Starting phenix.real_space_refine
on Wed Feb  4 10:02:13 2026 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/9qtu_53362/02_2026/9qtu_53362.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/9qtu_53362/02_2026/9qtu_53362.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=4.6
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/9qtu_53362/02_2026/9qtu_53362.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/9qtu_53362/02_2026/9qtu_53362.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/9qtu_53362/02_2026/9qtu_53362.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/9qtu_53362/02_2026/9qtu_53362.cif"
  }
  resolution = 4.6
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }


Starting job
===============================================================================
-------------------------------------------------------------------------------
Citation:
*********
Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams
PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography.
Acta Cryst. D74:531-544.

Validating inputs
Origin is already at (0, 0, 0), no shifts will be applied
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=  -0.001 sd=   0.028
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      53      5.16       5
     C    6242      2.51       5
     N    1697      2.21       5
     O    1808      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 4 residue(s): 0.01s

  Monomer Library directory:
    "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5952/lib/python3.9/site-packages/chem_data/mon_lib"
  Total number of atoms: 9800
  Number of models: 1
  Model: ""
    Number of chains: 3
    Chain: "A"
      Number of atoms: 3331
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 418, 3331
          Classifications: {'peptide': 418}
          Link IDs: {'PTRANS': 19, 'TRANS': 398}
    Chain: "B"
      Number of atoms: 3331
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 418, 3331
          Classifications: {'peptide': 418}
          Link IDs: {'PTRANS': 19, 'TRANS': 398}
    Chain: "C"
      Number of atoms: 3138
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 401, 3138
          Classifications: {'peptide': 401}
          Link IDs: {'PTRANS': 27, 'TRANS': 373}
  Time building chain proxies: 2.17, per 1000 atoms: 0.22
  Number of scatterers: 9800
  At special positions: 0
  Unit cell: (85.12, 113.21, 163.43, 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      53     16.00
     O    1808      8.00
     N    1697      7.00
     C    6242      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: 0.78
  Conformation dependent library (CDL) restraints added in 512.5 milliseconds
  

  2462 Ramachandran restraints generated.
    1231 Oldfield, 0 Emsley, 1231 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  2346

  Finding SS restraints...
    Secondary structure from input PDB file:
      42 helices and 15 sheets defined
      37.9% alpha, 19.4% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.27
  Creating SS restraints...
    Processing helix  chain 'A' and resid 479 through 489
    Processing helix  chain 'A' and resid 523 through 529
    Processing helix  chain 'A' and resid 531 through 540
      removed outlier: 3.992A  pdb=" N   ASP A 535 " --> pdb=" O   ASP A 531 " (cutoff:3.500A)
      removed outlier: 4.201A  pdb=" N   TYR A 537 " --> pdb=" O   ASN A 533 " (cutoff:3.500A)
      removed outlier: 5.241A  pdb=" N   PHE A 538 " --> pdb=" O   ALA A 534 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 559 through 581
      removed outlier: 3.634A  pdb=" N   ILE A 563 " --> pdb=" O   PRO A 559 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 588 through 590
      No H-bonds generated for 'chain 'A' and resid 588 through 590'
    Processing helix  chain 'A' and resid 606 through 612
    Processing helix  chain 'A' and resid 620 through 623
    Processing helix  chain 'A' and resid 624 through 645
    Processing helix  chain 'A' and resid 647 through 654
      removed outlier: 3.879A  pdb=" N   GLN A 652 " --> pdb=" O   ALA A 649 " (cutoff:3.500A)
      removed outlier: 5.652A  pdb=" N   ARG A 653 " --> pdb=" O   GLY A 650 " (cutoff:3.500A)
      removed outlier: 6.122A  pdb=" N   GLU A 654 " --> pdb=" O   ILE A 651 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 655 through 667
    Processing helix  chain 'A' and resid 668 through 680
    Processing helix  chain 'A' and resid 687 through 690
    Processing helix  chain 'A' and resid 691 through 696
      removed outlier: 4.061A  pdb=" N   ILE A 695 " --> pdb=" O   ILE A 691 " (cutoff:3.500A)
      removed outlier: 4.261A  pdb=" N   GLY A 696 " --> pdb=" O   MET A 692 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'A' and resid 691 through 696'
    Processing helix  chain 'A' and resid 697 through 718
      removed outlier: 3.843A  pdb=" N   THR A 701 " --> pdb=" O   ALA A 697 " (cutoff:3.500A)
      removed outlier: 3.905A  pdb=" N   ALA A 718 " --> pdb=" O   GLU A 714 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 719 through 721
      No H-bonds generated for 'chain 'A' and resid 719 through 721'
    Processing helix  chain 'A' and resid 722 through 737
    Processing helix  chain 'A' and resid 739 through 743
    Processing helix  chain 'A' and resid 745 through 749
    Processing helix  chain 'A' and resid 754 through 767
      removed outlier: 3.593A  pdb=" N   LYS A 758 " --> pdb=" O   ARG A 754 " (cutoff:3.500A)
      removed outlier: 3.872A  pdb=" N   GLN A 767 " --> pdb=" O   HIS A 763 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 777 through 791
    Processing helix  chain 'A' and resid 811 through 830
    Processing helix  chain 'B' and resid 478 through 489
      removed outlier: 4.207A  pdb=" N   LEU B 482 " --> pdb=" O   LYS B 478 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 523 through 528
    Processing helix  chain 'B' and resid 531 through 536
      removed outlier: 3.742A  pdb=" N   ASP B 535 " --> pdb=" O   ASP B 531 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 559 through 579
    Processing helix  chain 'B' and resid 588 through 590
      No H-bonds generated for 'chain 'B' and resid 588 through 590'
    Processing helix  chain 'B' and resid 607 through 612
    Processing helix  chain 'B' and resid 620 through 623
    Processing helix  chain 'B' and resid 624 through 646
    Processing helix  chain 'B' and resid 652 through 654
      No H-bonds generated for 'chain 'B' and resid 652 through 654'
    Processing helix  chain 'B' and resid 655 through 667
