Starting phenix.real_space_refine
on Sat Aug 23 09:26:15 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/8jcw_36167/08_2025/8jcw_36167.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/8jcw_36167/08_2025/8jcw_36167.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.0
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    model {
      file = "/net/cci-nas-00/data/ceres_data/8jcw_36167/08_2025/8jcw_36167.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/8jcw_36167/08_2025/8jcw_36167.cif"
    real_map_files = "/net/cci-nas-00/data/ceres_data/8jcw_36167/08_2025/8jcw_36167.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/8jcw_36167/08_2025/8jcw_36167.map"
  }
  resolution = 3.0
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }


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

Validating inputs
Origin is already at (0, 0, 0), no shifts will be applied
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=  -0.001 sd=   0.070
Set stop_for_unknowns flag
  Set to: True
Assert model is a single copy model
Assert all atoms have isotropic ADPs
Construct map_model_manager
Extract box with map and model
Check model and map are aligned
Set scattering table
  Set to: electron
  Number of scattering types: 4
    Type Number    sf(0)   Gaussians
     S      64      5.16       5
     C    6806      2.51       5
     N    1869      2.21       5
     O    2021      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 10 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: 10760
  Number of models: 1
  Model: ""
    Number of chains: 4
    Chain: "2"
      Number of atoms: 5266
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 762, 5266
          Classifications: {'peptide': 762}
          Incomplete info: {'truncation_to_alanine': 181}
          Link IDs: {'PTRANS': 37, 'TRANS': 724}
          Chain breaks: 2
          Unresolved non-hydrogen bonds: 696
          Unresolved non-hydrogen angles: 890
          Unresolved non-hydrogen dihedrals: 580
          Unresolved non-hydrogen chiralities: 70
          Planarities with less than four sites: {'GLU:plan': 13, 'ARG:plan': 21, 'ASP:plan': 6, 'GLN:plan1': 6, 'ASN:plan1': 6, 'HIS:plan': 4, 'PHE:plan': 14, 'TYR:plan': 7, 'TRP:plan': 3}
          Unresolved non-hydrogen planarities: 397
    Chain: "3"
      Number of atoms: 5358
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 765, 5358
          Classifications: {'peptide': 765}
          Incomplete info: {'truncation_to_alanine': 194}
          Link IDs: {'PTRANS': 30, 'TRANS': 734}
          Chain breaks: 2
          Unresolved non-hydrogen bonds: 732
          Unresolved non-hydrogen angles: 936
          Unresolved non-hydrogen dihedrals: 608
          Unresolved non-hydrogen chiralities: 76
          Planarities with less than four sites: {'GLU:plan': 12, 'ASN:plan1': 12, 'ARG:plan': 14, 'GLN:plan1': 5, 'HIS:plan': 4, 'ASP:plan': 11, 'TYR:plan': 9, 'TRP:plan': 3, 'PHE:plan': 12}
          Unresolved non-hydrogen planarities: 385
    Chain: "2"
      Number of atoms: 68
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 3, 68
          Unusual residues: {'CLR': 1, 'NAG': 1, 'Z99': 1}
          Classifications: {'undetermined': 3}
          Link IDs: {None: 2}
          Unresolved non-hydrogen bonds: 1
          Unresolved non-hydrogen angles: 2
          Unresolved non-hydrogen dihedrals: 3
          Unresolved non-hydrogen chiralities: 1
    Chain: "3"
      Number of atoms: 68
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 3, 68
          Unusual residues: {'CLR': 1, 'NAG': 1, 'Z99': 1}
          Classifications: {'undetermined': 3}
          Link IDs: {None: 2}
          Unresolved non-hydrogen bonds: 1
          Unresolved non-hydrogen angles: 2
          Unresolved non-hydrogen dihedrals: 3
          Unresolved non-hydrogen chiralities: 1
  Time building chain proxies: 2.84, per 1000 atoms: 0.26
  Number of scatterers: 10760
  At special positions: 0
  Unit cell: (88.893, 124.236, 184.212, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 4
    Type Number    sf(0)
     S      64     16.00
     O    2021      8.00
     N    1869      7.00
     C    6806      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=18, symmetry=0
    Simple disulfide: pdb=" SG  CYS 2  50 " - pdb=" SG  CYS 2  92 " distance=2.03
    Simple disulfide: pdb=" SG  CYS 2 234 " - pdb=" SG  CYS 2 518 " distance=2.04
    Simple disulfide: pdb=" SG  CYS 2 355 " - pdb=" SG  CYS 2 362 " distance=2.03
    Simple disulfide: pdb=" SG  CYS 2 400 " - pdb=" SG  CYS 2 407 " distance=2.03
    Simple disulfide: pdb=" SG  CYS 2 500 " - pdb=" SG  CYS 2 519 " distance=2.03
    Simple disulfide: pdb=" SG  CYS 2 504 " - pdb=" SG  CYS 2 522 " distance=2.03
    Simple disulfide: pdb=" SG  CYS 2 525 " - pdb=" SG  CYS 2 537 " distance=2.03
    Simple disulfide: pdb=" SG  CYS 2 540 " - pdb=" SG  CYS 2 553 " distance=2.03
    Simple disulfide: pdb=" SG  CYS 2 632 " - pdb=" SG  CYS 2 721 " distance=2.03
    Simple disulfide: pdb=" SG  CYS 3  57 " - pdb=" SG  CYS 3  99 " distance=2.03
    Simple disulfide: pdb=" SG  CYS 3 240 " - pdb=" SG  CYS 3 527 " distance=2.03
    Simple disulfide: pdb=" SG  CYS 3 361 " - pdb=" SG  CYS 3 373 " distance=2.03
    Simple disulfide: pdb=" SG  CYS 3 412 " - pdb=" SG  CYS 3 419 " distance=2.03
    Simple disulfide: pdb=" SG  CYS 3 509 " - pdb=" SG  CYS 3 528 " distance=2.03
    Simple disulfide: pdb=" SG  CYS 3 513 " - pdb=" SG  CYS 3 531 " distance=2.03
    Simple disulfide: pdb=" SG  CYS 3 534 " - pdb=" SG  CYS 3 546 " distance=2.03
    Simple disulfide: pdb=" SG  CYS 3 549 " - pdb=" SG  CYS 3 562 " distance=2.03
    Simple disulfide: pdb=" SG  CYS 3 641 " - pdb=" SG  CYS 3 730 " distance=2.03

  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
  Links applied
    NAG-ASN
      " NAG 21101 " - " ASN 2 203 "
      " NAG 31001 " - " ASN 3 209 "
  Time building additional restraints: 0.84
  Conformation dependent library (CDL) restraints added in 575.6 milliseconds
  
  Enol-peptide restraints added in 715.3 nanoseconds
  

  3030 Ramachandran restraints generated.
    1515 Oldfield, 0 Emsley, 1515 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  2866

