Starting phenix.real_space_refine
on Sun Aug 24 18:17:43 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/8uxt_42775/08_2025/8uxt_42775.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/8uxt_42775/08_2025/8uxt_42775.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=1.77
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    model {
      file = "/net/cci-nas-00/data/ceres_data/8uxt_42775/08_2025/8uxt_42775.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/8uxt_42775/08_2025/8uxt_42775.cif"
    real_map_files = "/net/cci-nas-00/data/ceres_data/8uxt_42775/08_2025/8uxt_42775.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/8uxt_42775/08_2025/8uxt_42775.map"
  }
  resolution = 1.77
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }


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

Validating inputs
Origin is already at (0, 0, 0), no shifts will be applied
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=  -0.002 sd=   0.047
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: 5
    Type Number    sf(0)   Gaussians
     S      27      5.16       5
     C    7132      2.51       5
     N    1942      2.21       5
     O    2169      1.98       5
     H   10719      0.53       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 15 residue(s): 0.01s

  Monomer Library directory:
    "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/chem_data/mon_lib"
  Total number of atoms: 21989
  Number of models: 1
  Model: ""
    Number of chains: 1
    Chain: "A"
      Number of atoms: 21989
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 1414, 21989
          Classifications: {'peptide': 1414}
          Incomplete info: {'truncation_to_alanine': 4}
          Link IDs: {'PTRANS': 45, 'TRANS': 1368}
          Chain breaks: 4
          Unresolved non-hydrogen bonds: 188
          Unresolved non-hydrogen angles: 237
          Unresolved non-hydrogen dihedrals: 156
          Unresolved non-hydrogen chiralities: 14
          Planarities with less than four sites: {'ASN:plan1': 1, 'ARG:plan': 2, 'GLN:plan1': 7, 'GLU:plan': 6, 'TYR:plan': 5, 'ASP:plan': 2, 'PHE:plan': 1}
          Unresolved non-hydrogen planarities: 112
  Time building chain proxies: 3.28, per 1000 atoms: 0.15
  Number of scatterers: 21989
  At special positions: 0
  Unit cell: (91, 96.2, 124.15, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 5
    Type Number    sf(0)
     S      27     16.00
     O    2169      8.00
     N    1942      7.00
     C    7132      6.00
     H   10719      1.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=0, symmetry=0

  Automatic linking
    Parameters for automatic linking
      Linking & cutoffs
        Metal                : Auto  - 3.00
        Amino acid           : True  - 1.90
        Carbohydrate         : True  - 1.99
        Ligands              : True  - 1.99
        Small molecules      : False - 1.98
        Amino acid - RNA/DNA : False
      
  Number of custom bonds: simple=0, symmetry=0
  Time building additional restraints: 1.85
  Conformation dependent library (CDL) restraints added in 569.5 milliseconds
  
  Enol-peptide restraints added in 476.8 nanoseconds
  

  2808 Ramachandran restraints generated.
    1404 Oldfield, 0 Emsley, 1404 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  2630

