Starting phenix.real_space_refine
on Sat May  2 13:56:01 2026 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/9i98_52755/05_2026/9i98_52755_trim.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/9i98_52755/05_2026/9i98_52755.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=2.86
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/9i98_52755/05_2026/9i98_52755.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/9i98_52755/05_2026/9i98_52755.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/9i98_52755/05_2026/9i98_52755_trim.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/9i98_52755/05_2026/9i98_52755_trim.cif"
  }
  resolution = 2.86
  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=   0.011
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      26      5.16       5
     C    3759      2.51       5
     N    1001      2.21       5
     O    1177      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 6 residue(s): 0.00s

  Monomer Library directory:
    "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.1rc2-6044/lib/python3.9/site-packages/chem_data/mon_lib"
  Total number of atoms: 5963
  Number of models: 1
  Model: ""
    Number of chains: 6
    Chain: "A"
      Number of atoms: 4535
      Number of conformers: 2
      Conformer: "A"
        Number of residues, atoms: 552, 4527
          Classifications: {'peptide': 552}
          Link IDs: {'PTRANS': 20, 'TRANS': 531}
          Chain breaks: 1
      Conformer: "B"
        Number of residues, atoms: 552, 4527
          Classifications: {'peptide': 552}
          Link IDs: {'PTRANS': 20, 'TRANS': 531}
          Chain breaks: 1
          bond proxies already assigned to first conformer: 4641
    Chain: "B"
      Number of atoms: 1170
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 149, 1170
          Classifications: {'peptide': 149}
          Link IDs: {'PTRANS': 8, 'TRANS': 140}
    Chain: "C"
      Number of atoms: 137
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 17, 137
          Classifications: {'peptide': 17}
          Link IDs: {'PTRANS': 1, 'TRANS': 15}
    Chain: "C"
      Number of atoms: 1
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 1, 1
          Unusual residues: {'NH2': 1}
          Classifications: {'undetermined': 1}
    Chain: "A"
      Number of atoms: 105
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 3, 105
          Unusual residues: {'LMT': 3}
          Classifications: {'undetermined': 3}
          Link IDs: {None: 2}
    Chain: "C"
      Number of atoms: 15
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 1, 15
          Unusual residues: {'R06': 1}
          Classifications: {'undetermined': 1}
          Unresolved non-hydrogen bonds: 3
          Unresolved non-hydrogen angles: 3
          Unresolved non-hydrogen dihedrals: 6
  Residues with excluded nonbonded symmetry interactions: 1
    residue:
      pdb=" N  AASN A 367 " occ=0.73
      ... (14 atoms not shown)
      pdb=" ND2BASN A 367 " occ=0.27
  Time building chain proxies: 2.37, per 1000 atoms: 0.40
  Number of scatterers: 5963
  At special positions: 0
  Unit cell: (85.293, 76.545, 88.209, 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      26     16.00
     O    1177      8.00
     N    1001      7.00
     C    3759      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=4, symmetry=0
  Number of additional bonds: simple=4, symmetry=0
  Coordination:
  Other bonds:
  Time building additional restraints: 0.51
  Conformation dependent library (CDL) restraints added in 326.2 milliseconds
  

  1426 Ramachandran restraints generated.
    713 Oldfield, 0 Emsley, 713 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  1356