  Finding SS restraints...
    Secondary structure from input PDB file:
      45 helices and 12 sheets defined
      47.3% alpha, 9.4% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.39
  Creating SS restraints...
    Processing helix  chain '2' and resid 44 through 48
      removed outlier: 4.052A  pdb=" N   ALA 2  47 " --> pdb=" O   GLY 2  44 " (cutoff:3.500A)
      removed outlier: 3.744A  pdb=" N   GLU 2  48 " --> pdb=" O   GLY 2  45 " (cutoff:3.500A)
      No H-bonds generated for 'chain '2' and resid 44 through 48'
    Processing helix  chain '2' and resid 58 through 74
      removed outlier: 3.639A  pdb=" N   LEU 2  62 " --> pdb=" O   GLY 2  58 " (cutoff:3.500A)
    Processing helix  chain '2' and resid 94 through 107
      removed outlier: 3.697A  pdb=" N   ASP 2 104 " --> pdb=" O   GLU 2 100 " (cutoff:3.500A)
      removed outlier: 3.507A  pdb=" N   PHE 2 105 " --> pdb=" O   GLN 2 101 " (cutoff:3.500A)
    Processing helix  chain '2' and resid 144 through 157
      removed outlier: 4.321A  pdb=" N   LEU 2 157 " --> pdb=" O   ASN 2 153 " (cutoff:3.500A)
    Processing helix  chain '2' and resid 169 through 173
      removed outlier: 3.619A  pdb=" N   LEU 2 172 " --> pdb=" O   SER 2 169 " (cutoff:3.500A)
      removed outlier: 3.973A  pdb=" N   SER 2 173 " --> pdb=" O   ALA 2 170 " (cutoff:3.500A)
      No H-bonds generated for 'chain '2' and resid 169 through 173'
    Processing helix  chain '2' and resid 189 through 202
    Processing helix  chain '2' and resid 214 through 230
      removed outlier: 6.384A  pdb=" N   GLY 2 220 " --> pdb=" O   TYR 2 216 " (cutoff:3.500A)
    Processing helix  chain '2' and resid 246 through 259
      removed outlier: 3.928A  pdb=" N   PHE 2 250 " --> pdb=" O   SER 2 246 " (cutoff:3.500A)
    Processing helix  chain '2' and resid 271 through 285
      removed outlier: 3.684A  pdb=" N   GLU 2 277 " --> pdb=" O   GLU 2 273 " (cutoff:3.500A)
      removed outlier: 4.112A  pdb=" N   LEU 2 278 " --> pdb=" O   ASP 2 274 " (cutoff:3.500A)
    Processing helix  chain '2' and resid 324 through 333
      removed outlier: 3.534A  pdb=" N   SER 2 333 " --> pdb=" O   SER 2 329 " (cutoff:3.500A)
    Processing helix  chain '2' and resid 344 through 354
    Processing helix  chain '2' and resid 377 through 400
    Processing helix  chain '2' and resid 414 through 422
    Processing helix  chain '2' and resid 569 through 592
    Processing helix  chain '2' and resid 593 through 595
      No H-bonds generated for 'chain '2' and resid 593 through 595'
    Processing helix  chain '2' and resid 602 through 624
    Processing helix  chain '2' and resid 630 through 659
      removed outlier: 4.389A  pdb=" N   LYS 2 653 " --> pdb=" O   ALA 2 649 " (cutoff:3.500A)
      removed outlier: 4.324A  pdb=" N   THR 2 654 " --> pdb=" O   LEU 2 650 " (cutoff:3.500A)
    Processing helix  chain '2' and resid 676 through 701
      removed outlier: 3.620A  pdb=" N   VAL 2 680 " --> pdb=" O   PRO 2 676 " (cutoff:3.500A)
    Processing helix  chain '2' and resid 724 through 748
      removed outlier: 3.776A  pdb=" N   MET 2 728 " --> pdb=" O   ARG 2 724 " (cutoff:3.500A)
    Processing helix  chain '2' and resid 755 through 784
      removed outlier: 4.871A  pdb=" N   PHE 2 761 " --> pdb=" O   ASN 2 757 " (cutoff:3.500A)
      removed outlier: 3.883A  pdb=" N   TYR 2 767 " --> pdb=" O   GLY 2 763 " (cutoff:3.500A)
      removed outlier: 3.870A  pdb=" N   THR 2 768 " --> pdb=" O   PHE 2 764 " (cutoff:3.500A)
      removed outlier: 3.813A  pdb=" N   LEU 2 777 " --> pdb=" O   TRP 2 773 " (cutoff:3.500A)
      Proline residue:  2 778  - end of helix
      removed outlier: 3.757A  pdb=" N   TYR 2 781 " --> pdb=" O   LEU 2 777 " (cutoff:3.500A)
    Processing helix  chain '2' and resid 787 through 818
      removed outlier: 3.629A  pdb=" N   THR 2 791 " --> pdb=" O   TYR 2 787 " (cutoff:3.500A)
      Proline residue:  2 812  - end of helix
    Processing helix  chain '3' and resid 65 through 81
    Processing helix  chain '3' and resid 101 through 109
    Processing helix  chain '3' and resid 109 through 114
      removed outlier: 3.656A  pdb=" N   VAL 3 113 " --> pdb=" O   SER 3 109 " (cutoff:3.500A)
    Processing helix  chain '3' and resid 115 through 117
      No H-bonds generated for 'chain '3' and resid 115 through 117'
    Processing helix  chain '3' and resid 150 through 162
    Processing helix  chain '3' and resid 175 through 180
    Processing helix  chain '3' and resid 194 through 208
      removed outlier: 3.815A  pdb=" N   ALA 3 198 " --> pdb=" O   ASP 3 194 " (cutoff:3.500A)
    Processing helix  chain '3' and resid 221 through 237
    Processing helix  chain '3' and resid 254 through 265
    Processing helix  chain '3' and resid 279 through 291
    Processing helix  chain '3' and resid 330 through 339
      removed outlier: 3.539A  pdb=" N   ASP 3 334 " --> pdb=" O   VAL 3 330 " (cutoff:3.500A)
      removed outlier: 3.557A  pdb=" N   ARG 3 335 " --> pdb=" O   ARG 3 331 " (cutoff:3.500A)
    Processing helix  chain '3' and resid 350 through 359
    Processing helix  chain '3' and resid 389 through 412
      removed outlier: 3.806A  pdb=" N   VAL 3 393 " --> pdb=" O   LYS 3 389 " (cutoff:3.500A)
    Processing helix  chain '3' and resid 419 through 423
    Processing helix  chain '3' and resid 426 through 435
    Processing helix  chain '3' and resid 578 through 601
    Processing helix  chain '3' and resid 611 through 632
      removed outlier: 3.773A  pdb=" N   PHE 3 632 " --> pdb=" O   MET 3 628 " (cutoff:3.500A)
    Processing helix  chain '3' and resid 637 through 664
      removed outlier: 3.747A  pdb=" N   LYS 3 662 " --> pdb=" O   ALA 3 658 " (cutoff:3.500A)
    Processing helix  chain '3' and resid 682 through 707
    Processing helix  chain '3' and resid 717 through 721
      removed outlier: 4.103A  pdb=" N   GLU 3 721 " --> pdb=" O   THR 3 718 " (cutoff:3.500A)
    Processing helix  chain '3' and resid 731 through 733
      No H-bonds generated for 'chain '3' and resid 731 through 733'
    Processing helix  chain '3' and resid 734 through 756
      removed outlier: 3.689A  pdb=" N   ASP 3 744 " --> pdb=" O   SER 3 740 " (cutoff:3.500A)
      removed outlier: 3.811A  pdb=" N   VAL 3 745 " --> pdb=" O   LEU 3 741 " (cutoff:3.500A)
    Processing helix  chain '3' and resid 764 through 792
      removed outlier: 4.193A  pdb=" N   ALA 3 768 " --> pdb=" O   ASN 3 764 " (cutoff:3.500A)
      Proline residue:  3 787  - end of helix
      removed outlier: 4.029A  pdb=" N   TYR 3 790 " --> pdb=" O   LEU 3 786 " (cutoff:3.500A)
    Processing helix  chain '3' and resid 796 through 826
      removed outlier: 3.885A  pdb=" N   THR 3 800 " --> pdb=" O   TYR 3 796 " (cutoff:3.500A)
      removed outlier: 3.874A  pdb=" N   CYS 3 817 " --> pdb=" O   VAL 3 813 " (cutoff:3.500A)
      removed outlier: 4.295A  pdb=" N   LEU 3 818 " --> pdb=" O   VAL 3 814 " (cutoff:3.500A)
      removed outlier: 3.572A  pdb=" N   PHE 3 819 " --> pdb=" O   LEU 3 815 " (cutoff:3.500A)
      removed outlier: 3.794A  pdb=" N   ALA 3 820 " --> pdb=" O   GLY 3 816 " (cutoff:3.500A)
      Proline residue:  3 821  - end of helix
    Processing sheet with id=AA1, first strand: chain '2' and resid 84 through 90
      removed outlier: 6.578A  pdb=" N   LEU 2  32 " --> pdb=" O   GLY 2  85 " (cutoff:3.500A)
      removed outlier: 7.418A  pdb=" N   HIS 2  87 " --> pdb=" O   LEU 2  32 " (cutoff:3.500A)
      removed outlier: 6.296A  pdb=" N   LEU 2  34 " --> pdb=" O   HIS 2  87 " (cutoff:3.500A)
      removed outlier: 7.473A  pdb=" N   LEU 2  89 " --> pdb=" O   LEU 2  34 " (cutoff:3.500A)
      removed outlier: 6.175A  pdb=" N   GLY 2  36 " --> pdb=" O   LEU 2  89 " (cutoff:3.500A)
      removed outlier: 6.926A  pdb=" N   VAL 2  33 " --> pdb=" O   GLY 2 138 " (cutoff:3.500A)
      removed outlier: 8.159A  pdb=" N   ILE 2 140 " --> pdb=" O   VAL 2  33 " (cutoff:3.500A)
      removed outlier: 6.450A  pdb=" N   GLY 2  35 " --> pdb=" O   ILE 2 140 " (cutoff:3.500A)
      removed outlier: 8.805A  pdb=" N   ILE 2 163 " --> pdb=" O   THR 2 137 " (cutoff:3.500A)
      removed outlier: 6.631A  pdb=" N   VAL 2 139 " --> pdb=" O   ILE 2 163 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain '2' and resid 234 through 240
      removed outlier: 7.938A  pdb=" N   VAL 2 207 " --> pdb=" O   ALA 2 236 " (cutoff:3.500A)
      removed outlier: 7.131A  pdb=" N   SER 2 238 " --> pdb=" O   VAL 2 207 " (cutoff:3.500A)
      removed outlier: 7.364A  pdb=" N   THR 2 209 " --> pdb=" O   SER 2 238 " (cutoff:3.500A)
      removed outlier: 6.260A  pdb=" N   LYS 2 240 " --> pdb=" O   THR 2 209 " (cutoff:3.500A)
      removed outlier: 6.693A  pdb=" N   ALA 2 211 " --> pdb=" O   LYS 2 240 " (cutoff:3.500A)
      removed outlier: 7.180A  pdb=" N   TYR 2 206 " --> pdb=" O   VAL 2 265 " (cutoff:3.500A)
      removed outlier: 8.471A  pdb=" N   VAL 2 267 " --> pdb=" O   TYR 2 206 " (cutoff:3.500A)
      removed outlier: 6.551A  pdb=" N   SER 2 208 " --> pdb=" O   VAL 2 267 " (cutoff:3.500A)
      removed outlier: 7.669A  pdb=" N   PHE 2 269 " --> pdb=" O   SER 2 208 " (cutoff:3.500A)
      removed outlier: 6.885A  pdb=" N   VAL 2 210 " --> pdb=" O   PHE 2 269 " (cutoff:3.500A)
      removed outlier: 6.602A  pdb=" N   ALA 2 266 " --> pdb=" O   VAL 2 292 " (cutoff:3.500A)
      removed outlier: 6.573A  pdb=" N   TYR 2 453 " --> pdb=" O   TYR 2 473 " (cutoff:3.500A)
      removed outlier: 4.539A  pdb=" N   TYR 2 473 " --> pdb=" O   TYR 2 453 " (cutoff:3.500A)
      removed outlier: 6.302A  pdb=" N   ILE 2 455 " --> pdb=" O   VAL 2 471 " (cutoff:3.500A)
      removed outlier: 3.551A  pdb=" N   ARG 2 467 " --> pdb=" O   LEU 2 459 " (cutoff:3.500A)
      removed outlier: 3.557A  pdb=" N   TYR 2 473 " --> pdb=" O   THR 2 479 " (cutoff:3.500A)
    Processing sheet with id=AA3, first strand: chain '2' and resid 428 through 429
      removed outlier: 3.693A  pdb=" N   PHE 2 428 " --> pdb=" O   VAL 2 441 " (cutoff:3.500A)
    Processing sheet with id=AA4, first strand: chain '2' and resid 508 through 511
    Processing sheet with id=AA5, first strand: chain '2' and resid 529 through 530
    Processing sheet with id=AA6, first strand: chain '3' and resid 33 through 34
      removed outlier: 6.394A  pdb=" N   LEU 3  39 " --> pdb=" O   GLY 3  92 " (cutoff:3.500A)
      removed outlier: 7.670A  pdb=" N   HIS 3  94 " --> pdb=" O   LEU 3  39 " (cutoff:3.500A)
      removed outlier: 6.738A  pdb=" N   LEU 3  41 " --> pdb=" O   HIS 3  94 " (cutoff:3.500A)
      removed outlier: 7.663A  pdb=" N   LEU 3  96 " --> pdb=" O   LEU 3  41 " (cutoff:3.500A)
      removed outlier: 6.354A  pdb=" N   GLY 3  43 " --> pdb=" O   LEU 3  96 " (cutoff:3.500A)
      removed outlier: 6.902A  pdb=" N   VAL 3  40 " --> pdb=" O   ILE 3 142 " (cutoff:3.500A)
      removed outlier: 4.271A  pdb=" N   GLY 3 144 " --> pdb=" O   VAL 3  40 " (cutoff:3.500A)
      removed outlier: 8.729A  pdb=" N   ILE 3 169 " --> pdb=" O   ALA 3 143 " (cutoff:3.500A)
      removed outlier: 6.536A  pdb=" N   VAL 3 145 " --> pdb=" O   ILE 3 169 " (cutoff:3.500A)
    Processing sheet with id=AA7, first strand: chain '3' and resid 48 through 50
      removed outlier: 5.370A  pdb=" N   ARG 3  59 " --> pdb=" O   GLU 3  49 " (cutoff:3.500A)
    Processing sheet with id=AA8, first strand: chain '3' and resid 240 through 246
      removed outlier: 7.779A  pdb=" N   VAL 3 213 " --> pdb=" O   ALA 3 242 " (cutoff:3.500A)
      removed outlier: 6.938A  pdb=" N   ALA 3 244 " --> pdb=" O   VAL 3 213 " (cutoff:3.500A)
      removed outlier: 7.225A  pdb=" N   THR 3 215 " --> pdb=" O   ALA 3 244 " (cutoff:3.500A)
      removed outlier: 5.746A  pdb=" N   LYS 3 246 " --> pdb=" O   THR 3 215 " (cutoff:3.500A)
      removed outlier: 6.612A  pdb=" N   ALA 3 217 " --> pdb=" O   LYS 3 246 " (cutoff:3.500A)
      removed outlier: 7.465A  pdb=" N   TYR 3 212 " --> pdb=" O   VAL 3 271 " (cutoff:3.500A)
      removed outlier: 8.422A  pdb=" N   VAL 3 273 " --> pdb=" O   TYR 3 212 " (cutoff:3.500A)
      removed outlier: 6.509A  pdb=" N   SER 3 214 " --> pdb=" O   VAL 3 273 " (cutoff:3.500A)
      removed outlier: 7.857A  pdb=" N   PHE 3 275 " --> pdb=" O   SER 3 214 " (cutoff:3.500A)
      removed outlier: 6.811A  pdb=" N   VAL 3 216 " --> pdb=" O   PHE 3 275 " (cutoff:3.500A)
      removed outlier: 6.020A  pdb=" N   TRP 3 297 " --> pdb=" O   ILE 3 321 " (cutoff:3.500A)
      removed outlier: 7.621A  pdb=" N   LEU 3 323 " --> pdb=" O   TRP 3 297 " (cutoff:3.500A)
      removed outlier: 7.131A  pdb=" N   ALA 3 299 " --> pdb=" O   LEU 3 323 " (cutoff:3.500A)
      removed outlier: 9.356A  pdb=" N   LEU 3 325 " --> pdb=" O   ALA 3 299 " (cutoff:3.500A)
      removed outlier: 6.291A  pdb=" N   ASN 3 470 " --> pdb=" O   LYS 3 482 " (cutoff:3.500A)
      removed outlier: 5.416A  pdb=" N   LYS 3 482 " --> pdb=" O   ASN 3 470 " (cutoff:3.500A)
      removed outlier: 5.786A  pdb=" N   GLN 3 472 " --> pdb=" O   TYR 3 480 " (cutoff:3.500A)
      removed outlier: 5.487A  pdb=" N   TYR 3 480 " --> pdb=" O   GLN 3 472 " (cutoff:3.500A)
    Processing sheet with id=AA9, first strand: chain '3' and resid 440 through 441
      removed outlier: 3.687A  pdb=" N   PHE 3 440 " --> pdb=" O   VAL 3 454 " (cutoff:3.500A)
    Processing sheet with id=AB1, first strand: chain '3' and resid 518 through 521
    Processing sheet with id=AB2, first strand: chain '3' and resid 538 through 539
    Processing sheet with id=AB3, first strand: chain '3' and resid 554 through 555