  Finding SS restraints...
    Secondary structure from input PDB file:
      19 helices and 7 sheets defined
      15.1% alpha, 48.9% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.78
  Creating SS restraints...
    Processing helix  chain 'A' and resid 25 through 27
      No H-bonds generated for 'chain 'A' and resid 25 through 27'
    Processing helix  chain 'A' and resid 30 through 48
    Processing helix  chain 'A' and resid 51 through 57
      removed outlier: 4.161A  pdb=" N   SER A  57 " --> pdb=" O   GLU A  53 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 66 through 83
    Processing helix  chain 'A' and resid 87 through 103
      removed outlier: 3.546A  pdb=" N   GLY A 103 " --> pdb=" O   ALA A  99 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 108 through 110
      No H-bonds generated for 'chain 'A' and resid 108 through 110'
    Processing helix  chain 'A' and resid 111 through 131
      Proline residue:  A 120  - end of helix
      removed outlier: 4.520A  pdb=" N   ARG A 131 " --> pdb=" O   GLU A 127 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 137 through 152
      removed outlier: 3.999A  pdb=" N   MET A 151 " --> pdb=" O   HIS A 147 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 155 through 166
    Processing helix  chain 'A' and resid 166 through 186
      removed outlier: 4.038A  pdb=" N   SER A 184 " --> pdb=" O   THR A 180 " (cutoff:3.500A)
      removed outlier: 4.354A  pdb=" N   MET A 185 " --> pdb=" O   ILE A 181 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 216 through 226
      removed outlier: 4.272A  pdb=" N   LEU A 220 " --> pdb=" O   TRP A 216 " (cutoff:3.500A)
      removed outlier: 3.742A  pdb=" N   LYS A 226 " --> pdb=" O   ASP A 222 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 244 through 261
      removed outlier: 4.476A  pdb=" N   SER A 256 " --> pdb=" O   ILE A 252 " (cutoff:3.500A)
      removed outlier: 4.720A  pdb=" N   GLN A 257 " --> pdb=" O   ALA A 253 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 262 through 264
      No H-bonds generated for 'chain 'A' and resid 262 through 264'
    Processing helix  chain 'A' and resid 270 through 286
    Processing helix  chain 'A' and resid 367 through 371
    Processing helix  chain 'A' and resid 407 through 412
      removed outlier: 3.981A  pdb=" N   ILE A 411 " --> pdb=" O   VAL A 408 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1330 through 1334
    Processing helix  chain 'A' and resid 1371 through 1376
    Processing helix  chain 'A' and resid 1405 through 1410
      removed outlier: 3.891A  pdb=" N   ALA A1410 " --> pdb=" O   PRO A1407 " (cutoff:3.500A)
    Processing sheet with id=AA1, first strand: chain 'A' and resid 20 through 23
    Processing sheet with id=AA2, first strand: chain 'A' and resid 60 through 65
      removed outlier: 6.146A  pdb=" N   ILE A  61 " --> pdb=" O   ASN A 215 " (cutoff:3.500A)
      removed outlier: 3.694A  pdb=" N   ASN A 215 " --> pdb=" O   ILE A  61 " (cutoff:3.500A)
      removed outlier: 6.231A  pdb=" N   LEU A 211 " --> pdb=" O   ALA A  65 " (cutoff:3.500A)
    Processing sheet with id=AA3, first strand: chain 'A' and resid 344 through 352
      removed outlier: 5.538A  pdb=" N   GLN A 346 " --> pdb=" O   TYR A 363 " (cutoff:3.500A)
      removed outlier: 7.254A  pdb=" N   TYR A 363 " --> pdb=" O   GLN A 346 " (cutoff:3.500A)
      removed outlier: 5.227A  pdb=" N   ALA A 348 " --> pdb=" O   ARG A 361 " (cutoff:3.500A)
      removed outlier: 6.657A  pdb=" N   ARG A 361 " --> pdb=" O   ALA A 348 " (cutoff:3.500A)
      removed outlier: 4.246A  pdb=" N   PHE A 350 " --> pdb=" O   PHE A 359 " (cutoff:3.500A)
    Processing sheet with id=AA4, first strand: chain 'A' and resid 403 through 406
      removed outlier: 3.503A  pdb=" N   MET A 386 " --> pdb=" O   ILE A 397 " (cutoff:3.500A)
      removed outlier: 14.545A  pdb=" N   ASN A 452 " --> pdb=" O   LEU A 473 " (cutoff:3.500A)
      removed outlier: 11.797A  pdb=" N   LEU A 473 " --> pdb=" O   ASN A 452 " (cutoff:3.500A)
      removed outlier: 11.115A  pdb=" N   TYR A 454 " --> pdb=" O   TYR A 471 " (cutoff:3.500A)
      removed outlier: 9.378A  pdb=" N   TYR A 471 " --> pdb=" O   TYR A 454 " (cutoff:3.500A)
      removed outlier: 5.359A  pdb=" N   VAL A 456 " --> pdb=" O   LEU A 469 " (cutoff:3.500A)
      removed outlier: 6.990A  pdb=" N   GLU A 466 " --> pdb=" O   PHE A 485 " (cutoff:3.500A)
      removed outlier: 5.260A  pdb=" N   PHE A 485 " --> pdb=" O   GLU A 466 " (cutoff:3.500A)
      removed outlier: 6.530A  pdb=" N   LEU A 468 " --> pdb=" O   ILE A 483 " (cutoff:3.500A)
      removed outlier: 4.497A  pdb=" N   ILE A 483 " --> pdb=" O   LEU A 468 " (cutoff:3.500A)
      removed outlier: 6.667A  pdb=" N   GLU A 470 " --> pdb=" O   LYS A 481 " (cutoff:3.500A)
      removed outlier: 12.817A  pdb=" N   TYR A 479 " --> pdb=" O   PHE A 498 " (cutoff:3.500A)
      removed outlier: 9.914A  pdb=" N   PHE A 498 " --> pdb=" O   TYR A 479 " (cutoff:3.500A)
      removed outlier: 6.752A  pdb=" N   LYS A 481 " --> pdb=" O   PHE A 496 " (cutoff:3.500A)
      removed outlier: 4.827A  pdb=" N   ILE A 505 " --> pdb=" O   TYR A 519 " (cutoff:3.500A)
      removed outlier: 3.551A  pdb=" N   LYS A 529 " --> pdb=" O   GLU A 520 " (cutoff:3.500A)
      removed outlier: 4.756A  pdb=" N   ILE A 528 " --> pdb=" O   TYR A 540 " (cutoff:3.500A)
      removed outlier: 4.029A  pdb=" N   THR A 539 " --> pdb=" O   THR A 552 " (cutoff:3.500A)
      removed outlier: 4.641A  pdb=" N   THR A 549 " --> pdb=" O   ILE A 561 " (cutoff:3.500A)
      removed outlier: 5.220A  pdb=" N   ILE A 573 " --> pdb=" O   LEU A 586 " (cutoff:3.500A)
      removed outlier: 5.498A  pdb=" N   TYR A 616 " --> pdb=" O   TYR A 628 " (cutoff:3.500A)
      removed outlier: 4.671A  pdb=" N   THR A 637 " --> pdb=" O   GLN A 649 " (cutoff:3.500A)
      removed outlier: 5.063A  pdb=" N   VAL A 658 " --> pdb=" O   PHE A 670 " (cutoff:3.500A)
      removed outlier: 4.788A  pdb=" N   VAL A 679 " --> pdb=" O   ARG A 691 " (cutoff:3.500A)
      removed outlier: 4.868A  pdb=" N   SER A 700 " --> pdb=" O   TYR A 712 " (cutoff:3.500A)
      removed outlier: 4.991A  pdb=" N   VAL A 721 " --> pdb=" O   ILE A 733 " (cutoff:3.500A)
      removed outlier: 4.909A  pdb=" N   ILE A 742 " --> pdb=" O   TRP A 754 " (cutoff:3.500A)
      removed outlier: 4.993A  pdb=" N   THR A 763 " --> pdb=" O   TYR A 775 " (cutoff:3.500A)
      removed outlier: 5.029A  pdb=" N   GLN A 788 " --> pdb=" O   PHE A 800 " (cutoff:3.500A)
      removed outlier: 6.713A  pdb=" N   TYR A 799 " --> pdb=" O   HIS A 811 " (cutoff:3.500A)
      removed outlier: 4.586A  pdb=" N   HIS A 811 " --> pdb=" O   TYR A 799 " (cutoff:3.500A)
      removed outlier: 6.573A  pdb=" N   GLU A 801 " --> pdb=" O   LEU A 809 " (cutoff:3.500A)
      removed outlier: 4.951A  pdb=" N   LEU A 809 " --> pdb=" O   TYR A 821 " (cutoff:3.500A)
      removed outlier: 4.787A  pdb=" N   GLU A 830 " --> pdb=" O   TYR A 842 " (cutoff:3.500A)
      removed outlier: 6.654A  pdb=" N   ALA A 841 " --> pdb=" O   LEU A 853 " (cutoff:3.500A)
      removed outlier: 4.596A  pdb=" N   LEU A 853 " --> pdb=" O   ALA A 841 " (cutoff:3.500A)
      removed outlier: 6.668A  pdb=" N   GLN A 843 " --> pdb=" O   GLN A 851 " (cutoff:3.500A)
      removed outlier: 5.262A  pdb=" N   GLN A 851 " --> pdb=" O   PHE A 863 " (cutoff:3.500A)
      removed outlier: 4.915A  pdb=" N   ILE A 872 " --> pdb=" O   TYR A 884 " (cutoff:3.500A)
      removed outlier: 5.653A  pdb=" N   PHE A 893 " --> pdb=" O   PHE A 904 " (cutoff:3.500A)
      removed outlier: 5.162A  pdb=" N   ALA A 913 " --> pdb=" O   PHE A 930 " (cutoff:3.500A)
      removed outlier: 5.169A  pdb=" N   SER A 939 " --> pdb=" O   LEU A 950 " (cutoff:3.500A)
      removed outlier: 4.995A  pdb=" N   VAL A 959 " --> pdb=" O   TYR A 979 " (cutoff:3.500A)
      removed outlier: 4.915A  pdb=" N   ILE A 988 " --> pdb=" O   HIS A1000 " (cutoff:3.500A)
      removed outlier: 3.502A  pdb=" N   ALA A1010 " --> pdb=" O   LEU A1001 " (cutoff:3.500A)
      removed outlier: 6.468A  pdb=" N   TYR A1003 " --> pdb=" O   ILE A1008 " (cutoff:3.500A)
      removed outlier: 5.532A  pdb=" N   ILE A1008 " --> pdb=" O   TYR A1003 " (cutoff:3.500A)
      removed outlier: 11.492A  pdb=" N   HIS A1007 " --> pdb=" O   GLN A1022 " (cutoff:3.500A)
      removed outlier: 9.125A  pdb=" N   GLN A1022 " --> pdb=" O   HIS A1007 " (cutoff:3.500A)
      removed outlier: 7.448A  pdb=" N   TYR A1009 " --> pdb=" O   SER A1020 " (cutoff:3.500A)
      removed outlier: 4.433A  pdb=" N   SER A1020 " --> pdb=" O   TYR A1009 " (cutoff:3.500A)
      removed outlier: 6.823A  pdb=" N   ILE A1011 " --> pdb=" O   VAL A1018 " (cutoff:3.500A)
      removed outlier: 4.773A  pdb=" N   THR A1030 " --> pdb=" O   LYS A1042 " (cutoff:3.500A)
      removed outlier: 3.933A  pdb=" N   LEU A1038 " --> pdb=" O   LEU A1034 " (cutoff:3.500A)
      removed outlier: 5.302A  pdb=" N   SER A1051 " --> pdb=" O   TYR A1073 " (cutoff:3.500A)
      removed outlier: 5.014A  pdb=" N   SER A1082 " --> pdb=" O   TYR A1094 " (cutoff:3.500A)
    Processing sheet with id=AA5, first strand: chain 'A' and resid 415 through 416
      removed outlier: 3.639A  pdb=" N   LYS A 457 " --> pdb=" O   HIS A 443 " (cutoff:3.500A)
      removed outlier: 6.393A  pdb=" N   GLN A 445 " --> pdb=" O   LEU A 455 " (cutoff:3.500A)
      removed outlier: 5.143A  pdb=" N   LEU A 455 " --> pdb=" O   GLN A 445 " (cutoff:3.500A)
      removed outlier: 14.545A  pdb=" N   ASN A 452 " --> pdb=" O   LEU A 473 " (cutoff:3.500A)
      removed outlier: 11.797A  pdb=" N   LEU A 473 " --> pdb=" O   ASN A 452 " (cutoff:3.500A)
      removed outlier: 11.115A  pdb=" N   TYR A 454 " --> pdb=" O   TYR A 471 " (cutoff:3.500A)
      removed outlier: 9.378A  pdb=" N   TYR A 471 " --> pdb=" O   TYR A 454 " (cutoff:3.500A)
      removed outlier: 5.359A  pdb=" N   VAL A 456 " --> pdb=" O   LEU A 469 " (cutoff:3.500A)
      removed outlier: 6.990A  pdb=" N   GLU A 466 " --> pdb=" O   PHE A 485 " (cutoff:3.500A)
      removed outlier: 5.260A  pdb=" N   PHE A 485 " --> pdb=" O   GLU A 466 " (cutoff:3.500A)
      removed outlier: 6.530A  pdb=" N   LEU A 468 " --> pdb=" O   ILE A 483 " (cutoff:3.500A)
      removed outlier: 4.497A  pdb=" N   ILE A 483 " --> pdb=" O   LEU A 468 " (cutoff:3.500A)
      removed outlier: 6.667A  pdb=" N   GLU A 470 " --> pdb=" O   LYS A 481 " (cutoff:3.500A)
      removed outlier: 12.817A  pdb=" N   TYR A 479 " --> pdb=" O   PHE A 498 " (cutoff:3.500A)
      removed outlier: 9.914A  pdb=" N   PHE A 498 " --> pdb=" O   TYR A 479 " (cutoff:3.500A)
      removed outlier: 6.752A  pdb=" N   LYS A 481 " --> pdb=" O   PHE A 496 " (cutoff:3.500A)
      removed outlier: 4.827A  pdb=" N   ILE A 505 " --> pdb=" O   TYR A 519 " (cutoff:3.500A)
      removed outlier: 3.551A  pdb=" N   LYS A 529 " --> pdb=" O   GLU A 520 " (cutoff:3.500A)
      removed outlier: 4.756A  pdb=" N   ILE A 528 " --> pdb=" O   TYR A 540 " (cutoff:3.500A)
      removed outlier: 4.029A  pdb=" N   THR A 539 " --> pdb=" O   THR A 552 " (cutoff:3.500A)
      removed outlier: 4.641A  pdb=" N   THR A 549 " --> pdb=" O   ILE A 561 " (cutoff:3.500A)
      removed outlier: 5.220A  pdb=" N   ILE A 573 " --> pdb=" O   LEU A 586 " (cutoff:3.500A)
      removed outlier: 5.498A  pdb=" N   TYR A 616 " --> pdb=" O   TYR A 628 " (cutoff:3.500A)
      removed outlier: 4.671A  pdb=" N   THR A 637 " --> pdb=" O   GLN A 649 " (cutoff:3.500A)
      removed outlier: 5.063A  pdb=" N   VAL A 658 " --> pdb=" O   PHE A 670 " (cutoff:3.500A)
      removed outlier: 4.788A  pdb=" N   VAL A 679 " --> pdb=" O   ARG A 691 " (cutoff:3.500A)
      removed outlier: 4.868A  pdb=" N   SER A 700 " --> pdb=" O   TYR A 712 " (cutoff:3.500A)
      removed outlier: 4.991A  pdb=" N   VAL A 721 " --> pdb=" O   ILE A 733 " (cutoff:3.500A)
      removed outlier: 4.909A  pdb=" N   ILE A 742 " --> pdb=" O   TRP A 754 " (cutoff:3.500A)
      removed outlier: 4.993A  pdb=" N   THR A 763 " --> pdb=" O   TYR A 775 " (cutoff:3.500A)
      removed outlier: 5.029A  pdb=" N   GLN A 788 " --> pdb=" O   PHE A 800 " (cutoff:3.500A)
      removed outlier: 6.713A  pdb=" N   TYR A 799 " --> pdb=" O   HIS A 811 " (cutoff:3.500A)
      removed outlier: 4.586A  pdb=" N   HIS A 811 " --> pdb=" O   TYR A 799 " (cutoff:3.500A)
      removed outlier: 6.573A  pdb=" N   GLU A 801 " --> pdb=" O   LEU A 809 " (cutoff:3.500A)
      removed outlier: 4.951A  pdb=" N   LEU A 809 " --> pdb=" O   TYR A 821 " (cutoff:3.500A)
      removed outlier: 4.787A  pdb=" N   GLU A 830 " --> pdb=" O   TYR A 842 " (cutoff:3.500A)
      removed outlier: 6.654A  pdb=" N   ALA A 841 " --> pdb=" O   LEU A 853 " (cutoff:3.500A)
      removed outlier: 4.596A  pdb=" N   LEU A 853 " --> pdb=" O   ALA A 841 " (cutoff:3.500A)
      removed outlier: 6.668A  pdb=" N   GLN A 843 " --> pdb=" O   GLN A 851 " (cutoff:3.500A)
      removed outlier: 5.262A  pdb=" N   GLN A 851 " --> pdb=" O   PHE A 863 " (cutoff:3.500A)
      removed outlier: 4.915A  pdb=" N   ILE A 872 " --> pdb=" O   TYR A 884 " (cutoff:3.500A)
      removed outlier: 5.653A  pdb=" N   PHE A 893 " --> pdb=" O   PHE A 904 " (cutoff:3.500A)
      removed outlier: 5.162A  pdb=" N   ALA A 913 " --> pdb=" O   PHE A 930 " (cutoff:3.500A)
      removed outlier: 5.169A  pdb=" N   SER A 939 " --> pdb=" O   LEU A 950 " (cutoff:3.500A)
      removed outlier: 4.995A  pdb=" N   VAL A 959 " --> pdb=" O   TYR A 979 " (cutoff:3.500A)
    Processing sheet with id=AA6, first strand: chain 'A' and resid 1141 through 1142
      removed outlier: 6.353A  pdb=" N   HIS A1146 " --> pdb=" O   ILE A1158 " (cutoff:3.500A)
      removed outlier: 4.318A  pdb=" N   ILE A1158 " --> pdb=" O   HIS A1146 " (cutoff:3.500A)
      removed outlier: 6.595A  pdb=" N   GLN A1148 " --> pdb=" O   THR A1156 " (cutoff:3.500A)
      removed outlier: 4.768A  pdb=" N   THR A1156 " --> pdb=" O   LEU A1167 " (cutoff:3.500A)
      removed outlier: 4.932A  pdb=" N   ILE A1176 " --> pdb=" O   TYR A1187 " (cutoff:3.500A)
      removed outlier: 3.526A  pdb=" N   TYR A1197 " --> pdb=" O   GLY A1188 " (cutoff:3.500A)
      removed outlier: 5.026A  pdb=" N   LEU A1196 " --> pdb=" O   PHE A1207 " (cutoff:3.500A)
      removed outlier: 6.686A  pdb=" N   LEU A1204 " --> pdb=" O   PHE A1219 " (cutoff:3.500A)
      removed outlier: 4.398A  pdb=" N   PHE A1219 " --> pdb=" O   LEU A1204 " (cutoff:3.500A)
      removed outlier: 6.370A  pdb=" N   LEU A1206 " --> pdb=" O   GLU A1217 " (cutoff:3.500A)
      removed outlier: 4.337A  pdb=" N   GLU A1217 " --> pdb=" O   LEU A1206 " (cutoff:3.500A)
      removed outlier: 6.777A  pdb=" N   GLY A1208 " --> pdb=" O   ILE A1215 " (cutoff:3.500A)
      removed outlier: 10.584A  pdb=" N   LEU A1213 " --> pdb=" O   TYR A1232 " (cutoff:3.500A)
      removed outlier: 9.084A  pdb=" N   TYR A1232 " --> pdb=" O   LEU A1213 " (cutoff:3.500A)
      removed outlier: 5.147A  pdb=" N   ILE A1215 " --> pdb=" O   TYR A1230 " (cutoff:3.500A)
      removed outlier: 5.950A  pdb=" N   LEU A1240 " --> pdb=" O   TYR A1290 " (cutoff:3.500A)
      removed outlier: 8.150A  pdb=" N   GLN A1299 " --> pdb=" O   GLU A1311 " (cutoff:3.500A)
      removed outlier: 4.746A  pdb=" N   GLU A1311 " --> pdb=" O   GLN A1299 " (cutoff:3.500A)
      removed outlier: 6.508A  pdb=" N   MET A1301 " --> pdb=" O   VAL A1309 " (cutoff:3.500A)
    Processing sheet with id=AA7, first strand: chain 'A' and resid 1343 through 1344

