386 (  617)
  hydrogen bonds       : angle       5.32018 ( 1779)

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

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

  3024 Ramachandran restraints generated.
    1512 Oldfield, 0 Emsley, 1512 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3024 Ramachandran restraints generated.
    1512 Oldfield, 0 Emsley, 1512 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  158 residues out of total 1365 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 157
  time to evaluate  : 0.464 
Fit side-chains
REVERT: B  655 MET cc_start: 0.7120 (mmt) cc_final: 0.6321 (mtp)
  outliers start: 1
  outliers final: 1
  residues processed: 158
  average time/residue: 0.6096
  time to fit residues: 104.3222
Evaluate side-chains
  111 residues out of total 1365 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 110
  time to evaluate  : 0.459 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  472 ARG
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 152
   random chunks:
   chunk 98 optimal weight:    3.9990
   chunk 107 optimal weight:    0.5980
   chunk 10 optimal weight:    0.7980
   chunk 66 optimal weight:    5.9990
   chunk 130 optimal weight:    2.9990
   chunk 124 optimal weight:    0.9980
   chunk 103 optimal weight:    1.9990
   chunk 77 optimal weight:    0.7980
   chunk 122 optimal weight:    7.9990
   chunk 91 optimal weight:    0.5980
   chunk 149 optimal weight:    0.7980
   overall best weight:    0.7180

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

Flipped N/Q/H residues before XYZ refinement:
A  73 GLN
** A 693 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 735 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 948 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 951 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A1060 ASN
** B  70 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 607 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
B 760 GLN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4025 r_free = 0.4025 target = 0.158868 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 61)----------------|
| r_work = 0.3462 r_free = 0.3462 target = 0.111524 restraints weight = 16591.174|
|-----------------------------------------------------------------------------|
r_work (start): 0.3425 rms_B_bonded: 2.35
r_work: 0.3309 rms_B_bonded: 2.79 restraints_weight: 0.5000
r_work: 0.3170 rms_B_bonded: 4.49 restraints_weight: 0.2500
r_work (final): 0.3170
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8039
moved from start:          0.0959

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.038  12639  Z= 0.139
  Angle     :  0.537   8.015  17127  Z= 0.276
  Chirality :  0.042   0.163   1932
  Planarity :  0.004   0.065   2179
  Dihedral  :  4.516  45.053   1658
  Min Nonbonded Distance : 2.570

Molprobity Statistics.
  All-atom Clashscore : 7.06
  Ramachandran Plot:
    Outliers :  0.20 %
    Allowed  :  3.31 %
    Favored  : 96.49 %
  Rotamer:
    Outliers :  1.47 %
    Allowed  :  7.47 %
    Favored  : 91.06 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.07 %

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 (0.22), residues: 1512
  helix:  1.57 (0.19), residues: 697
  sheet: -0.28 (0.33), residues: 231
  loop : -0.43 (0.27), residues: 584

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.008   0.000   ARG A 123 
 TYR   0.018   0.001   TYR B 730 
 PHE   0.012   0.001   PHE A 382 
 TRP   0.015   0.001   TRP A 812 
 HIS   0.009   0.001   HIS B 607 

Details of bonding type rmsd
  covalent geometry    : bond        0.00324 (12639)
  covalent geometry    : angle       0.53686 (17127)
  hydrogen bonds       : bond        0.03754 (  617)
  hydrogen bonds       : angle       4.41173 ( 1779)

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

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

  3024 Ramachandran restraints generated.
    1512 Oldfield, 0 Emsley, 1512 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3024 Ramachandran restraints generated.
    1512 Oldfield, 0 Emsley, 1512 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  142 residues out of total 1365 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 122
  time to evaluate  : 0.349 
Fit side-chains
REVERT: A  252 MET cc_start: 0.6645 (OUTLIER) cc_final: 0.6420 (ptm)
REVERT: A  571 ASP cc_start: 0.8251 (m-30) cc_final: 0.8026 (m-30)
REVERT: B   50 ARG cc_start: 0.7308 (ptp-170) cc_final: 0.6524 (tpp-160)
REVERT: B  223 LEU cc_start: 0.7068 (OUTLIER) cc_final: 0.6823 (tm)
REVERT: B  655 MET cc_start: 0.7544 (mmt) cc_final: 0.6752 (mtp)
REVERT: B  744 MET cc_start: 0.7170 (mpp) cc_final: 0.6892 (mpp)
REVERT: B  819 ASP cc_start: 0.5535 (m-30) cc_final: 0.5088 (m-30)
  outliers start: 20
  outliers final: 10
  residues processed: 131
  average time/residue: 0.5910
  time to fit residues: 84.0920
Evaluate side-chains
  119 residues out of total 1365 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 107
  time to evaluate  : 0.476 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  252 MET
Chi-restraints excluded: chain A residue  326 VAL
Chi-restraints excluded: chain A residue  346 HIS
Chi-restraints excluded: chain A residue  358 ASP
Chi-restraints excluded: chain A residue  435 CYS
Chi-restraints excluded: chain A residue  472 ARG
Chi-restraints excluded: chain A residue  551 LEU
Chi-restraints excluded: chain A residue  559 ILE
Chi-restraints excluded: chain A residue  870 ILE
Chi-restraints excluded: chain A residue  878 MET
Chi-restraints excluded: chain A residue 1047 ASP
Chi-restraints excluded: chain B residue  223 LEU
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 152
   random chunks:
   chunk 134 optimal weight:    0.9980
   chunk 13 optimal weight:    0.6980
   chunk 80 optimal weight:    5.9990
   chunk 77 optimal weight:    0.7980
   chunk 83 optimal weight:    2.9990
   chunk 125 optimal weight:    4.9990
   chunk 19 optimal weight:    0.9990
   chunk 147 optimal weight:    5.9990
   chunk 32 optimal weight:    0.8980
   chunk 8 optimal weight:    0.0970
   chunk 26 optimal weight:    1.9990
   overall best weight:    0.6978