    Processing helix  chain 'B' and resid 668 through 680
    Processing helix  chain 'B' and resid 687 through 696
      removed outlier: 3.952A  pdb=" N   ILE B 691 " --> pdb=" O   SER B 687 " (cutoff:3.500A)
      removed outlier: 3.753A  pdb=" N   MET B 692 " --> pdb=" O   VAL B 688 " (cutoff:3.500A)
      Proline residue:  B 693  - end of helix
      removed outlier: 3.832A  pdb=" N   GLY B 696 " --> pdb=" O   MET B 692 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'B' and resid 687 through 696'
    Processing helix  chain 'B' and resid 697 through 737
      removed outlier: 3.701A  pdb=" N   GLU B 715 " --> pdb=" O   ASP B 711 " (cutoff:3.500A)
      removed outlier: 3.978A  pdb=" N   GLN B 722 " --> pdb=" O   ALA B 718 " (cutoff:3.500A)
      removed outlier: 3.615A  pdb=" N   LEU B 729 " --> pdb=" O   ARG B 725 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 739 through 745
      removed outlier: 3.514A  pdb=" N   LYS B 744 " --> pdb=" O   PRO B 740 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 753 through 766
      removed outlier: 3.511A  pdb=" N   LEU B 757 " --> pdb=" O   ASP B 753 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 777 through 791
      removed outlier: 4.032A  pdb=" N   ILE B 781 " --> pdb=" O   ASP B 777 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 811 through 830
    Processing helix  chain 'C' and resid 319 through 321
      No H-bonds generated for 'chain 'C' and resid 319 through 321'
    Processing helix  chain 'C' and resid 394 through 398
      removed outlier: 3.734A  pdb=" N   LEU C 397 " --> pdb=" O   PRO C 394 " (cutoff:3.500A)
      removed outlier: 3.732A  pdb=" N   ILE C 398 " --> pdb=" O   LEU C 395 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'C' and resid 394 through 398'
    Processing helix  chain 'C' and resid 413 through 417
      removed outlier: 4.015A  pdb=" N   ALA C 417 " --> pdb=" O   ALA C 414 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 427 through 434
    Processing sheet with id=AA1, first strand: chain 'A' and resid 425 through 430
      removed outlier: 6.117A  pdb=" N   SER A 427 " --> pdb=" O   VAL A 456 " (cutoff:3.500A)
      removed outlier: 5.169A  pdb=" N   VAL A 456 " --> pdb=" O   SER A 427 " (cutoff:3.500A)
      removed outlier: 4.137A  pdb=" N   LEU A 511 " --> pdb=" O   ILE A 469 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'A' and resid 592 through 595
    Processing sheet with id=AA3, first strand: chain 'A' and resid 795 through 799
    Processing sheet with id=AA4, first strand: chain 'B' and resid 425 through 430
      removed outlier: 5.744A  pdb=" N   SER B 427 " --> pdb=" O   VAL B 456 " (cutoff:3.500A)
      removed outlier: 4.801A  pdb=" N   VAL B 456 " --> pdb=" O   SER B 427 " (cutoff:3.500A)
      removed outlier: 6.235A  pdb=" N   ASP B 516 " --> pdb=" O   LEU B 497 " (cutoff:3.500A)
      removed outlier: 6.748A  pdb=" N   LEU B 497 " --> pdb=" O   ASP B 516 " (cutoff:3.500A)
    Processing sheet with id=AA5, first strand: chain 'B' and resid 592 through 594
    Processing sheet with id=AA6, first strand: chain 'B' and resid 795 through 799
    Processing sheet with id=AA7, first strand: chain 'C' and resid 63 through 69
      removed outlier: 6.870A  pdb=" N   LEU C 356 " --> pdb=" O   LEU C  65 " (cutoff:3.500A)
      removed outlier: 4.442A  pdb=" N   SER C  67 " --> pdb=" O   VAL C 354 " (cutoff:3.500A)
      removed outlier: 6.567A  pdb=" N   VAL C 354 " --> pdb=" O   SER C  67 " (cutoff:3.500A)
      removed outlier: 4.505A  pdb=" N   CYS C 353 " --> pdb=" O   ASP C 349 " (cutoff:3.500A)
    Processing sheet with id=AA8, first strand: chain 'C' and resid 76 through 82
      removed outlier: 4.432A  pdb=" N   MET C  87 " --> pdb=" O   ASP C  82 " (cutoff:3.500A)
      removed outlier: 4.515A  pdb=" N   HIS C  96 " --> pdb=" O   SER C  92 " (cutoff:3.500A)
      removed outlier: 3.799A  pdb=" N   SER C 109 " --> pdb=" O   SER C  99 " (cutoff:3.500A)
      removed outlier: 5.956A  pdb=" N   PHE C 101 " --> pdb=" O   ARG C 107 " (cutoff:3.500A)
      removed outlier: 5.784A  pdb=" N   ARG C 107 " --> pdb=" O   PHE C 101 " (cutoff:3.500A)
    Processing sheet with id=AA9, first strand: chain 'C' and resid 121 through 124
      removed outlier: 3.841A  pdb=" N   GLN C 121 " --> pdb=" O   LEU C 132 " (cutoff:3.500A)
    Processing sheet with id=AB1, first strand: chain 'C' and resid 158 through 160
      removed outlier: 6.513A  pdb=" N   GLY C 172 " --> pdb=" O   HIS C 159 " (cutoff:3.500A)
      removed outlier: 4.582A  pdb=" N   GLY C 173 " --> pdb=" O   HIS C 177 " (cutoff:3.500A)
      removed outlier: 5.962A  pdb=" N   HIS C 177 " --> pdb=" O   GLY C 173 " (cutoff:3.500A)
      removed outlier: 6.415A  pdb=" N   ILE C 178 " --> pdb=" O   LYS C 191 " (cutoff:3.500A)
      removed outlier: 4.579A  pdb=" N   LYS C 191 " --> pdb=" O   ILE C 178 " (cutoff:3.500A)
      removed outlier: 6.687A  pdb=" N   GLU C 180 " --> pdb=" O   THR C 189 " (cutoff:3.500A)
    Processing sheet with id=AB2, first strand: chain 'C' and resid 199 through 204
      removed outlier: 3.615A  pdb=" N   ILE C 201 " --> pdb=" O   GLY C 212 " (cutoff:3.500A)
      removed outlier: 3.694A  pdb=" N   LYS C 217 " --> pdb=" O   HIS C 213 " (cutoff:3.500A)
      removed outlier: 6.470A  pdb=" N   ASP C 222 " --> pdb=" O   VAL C 228 " (cutoff:3.500A)
      removed outlier: 7.028A  pdb=" N   VAL C 228 " --> pdb=" O   ASP C 222 " (cutoff:3.500A)
    Processing sheet with id=AB3, first strand: chain 'C' and resid 238 through 245
      removed outlier: 4.893A  pdb=" N   LEU C 239 " --> pdb=" O   PHE C 254 " (cutoff:3.500A)
      removed outlier: 5.821A  pdb=" N   PHE C 254 " --> pdb=" O   LEU C 239 " (cutoff:3.500A)
      removed outlier: 6.411A  pdb=" N   GLY C 253 " --> pdb=" O   PHE C 266 " (cutoff:3.500A)
      removed outlier: 6.975A  pdb=" N   PHE C 266 " --> pdb=" O   GLY C 253 " (cutoff:3.500A)
      removed outlier: 3.574A  pdb=" N   ARG C 276 " --> pdb=" O   ASP C 271 " (cutoff:3.500A)
    Processing sheet with id=AB4, first strand: chain 'C' and resid 260 through 263
      removed outlier: 6.411A  pdb=" N   GLY C 253 " --> pdb=" O   PHE C 266 " (cutoff:3.500A)
      removed outlier: 6.975A  pdb=" N   PHE C 266 " --> pdb=" O   GLY C 253 " (cutoff:3.500A)
    Processing sheet with id=AB5, first strand: chain 'C' and resid 287 through 293
      removed outlier: 4.144A  pdb=" N   GLN C 308 " --> pdb=" O   SER C 304 " (cutoff:3.500A)
    Processing sheet with id=AB6, first strand: chain 'C' and resid 435 through 437

