Starting phenix.real_space_refine
on Thu Mar  5 02:53:27 2026 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/7lmb_23439/03_2026/7lmb_23439.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/7lmb_23439/03_2026/7lmb_23439.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.8
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    model {
      file = "/net/cci-nas-00/data/ceres_data/7lmb_23439/03_2026/7lmb_23439.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/7lmb_23439/03_2026/7lmb_23439.cif"
    real_map_files = "/net/cci-nas-00/data/ceres_data/7lmb_23439/03_2026/7lmb_23439.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/7lmb_23439/03_2026/7lmb_23439.map"
  }
  resolution = 3.8
  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=   0.000 sd=   0.004
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: 6
    Type Number    sf(0)   Gaussians
     Zn      1      6.06       5
     P     162      5.49       5
     S      65      5.16       5
     C   11247      2.51       5
     N    3115      2.21       5
     O    3908      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 37 residue(s): 0.01s

  Monomer Library directory:
    "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/chem_data/mon_lib"
  Total number of atoms: 18498
  Number of models: 1
  Model: ""
    Number of chains: 9
    Chain: "B"
      Number of atoms: 3189
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 151, 3189
          Classifications: {'RNA': 151}
          Modifications used: {'rna2p_pur': 9, 'rna2p_pyr': 18, 'rna3p_pur': 64, 'rna3p_pyr': 60}
          Link IDs: {'rna2p': 26, 'rna3p': 124}
          Chain breaks: 1
    Chain: "C"
      Number of atoms: 230
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 11, 230
          Classifications: {'DNA': 11}
          Link IDs: {'rna3p': 10}
          Chain breaks: 1
    Chain: "H"
      Number of atoms: 1367
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 199, 1367
          Classifications: {'peptide': 199}
          Incomplete info: {'truncation_to_alanine': 90}
          Link IDs: {'PTRANS': 4, 'TRANS': 194}
          Chain breaks: 3
          Unresolved chain link angles: 2
          Unresolved non-hydrogen bonds: 320
          Unresolved non-hydrogen angles: 395
          Unresolved non-hydrogen dihedrals: 270
          Unresolved non-hydrogen chiralities: 28
          Planarities with less than four sites: {'GLU:plan': 4, 'ASP:plan': 7, 'GLN:plan1': 3, 'TYR:plan': 3, 'PHE:plan': 5, 'ASN:plan1': 4, 'HIS:plan': 2, 'ARG:plan': 4}
          Unresolved non-hydrogen planarities: 142
    Chain: "A"
      Number of atoms: 8542
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 1012, 8542
          Classifications: {'peptide': 1012}
          Link IDs: {'PTRANS': 22, 'TRANS': 989}
          Chain breaks: 3
    Chain: "D"
      Number of atoms: 1554
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 187, 1554
          Classifications: {'peptide': 187}
          Link IDs: {'PTRANS': 3, 'TRANS': 183}
    Chain: "E"
      Number of atoms: 1188
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 147, 1188
          Classifications: {'peptide': 147}
          Link IDs: {'PTRANS': 4, 'TRANS': 142}
    Chain: "F"
      Number of atoms: 885
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 108, 885
          Classifications: {'peptide': 108}
          Link IDs: {'PTRANS': 2, 'TRANS': 105}
          Chain breaks: 2
    Chain: "G"
      Number of atoms: 1542
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 184, 1542
          Classifications: {'peptide': 184}
          Link IDs: {'PTRANS': 1, 'TRANS': 182}
    Chain: "D"
      Number of atoms: 1
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 1, 1
          Unusual residues: {' ZN': 1}
          Classifications: {'undetermined': 1}

List of CYS excluded from plausible disulfide bonds:
  (reason: may participate in coordination)
  ATOM  13842  SG  CYS D 572      72.985  72.349  83.189  1.00 61.65           S
  ATOM  13863  SG  CYS D 575      74.480  73.378  86.248  1.00 63.38           S

  Time building chain proxies: 4.22, per 1000 atoms: 0.23
  Number of scatterers: 18498
  At special positions: 0
  Unit cell: (148.24, 160.48, 118.32, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 6
    Type Number    sf(0)
     Zn      1     29.99
     S      65     16.00
     P     162     15.00
     O    3908      8.00
     N    3115      7.00
     C   11247      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=0, symmetry=0

  Automatic linking
    Parameters for automatic linking
      Linking & cutoffs
        Metal                : Auto  - 3.00
        Amino acid           : True  - 1.90
        Carbohydrate         : True  - 1.99
        Ligands              : True  - 1.99
        Small molecules      : False - 1.98
        Amino acid - RNA/DNA : False
      
  Number of custom bonds: simple=0, symmetry=0
  Time building additional restraints: 1.54
  Conformation dependent library (CDL) restraints added in 700.0 milliseconds
  
  Dynamic metal coordination
    Zn2+ tetrahedral coordination
      pdb="  ZN D 900 "
        pdb="ZN    ZN D 900 " - pdb=" SG  CYS D 575 "
        pdb="ZN    ZN D 900 " - pdb=" SG  CYS D 572 "


  3618 Ramachandran restraints generated.
    1809 Oldfield, 0 Emsley, 1809 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  3562