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

Flipped N/Q/H residues before XYZ refinement:
** A 693 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 735 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 773 ASN
** A 948 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 951 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A1060 ASN
** B  70 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 607 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4031 r_free = 0.4031 target = 0.158750 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 54)----------------|
| r_work = 0.3465 r_free = 0.3465 target = 0.111512 restraints weight = 16525.378|
|-----------------------------------------------------------------------------|
r_work (start): 0.3429 rms_B_bonded: 2.34
r_work: 0.3310 rms_B_bonded: 2.80 restraints_weight: 0.5000
r_work: 0.3168 rms_B_bonded: 4.51 restraints_weight: 0.2500
r_work (final): 0.3168
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8004
moved from start:          0.1140

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.033  12639  Z= 0.131
  Angle     :  0.508   7.691  17127  Z= 0.260
  Chirality :  0.041   0.159   1932
  Planarity :  0.004   0.064   2179
  Dihedral  :  4.247  28.559   1658
  Min Nonbonded Distance : 2.582

Molprobity Statistics.
  All-atom Clashscore : 7.30
  Ramachandran Plot:
    Outliers :  0.20 %
    Allowed  :  3.04 %
    Favored  : 96.76 %
  Rotamer:
    Outliers :  2.05 %
    Allowed  :  9.08 %
    Favored  : 88.86 %
  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:  0.83 (0.22), residues: 1512
  helix:  1.69 (0.19), residues: 698
  sheet: -0.24 (0.33), residues: 231
  loop : -0.45 (0.27), residues: 583

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.011   0.000   ARG B 217 
 TYR   0.013   0.001   TYR A 720 
 PHE   0.013   0.001   PHE A 382 
 TRP   0.014   0.001   TRP A 812 
 HIS   0.007   0.001   HIS B 607 

Details of bonding type rmsd
  covalent geometry    : bond        0.00306 (12639)
  covalent geometry    : angle       0.50791 (17127)
  hydrogen bonds       : bond        0.03479 (  617)
  hydrogen bonds       : angle       4.23014 ( 1779)

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

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

  3024 Ramachandran restraints generated.
    1512 Oldfield, 0 Emsley, 1512 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3024 Ramachandran restraints generated.
    1512 Oldfield, 0 Emsley, 1512 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  158 residues out of total 1365 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 28
    poor density    : 130
  time to evaluate  : 0.471 
Fit side-chains
REVERT: A  619 GLN cc_start: 0.8921 (OUTLIER) cc_final: 0.8631 (pm20)
REVERT: A  772 GLU cc_start: 0.7039 (OUTLIER) cc_final: 0.6780 (mp0)
REVERT: A  903 LYS cc_start: 0.8333 (tptp) cc_final: 0.8087 (tptp)
REVERT: B   50 ARG cc_start: 0.7594 (ptp-170) cc_final: 0.6565 (tpp-160)
REVERT: B  655 MET cc_start: 0.7484 (mmt) cc_final: 0.6740 (mtp)
  outliers start: 28
  outliers final: 11
  residues processed: 145
  average time/residue: 0.5215
  time to fit residues: 83.3613
Evaluate side-chains
  130 residues out of total 1365 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 117
  time to evaluate  : 0.393 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  326 VAL
Chi-restraints excluded: chain A residue  346 HIS
Chi-restraints excluded: chain A residue  358 ASP
Chi-restraints excluded: chain A residue  435 CYS
Chi-restraints excluded: chain A residue  551 LEU
Chi-restraints excluded: chain A residue  559 ILE
Chi-restraints excluded: chain A residue  619 GLN
Chi-restraints excluded: chain A residue  772 GLU
Chi-restraints excluded: chain A residue  878 MET
Chi-restraints excluded: chain A residue 1047 ASP
Chi-restraints excluded: chain A residue 1074 VAL
Chi-restraints excluded: chain B residue   47 LEU
Chi-restraints excluded: chain B residue  176 LEU
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 152
   random chunks:
   chunk 66 optimal weight:    4.9990
   chunk 94 optimal weight:    0.4980
   chunk 79 optimal weight:    0.4980
   chunk 61 optimal weight:    1.9990
   chunk 82 optimal weight:    1.9990
   chunk 65 optimal weight:    1.9990
   chunk 30 optimal weight:    2.9990
   chunk 29 optimal weight:    3.9990
   chunk 86 optimal weight:    3.9990
   chunk 105 optimal weight:    4.9990
   chunk 11 optimal weight:    0.9980
   overall best weight:    1.1984

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

Flipped N/Q/H residues before XYZ refinement:
** A 693 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 735 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 773 ASN
** A 948 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 951 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A1060 ASN
** B  70 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 607 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4004 r_free = 0.4004 target = 0.156998 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.3513 r_free = 0.3513 target = 0.113214 restraints weight = 16660.233|
|-----------------------------------------------------------------------------|
r_work (start): 0.3444 rms_B_bonded: 2.33
r_work: 0.3257 rms_B_bonded: 3.00 restraints_weight: 0.5000
r_work: 0.3118 rms_B_bonded: 4.80 restraints_weight: 0.2500
r_work (final): 0.3118
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8054
moved from start:          0.1281

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.041  12639  Z= 0.184
  Angle     :  0.543   7.018  17127  Z= 0.279
  Chirality :  0.043   0.167   1932
  Planarity :  0.004   0.065   2179
  Dihedral  :  4.261  26.786   1654
  Min Nonbonded Distance : 2.531