  Finding SS restraints...
    Secondary structure from input PDB file:
      11 helices and 3 sheets defined
      14.3% alpha, 52.5% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.12
  Creating SS restraints...
    Processing helix  chain 'A' and resid 295 through 302
    Processing helix  chain 'A' and resid 463 through 470
    Processing helix  chain 'A' and resid 536 through 541
      removed outlier: 4.267A  pdb=" N   PHE A 541 " --> pdb=" O   TYR A 537 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 660 through 668
    Processing helix  chain 'A' and resid 669 through 673
    Processing helix  chain 'A' and resid 768 through 774
    Processing helix  chain 'B' and resid 1025 through 1038
    Processing helix  chain 'B' and resid 1109 through 1111
      No H-bonds generated for 'chain 'B' and resid 1109 through 1111'
    Processing helix  chain 'B' and resid 1112 through 1138
      removed outlier: 4.164A  pdb=" N   ASP B1129 " --> pdb=" O   LYS B1125 " (cutoff:3.500A)
      removed outlier: 3.630A  pdb=" N   LEU B1135 " --> pdb=" O   ALA B1131 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 1138 through 1147
    Processing helix  chain 'C' and resid 4 through 9
      removed outlier: 3.635A  pdb=" N   ASP C   7 " --> pdb=" O   ASP C   4 " (cutoff:3.500A)
      removed outlier: 3.659A  pdb=" N   TRP C   8 " --> pdb=" O   PHE C   5 " (cutoff:3.500A)
    Processing sheet with id=AA1, first strand: chain 'A' and resid 227 through 228
      removed outlier: 6.569A  pdb=" N   MET A 255 " --> pdb=" O   ILE A 251 " (cutoff:3.500A)
      removed outlier: 6.590A  pdb=" N   HIS A 745 " --> pdb=" O   TRP A 739 " (cutoff:3.500A)
      removed outlier: 4.935A  pdb=" N   TRP A 739 " --> pdb=" O   HIS A 745 " (cutoff:3.500A)
      removed outlier: 5.106A  pdb=" N   VAL A 747 " --> pdb=" O   ASN A 737 " (cutoff:3.500A)
      removed outlier: 8.413A  pdb=" N   ALA A 713 " --> pdb=" O   LEU A 736 " (cutoff:3.500A)
      removed outlier: 13.123A  pdb=" N   GLY A 738 " --> pdb=" O   LYS A 711 " (cutoff:3.500A)
      removed outlier: 13.392A  pdb=" N   LYS A 711 " --> pdb=" O   GLY A 738 " (cutoff:3.500A)
      removed outlier: 6.753A  pdb=" N   TYR A 704 " --> pdb=" O   ALA A 713 " (cutoff:3.500A)
      removed outlier: 4.361A  pdb=" N   SER A 715 " --> pdb=" O   ALA A 702 " (cutoff:3.500A)
      removed outlier: 6.488A  pdb=" N   ALA A 702 " --> pdb=" O   SER A 715 " (cutoff:3.500A)
      removed outlier: 4.313A  pdb=" N   LEU A 717 " --> pdb=" O   VAL A 700 " (cutoff:3.500A)
      removed outlier: 6.538A  pdb=" N   VAL A 700 " --> pdb=" O   LEU A 717 " (cutoff:3.500A)
      removed outlier: 4.076A  pdb=" N   VAL A 719 " --> pdb=" O   SER A 698 " (cutoff:3.500A)
      removed outlier: 6.497A  pdb=" N   SER A 698 " --> pdb=" O   VAL A 719 " (cutoff:3.500A)
      removed outlier: 4.161A  pdb=" N   LEU A 651 " --> pdb=" O   SER A 690 " (cutoff:3.500A)
      removed outlier: 6.477A  pdb=" N   ARG A 650 " --> pdb=" O   ARG A 646 " (cutoff:3.500A)
      removed outlier: 5.529A  pdb=" N   VAL A 635 " --> pdb=" O   ASP A 629 " (cutoff:3.500A)
      removed outlier: 6.411A  pdb=" N   ASP A 629 " --> pdb=" O   VAL A 635 " (cutoff:3.500A)
      removed outlier: 3.604A  pdb=" N   THR A 637 " --> pdb=" O   GLN A 627 " (cutoff:3.500A)
      removed outlier: 5.544A  pdb=" N   SER A 605 " --> pdb=" O   TYR A 584 " (cutoff:3.500A)
      removed outlier: 6.944A  pdb=" N   TYR A 584 " --> pdb=" O   SER A 605 " (cutoff:3.500A)
      removed outlier: 3.757A  pdb=" N   VAL A 607 " --> pdb=" O   ILE A 582 " (cutoff:3.500A)
      removed outlier: 6.503A  pdb=" N   ILE A 566 " --> pdb=" O   ARG A 574 " (cutoff:3.500A)
      removed outlier: 4.065A  pdb=" N   ASN A 576 " --> pdb=" O   SER A 564 " (cutoff:3.500A)
      removed outlier: 6.480A  pdb=" N   SER A 564 " --> pdb=" O   ASN A 576 " (cutoff:3.500A)
      removed outlier: 4.329A  pdb=" N   SER A 578 " --> pdb=" O   VAL A 562 " (cutoff:3.500A)
      removed outlier: 6.755A  pdb=" N   VAL A 562 " --> pdb=" O   SER A 578 " (cutoff:3.500A)
      removed outlier: 4.441A  pdb=" N   GLY A 580 " --> pdb=" O   THR A 560 " (cutoff:3.500A)
      removed outlier: 6.849A  pdb=" N   THR A 560 " --> pdb=" O   GLY A 580 " (cutoff:3.500A)
      removed outlier: 4.759A  pdb=" N   ILE A 582 " --> pdb=" O   VAL A 558 " (cutoff:3.500A)
      removed outlier: 6.689A  pdb=" N   VAL A 558 " --> pdb=" O   ILE A 582 " (cutoff:3.500A)
      removed outlier: 4.825A  pdb=" N   TYR A 584 " --> pdb=" O   ASN A 556 " (cutoff:3.500A)
      removed outlier: 7.511A  pdb=" N   ASN A 556 " --> pdb=" O   TYR A 584 " (cutoff:3.500A)
      removed outlier: 4.718A  pdb=" N   TYR A 504 " --> pdb=" O   MET A 497 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'A' and resid 227 through 228
      removed outlier: 6.569A  pdb=" N   MET A 255 " --> pdb=" O   ILE A 251 " (cutoff:3.500A)
      removed outlier: 4.593A  pdb=" N   THR A 356 " --> pdb=" O   THR A 332 " (cutoff:3.500A)
      removed outlier: 9.153A  pdb=" N   VAL A 334 " --> pdb=" O   TYR A 354 " (cutoff:3.500A)
      removed outlier: 11.403A  pdb=" N   TYR A 354 " --> pdb=" O   VAL A 334 " (cutoff:3.500A)
      removed outlier: 3.565A  pdb=" N   PHE A 368 " --> pdb=" O   VAL A 365 " (cutoff:3.500A)
      removed outlier: 4.653A  pdb=" N   LYS A 375 " --> pdb=" O   GLU A 391 " (cutoff:3.500A)
      removed outlier: 4.747A  pdb=" N   GLU A 391 " --> pdb=" O   LYS A 375 " (cutoff:3.500A)
      removed outlier: 8.044A  pdb=" N   PHE A 377 " --> pdb=" O   SER A 389 " (cutoff:3.500A)
      removed outlier: 7.254A  pdb=" N   SER A 389 " --> pdb=" O   PHE A 377 " (cutoff:3.500A)
      removed outlier: 5.326A  pdb=" N   ALA A 390 " --> pdb=" O   VAL A 418 " (cutoff:3.500A)
      removed outlier: 7.036A  pdb=" N   VAL A 418 " --> pdb=" O   ALA A 390 " (cutoff:3.500A)
      removed outlier: 6.090A  pdb=" N   PHE A 406 " --> pdb=" O   ASP A 402 " (cutoff:3.500A)
      removed outlier: 4.718A  pdb=" N   TYR A 504 " --> pdb=" O   MET A 497 " (cutoff:3.500A)
    Processing sheet with id=AA3, first strand: chain 'B' and resid 1041 through 1043
      removed outlier: 6.770A  pdb=" N   MET B1016 " --> pdb=" O   LEU B1043 " (cutoff:3.500A)
      removed outlier: 7.148A  pdb=" N   SER B1054 " --> pdb=" O   ILE B1090 " (cutoff:3.500A)
      removed outlier: 5.337A  pdb=" N   ILE B1090 " --> pdb=" O   SER B1054 " (cutoff:3.500A)
      removed outlier: 7.138A  pdb=" N   ARG B1056 " --> pdb=" O   VAL B1088 " (cutoff:3.500A)
      removed outlier: 5.544A  pdb=" N   VAL B1088 " --> pdb=" O   ARG B1056 " (cutoff:3.500A)
      removed outlier: 6.138A  pdb=" N   GLY B1058 " --> pdb=" O   ALA B1086 " (cutoff:3.500A)
      removed outlier: 6.396A  pdb=" N   ALA B1086 " --> pdb=" O   GLY B1058 " (cutoff:3.500A)
      removed outlier: 7.098A  pdb=" N   VAL B1060 " --> pdb=" O   VAL B1084 " (cutoff:3.500A)
      removed outlier: 6.966A  pdb=" N   VAL B1084 " --> pdb=" O   VAL B1060 " (cutoff:3.500A)
      removed outlier: 6.885A  pdb=" N   ILE B1062 " --> pdb=" O   MET B1082 " (cutoff:3.500A)
      removed outlier: 6.898A  pdb=" N   MET B1082 " --> pdb=" O   ILE B1062 " (cutoff:3.500A)
      removed outlier: 6.784A  pdb=" N   LYS B1064 " --> pdb=" O   MET B1080 " (cutoff:3.500A)
      removed outlier: 6.742A  pdb=" N   MET B1080 " --> pdb=" O   LYS B1064 " (cutoff:3.500A)
      removed outlier: 6.872A  pdb=" N   THR B1066 " --> pdb=" O   TYR B1078 " (cutoff:3.500A)
      removed outlier: 6.769A  pdb=" N   TYR B1078 " --> pdb=" O   THR B1066 " (cutoff:3.500A)
      removed outlier: 6.583A  pdb=" N   SER B1068 " --> pdb=" O   ALA B1076 " (cutoff:3.500A)

    323 hydrogen bonds defined for protein.
    897 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: 1.04