    431 hydrogen bonds defined for protein.
    1224 hydrogen bond angles defined for protein.
    Restraints generated for nucleic acids:
      0 hydrogen bonds
      0 hydrogen bond angles
      0 basepair planarities
      0 basepair parallelities
      0 stacking parallelities
  Total time for adding SS restraints: 1.55

  Time building geometry restraints manager: 1.06 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: 3235
        1.34 -     1.46: 1652
        1.46 -     1.57: 5053
        1.57 -     1.69: 0
        1.69 -     1.81: 83
  Bond restraints: 10023
  Sorted by residual:
  bond pdb=" CG  LEU A 726 "
       pdb=" CD1 LEU A 726 "
    ideal  model  delta    sigma   weight residual
    1.521  1.467  0.054 3.30e-02 9.18e+02 2.66e+00
  bond pdb=" N   ARG B 585 "
       pdb=" CA  ARG B 585 "
    ideal  model  delta    sigma   weight residual
    1.457  1.475 -0.017 1.29e-02 6.01e+03 1.81e+00
  bond pdb=" C   GLY B 724 "
       pdb=" O   GLY B 724 "
    ideal  model  delta    sigma   weight residual
    1.234  1.249 -0.015 1.19e-02 7.06e+03 1.55e+00
  bond pdb=" N   ILE A 594 "
       pdb=" CA  ILE A 594 "
    ideal  model  delta    sigma   weight residual
    1.474  1.456  0.019 1.57e-02 4.06e+03 1.40e+00
  bond pdb=" CG  MET A 525 "
       pdb=" SD  MET A 525 "
    ideal  model  delta    sigma   weight residual
    1.803  1.774  0.029 2.50e-02 1.60e+03 1.38e+00
  ... (remaining 10018 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     1.98: 13223
        1.98 -     3.96: 344
        3.96 -     5.94: 35
        5.94 -     7.92: 5
        7.92 -     9.90: 3
  Bond angle restraints: 13610
  Sorted by residual:
  angle pdb=" C   ARG A 498 "
        pdb=" N   GLU A 499 "
        pdb=" CA  GLU A 499 "
      ideal   model   delta    sigma   weight residual
     121.87  112.84    9.03 1.64e+00 3.72e-01 3.03e+01
  angle pdb=" N   ILE A 594 "
        pdb=" CA  ILE A 594 "
        pdb=" C   ILE A 594 "
      ideal   model   delta    sigma   weight residual
     106.21  109.89   -3.68 1.07e+00 8.73e-01 1.18e+01
  angle pdb=" CA  LEU A 678 "
        pdb=" CB  LEU A 678 "
        pdb=" CG  LEU A 678 "
      ideal   model   delta    sigma   weight residual
     116.30  106.40    9.90 3.50e+00 8.16e-02 8.00e+00
  angle pdb=" CG  MET A 525 "
        pdb=" SD  MET A 525 "
        pdb=" CE  MET A 525 "
      ideal   model   delta    sigma   weight residual
     100.90   94.87    6.03 2.20e+00 2.07e-01 7.52e+00
  angle pdb=" C   ILE A 594 "
        pdb=" CA  ILE A 594 "
        pdb=" CB  ILE A 594 "
      ideal   model   delta    sigma   weight residual
     113.22  110.33    2.89 1.12e+00 7.97e-01 6.67e+00
  ... (remaining 13605 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    17.53: 5576
       17.53 -    35.05: 416
       35.05 -    52.58: 47
       52.58 -    70.11: 9
       70.11 -    87.64: 8
  Dihedral angle restraints: 6056
    sinusoidal: 2440
      harmonic: 3616
  Sorted by residual:
  dihedral pdb=" CA  TYR A 515 "
           pdb=" C   TYR A 515 "
           pdb=" N   ASP A 516 "
           pdb=" CA  ASP A 516 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  160.48   19.52     0      5.00e+00 4.00e-02 1.52e+01
  dihedral pdb=" CA  ASN B 737 "
           pdb=" C   ASN B 737 "
           pdb=" N   GLU B 738 "
           pdb=" CA  GLU B 738 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  161.39   18.61     0      5.00e+00 4.00e-02 1.39e+01
  dihedral pdb=" CA  PHE A 765 "
           pdb=" C   PHE A 765 "
           pdb=" N   HIS A 766 "
           pdb=" CA  HIS A 766 "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00 -161.44  -18.56     0      5.00e+00 4.00e-02 1.38e+01
  ... (remaining 6053 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.032: 896
       0.032 -    0.064: 407
       0.064 -    0.097: 164
       0.097 -    0.129: 62
       0.129 -    0.161: 10
  Chirality restraints: 1539
  Sorted by residual:
  chirality pdb=" CG  LEU A 674 "
            pdb=" CB  LEU A 674 "
            pdb=" CD1 LEU A 674 "
            pdb=" CD2 LEU A 674 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.59   -2.75    0.16 2.00e-01 2.50e+01 6.47e-01
  chirality pdb=" CA  ILE C 302 "
            pdb=" N   ILE C 302 "
            pdb=" C   ILE C 302 "
            pdb=" CB  ILE C 302 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.43    2.59   -0.16 2.00e-01 2.50e+01 6.30e-01
  chirality pdb=" CG  LEU A 726 "
            pdb=" CB  LEU A 726 "
            pdb=" CD1 LEU A 726 "
            pdb=" CD2 LEU A 726 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.59   -2.44   -0.15 2.00e-01 2.50e+01 5.63e-01
  ... (remaining 1536 not shown)

  Planarity restraints: 1761
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  ILE B 796 "   -0.013 2.00e-02 2.50e+03   2.59e-02 6.73e+00
        pdb=" C   ILE B 796 "    0.045 2.00e-02 2.50e+03
        pdb=" O   ILE B 796 "   -0.017 2.00e-02 2.50e+03
        pdb=" N   SER B 797 "   -0.015 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CD  ARG A 498 "    0.185 9.50e-02 1.11e+02   8.36e-02 5.35e+00
        pdb=" NE  ARG A 498 "   -0.017 2.00e-02 2.50e+03
        pdb=" CZ  ARG A 498 "    0.016 2.00e-02 2.50e+03
        pdb=" NH1 ARG A 498 "   -0.008 2.00e-02 2.50e+03
        pdb=" NH2 ARG A 498 "    0.001 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  LEU C 300 "    0.011 2.00e-02 2.50e+03   2.27e-02 5.15e+00
        pdb=" C   LEU C 300 "   -0.039 2.00e-02 2.50e+03
        pdb=" O   LEU C 300 "    0.015 2.00e-02 2.50e+03
        pdb=" N   ALA C 301 "    0.013 2.00e-02 2.50e+03
  ... (remaining 1758 not shown)

  Histogram of nonbonded interaction distances:
        2.44 -     2.93: 4366
        2.93 -     3.42: 10721
        3.42 -     3.92: 17092
        3.92 -     4.41: 19250
        4.41 -     4.90: 29700
  Nonbonded interactions: 81129
  Sorted by model distance:
  nonbonded pdb=" O   ASN B 786 "
            pdb=" OD1 ASP B 789 "
     model   vdw
     2.439 3.040
  nonbonded pdb=" O   ILE B 782 "
            pdb=" OD1 ASN B 786 "
     model   vdw
     2.506 3.040
  nonbonded pdb=" O   GLU A 714 "
            pdb=" OE1 GLU A 714 "
     model   vdw
     2.523 3.040
  nonbonded pdb=" O   ARG A 498 "
            pdb=" CA  GLU A 499 "
     model   vdw
     2.554 2.776
  nonbonded pdb=" O   ASN B 533 "
            pdb=" OD1 ASN B 533 "
     model   vdw
     2.559 3.040
  ... (remaining 81124 not shown)

  NOTE: a complete listing of the restraints can be obtained by requesting
        output of .geo file.
Find NCS groups from input model
Time spend for trying shortcut: 0.00
Found NCS groups:
ncs_group {
  reference = chain 'A'
  selection = chain 'B'
}

Set up NCS constraints
  No NCS constraints will be used in refinement.
Set refine NCS operators
Adjust number of macro_cycles
  Number of macro_cycles: 10
Reset NCS operators
Extract rigid body selections
Check and reset occupancies
  Occupancies: min=1.00 max=1.00 mean=1.00
Load rotamer database and sin/cos tables
Set ADP refinement strategy
  ADPs will be refined as group one per residue
Make a string to write initial .geo file
Internal consistency checks
Time:
  Set random seed:                         0.000
  Set model cs if undefined:               0.000
  Decide on map wrapping:                  0.000
  Normalize map: mean=0, sd=1:             6.520
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.000
  Construct map_model_manager:             0.010
  Extract box with map and model:          0.190
  Check model and map are aligned:         0.040
  Set scattering table:                    0.030
  Process input model:                     10.320
  Find NCS groups from input model:        0.110
  Set up NCS constraints:                  0.030
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.000
  Load rotamer database and sin/cos tables:1.140
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   18.390
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.5128
moved from start:          0.0000

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.054  10023  Z= 0.192
  Angle     :  0.727   9.901  13610  Z= 0.388
  Chirality :  0.045   0.161   1539
  Planarity :  0.005   0.084   1761
  Dihedral  : 12.600  87.636   3710
  Min Nonbonded Distance : 2.439

Molprobity Statistics.
  All-atom Clashscore : 18.95
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.06 %
    Favored  : 95.94 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.37 %
    Favored  : 99.63 %
  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: -0.08 (0.25), residues: 1231
  helix:  0.18 (0.25), residues: 395
  sheet: -0.16 (0.35), residues: 221
  loop : -0.01 (0.27), residues: 615

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.018   0.001   ARG A 498 
 TYR   0.026   0.002   TYR A 700 
 PHE   0.028   0.003   PHE A 699 
 TRP   0.031   0.002   TRP C 357 
 HIS   0.011   0.001   HIS A 780 

Details of bonding type rmsd
  covalent geometry    : bond        0.00392 (10023)
  covalent geometry    : angle       0.72652 (13610)
  hydrogen bonds       : bond        0.10511 (  427)
  hydrogen bonds       : angle       6.43933 ( 1224)