Molprobity Statistics.
  All-atom Clashscore : 7.91
  Ramachandran Plot:
    Outliers :  0.20 %
    Allowed  :  3.64 %
    Favored  : 96.16 %
  Rotamer:
    Outliers :  1.90 %
    Allowed  : 11.58 %
    Favored  : 86.52 %
  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 (0.22), residues: 1512
  helix:  1.64 (0.19), residues: 697
  sheet: -0.38 (0.34), residues: 224
  loop : -0.47 (0.27), residues: 591

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.009   0.000   ARG A 123 
 TYR   0.020   0.002   TYR B 730 
 PHE   0.015   0.001   PHE A 382 
 TRP   0.014   0.001   TRP A 812 
 HIS   0.006   0.001   HIS B 607 

Details of bonding type rmsd
  covalent geometry    : bond        0.00443 (12639)
  covalent geometry    : angle       0.54297 (17127)
  hydrogen bonds       : bond        0.03697 (  617)
  hydrogen bonds       : angle       4.25535 ( 1779)

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

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

  3024 Ramachandran restraints generated.
    1512 Oldfield, 0 Emsley, 1512 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3024 Ramachandran restraints generated.
    1512 Oldfield, 0 Emsley, 1512 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  147 residues out of total 1365 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 26
    poor density    : 121
  time to evaluate  : 0.472 
Fit side-chains
REVERT: A  571 ASP cc_start: 0.8292 (m-30) cc_final: 0.8091 (m-30)
REVERT: A  628 MET cc_start: 0.8819 (mmt) cc_final: 0.8616 (mmm)
REVERT: A  772 GLU cc_start: 0.7064 (OUTLIER) cc_final: 0.6752 (mp0)
REVERT: B   50 ARG cc_start: 0.7668 (ptp-170) cc_final: 0.6569 (tpp-160)
REVERT: B  239 LEU cc_start: 0.8621 (tt) cc_final: 0.8412 (tp)
REVERT: B  655 MET cc_start: 0.7536 (mmt) cc_final: 0.6763 (mtp)
  outliers start: 26
  outliers final: 11
  residues processed: 136
  average time/residue: 0.5334
  time to fit residues: 79.6995
Evaluate side-chains
  124 residues out of total 1365 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 112
  time to evaluate  : 0.287 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  326 VAL
Chi-restraints excluded: chain A residue  346 HIS
Chi-restraints excluded: chain A residue  358 ASP
Chi-restraints excluded: chain A residue  372 VAL
Chi-restraints excluded: chain A residue  435 CYS
Chi-restraints excluded: chain A residue  559 ILE
Chi-restraints excluded: chain A residue  772 GLU
Chi-restraints excluded: chain A residue  870 ILE
Chi-restraints excluded: chain A residue  890 LYS
Chi-restraints excluded: chain A residue 1047 ASP
Chi-restraints excluded: chain A residue 1074 VAL
Chi-restraints excluded: chain B residue   47 LEU
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 152
   random chunks:
   chunk 148 optimal weight:    0.9990
   chunk 94 optimal weight:    0.7980
   chunk 66 optimal weight:    4.9990
   chunk 88 optimal weight:    2.9990
   chunk 124 optimal weight:    1.9990
   chunk 81 optimal weight:    0.0870
   chunk 96 optimal weight:    2.9990
   chunk 43 optimal weight:    2.9990
   chunk 115 optimal weight:    3.9990
   chunk 125 optimal weight:    3.9990
   chunk 35 optimal weight:    0.9990
   overall best weight:    0.9764

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

Flipped N/Q/H residues before XYZ refinement:
** A 693 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 735 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 773 ASN
** A 948 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 951 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A1060 ASN
** B  70 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 607 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4104 r_free = 0.4104 target = 0.160657 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.3607 r_free = 0.3607 target = 0.115372 restraints weight = 16643.670|
|-----------------------------------------------------------------------------|
r_work (start): 0.3559 rms_B_bonded: 2.72
r_work: 0.3345 rms_B_bonded: 3.13 restraints_weight: 0.5000
r_work (final): 0.3345
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8027
moved from start:          0.1354

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.037  12639  Z= 0.160
  Angle     :  0.532   6.884  17127  Z= 0.272
  Chirality :  0.042   0.191   1932
  Planarity :  0.004   0.066   2179
  Dihedral  :  4.217  25.879   1654
  Min Nonbonded Distance : 2.525

Molprobity Statistics.
  All-atom Clashscore : 7.87
  Ramachandran Plot:
    Outliers :  0.13 %
    Allowed  :  3.64 %
    Favored  : 96.23 %
  Rotamer:
    Outliers :  2.34 %
    Allowed  : 12.09 %
    Favored  : 85.57 %
  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 (0.22), residues: 1512
  helix:  1.64 (0.19), residues: 697
  sheet: -0.39 (0.34), residues: 224
  loop : -0.47 (0.27), residues: 591

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.009   0.000   ARG A 123 
 TYR   0.014   0.001   TYR A 720 
 PHE   0.014   0.001   PHE A 175 
 TRP   0.035   0.001   TRP B 252 
 HIS   0.005   0.001   HIS B 607 

Details of bonding type rmsd
  covalent geometry    : bond        0.00382 (12639)
  covalent geometry    : angle       0.53170 (17127)
  hydrogen bonds       : bond        0.03532 (  617)
  hydrogen bonds       : angle       4.22374 ( 1779)