  Finding SS restraints...
    Secondary structure from input PDB file:
      69 helices and 19 sheets defined
      47.3% alpha, 16.7% beta
      43 base pairs and 73 stacking pairs defined.
    Time for finding SS restraints: 2.27
  Creating SS restraints...
    Processing helix  chain 'H' and resid 115 through 131
      removed outlier: 3.784A  pdb=" N   CYS H 131 " --> pdb=" O   GLU H 127 " (cutoff:3.500A)
    Processing helix  chain 'H' and resid 133 through 138
      removed outlier: 4.021A  pdb=" N   HIS H 137 " --> pdb=" O   THR H 133 " (cutoff:3.500A)
    Processing helix  chain 'H' and resid 141 through 147
    Processing helix  chain 'H' and resid 155 through 160
      removed outlier: 3.700A  pdb=" N   LEU H 159 " --> pdb=" O   ILE H 155 " (cutoff:3.500A)
      removed outlier: 3.519A  pdb=" N   LYS H 160 " --> pdb=" O   LYS H 156 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'H' and resid 155 through 160'
    Processing helix  chain 'H' and resid 162 through 167
      removed outlier: 3.530A  pdb=" N   GLN H 166 " --> pdb=" O   ASN H 162 " (cutoff:3.500A)
      removed outlier: 3.563A  pdb=" N   ILE H 167 " --> pdb=" O   LYS H 163 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'H' and resid 162 through 167'
    Processing helix  chain 'H' and resid 203 through 215
    Processing helix  chain 'H' and resid 391 through 401
      removed outlier: 4.185A  pdb=" N   VAL H 395 " --> pdb=" O   LEU H 391 " (cutoff:3.500A)
    Processing helix  chain 'H' and resid 470 through 480
      removed outlier: 4.828A  pdb=" N   GLN H 477 " --> pdb=" O   ARG H 473 " (cutoff:3.500A)
      removed outlier: 5.602A  pdb=" N   LYS H 478 " --> pdb=" O   LEU H 474 " (cutoff:3.500A)
    Processing helix  chain 'H' and resid 503 through 531
    Processing helix  chain 'A' and resid 19 through 26
      removed outlier: 3.890A  pdb=" N   VAL A  23 " --> pdb=" O   ASP A  19 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 35 through 44
    Processing helix  chain 'A' and resid 53 through 63
    Processing helix  chain 'A' and resid 88 through 100
    Processing helix  chain 'A' and resid 127 through 132
    Processing helix  chain 'A' and resid 134 through 144
    Processing helix  chain 'A' and resid 144 through 155
      removed outlier: 4.645A  pdb=" N   TYR A 150 " --> pdb=" O   GLU A 146 " (cutoff:3.500A)
      removed outlier: 4.575A  pdb=" N   ILE A 153 " --> pdb=" O   LYS A 149 " (cutoff:3.500A)
      removed outlier: 3.581A  pdb=" N   PHE A 155 " --> pdb=" O   PHE A 151 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 173 through 177
    Processing helix  chain 'A' and resid 225 through 229
      removed outlier: 3.878A  pdb=" N   GLN A 228 " --> pdb=" O   GLN A 225 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 245 through 249
    Processing helix  chain 'A' and resid 282 through 289
    Processing helix  chain 'A' and resid 300 through 319
      removed outlier: 3.562A  pdb=" N   ARG A 304 " --> pdb=" O   CYS A 300 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 322 through 331
      removed outlier: 3.845A  pdb=" N   PHE A 330 " --> pdb=" O   LEU A 326 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 336 through 350
    Processing helix  chain 'A' and resid 356 through 368
    Processing helix  chain 'A' and resid 372 through 386
      removed outlier: 4.160A  pdb=" N   ASN A 386 " --> pdb=" O   GLN A 382 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 394 through 410
      removed outlier: 3.573A  pdb=" N   PHE A 398 " --> pdb=" O   GLY A 394 " (cutoff:3.500A)
      removed outlier: 3.926A  pdb=" N   LYS A 399 " --> pdb=" O   LYS A 395 " (cutoff:3.500A)
      removed outlier: 4.458A  pdb=" N   TYR A 406 " --> pdb=" O   LEU A 402 " (cutoff:3.500A)
      removed outlier: 4.447A  pdb=" N   GLU A 407 " --> pdb=" O   GLU A 403 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 418 through 424
      removed outlier: 3.676A  pdb=" N   TYR A 422 " --> pdb=" O   LYS A 418 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 444 through 467
      removed outlier: 3.640A  pdb=" N   TYR A 448 " --> pdb=" O   GLN A 444 " (cutoff:3.500A)
      removed outlier: 4.594A  pdb=" N   ILE A 455 " --> pdb=" O   ASP A 451 " (cutoff:3.500A)
      removed outlier: 4.689A  pdb=" N   ASP A 458 " --> pdb=" O   LYS A 454 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 467 through 475
    Processing helix  chain 'A' and resid 493 through 508
      removed outlier: 3.532A  pdb=" N   GLU A 508 " --> pdb=" O   ILE A 504 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 521 through 528
    Processing helix  chain 'A' and resid 560 through 577
      removed outlier: 5.556A  pdb=" N   ASP A 567 " --> pdb=" O   GLN A 563 " (cutoff:3.500A)
      removed outlier: 5.195A  pdb=" N   SER A 568 " --> pdb=" O   ILE A 564 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 589 through 608
      removed outlier: 3.676A  pdb=" N   ILE A 593 " --> pdb=" O   ASP A 589 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 621 through 625
    Processing helix  chain 'A' and resid 627 through 637
    Processing helix  chain 'A' and resid 691 through 694
    Processing helix  chain 'A' and resid 742 through 755
    Processing helix  chain 'A' and resid 777 through 794
      removed outlier: 4.080A  pdb=" N   SER A 783 " --> pdb=" O   GLY A 779 " (cutoff:3.500A)
      removed outlier: 3.526A  pdb=" N   LEU A 789 " --> pdb=" O   TYR A 785 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 794 through 804
      removed outlier: 4.253A  pdb=" N   LYS A 798 " --> pdb=" O   THR A 794 " (cutoff:3.500A)
      removed outlier: 4.126A  pdb=" N   ASN A 799 " --> pdb=" O   GLN A 795 " (cutoff:3.500A)
      removed outlier: 4.481A  pdb=" N   GLU A 801 " --> pdb=" O   LEU A 797 " (cutoff:3.500A)
      removed outlier: 5.802A  pdb=" N   GLN A 802 " --> pdb=" O   LYS A 798 " (cutoff:3.500A)
      removed outlier: 3.828A  pdb=" N   ASN A 804 " --> pdb=" O   ALA A 800 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 823 through 842
      removed outlier: 3.579A  pdb=" N   ALA A 827 " --> pdb=" O   SER A 823 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 845 through 849
      removed outlier: 3.794A  pdb=" N   GLN A 848 " --> pdb=" O   PHE A 845 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 895 through 901
    Processing helix  chain 'A' and resid 911 through 926
      removed outlier: 3.987A  pdb=" N   LYS A 917 " --> pdb=" O   LYS A 913 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 938 through 965
      removed outlier: 3.648A  pdb=" N   MET A 955 " --> pdb=" O   LYS A 951 " (cutoff:3.500A)
      Proline residue:  A 959  - end of helix
    Processing helix  chain 'A' and resid 972 through 980
      removed outlier: 4.736A  pdb=" N   GLN A 978 " --> pdb=" O   GLN A 974 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 983 through 1009
      removed outlier: 4.013A  pdb=" N   ASN A 987 " --> pdb=" O   ASN A 983 " (cutoff:3.500A)
      removed outlier: 3.711A  pdb=" N   PHE A1009 " --> pdb=" O   CYS A1005 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1014 through 1038
      removed outlier: 3.754A  pdb=" N   LYS A1018 " --> pdb=" O   ASN A1014 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1046 through 1075
      removed outlier: 3.894A  pdb=" N   LEU A1050 " --> pdb=" O   TYR A1046 " (cutoff:3.500A)
      removed outlier: 4.340A  pdb=" N   GLN A1070 " --> pdb=" O   CYS A1066 " (cutoff:3.500A)
      removed outlier: 4.219A  pdb=" N   LEU A1071 " --> pdb=" O   LYS A1067 " (cutoff:3.500A)
      removed outlier: 3.891A  pdb=" N   GLN A1075 " --> pdb=" O   LEU A1071 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1081 through 1094
      removed outlier: 3.846A  pdb=" N   ASN A1094 " --> pdb=" O   PHE A1090 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1099 through 1103
      removed outlier: 4.354A  pdb=" N   THR A1102 " --> pdb=" O   ASP A1099 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1104 through 1109
      removed outlier: 4.342A  pdb=" N   ALA A1109 " --> pdb=" O   PRO A1105 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 516 through 526
      removed outlier: 3.793A  pdb=" N   ILE D 520 " --> pdb=" O   SER D 516 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 603 through 615
    Processing helix  chain 'D' and resid 622 through 634
      removed outlier: 3.561A  pdb=" N   GLY D 634 " --> pdb=" O   CYS D 630 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 636 through 645
    Processing helix  chain 'D' and resid 679 through 696
      removed outlier: 3.667A  pdb=" N   LYS D 685 " --> pdb=" O   LYS D 681 " (cutoff:3.500A)
    Processing helix  chain 'E' and resid 35 through 49
    Processing helix  chain 'E' and resid 110 through 123
      removed outlier: 4.205A  pdb=" N   TYR E 116 " --> pdb=" O   PHE E 112 " (cutoff:3.500A)
    Processing helix  chain 'E' and resid 153 through 175
      removed outlier: 3.871A  pdb=" N   SER E 157 " --> pdb=" O   ALA E 153 " (cutoff:3.500A)
      removed outlier: 4.502A  pdb=" N   GLY E 173 " --> pdb=" O   GLN E 169 " (cutoff:3.500A)
    Processing helix  chain 'F' and resid 15 through 22
      removed outlier: 3.874A  pdb=" N   ALA F  19 " --> pdb=" O   PHE F  15 " (cutoff:3.500A)
      removed outlier: 4.274A  pdb=" N   ARG F  22 " --> pdb=" O   MET F  18 " (cutoff:3.500A)
    Processing helix  chain 'F' and resid 99 through 111
    Processing helix  chain 'F' and resid 114 through 119
      removed outlier: 3.902A  pdb=" N   PHE F 118 " --> pdb=" O   LEU F 114 " (cutoff:3.500A)
      removed outlier: 3.528A  pdb=" N   THR F 119 " --> pdb=" O   SER F 115 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'F' and resid 114 through 119'
    Processing helix  chain 'G' and resid 2 through 7
    Processing helix  chain 'G' and resid 9 through 29
      removed outlier: 4.032A  pdb=" N   LYS G  13 " --> pdb=" O   ASN G   9 " (cutoff:3.500A)
    Processing helix  chain 'G' and resid 33 through 41
    Processing helix  chain 'G' and resid 87 through 94
      removed outlier: 3.952A  pdb=" N   LEU G  91 " --> pdb=" O   ASP G  87 " (cutoff:3.500A)
    Processing helix  chain 'G' and resid 150 through 156
      removed outlier: 3.516A  pdb=" N   ILE G 155 " --> pdb=" O   GLY G 151 " (cutoff:3.500A)
    Processing helix  chain 'G' and resid 158 through 161
    Processing helix  chain 'G' and resid 162 through 184
    Processing sheet with id=AA1, first strand: chain 'H' and resid 153 through 154
    Processing sheet with id=AA2, first strand: chain 'H' and resid 407 through 411
    Processing sheet with id=AA3, first strand: chain 'A' and resid 32 through 34
      removed outlier: 3.724A  pdb=" N   ALA A 170 " --> pdb=" O   VAL A 157 " (cutoff:3.500A)
      removed outlier: 6.607A  pdb=" N   THR A 159 " --> pdb=" O   GLN A 168 " (cutoff:3.500A)
      removed outlier: 5.373A  pdb=" N   GLN A 168 " --> pdb=" O   THR A 159 " (cutoff:3.500A)
      removed outlier: 5.703A  pdb=" N   ASN A 733 " --> pdb=" O   GLN A 168 " (cutoff:3.500A)
      removed outlier: 10.239A  pdb=" N   ALA A 170 " --> pdb=" O   ASN A 733 " (cutoff:3.500A)
    Processing sheet with id=AA4, first strand: chain 'A' and resid 32 through 34
      removed outlier: 3.724A  pdb=" N   ALA A 170 " --> pdb=" O   VAL A 157 " (cutoff:3.500A)
      removed outlier: 6.607A  pdb=" N   THR A 159 " --> pdb=" O   GLN A 168 " (cutoff:3.500A)
      removed outlier: 5.373A  pdb=" N   GLN A 168 " --> pdb=" O   THR A 159 " (cutoff:3.500A)
      removed outlier: 5.703A  pdb=" N   ASN A 733 " --> pdb=" O   GLN A 168 " (cutoff:3.500A)
      removed outlier: 10.239A  pdb=" N   ALA A 170 " --> pdb=" O   ASN A 733 " (cutoff:3.500A)
    Processing sheet with id=AA5, first strand: chain 'A' and resid 112 through 115
    Processing sheet with id=AA6, first strand: chain 'A' and resid 476 through 479
    Processing sheet with id=AA7, first strand: chain 'A' and resid 513 through 514
    Processing sheet with id=AA8, first strand: chain 'A' and resid 532 through 535
    Processing sheet with id=AA9, first strand: chain 'A' and resid 613 through 615
    Processing sheet with id=AB1, first strand: chain 'D' and resid 532 through 537
      removed outlier: 6.398A  pdb=" N   ILE D 652 " --> pdb=" O   ILE D 675 " (cutoff:3.500A)
      removed outlier: 4.282A  pdb=" N   ILE D 675 " --> pdb=" O   ILE D 652 " (cutoff:3.500A)
      removed outlier: 6.436A  pdb=" N   GLU D 654 " --> pdb=" O   LEU D 673 " (cutoff:3.500A)
      removed outlier: 3.527A  pdb=" N   ALA D 669 " --> pdb=" O   GLU D 658 " (cutoff:3.500A)
      removed outlier: 4.325A  pdb=" N   TYR D 670 " --> pdb=" O   PRO D 599 " (cutoff:3.500A)
      removed outlier: 3.583A  pdb=" N   LEU D 541 " --> pdb=" O   ALA D 649 " (cutoff:3.500A)
      removed outlier: 3.816A  pdb=" N   ALA D 649 " --> pdb=" O   LEU D 541 " (cutoff:3.500A)
    Processing sheet with id=AB2, first strand: chain 'D' and resid 552 through 554
    Processing sheet with id=AB3, first strand: chain 'D' and resid 661 through 662
    Processing sheet with id=AB4, first strand: chain 'E' and resid 31 through 33
    Processing sheet with id=AB5, first strand: chain 'E' and resid 31 through 33
      removed outlier: 5.886A  pdb=" N   LYS E 135 " --> pdb=" O   LEU E 144 " (cutoff:3.500A)
      removed outlier: 4.839A  pdb=" N   LEU E 144 " --> pdb=" O   LYS E 135 " (cutoff:3.500A)
      removed outlier: 3.965A  pdb=" N   VAL E  98 " --> pdb=" O   GLY E  87 " (cutoff:3.500A)
      removed outlier: 3.784A  pdb=" N   ILE E  85 " --> pdb=" O   ILE E 100 " (cutoff:3.500A)
    Processing sheet with id=AB6, first strand: chain 'E' and resid 58 through 59
      removed outlier: 3.800A  pdb=" N   PHE E  64 " --> pdb=" O   TYR E  58 " (cutoff:3.500A)
    Processing sheet with id=AB7, first strand: chain 'F' and resid 53 through 56
      removed outlier: 3.809A  pdb=" N   HIS F  53 " --> pdb=" O   PHE F  45 " (cutoff:3.500A)
      removed outlier: 3.746A  pdb=" N   LYS F  24 " --> pdb=" O   VAL F  77 " (cutoff:3.500A)
    Processing sheet with id=AB8, first strand: chain 'G' and resid 46 through 51
      removed outlier: 6.866A  pdb=" N   ILE G 114 " --> pdb=" O   LEU G  47 " (cutoff:3.500A)
      removed outlier: 4.718A  pdb=" N   ARG G  49 " --> pdb=" O   TYR G 112 " (cutoff:3.500A)
      removed outlier: 6.575A  pdb=" N   TYR G 112 " --> pdb=" O   ARG G  49 " (cutoff:3.500A)
      removed outlier: 5.121A  pdb=" N   SER G  51 " --> pdb=" O   TRP G 110 " (cutoff:3.500A)
      removed outlier: 7.353A  pdb=" N   TRP G 110 " --> pdb=" O   SER G  51 " (cutoff:3.500A)
      removed outlier: 15.980A  pdb=" N   LYS G  80 " --> pdb=" O   ILE G 123 " (cutoff:3.500A)
      removed outlier: 13.061A  pdb=" N   LEU G 125 " --> pdb=" O   LYS G  80 " (cutoff:3.500A)
      removed outlier: 9.104A  pdb=" N   ILE G  82 " --> pdb=" O   LEU G 125 " (cutoff:3.500A)
      removed outlier: 9.150A  pdb=" N   ILE G 127 " --> pdb=" O   ILE G  82 " (cutoff:3.500A)
      removed outlier: 7.143A  pdb=" N   ASN G  84 " --> pdb=" O   ILE G 127 " (cutoff:3.500A)
    Processing sheet with id=AB9, first strand: chain 'G' and resid 46 through 51
      removed outlier: 6.866A  pdb=" N   ILE G 114 " --> pdb=" O   LEU G  47 " (cutoff:3.500A)
      removed outlier: 4.718A  pdb=" N   ARG G  49 " --> pdb=" O   TYR G 112 " (cutoff:3.500A)
      removed outlier: 6.575A  pdb=" N   TYR G 112 " --> pdb=" O   ARG G  49 " (cutoff:3.500A)
      removed outlier: 5.121A  pdb=" N   SER G  51 " --> pdb=" O   TRP G 110 " (cutoff:3.500A)
      removed outlier: 7.353A  pdb=" N   TRP G 110 " --> pdb=" O   SER G  51 " (cutoff:3.500A)
      removed outlier: 15.980A  pdb=" N   LYS G  80 " --> pdb=" O   ILE G 123 " (cutoff:3.500A)
      removed outlier: 13.061A  pdb=" N   LEU G 125 " --> pdb=" O   LYS G  80 " (cutoff:3.500A)
      removed outlier: 9.104A  pdb=" N   ILE G  82 " --> pdb=" O   LEU G 125 " (cutoff:3.500A)
      removed outlier: 9.150A  pdb=" N   ILE G 127 " --> pdb=" O   ILE G  82 " (cutoff:3.500A)
      removed outlier: 7.143A  pdb=" N   ASN G  84 " --> pdb=" O   ILE G 127 " (cutoff:3.500A)
    Processing sheet with id=AC1, first strand: chain 'G' and resid 59 through 62
      removed outlier: 3.995A  pdb=" N   SER G 103 " --> pdb=" O   ILE G  62 " (cutoff:3.500A)
      removed outlier: 6.456A  pdb=" N   ILE G 106 " --> pdb=" O   CYS G 132 " (cutoff:3.500A)
      removed outlier: 5.390A  pdb=" N   CYS G 132 " --> pdb=" O   ILE G 106 " (cutoff:3.500A)