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

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

  2462 Ramachandran restraints generated.
    1231 Oldfield, 0 Emsley, 1231 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2462 Ramachandran restraints generated.
    1231 Oldfield, 0 Emsley, 1231 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  119 residues out of total 1086 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 119
  time to evaluate  : 0.379 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  485 MET cc_start: 0.7101 (mmp) cc_final: 0.6765 (mmp)
REVERT: A  575 ARG cc_start: 0.8350 (tmt170) cc_final: 0.7878 (tpt90)
REVERT: A  593 LEU cc_start: 0.9088 (mt) cc_final: 0.8806 (mt)
REVERT: A  600 LEU cc_start: 0.8414 (mt) cc_final: 0.8077 (mt)
REVERT: A  662 LEU cc_start: 0.8769 (mt) cc_final: 0.8394 (mt)
REVERT: A  674 LEU cc_start: 0.6683 (mt) cc_final: 0.6396 (mt)
REVERT: C  274 MET cc_start: 0.3150 (ptt) cc_final: 0.2627 (ptp)
  outliers start: 0
  outliers final: 0
  residues processed: 119
  average time/residue: 0.0926
  time to fit residues: 15.9621
Evaluate side-chains
  87 residues out of total 1086 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 87
  time to evaluate  : 0.326 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 122
   random chunks:
   chunk 108 optimal weight:    5.9990
   chunk 49 optimal weight:    2.9990
   chunk 97 optimal weight:   10.0000
   chunk 113 optimal weight:    5.9990
   chunk 53 optimal weight:    6.9990
   chunk 5 optimal weight:    2.9990
   chunk 33 optimal weight:    5.9990
   chunk 65 optimal weight:    5.9990
   chunk 62 optimal weight:    0.9980
   chunk 51 optimal weight:    3.9990
   chunk 117 optimal weight:    0.0970
   overall best weight:    2.2184

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

Flipped N/Q/H residues before XYZ refinement:
A 518 HIS
A 673 ASN
** A 707 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 780 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 491 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 554 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 707 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 710 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 766 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 780 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
C 245 HIS
C 325 HIS
C 355 HIS
C 390 GLN

Total number of N/Q/H flips: 6

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4162 r_free = 0.4162 target = 0.086866 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 56)----------------|
| r_work = 0.3709 r_free = 0.3709 target = 0.067784 restraints weight = 80710.508|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 41)----------------|
| r_work = 0.3738 r_free = 0.3738 target = 0.069031 restraints weight = 65024.766|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 30)----------------|
| r_work = 0.3757 r_free = 0.3757 target = 0.069765 restraints weight = 56105.079|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 27)----------------|
| r_work = 0.3772 r_free = 0.3772 target = 0.070424 restraints weight = 50677.324|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 29)----------------|
| r_work = 0.3780 r_free = 0.3780 target = 0.070741 restraints weight = 47216.993|
|-----------------------------------------------------------------------------|
r_work (final): 0.3721
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7136
moved from start:          0.0871

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.031  10023  Z= 0.188
  Angle     :  0.632  11.137  13610  Z= 0.327
  Chirality :  0.043   0.159   1539
  Planarity :  0.004   0.033   1761
  Dihedral  :  4.839  18.079   1339
  Min Nonbonded Distance : 2.490

Molprobity Statistics.
  All-atom Clashscore : 18.33
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.74 %
    Favored  : 96.26 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  4.42 %
    Favored  : 95.58 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  0.16 (0.25), residues: 1231
  helix:  0.56 (0.25), residues: 400
  sheet: -0.08 (0.35), residues: 231
  loop :  0.02 (0.28), residues: 600

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.009   0.001   ARG A 728 
 TYR   0.018   0.002   TYR B 515 
 PHE   0.018   0.002   PHE A 699 
 TRP   0.048   0.002   TRP C 411 
 HIS   0.007   0.001   HIS A 780 

Details of bonding type rmsd
  covalent geometry    : bond        0.00378 (10023)
  covalent geometry    : angle       0.63194 (13610)
  hydrogen bonds       : bond        0.05158 (  427)
  hydrogen bonds       : angle       5.70070 ( 1224)

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

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

  2462 Ramachandran restraints generated.
    1231 Oldfield, 0 Emsley, 1231 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2462 Ramachandran restraints generated.
    1231 Oldfield, 0 Emsley, 1231 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  121 residues out of total 1086 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 121
  time to evaluate  : 0.425 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  513 PHE cc_start: 0.8708 (m-80) cc_final: 0.8465 (m-80)
REVERT: A  524 MET cc_start: 0.8846 (tpt) cc_final: 0.8353 (tpp)
REVERT: A  554 HIS cc_start: 0.7658 (m-70) cc_final: 0.7190 (m-70)
REVERT: A  575 ARG cc_start: 0.8977 (tmt170) cc_final: 0.8524 (tpt90)
REVERT: A  587 MET cc_start: 0.8877 (mmp) cc_final: 0.8609 (mmp)
  outliers start: 0
  outliers final: 0
  residues processed: 121
  average time/residue: 0.0905
  time to fit residues: 15.8685
Evaluate side-chains
  86 residues out of total 1086 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 86
  time to evaluate  : 0.276 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 122
   random chunks:
   chunk 110 optimal weight:    8.9990
   chunk 84 optimal weight:   10.0000
   chunk 6 optimal weight:    4.9990
   chunk 47 optimal weight:    4.9990
   chunk 49 optimal weight:    3.9990
   chunk 113 optimal weight:    6.9990
   chunk 33 optimal weight:    5.9990
   chunk 44 optimal weight:    9.9990
   chunk 67 optimal weight:    3.9990
   chunk 76 optimal weight:    5.9990
   chunk 43 optimal weight:   10.0000
   overall best weight:    4.7990

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

Flipped N/Q/H residues before XYZ refinement:
** A 491 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 578 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
A 702 GLN
** A 707 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 780 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 491 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
B 493 ASN
** B 666 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 682 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 766 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 = 0.4044 r_free = 0.4044 target = 0.081149 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 43)----------------|
| r_work = 0.3593 r_free = 0.3593 target = 0.063279 restraints weight = 85729.548|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 49)----------------|
| r_work = 0.3618 r_free = 0.3618 target = 0.064298 restraints weight = 70334.926|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 34)----------------|
| r_work = 0.3636 r_free = 0.3636 target = 0.064976 restraints weight = 61373.261|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 33)----------------|
| r_work = 0.3649 r_free = 0.3649 target = 0.065487 restraints weight = 55904.751|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 27)----------------|
| r_work = 0.3655 r_free = 0.3655 target = 0.065730 restraints weight = 52339.146|
|-----------------------------------------------------------------------------|
r_work (final): 0.3516
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7317
moved from start:          0.2208

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.007   0.061  10023  Z= 0.354
  Angle     :  0.885  19.564  13610  Z= 0.457
  Chirality :  0.050   0.239   1539
  Planarity :  0.006   0.061   1761
  Dihedral  :  5.642  21.342   1339
  Min Nonbonded Distance : 2.416

Molprobity Statistics.
  All-atom Clashscore : 32.48
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.28 %
    Favored  : 94.72 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  5.71 %
    Favored  : 94.29 %
  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: -0.89 (0.24), residues: 1231
  helix: -0.74 (0.24), residues: 394
  sheet: -0.48 (0.35), residues: 214
  loop : -0.37 (0.26), residues: 623

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.011   0.001   ARG B 468 
 TYR   0.021   0.003   TYR B 515 
 PHE   0.029   0.003   PHE A 608 
 TRP   0.035   0.004   TRP C 411 
 HIS   0.009   0.002   HIS B 491 

Details of bonding type rmsd
  covalent geometry    : bond        0.00716 (10023)
  covalent geometry    : angle       0.88538 (13610)
  hydrogen bonds       : bond        0.06594 (  427)
  hydrogen bonds       : angle       6.59312 ( 1224)