  Time building geometry restraints manager: 0.56 seconds

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

  Histogram of bond lengths:
        1.18 -     1.31: 990
        1.31 -     1.44: 1818
        1.44 -     1.56: 3256
        1.56 -     1.69: 2
        1.69 -     1.81: 46
  Bond restraints: 6112
  Sorted by residual:
  bond pdb=" C2  R06 C 101 "
       pdb=" N1  R06 C 101 "
    ideal  model  delta    sigma   weight residual
    1.364  1.465 -0.101 2.00e-02 2.50e+03 2.54e+01
  bond pdb=" C4  R06 C 101 "
       pdb=" N2  R06 C 101 "
    ideal  model  delta    sigma   weight residual
    1.362  1.461 -0.099 2.00e-02 2.50e+03 2.44e+01
  bond pdb=" C7  R06 C 101 "
       pdb=" N3  R06 C 101 "
    ideal  model  delta    sigma   weight residual
    1.368  1.451 -0.083 2.00e-02 2.50e+03 1.72e+01
  bond pdb=" C3' LMT A 803 "
       pdb=" O3' LMT A 803 "
    ideal  model  delta    sigma   weight residual
    1.404  1.360  0.044 2.00e-02 2.50e+03 4.83e+00
  bond pdb=" C3' LMT A 802 "
       pdb=" O3' LMT A 802 "
    ideal  model  delta    sigma   weight residual
    1.404  1.360  0.044 2.00e-02 2.50e+03 4.81e+00
  ... (remaining 6107 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     2.16: 8084
        2.16 -     4.32: 166
        4.32 -     6.49: 41
        6.49 -     8.65: 6
        8.65 -    10.81: 6
  Bond angle restraints: 8303
  Sorted by residual:
  angle pdb=" C2  LMT A 801 "
        pdb=" C3  LMT A 801 "
        pdb=" C4  LMT A 801 "
      ideal   model   delta    sigma   weight residual
     117.09  106.82   10.27 3.00e+00 1.11e-01 1.17e+01
  angle pdb=" N2  R06 C 101 "
        pdb=" C6  R06 C 101 "
        pdb=" N3  R06 C 101 "
      ideal   model   delta    sigma   weight residual
     109.46  119.53  -10.07 3.00e+00 1.11e-01 1.13e+01
  angle pdb=" C2  LMT A 802 "
        pdb=" C3  LMT A 802 "
        pdb=" C4  LMT A 802 "
      ideal   model   delta    sigma   weight residual
     117.09  107.30    9.79 3.00e+00 1.11e-01 1.07e+01
  angle pdb=" CA  LEU A 500 "
        pdb=" CB  LEU A 500 "
        pdb=" CG  LEU A 500 "
      ideal   model   delta    sigma   weight residual
     116.30  127.11  -10.81 3.50e+00 8.16e-02 9.54e+00
  angle pdb=" C2  LMT A 803 "
        pdb=" C3  LMT A 803 "
        pdb=" C4  LMT A 803 "
      ideal   model   delta    sigma   weight residual
     117.09  108.09    9.00 3.00e+00 1.11e-01 8.99e+00
  ... (remaining 8298 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    27.47: 3540
       27.47 -    54.93: 130
       54.93 -    82.40: 34
       82.40 -   109.87: 16
      109.87 -   137.34: 13
  Dihedral angle restraints: 3733
    sinusoidal: 1607
      harmonic: 2126
  Sorted by residual:
  dihedral pdb=" CA  GLU A 391 "
           pdb=" C   GLU A 391 "
           pdb=" N   PRO A 392 "
           pdb=" CA  PRO A 392 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  157.38   22.62     0      5.00e+00 4.00e-02 2.05e+01
  dihedral pdb=" C2  R06 C 101 "
           pdb=" C3  R06 C 101 "
           pdb=" N1  R06 C 101 "
           pdb=" N2  R06 C 101 "
      ideal   model   delta sinusoidal    sigma   weight residual
     115.40 -107.26 -137.34     1      3.00e+01 1.11e-03 1.85e+01
  dihedral pdb=" C9  R06 C 101 "
           pdb=" C3  R06 C 101 "
           pdb=" N1  R06 C 101 "
           pdb=" N2  R06 C 101 "
      ideal   model   delta sinusoidal    sigma   weight residual
     -54.19   72.31 -126.50     1      3.00e+01 1.11e-03 1.70e+01
  ... (remaining 3730 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.044: 608
       0.044 -    0.088: 184
       0.088 -    0.132: 74
       0.132 -    0.176: 5
       0.176 -    0.219: 8
  Chirality restraints: 879
  Sorted by residual:
  chirality pdb=" C5' LMT A 802 "
            pdb=" C4' LMT A 802 "
            pdb=" C6' LMT A 802 "
            pdb=" O5' LMT A 802 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.51   -2.29   -0.22 2.00e-01 2.50e+01 1.20e+00
  chirality pdb=" C4' LMT A 803 "
            pdb=" C3' LMT A 803 "
            pdb=" C5' LMT A 803 "
            pdb=" O1B LMT A 803 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.55   -2.77    0.22 2.00e-01 2.50e+01 1.18e+00
  chirality pdb=" C5' LMT A 801 "
            pdb=" C4' LMT A 801 "
            pdb=" C6' LMT A 801 "
            pdb=" O5' LMT A 801 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.51   -2.30   -0.21 2.00e-01 2.50e+01 1.08e+00
  ... (remaining 876 not shown)

  Planarity restraints: 1075
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   GLU A 391 "    0.066 5.00e-02 4.00e+02   1.01e-01 1.62e+01
        pdb=" N   PRO A 392 "   -0.174 5.00e-02 4.00e+02
        pdb=" CA  PRO A 392 "    0.052 5.00e-02 4.00e+02
        pdb=" CD  PRO A 392 "    0.056 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   LEU A 668 "   -0.057 5.00e-02 4.00e+02   8.58e-02 1.18e+01
        pdb=" N   PRO A 669 "    0.148 5.00e-02 4.00e+02
        pdb=" CA  PRO A 669 "   -0.046 5.00e-02 4.00e+02
        pdb=" CD  PRO A 669 "   -0.046 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   ALA A 501 "   -0.044 5.00e-02 4.00e+02   6.79e-02 7.38e+00
        pdb=" N   PRO A 502 "    0.118 5.00e-02 4.00e+02
        pdb=" CA  PRO A 502 "   -0.036 5.00e-02 4.00e+02
        pdb=" CD  PRO A 502 "   -0.037 5.00e-02 4.00e+02
  ... (remaining 1072 not shown)

  Histogram of nonbonded interaction distances:
        2.11 -     2.67: 103
        2.67 -     3.23: 5348
        3.23 -     3.79: 8869
        3.79 -     4.34: 12968
        4.34 -     4.90: 22100
  Nonbonded interactions: 49388
  Sorted by model distance:
  nonbonded pdb=" O   SER A 441 "
            pdb=" O2' LMT A 803 "
     model   vdw
     2.114 3.040
  nonbonded pdb=" OH  TYR A 458 "
            pdb=" OD1 ASP A 550 "
     model   vdw
     2.179 3.040
  nonbonded pdb=" OH  TYR A 644 "
            pdb=" OD2 ASP C   4 "
     model   vdw
     2.183 3.040
  nonbonded pdb=" NH1 ARG A 691 "
            pdb=" O   PRO A 692 "
     model   vdw
     2.238 3.120
  nonbonded pdb=" OE2 GLU A 643 "
            pdb=" OH  TYR A 780 "
     model   vdw
     2.243 3.040
  ... (remaining 49383 not shown)

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

  No NCS relation were found !!!

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

Found NCS groups:
  found none.
Set up NCS constraints
  No NCS constraints will be used in refinement.
Set refine NCS operators
Adjust number of macro_cycles
  Number of macro_cycles: 10
Reset NCS operators
Extract rigid body selections
Check and reset occupancies
  Occupancies: min=0.27 max=1.00 mean=1.00
Load rotamer database and sin/cos tables
Set ADP refinement strategy
  ADPs will be refined as individual isotropic
Make a string to write initial .geo file
Internal consistency checks
Time:
  Set random seed:                         0.000
  Set model cs if undefined:               0.000
  Decide on map wrapping:                  0.000
  Normalize map: mean=0, sd=1:             2.730
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.000
  Construct map_model_manager:             0.000
  Extract box with map and model:          0.120
  Check model and map are aligned:         0.010
  Set scattering table:                    0.020
  Process input model:                     7.470
  Find NCS groups from input model:        0.020
  Set up NCS constraints:                  0.020
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.000
  Load rotamer database and sin/cos tables:6.370
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   16.760
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8718
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      :  0.006   0.101   6116  Z= 0.308
  Angle     :  0.821  10.811   8303  Z= 0.399
  Chirality :  0.051   0.219    879
  Planarity :  0.008   0.101   1075
  Dihedral  : 19.074 137.336   2377
  Min Nonbonded Distance : 2.114

Molprobity Statistics.
  All-atom Clashscore : 12.84
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.39 %
    Favored  : 97.61 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.16 %
    Favored  : 99.84 %
  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:  0.09 (0.31), residues: 713
  helix: -0.22 (0.51), residues: 92
  sheet:  0.42 (0.27), residues: 367
  loop : -0.17 (0.39), residues: 254

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.000   ARG A 645 
 TYR   0.021   0.002   TYR A 678 
 PHE   0.028   0.002   PHE C   5 
 TRP   0.038   0.002   TRP A 444 
 HIS   0.020   0.002   HIS A 262 

Details of bonding type rmsd
  covalent geometry    : bond        0.00573 ( 6112)
  covalent geometry    : angle       0.82122 ( 8303)
  hydrogen bonds       : bond        0.13195 (  309)
  hydrogen bonds       : angle       7.13084 (  897)
  Misc. bond           : bond        0.05857 (    4)