    613 hydrogen bonds defined for protein.
    1722 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: 7.76

  Time building geometry restraints manager: 2.60 seconds

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

  Histogram of bond lengths:
        0.84 -     1.03: 10711
        1.03 -     1.23: 12
        1.23 -     1.42: 5014
        1.42 -     1.62: 6452
        1.62 -     1.81: 46
  Bond restraints: 22235
  Sorted by residual:
  bond pdb=" C   GLU A 107 "
       pdb=" N   PRO A 108 "
    ideal  model  delta    sigma   weight residual
    1.334  1.367 -0.033 2.34e-02 1.83e+03 1.97e+00
  bond pdb=" CB  GLU A 758 "
       pdb=" CG  GLU A 758 "
    ideal  model  delta    sigma   weight residual
    1.520  1.550 -0.030 3.00e-02 1.11e+03 9.91e-01
  bond pdb=" CA  GLU A 107 "
       pdb=" C   GLU A 107 "
    ideal  model  delta    sigma   weight residual
    1.524  1.535 -0.011 1.26e-02 6.30e+03 7.25e-01
  bond pdb=" CB  GLN A 229 "
       pdb=" CG  GLN A 229 "
    ideal  model  delta    sigma   weight residual
    1.520  1.545 -0.025 3.00e-02 1.11e+03 6.94e-01
  bond pdb=" CA  ASP A 717 "
       pdb=" CB  ASP A 717 "
    ideal  model  delta    sigma   weight residual
    1.529  1.544 -0.015 1.78e-02 3.16e+03 6.65e-01
  ... (remaining 22230 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     1.43: 39210
        1.43 -     2.87: 654
        2.87 -     4.30: 60
        4.30 -     5.73: 2
        5.73 -     7.17: 2
  Bond angle restraints: 39928
  Sorted by residual:
  angle pdb=" C   GLY A1405 "
        pdb=" N   ILE A1406 "
        pdb=" CA  ILE A1406 "
      ideal   model   delta    sigma   weight residual
     120.24  122.71   -2.47 6.30e-01 2.52e+00 1.54e+01
  angle pdb=" C   ILE A1406 "
        pdb=" CA  ILE A1406 "
        pdb=" CB  ILE A1406 "
      ideal   model   delta    sigma   weight residual
     114.35  111.68    2.67 1.06e+00 8.90e-01 6.37e+00
  angle pdb=" N   ARG A1338 "
        pdb=" CA  ARG A1338 "
        pdb=" C   ARG A1338 "
      ideal   model   delta    sigma   weight residual
     110.80  105.58    5.22 2.13e+00 2.20e-01 6.00e+00
  angle pdb=" CA  GLU A 107 "
        pdb=" C   GLU A 107 "
        pdb=" N   PRO A 108 "
      ideal   model   delta    sigma   weight residual
     118.44  121.96   -3.52 1.59e+00 3.96e-01 4.90e+00
  angle pdb=" CA  GLU A 758 "
        pdb=" CB  GLU A 758 "
        pdb=" CG  GLU A 758 "
      ideal   model   delta    sigma   weight residual
     114.10  118.47   -4.37 2.00e+00 2.50e-01 4.78e+00
  ... (remaining 39923 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    17.81: 9531
       17.81 -    35.63: 713
       35.63 -    53.44: 203
       53.44 -    71.26: 61
       71.26 -    89.07: 33
  Dihedral angle restraints: 10541
    sinusoidal: 5608
      harmonic: 4933
  Sorted by residual:
  dihedral pdb=" CA  TYR A1422 "
           pdb=" C   TYR A1422 "
           pdb=" N   GLU A1423 "
           pdb=" CA  GLU A1423 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  160.87   19.13     0      5.00e+00 4.00e-02 1.46e+01
  dihedral pdb=" CA  MET A 459 "
           pdb=" C   MET A 459 "
           pdb=" N   ASN A 460 "
           pdb=" CA  ASN A 460 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  162.98   17.02     0      5.00e+00 4.00e-02 1.16e+01
  dihedral pdb=" CA  GLU A1430 "
           pdb=" C   GLU A1430 "
           pdb=" N   LEU A1431 "
           pdb=" CA  LEU A1431 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  163.32   16.68     0      5.00e+00 4.00e-02 1.11e+01
  ... (remaining 10538 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.028: 1021
       0.028 -    0.056: 459
       0.056 -    0.083: 74
       0.083 -    0.111: 73
       0.111 -    0.139: 34
  Chirality restraints: 1661
  Sorted by residual:
  chirality pdb=" CA  ILE A 467 "
            pdb=" N   ILE A 467 "
            pdb=" C   ILE A 467 "
            pdb=" CB  ILE A 467 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.43    2.57   -0.14 2.00e-01 2.50e+01 4.82e-01
  chirality pdb=" CA  ILE A 967 "
            pdb=" N   ILE A 967 "
            pdb=" C   ILE A 967 "
            pdb=" CB  ILE A 967 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.43    2.57   -0.14 2.00e-01 2.50e+01 4.58e-01
  chirality pdb=" CA  ILE A 790 "
            pdb=" N   ILE A 790 "
            pdb=" C   ILE A 790 "
            pdb=" CB  ILE A 790 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.43    2.57   -0.13 2.00e-01 2.50e+01 4.55e-01
  ... (remaining 1658 not shown)

  Planarity restraints: 3411
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  ALA A 251 "    0.007 2.00e-02 2.50e+03   1.33e-02 1.78e+00
        pdb=" C   ALA A 251 "   -0.023 2.00e-02 2.50e+03
        pdb=" O   ALA A 251 "    0.009 2.00e-02 2.50e+03
        pdb=" N   ILE A 252 "    0.008 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   ASP A1097 "   -0.019 5.00e-02 4.00e+02   2.90e-02 1.35e+00
        pdb=" N   PRO A1098 "    0.050 5.00e-02 4.00e+02
        pdb=" CA  PRO A1098 "   -0.015 5.00e-02 4.00e+02
        pdb=" CD  PRO A1098 "   -0.016 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  ASP A 717 "   -0.006 2.00e-02 2.50e+03   1.13e-02 1.27e+00
        pdb=" C   ASP A 717 "    0.019 2.00e-02 2.50e+03
        pdb=" O   ASP A 717 "   -0.007 2.00e-02 2.50e+03
        pdb=" N   ASN A 718 "   -0.007 2.00e-02 2.50e+03
  ... (remaining 3408 not shown)

  Histogram of nonbonded interaction distances:
        1.43 -     2.06: 448
        2.06 -     2.70: 35263
        2.70 -     3.33: 65543
        3.33 -     3.97: 89703
        3.97 -     4.60: 135721
  Nonbonded interactions: 326678
  Sorted by model distance:
  nonbonded pdb=" OE1 GLU A 758 "
            pdb=" H   GLU A 758 "
     model   vdw
     1.426 2.450
  nonbonded pdb=" OE1 GLN A1328 "
            pdb=" H   GLN A1328 "
     model   vdw
     1.527 2.450
  nonbonded pdb=" O   LEU A 871 "
            pdb=" HH  TYR A 886 "
     model   vdw
     1.584 2.450
  nonbonded pdb=" OD2 ASP A 994 "
            pdb=" HE2 HIS A1229 "
     model   vdw
     1.591 2.450
  nonbonded pdb=" OH  TYR A 608 "
            pdb="HH21 ARG A 619 "
     model   vdw
     1.595 2.450
  ... (remaining 326673 not shown)

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

  No NCS relation were found !!!

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

Found NCS groups:
  found none.
Set up NCS constraints
  No NCS constraints will be used in refinement.
Set refine NCS operators
Adjust number of macro_cycles
  Number of macro_cycles: 10
Reset NCS operators
Extract rigid body selections
Check and reset occupancies
  Occupancies: min=1.00 max=1.00 mean=1.00
Load rotamer database and sin/cos tables
Set ADP refinement strategy
  ADPs will be refined as individual isotropic
Make a string to write initial .geo file
Internal consistency checks
Time:
  Set random seed:                         0.000
  Set model cs if undefined:               0.000
  Decide on map wrapping:                  0.000
  Normalize map: mean=0, sd=1:             2.620
  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:             0.150
  Extract box with map and model:          0.300
  Check model and map are aligned:         0.070
  Set scattering table:                    0.050
  Process input model:                     23.040
  Find NCS groups from input model:        0.070
  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:8.700
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   35.030
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8426
moved from start:          0.0000

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.033  11516  Z= 0.118
  Angle     :  0.480   7.169  15600  Z= 0.261
  Chirality :  0.039   0.139   1661
  Planarity :  0.003   0.029   2054
  Dihedral  : 16.631  89.069   4221
  Min Nonbonded Distance : 2.053

Molprobity Statistics.
  All-atom Clashscore : 4.81
  Ramachandran Plot:
    Outliers :  0.50 %
    Allowed  :  4.49 %
    Favored  : 95.01 %
  Rotamer:
    Outliers :  1.45 %
    Allowed  : 15.08 %
    Favored  : 83.48 %
  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 aren not related in a simple way.
  whole:  1.15 (0.23), residues: 1404
  helix:  3.33 (0.40), residues: 165
  sheet:  1.54 (0.25), residues: 400
  loop : -0.15 (0.23), residues: 839

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG A 697 
 TYR   0.010   0.001   TYR A 601 
 PHE   0.008   0.001   PHE A 350 
 TRP   0.009   0.001   TRP A 422 
 HIS   0.003   0.001   HIS A1291 

Details of bonding type rmsd
  covalent geometry    : bond        0.00250 (11516)
  covalent geometry    : angle       0.48010 (15600)
  hydrogen bonds       : bond        0.18679 (  443)
  hydrogen bonds       : angle       8.64849 ( 1722)