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

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

  2462 Ramachandran restraints generated.
    1231 Oldfield, 0 Emsley, 1231 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2462 Ramachandran restraints generated.
    1231 Oldfield, 0 Emsley, 1231 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  111 residues out of total 1086 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 111
  time to evaluate  : 0.313 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  524 MET cc_start: 0.8963 (tpt) cc_final: 0.7883 (tpp)
REVERT: A  554 HIS cc_start: 0.7741 (m-70) cc_final: 0.7460 (m-70)
REVERT: A  575 ARG cc_start: 0.9193 (tmt170) cc_final: 0.8659 (tpt90)
REVERT: A  593 LEU cc_start: 0.9407 (mt) cc_final: 0.9193 (mt)
REVERT: A  600 LEU cc_start: 0.8900 (mt) cc_final: 0.8630 (mt)
REVERT: A  678 LEU cc_start: 0.8614 (mt) cc_final: 0.8369 (mt)
REVERT: B  485 MET cc_start: 0.9256 (mmp) cc_final: 0.9029 (mmp)
REVERT: C  357 TRP cc_start: 0.9036 (m100) cc_final: 0.8271 (m100)
  outliers start: 0
  outliers final: 0
  residues processed: 111
  average time/residue: 0.0899
  time to fit residues: 14.3540
Evaluate side-chains
  89 residues out of total 1086 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 89
  time to evaluate  : 0.332 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 122
   random chunks:
   chunk 71 optimal weight:    0.9980
   chunk 66 optimal weight:    0.9990
   chunk 72 optimal weight:    0.9980
   chunk 69 optimal weight:    0.6980
   chunk 82 optimal weight:    5.9990
   chunk 81 optimal weight:    0.9990
   chunk 20 optimal weight:    2.9990
   chunk 79 optimal weight:    6.9990
   chunk 26 optimal weight:    2.9990
   chunk 22 optimal weight:    0.6980
   chunk 35 optimal weight:    3.9990
   overall best weight:    0.8782

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

Flipped N/Q/H residues before XYZ refinement:
A 578 HIS
A 603 ASN
** A 707 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 780 HIS
** B 666 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 707 GLN
** B 766 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 780 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
C 123 GLN
C 305 GLN
C 355 HIS

Total number of N/Q/H flips: 7

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4153 r_free = 0.4153 target = 0.086268 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 54)----------------|
| r_work = 0.3706 r_free = 0.3706 target = 0.067497 restraints weight = 81104.657|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 32)----------------|
| r_work = 0.3736 r_free = 0.3736 target = 0.068710 restraints weight = 64755.954|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 34)----------------|
| r_work = 0.3757 r_free = 0.3757 target = 0.069683 restraints weight = 55476.535|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 26)----------------|
| r_work = 0.3771 r_free = 0.3771 target = 0.070271 restraints weight = 49728.821|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 25)----------------|
| r_work = 0.3778 r_free = 0.3778 target = 0.070524 restraints weight = 46135.809|
|-----------------------------------------------------------------------------|
r_work (final): 0.3722
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7128
moved from start:          0.2126

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.044  10023  Z= 0.133
  Angle     :  0.620   8.451  13610  Z= 0.315
  Chirality :  0.044   0.174   1539
  Planarity :  0.004   0.038   1761
  Dihedral  :  5.123  19.718   1339
  Min Nonbonded Distance : 2.537

Molprobity Statistics.
  All-atom Clashscore : 14.86
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.33 %
    Favored  : 96.67 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  3.50 %
    Favored  : 96.50 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -0.26 (0.24), residues: 1231
  helix:  0.22 (0.25), residues: 403
  sheet: -0.37 (0.37), residues: 202
  loop : -0.24 (0.27), residues: 626

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.001   ARG A 709 
 TYR   0.014   0.001   TYR B 515 
 PHE   0.017   0.002   PHE A 513 
 TRP   0.017   0.002   TRP C 411 
 HIS   0.005   0.001   HIS C  80 

Details of bonding type rmsd
  covalent geometry    : bond        0.00278 (10023)
  covalent geometry    : angle       0.62050 (13610)
  hydrogen bonds       : bond        0.04878 (  427)
  hydrogen bonds       : angle       5.69443 ( 1224)

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

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

  2462 Ramachandran restraints generated.
    1231 Oldfield, 0 Emsley, 1231 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2462 Ramachandran restraints generated.
    1231 Oldfield, 0 Emsley, 1231 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  120 residues out of total 1086 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 120
  time to evaluate  : 0.464 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  518 HIS cc_start: 0.8899 (m90) cc_final: 0.8632 (m90)
REVERT: A  524 MET cc_start: 0.8851 (tpt) cc_final: 0.7983 (tpt)
REVERT: A  554 HIS cc_start: 0.7851 (m-70) cc_final: 0.7453 (m-70)
REVERT: A  575 ARG cc_start: 0.8937 (tmt170) cc_final: 0.8448 (tpt90)
REVERT: A  587 MET cc_start: 0.8601 (mmp) cc_final: 0.8366 (mmp)
REVERT: A  678 LEU cc_start: 0.8721 (mt) cc_final: 0.8491 (mt)
REVERT: C  274 MET cc_start: 0.4955 (ptt) cc_final: 0.4492 (ppp)
REVERT: C  357 TRP cc_start: 0.8976 (m100) cc_final: 0.8396 (m100)
  outliers start: 0
  outliers final: 0
  residues processed: 120
  average time/residue: 0.0950
  time to fit residues: 16.6455
Evaluate side-chains
  86 residues out of total 1086 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 86
  time to evaluate  : 0.380 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 122
   random chunks:
   chunk 17 optimal weight:    3.9990
   chunk 33 optimal weight:    0.7980
   chunk 23 optimal weight:    0.9980
   chunk 114 optimal weight:    0.3980
   chunk 72 optimal weight:    1.9990
   chunk 47 optimal weight:    3.9990
   chunk 68 optimal weight:    0.4980
   chunk 88 optimal weight:    8.9990
   chunk 97 optimal weight:   10.0000
   chunk 24 optimal weight:    2.9990
   chunk 36 optimal weight:    0.9980
   overall best weight:    0.7380

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

Flipped N/Q/H residues before XYZ refinement:
A 707 GLN
** B 491 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 766 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 780 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
C 355 HIS

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4178 r_free = 0.4178 target = 0.087490 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 57)----------------|
| r_work = 0.3726 r_free = 0.3726 target = 0.068677 restraints weight = 79248.285|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 31)----------------|
| r_work = 0.3756 r_free = 0.3756 target = 0.069858 restraints weight = 63362.158|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 41)----------------|
| r_work = 0.3780 r_free = 0.3780 target = 0.070886 restraints weight = 54277.635|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 27)----------------|
| r_work = 0.3792 r_free = 0.3792 target = 0.071393 restraints weight = 48546.879|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 29)----------------|
| r_work = 0.3804 r_free = 0.3804 target = 0.071886 restraints weight = 45188.490|
|-----------------------------------------------------------------------------|
r_work (final): 0.3753
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7081
moved from start:          0.2260

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.041  10023  Z= 0.118
  Angle     :  0.588   8.426  13610  Z= 0.295
  Chirality :  0.042   0.153   1539
  Planarity :  0.004   0.036   1761
  Dihedral  :  4.817  19.507   1339
  Min Nonbonded Distance : 2.554

Molprobity Statistics.
  All-atom Clashscore : 13.53
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.49 %
    Favored  : 96.51 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  2.21 %
    Favored  : 97.79 %
  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:  0.14 (0.25), residues: 1231
  helix:  0.84 (0.26), residues: 403
  sheet: -0.30 (0.37), residues: 193
  loop : -0.17 (0.27), residues: 635

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.009   0.000   ARG C 257 
 TYR   0.012   0.001   TYR B 515 
 PHE   0.012   0.001   PHE C 148 
 TRP   0.008   0.001   TRP A 775 
 HIS   0.006   0.001   HIS A 578 

Details of bonding type rmsd
  covalent geometry    : bond        0.00249 (10023)
  covalent geometry    : angle       0.58809 (13610)
  hydrogen bonds       : bond        0.04410 (  427)
  hydrogen bonds       : angle       5.35535 ( 1224)