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

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

  1426 Ramachandran restraints generated.
    713 Oldfield, 0 Emsley, 713 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1426 Ramachandran restraints generated.
    713 Oldfield, 0 Emsley, 713 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  84 residues out of total 629 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 84
  time to evaluate  : 0.181 
Fit side-chains
REVERT: A  550 ASP cc_start: 0.8517 (m-30) cc_final: 0.8200 (m-30)
REVERT: B 1050 LYS cc_start: 0.8624 (mmpt) cc_final: 0.8415 (mmmt)
REVERT: B 1059 LYS cc_start: 0.8779 (tttp) cc_final: 0.8506 (ptmm)
  outliers start: 0
  outliers final: 0
  residues processed: 84
  average time/residue: 0.6743
  time to fit residues: 58.7748
Evaluate side-chains
  65 residues out of total 629 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 65
  time to evaluate  : 0.247 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 70
   random chunks:
   chunk 49 optimal weight:    4.9990
   chunk 53 optimal weight:    0.8980
   chunk 5 optimal weight:    0.9990
   chunk 33 optimal weight:    3.9990
   chunk 65 optimal weight:    0.7980
   chunk 62 optimal weight:    0.9990
   chunk 51 optimal weight:    0.7980
   chunk 38 optimal weight:    3.9990
   chunk 61 optimal weight:    2.9990
   chunk 45 optimal weight:    1.9990
   chunk 27 optimal weight:    5.9990
   overall best weight:    0.8984

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

Flipped N/Q/H residues before XYZ refinement:
A 770 GLN
A 781 GLN
B1033 ASN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3218 r_free = 0.3218 target = 0.085843 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.2869 r_free = 0.2869 target = 0.065274 restraints weight = 29089.676|
|-----------------------------------------------------------------------------|
r_work (start): 0.2861 rms_B_bonded: 4.15
r_work: 0.2655 rms_B_bonded: 4.25 restraints_weight: 0.5000
r_work (final): 0.2655
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2660
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2660 r_free = 0.2660    target_work(ls_wunit_k1) = 0.056         |
| occupancies: max = 1.00  min = 0.27   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2660 r_free = 0.2660    target_work(ls_wunit_k1) = 0.056         |
| occupancies: max = 1.00  min = 0.32   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.2660
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8748
moved from start:          0.1313

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.037   6116  Z= 0.154
  Angle     :  0.646   8.250   8303  Z= 0.331
  Chirality :  0.049   0.267    879
  Planarity :  0.007   0.083   1075
  Dihedral  : 14.086 121.832   1009
  Min Nonbonded Distance : 2.380

Molprobity Statistics.
  All-atom Clashscore : 5.86
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.39 %
    Favored  : 97.61 %
  Rotamer:
    Outliers :  1.43 %
    Allowed  :  6.66 %
    Favored  : 91.92 %
  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:  0.42 (0.32), residues: 713
  helix:  0.94 (0.55), residues: 92
  sheet:  0.48 (0.27), residues: 373
  loop : -0.11 (0.40), residues: 248

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.008   0.001   ARG A 589 
 TYR   0.011   0.001   TYR A 705 
 PHE   0.014   0.001   PHE B1107 
 TRP   0.017   0.001   TRP A 444 
 HIS   0.005   0.001   HIS A 317 

Details of bonding type rmsd
  covalent geometry    : bond        0.00360 ( 6112)
  covalent geometry    : angle       0.64641 ( 8303)
  hydrogen bonds       : bond        0.03665 (  309)
  hydrogen bonds       : angle       5.53963 (  897)
  Misc. bond           : bond        0.00166 (    4)

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

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

  1426 Ramachandran restraints generated.
    713 Oldfield, 0 Emsley, 713 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1426 Ramachandran restraints generated.
    713 Oldfield, 0 Emsley, 713 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  81 residues out of total 629 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 72
  time to evaluate  : 0.189 
Fit side-chains
REVERT: A  550 ASP cc_start: 0.8660 (m-30) cc_final: 0.8184 (m-30)
REVERT: A  648 GLU cc_start: 0.8753 (pm20) cc_final: 0.8550 (pm20)
REVERT: A  670 LYS cc_start: 0.8971 (tppt) cc_final: 0.8616 (mmtm)
REVERT: A  749 ASP cc_start: 0.8582 (t70) cc_final: 0.8253 (t70)
REVERT: A  781 GLN cc_start: 0.8308 (mm-40) cc_final: 0.8103 (mm110)
REVERT: B 1019 ASP cc_start: 0.8659 (t0) cc_final: 0.8444 (t0)
REVERT: B 1044 ASP cc_start: 0.7687 (t0) cc_final: 0.7287 (t0)
REVERT: B 1059 LYS cc_start: 0.8932 (tttp) cc_final: 0.8671 (ptmm)
REVERT: B 1117 ASP cc_start: 0.8576 (t70) cc_final: 0.8296 (t0)
REVERT: B 1121 ASP cc_start: 0.8421 (m-30) cc_final: 0.8204 (m-30)
  outliers start: 9
  outliers final: 6
  residues processed: 76
  average time/residue: 0.5641
  time to fit residues: 44.7216
Evaluate side-chains
  64 residues out of total 629 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 58
  time to evaluate  : 0.247 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  344 ASP
Chi-restraints excluded: chain A residue  754 PHE
Chi-restraints excluded: chain B residue 1037 LEU
Chi-restraints excluded: chain B residue 1074 GLN
Chi-restraints excluded: chain B residue 1105 SER
Chi-restraints excluded: chain C residue   10 TYR
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 70
   random chunks:
   chunk 58 optimal weight:    2.9990
   chunk 40 optimal weight:    0.9990
   chunk 61 optimal weight:    3.9990
   chunk 44 optimal weight:    0.1980
   chunk 65 optimal weight:    0.9990
   chunk 28 optimal weight:    2.9990
   chunk 39 optimal weight:    0.8980
   chunk 3 optimal weight:    4.9990
   chunk 62 optimal weight:    1.9990
   chunk 17 optimal weight:    3.9990
   chunk 34 optimal weight:    0.8980
   overall best weight:    0.7984

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3215 r_free = 0.3215 target = 0.085766 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 28)----------------|
| r_work = 0.2875 r_free = 0.2875 target = 0.065764 restraints weight = 22439.022|
|-----------------------------------------------------------------------------|
r_work (start): 0.2861 rms_B_bonded: 3.70
r_work: 0.2672 rms_B_bonded: 3.90 restraints_weight: 0.5000
r_work (final): 0.2672
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2684
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2684 r_free = 0.2684    target_work(ls_wunit_k1) = 0.057         |
| occupancies: max = 1.00  min = 0.32   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2684 r_free = 0.2684    target_work(ls_wunit_k1) = 0.057         |
| occupancies: max = 1.00  min = 0.35   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.2684
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8723
moved from start:          0.1515

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.034   6116  Z= 0.135
  Angle     :  0.607   8.810   8303  Z= 0.313
  Chirality :  0.047   0.185    879
  Planarity :  0.006   0.072   1075
  Dihedral  : 11.059 106.165   1009
  Min Nonbonded Distance : 2.552

Molprobity Statistics.
  All-atom Clashscore : 5.77
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.69 %
    Favored  : 98.31 %
  Rotamer:
    Outliers :  1.43 %
    Allowed  :  7.61 %
    Favored  : 90.97 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  0.44 (0.32), residues: 713
  helix:  1.08 (0.55), residues: 92
  sheet:  0.42 (0.27), residues: 375
  loop : -0.01 (0.40), residues: 246

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.000   ARG A 589 
 TYR   0.010   0.001   TYR A 705 
 PHE   0.011   0.001   PHE B1107 
 TRP   0.013   0.001   TRP A 465 
 HIS   0.004   0.001   HIS A 317 

Details of bonding type rmsd
  covalent geometry    : bond        0.00315 ( 6112)
  covalent geometry    : angle       0.60698 ( 8303)
  hydrogen bonds       : bond        0.03373 (  309)
  hydrogen bonds       : angle       5.35770 (  897)
  Misc. bond           : bond        0.00057 (    4)

