Starting phenix.real_space_refine
on Tue Jan 14 13:01:10 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/8xa6_38195/01_2025/8xa6_38195.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/8xa6_38195/01_2025/8xa6_38195.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.02
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/8xa6_38195/01_2025/8xa6_38195.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/8xa6_38195/01_2025/8xa6_38195.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/8xa6_38195/01_2025/8xa6_38195.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/8xa6_38195/01_2025/8xa6_38195.cif"
  }
  resolution = 3.02
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }
  qi {
    qm_restraints {
      package {
        program = *test
      }
    }
  }


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=   0.022
Set stop_for_unknowns flag
  Set to: True
Assert model is a single copy model
Assert all atoms have isotropic ADPs
Construct map_model_manager
Extract box with map and model
Check model and map are aligned
Set scattering table
  Set to: electron
  Number of scattering types: 5
    Type Number    sf(0)   Gaussians
     S      87      5.16       5
     C   15306      2.51       5
     N    4225      2.21       5
     O    4658      1.98       5
     H   24502      0.53       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 33 residue(s): 0.06s

  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/modules/chem_data/mon_lib"
  Total number of atoms: 48778
  Number of models: 1
  Model: ""
    Number of chains: 8
    Chain: "A"
      Number of atoms: 3456
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 224, 3456
          Classifications: {'peptide': 224}
          Link IDs: {'PCIS': 1, 'PTRANS': 8, 'TRANS': 214}
    Chain: "B"
      Number of atoms: 3456
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 224, 3456
          Classifications: {'peptide': 224}
          Link IDs: {'PCIS': 1, 'PTRANS': 8, 'TRANS': 214}
    Chain: "C"
      Number of atoms: 17931
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 1139, 17931
          Classifications: {'peptide': 1139}
          Link IDs: {'PTRANS': 54, 'TRANS': 1084}
          Chain breaks: 1
    Chain: "D"
      Number of atoms: 18775
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 1176, 18775
          Classifications: {'peptide': 1176}
          Link IDs: {'PTRANS': 52, 'TRANS': 1123}
          Chain breaks: 1
    Chain: "F"
      Number of atoms: 990
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 61, 990
          Classifications: {'peptide': 61}
          Modifications used: {'NH3': 1}
          Link IDs: {'PTRANS': 1, 'TRANS': 59}
    Chain: "L"
      Number of atoms: 1503
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 92, 1503
          Classifications: {'peptide': 92}
          Modifications used: {'NH3': 1}
          Link IDs: {'PTRANS': 3, 'TRANS': 88}
    Chain: "E"
      Number of atoms: 1113
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 69, 1113
          Classifications: {'peptide': 69}
          Modifications used: {'COO': 1, 'NH3': 1}
          Link IDs: {'PTRANS': 2, 'TRANS': 66}
          Unresolved non-hydrogen bonds: 20
          Unresolved non-hydrogen angles: 23
          Unresolved non-hydrogen dihedrals: 17
          Planarities with less than four sites: {'GLU:plan': 3}
          Unresolved non-hydrogen planarities: 12
    Chain: "H"
      Number of atoms: 1554
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 94, 1554
          Classifications: {'peptide': 94}
          Modifications used: {'NH3': 1}
          Link IDs: {'CIS': 2, 'TRANS': 91}
  Time building chain proxies: 19.73, per 1000 atoms: 0.40
  Number of scatterers: 48778
  At special positions: 0
  Unit cell: (133, 152.95, 176.7, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 5
    Type Number    sf(0)
     S      87     16.00
     O    4658      8.00
     N    4225      7.00
     C   15306      6.00
     H   24502      1.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=1, symmetry=0
    Simple disulfide: pdb=" SG  CYS D  62 " - pdb=" SG  CYS D  78 " distance=2.03

  Automatic linking
    Parameters for automatic linking
      Linking & cutoffs
        Metal                : Auto  - 3.00
        Amino acid           : True  - 1.90
        Carbohydrate         : True  - 1.99
        Ligands              : True  - 1.99
        Small molecules      : False - 1.98
        Amino acid - RNA/DNA : False
      
  Number of custom bonds: simple=0, symmetry=0
  Time building additional restraints: 9.78
  Conformation dependent library (CDL) restraints added in 3.4 seconds
  

  6118 Ramachandran restraints generated.
    3059 Oldfield, 0 Emsley, 3059 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  5686