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

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

  3024 Ramachandran restraints generated.
    1512 Oldfield, 0 Emsley, 1512 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3024 Ramachandran restraints generated.
    1512 Oldfield, 0 Emsley, 1512 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  157 residues out of total 1365 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 32
    poor density    : 125
  time to evaluate  : 0.491 
Fit side-chains
REVERT: A  571 ASP cc_start: 0.8136 (m-30) cc_final: 0.7906 (m-30)
REVERT: A  772 GLU cc_start: 0.7012 (OUTLIER) cc_final: 0.6762 (mp0)
REVERT: B   50 ARG cc_start: 0.7668 (ptp-170) cc_final: 0.6719 (tpp-160)
REVERT: B  655 MET cc_start: 0.7400 (mmt) cc_final: 0.6689 (mtp)
  outliers start: 32
  outliers final: 19
  residues processed: 143
  average time/residue: 0.5550
  time to fit residues: 87.0931
Evaluate side-chains
  138 residues out of total 1365 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 118
  time to evaluate  : 0.463 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  135 ILE
Chi-restraints excluded: chain A residue  287 ILE
Chi-restraints excluded: chain A residue  326 VAL
Chi-restraints excluded: chain A residue  346 HIS
Chi-restraints excluded: chain A residue  358 ASP
Chi-restraints excluded: chain A residue  372 VAL
Chi-restraints excluded: chain A residue  435 CYS
Chi-restraints excluded: chain A residue  559 ILE
Chi-restraints excluded: chain A residue  772 GLU
Chi-restraints excluded: chain A residue  870 ILE
Chi-restraints excluded: chain A residue  878 MET
Chi-restraints excluded: chain A residue  890 LYS
Chi-restraints excluded: chain A residue 1047 ASP
Chi-restraints excluded: chain A residue 1074 VAL
Chi-restraints excluded: chain B residue   69 VAL
Chi-restraints excluded: chain B residue  117 VAL
Chi-restraints excluded: chain B residue  176 LEU
Chi-restraints excluded: chain B residue  178 VAL
Chi-restraints excluded: chain B residue  304 ILE
Chi-restraints excluded: chain B residue  606 SER
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 152
   random chunks:
   chunk 104 optimal weight:    0.9980
   chunk 37 optimal weight:    1.9990
   chunk 67 optimal weight:    0.9990
   chunk 19 optimal weight:    0.6980
   chunk 77 optimal weight:    1.9990
   chunk 30 optimal weight:    2.9990
   chunk 81 optimal weight:    0.3980
   chunk 136 optimal weight:    8.9990
   chunk 130 optimal weight:    0.8980
   chunk 21 optimal weight:    0.9980
   chunk 1 optimal weight:    8.9990
   overall best weight:    0.7980

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

Flipped N/Q/H residues before XYZ refinement:
** A 693 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 735 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 948 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 951 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A1060 ASN
** B  70 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 607 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4109 r_free = 0.4109 target = 0.160994 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.3615 r_free = 0.3615 target = 0.116050 restraints weight = 16432.906|
|-----------------------------------------------------------------------------|
r_work (start): 0.3570 rms_B_bonded: 2.70
r_work: 0.3357 rms_B_bonded: 3.13 restraints_weight: 0.5000
r_work (final): 0.3357
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8022
moved from start:          0.1453

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.035  12639  Z= 0.141
  Angle     :  0.519   7.051  17127  Z= 0.265
  Chirality :  0.041   0.163   1932
  Planarity :  0.004   0.066   2179
  Dihedral  :  4.169  25.134   1654
  Min Nonbonded Distance : 2.554

Molprobity Statistics.
  All-atom Clashscore : 7.79
  Ramachandran Plot:
    Outliers :  0.13 %
    Allowed  :  3.64 %
    Favored  : 96.23 %
  Rotamer:
    Outliers :  2.12 %
    Allowed  : 12.82 %
    Favored  : 85.05 %
  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:  0.81 (0.22), residues: 1512
  helix:  1.68 (0.19), residues: 698
  sheet: -0.30 (0.34), residues: 233
  loop : -0.45 (0.27), residues: 581

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.011   0.000   ARG A 123 
 TYR   0.015   0.001   TYR A 720 
 PHE   0.014   0.001   PHE A 175 
 TRP   0.021   0.001   TRP B 252 
 HIS   0.005   0.001   HIS B 607 

Details of bonding type rmsd
  covalent geometry    : bond        0.00336 (12639)
  covalent geometry    : angle       0.51946 (17127)
  hydrogen bonds       : bond        0.03392 (  617)
  hydrogen bonds       : angle       4.17237 ( 1779)