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

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

  2808 Ramachandran restraints generated.
    1404 Oldfield, 0 Emsley, 1404 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2808 Ramachandran restraints generated.
    1404 Oldfield, 0 Emsley, 1404 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Residue LYS   84 is missing expected H atoms. Skipping.
Residue LYS  226 is missing expected H atoms. Skipping.
Residue ILE  240 is missing expected H atoms. Skipping.
Residue THR  241 is missing expected H atoms. Skipping.
Residue SER  242 is missing expected H atoms. Skipping.
Residue LEU  244 is missing expected H atoms. Skipping.
Residue LYS  306 is missing expected H atoms. Skipping.
Residue LEU 1414 is missing expected H atoms. Skipping.
Residue TYR 1416 is missing expected H atoms. Skipping.
Residue TYR 1422 is missing expected H atoms. Skipping.
Residue TYR 1425 is missing expected H atoms. Skipping.
Residue LYS 1433 is missing expected H atoms. Skipping.
Residue LYS 1435 is missing expected H atoms. Skipping.
Residue TYR 1442 is missing expected H atoms. Skipping.
Residue VAL 1443 is missing expected H atoms. Skipping.
Residue ALA 1444 is missing expected H atoms. Skipping.
Residue SER 1446 is missing expected H atoms. Skipping.
Residue LEU 1450 is missing expected H atoms. Skipping.
Residue ILE 1452 is missing expected H atoms. Skipping.
Residue VAL 1457 is missing expected H atoms. Skipping.
Residue LYS 1458 is missing expected H atoms. Skipping.
Residue TYR 1465 is missing expected H atoms. Skipping.
Residue ILE 1467 is missing expected H atoms. Skipping.
Residue LYS 1471 is missing expected H atoms. Skipping.
Residue LEU 1474 is missing expected H atoms. Skipping.
Residue LEU 1475 is missing expected H atoms. Skipping.
Residue ILE 1476 is missing expected H atoms. Skipping.
Residue VAL 1478 is missing expected H atoms. Skipping.
Residue LYS 1480 is missing expected H atoms. Skipping.
Evaluate side-chains
  105 residues out of total 1222 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 88
  time to evaluate  : 0.434 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
  outliers start: 17
  outliers final: 14
  residues processed: 104
  average time/residue: 1.2278
  time to fit residues: 137.5105
Evaluate side-chains
  101 residues out of total 1222 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 87
  time to evaluate  : 0.569 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  135 LYS
Chi-restraints excluded: chain A residue  184 SER
Chi-restraints excluded: chain A residue  228 SER
Chi-restraints excluded: chain A residue  325 CYS
Chi-restraints excluded: chain A residue  335 SER
Chi-restraints excluded: chain A residue  339 SER
Chi-restraints excluded: chain A residue  358 SER
Chi-restraints excluded: chain A residue  417 VAL
Chi-restraints excluded: chain A residue  436 PHE
Chi-restraints excluded: chain A residue  446 SER
Chi-restraints excluded: chain A residue 1068 GLN
Chi-restraints excluded: chain A residue 1141 SER
Chi-restraints excluded: chain A residue 1236 SER
Chi-restraints excluded: chain A residue 1473 SER
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 141
   random chunks:
   chunk 98 optimal weight:    5.9990
   chunk 107 optimal weight:    3.9990
   chunk 10 optimal weight:    6.9990
   chunk 66 optimal weight:    2.9990
   chunk 130 optimal weight:    2.9990
   chunk 124 optimal weight:    0.9990
   chunk 103 optimal weight:    1.9990
   chunk 77 optimal weight:    2.9990
   chunk 122 optimal weight:    1.9990
   chunk 91 optimal weight:    2.9990
   chunk 55 optimal weight:    0.7980
   overall best weight:    1.7588

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

Flipped N/Q/H residues before XYZ refinement:
A 404 HIS
A 594 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4127 r_free = 0.4127 target = 0.150093 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 54)----------------|
| r_work = 0.3579 r_free = 0.3579 target = 0.105791 restraints weight = 37181.638|
|-----------------------------------------------------------------------------|
r_work (start): 0.3511 rms_B_bonded: 1.92
r_work: 0.3383 rms_B_bonded: 2.03 restraints_weight: 0.5000
r_work: 0.3291 rms_B_bonded: 3.16 restraints_weight: 0.2500
r_work (final): 0.3291
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8343
moved from start:          0.0717

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.036  11516  Z= 0.182
  Angle     :  0.546   7.021  15600  Z= 0.302
  Chirality :  0.042   0.145   1661
  Planarity :  0.004   0.044   2054
  Dihedral  :  5.504  42.814   1575
  Min Nonbonded Distance : 2.256

Molprobity Statistics.
  All-atom Clashscore : 3.40
  Ramachandran Plot:
    Outliers :  0.50 %
    Allowed  :  5.13 %
    Favored  : 94.37 %
  Rotamer:
    Outliers :  1.70 %
    Allowed  : 14.65 %
    Favored  : 83.65 %
  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 aren not related in a simple way.
  whole:  0.94 (0.23), residues: 1404
  helix:  3.05 (0.40), residues: 166
  sheet:  1.30 (0.24), residues: 415
  loop : -0.24 (0.23), residues: 823

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG A 538 
 TYR   0.013   0.001   TYR A 965 
 PHE   0.009   0.001   PHE A 350 
 TRP   0.010   0.002   TRP A1317 
 HIS   0.003   0.001   HIS A1291 

Details of bonding type rmsd
  covalent geometry    : bond        0.00376 (11516)
  covalent geometry    : angle       0.54558 (15600)
  hydrogen bonds       : bond        0.04955 (  443)
  hydrogen bonds       : angle       6.24060 ( 1722)

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

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

  2808 Ramachandran restraints generated.
    1404 Oldfield, 0 Emsley, 1404 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2808 Ramachandran restraints generated.
    1404 Oldfield, 0 Emsley, 1404 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Residue LYS   84 is missing expected H atoms. Skipping.
Residue LYS  226 is missing expected H atoms. Skipping.
Residue ILE  240 is missing expected H atoms. Skipping.
Residue THR  241 is missing expected H atoms. Skipping.
Residue SER  242 is missing expected H atoms. Skipping.
Residue LEU  244 is missing expected H atoms. Skipping.
Residue LYS  306 is missing expected H atoms. Skipping.
Residue LEU 1414 is missing expected H atoms. Skipping.
Residue TYR 1416 is missing expected H atoms. Skipping.
Residue TYR 1422 is missing expected H atoms. Skipping.
Residue TYR 1425 is missing expected H atoms. Skipping.
Residue LYS 1433 is missing expected H atoms. Skipping.
Residue LYS 1435 is missing expected H atoms. Skipping.
Residue TYR 1442 is missing expected H atoms. Skipping.
Residue VAL 1443 is missing expected H atoms. Skipping.
Residue ALA 1444 is missing expected H atoms. Skipping.
Residue SER 1446 is missing expected H atoms. Skipping.
Residue LEU 1450 is missing expected H atoms. Skipping.
Residue ILE 1452 is missing expected H atoms. Skipping.
Residue VAL 1457 is missing expected H atoms. Skipping.
Residue LYS 1458 is missing expected H atoms. Skipping.
Residue TYR 1465 is missing expected H atoms. Skipping.
Residue ILE 1467 is missing expected H atoms. Skipping.
Residue LYS 1471 is missing expected H atoms. Skipping.
Residue LEU 1474 is missing expected H atoms. Skipping.
Residue LEU 1475 is missing expected H atoms. Skipping.
Residue ILE 1476 is missing expected H atoms. Skipping.
Residue VAL 1478 is missing expected H atoms. Skipping.
Residue LYS 1480 is missing expected H atoms. Skipping.
Evaluate side-chains
  109 residues out of total 1222 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 89
  time to evaluate  : 0.419 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  459 MET cc_start: 0.7602 (mmm) cc_final: 0.7396 (mmm)
REVERT: A 1346 ARG cc_start: 0.8348 (ptt90) cc_final: 0.8118 (ptt90)
REVERT: A 1359 GLU cc_start: 0.8911 (OUTLIER) cc_final: 0.8049 (tm-30)
  outliers start: 20
  outliers final: 9
  residues processed: 100
  average time/residue: 1.2427
  time to fit residues: 133.5687
Evaluate side-chains
  96 residues out of total 1222 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 86
  time to evaluate  : 0.559 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  228 SER
Chi-restraints excluded: chain A residue  318 ASP
Chi-restraints excluded: chain A residue  358 SER
Chi-restraints excluded: chain A residue  417 VAL
Chi-restraints excluded: chain A residue  436 PHE
Chi-restraints excluded: chain A residue  610 ASP
Chi-restraints excluded: chain A residue  973 LEU
Chi-restraints excluded: chain A residue 1359 GLU
Chi-restraints excluded: chain A residue 1377 MET
Chi-restraints excluded: chain A residue 1434 ILE
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 141
   random chunks:
   chunk 133 optimal weight:    0.4980
   chunk 82 optimal weight:    2.9990
   chunk 97 optimal weight:    0.8980
   chunk 5 optimal weight:    7.9990
   chunk 131 optimal weight:    4.9990
   chunk 11 optimal weight:   10.0000
   chunk 71 optimal weight:    1.9990
   chunk 107 optimal weight:    3.9990
   chunk 1 optimal weight:   10.0000
   chunk 54 optimal weight:    3.9990
   chunk 38 optimal weight:    4.9990
   overall best weight:    2.0786

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

Flipped N/Q/H residues before XYZ refinement:
A 404 HIS
A 594 GLN
A1327 ASN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4122 r_free = 0.4122 target = 0.149723 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 57)----------------|
| r_work = 0.3572 r_free = 0.3572 target = 0.105379 restraints weight = 37235.159|
|-----------------------------------------------------------------------------|
r_work (start): 0.3503 rms_B_bonded: 1.93
r_work: 0.3376 rms_B_bonded: 2.03 restraints_weight: 0.5000
r_work: 0.3264 rms_B_bonded: 3.23 restraints_weight: 0.2500
r_work (final): 0.3264
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8359
moved from start:          0.0816

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.040  11516  Z= 0.200
  Angle     :  0.541   6.980  15600  Z= 0.299
  Chirality :  0.042   0.139   1661
  Planarity :  0.004   0.039   2054
  Dihedral  :  4.947  38.787   1560
  Min Nonbonded Distance : 2.317

Molprobity Statistics.
  All-atom Clashscore : 3.13
  Ramachandran Plot:
    Outliers :  0.57 %
    Allowed  :  5.56 %
    Favored  : 93.87 %
  Rotamer:
    Outliers :  1.36 %
    Allowed  : 15.50 %
    Favored  : 83.13 %
  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 aren not related in a simple way.
  whole:  0.74 (0.23), residues: 1404
  helix:  2.94 (0.40), residues: 166
  sheet:  1.13 (0.24), residues: 409
  loop : -0.35 (0.23), residues: 829

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG A1305 
 TYR   0.013   0.001   TYR A 792 
 PHE   0.009   0.001   PHE A 350 
 TRP   0.010   0.002   TRP A1169 
 HIS   0.004   0.001   HIS A1291 

Details of bonding type rmsd
  covalent geometry    : bond        0.00413 (11516)
  covalent geometry    : angle       0.54073 (15600)
  hydrogen bonds       : bond        0.04612 (  443)
  hydrogen bonds       : angle       5.96150 ( 1722)