    731 hydrogen bonds defined for protein.
    2064 hydrogen bond angles defined for protein.
    Restraints generated for nucleic acids:
      105 hydrogen bonds
      208 hydrogen bond angles
      0 basepair planarities
      43 basepair parallelities
      73 stacking parallelities
  Total time for adding SS restraints: 4.21

  Time building geometry restraints manager: 2.07 seconds

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

  Histogram of bond lengths:
        1.21 -     1.33: 4796
        1.33 -     1.45: 4335
        1.45 -     1.57: 9620
        1.57 -     1.69: 320
        1.69 -     1.81: 97
  Bond restraints: 19168
  Sorted by residual:
  bond pdb=" CA  ASN A 465 "
       pdb=" C   ASN A 465 "
    ideal  model  delta    sigma   weight residual
    1.522  1.481  0.040 1.72e-02 3.38e+03 5.47e+00
  bond pdb=" CB  VAL A 119 "
       pdb=" CG2 VAL A 119 "
    ideal  model  delta    sigma   weight residual
    1.521  1.476  0.045 3.30e-02 9.18e+02 1.83e+00
  bond pdb=" O5'   C B  49 "
       pdb=" C5'   C B  49 "
    ideal  model  delta    sigma   weight residual
    1.420  1.439 -0.019 1.50e-02 4.44e+03 1.66e+00
  bond pdb=" CB  CYS A1001 "
       pdb=" SG  CYS A1001 "
    ideal  model  delta    sigma   weight residual
    1.808  1.767  0.041 3.30e-02 9.18e+02 1.53e+00
  bond pdb=" CB  ILE A 478 "
       pdb=" CG2 ILE A 478 "
    ideal  model  delta    sigma   weight residual
    1.521  1.481  0.040 3.30e-02 9.18e+02 1.47e+00
  ... (remaining 19163 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     1.37: 25349
        1.37 -     2.74: 1085
        2.74 -     4.11: 104
        4.11 -     5.48: 28
        5.48 -     6.85: 10
  Bond angle restraints: 26576
  Sorted by residual:
  angle pdb=" N   LYS A 657 "
        pdb=" CA  LYS A 657 "
        pdb=" C   LYS A 657 "
      ideal   model   delta    sigma   weight residual
     113.18  118.56   -5.38 1.21e+00 6.83e-01 1.97e+01
  angle pdb=" CA  ASN A 465 "
        pdb=" C   ASN A 465 "
        pdb=" N   LYS A 466 "
      ideal   model   delta    sigma   weight residual
     118.59  124.16   -5.57 1.63e+00 3.76e-01 1.17e+01
  angle pdb=" N   GLY D 596 "
        pdb=" CA  GLY D 596 "
        pdb=" C   GLY D 596 "
      ideal   model   delta    sigma   weight residual
     110.73  117.21   -6.48 1.90e+00 2.77e-01 1.16e+01
  angle pdb=" CA  TYR G  26 "
        pdb=" CB  TYR G  26 "
        pdb=" CG  TYR G  26 "
      ideal   model   delta    sigma   weight residual
     113.90  119.18   -5.28 1.80e+00 3.09e-01 8.61e+00
  angle pdb=" C   PHE G  25 "
        pdb=" N   TYR G  26 "
        pdb=" CA  TYR G  26 "
      ideal   model   delta    sigma   weight residual
     122.31  116.81    5.50 2.00e+00 2.50e-01 7.55e+00
  ... (remaining 26571 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    35.73: 11115
       35.73 -    71.45: 531
       71.45 -   107.18: 61
      107.18 -   142.91: 1
      142.91 -   178.63: 8
  Dihedral angle restraints: 11716
    sinusoidal: 6238
      harmonic: 5478
  Sorted by residual:
  dihedral pdb=" O4'   U B  17 "
           pdb=" C1'   U B  17 "
           pdb=" N1    U B  17 "
           pdb=" C2    U B  17 "
      ideal   model   delta sinusoidal    sigma   weight residual
     200.00   53.91  146.09     1      1.50e+01 4.44e-03 7.81e+01
  dihedral pdb=" O4'   C B  43 "
           pdb=" C1'   C B  43 "
           pdb=" N1    C B  43 "
           pdb=" C2    C B  43 "
      ideal   model   delta sinusoidal    sigma   weight residual
    -160.00  -26.18 -133.82     1      1.50e+01 4.44e-03 7.22e+01
  dihedral pdb=" O4'   U B  41 "
           pdb=" C1'   U B  41 "
           pdb=" N1    U B  41 "
           pdb=" C2    U B  41 "
      ideal   model   delta sinusoidal    sigma   weight residual
    -128.00   50.63 -178.63     1      1.70e+01 3.46e-03 6.64e+01
  ... (remaining 11713 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.047: 2334
       0.047 -    0.094: 604
       0.094 -    0.141: 112
       0.141 -    0.188: 14
       0.188 -    0.234: 1
  Chirality restraints: 3065
  Sorted by residual:
  chirality pdb=" CA  LYS A 657 "
            pdb=" N   LYS A 657 "
            pdb=" C   LYS A 657 "
            pdb=" CB  LYS A 657 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.28    0.23 2.00e-01 2.50e+01 1.37e+00
  chirality pdb=" C3'   C B  49 "
            pdb=" C4'   C B  49 "
            pdb=" O3'   C B  49 "
            pdb=" C2'   C B  49 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.48   -2.64    0.17 2.00e-01 2.50e+01 6.97e-01
  chirality pdb=" CB  ILE H 464 "
            pdb=" CA  ILE H 464 "
            pdb=" CG1 ILE H 464 "
            pdb=" CG2 ILE H 464 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.64    2.48    0.16 2.00e-01 2.50e+01 6.51e-01
  ... (remaining 3062 not shown)

  Planarity restraints: 2809
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C1'  DG C  17 "    0.015 2.00e-02 2.50e+03   1.54e-02 7.10e+00
        pdb=" N9   DG C  17 "   -0.012 2.00e-02 2.50e+03
        pdb=" C8   DG C  17 "   -0.004 2.00e-02 2.50e+03
        pdb=" N7   DG C  17 "    0.000 2.00e-02 2.50e+03
        pdb=" C5   DG C  17 "    0.001 2.00e-02 2.50e+03
        pdb=" C6   DG C  17 "    0.001 2.00e-02 2.50e+03
        pdb=" O6   DG C  17 "   -0.001 2.00e-02 2.50e+03
        pdb=" N1   DG C  17 "    0.024 2.00e-02 2.50e+03
        pdb=" C2   DG C  17 "   -0.041 2.00e-02 2.50e+03
        pdb=" N2   DG C  17 "    0.012 2.00e-02 2.50e+03
        pdb=" N3   DG C  17 "    0.000 2.00e-02 2.50e+03
        pdb=" C4   DG C  17 "    0.005 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   ILE A 536 "   -0.033 5.00e-02 4.00e+02   5.06e-02 4.09e+00
        pdb=" N   PRO A 537 "    0.088 5.00e-02 4.00e+02
        pdb=" CA  PRO A 537 "   -0.026 5.00e-02 4.00e+02
        pdb=" CD  PRO A 537 "   -0.028 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  ASN A 656 "   -0.010 2.00e-02 2.50e+03   1.96e-02 3.84e+00
        pdb=" C   ASN A 656 "    0.034 2.00e-02 2.50e+03
        pdb=" O   ASN A 656 "   -0.013 2.00e-02 2.50e+03
        pdb=" N   LYS A 657 "   -0.011 2.00e-02 2.50e+03
  ... (remaining 2806 not shown)

  Histogram of nonbonded interaction distances:
        2.16 -     2.71: 914
        2.71 -     3.26: 18684
        3.26 -     3.80: 29429
        3.80 -     4.35: 36553
        4.35 -     4.90: 58013
  Nonbonded interactions: 143593
  Sorted by model distance:
  nonbonded pdb=" N   CYS D 575 "
            pdb="ZN    ZN D 900 "
     model   vdw
     2.160 2.310
  nonbonded pdb=" OG  SER A 823 "
            pdb=" OD1 ASN A 826 "
     model   vdw
     2.198 3.040
  nonbonded pdb=" OP1   A B 136 "
            pdb=" OG  SER A 972 "
     model   vdw
     2.202 3.040
  nonbonded pdb=" OE1 GLN A1008 "
            pdb=" OH  TYR A1025 "
     model   vdw
     2.206 3.040
  nonbonded pdb=" O   PHE A 525 "
            pdb=" NZ  LYS A 555 "
     model   vdw
     2.213 3.120
  ... (remaining 143588 not shown)

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

  No NCS relation were found !!!

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

Found NCS groups:
  found none.
Set up NCS constraints
  No NCS constraints will be used in refinement.
Set refine NCS operators
Adjust number of macro_cycles
  Number of macro_cycles: 10
Reset NCS operators
Extract rigid body selections
Check and reset occupancies
  Occupancies: min=1.00 max=1.00 mean=1.00
Load rotamer database and sin/cos tables
Set ADP refinement strategy
  ADPs will be refined as group one per residue
Make a string to write initial .geo file
Internal consistency checks
Time:
  Set random seed:                         0.000
  Set model cs if undefined:               0.000
  Decide on map wrapping:                  0.000
  Normalize map: mean=0, sd=1:             1.040
  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:          0.250
  Check model and map are aligned:         0.050
  Set scattering table:                    0.050
  Process input model:                     22.140
  Find NCS groups from input model:        0.140
  Set up NCS constraints:                  0.040
  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:             0.010
  Load rotamer database and sin/cos tables:1.230
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   24.960
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7427
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      :  0.005   0.225  19170  Z= 0.197
  Angle     :  0.634   6.849  26576  Z= 0.358
  Chirality :  0.043   0.234   3065
  Planarity :  0.004   0.051   2809
  Dihedral  : 19.411 178.633   8154
  Min Nonbonded Distance : 2.160

Molprobity Statistics.
  All-atom Clashscore : 11.75
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.69 %
    Favored  : 93.31 %
  Rotamer:
    Outliers :  0.06 %
    Allowed  :  4.60 %
    Favored  : 95.34 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -3.71 (0.17), residues: 1809
  helix: -1.80 (0.16), residues: 731
  sheet: -2.61 (0.30), residues: 242
  loop : -3.01 (0.18), residues: 836

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG A 237 
 TYR   0.021   0.002   TYR G  26 
 PHE   0.022   0.002   PHE D 662 
 TRP   0.023   0.003   TRP A 604 
 HIS   0.006   0.001   HIS A 949 

Details of bonding type rmsd
  covalent geometry    : bond        0.00405 (19168)
  covalent geometry    : angle       0.63416 (26576)
  hydrogen bonds       : bond        0.13051 (  806)
  hydrogen bonds       : angle       6.45986 ( 2272)
  metal coordination   : bond        0.20586 (    2)