  Finding SS restraints...
    Secondary structure from input PDB file:
      103 helices and 36 sheets defined
      35.7% alpha, 13.9% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 3.06
  Creating SS restraints...
    Processing helix  chain 'A' and resid 32 through 47
      removed outlier: 3.775A  pdb=" N   SER A  46 " --> pdb=" O   ARG A  42 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 74 through 83
    Processing helix  chain 'A' and resid 110 through 112
      No H-bonds generated for 'chain 'A' and resid 110 through 112'
    Processing helix  chain 'A' and resid 150 through 155
      removed outlier: 3.511A  pdb=" N   ALA A 153 " --> pdb=" O   PRO A 150 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 205 through 227
      removed outlier: 3.606A  pdb=" N   ILE A 223 " --> pdb=" O   GLU A 219 " (cutoff:3.500A)
      removed outlier: 3.961A  pdb=" N   PHE A 224 " --> pdb=" O   HIS A 220 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 31 through 47
      removed outlier: 3.919A  pdb=" N   THR B  35 " --> pdb=" O   GLY B  31 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 74 through 85
      removed outlier: 4.258A  pdb=" N   ILE B  78 " --> pdb=" O   ASP B  74 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 150 through 155
      removed outlier: 3.507A  pdb=" N   LYS B 155 " --> pdb=" O   ASP B 152 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 205 through 227
      removed outlier: 4.410A  pdb=" N   ILE B 223 " --> pdb=" O   GLU B 219 " (cutoff:3.500A)
      removed outlier: 4.703A  pdb=" N   PHE B 224 " --> pdb=" O   HIS B 220 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 31 through 43
      removed outlier: 3.667A  pdb=" N   GLU C  43 " --> pdb=" O   TRP C  39 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 43 through 53
    Processing helix  chain 'C' and resid 77 through 84
    Processing helix  chain 'C' and resid 191 through 198
      removed outlier: 4.039A  pdb=" N   LEU C 195 " --> pdb=" O   PRO C 191 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 206 through 211
    Processing helix  chain 'C' and resid 217 through 224
      removed outlier: 3.886A  pdb=" N   LEU C 221 " --> pdb=" O   LEU C 217 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 229 through 239
    Processing helix  chain 'C' and resid 247 through 260
    Processing helix  chain 'C' and resid 268 through 279
      removed outlier: 3.915A  pdb=" N   ARG C 272 " --> pdb=" O   ALA C 268 " (cutoff:3.500A)
      removed outlier: 3.791A  pdb=" N   LEU C 279 " --> pdb=" O   ILE C 275 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 280 through 284
    Processing helix  chain 'C' and resid 377 through 394
      removed outlier: 3.851A  pdb=" N   ILE C 381 " --> pdb=" O   THR C 377 " (cutoff:3.500A)
      removed outlier: 3.610A  pdb=" N   SER C 383 " --> pdb=" O   ALA C 379 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 411 through 439
      removed outlier: 4.234A  pdb=" N   ARG C 429 " --> pdb=" O   SER C 425 " (cutoff:3.500A)
      removed outlier: 3.974A  pdb=" N   VAL C 430 " --> pdb=" O   ARG C 426 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 444 through 449
      removed outlier: 4.164A  pdb=" N   GLN C 447 " --> pdb=" O   THR C 444 " (cutoff:3.500A)
      removed outlier: 3.914A  pdb=" N   ILE C 449 " --> pdb=" O   GLN C 446 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 451 through 464
    Processing helix  chain 'C' and resid 475 through 483
    Processing helix  chain 'C' and resid 507 through 511
    Processing helix  chain 'C' and resid 565 through 571
      removed outlier: 4.507A  pdb=" N   ASN C 571 " --> pdb=" O   ASP C 567 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 628 through 632
    Processing helix  chain 'C' and resid 633 through 646
    Processing helix  chain 'C' and resid 661 through 669
      removed outlier: 4.322A  pdb=" N   VAL C 665 " --> pdb=" O   GLY C 661 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 779 through 784
    Processing helix  chain 'C' and resid 860 through 865
      removed outlier: 3.547A  pdb=" N   PHE C 865 " --> pdb=" O   HIS C 862 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 960 through 965
      removed outlier: 4.081A  pdb=" N   SER C 964 " --> pdb=" O   LEU C 960 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 967 through 984
      removed outlier: 4.052A  pdb=" N   VAL C 971 " --> pdb=" O   ASN C 967 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 996 through 1007
    Processing helix  chain 'C' and resid 1076 through 1086
    Processing helix  chain 'C' and resid 1088 through 1098
    Processing helix  chain 'C' and resid 1102 through 1116
      removed outlier: 3.510A  pdb=" N   ARG C1106 " --> pdb=" O   ASP C1102 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 1126 through 1138
    Processing helix  chain 'D' and resid 16 through 24
      removed outlier: 3.812A  pdb=" N   ILE D  20 " --> pdb=" O   SER D  16 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 113 through 118
    Processing helix  chain 'D' and resid 123 through 129
      removed outlier: 3.920A  pdb=" N   GLU D 127 " --> pdb=" O   ARG D 123 " (cutoff:3.500A)
      removed outlier: 4.514A  pdb=" N   ILE D 129 " --> pdb=" O   LEU D 125 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 153 through 159
    Processing helix  chain 'D' and resid 172 through 179
      removed outlier: 4.026A  pdb=" N   HIS D 176 " --> pdb=" O   ALA D 172 " (cutoff:3.500A)
      removed outlier: 3.567A  pdb=" N   LYS D 177 " --> pdb=" O   GLU D 173 " (cutoff:3.500A)
      removed outlier: 3.848A  pdb=" N   LEU D 179 " --> pdb=" O   ILE D 175 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 184 through 194
    Processing helix  chain 'D' and resid 200 through 219
    Processing helix  chain 'D' and resid 222 through 227
      removed outlier: 3.991A  pdb=" N   ILE D 227 " --> pdb=" O   SER D 224 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 235 through 239
    Processing helix  chain 'D' and resid 252 through 270
      removed outlier: 4.292A  pdb=" N   ARG D 267 " --> pdb=" O   ASN D 263 " (cutoff:3.500A)
      removed outlier: 4.459A  pdb=" N   LEU D 268 " --> pdb=" O   ARG D 264 " (cutoff:3.500A)
      removed outlier: 3.967A  pdb=" N   LYS D 269 " --> pdb=" O   ASN D 265 " (cutoff:3.500A)
      removed outlier: 4.380A  pdb=" N   ARG D 270 " --> pdb=" O   ASN D 266 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 278 through 297
      removed outlier: 4.283A  pdb=" N   GLN D 282 " --> pdb=" O   SER D 278 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 315 through 320
      removed outlier: 4.001A  pdb=" N   LEU D 320 " --> pdb=" O   LEU D 316 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 325 through 330
      removed outlier: 3.645A  pdb=" N   GLN D 329 " --> pdb=" O   GLY D 325 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 359 through 366
      removed outlier: 3.801A  pdb=" N   GLU D 364 " --> pdb=" O   GLU D 360 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 366 through 378
      removed outlier: 3.658A  pdb=" N   VAL D 370 " --> pdb=" O   PHE D 366 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 382 through 392
    Processing helix  chain 'D' and resid 395 through 405
      removed outlier: 3.577A  pdb=" N   ASP D 399 " --> pdb=" O   PRO D 395 " (cutoff:3.500A)
      removed outlier: 3.691A  pdb=" N   LEU D 401 " --> pdb=" O   VAL D 397 " (cutoff:3.500A)
      removed outlier: 4.214A  pdb=" N   GLU D 402 " --> pdb=" O   TRP D 398 " (cutoff:3.500A)
      removed outlier: 4.000A  pdb=" N   SER D 403 " --> pdb=" O   ASP D 399 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 419 through 421
      No H-bonds generated for 'chain 'D' and resid 419 through 421'
    Processing helix  chain 'D' and resid 439 through 444
      removed outlier: 3.619A  pdb=" N   CYS D 443 " --> pdb=" O   PRO D 440 " (cutoff:3.500A)
      removed outlier: 3.651A  pdb=" N   THR D 444 " --> pdb=" O   LEU D 441 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 462 through 472
    Processing helix  chain 'D' and resid 495 through 502
    Processing helix  chain 'D' and resid 518 through 529
      removed outlier: 3.612A  pdb=" N   ALA D 522 " --> pdb=" O   ASN D 518 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 563 through 569
    Processing helix  chain 'D' and resid 583 through 588
    Processing helix  chain 'D' and resid 601 through 609
      removed outlier: 3.563A  pdb=" N   VAL D 605 " --> pdb=" O   ASP D 601 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 616 through 631
      removed outlier: 3.705A  pdb=" N   LEU D 620 " --> pdb=" O   LYS D 616 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 633 through 653
    Processing helix  chain 'D' and resid 659 through 664
      removed outlier: 3.633A  pdb=" N   VAL D 664 " --> pdb=" O   SER D 661 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 666 through 677
      removed outlier: 3.703A  pdb=" N   GLN D 670 " --> pdb=" O   LEU D 666 " (cutoff:3.500A)
      removed outlier: 3.836A  pdb=" N   ILE D 672 " --> pdb=" O   ASP D 668 " (cutoff:3.500A)
      removed outlier: 3.932A  pdb=" N   LEU D 673 " --> pdb=" O   LYS D 669 " (cutoff:3.500A)
      removed outlier: 3.860A  pdb=" N   ALA D 676 " --> pdb=" O   ILE D 672 " (cutoff:3.500A)
      removed outlier: 3.739A  pdb=" N   GLN D 677 " --> pdb=" O   LEU D 673 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 677 through 690
      removed outlier: 3.864A  pdb=" N   ASP D 681 " --> pdb=" O   GLN D 677 " (cutoff:3.500A)
      removed outlier: 3.805A  pdb=" N   ASN D 682 " --> pdb=" O   SER D 678 " (cutoff:3.500A)
      removed outlier: 3.806A  pdb=" N   VAL D 683 " --> pdb=" O   LYS D 679 " (cutoff:3.500A)
      removed outlier: 4.040A  pdb=" N   MET D 684 " --> pdb=" O   VAL D 680 " (cutoff:3.500A)
      removed outlier: 3.838A  pdb=" N   LYS D 685 " --> pdb=" O   ASP D 681 " (cutoff:3.500A)
      removed outlier: 3.583A  pdb=" N   GLN D 686 " --> pdb=" O   ASN D 682 " (cutoff:3.500A)
      removed outlier: 3.581A  pdb=" N   PHE D 687 " --> pdb=" O   VAL D 683 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 693 through 720
    Processing helix  chain 'D' and resid 724 through 733
    Processing helix  chain 'D' and resid 737 through 746
    Processing helix  chain 'D' and resid 772 through 808
      removed outlier: 3.839A  pdb=" N   GLY D 782 " --> pdb=" O   ILE D 778 " (cutoff:3.500A)
      removed outlier: 3.933A  pdb=" N   ALA D 795 " --> pdb=" O   ALA D 791 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 838 through 843
    Processing helix  chain 'D' and resid 869 through 878
      removed outlier: 3.668A  pdb=" N   ALA D 873 " --> pdb=" O   ASP D 869 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 888 through 892
    Processing helix  chain 'D' and resid 899 through 904
    Processing helix  chain 'D' and resid 918 through 929
    Processing helix  chain 'D' and resid 930 through 932
      No H-bonds generated for 'chain 'D' and resid 930 through 932'
    Processing helix  chain 'D' and resid 952 through 961
    Processing helix  chain 'D' and resid 1030 through 1038
    Processing helix  chain 'D' and resid 1039 through 1059
      removed outlier: 3.686A  pdb=" N   VAL D1043 " --> pdb=" O   ASP D1039 " (cutoff:3.500A)
      removed outlier: 3.999A  pdb=" N   VAL D1054 " --> pdb=" O   GLU D1050 " (cutoff:3.500A)
      removed outlier: 4.248A  pdb=" N   TYR D1055 " --> pdb=" O   VAL D1051 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 1064 through 1073
      removed outlier: 3.760A  pdb=" N   GLN D1073 " --> pdb=" O   VAL D1069 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 1074 through 1076