    548 hydrogen bonds defined for protein.
    1602 hydrogen bond angles defined for protein.
    Restraints generated for nucleic acids:
      0 hydrogen bonds
      0 hydrogen bond angles
      0 basepair planarities
      0 basepair parallelities
      0 stacking parallelities
  Total time for adding SS restraints: 2.10

  Time building geometry restraints manager: 1.16 seconds

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

  Histogram of bond lengths:
        1.22 -     1.34: 3473
        1.34 -     1.46: 1630
        1.46 -     1.58: 5806
        1.58 -     1.70: 1
        1.70 -     1.82: 82
  Bond restraints: 10992
  Sorted by residual:
  bond pdb=" CAT Z99 31002 "
       pdb=" OAP Z99 31002 "
    ideal  model  delta    sigma   weight residual
    1.364  1.461 -0.097 2.00e-02 2.50e+03 2.36e+01
  bond pdb=" CAT Z99 21102 "
       pdb=" OAP Z99 21102 "
    ideal  model  delta    sigma   weight residual
    1.364  1.457 -0.093 2.00e-02 2.50e+03 2.18e+01
  bond pdb=" CAS Z99 31002 "
       pdb=" OAP Z99 31002 "
    ideal  model  delta    sigma   weight residual
    1.369  1.451 -0.082 2.00e-02 2.50e+03 1.66e+01
  bond pdb=" CAS Z99 21102 "
       pdb=" OAP Z99 21102 "
    ideal  model  delta    sigma   weight residual
    1.369  1.449 -0.080 2.00e-02 2.50e+03 1.60e+01
  bond pdb=" C   ASN 3 445 "
       pdb=" N   PRO 3 446 "
    ideal  model  delta    sigma   weight residual
    1.334  1.390 -0.056 2.34e-02 1.83e+03 5.77e+00
  ... (remaining 10987 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     2.26: 14854
        2.26 -     4.52: 156
        4.52 -     6.78: 28
        6.78 -     9.04: 12
        9.04 -    11.31: 4
  Bond angle restraints: 15054
  Sorted by residual:
  angle pdb=" CA  PRO 2 524 "
        pdb=" N   PRO 2 524 "
        pdb=" CD  PRO 2 524 "
      ideal   model   delta    sigma   weight residual
     112.00  104.92    7.08 1.40e+00 5.10e-01 2.56e+01
  angle pdb=" CB  ARG 3 183 "
        pdb=" CG  ARG 3 183 "
        pdb=" CD  ARG 3 183 "
      ideal   model   delta    sigma   weight residual
     111.30  100.30   11.00 2.30e+00 1.89e-01 2.29e+01
  angle pdb=" N   GLU 2 225 "
        pdb=" CA  GLU 2 225 "
        pdb=" CB  GLU 2 225 "
      ideal   model   delta    sigma   weight residual
     110.12  116.36   -6.24 1.47e+00 4.63e-01 1.80e+01
  angle pdb=" C   ARG 3 183 "
        pdb=" CA  ARG 3 183 "
        pdb=" CB  ARG 3 183 "
      ideal   model   delta    sigma   weight residual
     109.15  116.45   -7.30 1.78e+00 3.16e-01 1.68e+01
  angle pdb=" CAX Z99 21102 "
        pdb=" CAZ Z99 21102 "
        pdb=" CAY Z99 21102 "
      ideal   model   delta    sigma   weight residual
     120.67  109.36   11.31 3.00e+00 1.11e-01 1.42e+01
  ... (remaining 15049 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    34.72: 6571
       34.72 -    69.45: 99
       69.45 -   104.17: 17
      104.17 -   138.89: 2
      138.89 -   173.61: 2
  Dihedral angle restraints: 6691
    sinusoidal: 2260
      harmonic: 4431
  Sorted by residual:
  dihedral pdb=" CB  CYS 2 632 "
           pdb=" SG  CYS 2 632 "
           pdb=" SG  CYS 2 721 "
           pdb=" CB  CYS 2 721 "
      ideal   model   delta sinusoidal    sigma   weight residual
     -86.00    1.84  -87.84     1      1.00e+01 1.00e-02 9.24e+01
  dihedral pdb=" CB  CYS 3 412 "
           pdb=" SG  CYS 3 412 "
           pdb=" SG  CYS 3 419 "
           pdb=" CB  CYS 3 419 "
      ideal   model   delta sinusoidal    sigma   weight residual
      93.00  170.52  -77.52     1      1.00e+01 1.00e-02 7.53e+01
  dihedral pdb=" CB  CYS 2  50 "
           pdb=" SG  CYS 2  50 "
           pdb=" SG  CYS 2  92 "
           pdb=" CB  CYS 2  92 "
      ideal   model   delta sinusoidal    sigma   weight residual
      93.00   29.36   63.64     1      1.00e+01 1.00e-02 5.34e+01
  ... (remaining 6688 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.973: 1752
       0.973 -    1.947: 0
       1.947 -    2.920: 0
       2.920 -    3.893: 0
       3.893 -    4.866: 2
  Chirality restraints: 1754
  Sorted by residual:
  chirality pdb=" CAW Z99 21102 "
            pdb=" CAN Z99 21102 "
            pdb=" CAU Z99 21102 "
            pdb=" CAV Z99 21102 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.61   -2.26    4.87 2.00e-01 2.50e+01 5.92e+02
  chirality pdb=" CAW Z99 31002 "
            pdb=" CAN Z99 31002 "
            pdb=" CAU Z99 31002 "
            pdb=" CAV Z99 31002 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.61   -2.15    4.76 2.00e-01 2.50e+01 5.67e+02
  chirality pdb=" CAY Z99 31002 "
            pdb=" CAN Z99 31002 "
            pdb=" CAR Z99 31002 "
            pdb=" CAZ Z99 31002 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.97   -2.58   -0.39 2.00e-01 2.50e+01 3.82e+00
  ... (remaining 1751 not shown)

  Planarity restraints: 1974
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   ILE 2 523 "   -0.079 5.00e-02 4.00e+02   1.16e-01 2.14e+01
        pdb=" N   PRO 2 524 "    0.200 5.00e-02 4.00e+02
        pdb=" CA  PRO 2 524 "   -0.059 5.00e-02 4.00e+02
        pdb=" CD  PRO 2 524 "   -0.062 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CB  TRP 3 706 "    0.014 2.00e-02 2.50e+03   1.14e-02 3.27e+00
        pdb=" CG  TRP 3 706 "   -0.032 2.00e-02 2.50e+03
        pdb=" CD1 TRP 3 706 "    0.010 2.00e-02 2.50e+03
        pdb=" CD2 TRP 3 706 "    0.001 2.00e-02 2.50e+03
        pdb=" NE1 TRP 3 706 "    0.000 2.00e-02 2.50e+03
        pdb=" CE2 TRP 3 706 "    0.003 2.00e-02 2.50e+03
        pdb=" CE3 TRP 3 706 "    0.003 2.00e-02 2.50e+03
        pdb=" CZ2 TRP 3 706 "    0.001 2.00e-02 2.50e+03
        pdb=" CZ3 TRP 3 706 "    0.000 2.00e-02 2.50e+03
        pdb=" CH2 TRP 3 706 "    0.000 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  TYR 3 431 "    0.009 2.00e-02 2.50e+03   1.73e-02 2.99e+00
        pdb=" C   TYR 3 431 "   -0.030 2.00e-02 2.50e+03
        pdb=" O   TYR 3 431 "    0.011 2.00e-02 2.50e+03
        pdb=" N   LYS 3 432 "    0.010 2.00e-02 2.50e+03
  ... (remaining 1971 not shown)

  Histogram of nonbonded interaction distances:
        2.22 -     2.75: 1404
        2.75 -     3.29: 10446
        3.29 -     3.83: 18073
        3.83 -     4.36: 19713
        4.36 -     4.90: 34809
  Nonbonded interactions: 84445
  Sorted by model distance:
  nonbonded pdb=" OG  SER 2 262 "
            pdb=" O   SER 2 498 "
     model   vdw
     2.218 3.040
  nonbonded pdb=" OE1 GLN 3 232 "
            pdb=" NH2 ARG 3 235 "
     model   vdw
     2.243 3.120
  nonbonded pdb=" O   TYR 3 212 "
            pdb=" OG  SER 3 507 "
     model   vdw
     2.244 3.040
  nonbonded pdb=" OE2 GLU 3 224 "
            pdb=" NZ  LYS 3 246 "
     model   vdw
     2.295 3.120
  nonbonded pdb=" O   SER 2 169 "
            pdb=" NH1 ARG 2 183 "
     model   vdw
     2.312 3.120
  ... (remaining 84440 not shown)

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

  No NCS relation were found !!!

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

Found NCS groups:
  found none.
Set up NCS constraints
  No NCS constraints will be used in refinement.
Set refine NCS operators
Adjust number of macro_cycles
  Number of macro_cycles: 10
Reset NCS operators
Extract rigid body selections
Check and reset occupancies
  Occupancies: min=0.50 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:             3.960
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.000
  Construct map_model_manager:             0.010
  Extract box with map and model:          0.160
  Check model and map are aligned:         0.030
  Set scattering table:                    0.030
  Process input model:                     12.030
  Find NCS groups from input model:        0.170
  Set up NCS constraints:                  0.020
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.000
  Load rotamer database and sin/cos tables:8.950
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   25.360
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7405
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   0.109  11012  Z= 0.151
  Angle     :  0.611  11.306  15096  Z= 0.296
  Chirality :  0.168   4.866   1754
  Planarity :  0.004   0.116   1972
  Dihedral  : 13.684 173.613   3771
  Min Nonbonded Distance : 2.218

Molprobity Statistics.
  All-atom Clashscore : 5.85
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.54 %
    Favored  : 94.46 %
  Rotamer:
    Outliers :  0.22 %
    Allowed  :  0.00 %
    Favored  : 99.78 %
  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:  0.47 (0.22), residues: 1515
  helix:  2.39 (0.20), residues: 681
  sheet: -0.86 (0.44), residues: 149
  loop : -1.68 (0.22), residues: 685

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG 3 183 
 TYR   0.008   0.001   TYR 3 563 
 PHE   0.012   0.001   PHE 3 544 
 TRP   0.032   0.001   TRP 3 706 
 HIS   0.002   0.000   HIS 2  87 

Details of bonding type rmsd
  covalent geometry    : bond        0.00317 (10992)
  covalent geometry    : angle       0.61037 (15054)
  SS BOND              : bond        0.00238 (   18)
  SS BOND              : angle       0.78933 (   36)
  hydrogen bonds       : bond        0.15789 (  548)
  hydrogen bonds       : angle       5.00028 ( 1602)
  link_NAG-ASN         : bond        0.00205 (    2)
  link_NAG-ASN         : angle       1.00006 (    6)