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

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

  3618 Ramachandran restraints generated.
    1809 Oldfield, 0 Emsley, 1809 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3618 Ramachandran restraints generated.
    1809 Oldfield, 0 Emsley, 1809 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  336 residues out of total 1741 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 335
  time to evaluate  : 0.597 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: F   15 PHE cc_start: 0.4481 (t80) cc_final: 0.4007 (t80)
REVERT: F   21 PHE cc_start: 0.7468 (m-10) cc_final: 0.7124 (m-10)
REVERT: F  120 ASP cc_start: 0.5892 (p0) cc_final: 0.5201 (p0)
REVERT: G  130 MET cc_start: 0.7285 (mtm) cc_final: 0.7051 (mtm)
  outliers start: 1
  outliers final: 0
  residues processed: 335
  average time/residue: 0.1356
  time to fit residues: 70.2190
Evaluate side-chains
  198 residues out of total 1741 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 198
  time to evaluate  : 0.971 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 196
   random chunks:
   chunk 98 optimal weight:    5.9990
   chunk 194 optimal weight:    0.6980
   chunk 107 optimal weight:    0.6980
   chunk 10 optimal weight:    9.9990
   chunk 66 optimal weight:    4.9990
   chunk 130 optimal weight:    0.8980
   chunk 124 optimal weight:    0.7980
   chunk 103 optimal weight:    2.9990
   chunk 77 optimal weight:    0.5980
   chunk 122 optimal weight:    2.9990
   chunk 91 optimal weight:    3.9990
   overall best weight:    0.7380

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

Flipped N/Q/H residues before XYZ refinement:
H 468 ASN
H 484 ASN
H 485 ASN
** A  12 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 129 GLN
A 248 ASN
A 320 ASN
A 324 ASN
** A 349 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 364 ASN
A 440 GLN
A 482 HIS
A 733 ASN
A 747 ASN
A 748 HIS
A 756 ASN
A 826 ASN
A 835 GLN
A 839 ASN
A 841 ASN
A 872 ASN
A 901 GLN
A 904 ASN
A 918 ASN
D 531 GLN
D 629 ASN
D 633 ASN
D 635 GLN
E 159 HIS
** F  53 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
F 107 HIS
** F 110 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
G  34 GLN
** G  84 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** G 109 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
G 177 GLN

Total number of N/Q/H flips: 30

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4190 r_free = 0.4190 target = 0.150448 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.3781 r_free = 0.3781 target = 0.119777 restraints weight = 35685.596|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 26)----------------|
| r_work = 0.3764 r_free = 0.3764 target = 0.119378 restraints weight = 41782.716|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 27)----------------|
| r_work = 0.3776 r_free = 0.3776 target = 0.120619 restraints weight = 40231.437|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 25)----------------|
| r_work = 0.3779 r_free = 0.3779 target = 0.120917 restraints weight = 27817.212|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 23)----------------|
| r_work = 0.3782 r_free = 0.3782 target = 0.121194 restraints weight = 26770.671|
|-----------------------------------------------------------------------------|
r_work (final): 0.3773
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7479
moved from start:          0.1790

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.037  19170  Z= 0.129
  Angle     :  0.580   7.882  26576  Z= 0.309
  Chirality :  0.040   0.157   3065
  Planarity :  0.004   0.045   2809
  Dihedral  : 20.096 179.212   4331
  Min Nonbonded Distance : 2.183

Molprobity Statistics.
  All-atom Clashscore : 9.64
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.81 %
    Favored  : 95.19 %
  Rotamer:
    Outliers :  1.70 %
    Allowed  : 11.87 %
    Favored  : 86.43 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -1.97 (0.19), residues: 1809
  helix: -0.00 (0.18), residues: 747
  sheet: -2.00 (0.32), residues: 239
  loop : -2.34 (0.20), residues: 823

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.000   ARG E 158 
 TYR   0.029   0.001   TYR G  26 
 PHE   0.027   0.002   PHE H 524 
 TRP   0.022   0.002   TRP A 604 
 HIS   0.006   0.001   HIS F  53 

Details of bonding type rmsd
  covalent geometry    : bond        0.00285 (19168)
  covalent geometry    : angle       0.57991 (26576)
  hydrogen bonds       : bond        0.04507 (  806)
  hydrogen bonds       : angle       4.72650 ( 2272)
  metal coordination   : bond        0.00238 (    2)

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

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

  3618 Ramachandran restraints generated.
    1809 Oldfield, 0 Emsley, 1809 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3618 Ramachandran restraints generated.
    1809 Oldfield, 0 Emsley, 1809 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  270 residues out of total 1741 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 28
    poor density    : 242
  time to evaluate  : 0.693 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: H  473 ARG cc_start: 0.5910 (tpp-160) cc_final: 0.5492 (ptp-170)
REVERT: H  497 ASP cc_start: 0.6461 (t0) cc_final: 0.5953 (m-30)
REVERT: A   71 LEU cc_start: 0.9144 (mt) cc_final: 0.8942 (mp)
REVERT: A  285 ILE cc_start: 0.7462 (mt) cc_final: 0.7213 (mm)
REVERT: A  578 MET cc_start: 0.7258 (mtp) cc_final: 0.6673 (mmp)
REVERT: A  790 GLU cc_start: 0.6046 (pt0) cc_final: 0.5815 (pt0)
REVERT: A  991 ASP cc_start: 0.7355 (t0) cc_final: 0.6944 (m-30)
REVERT: A 1100 ILE cc_start: 0.6804 (OUTLIER) cc_final: 0.6446 (tp)
REVERT: D  654 GLU cc_start: 0.5315 (tt0) cc_final: 0.5093 (tt0)
REVERT: F   59 TYR cc_start: 0.4923 (t80) cc_final: 0.3735 (t80)
REVERT: G  130 MET cc_start: 0.7528 (mtm) cc_final: 0.7251 (mtm)
  outliers start: 28
  outliers final: 14
  residues processed: 259
  average time/residue: 0.1308
  time to fit residues: 52.7020
Evaluate side-chains
  213 residues out of total 1741 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 198
  time to evaluate  : 0.619 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain H residue  380 LEU
Chi-restraints excluded: chain H residue  516 PHE
Chi-restraints excluded: chain A residue   33 VAL
Chi-restraints excluded: chain A residue   37 TYR
Chi-restraints excluded: chain A residue  169 VAL
Chi-restraints excluded: chain A residue  241 VAL
Chi-restraints excluded: chain A residue  420 LEU
Chi-restraints excluded: chain A residue  877 ILE
Chi-restraints excluded: chain A residue  888 ILE
Chi-restraints excluded: chain A residue 1006 TYR
Chi-restraints excluded: chain A residue 1100 ILE
Chi-restraints excluded: chain D residue  610 LEU
Chi-restraints excluded: chain D residue  691 LEU
Chi-restraints excluded: chain G residue   79 VAL
Chi-restraints excluded: chain G residue  105 VAL
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 196
   random chunks:
   chunk 110 optimal weight:    1.9990
   chunk 165 optimal weight:    2.9990
   chunk 143 optimal weight:    1.9990
   chunk 106 optimal weight:    2.9990
   chunk 84 optimal weight:    0.9990
   chunk 103 optimal weight:    1.9990
   chunk 51 optimal weight:    3.9990
   chunk 62 optimal weight:    6.9990
   chunk 67 optimal weight:    1.9990
   chunk 21 optimal weight:   20.0000
   chunk 164 optimal weight:    2.9990
   overall best weight:    1.7990

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

Flipped N/Q/H residues before XYZ refinement:
A  12 GLN
A 349 GLN
A 636 ASN
E 114 GLN
E 151 ASN
F  53 HIS
** G  84 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** G 109 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 6

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4145 r_free = 0.4145 target = 0.146832 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.3727 r_free = 0.3727 target = 0.115993 restraints weight = 35892.554|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 26)----------------|
| r_work = 0.3709 r_free = 0.3709 target = 0.115549 restraints weight = 46000.414|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 24)----------------|
| r_work = 0.3721 r_free = 0.3721 target = 0.116645 restraints weight = 46992.997|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 25)----------------|
| r_work = 0.3727 r_free = 0.3727 target = 0.117221 restraints weight = 30714.067|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 23)----------------|
| r_work = 0.3730 r_free = 0.3730 target = 0.117544 restraints weight = 28686.056|
|-----------------------------------------------------------------------------|
r_work (final): 0.3724
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7566
moved from start:          0.2067

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.046  19170  Z= 0.196
  Angle     :  0.626   8.451  26576  Z= 0.332
  Chirality :  0.042   0.157   3065
  Planarity :  0.004   0.060   2809
  Dihedral  : 20.061 179.556   4331
  Min Nonbonded Distance : 2.096

Molprobity Statistics.
  All-atom Clashscore : 10.75
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.03 %
    Favored  : 93.97 %
  Rotamer:
    Outliers :  2.60 %
    Allowed  : 13.63 %
    Favored  : 83.77 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -1.63 (0.19), residues: 1809
  helix:  0.36 (0.19), residues: 748
  sheet: -2.09 (0.31), residues: 253
  loop : -2.13 (0.20), residues: 808

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.000   ARG A 812 
 TYR   0.026   0.002   TYR G  26 
 PHE   0.060   0.002   PHE H 524 
 TRP   0.021   0.002   TRP A 604 
 HIS   0.007   0.001   HIS A 949 

Details of bonding type rmsd
  covalent geometry    : bond        0.00453 (19168)
  covalent geometry    : angle       0.62556 (26576)
  hydrogen bonds       : bond        0.04931 (  806)
  hydrogen bonds       : angle       4.76145 ( 2272)
  metal coordination   : bond        0.00168 (    2)

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

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

  3618 Ramachandran restraints generated.
    1809 Oldfield, 0 Emsley, 1809 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3618 Ramachandran restraints generated.
    1809 Oldfield, 0 Emsley, 1809 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  248 residues out of total 1741 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 43
    poor density    : 205
  time to evaluate  : 0.458 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: H  473 ARG cc_start: 0.5897 (tpp-160) cc_final: 0.5521 (ptp-170)
REVERT: H  484 ASN cc_start: 0.6611 (p0) cc_final: 0.6381 (p0)
REVERT: A  228 GLN cc_start: 0.8465 (mm110) cc_final: 0.8149 (tt0)
REVERT: A  285 ILE cc_start: 0.7241 (mt) cc_final: 0.6932 (mm)
REVERT: A  575 LEU cc_start: 0.8267 (tp) cc_final: 0.7955 (tt)
REVERT: D  586 MET cc_start: 0.7811 (ppp) cc_final: 0.7584 (ppp)
REVERT: D  654 GLU cc_start: 0.5404 (tt0) cc_final: 0.5124 (tt0)
REVERT: E  126 ARG cc_start: 0.4791 (mmt180) cc_final: 0.4504 (mmt180)
REVERT: F   21 PHE cc_start: 0.8076 (m-80) cc_final: 0.7803 (m-80)
REVERT: G    1 MET cc_start: 0.8685 (tpp) cc_final: 0.8481 (tpp)
  outliers start: 43
  outliers final: 31
  residues processed: 228
  average time/residue: 0.1289
  time to fit residues: 46.4154
Evaluate side-chains
  215 residues out of total 1741 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 31
    poor density    : 184
  time to evaluate  : 0.606 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain H residue  380 LEU
Chi-restraints excluded: chain H residue  396 VAL
Chi-restraints excluded: chain H residue  464 ILE
Chi-restraints excluded: chain H residue  516 PHE
Chi-restraints excluded: chain A residue   33 VAL
Chi-restraints excluded: chain A residue   37 TYR
Chi-restraints excluded: chain A residue  169 VAL
Chi-restraints excluded: chain A residue  241 VAL
Chi-restraints excluded: chain A residue  289 LEU
Chi-restraints excluded: chain A residue  311 THR
Chi-restraints excluded: chain A residue  398 PHE
Chi-restraints excluded: chain A residue  420 LEU
Chi-restraints excluded: chain A residue  807 ILE
Chi-restraints excluded: chain A residue  809 LEU
Chi-restraints excluded: chain A residue  877 ILE
Chi-restraints excluded: chain A residue  950 SER
Chi-restraints excluded: chain A residue 1006 TYR
Chi-restraints excluded: chain D residue  520 ILE
Chi-restraints excluded: chain D residue  610 LEU
Chi-restraints excluded: chain D residue  619 HIS
Chi-restraints excluded: chain D residue  686 TYR
Chi-restraints excluded: chain D residue  691 LEU
Chi-restraints excluded: chain E residue   98 VAL
Chi-restraints excluded: chain E residue  150 VAL
Chi-restraints excluded: chain F residue   25 LYS
Chi-restraints excluded: chain F residue   53 HIS
Chi-restraints excluded: chain F residue   67 THR
Chi-restraints excluded: chain F residue   78 LEU
Chi-restraints excluded: chain F residue   79 ASN
Chi-restraints excluded: chain G residue    3 LEU
Chi-restraints excluded: chain G residue   10 ILE
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 196
   random chunks:
   chunk 169 optimal weight:    4.9990
   chunk 76 optimal weight:    0.6980
   chunk 178 optimal weight:    0.6980
   chunk 53 optimal weight:    0.6980
   chunk 102 optimal weight:    0.7980
   chunk 150 optimal weight:    4.9990
   chunk 124 optimal weight:    0.9990
   chunk 179 optimal weight:    0.8980
   chunk 57 optimal weight:    0.6980
   chunk 134 optimal weight:    0.6980
   chunk 125 optimal weight:    0.9990
   overall best weight:    0.6980