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

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

  2808 Ramachandran restraints generated.
    1404 Oldfield, 0 Emsley, 1404 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2808 Ramachandran restraints generated.
    1404 Oldfield, 0 Emsley, 1404 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Residue LYS   84 is missing expected H atoms. Skipping.
Residue LYS  226 is missing expected H atoms. Skipping.
Residue ILE  240 is missing expected H atoms. Skipping.
Residue THR  241 is missing expected H atoms. Skipping.
Residue SER  242 is missing expected H atoms. Skipping.
Residue LEU  244 is missing expected H atoms. Skipping.
Residue LYS  306 is missing expected H atoms. Skipping.
Residue LEU 1414 is missing expected H atoms. Skipping.
Residue TYR 1416 is missing expected H atoms. Skipping.
Residue TYR 1422 is missing expected H atoms. Skipping.
Residue TYR 1425 is missing expected H atoms. Skipping.
Residue LYS 1433 is missing expected H atoms. Skipping.
Residue LYS 1435 is missing expected H atoms. Skipping.
Residue TYR 1442 is missing expected H atoms. Skipping.
Residue VAL 1443 is missing expected H atoms. Skipping.
Residue ALA 1444 is missing expected H atoms. Skipping.
Residue SER 1446 is missing expected H atoms. Skipping.
Residue LEU 1450 is missing expected H atoms. Skipping.
Residue ILE 1452 is missing expected H atoms. Skipping.
Residue VAL 1457 is missing expected H atoms. Skipping.
Residue LYS 1458 is missing expected H atoms. Skipping.
Residue TYR 1465 is missing expected H atoms. Skipping.
Residue ILE 1467 is missing expected H atoms. Skipping.
Residue LYS 1471 is missing expected H atoms. Skipping.
Residue LEU 1474 is missing expected H atoms. Skipping.
Residue LEU 1475 is missing expected H atoms. Skipping.
Residue ILE 1476 is missing expected H atoms. Skipping.
Residue VAL 1478 is missing expected H atoms. Skipping.
Residue LYS 1480 is missing expected H atoms. Skipping.
Evaluate side-chains
  107 residues out of total 1222 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 91
  time to evaluate  : 0.393 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  229 GLN cc_start: 0.7024 (OUTLIER) cc_final: 0.5864 (tm130)
REVERT: A  459 MET cc_start: 0.7712 (mmm) cc_final: 0.7452 (mmm)
REVERT: A 1346 ARG cc_start: 0.8414 (ptt90) cc_final: 0.8186 (ptt90)
REVERT: A 1359 GLU cc_start: 0.8923 (OUTLIER) cc_final: 0.8084 (tm-30)
  outliers start: 16
  outliers final: 7
  residues processed: 98
  average time/residue: 1.2373
  time to fit residues: 130.2868
Evaluate side-chains
  94 residues out of total 1222 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 85
  time to evaluate  : 0.379 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  229 GLN
Chi-restraints excluded: chain A residue  318 ASP
Chi-restraints excluded: chain A residue  410 ILE
Chi-restraints excluded: chain A residue  610 ASP
Chi-restraints excluded: chain A residue  973 LEU
Chi-restraints excluded: chain A residue 1359 GLU
Chi-restraints excluded: chain A residue 1377 MET
Chi-restraints excluded: chain A residue 1434 ILE
Chi-restraints excluded: chain A residue 1473 SER
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 141
   random chunks:
   chunk 68 optimal weight:    3.9990
   chunk 126 optimal weight:    2.9990
   chunk 120 optimal weight:    0.2980
   chunk 124 optimal weight:    2.9990
   chunk 47 optimal weight:    0.7980
   chunk 123 optimal weight:    0.7980
   chunk 52 optimal weight:    0.2980
   chunk 72 optimal weight:    2.9990
   chunk 24 optimal weight:    8.9990
   chunk 75 optimal weight:    4.9990
   chunk 69 optimal weight:    0.9980
   overall best weight:    0.6380

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

Flipped N/Q/H residues before XYZ refinement:
A 404 HIS
A 594 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4150 r_free = 0.4150 target = 0.152016 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 50)----------------|
| r_work = 0.3619 r_free = 0.3619 target = 0.108282 restraints weight = 37132.767|
|-----------------------------------------------------------------------------|
r_work (start): 0.3551 rms_B_bonded: 1.90
r_work: 0.3429 rms_B_bonded: 2.02 restraints_weight: 0.5000
r_work: 0.3322 rms_B_bonded: 3.19 restraints_weight: 0.2500
r_work (final): 0.3322
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8311
moved from start:          0.0993

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.032  11516  Z= 0.108
  Angle     :  0.494   6.918  15600  Z= 0.271
  Chirality :  0.041   0.143   1661
  Planarity :  0.004   0.048   2054
  Dihedral  :  4.460  17.765   1555
  Min Nonbonded Distance : 2.427

Molprobity Statistics.
  All-atom Clashscore : 2.81
  Ramachandran Plot:
    Outliers :  0.50 %
    Allowed  :  5.34 %
    Favored  : 94.16 %
  Rotamer:
    Outliers :  1.45 %
    Allowed  : 14.99 %
    Favored  : 83.56 %
  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 aren not related in a simple way.
  whole:  0.68 (0.23), residues: 1404
  helix:  3.12 (0.41), residues: 166
  sheet:  0.85 (0.24), residues: 420
  loop : -0.31 (0.23), residues: 818

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG A 697 
 TYR   0.010   0.001   TYR A 965 
 PHE   0.007   0.001   PHE A 350 
 TRP   0.007   0.001   TRP A 422 
 HIS   0.002   0.001   HIS A1361 

Details of bonding type rmsd
  covalent geometry    : bond        0.00221 (11516)
  covalent geometry    : angle       0.49396 (15600)
  hydrogen bonds       : bond        0.03719 (  443)
  hydrogen bonds       : angle       5.51885 ( 1722)

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

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

  2808 Ramachandran restraints generated.
    1404 Oldfield, 0 Emsley, 1404 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2808 Ramachandran restraints generated.
    1404 Oldfield, 0 Emsley, 1404 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Residue LYS   84 is missing expected H atoms. Skipping.
Residue LYS  226 is missing expected H atoms. Skipping.
Residue ILE  240 is missing expected H atoms. Skipping.
Residue THR  241 is missing expected H atoms. Skipping.
Residue SER  242 is missing expected H atoms. Skipping.
Residue LEU  244 is missing expected H atoms. Skipping.
Residue LYS  306 is missing expected H atoms. Skipping.
Residue LEU 1414 is missing expected H atoms. Skipping.
Residue TYR 1416 is missing expected H atoms. Skipping.
Residue TYR 1422 is missing expected H atoms. Skipping.
Residue TYR 1425 is missing expected H atoms. Skipping.
Residue LYS 1433 is missing expected H atoms. Skipping.
Residue LYS 1435 is missing expected H atoms. Skipping.
Residue TYR 1442 is missing expected H atoms. Skipping.
Residue VAL 1443 is missing expected H atoms. Skipping.
Residue ALA 1444 is missing expected H atoms. Skipping.
Residue SER 1446 is missing expected H atoms. Skipping.
Residue LEU 1450 is missing expected H atoms. Skipping.
Residue ILE 1452 is missing expected H atoms. Skipping.
Residue VAL 1457 is missing expected H atoms. Skipping.
Residue LYS 1458 is missing expected H atoms. Skipping.
Residue TYR 1465 is missing expected H atoms. Skipping.
Residue ILE 1467 is missing expected H atoms. Skipping.
Residue LYS 1471 is missing expected H atoms. Skipping.
Residue LEU 1474 is missing expected H atoms. Skipping.
Residue LEU 1475 is missing expected H atoms. Skipping.
Residue ILE 1476 is missing expected H atoms. Skipping.
Residue VAL 1478 is missing expected H atoms. Skipping.
Residue LYS 1480 is missing expected H atoms. Skipping.
Evaluate side-chains
  109 residues out of total 1222 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 92
  time to evaluate  : 0.549 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  229 GLN cc_start: 0.7045 (OUTLIER) cc_final: 0.6157 (tm-30)
REVERT: A  459 MET cc_start: 0.7717 (mmm) cc_final: 0.7492 (mmm)
REVERT: A 1346 ARG cc_start: 0.8361 (ptt90) cc_final: 0.8129 (ptt90)
REVERT: A 1359 GLU cc_start: 0.8785 (OUTLIER) cc_final: 0.8036 (tm-30)
  outliers start: 17
  outliers final: 7
  residues processed: 104
  average time/residue: 1.0863
  time to fit residues: 122.4536
Evaluate side-chains
  97 residues out of total 1222 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 88
  time to evaluate  : 0.394 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  229 GLN
Chi-restraints excluded: chain A residue  410 ILE
Chi-restraints excluded: chain A residue  417 VAL
Chi-restraints excluded: chain A residue  610 ASP
Chi-restraints excluded: chain A residue  721 VAL
Chi-restraints excluded: chain A residue  973 LEU
Chi-restraints excluded: chain A residue 1141 SER
Chi-restraints excluded: chain A residue 1359 GLU
Chi-restraints excluded: chain A residue 1473 SER
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 141
   random chunks:
   chunk 0 optimal weight:    7.9990
   chunk 69 optimal weight:    3.9990
   chunk 78 optimal weight:    3.9990
   chunk 9 optimal weight:   10.0000
   chunk 120 optimal weight:    0.0570
   chunk 50 optimal weight:    2.9990
   chunk 122 optimal weight:    0.6980
   chunk 42 optimal weight:    6.9990
   chunk 17 optimal weight:   20.0000
   chunk 107 optimal weight:    2.9990
   chunk 95 optimal weight:    5.9990
   overall best weight:    2.1504

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

Flipped N/Q/H residues before XYZ refinement:
A 404 HIS
A 594 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4127 r_free = 0.4127 target = 0.150184 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 58)----------------|
| r_work = 0.3576 r_free = 0.3576 target = 0.105605 restraints weight = 36880.176|
|-----------------------------------------------------------------------------|
r_work (start): 0.3507 rms_B_bonded: 1.93
r_work: 0.3383 rms_B_bonded: 2.02 restraints_weight: 0.5000
r_work: 0.3271 rms_B_bonded: 3.22 restraints_weight: 0.2500
r_work (final): 0.3271
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8355
moved from start:          0.1030

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.040  11516  Z= 0.198
  Angle     :  0.531   6.911  15600  Z= 0.292
  Chirality :  0.041   0.139   1661
  Planarity :  0.004   0.045   2054
  Dihedral  :  4.631  18.273   1555
  Min Nonbonded Distance : 2.403

Molprobity Statistics.
  All-atom Clashscore : 3.08
  Ramachandran Plot:
    Outliers :  0.57 %
    Allowed  :  5.48 %
    Favored  : 93.95 %
  Rotamer:
    Outliers :  1.53 %
    Allowed  : 15.25 %
    Favored  : 83.22 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  0.65 (0.23), residues: 1404
  helix:  2.96 (0.40), residues: 166
  sheet:  0.93 (0.24), residues: 409
  loop : -0.35 (0.23), residues: 829

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG A 697 
 TYR   0.012   0.001   TYR A 792 
 PHE   0.009   0.001   PHE A 350 
 TRP   0.011   0.002   TRP A1169 
 HIS   0.004   0.001   HIS A1291 

Details of bonding type rmsd
  covalent geometry    : bond        0.00414 (11516)
  covalent geometry    : angle       0.53120 (15600)
  hydrogen bonds       : bond        0.04221 (  443)
  hydrogen bonds       : angle       5.65822 ( 1722)