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

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

  3030 Ramachandran restraints generated.
    1515 Oldfield, 0 Emsley, 1515 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3030 Ramachandran restraints generated.
    1515 Oldfield, 0 Emsley, 1515 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  136 residues out of total 1297 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 2
    poor density    : 134
  time to evaluate  : 0.437 
Fit side-chains
   revert: symmetry clash
REVERT: 2  259 GLN cc_start: 0.8104 (pt0) cc_final: 0.7724 (pp30)
REVERT: 2  518 CYS cc_start: 0.1891 (p) cc_final: 0.1307 (p)
  outliers start: 2
  outliers final: 0
  residues processed: 136
  average time/residue: 0.5289
  time to fit residues: 78.4324
Evaluate side-chains
  99 residues out of total 1297 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 99
  time to evaluate  : 0.401 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 152
   random chunks:
   chunk 98 optimal weight:    2.9990
   chunk 107 optimal weight:    1.9990
   chunk 10 optimal weight:    1.9990
   chunk 66 optimal weight:    0.5980
   chunk 130 optimal weight:   20.0000
   chunk 124 optimal weight:    4.9990
   chunk 103 optimal weight:    1.9990
   chunk 77 optimal weight:    0.7980
   chunk 122 optimal weight:    0.9990
   chunk 91 optimal weight:    0.5980
   chunk 149 optimal weight:   20.0000
   overall best weight:    0.9984

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

Flipped N/Q/H residues before XYZ refinement:
3  94 HIS
3 232 GLN
3 251 ASN
3 341 ASN
3 470 ASN
3 472 GLN

Total number of N/Q/H flips: 6

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4406 r_free = 0.4406 target = 0.206716 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 65)----------------|
| r_work = 0.3556 r_free = 0.3556 target = 0.128817 restraints weight = 12645.839|
|-----------------------------------------------------------------------------|
r_work (start): 0.3508 rms_B_bonded: 1.99
r_work: 0.3282 rms_B_bonded: 2.91 restraints_weight: 0.5000
r_work: 0.3126 rms_B_bonded: 4.56 restraints_weight: 0.2500
r_work (final): 0.3126
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3011
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3011 r_free = 0.3011    target_work(ls_wunit_k1) = 0.091         |
| occupancies: max = 1.00  min = 0.50   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3010 r_free = 0.3010    target_work(ls_wunit_k1) = 0.090         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        4 |
|-----------------------------------------------------------------------------|
r_final: 0.3010
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8115
moved from start:          0.1461

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.055  11012  Z= 0.202
  Angle     :  0.610   9.529  15096  Z= 0.305
  Chirality :  0.043   0.195   1754
  Planarity :  0.004   0.060   1972
  Dihedral  :  4.556  52.549   1845
  Min Nonbonded Distance : 2.471

Molprobity Statistics.
  All-atom Clashscore : 5.16
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.74 %
    Favored  : 94.26 %
  Rotamer:
    Outliers :  2.18 %
    Allowed  :  9.47 %
    Favored  : 88.36 %
  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:  0.40 (0.22), residues: 1515
  helix:  2.40 (0.20), residues: 678
  sheet: -0.78 (0.43), residues: 138
  loop : -1.79 (0.22), residues: 699

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.008   0.001   ARG 3 253 
 TYR   0.015   0.002   TYR 3 171 
 PHE   0.016   0.002   PHE 3 195 
 TRP   0.022   0.002   TRP 3 706 
 HIS   0.003   0.001   HIS 3 485 

Details of bonding type rmsd
  covalent geometry    : bond        0.00474 (10992)
  covalent geometry    : angle       0.60920 (15054)
  SS BOND              : bond        0.00243 (   18)
  SS BOND              : angle       0.78987 (   36)
  hydrogen bonds       : bond        0.04096 (  548)
  hydrogen bonds       : angle       4.02864 ( 1602)
  link_NAG-ASN         : bond        0.00335 (    2)
  link_NAG-ASN         : angle       0.77184 (    6)

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

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

  3030 Ramachandran restraints generated.
    1515 Oldfield, 0 Emsley, 1515 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3030 Ramachandran restraints generated.
    1515 Oldfield, 0 Emsley, 1515 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  129 residues out of total 1297 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 109
  time to evaluate  : 0.424 
Fit side-chains
   revert: symmetry clash
REVERT: 2  227 GLU cc_start: 0.7379 (OUTLIER) cc_final: 0.7007 (mp0)
REVERT: 2  259 GLN cc_start: 0.8071 (pt0) cc_final: 0.7576 (pp30)
REVERT: 2  356 SER cc_start: 0.8363 (m) cc_final: 0.7637 (p)
REVERT: 2  469 GLN cc_start: 0.8190 (mt0) cc_final: 0.7948 (tt0)
REVERT: 3   59 ARG cc_start: 0.8408 (OUTLIER) cc_final: 0.7962 (ptm160)
REVERT: 3  183 ARG cc_start: 0.9054 (OUTLIER) cc_final: 0.7455 (mtp85)
REVERT: 3  246 LYS cc_start: 0.8524 (mmmm) cc_final: 0.8318 (tptt)
REVERT: 3  803 MET cc_start: 0.6549 (mmm) cc_final: 0.6244 (mmm)
  outliers start: 20
  outliers final: 8
  residues processed: 121
  average time/residue: 0.5291
  time to fit residues: 69.7911
Evaluate side-chains
  106 residues out of total 1297 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 95
  time to evaluate  : 0.407 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain 2 residue   27 THR
Chi-restraints excluded: chain 2 residue  154 LEU
Chi-restraints excluded: chain 2 residue  227 GLU
Chi-restraints excluded: chain 2 residue  367 LEU
Chi-restraints excluded: chain 3 residue   59 ARG
Chi-restraints excluded: chain 3 residue   60 ILE
Chi-restraints excluded: chain 3 residue  177 LYS
Chi-restraints excluded: chain 3 residue  183 ARG
Chi-restraints excluded: chain 3 residue  227 ILE
Chi-restraints excluded: chain 3 residue  346 HIS
Chi-restraints excluded: chain 3 residue  518 MET
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 152
   random chunks:
   chunk 61 optimal weight:   40.0000
   chunk 124 optimal weight:    3.9990
   chunk 141 optimal weight:    1.9990
   chunk 128 optimal weight:    5.9990
   chunk 15 optimal weight:    0.2980
   chunk 56 optimal weight:   20.0000
   chunk 113 optimal weight:    3.9990
   chunk 2 optimal weight:    0.0870
   chunk 32 optimal weight:    6.9990
   chunk 11 optimal weight:    0.9990
   chunk 43 optimal weight:    1.9990
   overall best weight:    1.0764

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

Flipped N/Q/H residues before XYZ refinement:
3 232 GLN
3 251 ASN
3 470 ASN
3 508 GLN

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4394 r_free = 0.4394 target = 0.205533 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 67)----------------|
| r_work = 0.3466 r_free = 0.3466 target = 0.124658 restraints weight = 12723.194|
|-----------------------------------------------------------------------------|
r_work (start): 0.3440 rms_B_bonded: 2.58
r_work: 0.3162 rms_B_bonded: 3.48 restraints_weight: 0.5000
r_work (final): 0.3162
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3169
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3169 r_free = 0.3169    target_work(ls_wunit_k1) = 0.099         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        4 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3169 r_free = 0.3169    target_work(ls_wunit_k1) = 0.099         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        6 |
|-----------------------------------------------------------------------------|
r_final: 0.3169
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8067
moved from start:          0.2029

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.052  11012  Z= 0.201
  Angle     :  0.601  12.750  15096  Z= 0.301
  Chirality :  0.044   0.191   1754
  Planarity :  0.004   0.050   1972
  Dihedral  :  4.668  54.356   1845
  Min Nonbonded Distance : 2.466

Molprobity Statistics.
  All-atom Clashscore : 5.75
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.87 %
    Favored  : 94.13 %
  Rotamer:
    Outliers :  3.26 %
    Allowed  : 12.08 %
    Favored  : 84.66 %
  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:  0.27 (0.22), residues: 1515
  helix:  2.30 (0.20), residues: 685
  sheet: -1.01 (0.41), residues: 142
  loop : -1.87 (0.22), residues: 688

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.011   0.001   ARG 2 229 
 TYR   0.013   0.002   TYR 3 171 
 PHE   0.016   0.002   PHE 2 224 
 TRP   0.019   0.001   TRP 3 706 
 HIS   0.002   0.001   HIS 3  94 

Details of bonding type rmsd
  covalent geometry    : bond        0.00474 (10992)
  covalent geometry    : angle       0.60014 (15054)
  SS BOND              : bond        0.00443 (   18)
  SS BOND              : angle       0.87137 (   36)
  hydrogen bonds       : bond        0.04007 (  548)
  hydrogen bonds       : angle       3.89000 ( 1602)
  link_NAG-ASN         : bond        0.00125 (    2)
  link_NAG-ASN         : angle       0.87398 (    6)

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

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

  3030 Ramachandran restraints generated.
    1515 Oldfield, 0 Emsley, 1515 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3030 Ramachandran restraints generated.
    1515 Oldfield, 0 Emsley, 1515 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  131 residues out of total 1297 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 30
    poor density    : 101
  time to evaluate  : 0.266 
Fit side-chains
   revert: symmetry clash
REVERT: 2  227 GLU cc_start: 0.7572 (OUTLIER) cc_final: 0.7087 (mp0)
REVERT: 2  259 GLN cc_start: 0.8063 (pt0) cc_final: 0.7557 (pp30)
REVERT: 2  356 SER cc_start: 0.8344 (m) cc_final: 0.7553 (p)
REVERT: 2  469 GLN cc_start: 0.8157 (mt0) cc_final: 0.7909 (tt0)
REVERT: 2  520 TRP cc_start: 0.6526 (OUTLIER) cc_final: 0.5970 (p90)
REVERT: 3   59 ARG cc_start: 0.8437 (OUTLIER) cc_final: 0.7966 (ptm160)
REVERT: 3  183 ARG cc_start: 0.9017 (OUTLIER) cc_final: 0.7289 (mtp85)
REVERT: 3  246 LYS cc_start: 0.8494 (mmmm) cc_final: 0.8289 (tptt)
REVERT: 3  803 MET cc_start: 0.6537 (mmm) cc_final: 0.6211 (mmm)
  outliers start: 30
  outliers final: 15
  residues processed: 119
  average time/residue: 0.4506
  time to fit residues: 58.4845
Evaluate side-chains
  110 residues out of total 1297 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 91
  time to evaluate  : 0.369 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain 2 residue   27 THR
Chi-restraints excluded: chain 2 residue   82 VAL
Chi-restraints excluded: chain 2 residue  106 VAL
Chi-restraints excluded: chain 2 residue  154 LEU
Chi-restraints excluded: chain 2 residue  227 GLU
Chi-restraints excluded: chain 2 residue  262 SER
Chi-restraints excluded: chain 2 residue  367 LEU
Chi-restraints excluded: chain 2 residue  400 CYS
Chi-restraints excluded: chain 2 residue  484 LEU
Chi-restraints excluded: chain 2 residue  518 CYS
Chi-restraints excluded: chain 2 residue  520 TRP
Chi-restraints excluded: chain 3 residue   59 ARG
Chi-restraints excluded: chain 3 residue   60 ILE
Chi-restraints excluded: chain 3 residue  140 LEU
Chi-restraints excluded: chain 3 residue  183 ARG
Chi-restraints excluded: chain 3 residue  227 ILE
Chi-restraints excluded: chain 3 residue  346 HIS
Chi-restraints excluded: chain 3 residue  385 GLU
Chi-restraints excluded: chain 3 residue  391 MET
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 152
   random chunks:
   chunk 52 optimal weight:    0.0070
   chunk 145 optimal weight:   20.0000
   chunk 40 optimal weight:    0.9990
   chunk 18 optimal weight:    0.8980
   chunk 21 optimal weight:    0.7980
   chunk 114 optimal weight:    0.8980
   chunk 85 optimal weight:    0.1980
   chunk 93 optimal weight:    3.9990
   chunk 99 optimal weight:    0.9980
   chunk 61 optimal weight:    1.9990
   chunk 63 optimal weight:    5.9990
   overall best weight:    0.5598