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

Flipped N/Q/H residues before XYZ refinement:
** A  12 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 109 GLN
A 349 GLN
F  53 HIS
G  84 ASN

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4187 r_free = 0.4187 target = 0.150383 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.3782 r_free = 0.3782 target = 0.119960 restraints weight = 35821.271|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 26)----------------|
| r_work = 0.3766 r_free = 0.3766 target = 0.119718 restraints weight = 45004.925|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 27)----------------|
| r_work = 0.3778 r_free = 0.3778 target = 0.120937 restraints weight = 41928.146|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 25)----------------|
| r_work = 0.3785 r_free = 0.3785 target = 0.121624 restraints weight = 28054.381|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 23)----------------|
| r_work = 0.3787 r_free = 0.3787 target = 0.121885 restraints weight = 26936.755|
|-----------------------------------------------------------------------------|
r_work (final): 0.3779
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7471
moved from start:          0.2482

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.040  19170  Z= 0.118
  Angle     :  0.550   9.022  26576  Z= 0.292
  Chirality :  0.039   0.150   3065
  Planarity :  0.003   0.042   2809
  Dihedral  : 19.902 179.349   4331
  Min Nonbonded Distance : 2.180

Molprobity Statistics.
  All-atom Clashscore : 9.39
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.76 %
    Favored  : 96.24 %
  Rotamer:
    Outliers :  2.18 %
    Allowed  : 15.20 %
    Favored  : 82.62 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -1.02 (0.20), residues: 1809
  helix:  0.90 (0.19), residues: 757
  sheet: -1.72 (0.31), residues: 258
  loop : -1.89 (0.21), residues: 794

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.000   ARG A 812 
 TYR   0.024   0.001   TYR G  26 
 PHE   0.060   0.001   PHE H 524 
 TRP   0.015   0.001   TRP A 604 
 HIS   0.021   0.001   HIS F  53 

Details of bonding type rmsd
  covalent geometry    : bond        0.00263 (19168)
  covalent geometry    : angle       0.55006 (26576)
  hydrogen bonds       : bond        0.04152 (  806)
  hydrogen bonds       : angle       4.38928 ( 2272)
  metal coordination   : bond        0.00070 (    2)

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

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

  3618 Ramachandran restraints generated.
    1809 Oldfield, 0 Emsley, 1809 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3618 Ramachandran restraints generated.
    1809 Oldfield, 0 Emsley, 1809 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  261 residues out of total 1741 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 36
    poor density    : 225
  time to evaluate  : 0.613 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: H  473 ARG cc_start: 0.5871 (tpp-160) cc_final: 0.5450 (ptp-170)
REVERT: H  484 ASN cc_start: 0.6479 (p0) cc_final: 0.6110 (p0)
REVERT: A  560 ASN cc_start: 0.7585 (p0) cc_final: 0.7172 (p0)
REVERT: A  578 MET cc_start: 0.7117 (mtp) cc_final: 0.6611 (mmp)
REVERT: D  586 MET cc_start: 0.7776 (ppp) cc_final: 0.7547 (ppp)
REVERT: G  130 MET cc_start: 0.7368 (mtm) cc_final: 0.7134 (mtm)
  outliers start: 36
  outliers final: 27
  residues processed: 245
  average time/residue: 0.1290
  time to fit residues: 50.1241
Evaluate side-chains
  212 residues out of total 1741 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 27
    poor density    : 185
  time to evaluate  : 0.605 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain H residue  380 LEU
Chi-restraints excluded: chain H residue  464 ILE
Chi-restraints excluded: chain H residue  516 PHE
Chi-restraints excluded: chain A residue   21 LEU
Chi-restraints excluded: chain A residue   33 VAL
Chi-restraints excluded: chain A residue   72 VAL
Chi-restraints excluded: chain A residue  169 VAL
Chi-restraints excluded: chain A residue  241 VAL
Chi-restraints excluded: chain A residue  289 LEU
Chi-restraints excluded: chain A residue  311 THR
Chi-restraints excluded: chain A residue  420 LEU
Chi-restraints excluded: chain A residue  430 ASP
Chi-restraints excluded: chain A residue  732 ILE
Chi-restraints excluded: chain A residue  777 ILE
Chi-restraints excluded: chain A residue  877 ILE
Chi-restraints excluded: chain A residue 1006 TYR
Chi-restraints excluded: chain A residue 1100 ILE
Chi-restraints excluded: chain D residue  610 LEU
Chi-restraints excluded: chain D residue  686 TYR
Chi-restraints excluded: chain E residue   90 SER
Chi-restraints excluded: chain F residue   25 LYS
Chi-restraints excluded: chain F residue   62 VAL
Chi-restraints excluded: chain F residue   78 LEU
Chi-restraints excluded: chain F residue   85 CYS
Chi-restraints excluded: chain G residue   10 ILE
Chi-restraints excluded: chain G residue  105 VAL
Chi-restraints excluded: chain G residue  133 ILE
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 196
   random chunks:
   chunk 73 optimal weight:    0.8980
   chunk 9 optimal weight:   10.0000
   chunk 63 optimal weight:    0.9980
   chunk 15 optimal weight:    6.9990
   chunk 183 optimal weight:    3.9990
   chunk 184 optimal weight:    3.9990
   chunk 81 optimal weight:    1.9990
   chunk 97 optimal weight:    0.3980
   chunk 121 optimal weight:    0.9980
   chunk 162 optimal weight:    3.9990
   chunk 194 optimal weight:    0.8980
   overall best weight:    0.8380

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

Flipped N/Q/H residues before XYZ refinement:
H 477 GLN
** A  12 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** G 109 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** G 177 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4183 r_free = 0.4183 target = 0.150055 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.3779 r_free = 0.3779 target = 0.119531 restraints weight = 35473.758|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 26)----------------|
| r_work = 0.3780 r_free = 0.3780 target = 0.120476 restraints weight = 40567.761|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 27)----------------|
| r_work = 0.3786 r_free = 0.3786 target = 0.121264 restraints weight = 39278.396|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 23)----------------|
| r_work = 0.3789 r_free = 0.3789 target = 0.121561 restraints weight = 26560.730|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 23)----------------|
| r_work = 0.3793 r_free = 0.3793 target = 0.121907 restraints weight = 25759.345|
|-----------------------------------------------------------------------------|
r_work (final): 0.3785
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7461
moved from start:          0.2762

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.064  19170  Z= 0.126
  Angle     :  0.563   9.402  26576  Z= 0.295
  Chirality :  0.039   0.176   3065
  Planarity :  0.003   0.045   2809
  Dihedral  : 19.757 178.840   4331
  Min Nonbonded Distance : 2.169

Molprobity Statistics.
  All-atom Clashscore : 9.45
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.70 %
    Favored  : 95.30 %
  Rotamer:
    Outliers :  2.42 %
    Allowed  : 17.38 %
    Favored  : 80.19 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -0.78 (0.20), residues: 1809
  helix:  1.14 (0.19), residues: 751
  sheet: -1.58 (0.30), residues: 264
  loop : -1.78 (0.21), residues: 794

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.009   0.000   ARG E 158 
 TYR   0.020   0.001   TYR G  26 
 PHE   0.053   0.001   PHE H 524 
 TRP   0.014   0.001   TRP A 604 
 HIS   0.006   0.001   HIS F  53 

Details of bonding type rmsd
  covalent geometry    : bond        0.00287 (19168)
  covalent geometry    : angle       0.56277 (26576)
  hydrogen bonds       : bond        0.04154 (  806)
  hydrogen bonds       : angle       4.30349 ( 2272)
  metal coordination   : bond        0.00074 (    2)

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

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

  3618 Ramachandran restraints generated.
    1809 Oldfield, 0 Emsley, 1809 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3618 Ramachandran restraints generated.
    1809 Oldfield, 0 Emsley, 1809 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  244 residues out of total 1741 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 40
    poor density    : 204
  time to evaluate  : 0.614 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: H  484 ASN cc_start: 0.6291 (p0) cc_final: 0.5834 (p0)
REVERT: A  560 ASN cc_start: 0.7562 (p0) cc_final: 0.7151 (p0)
REVERT: A  575 LEU cc_start: 0.8195 (tp) cc_final: 0.7936 (tt)
REVERT: A  578 MET cc_start: 0.6835 (mtp) cc_final: 0.6428 (mmp)
  outliers start: 40
  outliers final: 34
  residues processed: 225
  average time/residue: 0.1309
  time to fit residues: 46.7527
Evaluate side-chains
  219 residues out of total 1741 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 34
    poor density    : 185
  time to evaluate  : 0.644 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain H residue  380 LEU
Chi-restraints excluded: chain H residue  464 ILE
Chi-restraints excluded: chain H residue  512 ASN
Chi-restraints excluded: chain H residue  516 PHE
Chi-restraints excluded: chain A residue   21 LEU
Chi-restraints excluded: chain A residue   33 VAL
Chi-restraints excluded: chain A residue  112 THR
Chi-restraints excluded: chain A residue  169 VAL
Chi-restraints excluded: chain A residue  241 VAL
Chi-restraints excluded: chain A residue  289 LEU
Chi-restraints excluded: chain A residue  420 LEU
Chi-restraints excluded: chain A residue  732 ILE
Chi-restraints excluded: chain A residue  792 GLU
Chi-restraints excluded: chain A residue  807 ILE
Chi-restraints excluded: chain A residue  809 LEU
Chi-restraints excluded: chain A residue  877 ILE
Chi-restraints excluded: chain A residue  950 SER
Chi-restraints excluded: chain A residue  962 THR
Chi-restraints excluded: chain A residue 1006 TYR
Chi-restraints excluded: chain D residue  610 LEU
Chi-restraints excluded: chain D residue  619 HIS
Chi-restraints excluded: chain D residue  686 TYR
Chi-restraints excluded: chain E residue  150 VAL
Chi-restraints excluded: chain F residue   25 LYS
Chi-restraints excluded: chain F residue   62 VAL
Chi-restraints excluded: chain F residue   67 THR
Chi-restraints excluded: chain F residue   78 LEU
Chi-restraints excluded: chain F residue   79 ASN
Chi-restraints excluded: chain F residue   85 CYS
Chi-restraints excluded: chain G residue    3 LEU
Chi-restraints excluded: chain G residue   10 ILE
Chi-restraints excluded: chain G residue   40 MET
Chi-restraints excluded: chain G residue   79 VAL
Chi-restraints excluded: chain G residue  105 VAL
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 196
   random chunks:
   chunk 170 optimal weight:    0.8980
   chunk 34 optimal weight:    0.0970
   chunk 127 optimal weight:    0.5980
   chunk 15 optimal weight:    6.9990
   chunk 130 optimal weight:    2.9990
   chunk 179 optimal weight:    0.9990
   chunk 48 optimal weight:    2.9990
   chunk 168 optimal weight:    0.9980
   chunk 192 optimal weight:    4.9990
   chunk 129 optimal weight:    0.7980
   chunk 187 optimal weight:    0.5980
   overall best weight:    0.5978