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

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

  2808 Ramachandran restraints generated.
    1404 Oldfield, 0 Emsley, 1404 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2808 Ramachandran restraints generated.
    1404 Oldfield, 0 Emsley, 1404 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Residue LYS   84 is missing expected H atoms. Skipping.
Residue LYS  226 is missing expected H atoms. Skipping.
Residue ILE  240 is missing expected H atoms. Skipping.
Residue THR  241 is missing expected H atoms. Skipping.
Residue SER  242 is missing expected H atoms. Skipping.
Residue LEU  244 is missing expected H atoms. Skipping.
Residue LYS  306 is missing expected H atoms. Skipping.
Residue LEU 1414 is missing expected H atoms. Skipping.
Residue TYR 1416 is missing expected H atoms. Skipping.
Residue TYR 1422 is missing expected H atoms. Skipping.
Residue TYR 1425 is missing expected H atoms. Skipping.
Residue LYS 1433 is missing expected H atoms. Skipping.
Residue LYS 1435 is missing expected H atoms. Skipping.
Residue TYR 1442 is missing expected H atoms. Skipping.
Residue VAL 1443 is missing expected H atoms. Skipping.
Residue ALA 1444 is missing expected H atoms. Skipping.
Residue SER 1446 is missing expected H atoms. Skipping.
Residue LEU 1450 is missing expected H atoms. Skipping.
Residue ILE 1452 is missing expected H atoms. Skipping.
Residue VAL 1457 is missing expected H atoms. Skipping.
Residue LYS 1458 is missing expected H atoms. Skipping.
Residue TYR 1465 is missing expected H atoms. Skipping.
Residue ILE 1467 is missing expected H atoms. Skipping.
Residue LYS 1471 is missing expected H atoms. Skipping.
Residue LEU 1474 is missing expected H atoms. Skipping.
Residue LEU 1475 is missing expected H atoms. Skipping.
Residue ILE 1476 is missing expected H atoms. Skipping.
Residue VAL 1478 is missing expected H atoms. Skipping.
Residue LYS 1480 is missing expected H atoms. Skipping.
Evaluate side-chains
  105 residues out of total 1222 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 87
  time to evaluate  : 0.503 
Fit side-chains
   revert: symmetry clash
REVERT: A  229 GLN cc_start: 0.7136 (OUTLIER) cc_final: 0.6243 (tm-30)
REVERT: A  458 LYS cc_start: 0.8281 (mtpp) cc_final: 0.7898 (mtpp)
REVERT: A  459 MET cc_start: 0.7734 (mmm) cc_final: 0.7510 (mmm)
REVERT: A  971 LYS cc_start: 0.8680 (mppt) cc_final: 0.8441 (ttpp)
REVERT: A 1346 ARG cc_start: 0.8421 (ptt90) cc_final: 0.8196 (ptt90)
REVERT: A 1359 GLU cc_start: 0.8862 (OUTLIER) cc_final: 0.8115 (tm-30)
  outliers start: 18
  outliers final: 12
  residues processed: 99
  average time/residue: 1.2094
  time to fit residues: 129.1536
Evaluate side-chains
  99 residues out of total 1222 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 85
  time to evaluate  : 0.702 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  228 SER
Chi-restraints excluded: chain A residue  229 GLN
Chi-restraints excluded: chain A residue  318 ASP
Chi-restraints excluded: chain A residue  358 SER
Chi-restraints excluded: chain A residue  410 ILE
Chi-restraints excluded: chain A residue  417 VAL
Chi-restraints excluded: chain A residue  610 ASP
Chi-restraints excluded: chain A residue  721 VAL
Chi-restraints excluded: chain A residue  965 TYR
Chi-restraints excluded: chain A residue 1141 SER
Chi-restraints excluded: chain A residue 1359 GLU
Chi-restraints excluded: chain A residue 1377 MET
Chi-restraints excluded: chain A residue 1434 ILE
Chi-restraints excluded: chain A residue 1473 SER
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 141
   random chunks:
   chunk 21 optimal weight:   20.0000
   chunk 17 optimal weight:   20.0000
   chunk 109 optimal weight:    4.9990
   chunk 119 optimal weight:    2.9990
   chunk 31 optimal weight:    4.9990
   chunk 95 optimal weight:    4.9990
   chunk 98 optimal weight:    5.9990
   chunk 128 optimal weight:    1.9990
   chunk 32 optimal weight:    4.9990
   chunk 22 optimal weight:    2.9990
   chunk 23 optimal weight:   10.0000
   overall best weight:    3.5990

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

Flipped N/Q/H residues before XYZ refinement:
A 404 HIS
A 484 ASN
A 594 GLN
A1327 ASN

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4106 r_free = 0.4106 target = 0.147743 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.3532 r_free = 0.3532 target = 0.103220 restraints weight = 37156.876|
|-----------------------------------------------------------------------------|
r_work (start): 0.3479 rms_B_bonded: 2.07
r_work: 0.3344 rms_B_bonded: 2.07 restraints_weight: 0.5000
r_work: 0.3231 rms_B_bonded: 3.30 restraints_weight: 0.2500
r_work (final): 0.3231
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8388
moved from start:          0.1102

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.006   0.061  11516  Z= 0.297
  Angle     :  0.588   6.910  15600  Z= 0.326
  Chirality :  0.043   0.145   1661
  Planarity :  0.004   0.047   2054
  Dihedral  :  4.906  19.876   1555
  Min Nonbonded Distance : 2.356

Molprobity Statistics.
  All-atom Clashscore : 3.86
  Ramachandran Plot:
    Outliers :  0.50 %
    Allowed  :  5.56 %
    Favored  : 93.95 %
  Rotamer:
    Outliers :  1.79 %
    Allowed  : 14.99 %
    Favored  : 83.22 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  0.55 (0.23), residues: 1404
  helix:  2.72 (0.40), residues: 166
  sheet:  0.98 (0.24), residues: 407
  loop : -0.45 (0.23), residues: 831

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.008   0.001   ARG A1305 
 TYR   0.016   0.002   TYR A 792 
 PHE   0.011   0.001   PHE A  22 
 TRP   0.017   0.002   TRP A1169 
 HIS   0.006   0.001   HIS A1291 

Details of bonding type rmsd
  covalent geometry    : bond        0.00625 (11516)
  covalent geometry    : angle       0.58817 (15600)
  hydrogen bonds       : bond        0.04735 (  443)
  hydrogen bonds       : angle       5.93548 ( 1722)

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

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

  2808 Ramachandran restraints generated.
    1404 Oldfield, 0 Emsley, 1404 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2808 Ramachandran restraints generated.
    1404 Oldfield, 0 Emsley, 1404 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Residue LYS   84 is missing expected H atoms. Skipping.
Residue LYS  226 is missing expected H atoms. Skipping.
Residue ILE  240 is missing expected H atoms. Skipping.
Residue THR  241 is missing expected H atoms. Skipping.
Residue SER  242 is missing expected H atoms. Skipping.
Residue LEU  244 is missing expected H atoms. Skipping.
Residue LYS  306 is missing expected H atoms. Skipping.
Residue LEU 1414 is missing expected H atoms. Skipping.
Residue TYR 1416 is missing expected H atoms. Skipping.
Residue TYR 1422 is missing expected H atoms. Skipping.
Residue TYR 1425 is missing expected H atoms. Skipping.
Residue LYS 1433 is missing expected H atoms. Skipping.
Residue LYS 1435 is missing expected H atoms. Skipping.
Residue TYR 1442 is missing expected H atoms. Skipping.
Residue VAL 1443 is missing expected H atoms. Skipping.
Residue ALA 1444 is missing expected H atoms. Skipping.
Residue SER 1446 is missing expected H atoms. Skipping.
Residue LEU 1450 is missing expected H atoms. Skipping.
Residue ILE 1452 is missing expected H atoms. Skipping.
Residue VAL 1457 is missing expected H atoms. Skipping.
Residue LYS 1458 is missing expected H atoms. Skipping.
Residue TYR 1465 is missing expected H atoms. Skipping.
Residue ILE 1467 is missing expected H atoms. Skipping.
Residue LYS 1471 is missing expected H atoms. Skipping.
Residue LEU 1474 is missing expected H atoms. Skipping.
Residue LEU 1475 is missing expected H atoms. Skipping.
Residue ILE 1476 is missing expected H atoms. Skipping.
Residue VAL 1478 is missing expected H atoms. Skipping.
Residue LYS 1480 is missing expected H atoms. Skipping.
Evaluate side-chains
  113 residues out of total 1222 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 92
  time to evaluate  : 0.383 
Fit side-chains
   revert: symmetry clash
REVERT: A  229 GLN cc_start: 0.7201 (OUTLIER) cc_final: 0.6265 (tm-30)
REVERT: A  459 MET cc_start: 0.7736 (mmm) cc_final: 0.7517 (mmm)
REVERT: A  487 LEU cc_start: 0.8628 (mp) cc_final: 0.8330 (mp)
REVERT: A 1346 ARG cc_start: 0.8481 (ptt90) cc_final: 0.8250 (ptt90)
REVERT: A 1359 GLU cc_start: 0.8985 (OUTLIER) cc_final: 0.8118 (tm-30)
  outliers start: 21
  outliers final: 11
  residues processed: 106
  average time/residue: 1.2033
  time to fit residues: 137.6709
Evaluate side-chains
  98 residues out of total 1222 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 85
  time to evaluate  : 0.371 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  228 SER
Chi-restraints excluded: chain A residue  229 GLN
Chi-restraints excluded: chain A residue  318 ASP
Chi-restraints excluded: chain A residue  358 SER
Chi-restraints excluded: chain A residue  410 ILE
Chi-restraints excluded: chain A residue  417 VAL
Chi-restraints excluded: chain A residue  610 ASP
Chi-restraints excluded: chain A residue  721 VAL
Chi-restraints excluded: chain A residue 1141 SER
Chi-restraints excluded: chain A residue 1359 GLU
Chi-restraints excluded: chain A residue 1377 MET
Chi-restraints excluded: chain A residue 1434 ILE
Chi-restraints excluded: chain A residue 1473 SER
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 141
   random chunks:
   chunk 12 optimal weight:    3.9990
   chunk 75 optimal weight:    3.9990
   chunk 38 optimal weight:    9.9990
   chunk 41 optimal weight:    0.5980
   chunk 77 optimal weight:    2.9990
   chunk 0 optimal weight:    6.9990
   chunk 7 optimal weight:    1.9990
   chunk 73 optimal weight:    1.9990
   chunk 103 optimal weight:    1.9990
   chunk 71 optimal weight:    0.9990
   chunk 40 optimal weight:    8.9990
   overall best weight:    1.5188

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

Flipped N/Q/H residues before XYZ refinement:
A 404 HIS
A 594 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4129 r_free = 0.4129 target = 0.150345 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 48)----------------|
| r_work = 0.3583 r_free = 0.3583 target = 0.106038 restraints weight = 36968.398|
|-----------------------------------------------------------------------------|
r_work (start): 0.3512 rms_B_bonded: 1.88
r_work: 0.3391 rms_B_bonded: 2.02 restraints_weight: 0.5000
r_work: 0.3276 rms_B_bonded: 3.22 restraints_weight: 0.2500
r_work (final): 0.3276
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8351
moved from start:          0.1134

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.044  11516  Z= 0.161
  Angle     :  0.532   6.824  15600  Z= 0.292
  Chirality :  0.041   0.142   1661
  Planarity :  0.004   0.040   2054
  Dihedral  :  4.704  18.640   1555
  Min Nonbonded Distance : 2.204

Molprobity Statistics.
  All-atom Clashscore : 3.40
  Ramachandran Plot:
    Outliers :  0.50 %
    Allowed  :  5.27 %
    Favored  : 94.23 %
  Rotamer:
    Outliers :  1.28 %
    Allowed  : 15.84 %
    Favored  : 82.88 %
  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 aren not related in a simple way.
  whole:  0.56 (0.23), residues: 1404
  helix:  2.89 (0.40), residues: 166
  sheet:  0.88 (0.24), residues: 409
  loop : -0.42 (0.23), residues: 829

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.000   ARG A1305 
 TYR   0.013   0.001   TYR A 965 
 PHE   0.008   0.001   PHE A  22 
 TRP   0.009   0.001   TRP A1317 
 HIS   0.003   0.001   HIS A1291 

Details of bonding type rmsd
  covalent geometry    : bond        0.00333 (11516)
  covalent geometry    : angle       0.53182 (15600)
  hydrogen bonds       : bond        0.04014 (  443)
  hydrogen bonds       : angle       5.62034 ( 1722)