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

Flipped N/Q/H residues before XYZ refinement:
2 232 ASN
3 168 GLN
3 232 GLN
3 251 ASN
3 344 ASN

Total number of N/Q/H flips: 5

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4410 r_free = 0.4410 target = 0.207352 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 67)----------------|
| r_work = 0.3504 r_free = 0.3504 target = 0.127271 restraints weight = 12866.847|
|-----------------------------------------------------------------------------|
r_work (start): 0.3469 rms_B_bonded: 2.73
r_work: 0.3184 rms_B_bonded: 3.54 restraints_weight: 0.5000
r_work (final): 0.3184
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3186
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3186 r_free = 0.3186    target_work(ls_wunit_k1) = 0.101         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        6 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3186 r_free = 0.3186    target_work(ls_wunit_k1) = 0.101         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        7 |
|-----------------------------------------------------------------------------|
r_final: 0.3186
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8019
moved from start:          0.2096

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.050  11012  Z= 0.131
  Angle     :  0.541   9.664  15096  Z= 0.271
  Chirality :  0.042   0.169   1754
  Planarity :  0.004   0.055   1972
  Dihedral  :  4.485  53.313   1845
  Min Nonbonded Distance : 2.499

Molprobity Statistics.
  All-atom Clashscore : 5.31
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.61 %
    Favored  : 94.39 %
  Rotamer:
    Outliers :  3.16 %
    Allowed  : 13.93 %
    Favored  : 82.92 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  0.41 (0.22), residues: 1515
  helix:  2.43 (0.20), residues: 684
  sheet: -0.95 (0.42), residues: 142
  loop : -1.82 (0.22), residues: 689

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.012   0.000   ARG 2 229 
 TYR   0.010   0.001   TYR 3 171 
 PHE   0.011   0.001   PHE 2 327 
 TRP   0.017   0.001   TRP 3 706 
 HIS   0.001   0.000   HIS 2 396 

Details of bonding type rmsd
  covalent geometry    : bond        0.00299 (10992)
  covalent geometry    : angle       0.54089 (15054)
  SS BOND              : bond        0.00204 (   18)
  SS BOND              : angle       0.65688 (   36)
  hydrogen bonds       : bond        0.03425 (  548)
  hydrogen bonds       : angle       3.74922 ( 1602)
  link_NAG-ASN         : bond        0.00163 (    2)
  link_NAG-ASN         : angle       0.93551 (    6)

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

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

  3030 Ramachandran restraints generated.
    1515 Oldfield, 0 Emsley, 1515 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3030 Ramachandran restraints generated.
    1515 Oldfield, 0 Emsley, 1515 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  125 residues out of total 1297 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 29
    poor density    : 96
  time to evaluate  : 0.254 
Fit side-chains
   revert: symmetry clash
REVERT: 2   65 MET cc_start: 0.8567 (OUTLIER) cc_final: 0.7621 (ttt)
REVERT: 2  227 GLU cc_start: 0.7642 (OUTLIER) cc_final: 0.7127 (mp0)
REVERT: 2  259 GLN cc_start: 0.8034 (pt0) cc_final: 0.7518 (pp30)
REVERT: 2  356 SER cc_start: 0.8371 (m) cc_final: 0.7549 (p)
REVERT: 2  469 GLN cc_start: 0.8064 (mt0) cc_final: 0.7859 (tt0)
REVERT: 2  520 TRP cc_start: 0.6576 (OUTLIER) cc_final: 0.6043 (p90)
REVERT: 3   59 ARG cc_start: 0.8397 (OUTLIER) cc_final: 0.7915 (ptm160)
REVERT: 3  183 ARG cc_start: 0.8990 (OUTLIER) cc_final: 0.7294 (mtp85)
REVERT: 3  246 LYS cc_start: 0.8388 (mmmm) cc_final: 0.8180 (tptt)
REVERT: 3  803 MET cc_start: 0.6514 (mmm) cc_final: 0.6155 (mmm)
  outliers start: 29
  outliers final: 12
  residues processed: 112
  average time/residue: 0.3889
  time to fit residues: 48.3435
Evaluate side-chains
  106 residues out of total 1297 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 89
  time to evaluate  : 0.364 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain 2 residue   27 THR
Chi-restraints excluded: chain 2 residue   65 MET
Chi-restraints excluded: chain 2 residue  106 VAL
Chi-restraints excluded: chain 2 residue  154 LEU
Chi-restraints excluded: chain 2 residue  227 GLU
Chi-restraints excluded: chain 2 residue  262 SER
Chi-restraints excluded: chain 2 residue  367 LEU
Chi-restraints excluded: chain 2 residue  518 CYS
Chi-restraints excluded: chain 2 residue  520 TRP
Chi-restraints excluded: chain 3 residue   59 ARG
Chi-restraints excluded: chain 3 residue   60 ILE
Chi-restraints excluded: chain 3 residue  140 LEU
Chi-restraints excluded: chain 3 residue  183 ARG
Chi-restraints excluded: chain 3 residue  227 ILE
Chi-restraints excluded: chain 3 residue  315 HIS
Chi-restraints excluded: chain 3 residue  385 GLU
Chi-restraints excluded: chain 3 residue  391 MET
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 152
   random chunks:
   chunk 149 optimal weight:   30.0000
   chunk 67 optimal weight:    6.9990
   chunk 124 optimal weight:    5.9990
   chunk 31 optimal weight:    1.9990
   chunk 128 optimal weight:   20.0000
   chunk 93 optimal weight:    3.9990
   chunk 28 optimal weight:    0.9990
   chunk 81 optimal weight:    0.6980
   chunk 43 optimal weight:    2.9990
   chunk 63 optimal weight:   10.0000
   chunk 33 optimal weight:    0.3980
   overall best weight:    1.4186

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

Flipped N/Q/H residues before XYZ refinement:
2 232 ASN
3 168 GLN
** 3 197 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
3 232 GLN
3 251 ASN
3 344 ASN
3 473 ASN

Total number of N/Q/H flips: 6

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4370 r_free = 0.4370 target = 0.202998 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 81)----------------|
| r_work = 0.3407 r_free = 0.3407 target = 0.119614 restraints weight = 12666.096|
|-----------------------------------------------------------------------------|
r_work (start): 0.3371 rms_B_bonded: 2.52
r_work: 0.3109 rms_B_bonded: 3.63 restraints_weight: 0.5000
r_work (final): 0.3109
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3114
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3114 r_free = 0.3114    target_work(ls_wunit_k1) = 0.096         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        7 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3114 r_free = 0.3114    target_work(ls_wunit_k1) = 0.096         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        9 |
|-----------------------------------------------------------------------------|
r_final: 0.3114
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8189
moved from start:          0.2526

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.006   0.057  11012  Z= 0.255
  Angle     :  0.648  13.673  15096  Z= 0.323
  Chirality :  0.046   0.199   1754
  Planarity :  0.005   0.066   1972
  Dihedral  :  4.967  55.811   1845
  Min Nonbonded Distance : 2.494

Molprobity Statistics.
  All-atom Clashscore : 6.00
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.47 %
    Favored  : 93.53 %
  Rotamer:
    Outliers :  4.35 %
    Allowed  : 13.82 %
    Favored  : 81.83 %
  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:  0.11 (0.22), residues: 1515
  helix:  2.16 (0.20), residues: 689
  sheet: -1.21 (0.41), residues: 148
  loop : -1.96 (0.22), residues: 678

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.012   0.001   ARG 2 229 
 TYR   0.015   0.002   TYR 3 171 
 PHE   0.015   0.002   PHE 2 327 
 TRP   0.017   0.002   TRP 3 706 
 HIS   0.002   0.001   HIS 3  94 

Details of bonding type rmsd
  covalent geometry    : bond        0.00610 (10992)
  covalent geometry    : angle       0.64780 (15054)
  SS BOND              : bond        0.00206 (   18)
  SS BOND              : angle       0.84981 (   36)
  hydrogen bonds       : bond        0.04151 (  548)
  hydrogen bonds       : angle       3.92932 ( 1602)
  link_NAG-ASN         : bond        0.00096 (    2)
  link_NAG-ASN         : angle       0.92323 (    6)

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

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

  3030 Ramachandran restraints generated.
    1515 Oldfield, 0 Emsley, 1515 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3030 Ramachandran restraints generated.
    1515 Oldfield, 0 Emsley, 1515 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  139 residues out of total 1297 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 40
    poor density    : 99
  time to evaluate  : 0.250 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: 2  227 GLU cc_start: 0.7872 (OUTLIER) cc_final: 0.7374 (mp0)
REVERT: 2  259 GLN cc_start: 0.8127 (pt0) cc_final: 0.7559 (pp30)
REVERT: 2  356 SER cc_start: 0.8381 (m) cc_final: 0.7580 (p)
REVERT: 2  469 GLN cc_start: 0.8224 (mt0) cc_final: 0.7996 (tt0)
REVERT: 2  520 TRP cc_start: 0.6450 (OUTLIER) cc_final: 0.5662 (p90)
REVERT: 3   59 ARG cc_start: 0.8430 (OUTLIER) cc_final: 0.7980 (ptm160)
REVERT: 3  183 ARG cc_start: 0.9039 (OUTLIER) cc_final: 0.7638 (mtp85)
REVERT: 3  246 LYS cc_start: 0.8504 (mmmm) cc_final: 0.8266 (tptt)
REVERT: 3  335 ARG cc_start: 0.8493 (ttp-110) cc_final: 0.8209 (ttp-110)
REVERT: 3  363 LEU cc_start: 0.6987 (OUTLIER) cc_final: 0.6454 (mm)
REVERT: 3  803 MET cc_start: 0.6599 (mmm) cc_final: 0.6223 (mmm)
  outliers start: 40
  outliers final: 21
  residues processed: 125
  average time/residue: 0.3929
  time to fit residues: 54.2221
Evaluate side-chains
  118 residues out of total 1297 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 26
    poor density    : 92
  time to evaluate  : 0.343 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain 2 residue   27 THR
Chi-restraints excluded: chain 2 residue   50 CYS
Chi-restraints excluded: chain 2 residue   82 VAL
Chi-restraints excluded: chain 2 residue  106 VAL
Chi-restraints excluded: chain 2 residue  139 VAL
Chi-restraints excluded: chain 2 residue  154 LEU
Chi-restraints excluded: chain 2 residue  227 GLU
Chi-restraints excluded: chain 2 residue  262 SER
Chi-restraints excluded: chain 2 residue  367 LEU
Chi-restraints excluded: chain 2 residue  400 CYS
Chi-restraints excluded: chain 2 residue  484 LEU
Chi-restraints excluded: chain 2 residue  518 CYS
Chi-restraints excluded: chain 2 residue  519 CYS
Chi-restraints excluded: chain 2 residue  520 TRP
Chi-restraints excluded: chain 3 residue   59 ARG
Chi-restraints excluded: chain 3 residue   60 ILE
Chi-restraints excluded: chain 3 residue  140 LEU
Chi-restraints excluded: chain 3 residue  183 ARG
Chi-restraints excluded: chain 3 residue  227 ILE
Chi-restraints excluded: chain 3 residue  236 LEU
Chi-restraints excluded: chain 3 residue  315 HIS
Chi-restraints excluded: chain 3 residue  316 VAL
Chi-restraints excluded: chain 3 residue  346 HIS
Chi-restraints excluded: chain 3 residue  363 LEU
Chi-restraints excluded: chain 3 residue  385 GLU
Chi-restraints excluded: chain 3 residue  391 MET
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 152
   random chunks:
   chunk 29 optimal weight:    0.0770
   chunk 6 optimal weight:    0.9990
   chunk 15 optimal weight:    0.7980
   chunk 93 optimal weight:    0.7980
   chunk 126 optimal weight:    9.9990
   chunk 149 optimal weight:    0.0570
   chunk 18 optimal weight:    0.8980
   chunk 131 optimal weight:    8.9990
   chunk 86 optimal weight:    0.8980
   chunk 57 optimal weight:    6.9990
   chunk 48 optimal weight:    2.9990
   overall best weight:    0.5256