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

Flipped N/Q/H residues before XYZ refinement:
D 584 HIS
F  20 GLN
** G 109 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4202 r_free = 0.4202 target = 0.151575 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.3810 r_free = 0.3810 target = 0.122263 restraints weight = 35420.736|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 24)----------------|
| r_work = 0.3793 r_free = 0.3793 target = 0.121816 restraints weight = 38962.510|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 27)----------------|
| r_work = 0.3801 r_free = 0.3801 target = 0.122718 restraints weight = 40038.999|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 25)----------------|
| r_work = 0.3806 r_free = 0.3806 target = 0.123158 restraints weight = 29282.510|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 23)----------------|
| r_work = 0.3816 r_free = 0.3816 target = 0.124102 restraints weight = 25906.836|
|-----------------------------------------------------------------------------|
r_work (final): 0.3810
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7424
moved from start:          0.3063

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.037  19170  Z= 0.110
  Angle     :  0.543  11.019  26576  Z= 0.283
  Chirality :  0.038   0.157   3065
  Planarity :  0.003   0.046   2809
  Dihedral  : 19.638 179.965   4331
  Min Nonbonded Distance : 2.204

Molprobity Statistics.
  All-atom Clashscore : 9.02
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.76 %
    Favored  : 96.24 %
  Rotamer:
    Outliers :  2.73 %
    Allowed  : 17.38 %
    Favored  : 79.89 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -0.47 (0.20), residues: 1809
  helix:  1.36 (0.19), residues: 754
  sheet: -1.48 (0.30), residues: 270
  loop : -1.55 (0.21), residues: 785

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.000   ARG E 158 
 TYR   0.016   0.001   TYR G  26 
 PHE   0.048   0.001   PHE H 524 
 TRP   0.012   0.001   TRP A 604 
 HIS   0.003   0.001   HIS A 949 

Details of bonding type rmsd
  covalent geometry    : bond        0.00247 (19168)
  covalent geometry    : angle       0.54300 (26576)
  hydrogen bonds       : bond        0.03857 (  806)
  hydrogen bonds       : angle       4.15233 ( 2272)
  metal coordination   : bond        0.00068 (    2)

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

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

  3618 Ramachandran restraints generated.
    1809 Oldfield, 0 Emsley, 1809 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3618 Ramachandran restraints generated.
    1809 Oldfield, 0 Emsley, 1809 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  248 residues out of total 1741 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 45
    poor density    : 203
  time to evaluate  : 0.680 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: H  484 ASN cc_start: 0.6410 (p0) cc_final: 0.5925 (p0)
REVERT: H  497 ASP cc_start: 0.6103 (t0) cc_final: 0.5840 (m-30)
REVERT: A   68 GLU cc_start: 0.6696 (tm-30) cc_final: 0.6454 (tm-30)
REVERT: A  578 MET cc_start: 0.6770 (mtp) cc_final: 0.6377 (mmp)
REVERT: D  647 ASP cc_start: 0.8274 (m-30) cc_final: 0.8063 (m-30)
REVERT: D  650 ARG cc_start: 0.7155 (mmm160) cc_final: 0.6921 (mmm-85)
REVERT: G  136 ILE cc_start: 0.9189 (mp) cc_final: 0.8987 (pt)
  outliers start: 45
  outliers final: 39
  residues processed: 229
  average time/residue: 0.1292
  time to fit residues: 47.3491
Evaluate side-chains
  221 residues out of total 1741 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 39
    poor density    : 182
  time to evaluate  : 0.514 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain H residue  380 LEU
Chi-restraints excluded: chain H residue  396 VAL
Chi-restraints excluded: chain H residue  464 ILE
Chi-restraints excluded: chain H residue  516 PHE
Chi-restraints excluded: chain A residue   21 LEU
Chi-restraints excluded: chain A residue   33 VAL
Chi-restraints excluded: chain A residue   37 TYR
Chi-restraints excluded: chain A residue  112 THR
Chi-restraints excluded: chain A residue  169 VAL
Chi-restraints excluded: chain A residue  241 VAL
Chi-restraints excluded: chain A residue  289 LEU
Chi-restraints excluded: chain A residue  324 ASN
Chi-restraints excluded: chain A residue  393 LEU
Chi-restraints excluded: chain A residue  420 LEU
Chi-restraints excluded: chain A residue  430 ASP
Chi-restraints excluded: chain A residue  732 ILE
Chi-restraints excluded: chain A residue  777 ILE
Chi-restraints excluded: chain A residue  792 GLU
Chi-restraints excluded: chain A residue  807 ILE
Chi-restraints excluded: chain A residue  809 LEU
Chi-restraints excluded: chain A residue  877 ILE
Chi-restraints excluded: chain A residue  888 ILE
Chi-restraints excluded: chain A residue  962 THR
Chi-restraints excluded: chain A residue 1006 TYR
Chi-restraints excluded: chain A residue 1100 ILE
Chi-restraints excluded: chain D residue  619 HIS
Chi-restraints excluded: chain D residue  686 TYR
Chi-restraints excluded: chain E residue  150 VAL
Chi-restraints excluded: chain F residue   14 LEU
Chi-restraints excluded: chain F residue   20 GLN
Chi-restraints excluded: chain F residue   25 LYS
Chi-restraints excluded: chain F residue   62 VAL
Chi-restraints excluded: chain F residue   67 THR
Chi-restraints excluded: chain F residue   85 CYS
Chi-restraints excluded: chain G residue   10 ILE
Chi-restraints excluded: chain G residue   40 MET
Chi-restraints excluded: chain G residue   42 VAL
Chi-restraints excluded: chain G residue   79 VAL
Chi-restraints excluded: chain G residue  105 VAL
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 196
   random chunks:
   chunk 13 optimal weight:    8.9990
   chunk 26 optimal weight:    7.9990
   chunk 70 optimal weight:    0.2980
   chunk 195 optimal weight:    4.9990
   chunk 145 optimal weight:    4.9990
   chunk 182 optimal weight:    0.4980
   chunk 27 optimal weight:    0.7980
   chunk 115 optimal weight:    1.9990
   chunk 163 optimal weight:    7.9990
   chunk 114 optimal weight:    7.9990
   chunk 86 optimal weight:    0.5980
   overall best weight:    0.8382

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

Flipped N/Q/H residues before XYZ refinement:
H 385 ASN
** H 481 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 297 ASN
A 949 HIS
F  20 GLN
** G 109 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4194 r_free = 0.4194 target = 0.150841 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.3797 r_free = 0.3797 target = 0.121273 restraints weight = 35947.278|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 24)----------------|
| r_work = 0.3786 r_free = 0.3786 target = 0.121060 restraints weight = 38582.449|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 29)----------------|
| r_work = 0.3791 r_free = 0.3791 target = 0.121592 restraints weight = 38372.850|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 25)----------------|
| r_work = 0.3804 r_free = 0.3804 target = 0.122811 restraints weight = 29200.051|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 23)----------------|
| r_work = 0.3803 r_free = 0.3803 target = 0.122797 restraints weight = 25107.281|
|-----------------------------------------------------------------------------|
r_work (final): 0.3796
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7449
moved from start:          0.3171

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.041  19170  Z= 0.122
  Angle     :  0.560  12.040  26576  Z= 0.289
  Chirality :  0.039   0.163   3065
  Planarity :  0.003   0.045   2809
  Dihedral  : 19.586 179.159   4331
  Min Nonbonded Distance : 2.133

Molprobity Statistics.
  All-atom Clashscore : 9.36
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.26 %
    Favored  : 95.74 %
  Rotamer:
    Outliers :  3.09 %
    Allowed  : 17.99 %
    Favored  : 78.92 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -0.40 (0.20), residues: 1809
  helix:  1.40 (0.19), residues: 752
  sheet: -1.43 (0.30), residues: 277
  loop : -1.49 (0.22), residues: 780

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.000   ARG E 158 
 TYR   0.014   0.001   TYR G  26 
 PHE   0.065   0.001   PHE H 524 
 TRP   0.011   0.001   TRP A 604 
 HIS   0.002   0.001   HIS F  53 

Details of bonding type rmsd
  covalent geometry    : bond        0.00277 (19168)
  covalent geometry    : angle       0.56029 (26576)
  hydrogen bonds       : bond        0.03982 (  806)
  hydrogen bonds       : angle       4.16675 ( 2272)
  metal coordination   : bond        0.00071 (    2)

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

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

  3618 Ramachandran restraints generated.
    1809 Oldfield, 0 Emsley, 1809 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3618 Ramachandran restraints generated.
    1809 Oldfield, 0 Emsley, 1809 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  244 residues out of total 1741 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 51
    poor density    : 193
  time to evaluate  : 0.654 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: H  484 ASN cc_start: 0.6335 (p0) cc_final: 0.5836 (p0)
REVERT: H  492 ARG cc_start: 0.6147 (ptm-80) cc_final: 0.5842 (ptt-90)
REVERT: H  497 ASP cc_start: 0.6223 (t0) cc_final: 0.5879 (m-30)
REVERT: A  575 LEU cc_start: 0.8271 (tp) cc_final: 0.8058 (tt)
REVERT: A  578 MET cc_start: 0.6756 (mtp) cc_final: 0.6358 (mmp)
REVERT: D  647 ASP cc_start: 0.8289 (m-30) cc_final: 0.8053 (m-30)
REVERT: E   51 GLN cc_start: 0.3543 (pm20) cc_final: 0.2821 (pm20)
REVERT: E   86 MET cc_start: 0.7548 (mpp) cc_final: 0.7254 (mpp)
REVERT: E  126 ARG cc_start: 0.4530 (mmt180) cc_final: 0.4125 (mtt180)
  outliers start: 51
  outliers final: 45
  residues processed: 221
  average time/residue: 0.1292
  time to fit residues: 45.8701
Evaluate side-chains
  232 residues out of total 1741 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 45
    poor density    : 187
  time to evaluate  : 0.621 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain H residue  380 LEU
Chi-restraints excluded: chain H residue  396 VAL
Chi-restraints excluded: chain H residue  412 ASP
Chi-restraints excluded: chain H residue  464 ILE
Chi-restraints excluded: chain H residue  512 ASN
Chi-restraints excluded: chain H residue  516 PHE
Chi-restraints excluded: chain A residue   21 LEU
Chi-restraints excluded: chain A residue   33 VAL
Chi-restraints excluded: chain A residue  112 THR
Chi-restraints excluded: chain A residue  159 THR
Chi-restraints excluded: chain A residue  169 VAL
Chi-restraints excluded: chain A residue  241 VAL
Chi-restraints excluded: chain A residue  289 LEU
Chi-restraints excluded: chain A residue  324 ASN
Chi-restraints excluded: chain A residue  384 ILE
Chi-restraints excluded: chain A residue  393 LEU
Chi-restraints excluded: chain A residue  420 LEU
Chi-restraints excluded: chain A residue  430 ASP
Chi-restraints excluded: chain A residue  732 ILE
Chi-restraints excluded: chain A residue  792 GLU
Chi-restraints excluded: chain A residue  807 ILE
Chi-restraints excluded: chain A residue  809 LEU
Chi-restraints excluded: chain A residue  814 THR
Chi-restraints excluded: chain A residue  877 ILE
Chi-restraints excluded: chain A residue  888 ILE
Chi-restraints excluded: chain A residue  903 ILE
Chi-restraints excluded: chain A residue  950 SER
Chi-restraints excluded: chain A residue  962 THR
Chi-restraints excluded: chain A residue 1006 TYR
Chi-restraints excluded: chain A residue 1100 ILE
Chi-restraints excluded: chain D residue  627 VAL
Chi-restraints excluded: chain D residue  686 TYR
Chi-restraints excluded: chain E residue  150 VAL
Chi-restraints excluded: chain F residue   14 LEU
Chi-restraints excluded: chain F residue   20 GLN
Chi-restraints excluded: chain F residue   62 VAL
Chi-restraints excluded: chain F residue   67 THR
Chi-restraints excluded: chain F residue   78 LEU
Chi-restraints excluded: chain F residue   85 CYS
Chi-restraints excluded: chain G residue    3 LEU
Chi-restraints excluded: chain G residue   10 ILE
Chi-restraints excluded: chain G residue   40 MET
Chi-restraints excluded: chain G residue   42 VAL
Chi-restraints excluded: chain G residue   79 VAL
Chi-restraints excluded: chain G residue  105 VAL
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 196
   random chunks:
   chunk 19 optimal weight:    0.7980
   chunk 73 optimal weight:    0.6980
   chunk 141 optimal weight:    0.3980
   chunk 109 optimal weight:    0.7980
   chunk 55 optimal weight:    0.0370
   chunk 79 optimal weight:    0.1980
   chunk 110 optimal weight:    0.6980
   chunk 53 optimal weight:    0.0010
   chunk 115 optimal weight:    0.7980
   chunk 31 optimal weight:    0.0270
   chunk 60 optimal weight:    0.5980
   overall best weight:    0.1322