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

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

  2462 Ramachandran restraints generated.
    1231 Oldfield, 0 Emsley, 1231 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2462 Ramachandran restraints generated.
    1231 Oldfield, 0 Emsley, 1231 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  115 residues out of total 1086 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 115
  time to evaluate  : 0.357 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  518 HIS cc_start: 0.8881 (m90) cc_final: 0.8591 (m90)
REVERT: A  524 MET cc_start: 0.8791 (tpt) cc_final: 0.7726 (tpp)
REVERT: A  554 HIS cc_start: 0.7775 (m-70) cc_final: 0.7405 (m-70)
REVERT: A  575 ARG cc_start: 0.8956 (tmt170) cc_final: 0.8536 (tpt90)
REVERT: A  587 MET cc_start: 0.8762 (mmp) cc_final: 0.8422 (mmp)
REVERT: A  600 LEU cc_start: 0.9027 (mt) cc_final: 0.8810 (mt)
REVERT: A  678 LEU cc_start: 0.8774 (mt) cc_final: 0.8563 (mt)
REVERT: C  274 MET cc_start: 0.4832 (ptt) cc_final: 0.4198 (ppp)
REVERT: C  357 TRP cc_start: 0.8945 (m100) cc_final: 0.8257 (m100)
  outliers start: 0
  outliers final: 0
  residues processed: 115
  average time/residue: 0.0912
  time to fit residues: 15.5419
Evaluate side-chains
  88 residues out of total 1086 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 88
  time to evaluate  : 0.318 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 122
   random chunks:
   chunk 54 optimal weight:    0.0980
   chunk 118 optimal weight:    0.0000
   chunk 87 optimal weight:    4.9990
   chunk 79 optimal weight:    0.9990
   chunk 61 optimal weight:    1.9990
   chunk 50 optimal weight:   10.0000
   chunk 9 optimal weight:    5.9990
   chunk 16 optimal weight:    4.9990
   chunk 35 optimal weight:    3.9990
   chunk 19 optimal weight:    4.9990
   chunk 103 optimal weight:    8.9990
   overall best weight:    1.4190

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

Flipped N/Q/H residues before XYZ refinement:
** B 491 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 737 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 766 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 780 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
C  93 HIS
C 355 HIS

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4151 r_free = 0.4151 target = 0.086332 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 51)----------------|
| r_work = 0.3707 r_free = 0.3707 target = 0.067707 restraints weight = 80387.173|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 37)----------------|
| r_work = 0.3737 r_free = 0.3737 target = 0.068962 restraints weight = 64064.177|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 28)----------------|
| r_work = 0.3754 r_free = 0.3754 target = 0.069681 restraints weight = 54961.348|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 46)----------------|
| r_work = 0.3770 r_free = 0.3770 target = 0.070434 restraints weight = 49641.590|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 24)----------------|
| r_work = 0.3779 r_free = 0.3779 target = 0.070742 restraints weight = 45894.122|
|-----------------------------------------------------------------------------|
r_work (final): 0.3734
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7127
moved from start:          0.2468

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.033  10023  Z= 0.141
  Angle     :  0.590   8.306  13610  Z= 0.301
  Chirality :  0.042   0.157   1539
  Planarity :  0.004   0.041   1761
  Dihedral  :  4.765  18.701   1339
  Min Nonbonded Distance : 2.525

Molprobity Statistics.
  All-atom Clashscore : 15.47
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.66 %
    Favored  : 96.34 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  1.38 %
    Favored  : 98.62 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  0.18 (0.25), residues: 1231
  helix:  0.89 (0.26), residues: 403
  sheet: -0.34 (0.38), residues: 195
  loop : -0.12 (0.27), residues: 633

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.001   ARG A 709 
 TYR   0.013   0.001   TYR B 515 
 PHE   0.012   0.001   PHE A 506 
 TRP   0.011   0.001   TRP A 486 
 HIS   0.007   0.001   HIS A 578 

Details of bonding type rmsd
  covalent geometry    : bond        0.00295 (10023)
  covalent geometry    : angle       0.59044 (13610)
  hydrogen bonds       : bond        0.04478 (  427)
  hydrogen bonds       : angle       5.32636 ( 1224)

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

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

  2462 Ramachandran restraints generated.
    1231 Oldfield, 0 Emsley, 1231 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2462 Ramachandran restraints generated.
    1231 Oldfield, 0 Emsley, 1231 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  116 residues out of total 1086 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 116
  time to evaluate  : 0.341 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  518 HIS cc_start: 0.8864 (m90) cc_final: 0.8609 (m90)
REVERT: A  524 MET cc_start: 0.8836 (tpt) cc_final: 0.7937 (tpt)
REVERT: A  554 HIS cc_start: 0.7792 (m-70) cc_final: 0.7458 (m-70)
REVERT: A  575 ARG cc_start: 0.8971 (tmt170) cc_final: 0.8507 (tpt90)
REVERT: A  587 MET cc_start: 0.8743 (mmp) cc_final: 0.8489 (mmm)
REVERT: A  674 LEU cc_start: 0.7545 (mt) cc_final: 0.7312 (mt)
REVERT: A  678 LEU cc_start: 0.8754 (mt) cc_final: 0.8528 (mt)
REVERT: C  158 MET cc_start: 0.8305 (tpt) cc_final: 0.5859 (mmm)
REVERT: C  357 TRP cc_start: 0.8968 (m100) cc_final: 0.8263 (m100)
  outliers start: 0
  outliers final: 0
  residues processed: 116
  average time/residue: 0.0917
  time to fit residues: 15.3790
Evaluate side-chains
  89 residues out of total 1086 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 89
  time to evaluate  : 0.417 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 122
   random chunks:
   chunk 13 optimal weight:    7.9990
   chunk 7 optimal weight:    1.9990
   chunk 43 optimal weight:    9.9990
   chunk 41 optimal weight:   20.0000
   chunk 40 optimal weight:    0.8980
   chunk 94 optimal weight:    2.9990
   chunk 87 optimal weight:    0.3980
   chunk 36 optimal weight:    2.9990
   chunk 73 optimal weight:    3.9990
   chunk 113 optimal weight:    9.9990
   chunk 58 optimal weight:    0.1980
   overall best weight:    1.2984

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

Flipped N/Q/H residues before XYZ refinement:
** B 491 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 737 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 766 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
C 355 HIS

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4152 r_free = 0.4152 target = 0.086375 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 49)----------------|
| r_work = 0.3712 r_free = 0.3712 target = 0.067989 restraints weight = 79783.706|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 27)----------------|
| r_work = 0.3742 r_free = 0.3742 target = 0.069251 restraints weight = 63525.463|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 36)----------------|
| r_work = 0.3762 r_free = 0.3762 target = 0.070151 restraints weight = 54229.523|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 39)----------------|
| r_work = 0.3777 r_free = 0.3777 target = 0.070785 restraints weight = 48606.818|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 25)----------------|
| r_work = 0.3784 r_free = 0.3784 target = 0.071022 restraints weight = 44953.612|
|-----------------------------------------------------------------------------|
r_work (final): 0.3733
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7112
moved from start:          0.2603

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.043  10023  Z= 0.131
  Angle     :  0.576   8.389  13610  Z= 0.291
  Chirality :  0.042   0.148   1539
  Planarity :  0.004   0.035   1761
  Dihedral  :  4.700  19.165   1339
  Min Nonbonded Distance : 2.521

Molprobity Statistics.
  All-atom Clashscore : 14.96
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.06 %
    Favored  : 95.94 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  1.84 %
    Favored  : 98.16 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  0.22 (0.25), residues: 1231
  helix:  1.01 (0.26), residues: 400
  sheet: -0.38 (0.38), residues: 195
  loop : -0.13 (0.27), residues: 636

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.001   ARG A 709 
 TYR   0.013   0.001   TYR B 515 
 PHE   0.012   0.001   PHE C 148 
 TRP   0.010   0.001   TRP A 486 
 HIS   0.012   0.001   HIS B 470 

Details of bonding type rmsd
  covalent geometry    : bond        0.00278 (10023)
  covalent geometry    : angle       0.57591 (13610)
  hydrogen bonds       : bond        0.04301 (  427)
  hydrogen bonds       : angle       5.23224 ( 1224)