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

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

  3024 Ramachandran restraints generated.
    1512 Oldfield, 0 Emsley, 1512 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3024 Ramachandran restraints generated.
    1512 Oldfield, 0 Emsley, 1512 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  157 residues out of total 1365 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 29
    poor density    : 128
  time to evaluate  : 0.462 
Fit side-chains
REVERT: A  571 ASP cc_start: 0.8143 (m-30) cc_final: 0.7920 (m-30)
REVERT: A  772 GLU cc_start: 0.6999 (OUTLIER) cc_final: 0.6756 (mp0)
REVERT: B   50 ARG cc_start: 0.7676 (ptp-170) cc_final: 0.6747 (tpp-160)
REVERT: B  251 GLN cc_start: 0.8238 (tp-100) cc_final: 0.7953 (tp-100)
REVERT: B  304 ILE cc_start: 0.2589 (mm) cc_final: 0.2200 (tp)
REVERT: B  655 MET cc_start: 0.7397 (mmt) cc_final: 0.6760 (mtp)
  outliers start: 29
  outliers final: 18
  residues processed: 143
  average time/residue: 0.5538
  time to fit residues: 86.7785
Evaluate side-chains
  137 residues out of total 1365 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 118
  time to evaluate  : 0.475 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  287 ILE
Chi-restraints excluded: chain A residue  326 VAL
Chi-restraints excluded: chain A residue  346 HIS
Chi-restraints excluded: chain A residue  358 ASP
Chi-restraints excluded: chain A residue  372 VAL
Chi-restraints excluded: chain A residue  435 CYS
Chi-restraints excluded: chain A residue  472 ARG
Chi-restraints excluded: chain A residue  559 ILE
Chi-restraints excluded: chain A residue  772 GLU
Chi-restraints excluded: chain A residue  823 LEU
Chi-restraints excluded: chain A residue  870 ILE
Chi-restraints excluded: chain A residue  878 MET
Chi-restraints excluded: chain A residue 1047 ASP
Chi-restraints excluded: chain A residue 1074 VAL
Chi-restraints excluded: chain B residue   47 LEU
Chi-restraints excluded: chain B residue   69 VAL
Chi-restraints excluded: chain B residue  176 LEU
Chi-restraints excluded: chain B residue  178 VAL
Chi-restraints excluded: chain B residue  606 SER
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 152
   random chunks:
   chunk 105 optimal weight:    3.9990
   chunk 82 optimal weight:    1.9990
   chunk 58 optimal weight:    0.7980
   chunk 148 optimal weight:    0.9980
   chunk 129 optimal weight:    4.9990
   chunk 93 optimal weight:    0.5980
   chunk 116 optimal weight:    9.9990
   chunk 131 optimal weight:    0.9990
   chunk 149 optimal weight:    5.9990
   chunk 100 optimal weight:    0.6980
   chunk 20 optimal weight:    1.9990
   overall best weight:    0.8182

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

Flipped N/Q/H residues before XYZ refinement:
** A 105 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 693 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 735 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 773 ASN
A 893 GLN
** A 948 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 951 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A1060 ASN
** B  70 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 607 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 = 0.4101 r_free = 0.4101 target = 0.160103 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 57)----------------|
| r_work = 0.3563 r_free = 0.3563 target = 0.113798 restraints weight = 16262.890|
|-----------------------------------------------------------------------------|
r_work (start): 0.3527 rms_B_bonded: 2.32
r_work: 0.3383 rms_B_bonded: 2.80 restraints_weight: 0.5000
r_work: 0.3236 rms_B_bonded: 4.57 restraints_weight: 0.2500
r_work (final): 0.3236
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8104
moved from start:          0.1513

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.037  12639  Z= 0.144
  Angle     :  0.527   6.884  17127  Z= 0.269
  Chirality :  0.042   0.164   1932
  Planarity :  0.004   0.066   2179
  Dihedral  :  4.169  24.926   1654
  Min Nonbonded Distance : 2.501

Molprobity Statistics.
  All-atom Clashscore : 7.95
  Ramachandran Plot:
    Outliers :  0.13 %
    Allowed  :  3.57 %
    Favored  : 96.30 %
  Rotamer:
    Outliers :  2.34 %
    Allowed  : 13.26 %
    Favored  : 84.40 %
  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:  0.79 (0.22), residues: 1512
  helix:  1.67 (0.19), residues: 698
  sheet: -0.30 (0.34), residues: 226
  loop : -0.47 (0.27), residues: 588

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.012   0.000   ARG A 123 
 TYR   0.014   0.001   TYR A 720 
 PHE   0.013   0.001   PHE A 382 
 TRP   0.041   0.001   TRP B 252 
 HIS   0.004   0.001   HIS B 607 

Details of bonding type rmsd
  covalent geometry    : bond        0.00343 (12639)
  covalent geometry    : angle       0.52650 (17127)
  hydrogen bonds       : bond        0.03403 (  617)
  hydrogen bonds       : angle       4.17338 ( 1779)

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

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

  3024 Ramachandran restraints generated.
    1512 Oldfield, 0 Emsley, 1512 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3024 Ramachandran restraints generated.
    1512 Oldfield, 0 Emsley, 1512 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  159 residues out of total 1365 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 32
    poor density    : 127
  time to evaluate  : 0.467 
Fit side-chains
REVERT: A  619 GLN cc_start: 0.8937 (OUTLIER) cc_final: 0.8695 (pm20)
REVERT: B   50 ARG cc_start: 0.7703 (ptp-170) cc_final: 0.6726 (tpp-160)
REVERT: B  252 TRP cc_start: 0.7180 (t60) cc_final: 0.6858 (t60)
REVERT: B  304 ILE cc_start: 0.2667 (mm) cc_final: 0.2220 (tp)
REVERT: B  655 MET cc_start: 0.7505 (mmt) cc_final: 0.6848 (mtp)
  outliers start: 32
  outliers final: 16
  residues processed: 145
  average time/residue: 0.5249
  time to fit residues: 83.8740
Evaluate side-chains
  134 residues out of total 1365 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 117
  time to evaluate  : 0.462 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  326 VAL
Chi-restraints excluded: chain A residue  346 HIS
Chi-restraints excluded: chain A residue  358 ASP
Chi-restraints excluded: chain A residue  372 VAL
Chi-restraints excluded: chain A residue  435 CYS
Chi-restraints excluded: chain A residue  472 ARG
Chi-restraints excluded: chain A residue  619 GLN
Chi-restraints excluded: chain A residue  823 LEU
Chi-restraints excluded: chain A residue  870 ILE
Chi-restraints excluded: chain A residue  876 ILE
Chi-restraints excluded: chain A residue  890 LYS
Chi-restraints excluded: chain A residue 1074 VAL
Chi-restraints excluded: chain B residue   47 LEU
Chi-restraints excluded: chain B residue   69 VAL
Chi-restraints excluded: chain B residue  176 LEU
Chi-restraints excluded: chain B residue  178 VAL
Chi-restraints excluded: chain B residue  606 SER
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 152
   random chunks:
   chunk 4 optimal weight:    0.0670
   chunk 74 optimal weight:    0.6980
   chunk 147 optimal weight:    5.9990
   chunk 108 optimal weight:    0.9990
   chunk 123 optimal weight:    3.9990
   chunk 48 optimal weight:    2.9990
   chunk 107 optimal weight:    0.6980
   chunk 24 optimal weight:    2.9990
   chunk 39 optimal weight:    2.9990
   chunk 72 optimal weight:    0.9980
   chunk 65 optimal weight:    0.9990
   overall best weight:    0.6920