      No H-bonds generated for 'chain 'D' and resid 1074 through 1076'
    Processing helix  chain 'D' and resid 1095 through 1108
    Processing helix  chain 'D' and resid 1122 through 1128
      removed outlier: 4.149A  pdb=" N   LEU D1128 " --> pdb=" O   THR D1124 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 1142 through 1153
    Processing helix  chain 'D' and resid 1160 through 1168
      removed outlier: 3.525A  pdb=" N   ASN D1164 " --> pdb=" O   GLY D1160 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 1173 through 1182
      removed outlier: 3.689A  pdb=" N   MET D1177 " --> pdb=" O   GLY D1174 " (cutoff:3.500A)
      removed outlier: 6.025A  pdb=" N   MET D1178 " --> pdb=" O   THR D1175 " (cutoff:3.500A)
      removed outlier: 5.938A  pdb=" N   LYS D1179 " --> pdb=" O   GLY D1176 " (cutoff:3.500A)
      removed outlier: 3.646A  pdb=" N   LYS D1182 " --> pdb=" O   LYS D1179 " (cutoff:3.500A)
    Processing helix  chain 'F' and resid 6 through 11
    Processing helix  chain 'F' and resid 15 through 34
    Processing helix  chain 'F' and resid 45 through 55
      removed outlier: 3.588A  pdb=" N   ASP F  55 " --> pdb=" O   LEU F  51 " (cutoff:3.500A)
    Processing helix  chain 'L' and resid 7 through 14
      removed outlier: 3.802A  pdb=" N   GLU L  13 " --> pdb=" O   GLU L   9 " (cutoff:3.500A)
    Processing helix  chain 'L' and resid 22 through 27
      removed outlier: 3.969A  pdb=" N   GLU L  26 " --> pdb=" O   GLU L  22 " (cutoff:3.500A)
      removed outlier: 3.961A  pdb=" N   HIS L  27 " --> pdb=" O   LEU L  23 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'L' and resid 22 through 27'
    Processing helix  chain 'L' and resid 33 through 42
    Processing helix  chain 'L' and resid 51 through 53
      No H-bonds generated for 'chain 'L' and resid 51 through 53'
    Processing helix  chain 'L' and resid 54 through 65
      removed outlier: 4.567A  pdb=" N   ASP L  65 " --> pdb=" O   ASP L  61 " (cutoff:3.500A)
    Processing helix  chain 'L' and resid 84 through 92
      removed outlier: 3.605A  pdb=" N   GLN L  92 " --> pdb=" O   ASP L  88 " (cutoff:3.500A)
    Processing helix  chain 'E' and resid 29 through 37
    Processing helix  chain 'E' and resid 38 through 40
      No H-bonds generated for 'chain 'E' and resid 38 through 40'
    Processing helix  chain 'E' and resid 53 through 61
    Processing helix  chain 'H' and resid 2 through 8
    Processing helix  chain 'H' and resid 22 through 38
      removed outlier: 3.788A  pdb=" N   ARG H  26 " --> pdb=" O   SER H  22 " (cutoff:3.500A)
    Processing helix  chain 'H' and resid 87 through 93
      removed outlier: 3.539A  pdb=" N   GLY H  93 " --> pdb=" O   ALA H  89 " (cutoff:3.500A)
    Processing sheet with id=AA1, first strand: chain 'A' and resid 8 through 14
      removed outlier: 6.857A  pdb=" N   LYS A  22 " --> pdb=" O   VAL A  12 " (cutoff:3.500A)
      removed outlier: 4.482A  pdb=" N   ILE A  14 " --> pdb=" O   PHE A  20 " (cutoff:3.500A)
      removed outlier: 6.678A  pdb=" N   PHE A  20 " --> pdb=" O   ILE A  14 " (cutoff:3.500A)
      removed outlier: 6.346A  pdb=" N   ASP A 192 " --> pdb=" O   PRO A  27 " (cutoff:3.500A)
      removed outlier: 5.833A  pdb=" N   ALA A 189 " --> pdb=" O   VAL A 185 " (cutoff:3.500A)
      removed outlier: 7.052A  pdb=" N   VAL A 185 " --> pdb=" O   ALA A 189 " (cutoff:3.500A)
      removed outlier: 4.452A  pdb=" N   TYR A 191 " --> pdb=" O   THR A 183 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'A' and resid 95 through 102
      removed outlier: 6.318A  pdb=" N   GLN A 143 " --> pdb=" O   VAL A  53 " (cutoff:3.500A)
      removed outlier: 5.239A  pdb=" N   VAL A  53 " --> pdb=" O   GLN A 143 " (cutoff:3.500A)
      removed outlier: 6.357A  pdb=" N   GLY A 145 " --> pdb=" O   ALA A  51 " (cutoff:3.500A)
      removed outlier: 4.772A  pdb=" N   ALA A  51 " --> pdb=" O   GLY A 145 " (cutoff:3.500A)
    Processing sheet with id=AA3, first strand: chain 'A' and resid 87 through 89
    Processing sheet with id=AA4, first strand: chain 'A' and resid 107 through 108
    Processing sheet with id=AA5, first strand: chain 'A' and resid 148 through 149
      removed outlier: 3.756A  pdb=" N   SER A 168 " --> pdb=" O   THR A 149 " (cutoff:3.500A)
    Processing sheet with id=AA6, first strand: chain 'B' and resid 8 through 12
      removed outlier: 4.126A  pdb=" N   LYS B  22 " --> pdb=" O   VAL B  12 " (cutoff:3.500A)
      removed outlier: 5.413A  pdb=" N   LYS B  22 " --> pdb=" O   VAL B 198 " (cutoff:3.500A)
      removed outlier: 7.238A  pdb=" N   VAL B 198 " --> pdb=" O   LYS B  22 " (cutoff:3.500A)
      removed outlier: 5.432A  pdb=" N   VAL B  24 " --> pdb=" O   LEU B 196 " (cutoff:3.500A)
      removed outlier: 7.061A  pdb=" N   LEU B 196 " --> pdb=" O   VAL B  24 " (cutoff:3.500A)
      removed outlier: 5.580A  pdb=" N   GLU B  26 " --> pdb=" O   LEU B 194 " (cutoff:3.500A)
      removed outlier: 7.723A  pdb=" N   LEU B 194 " --> pdb=" O   GLU B  26 " (cutoff:3.500A)
      removed outlier: 5.352A  pdb=" N   ALA B 189 " --> pdb=" O   VAL B 185 " (cutoff:3.500A)
      removed outlier: 7.374A  pdb=" N   VAL B 185 " --> pdb=" O   ALA B 189 " (cutoff:3.500A)
      removed outlier: 4.090A  pdb=" N   TYR B 191 " --> pdb=" O   THR B 183 " (cutoff:3.500A)
    Processing sheet with id=AA7, first strand: chain 'B' and resid 49 through 50
      removed outlier: 3.652A  pdb=" N   GLY B 145 " --> pdb=" O   GLY B  50 " (cutoff:3.500A)
    Processing sheet with id=AA8, first strand: chain 'B' and resid 53 through 58
      removed outlier: 6.598A  pdb=" N   THR B 141 " --> pdb=" O   THR B  54 " (cutoff:3.500A)
      removed outlier: 4.361A  pdb=" N   ILE B  56 " --> pdb=" O   ARG B 139 " (cutoff:3.500A)
      removed outlier: 6.635A  pdb=" N   ARG B 139 " --> pdb=" O   ILE B  56 " (cutoff:3.500A)
      removed outlier: 4.947A  pdb=" N   ILE B  58 " --> pdb=" O   ARG B 137 " (cutoff:3.500A)
      removed outlier: 7.931A  pdb=" N   ARG B 137 " --> pdb=" O   ILE B  58 " (cutoff:3.500A)
    Processing sheet with id=AA9, first strand: chain 'B' and resid 105 through 108
    Processing sheet with id=AB1, first strand: chain 'C' and resid 4 through 7
      removed outlier: 8.623A  pdb=" N   ALA C 988 " --> pdb=" O   GLN C  13 " (cutoff:3.500A)
      removed outlier: 6.448A  pdb=" N   ARG C  15 " --> pdb=" O   ALA C 988 " (cutoff:3.500A)
    Processing sheet with id=AB2, first strand: chain 'C' and resid 55 through 57
      removed outlier: 4.301A  pdb=" N   LEU C  62 " --> pdb=" O   ASP C  57 " (cutoff:3.500A)
      removed outlier: 7.056A  pdb=" N   LYS C  95 " --> pdb=" O   ILE C  67 " (cutoff:3.500A)
      removed outlier: 4.475A  pdb=" N   TYR C  69 " --> pdb=" O   ARG C  93 " (cutoff:3.500A)
      removed outlier: 6.255A  pdb=" N   ARG C  93 " --> pdb=" O   TYR C  69 " (cutoff:3.500A)
    Processing sheet with id=AB3, first strand: chain 'C' and resid 89 through 91
    Processing sheet with id=AB4, first strand: chain 'C' and resid 125 through 127
    Processing sheet with id=AB5, first strand: chain 'C' and resid 137 through 138
    Processing sheet with id=AB6, first strand: chain 'C' and resid 143 through 147
      removed outlier: 3.815A  pdb=" N   SER C 143 " --> pdb=" O   ILE C 163 " (cutoff:3.500A)
    Processing sheet with id=AB7, first strand: chain 'C' and resid 345 through 350
    Processing sheet with id=AB8, first strand: chain 'C' and resid 485 through 487
      removed outlier: 4.486A  pdb=" N   SER C 530 " --> pdb=" O   CYS C 515 " (cutoff:3.500A)
    Processing sheet with id=AB9, first strand: chain 'C' and resid 536 through 537
      removed outlier: 5.334A  pdb=" N   ARG C 560 " --> pdb=" O   ARG C 549 " (cutoff:3.500A)
    Processing sheet with id=AC1, first strand: chain 'C' and resid 574 through 575
    Processing sheet with id=AC2, first strand: chain 'C' and resid 592 through 595
    Processing sheet with id=AC3, first strand: chain 'C' and resid 681 through 684
      removed outlier: 5.470A  pdb=" N   VAL C 682 " --> pdb=" O   ARG C 693 " (cutoff:3.500A)
      removed outlier: 6.126A  pdb=" N   ARG C 693 " --> pdb=" O   VAL C 682 " (cutoff:3.500A)
      removed outlier: 3.543A  pdb=" N   ASN C 706 " --> pdb=" O   ARG C 694 " (cutoff:3.500A)
    Processing sheet with id=AC4, first strand: chain 'C' and resid 716 through 717
    Processing sheet with id=AC5, first strand: chain 'C' and resid 1014 through 1015
      removed outlier: 4.193A  pdb=" N   GLY C 927 " --> pdb=" O   ASN C 931 " (cutoff:3.500A)
      removed outlier: 5.137A  pdb=" N   ASN C 931 " --> pdb=" O   GLY C 927 " (cutoff:3.500A)
      removed outlier: 7.863A  pdb=" N   ILE C 775 " --> pdb=" O   SER C 936 " (cutoff:3.500A)
      removed outlier: 6.626A  pdb=" N   ILE C 938 " --> pdb=" O   ILE C 775 " (cutoff:3.500A)
      removed outlier: 6.736A  pdb=" N   MET C 777 " --> pdb=" O   ILE C 938 " (cutoff:3.500A)
      removed outlier: 4.820A  pdb=" N   SER C1031 " --> pdb=" O   PHE C 763 " (cutoff:3.500A)
    Processing sheet with id=AC6, first strand: chain 'C' and resid 788 through 799
      removed outlier: 4.350A  pdb=" N   ASP C 889 " --> pdb=" O   TYR C 912 " (cutoff:3.500A)
      removed outlier: 7.001A  pdb=" N   VAL C 914 " --> pdb=" O   ILE C 887 " (cutoff:3.500A)
      removed outlier: 6.625A  pdb=" N   ILE C 887 " --> pdb=" O   VAL C 914 " (cutoff:3.500A)
    Processing sheet with id=AC7, first strand: chain 'C' and resid 845 through 847
      removed outlier: 3.894A  pdb=" N   ARG C 873 " --> pdb=" O   THR C 847 " (cutoff:3.500A)
    Processing sheet with id=AC8, first strand: chain 'C' and resid 1049 through 1051
      removed outlier: 3.819A  pdb=" N   ARG C1051 " --> pdb=" O   SER D 339 " (cutoff:3.500A)
      removed outlier: 4.531A  pdb=" N   SER D 339 " --> pdb=" O   ARG C1051 " (cutoff:3.500A)
    Processing sheet with id=AC9, first strand: chain 'C' and resid 1074 through 1075
    Processing sheet with id=AD1, first strand: chain 'C' and resid 1142 through 1143
      removed outlier: 3.817A  pdb=" N   LYS C1143 " --> pdb=" O   ASN D  11 " (cutoff:3.500A)
      removed outlier: 4.314A  pdb=" N   ASN D  11 " --> pdb=" O   LYS C1143 " (cutoff:3.500A)
    Processing sheet with id=AD2, first strand: chain 'D' and resid 515 through 516
      removed outlier: 3.750A  pdb=" N   PHE D 516 " --> pdb=" O   ALA D 538 " (cutoff:3.500A)
      removed outlier: 4.090A  pdb=" N   ALA D 540 " --> pdb=" O   PHE D 516 " (cutoff:3.500A)
    Processing sheet with id=AD3, first strand: chain 'D' and resid 824 through 826
    Processing sheet with id=AD4, first strand: chain 'D' and resid 829 through 831
      removed outlier: 6.077A  pdb=" N   GLU D 831 " --> pdb=" O   THR D 835 " (cutoff:3.500A)
      removed outlier: 5.533A  pdb=" N   THR D 835 " --> pdb=" O   GLU D 831 " (cutoff:3.500A)
    Processing sheet with id=AD5, first strand: chain 'D' and resid 977 through 981
    Processing sheet with id=AD6, first strand: chain 'D' and resid 1078 through 1080
    Processing sheet with id=AD7, first strand: chain 'L' and resid 69 through 71
    Processing sheet with id=AD8, first strand: chain 'E' and resid 21 through 26
    Processing sheet with id=AD9, first strand: chain 'H' and resid 58 through 61
      removed outlier: 5.848A  pdb=" N   ILE H  58 " --> pdb=" O   SER H  69 " (cutoff:3.500A)
      removed outlier: 5.795A  pdb=" N   SER H  69 " --> pdb=" O   ILE H  58 " (cutoff:3.500A)
      removed outlier: 3.975A  pdb=" N   TYR H  70 " --> pdb=" O   THR H  81 " (cutoff:3.500A)
      removed outlier: 3.833A  pdb=" N   THR H  81 " --> pdb=" O   TYR H  70 " (cutoff:3.500A)