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

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

  2462 Ramachandran restraints generated.
    1231 Oldfield, 0 Emsley, 1231 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2462 Ramachandran restraints generated.
    1231 Oldfield, 0 Emsley, 1231 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  114 residues out of total 1086 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 114
  time to evaluate  : 0.385 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  518 HIS cc_start: 0.8838 (m90) cc_final: 0.8595 (m90)
REVERT: A  524 MET cc_start: 0.8864 (tpt) cc_final: 0.7856 (tpp)
REVERT: A  554 HIS cc_start: 0.7840 (m-70) cc_final: 0.7492 (m-70)
REVERT: A  575 ARG cc_start: 0.8968 (tmt170) cc_final: 0.8505 (tpt90)
REVERT: A  587 MET cc_start: 0.8744 (mmp) cc_final: 0.8441 (mmp)
REVERT: A  674 LEU cc_start: 0.7502 (mt) cc_final: 0.7268 (mt)
REVERT: A  678 LEU cc_start: 0.8782 (mt) cc_final: 0.8575 (mt)
REVERT: C  158 MET cc_start: 0.8250 (tpt) cc_final: 0.5844 (mmm)
REVERT: C  357 TRP cc_start: 0.8989 (m100) cc_final: 0.8268 (m100)
  outliers start: 0
  outliers final: 0
  residues processed: 114
  average time/residue: 0.0953
  time to fit residues: 15.8352
Evaluate side-chains
  87 residues out of total 1086 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 87
  time to evaluate  : 0.442 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 122
   random chunks:
   chunk 94 optimal weight:    0.0980
   chunk 8 optimal weight:    8.9990
   chunk 80 optimal weight:    3.9990
   chunk 49 optimal weight:    0.9980
   chunk 78 optimal weight:    2.9990
   chunk 87 optimal weight:    4.9990
   chunk 117 optimal weight:    0.0870
   chunk 27 optimal weight:    0.0370
   chunk 37 optimal weight:    3.9990
   chunk 83 optimal weight:    0.6980
   chunk 99 optimal weight:   10.0000
   overall best weight:    0.3836

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

Flipped N/Q/H residues before XYZ refinement:
** A 528 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
A 702 GLN
** B 491 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 646 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 766 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
C 355 HIS

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4206 r_free = 0.4206 target = 0.089114 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 42)----------------|
| r_work = 0.3768 r_free = 0.3768 target = 0.070333 restraints weight = 77669.917|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 37)----------------|
| r_work = 0.3799 r_free = 0.3799 target = 0.071679 restraints weight = 61388.368|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 34)----------------|
| r_work = 0.3821 r_free = 0.3821 target = 0.072606 restraints weight = 52181.311|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 42)----------------|
| r_work = 0.3837 r_free = 0.3837 target = 0.073342 restraints weight = 46460.754|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 33)----------------|
| r_work = 0.3846 r_free = 0.3846 target = 0.073756 restraints weight = 42780.029|
|-----------------------------------------------------------------------------|
r_work (final): 0.3796
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7016
moved from start:          0.2784

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.034  10023  Z= 0.100
  Angle     :  0.566   8.728  13610  Z= 0.282
  Chirality :  0.042   0.166   1539
  Planarity :  0.004   0.037   1761
  Dihedral  :  4.460  17.908   1339
  Min Nonbonded Distance : 2.552

Molprobity Statistics.
  All-atom Clashscore : 11.54
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.09 %
    Favored  : 96.91 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.92 %
    Favored  : 99.08 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  0.41 (0.25), residues: 1231
  helix:  1.31 (0.26), residues: 400
  sheet: -0.08 (0.38), residues: 188
  loop : -0.20 (0.27), residues: 643

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.009   0.000   ARG A 709 
 TYR   0.014   0.001   TYR A 537 
 PHE   0.011   0.001   PHE C 148 
 TRP   0.006   0.001   TRP B 543 
 HIS   0.008   0.001   HIS A 528 

Details of bonding type rmsd
  covalent geometry    : bond        0.00212 (10023)
  covalent geometry    : angle       0.56625 (13610)
  hydrogen bonds       : bond        0.03885 (  427)
  hydrogen bonds       : angle       4.94861 ( 1224)

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

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

  2462 Ramachandran restraints generated.
    1231 Oldfield, 0 Emsley, 1231 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2462 Ramachandran restraints generated.
    1231 Oldfield, 0 Emsley, 1231 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  122 residues out of total 1086 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 122
  time to evaluate  : 0.382 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  466 LEU cc_start: 0.9635 (pp) cc_final: 0.9312 (mp)
REVERT: A  518 HIS cc_start: 0.8842 (m90) cc_final: 0.8596 (m90)
REVERT: A  554 HIS cc_start: 0.7855 (m-70) cc_final: 0.7452 (m-70)
REVERT: A  575 ARG cc_start: 0.8923 (tmt170) cc_final: 0.8470 (tpt90)
REVERT: A  587 MET cc_start: 0.8679 (mmp) cc_final: 0.8348 (mmp)
REVERT: A  600 LEU cc_start: 0.9037 (mt) cc_final: 0.8824 (mt)
REVERT: A  674 LEU cc_start: 0.7388 (mt) cc_final: 0.7153 (mt)
REVERT: C  108 TYR cc_start: 0.8845 (t80) cc_final: 0.8597 (t80)
REVERT: C  357 TRP cc_start: 0.8807 (m100) cc_final: 0.8198 (m100)
  outliers start: 0
  outliers final: 0
  residues processed: 122
  average time/residue: 0.0930
  time to fit residues: 16.4529
Evaluate side-chains
  87 residues out of total 1086 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 87
  time to evaluate  : 0.410 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 122
   random chunks:
   chunk 11 optimal weight:   10.0000
   chunk 43 optimal weight:    0.8980
   chunk 120 optimal weight:    2.9990
   chunk 8 optimal weight:    5.9990
   chunk 60 optimal weight:    0.9990
   chunk 91 optimal weight:    2.9990
   chunk 82 optimal weight:    2.9990
   chunk 29 optimal weight:    3.9990
   chunk 77 optimal weight:    3.9990
   chunk 68 optimal weight:    4.9990
   chunk 101 optimal weight:    5.9990
   overall best weight:    2.1788

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

Flipped N/Q/H residues before XYZ refinement:
** B 491 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
B 682 GLN
** B 766 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
C 355 HIS

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4126 r_free = 0.4126 target = 0.084822 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 44)----------------|
| r_work = 0.3679 r_free = 0.3679 target = 0.066417 restraints weight = 81489.842|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 37)----------------|
| r_work = 0.3707 r_free = 0.3707 target = 0.067633 restraints weight = 65678.900|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 36)----------------|
| r_work = 0.3728 r_free = 0.3728 target = 0.068522 restraints weight = 56440.277|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 29)----------------|
| r_work = 0.3739 r_free = 0.3739 target = 0.068995 restraints weight = 50612.224|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 35)----------------|
| r_work = 0.3750 r_free = 0.3750 target = 0.069453 restraints weight = 47304.665|
|-----------------------------------------------------------------------------|
r_work (final): 0.3713
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7166
moved from start:          0.3040

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.033  10023  Z= 0.188
  Angle     :  0.655  11.585  13610  Z= 0.333
  Chirality :  0.044   0.164   1539
  Planarity :  0.004   0.034   1761
  Dihedral  :  4.700  19.408   1339
  Min Nonbonded Distance : 2.437

Molprobity Statistics.
  All-atom Clashscore : 18.44
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.47 %
    Favored  : 95.53 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.83 %
    Favored  : 99.17 %
  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:  0.15 (0.25), residues: 1231
  helix:  0.88 (0.26), residues: 398
  sheet: -0.39 (0.37), residues: 202
  loop : -0.12 (0.27), residues: 631

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.008   0.001   ARG A 698 
 TYR   0.015   0.002   TYR B 515 
 PHE   0.016   0.002   PHE A 699 
 TRP   0.015   0.002   TRP A 486 
 HIS   0.007   0.002   HIS B 470 

Details of bonding type rmsd
  covalent geometry    : bond        0.00393 (10023)
  covalent geometry    : angle       0.65534 (13610)
  hydrogen bonds       : bond        0.04459 (  427)
  hydrogen bonds       : angle       5.35947 ( 1224)