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

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

  1426 Ramachandran restraints generated.
    713 Oldfield, 0 Emsley, 713 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1426 Ramachandran restraints generated.
    713 Oldfield, 0 Emsley, 713 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  73 residues out of total 629 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 64
  time to evaluate  : 0.232 
Fit side-chains
REVERT: A  550 ASP cc_start: 0.8658 (m-30) cc_final: 0.8193 (m-30)
REVERT: A  648 GLU cc_start: 0.8678 (pm20) cc_final: 0.8426 (pm20)
REVERT: A  670 LYS cc_start: 0.8969 (tppt) cc_final: 0.8616 (mmtm)
REVERT: A  749 ASP cc_start: 0.8529 (t70) cc_final: 0.8183 (t70)
REVERT: A  752 ILE cc_start: 0.8755 (OUTLIER) cc_final: 0.8444 (tp)
REVERT: B 1059 LYS cc_start: 0.8918 (tttp) cc_final: 0.8654 (ptmm)
  outliers start: 9
  outliers final: 3
  residues processed: 69
  average time/residue: 0.6160
  time to fit residues: 44.4353
Evaluate side-chains
  62 residues out of total 629 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 4
    poor density    : 58
  time to evaluate  : 0.239 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  752 ILE
Chi-restraints excluded: chain B residue 1074 GLN
Chi-restraints excluded: chain B residue 1105 SER
Chi-restraints excluded: chain C residue   10 TYR
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 70
   random chunks:
   chunk 43 optimal weight:    1.9990
   chunk 48 optimal weight:    0.8980
   chunk 9 optimal weight:    1.9990
   chunk 12 optimal weight:    3.9990
   chunk 60 optimal weight:    1.9990
   chunk 8 optimal weight:    1.9990
   chunk 16 optimal weight:    3.9990
   chunk 42 optimal weight:    0.8980
   chunk 46 optimal weight:    0.6980
   chunk 52 optimal weight:    3.9990
   chunk 35 optimal weight:    3.9990
   overall best weight:    1.2984

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

Flipped N/Q/H residues before XYZ refinement:
A 345 ASN
A 781 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3186 r_free = 0.3186 target = 0.084223 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.2827 r_free = 0.2827 target = 0.063254 restraints weight = 30005.302|
|-----------------------------------------------------------------------------|
r_work (start): 0.2814 rms_B_bonded: 4.22
r_work: 0.2605 rms_B_bonded: 4.27 restraints_weight: 0.5000
r_work (final): 0.2605
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2611
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2611 r_free = 0.2611    target_work(ls_wunit_k1) = 0.053         |
| occupancies: max = 1.00  min = 0.35   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2611 r_free = 0.2611    target_work(ls_wunit_k1) = 0.053         |
| occupancies: max = 1.00  min = 0.35   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.2611
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8782
moved from start:          0.1673

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.032   6116  Z= 0.180
  Angle     :  0.607   8.708   8303  Z= 0.316
  Chirality :  0.047   0.156    879
  Planarity :  0.006   0.063   1075
  Dihedral  :  8.336  72.710   1009
  Min Nonbonded Distance : 2.587

Molprobity Statistics.
  All-atom Clashscore : 5.34
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.11 %
    Favored  : 97.89 %
  Rotamer:
    Outliers :  0.95 %
    Allowed  :  8.24 %
    Favored  : 90.81 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  0.55 (0.32), residues: 713
  helix:  1.42 (0.55), residues: 92
  sheet:  0.41 (0.27), residues: 375
  loop :  0.09 (0.41), residues: 246

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.001   ARG B1049 
 TYR   0.012   0.001   TYR A 678 
 PHE   0.014   0.002   PHE B1107 
 TRP   0.011   0.001   TRP A 465 
 HIS   0.004   0.001   HIS A 317 

Details of bonding type rmsd
  covalent geometry    : bond        0.00423 ( 6112)
  covalent geometry    : angle       0.60716 ( 8303)
  hydrogen bonds       : bond        0.03420 (  309)
  hydrogen bonds       : angle       5.29356 (  897)
  Misc. bond           : bond        0.00049 (    4)

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

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

  1426 Ramachandran restraints generated.
    713 Oldfield, 0 Emsley, 713 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1426 Ramachandran restraints generated.
    713 Oldfield, 0 Emsley, 713 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  73 residues out of total 629 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 67
  time to evaluate  : 0.238 
Fit side-chains
REVERT: A  550 ASP cc_start: 0.8696 (m-30) cc_final: 0.8219 (m-30)
REVERT: A  648 GLU cc_start: 0.8717 (pm20) cc_final: 0.8480 (pm20)
REVERT: A  670 LYS cc_start: 0.9019 (tppt) cc_final: 0.8663 (mmtm)
REVERT: A  749 ASP cc_start: 0.8609 (t70) cc_final: 0.8317 (t70)
  outliers start: 6
  outliers final: 5
  residues processed: 69
  average time/residue: 0.5787
  time to fit residues: 41.6802
Evaluate side-chains
  66 residues out of total 629 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 5
    poor density    : 61
  time to evaluate  : 0.172 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  344 ASP
Chi-restraints excluded: chain B residue 1061 SER
Chi-restraints excluded: chain B residue 1074 GLN
Chi-restraints excluded: chain B residue 1105 SER
Chi-restraints excluded: chain C residue   10 TYR
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 70
   random chunks:
   chunk 27 optimal weight:    0.0570
   chunk 19 optimal weight:    0.7980
   chunk 51 optimal weight:    3.9990
   chunk 54 optimal weight:    1.9990
   chunk 0 optimal weight:    4.9990
   chunk 29 optimal weight:    0.0470
   chunk 53 optimal weight:    2.9990
   chunk 2 optimal weight:    0.5980
   chunk 64 optimal weight:    4.9990
   chunk 28 optimal weight:    0.7980
   chunk 31 optimal weight:    2.9990
   overall best weight:    0.4596

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

Flipped N/Q/H residues before XYZ refinement:
A 781 GLN
B1079 GLN
B1120 GLN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3227 r_free = 0.3227 target = 0.086576 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.2881 r_free = 0.2881 target = 0.065778 restraints weight = 29300.177|
|-----------------------------------------------------------------------------|
r_work (start): 0.2868 rms_B_bonded: 4.17
r_work: 0.2664 rms_B_bonded: 4.25 restraints_weight: 0.5000
r_work (final): 0.2664
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2674
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2674 r_free = 0.2674    target_work(ls_wunit_k1) = 0.056         |
| occupancies: max = 1.00  min = 0.35   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2674 r_free = 0.2674    target_work(ls_wunit_k1) = 0.056         |
| occupancies: max = 1.00  min = 0.34   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.2674
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8734
moved from start:          0.1885

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.034   6116  Z= 0.106
  Angle     :  0.560   8.667   8303  Z= 0.292
  Chirality :  0.044   0.157    879
  Planarity :  0.005   0.056   1075
  Dihedral  :  6.849  53.334   1009
  Min Nonbonded Distance : 2.533

Molprobity Statistics.
  All-atom Clashscore : 5.26
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.69 %
    Favored  : 98.31 %
  Rotamer:
    Outliers :  1.43 %
    Allowed  :  9.19 %
    Favored  : 89.38 %
  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:  0.55 (0.32), residues: 713
  helix:  1.62 (0.56), residues: 92
  sheet:  0.41 (0.27), residues: 376
  loop : -0.01 (0.41), residues: 245

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.000   ARG A 589 
 TYR   0.009   0.001   TYR A 705 
 PHE   0.009   0.001   PHE A 417 
 TRP   0.014   0.001   TRP A 465 
 HIS   0.004   0.001   HIS A 317 

Details of bonding type rmsd
  covalent geometry    : bond        0.00239 ( 6112)
  covalent geometry    : angle       0.56019 ( 8303)
  hydrogen bonds       : bond        0.02990 (  309)
  hydrogen bonds       : angle       5.04549 (  897)
  Misc. bond           : bond        0.00095 (    4)