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

Flipped N/Q/H residues before XYZ refinement:
** A 693 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 735 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 893 GLN
** A 948 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 951 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A1060 ASN
** B  70 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4112 r_free = 0.4112 target = 0.161363 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.3596 r_free = 0.3596 target = 0.116113 restraints weight = 16396.377|
|-----------------------------------------------------------------------------|
r_work (start): 0.3570 rms_B_bonded: 2.94
r_work: 0.3346 rms_B_bonded: 3.30 restraints_weight: 0.5000
r_work (final): 0.3346
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8004
moved from start:          0.1593

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.038  12639  Z= 0.132
  Angle     :  0.524   6.970  17127  Z= 0.268
  Chirality :  0.041   0.162   1932
  Planarity :  0.004   0.065   2179
  Dihedral  :  4.140  24.580   1654
  Min Nonbonded Distance : 2.521

Molprobity Statistics.
  All-atom Clashscore : 7.99
  Ramachandran Plot:
    Outliers :  0.13 %
    Allowed  :  3.77 %
    Favored  : 96.10 %
  Rotamer:
    Outliers :  2.05 %
    Allowed  : 13.92 %
    Favored  : 84.03 %
  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:  0.84 (0.22), residues: 1512
  helix:  1.71 (0.19), residues: 698
  sheet: -0.24 (0.33), residues: 238
  loop : -0.47 (0.27), residues: 576

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.012   0.000   ARG A 123 
 TYR   0.015   0.001   TYR A 720 
 PHE   0.012   0.001   PHE A 382 
 TRP   0.048   0.001   TRP B 252 
 HIS   0.011   0.001   HIS B 607 

Details of bonding type rmsd
  covalent geometry    : bond        0.00313 (12639)
  covalent geometry    : angle       0.52379 (17127)
  hydrogen bonds       : bond        0.03319 (  617)
  hydrogen bonds       : angle       4.12995 ( 1779)

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

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

  3024 Ramachandran restraints generated.
    1512 Oldfield, 0 Emsley, 1512 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3024 Ramachandran restraints generated.
    1512 Oldfield, 0 Emsley, 1512 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  147 residues out of total 1365 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 28
    poor density    : 119
  time to evaluate  : 0.455 
Fit side-chains
REVERT: B   50 ARG cc_start: 0.7644 (ptp-170) cc_final: 0.6710 (tpp-160)
REVERT: B  304 ILE cc_start: 0.2585 (mm) cc_final: 0.2220 (tp)
REVERT: B  655 MET cc_start: 0.7392 (mmt) cc_final: 0.6754 (mtp)
  outliers start: 28
  outliers final: 16
  residues processed: 135
  average time/residue: 0.5169
  time to fit residues: 77.0104
Evaluate side-chains
  132 residues out of total 1365 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 116
  time to evaluate  : 0.319 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  326 VAL
Chi-restraints excluded: chain A residue  346 HIS
Chi-restraints excluded: chain A residue  358 ASP
Chi-restraints excluded: chain A residue  372 VAL
Chi-restraints excluded: chain A residue  435 CYS
Chi-restraints excluded: chain A residue  823 LEU
Chi-restraints excluded: chain A residue  870 ILE
Chi-restraints excluded: chain A residue  876 ILE
Chi-restraints excluded: chain A residue  878 MET
Chi-restraints excluded: chain A residue 1047 ASP
Chi-restraints excluded: chain A residue 1074 VAL
Chi-restraints excluded: chain B residue   47 LEU
Chi-restraints excluded: chain B residue   69 VAL
Chi-restraints excluded: chain B residue  178 VAL
Chi-restraints excluded: chain B residue  606 SER
Chi-restraints excluded: chain B residue  700 THR
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 152
   random chunks:
   chunk 117 optimal weight:    2.9990
   chunk 15 optimal weight:    2.9990
   chunk 18 optimal weight:    5.9990
   chunk 60 optimal weight:    0.7980
   chunk 6 optimal weight:    1.9990
   chunk 123 optimal weight:    3.9990
   chunk 68 optimal weight:    0.8980
   chunk 69 optimal weight:    0.0970
   chunk 44 optimal weight:    0.5980
   chunk 8 optimal weight:    0.9980
   chunk 1 optimal weight:    7.9990
   overall best weight:    0.6778

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

Flipped N/Q/H residues before XYZ refinement:
** A 693 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 735 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 773 ASN
A 893 GLN
** A 948 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 951 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A1060 ASN
** B  70 GLN ** 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 = 0.4116 r_free = 0.4116 target = 0.161686 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 50)----------------|
| r_work = 0.3556 r_free = 0.3556 target = 0.113552 restraints weight = 16402.392|
|-----------------------------------------------------------------------------|
r_work (start): 0.3530 rms_B_bonded: 2.41
r_work: 0.3387 rms_B_bonded: 2.87 restraints_weight: 0.5000
r_work: 0.3242 rms_B_bonded: 4.66 restraints_weight: 0.2500
r_work (final): 0.3242
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8093
moved from start:          0.1639