    867 hydrogen bonds defined for protein.
    2406 hydrogen bond angles defined for protein.
    Restraints generated for nucleic acids:
      0 hydrogen bonds
      0 hydrogen bond angles
      0 basepair planarities
      0 basepair parallelities
      0 stacking parallelities
  Total time for adding SS restraints: 15.24

  Time building geometry restraints manager: 11.97 seconds

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

  Histogram of bond lengths:
        0.86 -     1.13: 24488
        1.13 -     1.40: 9776
        1.40 -     1.67: 14751
        1.67 -     1.94: 163
        1.94 -     2.21: 2
  Bond restraints: 49180
  Sorted by residual:
  bond pdb=" CD2 TYR D  70 "
       pdb=" CE2 TYR D  70 "
    ideal  model  delta    sigma   weight residual
    1.382  2.206 -0.824 3.00e-02 1.11e+03 7.54e+02
  bond pdb=" CD1 TYR D  70 "
       pdb=" CE1 TYR D  70 "
    ideal  model  delta    sigma   weight residual
    1.382  2.203 -0.821 3.00e-02 1.11e+03 7.49e+02
  bond pdb=" N   GLY D  79 "
       pdb=" CA  GLY D  79 "
    ideal  model  delta    sigma   weight residual
    1.449  1.793 -0.344 1.45e-02 4.76e+03 5.61e+02
  bond pdb=" CE2 TYR D  70 "
       pdb=" CZ  TYR D  70 "
    ideal  model  delta    sigma   weight residual
    1.378  1.880 -0.502 2.40e-02 1.74e+03 4.37e+02
  bond pdb=" CE1 TYR D  70 "
       pdb=" CZ  TYR D  70 "
    ideal  model  delta    sigma   weight residual
    1.378  1.846 -0.468 2.40e-02 1.74e+03 3.80e+02
  ... (remaining 49175 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     9.83: 89184
        9.83 -    19.65: 2
       19.65 -    29.48: 0
       29.48 -    39.31: 2
       39.31 -    49.14: 1
  Bond angle restraints: 89189
  Sorted by residual:
  angle pdb=" CA  ARG C 312 "
        pdb=" N   ARG C 312 "
        pdb=" H   ARG C 312 "
      ideal   model   delta    sigma   weight residual
     114.00  163.14  -49.14 3.00e+00 1.11e-01 2.68e+02
  angle pdb=" C   CYS D  78 "
        pdb=" N   GLY D  79 "
        pdb=" CA  GLY D  79 "
      ideal   model   delta    sigma   weight residual
     121.41  151.91  -30.50 1.96e+00 2.60e-01 2.42e+02
  angle pdb=" CA  GLY D  79 "
        pdb=" N   GLY D  79 "
        pdb=" H   GLY D  79 "
      ideal   model   delta    sigma   weight residual
     114.15   83.08   31.07 3.00e+00 1.11e-01 1.07e+02
  angle pdb=" N   GLY D  79 "
        pdb=" CA  GLY D  79 "
        pdb=" C   GLY D  79 "
      ideal   model   delta    sigma   weight residual
     113.18  131.37  -18.19 2.37e+00 1.78e-01 5.89e+01
  angle pdb=" CA  PRO D 610 "
        pdb=" N   PRO D 610 "
        pdb=" CD  PRO D 610 "
      ideal   model   delta    sigma   weight residual
     112.00  102.31    9.69 1.40e+00 5.10e-01 4.79e+01
  ... (remaining 89184 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    17.96: 20005
       17.96 -    35.93: 1969
       35.93 -    53.89: 634
       53.89 -    71.86: 183
       71.86 -    89.82: 65
  Dihedral angle restraints: 22856
    sinusoidal: 12863
      harmonic: 9993
  Sorted by residual:
  dihedral pdb=" CB  CYS D  62 "
           pdb=" SG  CYS D  62 "
           pdb=" SG  CYS D  78 "
           pdb=" CB  CYS D  78 "
      ideal   model   delta sinusoidal    sigma   weight residual
      93.00  148.53  -55.53     1      1.00e+01 1.00e-02 4.17e+01
  dihedral pdb=" CA  CYS D  78 "
           pdb=" C   CYS D  78 "
           pdb=" N   GLY D  79 "
           pdb=" CA  GLY D  79 "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00 -149.81  -30.19     0      5.00e+00 4.00e-02 3.64e+01
  dihedral pdb=" CA  GLY D  79 "
           pdb=" C   GLY D  79 "
           pdb=" N   VAL D  80 "
           pdb=" CA  VAL D  80 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  154.12   25.88     0      5.00e+00 4.00e-02 2.68e+01
  ... (remaining 22853 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.038: 2787
       0.038 -    0.076: 653
       0.076 -    0.115: 261
       0.115 -    0.153: 71
       0.153 -    0.191: 2
  Chirality restraints: 3774
  Sorted by residual:
  chirality pdb=" CB  ILE C 792 "
            pdb=" CA  ILE C 792 "
            pdb=" CG1 ILE C 792 "
            pdb=" CG2 ILE C 792 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.64    2.45    0.19 2.00e-01 2.50e+01 9.13e-01
  chirality pdb=" CA  PRO D 610 "
            pdb=" N   PRO D 610 "
            pdb=" C   PRO D 610 "
            pdb=" CB  PRO D 610 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.72    2.55    0.17 2.00e-01 2.50e+01 7.39e-01
  chirality pdb=" CA  ILE D 234 "
            pdb=" N   ILE D 234 "
            pdb=" C   ILE D 234 "
            pdb=" CB  ILE D 234 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.43    2.58   -0.15 2.00e-01 2.50e+01 5.62e-01
  ... (remaining 3771 not shown)

  Planarity restraints: 7287
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CB  TYR D  70 "    0.026 2.00e-02 2.50e+03   3.76e-02 4.24e+01
        pdb=" CG  TYR D  70 "    0.028 2.00e-02 2.50e+03
        pdb=" CD1 TYR D  70 "   -0.027 2.00e-02 2.50e+03
        pdb=" CD2 TYR D  70 "    0.014 2.00e-02 2.50e+03
        pdb=" CE1 TYR D  70 "    0.025 2.00e-02 2.50e+03
        pdb=" CE2 TYR D  70 "   -0.016 2.00e-02 2.50e+03
        pdb=" CZ  TYR D  70 "   -0.000 2.00e-02 2.50e+03
        pdb=" OH  TYR D  70 "   -0.008 2.00e-02 2.50e+03
        pdb=" HD1 TYR D  70 "   -0.087 2.00e-02 2.50e+03
        pdb=" HD2 TYR D  70 "    0.021 2.00e-02 2.50e+03
        pdb=" HE1 TYR D  70 "    0.064 2.00e-02 2.50e+03
        pdb=" HE2 TYR D  70 "   -0.039 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   GLN D 609 "   -0.064 5.00e-02 4.00e+02   9.03e-02 1.31e+01
        pdb=" N   PRO D 610 "    0.156 5.00e-02 4.00e+02
        pdb=" CA  PRO D 610 "   -0.042 5.00e-02 4.00e+02
        pdb=" CD  PRO D 610 "   -0.050 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  CYS D  78 "    0.012 2.00e-02 2.50e+03   2.39e-02 5.71e+00
        pdb=" C   CYS D  78 "   -0.041 2.00e-02 2.50e+03
        pdb=" O   CYS D  78 "    0.016 2.00e-02 2.50e+03
        pdb=" N   GLY D  79 "    0.013 2.00e-02 2.50e+03
  ... (remaining 7284 not shown)

  Histogram of nonbonded interaction distances:
        1.16 -     1.85: 339
        1.85 -     2.53: 41283
        2.53 -     3.22: 142076
        3.22 -     3.91: 170841
        3.91 -     4.60: 261670
  Nonbonded interactions: 616209
  Sorted by model distance:
  nonbonded pdb=" CD1 TYR D  70 "
            pdb=" H   GLY D  79 "
     model   vdw
     1.158 2.800
  nonbonded pdb=" HH  TYR C 664 "
            pdb="HD11 ILE C 741 "
     model   vdw
     1.220 2.270
  nonbonded pdb=" HG  SER A  47 "
            pdb=" HE1 TYR B  32 "
     model   vdw
     1.290 2.100
  nonbonded pdb=" O   VAL D 915 "
            pdb=" HH  TYR D1180 "
     model   vdw
     1.304 2.450
  nonbonded pdb="HD22 LEU C 947 "
            pdb=" HG1 THR C1015 "
     model   vdw
     1.328 2.270
  ... (remaining 616204 not shown)