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

Flipped N/Q/H residues before XYZ refinement:
H 385 ASN
A 949 HIS
D 592 GLN
F  20 GLN

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4248 r_free = 0.4248 target = 0.155366 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 33)----------------|
| r_work = 0.3862 r_free = 0.3862 target = 0.125752 restraints weight = 35575.404|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 28)----------------|
| r_work = 0.3852 r_free = 0.3852 target = 0.125563 restraints weight = 36611.565|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 26)----------------|
| r_work = 0.3855 r_free = 0.3855 target = 0.125989 restraints weight = 36450.201|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 23)----------------|
| r_work = 0.3863 r_free = 0.3863 target = 0.126769 restraints weight = 29592.874|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 23)----------------|
| r_work = 0.3864 r_free = 0.3864 target = 0.126894 restraints weight = 26335.205|
|-----------------------------------------------------------------------------|
r_work (final): 0.3864
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7354
moved from start:          0.3608

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.052  19170  Z= 0.100
  Angle     :  0.541  12.025  26576  Z= 0.278
  Chirality :  0.037   0.161   3065
  Planarity :  0.003   0.045   2809
  Dihedral  : 19.418 178.140   4331
  Min Nonbonded Distance : 2.118

Molprobity Statistics.
  All-atom Clashscore : 8.45
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.99 %
    Favored  : 97.01 %
  Rotamer:
    Outliers :  2.36 %
    Allowed  : 18.96 %
    Favored  : 78.68 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -0.10 (0.20), residues: 1809
  helix:  1.63 (0.20), residues: 759
  sheet: -1.22 (0.30), residues: 284
  loop : -1.35 (0.22), residues: 766

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG A 446 
 TYR   0.016   0.001   TYR H 410 
 PHE   0.060   0.001   PHE H 524 
 TRP   0.011   0.001   TRP A1027 
 HIS   0.002   0.000   HIS A 751 

Details of bonding type rmsd
  covalent geometry    : bond        0.00214 (19168)
  covalent geometry    : angle       0.54073 (26576)
  hydrogen bonds       : bond        0.03494 (  806)
  hydrogen bonds       : angle       3.98365 ( 2272)
  metal coordination   : bond        0.00031 (    2)

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

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

  3618 Ramachandran restraints generated.
    1809 Oldfield, 0 Emsley, 1809 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3618 Ramachandran restraints generated.
    1809 Oldfield, 0 Emsley, 1809 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  269 residues out of total 1741 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 39
    poor density    : 230
  time to evaluate  : 0.577 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: H  484 ASN cc_start: 0.6004 (p0) cc_final: 0.5727 (p0)
REVERT: H  492 ARG cc_start: 0.6182 (ptm-80) cc_final: 0.5725 (ptt-90)
REVERT: H  497 ASP cc_start: 0.6068 (t0) cc_final: 0.5785 (m-30)
REVERT: A  129 GLN cc_start: 0.8369 (mt0) cc_final: 0.8139 (mt0)
REVERT: A  290 LEU cc_start: 0.7752 (mt) cc_final: 0.7161 (pp)
REVERT: A  578 MET cc_start: 0.6512 (mtp) cc_final: 0.6186 (mmp)
REVERT: A  687 MET cc_start: 0.5779 (tpt) cc_final: 0.5264 (mtm)
REVERT: D  647 ASP cc_start: 0.8111 (m-30) cc_final: 0.7861 (m-30)
REVERT: E   86 MET cc_start: 0.7664 (mpp) cc_final: 0.7191 (mpp)
  outliers start: 39
  outliers final: 35
  residues processed: 253
  average time/residue: 0.1210
  time to fit residues: 48.8558
Evaluate side-chains
  230 residues out of total 1741 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 35
    poor density    : 195
  time to evaluate  : 0.621 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain H residue  380 LEU
Chi-restraints excluded: chain H residue  385 ASN
Chi-restraints excluded: chain H residue  464 ILE
Chi-restraints excluded: chain H residue  516 PHE
Chi-restraints excluded: chain A residue   21 LEU
Chi-restraints excluded: chain A residue   33 VAL
Chi-restraints excluded: chain A residue   37 TYR
Chi-restraints excluded: chain A residue  139 LEU
Chi-restraints excluded: chain A residue  241 VAL
Chi-restraints excluded: chain A residue  289 LEU
Chi-restraints excluded: chain A residue  324 ASN
Chi-restraints excluded: chain A residue  384 ILE
Chi-restraints excluded: chain A residue  430 ASP
Chi-restraints excluded: chain A residue  579 LEU
Chi-restraints excluded: chain A residue  792 GLU
Chi-restraints excluded: chain A residue  814 THR
Chi-restraints excluded: chain A residue  877 ILE
Chi-restraints excluded: chain A residue  888 ILE
Chi-restraints excluded: chain A residue  903 ILE
Chi-restraints excluded: chain A residue  962 THR
Chi-restraints excluded: chain A residue 1006 TYR
Chi-restraints excluded: chain A residue 1100 ILE
Chi-restraints excluded: chain D residue  627 VAL
Chi-restraints excluded: chain D residue  686 TYR
Chi-restraints excluded: chain E residue  150 VAL
Chi-restraints excluded: chain F residue   14 LEU
Chi-restraints excluded: chain F residue   20 GLN
Chi-restraints excluded: chain F residue   62 VAL
Chi-restraints excluded: chain F residue   67 THR
Chi-restraints excluded: chain F residue   73 ILE
Chi-restraints excluded: chain F residue   85 CYS
Chi-restraints excluded: chain G residue   10 ILE
Chi-restraints excluded: chain G residue   40 MET
Chi-restraints excluded: chain G residue   79 VAL
Chi-restraints excluded: chain G residue  105 VAL
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 196
   random chunks:
   chunk 190 optimal weight:    0.6980
   chunk 151 optimal weight:    0.0670
   chunk 97 optimal weight:    0.0980
   chunk 122 optimal weight:    0.0470
   chunk 5 optimal weight:   10.0000
   chunk 22 optimal weight:   20.0000
   chunk 172 optimal weight:    4.9990
   chunk 166 optimal weight:    4.9990
   chunk 140 optimal weight:    5.9990
   chunk 2 optimal weight:    9.9990
   chunk 157 optimal weight:    0.5980
   overall best weight:    0.3016

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

Flipped N/Q/H residues before XYZ refinement:
H 385 ASN
H 481 ASN
A 949 HIS
F  20 GLN
F  53 HIS
G  63 GLN
** G 177 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 6

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4238 r_free = 0.4238 target = 0.154341 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.3854 r_free = 0.3854 target = 0.125236 restraints weight = 35947.877|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 28)----------------|
| r_work = 0.3836 r_free = 0.3836 target = 0.124771 restraints weight = 37999.178|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 27)----------------|
| r_work = 0.3844 r_free = 0.3844 target = 0.125684 restraints weight = 38935.299|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 23)----------------|
| r_work = 0.3851 r_free = 0.3851 target = 0.126309 restraints weight = 27876.924|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 23)----------------|
| r_work = 0.3853 r_free = 0.3853 target = 0.126502 restraints weight = 24717.578|
|-----------------------------------------------------------------------------|
r_work (final): 0.3854
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7368
moved from start:          0.3768

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.084  19170  Z= 0.102
  Angle     :  0.548  12.412  26576  Z= 0.280
  Chirality :  0.038   0.161   3065
  Planarity :  0.003   0.044   2809
  Dihedral  : 19.332 178.377   4331
  Min Nonbonded Distance : 2.089

Molprobity Statistics.
  All-atom Clashscore : 8.02
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.21 %
    Favored  : 96.79 %
  Rotamer:
    Outliers :  2.36 %
    Allowed  : 19.93 %
    Favored  : 77.71 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  0.01 (0.20), residues: 1809
  helix:  1.72 (0.20), residues: 761
  sheet: -1.25 (0.31), residues: 256
  loop : -1.27 (0.21), residues: 792

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG E 126 
 TYR   0.010   0.001   TYR A 249 
 PHE   0.060   0.001   PHE H 524 
 TRP   0.011   0.001   TRP A 604 
 HIS   0.004   0.001   HIS F  53 

Details of bonding type rmsd
  covalent geometry    : bond        0.00229 (19168)
  covalent geometry    : angle       0.54754 (26576)
  hydrogen bonds       : bond        0.03529 (  806)
  hydrogen bonds       : angle       3.96134 ( 2272)
  metal coordination   : bond        0.00018 (    2)