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.040  12639  Z= 0.130
  Angle     :  0.521   7.233  17127  Z= 0.267
  Chirality :  0.041   0.163   1932
  Planarity :  0.004   0.063   2179
  Dihedral  :  4.114  24.429   1654
  Min Nonbonded Distance : 2.472

Molprobity Statistics.
  All-atom Clashscore : 7.58
  Ramachandran Plot:
    Outliers :  0.13 %
    Allowed  :  3.70 %
    Favored  : 96.16 %
  Rotamer:
    Outliers :  1.61 %
    Allowed  : 14.65 %
    Favored  : 83.74 %
  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:  0.84 (0.22), residues: 1512
  helix:  1.71 (0.19), residues: 699
  sheet: -0.22 (0.34), residues: 232
  loop : -0.47 (0.27), residues: 581

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.014   0.000   ARG A 123 
 TYR   0.014   0.001   TYR A 720 
 PHE   0.012   0.001   PHE A 382 
 TRP   0.049   0.001   TRP B 252 
 HIS   0.010   0.001   HIS B 607 

Details of bonding type rmsd
  covalent geometry    : bond        0.00308 (12639)
  covalent geometry    : angle       0.52091 (17127)
  hydrogen bonds       : bond        0.03279 (  617)
  hydrogen bonds       : angle       4.10323 ( 1779)

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

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

  3024 Ramachandran restraints generated.
    1512 Oldfield, 0 Emsley, 1512 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3024 Ramachandran restraints generated.
    1512 Oldfield, 0 Emsley, 1512 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  143 residues out of total 1365 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 22
    poor density    : 121
  time to evaluate  : 0.471 
Fit side-chains
REVERT: A  139 GLN cc_start: 0.8661 (tt0) cc_final: 0.8354 (tt0)
REVERT: A  982 ARG cc_start: 0.7380 (ttp-170) cc_final: 0.7091 (ttm170)
REVERT: B   50 ARG cc_start: 0.7637 (ptp-170) cc_final: 0.6701 (tpp-160)
REVERT: B  304 ILE cc_start: 0.2646 (mm) cc_final: 0.2217 (tp)
REVERT: B  655 MET cc_start: 0.7508 (mmt) cc_final: 0.6880 (mtp)
  outliers start: 22
  outliers final: 19
  residues processed: 133
  average time/residue: 0.4947
  time to fit residues: 72.5997
Evaluate side-chains
  137 residues out of total 1365 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 118
  time to evaluate  : 0.461 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  105 GLN
Chi-restraints excluded: chain A residue  287 ILE
Chi-restraints excluded: chain A residue  326 VAL
Chi-restraints excluded: chain A residue  346 HIS
Chi-restraints excluded: chain A residue  358 ASP
Chi-restraints excluded: chain A residue  372 VAL
Chi-restraints excluded: chain A residue  435 CYS
Chi-restraints excluded: chain A residue  823 LEU
Chi-restraints excluded: chain A residue  870 ILE
Chi-restraints excluded: chain A residue  876 ILE
Chi-restraints excluded: chain A residue  878 MET
Chi-restraints excluded: chain A residue 1047 ASP
Chi-restraints excluded: chain A residue 1074 VAL
Chi-restraints excluded: chain B residue   47 LEU
Chi-restraints excluded: chain B residue   69 VAL
Chi-restraints excluded: chain B residue  176 LEU
Chi-restraints excluded: chain B residue  178 VAL
Chi-restraints excluded: chain B residue  606 SER
Chi-restraints excluded: chain B residue  700 THR
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 152
   random chunks:
   chunk 138 optimal weight:    1.9990
   chunk 134 optimal weight:    0.6980
   chunk 146 optimal weight:    6.9990
   chunk 130 optimal weight:    0.7980
   chunk 144 optimal weight:    0.9980
   chunk 60 optimal weight:    0.6980
   chunk 20 optimal weight:    1.9990
   chunk 128 optimal weight:    6.9990
   chunk 3 optimal weight:    5.9990
   chunk 32 optimal weight:    0.7980
   chunk 1 optimal weight:    0.9990
   overall best weight:    0.7980

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

Flipped N/Q/H residues before XYZ refinement:
A 105 GLN
** A 693 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 735 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 893 GLN
** A 948 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 951 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A1060 ASN
** B  70 GLN ** 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 = 0.4105 r_free = 0.4105 target = 0.161185 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 51)----------------|
| r_work = 0.3544 r_free = 0.3544 target = 0.113131 restraints weight = 16489.352|
|-----------------------------------------------------------------------------|
r_work (start): 0.3523 rms_B_bonded: 2.41
r_work: 0.3380 rms_B_bonded: 2.87 restraints_weight: 0.5000
r_work: 0.3236 rms_B_bonded: 4.64 restraints_weight: 0.2500
r_work (final): 0.3236
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8088
moved from start:          0.1704

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.051  12639  Z= 0.143
  Angle     :  0.540   7.802  17127  Z= 0.276
  Chirality :  0.041   0.163   1932
  Planarity :  0.004   0.064   2179
  Dihedral  :  4.140  24.480   1654
  Min Nonbonded Distance : 2.421

Molprobity Statistics.
  All-atom Clashscore : 7.83
  Ramachandran Plot:
    Outliers :  0.13 %
    Allowed  :  3.77 %
    Favored  : 96.10 %
  Rotamer:
    Outliers :  1.76 %
    Allowed  : 15.02 %
    Favored  : 83.22 %
  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:  0.85 (0.22), residues: 1512
  helix:  1.73 (0.19), residues: 699
  sheet: -0.21 (0.33), residues: 237
  loop : -0.47 (0.27), residues: 576