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

Set up NCS constraints
  No NCS constraints will be used in refinement.
Set refine NCS operators
Adjust number of macro_cycles
  Number of macro_cycles: 10
Reset NCS operators
Extract rigid body selections
Check and reset occupancies
  Occupancies: min=0.00 max=1.00 mean=1.00
Load rotamer database and sin/cos tables
Set ADP refinement strategy
  ADPs will be refined as individual isotropic
Make a string to write initial .geo file
Internal consistency checks
Time:
  Set random seed:                         0.000
  Set model cs if undefined:               0.000
  Decide on map wrapping:                  0.000
  Normalize map: mean=0, sd=1:             2.370
  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:             0.670
  Extract box with map and model:          1.820
  Check model and map are aligned:         0.280
  Set scattering table:                    0.360
  Process input model:                     78.460
  Find NCS groups from input model:        0.490
  Set up NCS constraints:                  0.120
  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:2.890
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   87.470
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.4755
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      :  0.010   0.824  24678  Z= 0.715
  Angle     :  0.611  30.500  33339  Z= 0.331
  Chirality :  0.041   0.191   3774
  Planarity :  0.004   0.090   4348
  Dihedral  : 18.050  89.822   9443
  Min Nonbonded Distance : 1.878

Molprobity Statistics.
  All-atom Clashscore : 7.36
  Ramachandran Plot:
    Outliers :  0.26 %
    Allowed  :  5.30 %
    Favored  : 94.44 %
  Rotamer:
    Outliers :  0.19 %
    Allowed  : 25.48 %
    Favored  : 74.33 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 1.54 %
    Cis-general     : 0.07 %
    Twisted Proline : 0.00 %
    Twisted General : 0.03 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.87 (0.15), residues: 3059
  helix:  0.69 (0.18), residues: 933
  sheet:  0.33 (0.27), residues: 349
  loop : -1.54 (0.15), residues: 1777

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.016   0.001   TRP B 199 
 HIS   0.004   0.001   HIS D 534 
 PHE   0.012   0.001   PHE C1075 
 TYR   0.037   0.001   TYR D  70 
 ARG   0.006   0.000   ARG D 341 

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

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

  6118 Ramachandran restraints generated.
    3059 Oldfield, 0 Emsley, 3059 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  6118 Ramachandran restraints generated.
    3059 Oldfield, 0 Emsley, 3059 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Residue LYS   19 is missing expected H atoms. Skipping.
Residue LYS   65 is missing expected H atoms. Skipping.
Evaluate side-chains
  211 residues out of total 2658 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 5
    poor density    : 206
  time to evaluate  : 2.823 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: C  121 ASP cc_start: 0.5496 (m-30) cc_final: 0.5076 (m-30)
REVERT: C  131 GLU cc_start: 0.7057 (OUTLIER) cc_final: 0.6634 (tm-30)
REVERT: D  866 GLU cc_start: 0.0903 (pm20) cc_final: -0.0972 (pm20)
REVERT: H   75 MET cc_start: 0.2836 (mmt) cc_final: 0.1057 (ppp)
  outliers start: 5
  outliers final: 4
  residues processed: 208
  average time/residue: 0.6251
  time to fit residues: 208.8477
Evaluate side-chains
  199 residues out of total 2658 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 5
    poor density    : 194
  time to evaluate  : 2.860 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain C residue  131 GLU
Chi-restraints excluded: chain C residue  510 HIS
Chi-restraints excluded: chain C residue  601 THR
Chi-restraints excluded: chain C residue 1043 MET
Chi-restraints excluded: chain D residue  120 MET
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 304
   random chunks:
   chunk 256 optimal weight:    5.9990
   chunk 230 optimal weight:    0.7980
   chunk 127 optimal weight:    8.9990
   chunk 78 optimal weight:   20.0000
   chunk 155 optimal weight:    0.9990
   chunk 123 optimal weight:    6.9990
   chunk 238 optimal weight:    0.9990
   chunk 92 optimal weight:    0.9980
   chunk 144 optimal weight:    0.8980
   chunk 177 optimal weight:    5.9990
   chunk 276 optimal weight:    0.9990
   overall best weight:    0.9384

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

Flipped N/Q/H residues before XYZ refinement:
** B 143 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** C 931 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
D 318 HIS

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.5512 r_free = 0.5512 target = 0.310050 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 43)----------------|
| r_work = 0.5200 r_free = 0.5200 target = 0.267180 restraints weight = 86729.889|
|-----------------------------------------------------------------------------|
r_work (start): 0.5208 rms_B_bonded: 3.14
r_work: 0.5017 rms_B_bonded: 3.19 restraints_weight: 0.5000
r_work (final): 0.5017
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.4923
moved from start:          0.0887

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.010   0.820  24678  Z= 0.718
  Angle     :  0.600  30.804  33339  Z= 0.309
  Chirality :  0.042   0.154   3774
  Planarity :  0.004   0.058   4348
  Dihedral  :  4.379  45.092   3385
  Min Nonbonded Distance : 1.966

Molprobity Statistics.
  All-atom Clashscore : 3.79
  Ramachandran Plot:
    Outliers :  0.26 %
    Allowed  :  5.88 %
    Favored  : 93.85 %
  Rotamer:
    Outliers :  1.81 %
    Allowed  : 23.11 %
    Favored  : 75.08 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 1.54 %
    Cis-general     : 0.07 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.92 (0.15), residues: 3059
  helix:  0.64 (0.17), residues: 955
  sheet:  0.29 (0.28), residues: 339
  loop : -1.58 (0.15), residues: 1765

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.010   0.001   TRP B 199 
 HIS   0.007   0.001   HIS D 781 
 PHE   0.012   0.001   PHE D 777 
 TYR   0.038   0.001   TYR D  70 
 ARG   0.005   0.000   ARG A  41 

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

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

  6118 Ramachandran restraints generated.
    3059 Oldfield, 0 Emsley, 3059 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  6118 Ramachandran restraints generated.
    3059 Oldfield, 0 Emsley, 3059 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Residue LYS   19 is missing expected H atoms. Skipping.
Residue LYS   65 is missing expected H atoms. Skipping.
Evaluate side-chains
  242 residues out of total 2658 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 48
    poor density    : 194
  time to evaluate  : 2.829 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: C    8 TYR cc_start: 0.3152 (OUTLIER) cc_final: 0.2749 (m-80)
REVERT: C   29 LEU cc_start: 0.3723 (OUTLIER) cc_final: 0.3504 (pp)
REVERT: C  121 ASP cc_start: 0.5981 (m-30) cc_final: 0.5194 (m-30)
REVERT: C  131 GLU cc_start: 0.6943 (OUTLIER) cc_final: 0.4345 (tt0)
REVERT: C  219 ASN cc_start: 0.5863 (t0) cc_final: 0.5131 (p0)
REVERT: C  274 LYS cc_start: 0.7149 (mmmt) cc_final: 0.6921 (mmmt)
REVERT: C  660 THR cc_start: 0.4546 (OUTLIER) cc_final: 0.4107 (p)
REVERT: D  684 MET cc_start: 0.5234 (OUTLIER) cc_final: 0.5001 (mtm)
REVERT: F   44 HIS cc_start: 0.2050 (OUTLIER) cc_final: 0.1367 (m170)
REVERT: H   75 MET cc_start: 0.2698 (mmt) cc_final: 0.1179 (ppp)
  outliers start: 48
  outliers final: 27
  residues processed: 227
  average time/residue: 0.6274
  time to fit residues: 229.4050
Evaluate side-chains
  222 residues out of total 2658 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 33
    poor density    : 189
  time to evaluate  : 2.866 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  136 PHE
Chi-restraints excluded: chain B residue   45 LEU
Chi-restraints excluded: chain B residue  129 THR
Chi-restraints excluded: chain B residue  183 THR
Chi-restraints excluded: chain C residue    6 VAL
Chi-restraints excluded: chain C residue    8 TYR
Chi-restraints excluded: chain C residue   29 LEU
Chi-restraints excluded: chain C residue  124 THR
Chi-restraints excluded: chain C residue  131 GLU
Chi-restraints excluded: chain C residue  414 GLU
Chi-restraints excluded: chain C residue  470 PHE
Chi-restraints excluded: chain C residue  510 HIS
Chi-restraints excluded: chain C residue  623 THR
Chi-restraints excluded: chain C residue  660 THR
Chi-restraints excluded: chain C residue  713 LEU
Chi-restraints excluded: chain C residue  741 ILE
Chi-restraints excluded: chain C residue  965 ARG
Chi-restraints excluded: chain C residue 1094 GLU
Chi-restraints excluded: chain D residue   62 CYS
Chi-restraints excluded: chain D residue  176 HIS
Chi-restraints excluded: chain D residue  533 LEU
Chi-restraints excluded: chain D residue  631 PHE
Chi-restraints excluded: chain D residue  684 MET
Chi-restraints excluded: chain D residue  787 LEU
Chi-restraints excluded: chain D residue  796 ASP
Chi-restraints excluded: chain D residue  871 ASP
Chi-restraints excluded: chain D residue  892 CYS
Chi-restraints excluded: chain D residue 1038 THR
Chi-restraints excluded: chain D residue 1070 MET
Chi-restraints excluded: chain D residue 1135 SER
Chi-restraints excluded: chain F residue   44 HIS
Chi-restraints excluded: chain E residue   45 GLU
Chi-restraints excluded: chain H residue   38 LEU
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 304
   random chunks:
   chunk 296 optimal weight:   10.0000
   chunk 76 optimal weight:    3.9990
   chunk 298 optimal weight:    6.9990
   chunk 150 optimal weight:    1.9990
   chunk 165 optimal weight:    6.9990
   chunk 193 optimal weight:    0.6980
   chunk 169 optimal weight:    0.1980
   chunk 217 optimal weight:    4.9990
   chunk 16 optimal weight:    0.6980
   chunk 4 optimal weight:    0.9990
   chunk 289 optimal weight:    2.9990
   overall best weight:    0.9184

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

Flipped N/Q/H residues before XYZ refinement:
B 143 GLN
C 931 ASN
D 568 ASN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.5514 r_free = 0.5514 target = 0.311730 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 43)----------------|
| r_work = 0.5193 r_free = 0.5193 target = 0.269911 restraints weight = 86976.556|
|-----------------------------------------------------------------------------|
r_work (start): 0.5189 rms_B_bonded: 3.18
r_work: 0.4997 rms_B_bonded: 3.20 restraints_weight: 0.5000
r_work (final): 0.4997
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.4960
moved from start:          0.1184