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

Flipped N/Q/H residues before XYZ refinement:
2 232 ASN
3 168 GLN
** 3 197 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
3 232 GLN
3 251 ASN
3 341 ASN

Total number of N/Q/H flips: 5

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4399 r_free = 0.4399 target = 0.206257 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 65)----------------|
| r_work = 0.3494 r_free = 0.3494 target = 0.124641 restraints weight = 12745.924|
|-----------------------------------------------------------------------------|
r_work (start): 0.3452 rms_B_bonded: 2.03
r_work: 0.3214 rms_B_bonded: 3.32 restraints_weight: 0.5000
r_work (final): 0.3214
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3215
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3215 r_free = 0.3215    target_work(ls_wunit_k1) = 0.103         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        9 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3215 r_free = 0.3215    target_work(ls_wunit_k1) = 0.103         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        9 |
|-----------------------------------------------------------------------------|
r_final: 0.3215
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8047
moved from start:          0.2484

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.048  11012  Z= 0.129
  Angle     :  0.553  10.066  15096  Z= 0.276
  Chirality :  0.042   0.188   1754
  Planarity :  0.004   0.068   1972
  Dihedral  :  4.643  53.579   1845
  Min Nonbonded Distance : 2.523

Molprobity Statistics.
  All-atom Clashscore : 6.00
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.61 %
    Favored  : 94.39 %
  Rotamer:
    Outliers :  4.35 %
    Allowed  : 14.15 %
    Favored  : 81.50 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  0.31 (0.22), residues: 1515
  helix:  2.35 (0.20), residues: 685
  sheet: -1.00 (0.42), residues: 143
  loop : -1.89 (0.22), residues: 687

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.014   0.000   ARG 2 229 
 TYR   0.010   0.001   TYR 3 171 
 PHE   0.012   0.001   PHE 2  67 
 TRP   0.015   0.001   TRP 3 706 
 HIS   0.002   0.000   HIS 3 485 

Details of bonding type rmsd
  covalent geometry    : bond        0.00294 (10992)
  covalent geometry    : angle       0.55241 (15054)
  SS BOND              : bond        0.00181 (   18)
  SS BOND              : angle       0.67190 (   36)
  hydrogen bonds       : bond        0.03396 (  548)
  hydrogen bonds       : angle       3.74459 ( 1602)
  link_NAG-ASN         : bond        0.00152 (    2)
  link_NAG-ASN         : angle       0.97841 (    6)

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

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

  3030 Ramachandran restraints generated.
    1515 Oldfield, 0 Emsley, 1515 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3030 Ramachandran restraints generated.
    1515 Oldfield, 0 Emsley, 1515 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  132 residues out of total 1297 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 40
    poor density    : 92
  time to evaluate  : 0.383 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: 2  227 GLU cc_start: 0.7724 (OUTLIER) cc_final: 0.7165 (mp0)
REVERT: 2  259 GLN cc_start: 0.8034 (pt0) cc_final: 0.7569 (pp30)
REVERT: 2  356 SER cc_start: 0.8501 (m) cc_final: 0.7724 (p)
REVERT: 2  520 TRP cc_start: 0.6568 (OUTLIER) cc_final: 0.5826 (p90)
REVERT: 3   59 ARG cc_start: 0.8426 (OUTLIER) cc_final: 0.7956 (ptm160)
REVERT: 3   72 MET cc_start: 0.8398 (OUTLIER) cc_final: 0.7286 (ttt)
REVERT: 3  183 ARG cc_start: 0.8974 (OUTLIER) cc_final: 0.7302 (mtp85)
REVERT: 3  246 LYS cc_start: 0.8400 (mmmm) cc_final: 0.8176 (tptt)
REVERT: 3  328 GLN cc_start: 0.8093 (OUTLIER) cc_final: 0.7508 (pt0)
REVERT: 3  335 ARG cc_start: 0.8368 (ttp-110) cc_final: 0.8161 (ttp-110)
REVERT: 3  363 LEU cc_start: 0.7203 (OUTLIER) cc_final: 0.6716 (mm)
REVERT: 3  803 MET cc_start: 0.6472 (mmm) cc_final: 0.6044 (mmm)
  outliers start: 40
  outliers final: 21
  residues processed: 121
  average time/residue: 0.4183
  time to fit residues: 55.9870
Evaluate side-chains
  116 residues out of total 1297 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 28
    poor density    : 88
  time to evaluate  : 0.328 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain 2 residue   27 THR
Chi-restraints excluded: chain 2 residue   50 CYS
Chi-restraints excluded: chain 2 residue   82 VAL
Chi-restraints excluded: chain 2 residue  106 VAL
Chi-restraints excluded: chain 2 residue  154 LEU
Chi-restraints excluded: chain 2 residue  221 ILE
Chi-restraints excluded: chain 2 residue  227 GLU
Chi-restraints excluded: chain 2 residue  262 SER
Chi-restraints excluded: chain 2 residue  367 LEU
Chi-restraints excluded: chain 2 residue  400 CYS
Chi-restraints excluded: chain 2 residue  518 CYS
Chi-restraints excluded: chain 2 residue  519 CYS
Chi-restraints excluded: chain 2 residue  520 TRP
Chi-restraints excluded: chain 2 residue  597 VAL
Chi-restraints excluded: chain 3 residue   50 LYS
Chi-restraints excluded: chain 3 residue   59 ARG
Chi-restraints excluded: chain 3 residue   60 ILE
Chi-restraints excluded: chain 3 residue   72 MET
Chi-restraints excluded: chain 3 residue  140 LEU
Chi-restraints excluded: chain 3 residue  183 ARG
Chi-restraints excluded: chain 3 residue  227 ILE
Chi-restraints excluded: chain 3 residue  315 HIS
Chi-restraints excluded: chain 3 residue  316 VAL
Chi-restraints excluded: chain 3 residue  328 GLN
Chi-restraints excluded: chain 3 residue  363 LEU
Chi-restraints excluded: chain 3 residue  385 GLU
Chi-restraints excluded: chain 3 residue  391 MET
Chi-restraints excluded: chain 3 residue  438 ILE
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 152
   random chunks:
   chunk 77 optimal weight:    0.4980
   chunk 119 optimal weight:    0.8980
   chunk 150 optimal weight:   20.0000
   chunk 61 optimal weight:    0.8980
   chunk 118 optimal weight:    0.9980
   chunk 70 optimal weight:    7.9990
   chunk 7 optimal weight:    0.7980
   chunk 139 optimal weight:    8.9990
   chunk 40 optimal weight:    0.4980
   chunk 55 optimal weight:    1.9990
   chunk 17 optimal weight:    0.8980
   overall best weight:    0.7180

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

Flipped N/Q/H residues before XYZ refinement:
2 232 ASN
2 414 ASN
** 3 197 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
3 232 GLN
3 251 ASN
3 341 ASN

Total number of N/Q/H flips: 5

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4394 r_free = 0.4394 target = 0.205828 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 60)----------------|
| r_work = 0.3484 r_free = 0.3484 target = 0.128155 restraints weight = 12770.412|
|-----------------------------------------------------------------------------|
r_work (start): 0.3445 rms_B_bonded: 3.03
r_work: 0.3144 rms_B_bonded: 3.56 restraints_weight: 0.5000
r_work (final): 0.3144
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3146
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3146 r_free = 0.3146    target_work(ls_wunit_k1) = 0.098         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        9 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3146 r_free = 0.3146    target_work(ls_wunit_k1) = 0.098         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        9 |
|-----------------------------------------------------------------------------|
r_final: 0.3146
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8043
moved from start:          0.2549

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.048  11012  Z= 0.150
  Angle     :  0.564  13.666  15096  Z= 0.280
  Chirality :  0.042   0.169   1754
  Planarity :  0.004   0.071   1972
  Dihedral  :  4.600  53.459   1845
  Min Nonbonded Distance : 2.531

Molprobity Statistics.
  All-atom Clashscore : 5.66
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.34 %
    Favored  : 93.66 %
  Rotamer:
    Outliers :  3.81 %
    Allowed  : 15.02 %
    Favored  : 81.18 %
  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:  0.36 (0.22), residues: 1515
  helix:  2.43 (0.20), residues: 679
  sheet: -0.96 (0.42), residues: 143
  loop : -1.87 (0.22), residues: 693

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.014   0.000   ARG 2 229 
 TYR   0.010   0.001   TYR 3 171 
 PHE   0.013   0.001   PHE 3 195 
 TRP   0.015   0.001   TRP 3 706 
 HIS   0.002   0.001   HIS 3 485 

Details of bonding type rmsd
  covalent geometry    : bond        0.00351 (10992)
  covalent geometry    : angle       0.56376 (15054)
  SS BOND              : bond        0.00174 (   18)
  SS BOND              : angle       0.69407 (   36)
  hydrogen bonds       : bond        0.03422 (  548)
  hydrogen bonds       : angle       3.71415 ( 1602)
  link_NAG-ASN         : bond        0.00100 (    2)
  link_NAG-ASN         : angle       0.96818 (    6)