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.015   0.000   ARG A 123 
 TYR   0.014   0.001   TYR A 720 
 PHE   0.013   0.001   PHE A 382 
 TRP   0.056   0.001   TRP B 252 
 HIS   0.010   0.001   HIS B 607 

Details of bonding type rmsd
  covalent geometry    : bond        0.00343 (12639)
  covalent geometry    : angle       0.53998 (17127)
  hydrogen bonds       : bond        0.03380 (  617)
  hydrogen bonds       : angle       4.09857 ( 1779)

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

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

  3024 Ramachandran restraints generated.
    1512 Oldfield, 0 Emsley, 1512 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3024 Ramachandran restraints generated.
    1512 Oldfield, 0 Emsley, 1512 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  142 residues out of total 1365 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 24
    poor density    : 118
  time to evaluate  : 0.475 
Fit side-chains
REVERT: A   97 LEU cc_start: 0.8716 (mt) cc_final: 0.8467 (mp)
REVERT: A  139 GLN cc_start: 0.8653 (tt0) cc_final: 0.8338 (tt0)
REVERT: A  252 MET cc_start: 0.6245 (ppp) cc_final: 0.5988 (pp-130)
REVERT: A  982 ARG cc_start: 0.7322 (ttp-170) cc_final: 0.7094 (mtp180)
REVERT: A 1053 ASP cc_start: 0.8644 (OUTLIER) cc_final: 0.8283 (m-30)
REVERT: B   50 ARG cc_start: 0.7645 (ptp-170) cc_final: 0.6696 (tpp-160)
REVERT: B  304 ILE cc_start: 0.2560 (mm) cc_final: 0.2183 (tp)
REVERT: B  655 MET cc_start: 0.7477 (mmt) cc_final: 0.6842 (mtp)
  outliers start: 24
  outliers final: 17
  residues processed: 131
  average time/residue: 0.4932
  time to fit residues: 71.3615
Evaluate side-chains
  133 residues out of total 1365 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 115
  time to evaluate  : 0.463 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  326 VAL
Chi-restraints excluded: chain A residue  346 HIS
Chi-restraints excluded: chain A residue  358 ASP
Chi-restraints excluded: chain A residue  372 VAL
Chi-restraints excluded: chain A residue  435 CYS
Chi-restraints excluded: chain A residue  823 LEU
Chi-restraints excluded: chain A residue  870 ILE
Chi-restraints excluded: chain A residue  876 ILE
Chi-restraints excluded: chain A residue  878 MET
Chi-restraints excluded: chain A residue  890 LYS
Chi-restraints excluded: chain A residue 1047 ASP
Chi-restraints excluded: chain A residue 1053 ASP
Chi-restraints excluded: chain A residue 1074 VAL
Chi-restraints excluded: chain B residue   47 LEU
Chi-restraints excluded: chain B residue   69 VAL
Chi-restraints excluded: chain B residue  178 VAL
Chi-restraints excluded: chain B residue  606 SER
Chi-restraints excluded: chain B residue  700 THR
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 152
   random chunks:
   chunk 60 optimal weight:    0.5980
   chunk 35 optimal weight:    1.9990
   chunk 151 optimal weight:    0.7980
   chunk 1 optimal weight:    4.9990
   chunk 105 optimal weight:    3.9990
   chunk 68 optimal weight:    0.0970
   chunk 43 optimal weight:    0.7980
   chunk 28 optimal weight:    2.9990
   chunk 123 optimal weight:    0.0770
   chunk 41 optimal weight:    0.7980
   chunk 6 optimal weight:    0.9990
   overall best weight:    0.4736

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

Flipped N/Q/H residues before XYZ refinement:
** A 693 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 735 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 893 GLN
** A 948 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 951 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A1060 ASN
B  70 GLN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4124 r_free = 0.4124 target = 0.162364 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 52)----------------|
| r_work = 0.3572 r_free = 0.3572 target = 0.114608 restraints weight = 16341.854|
|-----------------------------------------------------------------------------|
r_work (start): 0.3549 rms_B_bonded: 2.40
r_work: 0.3407 rms_B_bonded: 2.86 restraints_weight: 0.5000
r_work: 0.3263 rms_B_bonded: 4.64 restraints_weight: 0.2500
r_work (final): 0.3263
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8069
moved from start:          0.1770

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.035  12639  Z= 0.113
  Angle     :  0.516   7.964  17127  Z= 0.265
  Chirality :  0.040   0.160   1932
  Planarity :  0.004   0.062   2179
  Dihedral  :  4.057  23.794   1654
  Min Nonbonded Distance : 2.481

Molprobity Statistics.
  All-atom Clashscore : 7.71
  Ramachandran Plot:
    Outliers :  0.13 %
    Allowed  :  3.64 %
    Favored  : 96.23 %
  Rotamer:
    Outliers :  1.32 %
    Allowed  : 15.68 %
    Favored  : 83.00 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  0.98 (0.22), residues: 1512
  helix:  1.83 (0.19), residues: 701
  sheet: -0.12 (0.34), residues: 237
  loop : -0.44 (0.27), residues: 574

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.014   0.000   ARG A 123 
 TYR   0.015   0.001   TYR A 720 
 PHE   0.011   0.001   PHE A 382 
 TRP   0.058   0.001   TRP B 252 
 HIS   0.010   0.001   HIS B 607 

Details of bonding type rmsd
  covalent geometry    : bond        0.00262 (12639)
  covalent geometry    : angle       0.51587 (17127)
  hydrogen bonds       : bond        0.03143 (  617)
  hydrogen bonds       : angle       4.02325 ( 1779)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 4371.80 seconds
wall clock time: 75 minutes 8.44 seconds (4508.44 seconds total)