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.010   0.826  24678  Z= 0.715
  Angle     :  0.569  30.428  33339  Z= 0.293
  Chirality :  0.041   0.156   3774
  Planarity :  0.004   0.059   4348
  Dihedral  :  4.293  57.587   3378
  Min Nonbonded Distance : 1.972

Molprobity Statistics.
  All-atom Clashscore : 3.79
  Ramachandran Plot:
    Outliers :  0.26 %
    Allowed  :  5.82 %
    Favored  : 93.92 %
  Rotamer:
    Outliers :  2.37 %
    Allowed  : 22.16 %
    Favored  : 75.46 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 1.54 %
    Cis-general     : 0.07 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.94 (0.15), residues: 3059
  helix:  0.66 (0.17), residues: 950
  sheet:  0.25 (0.28), residues: 345
  loop : -1.60 (0.14), residues: 1764

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.009   0.001   TRP B 199 
 HIS   0.004   0.001   HIS D 781 
 PHE   0.009   0.001   PHE C  40 
 TYR   0.037   0.001   TYR D  70 
 ARG   0.010   0.000   ARG E  17 

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

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

  6118 Ramachandran restraints generated.
    3059 Oldfield, 0 Emsley, 3059 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  6118 Ramachandran restraints generated.
    3059 Oldfield, 0 Emsley, 3059 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Residue LYS   19 is missing expected H atoms. Skipping.
Residue LYS   65 is missing expected H atoms. Skipping.
Evaluate side-chains
  271 residues out of total 2658 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 63
    poor density    : 208
  time to evaluate  : 2.862 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: C  131 GLU cc_start: 0.7146 (OUTLIER) cc_final: 0.4606 (tt0)
REVERT: C  171 GLU cc_start: 0.6629 (OUTLIER) cc_final: 0.6381 (pm20)
REVERT: C  219 ASN cc_start: 0.5666 (t0) cc_final: 0.4991 (p0)
REVERT: C  274 LYS cc_start: 0.7129 (mmmt) cc_final: 0.6746 (mmmt)
REVERT: C  660 THR cc_start: 0.4642 (OUTLIER) cc_final: 0.4246 (p)
REVERT: C  696 GLU cc_start: 0.4596 (mm-30) cc_final: 0.4351 (mm-30)
REVERT: C  889 ASP cc_start: 0.4969 (OUTLIER) cc_final: 0.4716 (p0)
REVERT: D  120 MET cc_start: 0.1222 (OUTLIER) cc_final: 0.0957 (tmm)
REVERT: D  684 MET cc_start: 0.5049 (OUTLIER) cc_final: 0.4819 (mtm)
REVERT: D  767 PHE cc_start: 0.3705 (m-80) cc_final: 0.3178 (m-80)
REVERT: D  843 LEU cc_start: 0.5818 (OUTLIER) cc_final: 0.5554 (mm)
REVERT: F   37 MET cc_start: -0.1740 (mpp) cc_final: -0.2036 (mpp)
REVERT: F   44 HIS cc_start: 0.2218 (OUTLIER) cc_final: 0.1422 (m170)
REVERT: L   14 MET cc_start: -0.0314 (ppp) cc_final: -0.1214 (ptm)
REVERT: H   75 MET cc_start: 0.2748 (mmt) cc_final: 0.1424 (ppp)
  outliers start: 63
  outliers final: 39
  residues processed: 255
  average time/residue: 0.5878
  time to fit residues: 245.1748
Evaluate side-chains
  247 residues out of total 2658 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 47
    poor density    : 200
  time to evaluate  : 2.822 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   45 LEU
Chi-restraints excluded: chain A residue   47 SER
Chi-restraints excluded: chain A residue   66 SER
Chi-restraints excluded: chain A residue  136 PHE
Chi-restraints excluded: chain B residue   25 VAL
Chi-restraints excluded: chain B residue   45 LEU
Chi-restraints excluded: chain B residue  129 THR
Chi-restraints excluded: chain B residue  183 THR
Chi-restraints excluded: chain C residue    6 VAL
Chi-restraints excluded: chain C residue  124 THR
Chi-restraints excluded: chain C residue  131 GLU
Chi-restraints excluded: chain C residue  171 GLU
Chi-restraints excluded: chain C residue  414 GLU
Chi-restraints excluded: chain C residue  470 PHE
Chi-restraints excluded: chain C residue  510 HIS
Chi-restraints excluded: chain C residue  623 THR
Chi-restraints excluded: chain C residue  644 GLN
Chi-restraints excluded: chain C residue  660 THR
Chi-restraints excluded: chain C residue  681 ILE
Chi-restraints excluded: chain C residue  708 ASP
Chi-restraints excluded: chain C residue  713 LEU
Chi-restraints excluded: chain C residue  764 MET
Chi-restraints excluded: chain C residue  792 ILE
Chi-restraints excluded: chain C residue  889 ASP
Chi-restraints excluded: chain C residue  965 ARG
Chi-restraints excluded: chain C residue 1043 MET
Chi-restraints excluded: chain C residue 1094 GLU
Chi-restraints excluded: chain D residue   62 CYS
Chi-restraints excluded: chain D residue  120 MET
Chi-restraints excluded: chain D residue  176 HIS
Chi-restraints excluded: chain D residue  419 HIS
Chi-restraints excluded: chain D residue  533 LEU
Chi-restraints excluded: chain D residue  588 GLU
Chi-restraints excluded: chain D residue  631 PHE
Chi-restraints excluded: chain D residue  666 LEU
Chi-restraints excluded: chain D residue  684 MET
Chi-restraints excluded: chain D residue  787 LEU
Chi-restraints excluded: chain D residue  796 ASP
Chi-restraints excluded: chain D residue  843 LEU
Chi-restraints excluded: chain D residue  871 ASP
Chi-restraints excluded: chain D residue  892 CYS
Chi-restraints excluded: chain D residue 1038 THR
Chi-restraints excluded: chain D residue 1070 MET
Chi-restraints excluded: chain F residue   44 HIS
Chi-restraints excluded: chain L residue   64 ILE
Chi-restraints excluded: chain E residue   45 GLU
Chi-restraints excluded: chain H residue   38 LEU
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 304
   random chunks:
   chunk 203 optimal weight:    2.9990
   chunk 103 optimal weight:    4.9990
   chunk 76 optimal weight:    5.9990
   chunk 24 optimal weight:    2.9990
   chunk 125 optimal weight:    5.9990
   chunk 184 optimal weight:    3.9990
   chunk 57 optimal weight:    0.1980
   chunk 134 optimal weight:    0.8980
   chunk 259 optimal weight:    8.9990
   chunk 222 optimal weight:    2.9990
   chunk 244 optimal weight:    0.8980
   overall best weight:    1.5984

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

Flipped N/Q/H residues before XYZ refinement:
C 907 GLN
** C 931 ASN ** 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 = 0.5485 r_free = 0.5485 target = 0.308225 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 49)----------------|
| r_work = 0.5164 r_free = 0.5164 target = 0.265646 restraints weight = 86915.081|
|-----------------------------------------------------------------------------|
r_work (start): 0.5161 rms_B_bonded: 3.14
r_work: 0.4958 rms_B_bonded: 2.95 restraints_weight: 0.5000
r_work: 0.4839 rms_B_bonded: 4.95 restraints_weight: 0.2500
r_work (final): 0.4839
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.5187
moved from start:          0.1650

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.010   0.827  24678  Z= 0.738
  Angle     :  0.627  30.739  33339  Z= 0.328
  Chirality :  0.043   0.183   3774
  Planarity :  0.005   0.060   4348
  Dihedral  :  4.647  58.323   3378
  Min Nonbonded Distance : 1.969

Molprobity Statistics.
  All-atom Clashscore : 6.40
  Ramachandran Plot:
    Outliers :  0.26 %
    Allowed  :  7.16 %
    Favored  : 92.58 %
  Rotamer:
    Outliers :  3.17 %
    Allowed  : 22.65 %
    Favored  : 74.18 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 1.54 %
    Cis-general     : 0.07 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -1.28 (0.15), residues: 3059
  helix:  0.34 (0.17), residues: 950
  sheet: -0.02 (0.28), residues: 346
  loop : -1.78 (0.14), residues: 1763

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.011   0.001   TRP A 199 
 HIS   0.005   0.001   HIS D 781 
 PHE   0.020   0.002   PHE C  40 
 TYR   0.038   0.002   TYR D  70 
 ARG   0.026   0.000   ARG D 963 