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

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

  1426 Ramachandran restraints generated.
    713 Oldfield, 0 Emsley, 713 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1426 Ramachandran restraints generated.
    713 Oldfield, 0 Emsley, 713 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  78 residues out of total 629 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 69
  time to evaluate  : 0.205 
Fit side-chains
REVERT: A  347 TYR cc_start: 0.7717 (m-80) cc_final: 0.7360 (m-80)
REVERT: A  550 ASP cc_start: 0.8666 (m-30) cc_final: 0.8194 (m-30)
REVERT: A  648 GLU cc_start: 0.8692 (pm20) cc_final: 0.8443 (pm20)
REVERT: A  670 LYS cc_start: 0.8953 (tppt) cc_final: 0.8590 (mmtm)
REVERT: A  749 ASP cc_start: 0.8593 (t70) cc_final: 0.8303 (t70)
  outliers start: 9
  outliers final: 3
  residues processed: 73
  average time/residue: 0.5467
  time to fit residues: 41.6389
Evaluate side-chains
  61 residues out of total 629 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 3
    poor density    : 58
  time to evaluate  : 0.183 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue 1061 SER
Chi-restraints excluded: chain B residue 1074 GLN
Chi-restraints excluded: chain C residue   10 TYR
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 70
   random chunks:
   chunk 0 optimal weight:    4.9990
   chunk 11 optimal weight:    0.0370
   chunk 22 optimal weight:    3.9990
   chunk 62 optimal weight:    3.9990
   chunk 40 optimal weight:    3.9990
   chunk 1 optimal weight:    0.8980
   chunk 26 optimal weight:    1.9990
   chunk 45 optimal weight:    0.9980
   chunk 15 optimal weight:    0.7980
   chunk 5 optimal weight:    0.9980
   chunk 58 optimal weight:    1.9990
   overall best weight:    0.7458

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

Flipped N/Q/H residues before XYZ refinement:
A 781 GLN
B1120 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3216 r_free = 0.3216 target = 0.085702 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.2875 r_free = 0.2875 target = 0.065621 restraints weight = 22083.025|
|-----------------------------------------------------------------------------|
r_work (start): 0.2861 rms_B_bonded: 3.69
r_work: 0.2672 rms_B_bonded: 3.93 restraints_weight: 0.5000
r_work (final): 0.2672
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2683
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2683 r_free = 0.2683    target_work(ls_wunit_k1) = 0.057         |
| occupancies: max = 1.00  min = 0.34   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2683 r_free = 0.2683    target_work(ls_wunit_k1) = 0.057         |
| occupancies: max = 1.00  min = 0.33   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.2683
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8718
moved from start:          0.1968

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.031   6116  Z= 0.124
  Angle     :  0.543   5.786   8303  Z= 0.287
  Chirality :  0.044   0.156    879
  Planarity :  0.005   0.055   1075
  Dihedral  :  6.558  52.469   1009
  Min Nonbonded Distance : 2.539

Molprobity Statistics.
  All-atom Clashscore : 5.26
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.11 %
    Favored  : 97.89 %
  Rotamer:
    Outliers :  1.11 %
    Allowed  : 10.62 %
    Favored  : 88.27 %
  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:  0.57 (0.32), residues: 713
  helix:  1.76 (0.56), residues: 92
  sheet:  0.40 (0.27), residues: 377
  loop : -0.01 (0.41), residues: 244

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.000   ARG B1049 
 TYR   0.009   0.001   TYR A 705 
 PHE   0.009   0.001   PHE B1107 
 TRP   0.013   0.001   TRP A 465 
 HIS   0.004   0.001   HIS A 317 

Details of bonding type rmsd
  covalent geometry    : bond        0.00290 ( 6112)
  covalent geometry    : angle       0.54269 ( 8303)
  hydrogen bonds       : bond        0.03026 (  309)
  hydrogen bonds       : angle       4.99242 (  897)
  Misc. bond           : bond        0.00049 (    4)

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

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

  1426 Ramachandran restraints generated.
    713 Oldfield, 0 Emsley, 713 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1426 Ramachandran restraints generated.
    713 Oldfield, 0 Emsley, 713 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  67 residues out of total 629 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 60
  time to evaluate  : 0.223 
Fit side-chains
REVERT: A  550 ASP cc_start: 0.8574 (m-30) cc_final: 0.8153 (m-30)
REVERT: A  648 GLU cc_start: 0.8665 (pm20) cc_final: 0.8410 (pm20)
REVERT: A  670 LYS cc_start: 0.8938 (tppt) cc_final: 0.8585 (mmtm)
REVERT: A  749 ASP cc_start: 0.8539 (OUTLIER) cc_final: 0.8276 (t70)
REVERT: A  752 ILE cc_start: 0.8797 (OUTLIER) cc_final: 0.8492 (tp)
REVERT: B 1050 LYS cc_start: 0.8847 (mmmt) cc_final: 0.8569 (tppt)
  outliers start: 7
  outliers final: 4
  residues processed: 63
  average time/residue: 0.6188
  time to fit residues: 40.7703
Evaluate side-chains
  62 residues out of total 629 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 56
  time to evaluate  : 0.232 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  749 ASP
Chi-restraints excluded: chain A residue  752 ILE
Chi-restraints excluded: chain B residue 1061 SER
Chi-restraints excluded: chain B residue 1074 GLN
Chi-restraints excluded: chain B residue 1105 SER
Chi-restraints excluded: chain C residue   10 TYR
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 70
   random chunks:
   chunk 24 optimal weight:    3.9990
   chunk 19 optimal weight:    0.7980
   chunk 10 optimal weight:    2.9990
   chunk 27 optimal weight:    0.6980
   chunk 15 optimal weight:    3.9990
   chunk 61 optimal weight:    6.9990
   chunk 60 optimal weight:    2.9990
   chunk 18 optimal weight:    1.9990
   chunk 29 optimal weight:    0.3980
   chunk 40 optimal weight:    3.9990
   chunk 68 optimal weight:    0.4980
   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 781 GLN
B1120 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3210 r_free = 0.3210 target = 0.085299 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.2859 r_free = 0.2859 target = 0.064715 restraints weight = 26712.329|
|-----------------------------------------------------------------------------|
r_work (start): 0.2847 rms_B_bonded: 4.03
r_work: 0.2645 rms_B_bonded: 4.15 restraints_weight: 0.5000
r_work (final): 0.2645
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2650
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2650 r_free = 0.2650    target_work(ls_wunit_k1) = 0.055         |
| occupancies: max = 1.00  min = 0.33   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2650 r_free = 0.2650    target_work(ls_wunit_k1) = 0.055         |
| occupancies: max = 1.00  min = 0.33   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.2650
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8761
moved from start:          0.1988

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.030   6116  Z= 0.135
  Angle     :  0.551   8.428   8303  Z= 0.290
  Chirality :  0.045   0.160    879
  Planarity :  0.005   0.054   1075
  Dihedral  :  6.467  51.237   1009
  Min Nonbonded Distance : 2.486

Molprobity Statistics.
  All-atom Clashscore : 5.26
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.97 %
    Favored  : 98.03 %
  Rotamer:
    Outliers :  1.58 %
    Allowed  : 10.46 %
    Favored  : 87.96 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  0.61 (0.32), residues: 713
  helix:  1.75 (0.56), residues: 92
  sheet:  0.43 (0.27), residues: 377
  loop :  0.04 (0.41), residues: 244

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.000   ARG A 589 
 TYR   0.010   0.001   TYR A 678 
 PHE   0.009   0.001   PHE B1107 
 TRP   0.011   0.001   TRP A 465 
 HIS   0.004   0.001   HIS A 317 

Details of bonding type rmsd
  covalent geometry    : bond        0.00315 ( 6112)
  covalent geometry    : angle       0.55116 ( 8303)
  hydrogen bonds       : bond        0.03074 (  309)
  hydrogen bonds       : angle       5.01216 (  897)
  Misc. bond           : bond        0.00027 (    4)