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

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

  2808 Ramachandran restraints generated.
    1404 Oldfield, 0 Emsley, 1404 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2808 Ramachandran restraints generated.
    1404 Oldfield, 0 Emsley, 1404 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Residue LYS   84 is missing expected H atoms. Skipping.
Residue LYS  226 is missing expected H atoms. Skipping.
Residue ILE  240 is missing expected H atoms. Skipping.
Residue THR  241 is missing expected H atoms. Skipping.
Residue SER  242 is missing expected H atoms. Skipping.
Residue LEU  244 is missing expected H atoms. Skipping.
Residue LYS  306 is missing expected H atoms. Skipping.
Residue LEU 1414 is missing expected H atoms. Skipping.
Residue TYR 1416 is missing expected H atoms. Skipping.
Residue TYR 1422 is missing expected H atoms. Skipping.
Residue TYR 1425 is missing expected H atoms. Skipping.
Residue LYS 1433 is missing expected H atoms. Skipping.
Residue LYS 1435 is missing expected H atoms. Skipping.
Residue TYR 1442 is missing expected H atoms. Skipping.
Residue VAL 1443 is missing expected H atoms. Skipping.
Residue ALA 1444 is missing expected H atoms. Skipping.
Residue SER 1446 is missing expected H atoms. Skipping.
Residue LEU 1450 is missing expected H atoms. Skipping.
Residue ILE 1452 is missing expected H atoms. Skipping.
Residue VAL 1457 is missing expected H atoms. Skipping.
Residue LYS 1458 is missing expected H atoms. Skipping.
Residue TYR 1465 is missing expected H atoms. Skipping.
Residue ILE 1467 is missing expected H atoms. Skipping.
Residue LYS 1471 is missing expected H atoms. Skipping.
Residue LEU 1474 is missing expected H atoms. Skipping.
Residue LEU 1475 is missing expected H atoms. Skipping.
Residue ILE 1476 is missing expected H atoms. Skipping.
Residue VAL 1478 is missing expected H atoms. Skipping.
Residue LYS 1480 is missing expected H atoms. Skipping.
Evaluate side-chains
  105 residues out of total 1222 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 90
  time to evaluate  : 0.555 
Fit side-chains
   revert: symmetry clash
REVERT: A  229 GLN cc_start: 0.7180 (OUTLIER) cc_final: 0.6266 (tm-30)
REVERT: A  459 MET cc_start: 0.7734 (mmm) cc_final: 0.7523 (mmm)
REVERT: A  487 LEU cc_start: 0.8571 (mp) cc_final: 0.8296 (mp)
REVERT: A 1346 ARG cc_start: 0.8386 (ptt90) cc_final: 0.8147 (ptt90)
REVERT: A 1359 GLU cc_start: 0.8864 (OUTLIER) cc_final: 0.8073 (tm-30)
  outliers start: 15
  outliers final: 8
  residues processed: 100
  average time/residue: 1.1571
  time to fit residues: 125.6978
Evaluate side-chains
  98 residues out of total 1222 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 88
  time to evaluate  : 0.559 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  229 GLN
Chi-restraints excluded: chain A residue  358 SER
Chi-restraints excluded: chain A residue  410 ILE
Chi-restraints excluded: chain A residue  417 VAL
Chi-restraints excluded: chain A residue  610 ASP
Chi-restraints excluded: chain A residue  721 VAL
Chi-restraints excluded: chain A residue 1141 SER
Chi-restraints excluded: chain A residue 1359 GLU
Chi-restraints excluded: chain A residue 1434 ILE
Chi-restraints excluded: chain A residue 1473 SER
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 141
   random chunks:
   chunk 118 optimal weight:    2.9990
   chunk 124 optimal weight:    2.9990
   chunk 83 optimal weight:    4.9990
   chunk 120 optimal weight:    2.9990
   chunk 56 optimal weight:    3.9990
   chunk 42 optimal weight:    6.9990
   chunk 107 optimal weight:    2.9990
   chunk 57 optimal weight:    0.9990
   chunk 79 optimal weight:    2.9990
   chunk 71 optimal weight:    0.9990
   chunk 23 optimal weight:    8.9990
   overall best weight:    2.1990

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

Flipped N/Q/H residues before XYZ refinement:
A 404 HIS
A 594 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4120 r_free = 0.4120 target = 0.149423 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 46)----------------|
| r_work = 0.3565 r_free = 0.3565 target = 0.104911 restraints weight = 37125.956|
|-----------------------------------------------------------------------------|
r_work (start): 0.3497 rms_B_bonded: 1.91
r_work: 0.3371 rms_B_bonded: 2.02 restraints_weight: 0.5000
r_work: 0.3258 rms_B_bonded: 3.23 restraints_weight: 0.2500
r_work (final): 0.3258
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8363
moved from start:          0.1174

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.042  11516  Z= 0.207
  Angle     :  0.552   6.805  15600  Z= 0.304
  Chirality :  0.041   0.139   1661
  Planarity :  0.004   0.054   2054
  Dihedral  :  4.758  19.276   1555
  Min Nonbonded Distance : 2.198

Molprobity Statistics.
  All-atom Clashscore : 3.54
  Ramachandran Plot:
    Outliers :  0.50 %
    Allowed  :  5.98 %
    Favored  : 93.52 %
  Rotamer:
    Outliers :  1.36 %
    Allowed  : 15.93 %
    Favored  : 82.71 %
  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 aren not related in a simple way.
  whole:  0.52 (0.23), residues: 1404
  helix:  2.80 (0.40), residues: 166
  sheet:  0.92 (0.24), residues: 407
  loop : -0.47 (0.23), residues: 831

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.000   ARG A 697 
 TYR   0.013   0.001   TYR A 792 
 PHE   0.009   0.001   PHE A  22 
 TRP   0.011   0.002   TRP A1169 
 HIS   0.004   0.001   HIS A1291 

Details of bonding type rmsd
  covalent geometry    : bond        0.00431 (11516)
  covalent geometry    : angle       0.55235 (15600)
  hydrogen bonds       : bond        0.04236 (  443)
  hydrogen bonds       : angle       5.67532 ( 1722)

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

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

  2808 Ramachandran restraints generated.
    1404 Oldfield, 0 Emsley, 1404 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2808 Ramachandran restraints generated.
    1404 Oldfield, 0 Emsley, 1404 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Residue LYS   84 is missing expected H atoms. Skipping.
Residue LYS  226 is missing expected H atoms. Skipping.
Residue ILE  240 is missing expected H atoms. Skipping.
Residue THR  241 is missing expected H atoms. Skipping.
Residue SER  242 is missing expected H atoms. Skipping.
Residue LEU  244 is missing expected H atoms. Skipping.
Residue LYS  306 is missing expected H atoms. Skipping.
Residue LEU 1414 is missing expected H atoms. Skipping.
Residue TYR 1416 is missing expected H atoms. Skipping.
Residue TYR 1422 is missing expected H atoms. Skipping.
Residue TYR 1425 is missing expected H atoms. Skipping.
Residue LYS 1433 is missing expected H atoms. Skipping.
Residue LYS 1435 is missing expected H atoms. Skipping.
Residue TYR 1442 is missing expected H atoms. Skipping.
Residue VAL 1443 is missing expected H atoms. Skipping.
Residue ALA 1444 is missing expected H atoms. Skipping.
Residue SER 1446 is missing expected H atoms. Skipping.
Residue LEU 1450 is missing expected H atoms. Skipping.
Residue ILE 1452 is missing expected H atoms. Skipping.
Residue VAL 1457 is missing expected H atoms. Skipping.
Residue LYS 1458 is missing expected H atoms. Skipping.
Residue TYR 1465 is missing expected H atoms. Skipping.
Residue ILE 1467 is missing expected H atoms. Skipping.
Residue LYS 1471 is missing expected H atoms. Skipping.
Residue LEU 1474 is missing expected H atoms. Skipping.
Residue LEU 1475 is missing expected H atoms. Skipping.
Residue ILE 1476 is missing expected H atoms. Skipping.
Residue VAL 1478 is missing expected H atoms. Skipping.
Residue LYS 1480 is missing expected H atoms. Skipping.
Evaluate side-chains
  105 residues out of total 1222 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 89
  time to evaluate  : 0.556 
Fit side-chains
   revert: symmetry clash
REVERT: A  229 GLN cc_start: 0.7193 (OUTLIER) cc_final: 0.6262 (tm-30)
REVERT: A  459 MET cc_start: 0.7724 (mmm) cc_final: 0.7512 (mmm)
REVERT: A  971 LYS cc_start: 0.8720 (mppt) cc_final: 0.8450 (ttpp)
REVERT: A 1346 ARG cc_start: 0.8423 (ptt90) cc_final: 0.8193 (ptt90)
REVERT: A 1359 GLU cc_start: 0.8894 (OUTLIER) cc_final: 0.8076 (tm-30)
  outliers start: 16
  outliers final: 10
  residues processed: 99
  average time/residue: 1.1883
  time to fit residues: 127.9760
Evaluate side-chains
  96 residues out of total 1222 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 84
  time to evaluate  : 0.582 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  228 SER
Chi-restraints excluded: chain A residue  229 GLN
Chi-restraints excluded: chain A residue  318 ASP
Chi-restraints excluded: chain A residue  358 SER
Chi-restraints excluded: chain A residue  410 ILE
Chi-restraints excluded: chain A residue  417 VAL
Chi-restraints excluded: chain A residue  610 ASP
Chi-restraints excluded: chain A residue  721 VAL
Chi-restraints excluded: chain A residue 1141 SER
Chi-restraints excluded: chain A residue 1359 GLU
Chi-restraints excluded: chain A residue 1434 ILE
Chi-restraints excluded: chain A residue 1473 SER
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 141
   random chunks:
   chunk 22 optimal weight:    9.9990
   chunk 113 optimal weight:    0.9980
   chunk 35 optimal weight:   10.0000
   chunk 139 optimal weight:    9.9990
   chunk 23 optimal weight:    0.8980
   chunk 96 optimal weight:    3.9990
   chunk 32 optimal weight:    5.9990
   chunk 3 optimal weight:   10.0000
   chunk 105 optimal weight:    0.6980
   chunk 82 optimal weight:    0.7980
   chunk 102 optimal weight:    2.9990
   overall best weight:    1.2782

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

Flipped N/Q/H residues before XYZ refinement:
A 594 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4134 r_free = 0.4134 target = 0.150625 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 43)----------------|
| r_work = 0.3591 r_free = 0.3591 target = 0.106520 restraints weight = 37168.489|
|-----------------------------------------------------------------------------|
r_work (start): 0.3523 rms_B_bonded: 1.88
r_work: 0.3398 rms_B_bonded: 2.01 restraints_weight: 0.5000
r_work: 0.3287 rms_B_bonded: 3.22 restraints_weight: 0.2500
r_work (final): 0.3287
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8342
moved from start:          0.1217

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.050  11516  Z= 0.147
  Angle     :  0.527   6.747  15600  Z= 0.288
  Chirality :  0.041   0.140   1661
  Planarity :  0.004   0.096   2054
  Dihedral  :  4.625  18.323   1555
  Min Nonbonded Distance : 2.208

Molprobity Statistics.
  All-atom Clashscore : 3.49
  Ramachandran Plot:
    Outliers :  0.43 %
    Allowed  :  5.63 %
    Favored  : 93.95 %
  Rotamer:
    Outliers :  1.11 %
    Allowed  : 16.27 %
    Favored  : 82.62 %
  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 aren not related in a simple way.
  whole:  0.52 (0.23), residues: 1404
  helix:  2.91 (0.40), residues: 166
  sheet:  0.81 (0.24), residues: 410
  loop : -0.43 (0.23), residues: 828

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.013   0.000   ARG A 697 
 TYR   0.011   0.001   TYR A 792 
 PHE   0.007   0.001   PHE A  22 
 TRP   0.009   0.001   TRP A1317 
 HIS   0.003   0.001   HIS A1291 

Details of bonding type rmsd
  covalent geometry    : bond        0.00307 (11516)
  covalent geometry    : angle       0.52733 (15600)
  hydrogen bonds       : bond        0.03851 (  443)
  hydrogen bonds       : angle       5.49293 ( 1722)