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

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

  6118 Ramachandran restraints generated.
    3059 Oldfield, 0 Emsley, 3059 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  6118 Ramachandran restraints generated.
    3059 Oldfield, 0 Emsley, 3059 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Residue LYS   19 is missing expected H atoms. Skipping.
Residue LYS   65 is missing expected H atoms. Skipping.
Evaluate side-chains
  283 residues out of total 2658 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 84
    poor density    : 199
  time to evaluate  : 2.840 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: B   24 VAL cc_start: 0.6306 (OUTLIER) cc_final: 0.5862 (t)
REVERT: B  169 ILE cc_start: 0.7558 (OUTLIER) cc_final: 0.7332 (mt)
REVERT: C   40 PHE cc_start: 0.6051 (OUTLIER) cc_final: 0.5811 (t80)
REVERT: C  219 ASN cc_start: 0.5606 (t0) cc_final: 0.5171 (p0)
REVERT: C  274 LYS cc_start: 0.6708 (mmmt) cc_final: 0.6127 (mmmt)
REVERT: C  611 MET cc_start: 0.3828 (tmm) cc_final: 0.3430 (ttp)
REVERT: C  660 THR cc_start: 0.4743 (OUTLIER) cc_final: 0.4371 (p)
REVERT: C  696 GLU cc_start: 0.4777 (mm-30) cc_final: 0.4524 (mm-30)
REVERT: C  889 ASP cc_start: 0.5454 (OUTLIER) cc_final: 0.4949 (p0)
REVERT: C 1015 THR cc_start: 0.5391 (OUTLIER) cc_final: 0.4565 (t)
REVERT: C 1074 ARG cc_start: 0.5461 (mtm-85) cc_final: 0.4320 (ttt90)
REVERT: D  470 ARG cc_start: 0.6281 (OUTLIER) cc_final: 0.5957 (mtp180)
REVERT: D  684 MET cc_start: 0.5070 (OUTLIER) cc_final: 0.4813 (mtm)
REVERT: D  843 LEU cc_start: 0.5982 (OUTLIER) cc_final: 0.5679 (mm)
REVERT: D  866 GLU cc_start: 0.0949 (pm20) cc_final: -0.0271 (pm20)
REVERT: F   37 MET cc_start: -0.1487 (mpp) cc_final: -0.1922 (mpp)
REVERT: F   44 HIS cc_start: 0.2633 (OUTLIER) cc_final: 0.1317 (m90)
REVERT: L   14 MET cc_start: -0.0255 (ppp) cc_final: -0.0549 (ppp)
REVERT: H   75 MET cc_start: 0.2726 (mmt) cc_final: 0.1288 (ppp)
  outliers start: 84
  outliers final: 56
  residues processed: 269
  average time/residue: 0.6295
  time to fit residues: 270.0822
Evaluate side-chains
  258 residues out of total 2658 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 66
    poor density    : 192
  time to evaluate  : 3.032 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   46 SER
Chi-restraints excluded: chain A residue   47 SER
Chi-restraints excluded: chain A residue   66 SER
Chi-restraints excluded: chain A residue  136 PHE
Chi-restraints excluded: chain A residue  197 ASP
Chi-restraints excluded: chain B residue   24 VAL
Chi-restraints excluded: chain B residue   25 VAL
Chi-restraints excluded: chain B residue   45 LEU
Chi-restraints excluded: chain B residue  129 THR
Chi-restraints excluded: chain B residue  141 THR
Chi-restraints excluded: chain B residue  169 ILE
Chi-restraints excluded: chain B residue  183 THR
Chi-restraints excluded: chain C residue   25 GLU
Chi-restraints excluded: chain C residue   40 PHE
Chi-restraints excluded: chain C residue  124 THR
Chi-restraints excluded: chain C residue  127 ILE
Chi-restraints excluded: chain C residue  131 GLU
Chi-restraints excluded: chain C residue  136 SER
Chi-restraints excluded: chain C residue  414 GLU
Chi-restraints excluded: chain C residue  470 PHE
Chi-restraints excluded: chain C residue  510 HIS
Chi-restraints excluded: chain C residue  511 TYR
Chi-restraints excluded: chain C residue  570 ASP
Chi-restraints excluded: chain C residue  613 VAL
Chi-restraints excluded: chain C residue  623 THR
Chi-restraints excluded: chain C residue  644 GLN
Chi-restraints excluded: chain C residue  660 THR
Chi-restraints excluded: chain C residue  681 ILE
Chi-restraints excluded: chain C residue  708 ASP
Chi-restraints excluded: chain C residue  713 LEU
Chi-restraints excluded: chain C residue  723 CYS
Chi-restraints excluded: chain C residue  741 ILE
Chi-restraints excluded: chain C residue  764 MET
Chi-restraints excluded: chain C residue  778 SER
Chi-restraints excluded: chain C residue  792 ILE
Chi-restraints excluded: chain C residue  889 ASP
Chi-restraints excluded: chain C residue  965 ARG
Chi-restraints excluded: chain C residue 1015 THR
Chi-restraints excluded: chain C residue 1043 MET
Chi-restraints excluded: chain C residue 1094 GLU
Chi-restraints excluded: chain D residue   62 CYS
Chi-restraints excluded: chain D residue  176 HIS
Chi-restraints excluded: chain D residue  419 HIS
Chi-restraints excluded: chain D residue  470 ARG
Chi-restraints excluded: chain D residue  528 ASN
Chi-restraints excluded: chain D residue  533 LEU
Chi-restraints excluded: chain D residue  559 ILE
Chi-restraints excluded: chain D residue  588 GLU
Chi-restraints excluded: chain D residue  623 ILE
Chi-restraints excluded: chain D residue  631 PHE
Chi-restraints excluded: chain D residue  657 THR
Chi-restraints excluded: chain D residue  666 LEU
Chi-restraints excluded: chain D residue  684 MET
Chi-restraints excluded: chain D residue  787 LEU
Chi-restraints excluded: chain D residue  796 ASP
Chi-restraints excluded: chain D residue  843 LEU
Chi-restraints excluded: chain D residue  871 ASP
Chi-restraints excluded: chain D residue  892 CYS
Chi-restraints excluded: chain D residue 1038 THR
Chi-restraints excluded: chain D residue 1070 MET
Chi-restraints excluded: chain D residue 1138 SER
Chi-restraints excluded: chain F residue   44 HIS
Chi-restraints excluded: chain L residue   64 ILE
Chi-restraints excluded: chain E residue   45 GLU
Chi-restraints excluded: chain E residue   50 VAL
Chi-restraints excluded: chain H residue   38 LEU
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 304
   random chunks:
   chunk 284 optimal weight:    8.9990
   chunk 235 optimal weight:    2.9990
   chunk 37 optimal weight:    2.9990
   chunk 62 optimal weight:    0.0570
   chunk 13 optimal weight:    0.5980
   chunk 118 optimal weight:    0.7980
   chunk 287 optimal weight:    6.9990
   chunk 238 optimal weight:    3.9990
   chunk 217 optimal weight:    0.9980
   chunk 77 optimal weight:    7.9990
   chunk 115 optimal weight:    0.9990
   overall best weight:    0.6900

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

Flipped N/Q/H residues before XYZ refinement:
C 931 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.5509 r_free = 0.5509 target = 0.311239 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 46)----------------|
| r_work = 0.5182 r_free = 0.5182 target = 0.268984 restraints weight = 86732.178|
|-----------------------------------------------------------------------------|
r_work (start): 0.5171 rms_B_bonded: 2.96
r_work: 0.4985 rms_B_bonded: 3.07 restraints_weight: 0.5000
r_work (final): 0.4985
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.5001
moved from start:          0.1776

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.010   0.824  24678  Z= 0.709
  Angle     :  0.551  30.579  33339  Z= 0.285
  Chirality :  0.041   0.155   3774
  Planarity :  0.004   0.058   4348
  Dihedral  :  4.409  61.479   3378
  Min Nonbonded Distance : 1.970

Molprobity Statistics.
  All-atom Clashscore : 4.59
  Ramachandran Plot:
    Outliers :  0.26 %
    Allowed  :  5.30 %
    Favored  : 94.44 %
  Rotamer:
    Outliers :  2.45 %
    Allowed  : 23.22 %
    Favored  : 74.33 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 1.54 %
    Cis-general     : 0.07 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -1.03 (0.15), residues: 3059
  helix:  0.61 (0.17), residues: 951
  sheet:  0.08 (0.28), residues: 342
  loop : -1.65 (0.15), residues: 1766

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.009   0.001   TRP B 199 
 HIS   0.004   0.001   HIS D 419 
 PHE   0.009   0.001   PHE A 136 
 TYR   0.037   0.001   TYR D  70 
 ARG   0.004   0.000   ARG B  30 

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

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

  6118 Ramachandran restraints generated.
    3059 Oldfield, 0 Emsley, 3059 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  6118 Ramachandran restraints generated.
    3059 Oldfield, 0 Emsley, 3059 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Residue LYS   19 is missing expected H atoms. Skipping.
Residue LYS   65 is missing expected H atoms. Skipping.
Evaluate side-chains
  267 residues out of total 2658 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 65
    poor density    : 202
  time to evaluate  : 2.932 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: B   24 VAL cc_start: 0.6263 (OUTLIER) cc_final: 0.5828 (t)
REVERT: B  169 ILE cc_start: 0.7396 (OUTLIER) cc_final: 0.7174 (mt)
REVERT: C   40 PHE cc_start: 0.5878 (OUTLIER) cc_final: 0.5381 (t80)
REVERT: C  121 ASP cc_start: 0.6158 (m-30) cc_final: 0.5407 (m-30)
REVERT: C  219 ASN cc_start: 0.5679 (t0) cc_final: 0.5228 (p0)
REVERT: C  274 LYS cc_start: 0.6705 (mmmt) cc_final: 0.6011 (mmmt)
REVERT: C  403 HIS cc_start: 0.5985 (OUTLIER) cc_final: 0.5417 (t-90)
REVERT: C  696 GLU cc_start: 0.4460 (mm-30) cc_final: 0.4256 (mm-30)
REVERT: C 1074 ARG cc_start: 0.5271 (mtm-85) cc_final: 0.4261 (ttt90)
REVERT: D  539 VAL cc_start: 0.3765 (p) cc_final: 0.3538 (p)
REVERT: D  684 MET cc_start: 0.5055 (OUTLIER) cc_final: 0.4781 (mtm)
REVERT: D  843 LEU cc_start: 0.5808 (OUTLIER) cc_final: 0.5495 (mm)
REVERT: D  866 GLU cc_start: 0.0803 (pm20) cc_final: 0.0027 (pm20)
REVERT: F   37 MET cc_start: -0.1499 (mpp) cc_final: -0.1884 (mpp)
REVERT: F   44 HIS cc_start: 0.2429 (OUTLIER) cc_final: 0.1458 (m170)
REVERT: L   14 MET cc_start: -0.0085 (ppp) cc_final: -0.0426 (ppp)
REVERT: H   75 MET cc_start: 0.2715 (mmt) cc_final: 0.1285 (ppp)
  outliers start: 65
  outliers final: 48
  residues processed: 253
  average time/residue: 0.6271
  time to fit residues: 254.3215
Evaluate side-chains
  246 residues out of total 2658 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 55
    poor density    : 191
  time to evaluate  : 2.848 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   45 LEU
Chi-restraints excluded: chain A residue   47 SER
Chi-restraints excluded: chain A residue  136 PHE
Chi-restraints excluded: chain A residue  197 ASP
Chi-restraints excluded: chain A residue  224 PHE
Chi-restraints excluded: chain B residue   24 VAL
Chi-restraints excluded: chain B residue   25 VAL
Chi-restraints excluded: chain B residue   45 LEU
Chi-restraints excluded: chain B residue  129 THR
Chi-restraints excluded: chain B residue  169 ILE
Chi-restraints excluded: chain B residue  183 THR
Chi-restraints excluded: chain B residue  195 THR
Chi-restraints excluded: chain C residue   40 PHE
Chi-restraints excluded: chain C residue  124 THR
Chi-restraints excluded: chain C residue  127 ILE
Chi-restraints excluded: chain C residue  131 GLU
Chi-restraints excluded: chain C residue  136 SER
Chi-restraints excluded: chain C residue  403 HIS
Chi-restraints excluded: chain C residue  414 GLU
Chi-restraints excluded: chain C residue  510 HIS
Chi-restraints excluded: chain C residue  511 TYR
Chi-restraints excluded: chain C residue  570 ASP
Chi-restraints excluded: chain C residue  613 VAL
Chi-restraints excluded: chain C residue  623 THR
Chi-restraints excluded: chain C residue  644 GLN
Chi-restraints excluded: chain C residue  654 GLU
Chi-restraints excluded: chain C residue  681 ILE
Chi-restraints excluded: chain C residue  708 ASP
Chi-restraints excluded: chain C residue  713 LEU
Chi-restraints excluded: chain C residue  741 ILE
Chi-restraints excluded: chain C residue  764 MET
Chi-restraints excluded: chain C residue  779 GLU
Chi-restraints excluded: chain C residue  792 ILE
Chi-restraints excluded: chain C residue  965 ARG
Chi-restraints excluded: chain C residue 1094 GLU
Chi-restraints excluded: chain D residue   12 ILE
Chi-restraints excluded: chain D residue   62 CYS
Chi-restraints excluded: chain D residue  176 HIS
Chi-restraints excluded: chain D residue  528 ASN
Chi-restraints excluded: chain D residue  533 LEU
Chi-restraints excluded: chain D residue  534 HIS
Chi-restraints excluded: chain D residue  588 GLU
Chi-restraints excluded: chain D residue  631 PHE
Chi-restraints excluded: chain D residue  666 LEU
Chi-restraints excluded: chain D residue  684 MET
Chi-restraints excluded: chain D residue  787 LEU
Chi-restraints excluded: chain D residue  843 LEU
Chi-restraints excluded: chain D residue  871 ASP
Chi-restraints excluded: chain D residue  892 CYS
Chi-restraints excluded: chain D residue 1038 THR
Chi-restraints excluded: chain D residue 1070 MET
Chi-restraints excluded: chain F residue   44 HIS
Chi-restraints excluded: chain L residue   64 ILE
Chi-restraints excluded: chain E residue   45 GLU
Chi-restraints excluded: chain H residue   38 LEU
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 304
   random chunks:
   chunk 291 optimal weight:    1.9990
   chunk 35 optimal weight:    3.9990
   chunk 192 optimal weight:    1.9990
   chunk 15 optimal weight:    0.4980
   chunk 148 optimal weight:    2.9990
   chunk 126 optimal weight:    4.9990
   chunk 264 optimal weight:    5.9990
   chunk 214 optimal weight:    0.0030
   chunk 187 optimal weight:    0.0570
   chunk 29 optimal weight:    2.9990
   chunk 146 optimal weight:    0.9980
   overall best weight:    0.7110