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

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

  2462 Ramachandran restraints generated.
    1231 Oldfield, 0 Emsley, 1231 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2462 Ramachandran restraints generated.
    1231 Oldfield, 0 Emsley, 1231 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  106 residues out of total 1086 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 106
  time to evaluate  : 0.411 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  513 PHE cc_start: 0.8752 (m-80) cc_final: 0.8481 (m-80)
REVERT: A  518 HIS cc_start: 0.8840 (m90) cc_final: 0.8633 (m90)
REVERT: A  554 HIS cc_start: 0.7813 (m-70) cc_final: 0.7521 (m-70)
REVERT: A  575 ARG cc_start: 0.9038 (tmt170) cc_final: 0.8558 (tpt90)
REVERT: A  587 MET cc_start: 0.8799 (mmp) cc_final: 0.8488 (mmp)
REVERT: A  674 LEU cc_start: 0.7474 (mt) cc_final: 0.7222 (mt)
REVERT: A  678 LEU cc_start: 0.8739 (mt) cc_final: 0.8532 (mt)
REVERT: C  158 MET cc_start: 0.8464 (tpt) cc_final: 0.6267 (mmm)
REVERT: C  357 TRP cc_start: 0.8929 (m100) cc_final: 0.8235 (m100)
  outliers start: 0
  outliers final: 0
  residues processed: 106
  average time/residue: 0.1011
  time to fit residues: 15.4588
Evaluate side-chains
  82 residues out of total 1086 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 82
  time to evaluate  : 0.384 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 122
   random chunks:
   chunk 105 optimal weight:    0.7980
   chunk 31 optimal weight:    0.5980
   chunk 52 optimal weight:    8.9990
   chunk 49 optimal weight:    6.9990
   chunk 93 optimal weight:   20.0000
   chunk 98 optimal weight:    5.9990
   chunk 45 optimal weight:    0.9990
   chunk 99 optimal weight:    8.9990
   chunk 69 optimal weight:    2.9990
   chunk 57 optimal weight:    3.9990
   chunk 2 optimal weight:    6.9990
   overall best weight:    1.8786

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

Flipped N/Q/H residues before XYZ refinement:
** B 491 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 766 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
C 355 HIS

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4126 r_free = 0.4126 target = 0.084772 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 52)----------------|
| r_work = 0.3685 r_free = 0.3685 target = 0.066514 restraints weight = 80294.790|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 42)----------------|
| r_work = 0.3712 r_free = 0.3712 target = 0.067715 restraints weight = 64757.971|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 37)----------------|
| r_work = 0.3731 r_free = 0.3731 target = 0.068513 restraints weight = 55829.548|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 34)----------------|
| r_work = 0.3744 r_free = 0.3744 target = 0.069051 restraints weight = 50417.234|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 32)----------------|
| r_work = 0.3754 r_free = 0.3754 target = 0.069484 restraints weight = 47049.829|
|-----------------------------------------------------------------------------|
r_work (final): 0.3722
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7163
moved from start:          0.3205

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.033  10023  Z= 0.161
  Angle     :  0.627  10.079  13610  Z= 0.317
  Chirality :  0.043   0.175   1539
  Planarity :  0.004   0.034   1761
  Dihedral  :  4.803  18.964   1339
  Min Nonbonded Distance : 2.410

Molprobity Statistics.
  All-atom Clashscore : 17.36
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.22 %
    Favored  : 95.78 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.28 %
    Favored  : 99.72 %
  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:  0.07 (0.25), residues: 1231
  helix:  0.84 (0.26), residues: 400
  sheet: -0.42 (0.38), residues: 193
  loop : -0.22 (0.27), residues: 638

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.001   ARG A 698 
 TYR   0.015   0.001   TYR B 515 
 PHE   0.012   0.002   PHE C 210 
 TRP   0.014   0.001   TRP A 486 
 HIS   0.007   0.001   HIS B 470 

Details of bonding type rmsd
  covalent geometry    : bond        0.00337 (10023)
  covalent geometry    : angle       0.62726 (13610)
  hydrogen bonds       : bond        0.04412 (  427)
  hydrogen bonds       : angle       5.38817 ( 1224)

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

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

  2462 Ramachandran restraints generated.
    1231 Oldfield, 0 Emsley, 1231 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2462 Ramachandran restraints generated.
    1231 Oldfield, 0 Emsley, 1231 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  111 residues out of total 1086 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 111
  time to evaluate  : 0.417 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  513 PHE cc_start: 0.8739 (m-80) cc_final: 0.8538 (m-80)
REVERT: A  554 HIS cc_start: 0.7918 (m-70) cc_final: 0.7551 (m-70)
REVERT: A  575 ARG cc_start: 0.9011 (tmt170) cc_final: 0.8553 (tpt90)
REVERT: A  587 MET cc_start: 0.8734 (mmp) cc_final: 0.8437 (mmp)
REVERT: A  674 LEU cc_start: 0.7578 (mt) cc_final: 0.7330 (mt)
REVERT: A  678 LEU cc_start: 0.8738 (mt) cc_final: 0.8526 (mt)
REVERT: C  158 MET cc_start: 0.8461 (tpt) cc_final: 0.6316 (mmm)
REVERT: C  202 MET cc_start: 0.6297 (tpt) cc_final: 0.6092 (tpt)
REVERT: C  357 TRP cc_start: 0.8938 (m100) cc_final: 0.8235 (m100)
  outliers start: 0
  outliers final: 0
  residues processed: 111
  average time/residue: 0.0946
  time to fit residues: 15.0691
Evaluate side-chains
  84 residues out of total 1086 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 84
  time to evaluate  : 0.341 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 122
   random chunks:
   chunk 23 optimal weight:    0.2980
   chunk 116 optimal weight:    5.9990
   chunk 12 optimal weight:    1.9990
   chunk 44 optimal weight:    9.9990
   chunk 50 optimal weight:    3.9990
   chunk 38 optimal weight:    5.9990
   chunk 76 optimal weight:    0.7980
   chunk 89 optimal weight:    2.9990
   chunk 57 optimal weight:    0.9990
   chunk 79 optimal weight:    5.9990
   chunk 90 optimal weight:    3.9990
   overall best weight:    1.4186

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

Flipped N/Q/H residues before XYZ refinement:
** B 491 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 766 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
C 355 HIS

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4146 r_free = 0.4146 target = 0.085623 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 52)----------------|
| r_work = 0.3700 r_free = 0.3700 target = 0.067104 restraints weight = 80926.448|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 39)----------------|
| r_work = 0.3729 r_free = 0.3729 target = 0.068317 restraints weight = 65004.464|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 28)----------------|
| r_work = 0.3748 r_free = 0.3748 target = 0.069084 restraints weight = 55965.269|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 39)----------------|
| r_work = 0.3763 r_free = 0.3763 target = 0.069768 restraints weight = 50667.460|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 19)----------------|
| r_work = 0.3770 r_free = 0.3770 target = 0.070025 restraints weight = 46889.338|
|-----------------------------------------------------------------------------|
r_work (final): 0.3723
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7151
moved from start:          0.3310

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.038  10023  Z= 0.139
  Angle     :  0.613   9.384  13610  Z= 0.307
  Chirality :  0.043   0.177   1539
  Planarity :  0.004   0.033   1761
  Dihedral  :  4.762  18.745   1339
  Min Nonbonded Distance : 2.453

Molprobity Statistics.
  All-atom Clashscore : 16.04
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.31 %
    Favored  : 95.69 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.37 %
    Favored  : 99.63 %
  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:  0.12 (0.25), residues: 1231
  helix:  0.91 (0.26), residues: 400
  sheet: -0.26 (0.39), residues: 184
  loop : -0.27 (0.26), residues: 647

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.001   ARG A 709 
 TYR   0.014   0.001   TYR B 515 
 PHE   0.010   0.001   PHE C 148 
 TRP   0.010   0.001   TRP A 486 
 HIS   0.006   0.001   HIS B 470 

Details of bonding type rmsd
  covalent geometry    : bond        0.00293 (10023)
  covalent geometry    : angle       0.61298 (13610)
  hydrogen bonds       : bond        0.04263 (  427)
  hydrogen bonds       : angle       5.32138 ( 1224)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 1903.31 seconds
wall clock time: 33 minutes 47.09 seconds (2027.09 seconds total)