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

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

  1426 Ramachandran restraints generated.
    713 Oldfield, 0 Emsley, 713 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1426 Ramachandran restraints generated.
    713 Oldfield, 0 Emsley, 713 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  71 residues out of total 629 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 61
  time to evaluate  : 0.252 
Fit side-chains
REVERT: A  550 ASP cc_start: 0.8618 (m-30) cc_final: 0.8199 (m-30)
REVERT: A  648 GLU cc_start: 0.8675 (pm20) cc_final: 0.8416 (pm20)
REVERT: A  670 LYS cc_start: 0.8961 (tppt) cc_final: 0.8608 (mmtm)
REVERT: A  749 ASP cc_start: 0.8529 (OUTLIER) cc_final: 0.8275 (t70)
REVERT: A  752 ILE cc_start: 0.8835 (OUTLIER) cc_final: 0.8541 (tp)
REVERT: B 1050 LYS cc_start: 0.8952 (mmmt) cc_final: 0.8633 (tppt)
REVERT: B 1079 GLN cc_start: 0.8770 (OUTLIER) cc_final: 0.7634 (tp40)
  outliers start: 10
  outliers final: 5
  residues processed: 65
  average time/residue: 0.6278
  time to fit residues: 42.6973
Evaluate side-chains
  65 residues out of total 629 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 57
  time to evaluate  : 0.235 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  403 VAL
Chi-restraints excluded: chain A residue  749 ASP
Chi-restraints excluded: chain A residue  752 ILE
Chi-restraints excluded: chain B residue 1061 SER
Chi-restraints excluded: chain B residue 1074 GLN
Chi-restraints excluded: chain B residue 1079 GLN
Chi-restraints excluded: chain B residue 1105 SER
Chi-restraints excluded: chain C residue   10 TYR
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 70
   random chunks:
   chunk 68 optimal weight:    0.8980
   chunk 48 optimal weight:    0.4980
   chunk 37 optimal weight:    6.9990
   chunk 28 optimal weight:    1.9990
   chunk 67 optimal weight:    0.5980
   chunk 46 optimal weight:    0.7980
   chunk 62 optimal weight:    3.9990
   chunk 35 optimal weight:    3.9990
   chunk 54 optimal weight:    0.6980
   chunk 43 optimal weight:    0.6980
   chunk 4 optimal weight:    0.8980
   overall best weight:    0.6580

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

Flipped N/Q/H residues before XYZ refinement:
A 781 GLN
B1079 GLN
B1120 GLN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3233 r_free = 0.3233 target = 0.087819 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 46)----------------|
| r_work = 0.2930 r_free = 0.2930 target = 0.069118 restraints weight = 15681.200|
|-----------------------------------------------------------------------------|
r_work (start): 0.2892 rms_B_bonded: 3.07
r_work: 0.2720 rms_B_bonded: 3.43 restraints_weight: 0.5000
r_work (final): 0.2720
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2724
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2724 r_free = 0.2724    target_work(ls_wunit_k1) = 0.059         |
| occupancies: max = 1.00  min = 0.33   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2724 r_free = 0.2724    target_work(ls_wunit_k1) = 0.059         |
| occupancies: max = 1.00  min = 0.35   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.2724
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8707
moved from start:          0.2081

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.042   6116  Z= 0.118
  Angle     :  0.549   7.819   8303  Z= 0.289
  Chirality :  0.044   0.156    879
  Planarity :  0.005   0.053   1075
  Dihedral  :  6.493  50.348   1009
  Min Nonbonded Distance : 2.509

Molprobity Statistics.
  All-atom Clashscore : 5.08
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.11 %
    Favored  : 97.89 %
  Rotamer:
    Outliers :  1.90 %
    Allowed  : 10.30 %
    Favored  : 87.80 %
  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:  0.65 (0.32), residues: 713
  helix:  1.78 (0.56), residues: 92
  sheet:  0.47 (0.27), residues: 376
  loop :  0.03 (0.41), residues: 245

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.000   ARG A 589 
 TYR   0.009   0.001   TYR A 705 
 PHE   0.009   0.001   PHE B1107 
 TRP   0.011   0.001   TRP A 465 
 HIS   0.004   0.001   HIS A 317 

Details of bonding type rmsd
  covalent geometry    : bond        0.00274 ( 6112)
  covalent geometry    : angle       0.54884 ( 8303)
  hydrogen bonds       : bond        0.02970 (  309)
  hydrogen bonds       : angle       4.95595 (  897)
  Misc. bond           : bond        0.00067 (    4)

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

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

  1426 Ramachandran restraints generated.
    713 Oldfield, 0 Emsley, 713 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1426 Ramachandran restraints generated.
    713 Oldfield, 0 Emsley, 713 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  69 residues out of total 629 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 57
  time to evaluate  : 0.268 
Fit side-chains
REVERT: A  550 ASP cc_start: 0.8540 (m-30) cc_final: 0.8113 (m-30)
REVERT: A  648 GLU cc_start: 0.8590 (pm20) cc_final: 0.8333 (pm20)
REVERT: A  670 LYS cc_start: 0.8918 (tppt) cc_final: 0.8567 (mmtm)
REVERT: A  749 ASP cc_start: 0.8417 (OUTLIER) cc_final: 0.8184 (t70)
REVERT: A  752 ILE cc_start: 0.8748 (OUTLIER) cc_final: 0.8499 (tp)
  outliers start: 12
  outliers final: 6
  residues processed: 62
  average time/residue: 0.6132
  time to fit residues: 39.7058
Evaluate side-chains
  62 residues out of total 629 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 54
  time to evaluate  : 0.197 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  403 VAL
Chi-restraints excluded: chain A residue  724 CYS
Chi-restraints excluded: chain A residue  749 ASP
Chi-restraints excluded: chain A residue  752 ILE
Chi-restraints excluded: chain B residue 1061 SER
Chi-restraints excluded: chain B residue 1074 GLN
Chi-restraints excluded: chain B residue 1105 SER
Chi-restraints excluded: chain C residue   10 TYR
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 70
   random chunks:
   chunk 13 optimal weight:    4.9990
   chunk 56 optimal weight:    4.9990
   chunk 19 optimal weight:    0.9990
   chunk 40 optimal weight:    2.9990
   chunk 24 optimal weight:    3.9990
   chunk 41 optimal weight:    5.9990
   chunk 47 optimal weight:    3.9990
   chunk 18 optimal weight:    1.9990
   chunk 50 optimal weight:    5.9990
   chunk 2 optimal weight:    0.0980
   chunk 21 optimal weight:    0.8980
   overall best weight:    1.3986

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

Flipped N/Q/H residues before XYZ refinement:
A 393 GLN
A 781 GLN
B1120 GLN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3186 r_free = 0.3186 target = 0.083931 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.2837 r_free = 0.2837 target = 0.063776 restraints weight = 21805.318|
|-----------------------------------------------------------------------------|
r_work (start): 0.2823 rms_B_bonded: 3.70
r_work: 0.2636 rms_B_bonded: 3.84 restraints_weight: 0.5000
r_work (final): 0.2636
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2646
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2646 r_free = 0.2646    target_work(ls_wunit_k1) = 0.055         |
| occupancies: max = 1.00  min = 0.35   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2646 r_free = 0.2646    target_work(ls_wunit_k1) = 0.055         |
| occupancies: max = 1.00  min = 0.34   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.2646
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8748
moved from start:          0.2017

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.039   6116  Z= 0.189
  Angle     :  0.583   8.086   8303  Z= 0.306
  Chirality :  0.046   0.158    879
  Planarity :  0.005   0.054   1075
  Dihedral  :  6.693  51.695   1009
  Min Nonbonded Distance : 2.444

Molprobity Statistics.
  All-atom Clashscore : 5.52
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.97 %
    Favored  : 98.03 %
  Rotamer:
    Outliers :  1.43 %
    Allowed  : 11.25 %
    Favored  : 87.32 %
  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:  0.59 (0.32), residues: 713
  helix:  1.73 (0.57), residues: 92
  sheet:  0.42 (0.27), residues: 377
  loop :  0.03 (0.41), residues: 244

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.000   ARG A 589 
 TYR   0.013   0.001   TYR A 678 
 PHE   0.011   0.001   PHE B1107 
 TRP   0.009   0.001   TRP A 465 
 HIS   0.004   0.001   HIS A 317 

Details of bonding type rmsd
  covalent geometry    : bond        0.00445 ( 6112)
  covalent geometry    : angle       0.58251 ( 8303)
  hydrogen bonds       : bond        0.03288 (  309)
  hydrogen bonds       : angle       5.15886 (  897)
  Misc. bond           : bond        0.00081 (    4)