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

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

  3618 Ramachandran restraints generated.
    1809 Oldfield, 0 Emsley, 1809 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3618 Ramachandran restraints generated.
    1809 Oldfield, 0 Emsley, 1809 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  248 residues out of total 1741 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 39
    poor density    : 209
  time to evaluate  : 0.609 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: H  484 ASN cc_start: 0.6147 (p0) cc_final: 0.5877 (p0)
REVERT: H  492 ARG cc_start: 0.6137 (ptm-80) cc_final: 0.5761 (ptt-90)
REVERT: A  290 LEU cc_start: 0.7922 (mt) cc_final: 0.7185 (pp)
REVERT: A  575 LEU cc_start: 0.8016 (OUTLIER) cc_final: 0.7777 (tt)
REVERT: A  578 MET cc_start: 0.6588 (mtp) cc_final: 0.6221 (mmp)
REVERT: A  687 MET cc_start: 0.5781 (tpt) cc_final: 0.5258 (mtm)
REVERT: A  876 TRP cc_start: 0.7704 (t60) cc_final: 0.7337 (t60)
REVERT: D  546 MET cc_start: 0.7693 (mtp) cc_final: 0.7247 (mtt)
REVERT: D  551 TYR cc_start: 0.7017 (p90) cc_final: 0.6786 (p90)
REVERT: D  647 ASP cc_start: 0.8127 (m-30) cc_final: 0.7903 (m-30)
REVERT: E   86 MET cc_start: 0.7692 (mpp) cc_final: 0.7313 (mpp)
REVERT: E  105 MET cc_start: 0.6789 (pmm) cc_final: 0.6481 (pmm)
REVERT: F   14 LEU cc_start: 0.7782 (OUTLIER) cc_final: 0.7323 (mm)
REVERT: F   88 LEU cc_start: 0.7623 (tp) cc_final: 0.7406 (tt)
  outliers start: 39
  outliers final: 36
  residues processed: 234
  average time/residue: 0.1253
  time to fit residues: 47.0800
Evaluate side-chains
  234 residues out of total 1741 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 38
    poor density    : 196
  time to evaluate  : 0.597 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain H residue  380 LEU
Chi-restraints excluded: chain H residue  385 ASN
Chi-restraints excluded: chain H residue  464 ILE
Chi-restraints excluded: chain H residue  516 PHE
Chi-restraints excluded: chain A residue   19 ASP
Chi-restraints excluded: chain A residue   21 LEU
Chi-restraints excluded: chain A residue   33 VAL
Chi-restraints excluded: chain A residue   37 TYR
Chi-restraints excluded: chain A residue  112 THR
Chi-restraints excluded: chain A residue  139 LEU
Chi-restraints excluded: chain A residue  289 LEU
Chi-restraints excluded: chain A residue  324 ASN
Chi-restraints excluded: chain A residue  384 ILE
Chi-restraints excluded: chain A residue  430 ASP
Chi-restraints excluded: chain A residue  575 LEU
Chi-restraints excluded: chain A residue  579 LEU
Chi-restraints excluded: chain A residue  807 ILE
Chi-restraints excluded: chain A residue  814 THR
Chi-restraints excluded: chain A residue  877 ILE
Chi-restraints excluded: chain A residue  888 ILE
Chi-restraints excluded: chain A residue  962 THR
Chi-restraints excluded: chain A residue  984 THR
Chi-restraints excluded: chain A residue 1006 TYR
Chi-restraints excluded: chain A residue 1100 ILE
Chi-restraints excluded: chain D residue  610 LEU
Chi-restraints excluded: chain D residue  627 VAL
Chi-restraints excluded: chain D residue  686 TYR
Chi-restraints excluded: chain E residue  150 VAL
Chi-restraints excluded: chain F residue   14 LEU
Chi-restraints excluded: chain F residue   20 GLN
Chi-restraints excluded: chain F residue   62 VAL
Chi-restraints excluded: chain F residue   73 ILE
Chi-restraints excluded: chain F residue   85 CYS
Chi-restraints excluded: chain G residue    3 LEU
Chi-restraints excluded: chain G residue   10 ILE
Chi-restraints excluded: chain G residue   40 MET
Chi-restraints excluded: chain G residue   79 VAL
Chi-restraints excluded: chain G residue  105 VAL
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 196
   random chunks:
   chunk 123 optimal weight:    0.8980
   chunk 177 optimal weight:    0.8980
   chunk 82 optimal weight:    5.9990
   chunk 139 optimal weight:    6.9990
   chunk 103 optimal weight:    1.9990
   chunk 25 optimal weight:   10.0000
   chunk 94 optimal weight:    0.6980
   chunk 39 optimal weight:    2.9990
   chunk 120 optimal weight:    0.8980
   chunk 38 optimal weight:    0.4980
   chunk 184 optimal weight:    3.9990
   overall best weight:    0.7780

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

Flipped N/Q/H residues before XYZ refinement:
H 385 ASN
H 482 HIS
A 949 HIS
** E  51 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
F  20 GLN
G  63 GLN
** G 177 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 5

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4215 r_free = 0.4215 target = 0.152515 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.3830 r_free = 0.3830 target = 0.123443 restraints weight = 35715.977|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 34)----------------|
| r_work = 0.3818 r_free = 0.3818 target = 0.123272 restraints weight = 38853.880|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 24)----------------|
| r_work = 0.3828 r_free = 0.3828 target = 0.124291 restraints weight = 39101.038|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 27)----------------|
| r_work = 0.3830 r_free = 0.3830 target = 0.124449 restraints weight = 27185.836|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 23)----------------|
| r_work = 0.3833 r_free = 0.3833 target = 0.124795 restraints weight = 24701.596|
|-----------------------------------------------------------------------------|
r_work (final): 0.3828
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7400
moved from start:          0.3747

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.039  19170  Z= 0.122
  Angle     :  0.575  12.885  26576  Z= 0.295
  Chirality :  0.038   0.158   3065
  Planarity :  0.003   0.057   2809
  Dihedral  : 19.334 179.936   4331
  Min Nonbonded Distance : 2.123

Molprobity Statistics.
  All-atom Clashscore : 9.05
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.92 %
    Favored  : 96.08 %
  Rotamer:
    Outliers :  2.42 %
    Allowed  : 20.47 %
    Favored  : 77.10 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -0.03 (0.20), residues: 1809
  helix:  1.70 (0.20), residues: 756
  sheet: -1.26 (0.31), residues: 267
  loop : -1.29 (0.21), residues: 786

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.015   0.000   ARG G  70 
 TYR   0.017   0.001   TYR H 410 
 PHE   0.061   0.001   PHE H 524 
 TRP   0.011   0.001   TRP A 604 
 HIS   0.002   0.001   HIS A 751 

Details of bonding type rmsd
  covalent geometry    : bond        0.00279 (19168)
  covalent geometry    : angle       0.57465 (26576)
  hydrogen bonds       : bond        0.03774 (  806)
  hydrogen bonds       : angle       4.00792 ( 2272)
  metal coordination   : bond        0.00069 (    2)

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

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

  3618 Ramachandran restraints generated.
    1809 Oldfield, 0 Emsley, 1809 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3618 Ramachandran restraints generated.
    1809 Oldfield, 0 Emsley, 1809 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  238 residues out of total 1741 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 40
    poor density    : 198
  time to evaluate  : 0.536 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: H  484 ASN cc_start: 0.6136 (p0) cc_final: 0.5821 (p0)
REVERT: H  492 ARG cc_start: 0.6215 (ptm-80) cc_final: 0.5768 (ptt-90)
REVERT: A  575 LEU cc_start: 0.7965 (tt) cc_final: 0.7739 (tt)
REVERT: A  578 MET cc_start: 0.6571 (mtp) cc_final: 0.6203 (mmp)
REVERT: A  687 MET cc_start: 0.5545 (tpt) cc_final: 0.4931 (mtm)
REVERT: A  876 TRP cc_start: 0.7707 (t60) cc_final: 0.7238 (t60)
REVERT: D  546 MET cc_start: 0.7758 (mtp) cc_final: 0.7277 (mtt)
REVERT: D  647 ASP cc_start: 0.8193 (m-30) cc_final: 0.7985 (m-30)
REVERT: E   86 MET cc_start: 0.7673 (mpp) cc_final: 0.7242 (mpp)
  outliers start: 40
  outliers final: 37
  residues processed: 225
  average time/residue: 0.1230
  time to fit residues: 44.8013
Evaluate side-chains
  227 residues out of total 1741 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 37
    poor density    : 190
  time to evaluate  : 0.478 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain H residue  380 LEU
Chi-restraints excluded: chain H residue  385 ASN
Chi-restraints excluded: chain H residue  464 ILE
Chi-restraints excluded: chain H residue  516 PHE
Chi-restraints excluded: chain A residue   19 ASP
Chi-restraints excluded: chain A residue   21 LEU
Chi-restraints excluded: chain A residue   33 VAL
Chi-restraints excluded: chain A residue   37 TYR
Chi-restraints excluded: chain A residue  112 THR
Chi-restraints excluded: chain A residue  139 LEU
Chi-restraints excluded: chain A residue  284 ILE
Chi-restraints excluded: chain A residue  289 LEU
Chi-restraints excluded: chain A residue  384 ILE
Chi-restraints excluded: chain A residue  430 ASP
Chi-restraints excluded: chain A residue  579 LEU
Chi-restraints excluded: chain A residue  814 THR
Chi-restraints excluded: chain A residue  877 ILE
Chi-restraints excluded: chain A residue  903 ILE
Chi-restraints excluded: chain A residue  950 SER
Chi-restraints excluded: chain A residue  962 THR
Chi-restraints excluded: chain A residue  984 THR
Chi-restraints excluded: chain A residue 1006 TYR
Chi-restraints excluded: chain A residue 1100 ILE
Chi-restraints excluded: chain D residue  610 LEU
Chi-restraints excluded: chain D residue  627 VAL
Chi-restraints excluded: chain D residue  641 GLN
Chi-restraints excluded: chain D residue  686 TYR
Chi-restraints excluded: chain E residue  150 VAL
Chi-restraints excluded: chain F residue   20 GLN
Chi-restraints excluded: chain F residue   62 VAL
Chi-restraints excluded: chain F residue   73 ILE
Chi-restraints excluded: chain F residue   85 CYS
Chi-restraints excluded: chain G residue    3 LEU
Chi-restraints excluded: chain G residue   10 ILE
Chi-restraints excluded: chain G residue   40 MET
Chi-restraints excluded: chain G residue   79 VAL
Chi-restraints excluded: chain G residue  105 VAL
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 196
   random chunks:
   chunk 69 optimal weight:    0.5980
   chunk 99 optimal weight:    0.8980
   chunk 54 optimal weight:    0.9990
   chunk 109 optimal weight:    3.9990
   chunk 153 optimal weight:    0.8980
   chunk 77 optimal weight:    0.8980
   chunk 163 optimal weight:    7.9990
   chunk 120 optimal weight:    2.9990
   chunk 50 optimal weight:    2.9990
   chunk 166 optimal weight:    5.9990
   chunk 26 optimal weight:    6.9990
   overall best weight:    0.8582

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

Flipped N/Q/H residues before XYZ refinement:
H 385 ASN
A 949 HIS
** E  51 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** E 143 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
F  20 GLN
G  63 GLN
** G 177 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4211 r_free = 0.4211 target = 0.152071 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.3825 r_free = 0.3825 target = 0.123125 restraints weight = 35820.603|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 28)----------------|
| r_work = 0.3806 r_free = 0.3806 target = 0.122353 restraints weight = 38834.256|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 24)----------------|
| r_work = 0.3813 r_free = 0.3813 target = 0.123087 restraints weight = 43115.992|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 25)----------------|
| r_work = 0.3820 r_free = 0.3820 target = 0.123782 restraints weight = 30356.877|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 23)----------------|
| r_work = 0.3822 r_free = 0.3822 target = 0.124072 restraints weight = 26634.257|
|-----------------------------------------------------------------------------|
r_work (final): 0.3815
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7423
moved from start:          0.3759

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.045  19170  Z= 0.125
  Angle     :  0.571  12.743  26576  Z= 0.294
  Chirality :  0.039   0.164   3065
  Planarity :  0.003   0.041   2809
  Dihedral  : 19.332 179.386   4331
  Min Nonbonded Distance : 2.107

Molprobity Statistics.
  All-atom Clashscore : 9.25
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.92 %
    Favored  : 96.08 %
  Rotamer:
    Outliers :  2.36 %
    Allowed  : 20.35 %
    Favored  : 77.29 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -0.08 (0.20), residues: 1809
  helix:  1.58 (0.19), residues: 767
  sheet: -1.26 (0.30), residues: 277
  loop : -1.28 (0.22), residues: 765

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.000   ARG E 126 
 TYR   0.010   0.001   TYR A1006 
 PHE   0.063   0.001   PHE H 524 
 TRP   0.011   0.001   TRP A 604 
 HIS   0.002   0.001   HIS A 751 

Details of bonding type rmsd
  covalent geometry    : bond        0.00289 (19168)
  covalent geometry    : angle       0.57060 (26576)
  hydrogen bonds       : bond        0.03831 (  806)
  hydrogen bonds       : angle       4.02274 ( 2272)
  metal coordination   : bond        0.00078 (    2)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 2570.75 seconds
wall clock time: 45 minutes 38.90 seconds (2738.90 seconds total)