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

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

  2808 Ramachandran restraints generated.
    1404 Oldfield, 0 Emsley, 1404 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2808 Ramachandran restraints generated.
    1404 Oldfield, 0 Emsley, 1404 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Residue LYS   84 is missing expected H atoms. Skipping.
Residue LYS  226 is missing expected H atoms. Skipping.
Residue ILE  240 is missing expected H atoms. Skipping.
Residue THR  241 is missing expected H atoms. Skipping.
Residue SER  242 is missing expected H atoms. Skipping.
Residue LEU  244 is missing expected H atoms. Skipping.
Residue LYS  306 is missing expected H atoms. Skipping.
Residue LEU 1414 is missing expected H atoms. Skipping.
Residue TYR 1416 is missing expected H atoms. Skipping.
Residue TYR 1422 is missing expected H atoms. Skipping.
Residue TYR 1425 is missing expected H atoms. Skipping.
Residue LYS 1433 is missing expected H atoms. Skipping.
Residue LYS 1435 is missing expected H atoms. Skipping.
Residue TYR 1442 is missing expected H atoms. Skipping.
Residue VAL 1443 is missing expected H atoms. Skipping.
Residue ALA 1444 is missing expected H atoms. Skipping.
Residue SER 1446 is missing expected H atoms. Skipping.
Residue LEU 1450 is missing expected H atoms. Skipping.
Residue ILE 1452 is missing expected H atoms. Skipping.
Residue VAL 1457 is missing expected H atoms. Skipping.
Residue LYS 1458 is missing expected H atoms. Skipping.
Residue TYR 1465 is missing expected H atoms. Skipping.
Residue ILE 1467 is missing expected H atoms. Skipping.
Residue LYS 1471 is missing expected H atoms. Skipping.
Residue LEU 1474 is missing expected H atoms. Skipping.
Residue LEU 1475 is missing expected H atoms. Skipping.
Residue ILE 1476 is missing expected H atoms. Skipping.
Residue VAL 1478 is missing expected H atoms. Skipping.
Residue LYS 1480 is missing expected H atoms. Skipping.
Evaluate side-chains
  99 residues out of total 1222 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 86
  time to evaluate  : 0.591 
Fit side-chains
   revert: symmetry clash
REVERT: A  229 GLN cc_start: 0.7214 (OUTLIER) cc_final: 0.6403 (tm-30)
REVERT: A  459 MET cc_start: 0.7762 (mmm) cc_final: 0.7557 (mmm)
REVERT: A  971 LYS cc_start: 0.8714 (mppt) cc_final: 0.8451 (ttpp)
REVERT: A 1346 ARG cc_start: 0.8386 (ptt90) cc_final: 0.8145 (ptt90)
REVERT: A 1359 GLU cc_start: 0.8832 (OUTLIER) cc_final: 0.8106 (tm-30)
  outliers start: 13
  outliers final: 7
  residues processed: 96
  average time/residue: 1.1988
  time to fit residues: 124.8673
Evaluate side-chains
  94 residues out of total 1222 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 85
  time to evaluate  : 0.610 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  228 SER
Chi-restraints excluded: chain A residue  229 GLN
Chi-restraints excluded: chain A residue  410 ILE
Chi-restraints excluded: chain A residue  417 VAL
Chi-restraints excluded: chain A residue  610 ASP
Chi-restraints excluded: chain A residue  721 VAL
Chi-restraints excluded: chain A residue 1141 SER
Chi-restraints excluded: chain A residue 1359 GLU
Chi-restraints excluded: chain A residue 1473 SER
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 141
   random chunks:
   chunk 74 optimal weight:    0.9980
   chunk 116 optimal weight:    2.9990
   chunk 109 optimal weight:    3.9990
   chunk 63 optimal weight:    0.0980
   chunk 45 optimal weight:    0.3980
   chunk 67 optimal weight:    4.9990
   chunk 12 optimal weight:    9.9990
   chunk 93 optimal weight:    0.7980
   chunk 23 optimal weight:    6.9990
   chunk 130 optimal weight:    1.9990
   chunk 19 optimal weight:    0.8980
   overall best weight:    0.6380

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

Flipped N/Q/H residues before XYZ refinement:
A 594 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4155 r_free = 0.4155 target = 0.152323 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 48)----------------|
| r_work = 0.3626 r_free = 0.3626 target = 0.108531 restraints weight = 37315.146|
|-----------------------------------------------------------------------------|
r_work (start): 0.3557 rms_B_bonded: 1.89
r_work: 0.3435 rms_B_bonded: 2.03 restraints_weight: 0.5000
r_work: 0.3328 rms_B_bonded: 3.21 restraints_weight: 0.2500
r_work (final): 0.3328
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8313
moved from start:          0.1364

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.049  11516  Z= 0.109
  Angle     :  0.506   6.680  15600  Z= 0.275
  Chirality :  0.041   0.142   1661
  Planarity :  0.004   0.085   2054
  Dihedral  :  4.441  17.362   1555
  Min Nonbonded Distance : 2.231

Molprobity Statistics.
  All-atom Clashscore : 3.04
  Ramachandran Plot:
    Outliers :  0.36 %
    Allowed  :  5.98 %
    Favored  : 93.66 %
  Rotamer:
    Outliers :  1.02 %
    Allowed  : 16.35 %
    Favored  : 82.62 %
  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 aren not related in a simple way.
  whole:  0.49 (0.23), residues: 1404
  helix:  3.09 (0.41), residues: 166
  sheet:  0.58 (0.24), residues: 427
  loop : -0.39 (0.24), residues: 811

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.011   0.000   ARG A 697 
 TYR   0.012   0.001   TYR A 454 
 PHE   0.011   0.001   PHE A1398 
 TRP   0.009   0.001   TRP A 422 
 HIS   0.002   0.001   HIS A 443 

Details of bonding type rmsd
  covalent geometry    : bond        0.00233 (11516)
  covalent geometry    : angle       0.50641 (15600)
  hydrogen bonds       : bond        0.03470 (  443)
  hydrogen bonds       : angle       5.23715 ( 1722)

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

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

  2808 Ramachandran restraints generated.
    1404 Oldfield, 0 Emsley, 1404 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2808 Ramachandran restraints generated.
    1404 Oldfield, 0 Emsley, 1404 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Residue LYS   84 is missing expected H atoms. Skipping.
Residue LYS  226 is missing expected H atoms. Skipping.
Residue ILE  240 is missing expected H atoms. Skipping.
Residue THR  241 is missing expected H atoms. Skipping.
Residue SER  242 is missing expected H atoms. Skipping.
Residue LEU  244 is missing expected H atoms. Skipping.
Residue LYS  306 is missing expected H atoms. Skipping.
Residue LEU 1414 is missing expected H atoms. Skipping.
Residue TYR 1416 is missing expected H atoms. Skipping.
Residue TYR 1422 is missing expected H atoms. Skipping.
Residue TYR 1425 is missing expected H atoms. Skipping.
Residue LYS 1433 is missing expected H atoms. Skipping.
Residue LYS 1435 is missing expected H atoms. Skipping.
Residue TYR 1442 is missing expected H atoms. Skipping.
Residue VAL 1443 is missing expected H atoms. Skipping.
Residue ALA 1444 is missing expected H atoms. Skipping.
Residue SER 1446 is missing expected H atoms. Skipping.
Residue LEU 1450 is missing expected H atoms. Skipping.
Residue ILE 1452 is missing expected H atoms. Skipping.
Residue VAL 1457 is missing expected H atoms. Skipping.
Residue LYS 1458 is missing expected H atoms. Skipping.
Residue TYR 1465 is missing expected H atoms. Skipping.
Residue ILE 1467 is missing expected H atoms. Skipping.
Residue LYS 1471 is missing expected H atoms. Skipping.
Residue LEU 1474 is missing expected H atoms. Skipping.
Residue LEU 1475 is missing expected H atoms. Skipping.
Residue ILE 1476 is missing expected H atoms. Skipping.
Residue VAL 1478 is missing expected H atoms. Skipping.
Residue LYS 1480 is missing expected H atoms. Skipping.
Evaluate side-chains
  105 residues out of total 1222 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 93
  time to evaluate  : 0.508 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  229 GLN cc_start: 0.7235 (OUTLIER) cc_final: 0.6415 (tm-30)
REVERT: A  459 MET cc_start: 0.7750 (mmm) cc_final: 0.7542 (mmm)
REVERT: A  971 LYS cc_start: 0.8718 (mppt) cc_final: 0.8458 (ttpp)
REVERT: A 1346 ARG cc_start: 0.8314 (ptt90) cc_final: 0.8093 (ptt90)
REVERT: A 1359 GLU cc_start: 0.8714 (OUTLIER) cc_final: 0.8060 (tm-30)
  outliers start: 12
  outliers final: 6
  residues processed: 104
  average time/residue: 1.2166
  time to fit residues: 136.8288
Evaluate side-chains
  95 residues out of total 1222 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 87
  time to evaluate  : 0.582 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  228 SER
Chi-restraints excluded: chain A residue  229 GLN
Chi-restraints excluded: chain A residue  358 SER
Chi-restraints excluded: chain A residue  410 ILE
Chi-restraints excluded: chain A residue  417 VAL
Chi-restraints excluded: chain A residue  721 VAL
Chi-restraints excluded: chain A residue 1359 GLU
Chi-restraints excluded: chain A residue 1473 SER
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 141
   random chunks:
   chunk 92 optimal weight:    2.9990
   chunk 82 optimal weight:    3.9990
   chunk 53 optimal weight:    2.9990
   chunk 28 optimal weight:    5.9990
   chunk 140 optimal weight:   20.0000
   chunk 135 optimal weight:   30.0000
   chunk 111 optimal weight:    0.9990
   chunk 16 optimal weight:    7.9990
   chunk 95 optimal weight:    4.9990
   chunk 38 optimal weight:    6.9990
   chunk 89 optimal weight:    0.9990
   overall best weight:    2.3990

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

Flipped N/Q/H residues before XYZ refinement:
A 594 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4125 r_free = 0.4125 target = 0.149853 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 51)----------------|
| r_work = 0.3574 r_free = 0.3574 target = 0.105281 restraints weight = 37188.136|
|-----------------------------------------------------------------------------|
r_work (start): 0.3502 rms_B_bonded: 1.90
r_work: 0.3378 rms_B_bonded: 2.01 restraints_weight: 0.5000
r_work: 0.3265 rms_B_bonded: 3.21 restraints_weight: 0.2500
r_work (final): 0.3265
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8346
moved from start:          0.1257

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.051  11516  Z= 0.215
  Angle     :  0.556   6.805  15600  Z= 0.304
  Chirality :  0.042   0.140   1661
  Planarity :  0.004   0.067   2054
  Dihedral  :  4.655  18.546   1555
  Min Nonbonded Distance : 2.224

Molprobity Statistics.
  All-atom Clashscore : 3.72
  Ramachandran Plot:
    Outliers :  0.43 %
    Allowed  :  5.56 %
    Favored  : 94.02 %
  Rotamer:
    Outliers :  0.94 %
    Allowed  : 16.35 %
    Favored  : 82.71 %
  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 aren not related in a simple way.
  whole:  0.56 (0.23), residues: 1404
  helix:  2.93 (0.40), residues: 166
  sheet:  0.91 (0.24), residues: 407
  loop : -0.44 (0.23), residues: 831

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.000   ARG A 697 
 TYR   0.013   0.002   TYR A 792 
 PHE   0.009   0.001   PHE A 350 
 TRP   0.011   0.002   TRP A1169 
 HIS   0.004   0.001   HIS A1291 

Details of bonding type rmsd
  covalent geometry    : bond        0.00455 (11516)
  covalent geometry    : angle       0.55581 (15600)
  hydrogen bonds       : bond        0.04165 (  443)
  hydrogen bonds       : angle       5.52372 ( 1722)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 12219.46 seconds
wall clock time: 206 minutes 22.19 seconds (12382.19 seconds total)