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

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

  1426 Ramachandran restraints generated.
    713 Oldfield, 0 Emsley, 713 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1426 Ramachandran restraints generated.
    713 Oldfield, 0 Emsley, 713 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  67 residues out of total 629 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 58
  time to evaluate  : 0.244 
Fit side-chains
REVERT: A  550 ASP cc_start: 0.8644 (m-30) cc_final: 0.8173 (m-30)
REVERT: A  648 GLU cc_start: 0.8630 (pm20) cc_final: 0.8355 (pm20)
REVERT: A  670 LYS cc_start: 0.8980 (tppt) cc_final: 0.8620 (mmtm)
REVERT: A  749 ASP cc_start: 0.8506 (OUTLIER) cc_final: 0.8260 (t70)
REVERT: A  752 ILE cc_start: 0.8814 (OUTLIER) cc_final: 0.8501 (tp)
  outliers start: 9
  outliers final: 6
  residues processed: 61
  average time/residue: 0.6096
  time to fit residues: 38.7550
Evaluate side-chains
  63 residues out of total 629 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 55
  time to evaluate  : 0.147 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  403 VAL
Chi-restraints excluded: chain A residue  724 CYS
Chi-restraints excluded: chain A residue  749 ASP
Chi-restraints excluded: chain A residue  752 ILE
Chi-restraints excluded: chain B residue 1061 SER
Chi-restraints excluded: chain B residue 1074 GLN
Chi-restraints excluded: chain B residue 1105 SER
Chi-restraints excluded: chain C residue   10 TYR
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 70
   random chunks:
   chunk 11 optimal weight:    2.9990
   chunk 4 optimal weight:    3.9990
   chunk 38 optimal weight:    1.9990
   chunk 19 optimal weight:    0.9990
   chunk 52 optimal weight:    1.9990
   chunk 51 optimal weight:    0.8980
   chunk 10 optimal weight:    3.9990
   chunk 54 optimal weight:    0.8980
   chunk 8 optimal weight:    0.7980
   chunk 48 optimal weight:    0.5980
   chunk 59 optimal weight:    3.9990
   overall best weight:    0.8382

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

Flipped N/Q/H residues before XYZ refinement:
A 781 GLN
B1120 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3208 r_free = 0.3208 target = 0.085109 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.2870 r_free = 0.2870 target = 0.065511 restraints weight = 17255.600|
|-----------------------------------------------------------------------------|
r_work (start): 0.2860 rms_B_bonded: 3.34
r_work: 0.2683 rms_B_bonded: 3.58 restraints_weight: 0.5000
r_work (final): 0.2683
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2694
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2694 r_free = 0.2694    target_work(ls_wunit_k1) = 0.057         |
| occupancies: max = 1.00  min = 0.34   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2694 r_free = 0.2694    target_work(ls_wunit_k1) = 0.057         |
| occupancies: max = 1.00  min = 0.34   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.2694
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8724
moved from start:          0.2081

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.037   6116  Z= 0.135
  Angle     :  0.564   7.787   8303  Z= 0.296
  Chirality :  0.045   0.157    879
  Planarity :  0.005   0.053   1075
  Dihedral  :  6.530  52.637   1009
  Min Nonbonded Distance : 2.472

Molprobity Statistics.
  All-atom Clashscore : 5.95
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.25 %
    Favored  : 97.75 %
  Rotamer:
    Outliers :  1.43 %
    Allowed  : 11.25 %
    Favored  : 87.32 %
  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:  0.59 (0.32), residues: 713
  helix:  1.74 (0.56), residues: 92
  sheet:  0.42 (0.27), residues: 376
  loop :  0.00 (0.40), residues: 245

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.000   ARG A 589 
 TYR   0.010   0.001   TYR A 705 
 PHE   0.009   0.001   PHE B1107 
 TRP   0.011   0.001   TRP A 465 
 HIS   0.004   0.001   HIS A 317 

Details of bonding type rmsd
  covalent geometry    : bond        0.00318 ( 6112)
  covalent geometry    : angle       0.56402 ( 8303)
  hydrogen bonds       : bond        0.03063 (  309)
  hydrogen bonds       : angle       5.04848 (  897)
  Misc. bond           : bond        0.00064 (    4)

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

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

  1426 Ramachandran restraints generated.
    713 Oldfield, 0 Emsley, 713 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1426 Ramachandran restraints generated.
    713 Oldfield, 0 Emsley, 713 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  67 residues out of total 629 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 58
  time to evaluate  : 0.254 
Fit side-chains
REVERT: A  550 ASP cc_start: 0.8571 (m-30) cc_final: 0.8138 (m-30)
REVERT: A  648 GLU cc_start: 0.8579 (pm20) cc_final: 0.8311 (pm20)
REVERT: A  670 LYS cc_start: 0.8937 (tppt) cc_final: 0.8582 (mmtm)
REVERT: A  749 ASP cc_start: 0.8469 (OUTLIER) cc_final: 0.8223 (t70)
REVERT: A  752 ILE cc_start: 0.8784 (OUTLIER) cc_final: 0.8515 (tp)
REVERT: B 1077 GLU cc_start: 0.8218 (mt-10) cc_final: 0.7988 (mt-10)
  outliers start: 9
  outliers final: 6
  residues processed: 60
  average time/residue: 0.6193
  time to fit residues: 38.9017
Evaluate side-chains
  62 residues out of total 629 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 54
  time to evaluate  : 0.224 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  403 VAL
Chi-restraints excluded: chain A residue  724 CYS
Chi-restraints excluded: chain A residue  749 ASP
Chi-restraints excluded: chain A residue  752 ILE
Chi-restraints excluded: chain B residue 1061 SER
Chi-restraints excluded: chain B residue 1074 GLN
Chi-restraints excluded: chain B residue 1105 SER
Chi-restraints excluded: chain C residue   10 TYR
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 70
   random chunks:
   chunk 51 optimal weight:    0.0070
   chunk 20 optimal weight:    1.9990
   chunk 12 optimal weight:    1.9990
   chunk 29 optimal weight:    0.0060
   chunk 43 optimal weight:    0.8980
   chunk 62 optimal weight:    0.7980
   chunk 41 optimal weight:    0.9980
   chunk 10 optimal weight:    3.9990
   chunk 57 optimal weight:    0.9990
   chunk 54 optimal weight:    0.7980
   chunk 49 optimal weight:    2.9990
   overall best weight:    0.5014

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

Flipped N/Q/H residues before XYZ refinement:
A 576 ASN
A 781 GLN
B1079 GLN
B1120 GLN

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3230 r_free = 0.3230 target = 0.086467 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 43)----------------|
| r_work = 0.2881 r_free = 0.2881 target = 0.065755 restraints weight = 28450.626|
|-----------------------------------------------------------------------------|
r_work (start): 0.2864 rms_B_bonded: 4.12
r_work: 0.2664 rms_B_bonded: 4.22 restraints_weight: 0.5000
r_work (final): 0.2664
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2680
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2680 r_free = 0.2680    target_work(ls_wunit_k1) = 0.057         |
| occupancies: max = 1.00  min = 0.34   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2680 r_free = 0.2680    target_work(ls_wunit_k1) = 0.057         |
| occupancies: max = 1.00  min = 0.33   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.2680
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8723
moved from start:          0.2221

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.033   6116  Z= 0.108
  Angle     :  0.539   7.561   8303  Z= 0.284
  Chirality :  0.044   0.156    879
  Planarity :  0.005   0.053   1075
  Dihedral  :  6.243  49.222   1009
  Min Nonbonded Distance : 2.413

Molprobity Statistics.
  All-atom Clashscore : 4.91
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.39 %
    Favored  : 97.61 %
  Rotamer:
    Outliers :  1.43 %
    Allowed  : 11.41 %
    Favored  : 87.16 %
  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:  0.62 (0.32), residues: 713
  helix:  1.76 (0.56), residues: 92
  sheet:  0.44 (0.27), residues: 376
  loop :  0.02 (0.40), residues: 245

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.000   ARG A 589 
 TYR   0.009   0.001   TYR A 705 
 PHE   0.008   0.001   PHE A 417 
 TRP   0.012   0.001   TRP A 465 
 HIS   0.004   0.001   HIS A 317 

Details of bonding type rmsd
  covalent geometry    : bond        0.00251 ( 6112)
  covalent geometry    : angle       0.53902 ( 8303)
  hydrogen bonds       : bond        0.02881 (  309)
  hydrogen bonds       : angle       4.88457 (  897)
  Misc. bond           : bond        0.00055 (    4)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 1908.77 seconds
wall clock time: 33 minutes 20.55 seconds (2000.55 seconds total)