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

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

  3030 Ramachandran restraints generated.
    1515 Oldfield, 0 Emsley, 1515 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3030 Ramachandran restraints generated.
    1515 Oldfield, 0 Emsley, 1515 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  128 residues out of total 1297 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 35
    poor density    : 93
  time to evaluate  : 0.393 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: 2  227 GLU cc_start: 0.7823 (OUTLIER) cc_final: 0.7244 (mp0)
REVERT: 2  245 MET cc_start: 0.5950 (ptp) cc_final: 0.5665 (mmm)
REVERT: 2  259 GLN cc_start: 0.7985 (pt0) cc_final: 0.7387 (pp30)
REVERT: 2  262 SER cc_start: 0.6702 (OUTLIER) cc_final: 0.6481 (t)
REVERT: 2  356 SER cc_start: 0.8279 (m) cc_final: 0.7430 (p)
REVERT: 2  520 TRP cc_start: 0.6607 (OUTLIER) cc_final: 0.5865 (p90)
REVERT: 3   59 ARG cc_start: 0.8364 (OUTLIER) cc_final: 0.7898 (ptm160)
REVERT: 3   72 MET cc_start: 0.8526 (OUTLIER) cc_final: 0.7424 (ttt)
REVERT: 3  183 ARG cc_start: 0.8994 (OUTLIER) cc_final: 0.7254 (mtp85)
REVERT: 3  246 LYS cc_start: 0.8475 (mmmm) cc_final: 0.8181 (tptt)
REVERT: 3  328 GLN cc_start: 0.8078 (OUTLIER) cc_final: 0.7511 (pt0)
REVERT: 3  363 LEU cc_start: 0.7067 (OUTLIER) cc_final: 0.6509 (mm)
REVERT: 3  803 MET cc_start: 0.6670 (mmm) cc_final: 0.6274 (mmm)
  outliers start: 35
  outliers final: 23
  residues processed: 120
  average time/residue: 0.4001
  time to fit residues: 52.8691
Evaluate side-chains
  119 residues out of total 1297 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 31
    poor density    : 88
  time to evaluate  : 0.394 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain 2 residue   27 THR
Chi-restraints excluded: chain 2 residue   50 CYS
Chi-restraints excluded: chain 2 residue   82 VAL
Chi-restraints excluded: chain 2 residue  106 VAL
Chi-restraints excluded: chain 2 residue  154 LEU
Chi-restraints excluded: chain 2 residue  227 GLU
Chi-restraints excluded: chain 2 residue  262 SER
Chi-restraints excluded: chain 2 residue  267 VAL
Chi-restraints excluded: chain 2 residue  367 LEU
Chi-restraints excluded: chain 2 residue  400 CYS
Chi-restraints excluded: chain 2 residue  469 GLN
Chi-restraints excluded: chain 2 residue  518 CYS
Chi-restraints excluded: chain 2 residue  519 CYS
Chi-restraints excluded: chain 2 residue  520 TRP
Chi-restraints excluded: chain 2 residue  598 VAL
Chi-restraints excluded: chain 3 residue   50 LYS
Chi-restraints excluded: chain 3 residue   59 ARG
Chi-restraints excluded: chain 3 residue   60 ILE
Chi-restraints excluded: chain 3 residue   72 MET
Chi-restraints excluded: chain 3 residue  140 LEU
Chi-restraints excluded: chain 3 residue  183 ARG
Chi-restraints excluded: chain 3 residue  227 ILE
Chi-restraints excluded: chain 3 residue  315 HIS
Chi-restraints excluded: chain 3 residue  316 VAL
Chi-restraints excluded: chain 3 residue  328 GLN
Chi-restraints excluded: chain 3 residue  346 HIS
Chi-restraints excluded: chain 3 residue  363 LEU
Chi-restraints excluded: chain 3 residue  385 GLU
Chi-restraints excluded: chain 3 residue  391 MET
Chi-restraints excluded: chain 3 residue  438 ILE
Chi-restraints excluded: chain 3 residue  494 VAL
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 152
   random chunks:
   chunk 80 optimal weight:    0.9980
   chunk 23 optimal weight:    2.9990
   chunk 83 optimal weight:    0.8980
   chunk 149 optimal weight:    0.9980
   chunk 101 optimal weight:    0.6980
   chunk 147 optimal weight:   20.0000
   chunk 68 optimal weight:   40.0000
   chunk 135 optimal weight:    7.9990
   chunk 71 optimal weight:   30.0000
   chunk 131 optimal weight:    3.9990
   chunk 120 optimal weight:    1.9990
   overall best weight:    1.1182

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

Flipped N/Q/H residues before XYZ refinement:
2 232 ASN
3 168 GLN
** 3 197 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
3 232 GLN
3 251 ASN
3 341 ASN

Total number of N/Q/H flips: 5

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4387 r_free = 0.4387 target = 0.204415 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 59)----------------|
| r_work = 0.3464 r_free = 0.3464 target = 0.124120 restraints weight = 12711.879|
|-----------------------------------------------------------------------------|
r_work (start): 0.3425 rms_B_bonded: 2.87
r_work: 0.3123 rms_B_bonded: 3.54 restraints_weight: 0.5000
r_work (final): 0.3123
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3122
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3122 r_free = 0.3122    target_work(ls_wunit_k1) = 0.096         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        9 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3122 r_free = 0.3122    target_work(ls_wunit_k1) = 0.096         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        9 |
|-----------------------------------------------------------------------------|
r_final: 0.3122
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8094
moved from start:          0.2729

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.049  11012  Z= 0.208
  Angle     :  0.616  14.576  15096  Z= 0.305
  Chirality :  0.044   0.189   1754
  Planarity :  0.005   0.075   1972
  Dihedral  :  4.841  53.609   1845
  Min Nonbonded Distance : 2.526

Molprobity Statistics.
  All-atom Clashscore : 6.05
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.40 %
    Favored  : 93.60 %
  Rotamer:
    Outliers :  4.46 %
    Allowed  : 15.13 %
    Favored  : 80.41 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.07 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  0.24 (0.22), residues: 1515
  helix:  2.33 (0.20), residues: 682
  sheet: -1.08 (0.42), residues: 143
  loop : -1.95 (0.22), residues: 690

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.017   0.001   ARG 2 229 
 TYR   0.013   0.002   TYR 3 171 
 PHE   0.015   0.002   PHE 3 195 
 TRP   0.016   0.001   TRP 3 706 
 HIS   0.002   0.001   HIS 2 365 

Details of bonding type rmsd
  covalent geometry    : bond        0.00495 (10992)
  covalent geometry    : angle       0.61492 (15054)
  SS BOND              : bond        0.00187 (   18)
  SS BOND              : angle       0.79037 (   36)
  hydrogen bonds       : bond        0.03780 (  548)
  hydrogen bonds       : angle       3.81095 ( 1602)
  link_NAG-ASN         : bond        0.00086 (    2)
  link_NAG-ASN         : angle       0.95195 (    6)

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

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

  3030 Ramachandran restraints generated.
    1515 Oldfield, 0 Emsley, 1515 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3030 Ramachandran restraints generated.
    1515 Oldfield, 0 Emsley, 1515 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  127 residues out of total 1297 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 41
    poor density    : 86
  time to evaluate  : 0.243 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: 2  227 GLU cc_start: 0.7949 (OUTLIER) cc_final: 0.7382 (mp0)
REVERT: 2  259 GLN cc_start: 0.7917 (pt0) cc_final: 0.7329 (pp30)
REVERT: 2  356 SER cc_start: 0.8327 (m) cc_final: 0.7484 (p)
REVERT: 2  520 TRP cc_start: 0.6341 (OUTLIER) cc_final: 0.5575 (p90)
REVERT: 3   59 ARG cc_start: 0.8332 (OUTLIER) cc_final: 0.7867 (ptm160)
REVERT: 3   72 MET cc_start: 0.8570 (OUTLIER) cc_final: 0.7499 (ttt)
REVERT: 3  183 ARG cc_start: 0.9014 (OUTLIER) cc_final: 0.7243 (mtp85)
REVERT: 3  246 LYS cc_start: 0.8520 (mmmm) cc_final: 0.8198 (tptt)
REVERT: 3  328 GLN cc_start: 0.8179 (OUTLIER) cc_final: 0.7682 (pt0)
REVERT: 3  335 ARG cc_start: 0.8363 (ttp-110) cc_final: 0.8093 (ttp-110)
REVERT: 3  363 LEU cc_start: 0.7098 (OUTLIER) cc_final: 0.6552 (mm)
REVERT: 3  803 MET cc_start: 0.6621 (mmm) cc_final: 0.6203 (mmm)
  outliers start: 41
  outliers final: 24
  residues processed: 117
  average time/residue: 0.3702
  time to fit residues: 48.0084
Evaluate side-chains
  119 residues out of total 1297 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 31
    poor density    : 88
  time to evaluate  : 0.315 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain 2 residue   27 THR
Chi-restraints excluded: chain 2 residue   50 CYS
Chi-restraints excluded: chain 2 residue   82 VAL
Chi-restraints excluded: chain 2 residue  106 VAL
Chi-restraints excluded: chain 2 residue  154 LEU
Chi-restraints excluded: chain 2 residue  227 GLU
Chi-restraints excluded: chain 2 residue  267 VAL
Chi-restraints excluded: chain 2 residue  367 LEU
Chi-restraints excluded: chain 2 residue  400 CYS
Chi-restraints excluded: chain 2 residue  469 GLN
Chi-restraints excluded: chain 2 residue  485 ILE
Chi-restraints excluded: chain 2 residue  489 SER
Chi-restraints excluded: chain 2 residue  518 CYS
Chi-restraints excluded: chain 2 residue  519 CYS
Chi-restraints excluded: chain 2 residue  520 TRP
Chi-restraints excluded: chain 2 residue  598 VAL
Chi-restraints excluded: chain 3 residue   59 ARG
Chi-restraints excluded: chain 3 residue   60 ILE
Chi-restraints excluded: chain 3 residue   72 MET
Chi-restraints excluded: chain 3 residue  140 LEU
Chi-restraints excluded: chain 3 residue  183 ARG
Chi-restraints excluded: chain 3 residue  227 ILE
Chi-restraints excluded: chain 3 residue  315 HIS
Chi-restraints excluded: chain 3 residue  316 VAL
Chi-restraints excluded: chain 3 residue  328 GLN
Chi-restraints excluded: chain 3 residue  346 HIS
Chi-restraints excluded: chain 3 residue  363 LEU
Chi-restraints excluded: chain 3 residue  385 GLU
Chi-restraints excluded: chain 3 residue  391 MET
Chi-restraints excluded: chain 3 residue  438 ILE
Chi-restraints excluded: chain 3 residue  494 VAL
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 152
   random chunks:
   chunk 117 optimal weight:    0.9980
   chunk 73 optimal weight:    8.9990
   chunk 136 optimal weight:    7.9990
   chunk 59 optimal weight:    9.9990
   chunk 110 optimal weight:    0.3980
   chunk 135 optimal weight:    5.9990
   chunk 36 optimal weight:    0.6980
   chunk 139 optimal weight:    6.9990
   chunk 118 optimal weight:    0.5980
   chunk 132 optimal weight:   30.0000
   chunk 75 optimal weight:    8.9990
   overall best weight:    1.7382

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

Flipped N/Q/H residues before XYZ refinement:
2 232 ASN
** 3 197 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
3 232 GLN
3 251 ASN
3 341 ASN

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4365 r_free = 0.4365 target = 0.202268 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 57)----------------|
| r_work = 0.3459 r_free = 0.3459 target = 0.124782 restraints weight = 12736.892|
|-----------------------------------------------------------------------------|
r_work (start): 0.3427 rms_B_bonded: 2.87
r_work: 0.3063 rms_B_bonded: 3.81 restraints_weight: 0.5000
r_work (final): 0.3063
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2980
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2980 r_free = 0.2980    target_work(ls_wunit_k1) = 0.088         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        9 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2980 r_free = 0.2980    target_work(ls_wunit_k1) = 0.088         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        9 |
|-----------------------------------------------------------------------------|
r_final: 0.2980
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8150
moved from start:          0.3005

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.007   0.062  11012  Z= 0.297
  Angle     :  0.696  15.830  15096  Z= 0.345
  Chirality :  0.047   0.213   1754
  Planarity :  0.006   0.078   1972
  Dihedral  :  5.384  54.752   1845
  Min Nonbonded Distance : 2.512

Molprobity Statistics.
  All-atom Clashscore : 7.24
  Ramachandran Plot:
    Outliers :  0.13 %
    Allowed  :  6.67 %
    Favored  : 93.20 %
  Rotamer:
    Outliers :  4.24 %
    Allowed  : 15.78 %
    Favored  : 79.98 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.07 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  0.05 (0.22), residues: 1515
  helix:  2.19 (0.21), residues: 683
  sheet: -1.22 (0.42), residues: 143
  loop : -2.05 (0.22), residues: 689

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.016   0.001   ARG 2 229 
 TYR   0.016   0.002   TYR 3 171 
 PHE   0.019   0.002   PHE 3 195 
 TRP   0.017   0.002   TRP 3 706 
 HIS   0.003   0.001   HIS 2 365 

Details of bonding type rmsd
  covalent geometry    : bond        0.00713 (10992)
  covalent geometry    : angle       0.69497 (15054)
  SS BOND              : bond        0.00200 (   18)
  SS BOND              : angle       0.95532 (   36)
  hydrogen bonds       : bond        0.04294 (  548)
  hydrogen bonds       : angle       3.98176 ( 1602)
  link_NAG-ASN         : bond        0.00306 (    2)
  link_NAG-ASN         : angle       1.17070 (    6)

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

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

  3030 Ramachandran restraints generated.
    1515 Oldfield, 0 Emsley, 1515 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3030 Ramachandran restraints generated.
    1515 Oldfield, 0 Emsley, 1515 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  121 residues out of total 1297 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 39
    poor density    : 82
  time to evaluate  : 0.396 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: 2  227 GLU cc_start: 0.8086 (OUTLIER) cc_final: 0.7567 (mp0)
REVERT: 2  356 SER cc_start: 0.8364 (m) cc_final: 0.7555 (p)
REVERT: 2  520 TRP cc_start: 0.6350 (OUTLIER) cc_final: 0.5624 (p90)
REVERT: 3   59 ARG cc_start: 0.8359 (OUTLIER) cc_final: 0.7873 (ptm160)
REVERT: 3   72 MET cc_start: 0.8679 (OUTLIER) cc_final: 0.7655 (ttt)
REVERT: 3  335 ARG cc_start: 0.8444 (ttp-110) cc_final: 0.8120 (ttp-110)
REVERT: 3  363 LEU cc_start: 0.7122 (OUTLIER) cc_final: 0.6522 (mm)
REVERT: 3  803 MET cc_start: 0.6559 (mmm) cc_final: 0.6182 (mmm)
  outliers start: 39
  outliers final: 25
  residues processed: 109
  average time/residue: 0.4076
  time to fit residues: 48.9015
Evaluate side-chains
  107 residues out of total 1297 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 30
    poor density    : 77
  time to evaluate  : 0.384 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain 2 residue   27 THR
Chi-restraints excluded: chain 2 residue   50 CYS
Chi-restraints excluded: chain 2 residue   82 VAL
Chi-restraints excluded: chain 2 residue  106 VAL
Chi-restraints excluded: chain 2 residue  139 VAL
Chi-restraints excluded: chain 2 residue  154 LEU
Chi-restraints excluded: chain 2 residue  227 GLU
Chi-restraints excluded: chain 2 residue  267 VAL
Chi-restraints excluded: chain 2 residue  367 LEU
Chi-restraints excluded: chain 2 residue  400 CYS
Chi-restraints excluded: chain 2 residue  410 MET
Chi-restraints excluded: chain 2 residue  469 GLN
Chi-restraints excluded: chain 2 residue  485 ILE
Chi-restraints excluded: chain 2 residue  489 SER
Chi-restraints excluded: chain 2 residue  518 CYS
Chi-restraints excluded: chain 2 residue  519 CYS
Chi-restraints excluded: chain 2 residue  520 TRP
Chi-restraints excluded: chain 2 residue  598 VAL
Chi-restraints excluded: chain 3 residue   59 ARG
Chi-restraints excluded: chain 3 residue   60 ILE
Chi-restraints excluded: chain 3 residue   72 MET
Chi-restraints excluded: chain 3 residue  140 LEU
Chi-restraints excluded: chain 3 residue  183 ARG
Chi-restraints excluded: chain 3 residue  227 ILE
Chi-restraints excluded: chain 3 residue  315 HIS
Chi-restraints excluded: chain 3 residue  316 VAL
Chi-restraints excluded: chain 3 residue  363 LEU
Chi-restraints excluded: chain 3 residue  385 GLU
Chi-restraints excluded: chain 3 residue  391 MET
Chi-restraints excluded: chain 3 residue  494 VAL
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 152
   random chunks:
   chunk 29 optimal weight:    0.0870
   chunk 136 optimal weight:   10.0000
   chunk 5 optimal weight:    0.0010
   chunk 78 optimal weight:    0.7980
   chunk 23 optimal weight:    0.9990
   chunk 38 optimal weight:    0.5980
   chunk 16 optimal weight:    0.9990
   chunk 132 optimal weight:    0.0170
   chunk 48 optimal weight:    0.9980
   chunk 87 optimal weight:    0.5980
   chunk 137 optimal weight:    6.9990
   overall best weight:    0.2602

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

Flipped N/Q/H residues before XYZ refinement:
2 232 ASN
3 168 GLN
** 3 197 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
3 232 GLN
3 341 ASN

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4403 r_free = 0.4403 target = 0.206237 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 61)----------------|
| r_work = 0.3469 r_free = 0.3469 target = 0.125252 restraints weight = 12648.832|
|-----------------------------------------------------------------------------|
r_work (start): 0.3432 rms_B_bonded: 2.84
r_work: 0.3188 rms_B_bonded: 3.33 restraints_weight: 0.5000
r_work (final): 0.3188
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3192
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3192 r_free = 0.3192    target_work(ls_wunit_k1) = 0.101         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        9 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3192 r_free = 0.3192    target_work(ls_wunit_k1) = 0.101         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        9 |
|-----------------------------------------------------------------------------|
r_final: 0.3192
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8018
moved from start:          0.2826

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.049  11012  Z= 0.113
  Angle     :  0.565  12.117  15096  Z= 0.281
  Chirality :  0.041   0.174   1754
  Planarity :  0.005   0.072   1972
  Dihedral  :  4.743  52.873   1845
  Min Nonbonded Distance : 2.550

Molprobity Statistics.
  All-atom Clashscore : 6.00
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.21 %
    Favored  : 94.79 %
  Rotamer:
    Outliers :  2.83 %
    Allowed  : 17.30 %
    Favored  : 79.87 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.07 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  0.31 (0.22), residues: 1515
  helix:  2.40 (0.20), residues: 683
  sheet: -1.24 (0.42), residues: 150
  loop : -1.88 (0.22), residues: 682

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.017   0.001   ARG 2 229 
 TYR   0.009   0.001   TYR 3 222 
 PHE   0.011   0.001   PHE 2  67 
 TRP   0.015   0.001   TRP 3 706 
 HIS   0.002   0.000   HIS 3 485 

Details of bonding type rmsd
  covalent geometry    : bond        0.00244 (10992)
  covalent geometry    : angle       0.56424 (15054)
  SS BOND              : bond        0.00180 (   18)
  SS BOND              : angle       0.66237 (   36)
  hydrogen bonds       : bond        0.03169 (  548)
  hydrogen bonds       : angle       3.70186 ( 1602)
  link_NAG-ASN         : bond        0.00201 (    2)
  link_NAG-ASN         : angle       0.98221 (    6)

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

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

  3030 Ramachandran restraints generated.
    1515 Oldfield, 0 Emsley, 1515 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3030 Ramachandran restraints generated.
    1515 Oldfield, 0 Emsley, 1515 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  111 residues out of total 1297 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 26
    poor density    : 85
  time to evaluate  : 0.307 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: 2  227 GLU cc_start: 0.7849 (OUTLIER) cc_final: 0.7348 (mp0)
REVERT: 2  356 SER cc_start: 0.8310 (m) cc_final: 0.7472 (p)
REVERT: 3   59 ARG cc_start: 0.8323 (OUTLIER) cc_final: 0.7840 (ptm160)
REVERT: 3  236 LEU cc_start: 0.8564 (tp) cc_final: 0.8018 (mm)
REVERT: 3  335 ARG cc_start: 0.8306 (ttp-110) cc_final: 0.8003 (ttp-110)
REVERT: 3  363 LEU cc_start: 0.7224 (OUTLIER) cc_final: 0.6713 (mm)
REVERT: 3  425 LEU cc_start: 0.6445 (mm) cc_final: 0.6187 (tm)
REVERT: 3  803 MET cc_start: 0.6657 (mmm) cc_final: 0.6259 (mmm)
  outliers start: 26
  outliers final: 18
  residues processed: 105
  average time/residue: 0.4142
  time to fit residues: 47.9797
Evaluate side-chains
  102 residues out of total 1297 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 81
  time to evaluate  : 0.348 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain 2 residue   27 THR
Chi-restraints excluded: chain 2 residue   50 CYS
Chi-restraints excluded: chain 2 residue   82 VAL
Chi-restraints excluded: chain 2 residue  106 VAL
Chi-restraints excluded: chain 2 residue  154 LEU
Chi-restraints excluded: chain 2 residue  227 GLU
Chi-restraints excluded: chain 2 residue  367 LEU
Chi-restraints excluded: chain 2 residue  400 CYS
Chi-restraints excluded: chain 2 residue  469 GLN
Chi-restraints excluded: chain 2 residue  518 CYS
Chi-restraints excluded: chain 2 residue  519 CYS
Chi-restraints excluded: chain 2 residue  597 VAL
Chi-restraints excluded: chain 3 residue   59 ARG
Chi-restraints excluded: chain 3 residue   60 ILE
Chi-restraints excluded: chain 3 residue  140 LEU
Chi-restraints excluded: chain 3 residue  227 ILE
Chi-restraints excluded: chain 3 residue  315 HIS
Chi-restraints excluded: chain 3 residue  316 VAL
Chi-restraints excluded: chain 3 residue  363 LEU
Chi-restraints excluded: chain 3 residue  438 ILE
Chi-restraints excluded: chain 3 residue  494 VAL
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 152
   random chunks:
   chunk 63 optimal weight:    5.9990
   chunk 50 optimal weight:   20.0000
   chunk 129 optimal weight:    5.9990
   chunk 22 optimal weight:    1.9990
   chunk 7 optimal weight:    1.9990
   chunk 35 optimal weight:    3.9990
   chunk 67 optimal weight:    8.9990
   chunk 118 optimal weight:    0.7980
   chunk 122 optimal weight:    0.9990
   chunk 20 optimal weight:    2.9990
   chunk 114 optimal weight:    0.6980
   overall best weight:    1.2986

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

Flipped N/Q/H residues before XYZ refinement:
2 232 ASN
2 259 GLN
2 414 ASN
3 168 GLN
** 3 197 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
3 232 GLN
3 341 ASN

Total number of N/Q/H flips: 6

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4378 r_free = 0.4378 target = 0.203576 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 70)----------------|
| r_work = 0.3425 r_free = 0.3425 target = 0.121151 restraints weight = 12794.361|
|-----------------------------------------------------------------------------|
r_work (start): 0.3384 rms_B_bonded: 2.58
r_work: 0.3152 rms_B_bonded: 3.16 restraints_weight: 0.5000
r_work: 0.3003 rms_B_bonded: 4.80 restraints_weight: 0.2500
r_work (final): 0.3003
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2863
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2863 r_free = 0.2863    target_work(ls_wunit_k1) = 0.082         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        9 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2863 r_free = 0.2863    target_work(ls_wunit_k1) = 0.082         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        9 |
|-----------------------------------------------------------------------------|
r_final: 0.2863
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8201
moved from start:          0.2946

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.053  11012  Z= 0.229
  Angle     :  0.635  14.450  15096  Z= 0.315
  Chirality :  0.044   0.193   1754
  Planarity :  0.005   0.071   1972
  Dihedral  :  4.971  53.509   1845
  Min Nonbonded Distance : 2.436

Molprobity Statistics.
  All-atom Clashscore : 6.45
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.67 %
    Favored  : 93.33 %
  Rotamer:
    Outliers :  3.59 %
    Allowed  : 16.65 %
    Favored  : 79.76 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.07 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  0.23 (0.22), residues: 1515
  helix:  2.33 (0.21), residues: 683
  sheet: -1.08 (0.42), residues: 143
  loop : -1.96 (0.22), residues: 689

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.013   0.001   ARG 2 229 
 TYR   0.020   0.002   TYR 3 318 
 PHE   0.017   0.002   PHE 3 195 
 TRP   0.016   0.002   TRP 3 706 
 HIS   0.002   0.001   HIS 2 365 

Details of bonding type rmsd
  covalent geometry    : bond        0.00545 (10992)
  covalent geometry    : angle       0.63386 (15054)
  SS BOND              : bond        0.00178 (   18)
  SS BOND              : angle       0.81941 (   36)
  hydrogen bonds       : bond        0.03833 (  548)
  hydrogen bonds       : angle       3.81285 ( 1602)
  link_NAG-ASN         : bond        0.00149 (    2)
  link_NAG-ASN         : angle       1.05057 (    6)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 3915.20 seconds
wall clock time: 67 minutes 12.96 seconds (4032.96 seconds total)