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

Flipped N/Q/H residues before XYZ refinement:

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.5503 r_free = 0.5503 target = 0.310665 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 53)----------------|
| r_work = 0.5127 r_free = 0.5127 target = 0.264128 restraints weight = 87057.849|
|-----------------------------------------------------------------------------|
r_work (start): 0.5135 rms_B_bonded: 2.84
r_work: 0.4972 rms_B_bonded: 3.23 restraints_weight: 0.5000
r_work (final): 0.4972
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.5014
moved from start:          0.1883

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.010   0.824  24678  Z= 0.710
  Angle     :  0.545  30.613  33339  Z= 0.281
  Chirality :  0.041   0.154   3774
  Planarity :  0.004   0.056   4348
  Dihedral  :  4.332  60.473   3378
  Min Nonbonded Distance : 1.970

Molprobity Statistics.
  All-atom Clashscore : 4.70
  Ramachandran Plot:
    Outliers :  0.26 %
    Allowed  :  6.11 %
    Favored  : 93.63 %
  Rotamer:
    Outliers :  2.37 %
    Allowed  : 22.92 %
    Favored  : 74.71 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 1.54 %
    Cis-general     : 0.07 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.97 (0.15), residues: 3059
  helix:  0.70 (0.17), residues: 951
  sheet:  0.09 (0.28), residues: 342
  loop : -1.63 (0.15), residues: 1766

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.009   0.001   TRP B 199 
 HIS   0.004   0.001   HIS D 419 
 PHE   0.009   0.001   PHE C  40 
 TYR   0.037   0.001   TYR D  70 
 ARG   0.004   0.000   ARG F  25 

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

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

  6118 Ramachandran restraints generated.
    3059 Oldfield, 0 Emsley, 3059 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  6118 Ramachandran restraints generated.
    3059 Oldfield, 0 Emsley, 3059 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Residue LYS   19 is missing expected H atoms. Skipping.
Residue LYS   65 is missing expected H atoms. Skipping.
Evaluate side-chains
  263 residues out of total 2658 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 63
    poor density    : 200
  time to evaluate  : 2.884 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: B   24 VAL cc_start: 0.6344 (OUTLIER) cc_final: 0.5925 (t)
REVERT: B  169 ILE cc_start: 0.7407 (OUTLIER) cc_final: 0.7200 (mt)
REVERT: C   40 PHE cc_start: 0.5894 (OUTLIER) cc_final: 0.5382 (t80)
REVERT: C  219 ASN cc_start: 0.5688 (t0) cc_final: 0.5282 (p0)
REVERT: C  274 LYS cc_start: 0.6632 (mmmt) cc_final: 0.5976 (mmmt)
REVERT: C  403 HIS cc_start: 0.6031 (OUTLIER) cc_final: 0.5429 (t-90)
REVERT: C 1074 ARG cc_start: 0.5330 (mtm-85) cc_final: 0.4276 (ttt90)
REVERT: D  684 MET cc_start: 0.5041 (OUTLIER) cc_final: 0.4768 (mtm)
REVERT: D  843 LEU cc_start: 0.5801 (OUTLIER) cc_final: 0.5502 (mm)
REVERT: D  866 GLU cc_start: 0.0777 (pm20) cc_final: -0.0003 (pm20)
REVERT: F   37 MET cc_start: -0.1430 (mpp) cc_final: -0.1781 (mpp)
REVERT: F   44 HIS cc_start: 0.2482 (OUTLIER) cc_final: 0.1478 (m170)
REVERT: L   14 MET cc_start: -0.0010 (ppp) cc_final: -0.0348 (ppp)
REVERT: H   75 MET cc_start: 0.2701 (mmt) cc_final: 0.1297 (ppp)
  outliers start: 63
  outliers final: 49
  residues processed: 252
  average time/residue: 0.6412
  time to fit residues: 261.0603
Evaluate side-chains
  253 residues out of total 2658 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 56
    poor density    : 197
  time to evaluate  : 2.863 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   45 LEU
Chi-restraints excluded: chain A residue  136 PHE
Chi-restraints excluded: chain A residue  197 ASP
Chi-restraints excluded: chain A residue  224 PHE
Chi-restraints excluded: chain B residue   10 GLU
Chi-restraints excluded: chain B residue   24 VAL
Chi-restraints excluded: chain B residue   25 VAL
Chi-restraints excluded: chain B residue   45 LEU
Chi-restraints excluded: chain B residue   47 SER
Chi-restraints excluded: chain B residue  129 THR
Chi-restraints excluded: chain B residue  141 THR
Chi-restraints excluded: chain B residue  169 ILE
Chi-restraints excluded: chain B residue  183 THR
Chi-restraints excluded: chain B residue  195 THR
Chi-restraints excluded: chain C residue   13 GLN
Chi-restraints excluded: chain C residue   40 PHE
Chi-restraints excluded: chain C residue  124 THR
Chi-restraints excluded: chain C residue  127 ILE
Chi-restraints excluded: chain C residue  131 GLU
Chi-restraints excluded: chain C residue  136 SER
Chi-restraints excluded: chain C residue  403 HIS
Chi-restraints excluded: chain C residue  414 GLU
Chi-restraints excluded: chain C residue  510 HIS
Chi-restraints excluded: chain C residue  511 TYR
Chi-restraints excluded: chain C residue  570 ASP
Chi-restraints excluded: chain C residue  613 VAL
Chi-restraints excluded: chain C residue  623 THR
Chi-restraints excluded: chain C residue  644 GLN
Chi-restraints excluded: chain C residue  654 GLU
Chi-restraints excluded: chain C residue  681 ILE
Chi-restraints excluded: chain C residue  708 ASP
Chi-restraints excluded: chain C residue  713 LEU
Chi-restraints excluded: chain C residue  764 MET
Chi-restraints excluded: chain C residue  792 ILE
Chi-restraints excluded: chain C residue  965 ARG
Chi-restraints excluded: chain C residue 1015 THR
Chi-restraints excluded: chain C residue 1094 GLU
Chi-restraints excluded: chain D residue   12 ILE
Chi-restraints excluded: chain D residue   62 CYS
Chi-restraints excluded: chain D residue  419 HIS
Chi-restraints excluded: chain D residue  528 ASN
Chi-restraints excluded: chain D residue  588 GLU
Chi-restraints excluded: chain D residue  631 PHE
Chi-restraints excluded: chain D residue  666 LEU
Chi-restraints excluded: chain D residue  684 MET
Chi-restraints excluded: chain D residue  787 LEU
Chi-restraints excluded: chain D residue  843 LEU
Chi-restraints excluded: chain D residue  871 ASP
Chi-restraints excluded: chain D residue 1038 THR
Chi-restraints excluded: chain D residue 1070 MET
Chi-restraints excluded: chain D residue 1138 SER
Chi-restraints excluded: chain F residue   44 HIS
Chi-restraints excluded: chain L residue   64 ILE
Chi-restraints excluded: chain E residue   45 GLU
Chi-restraints excluded: chain E residue   50 VAL
Chi-restraints excluded: chain H residue   38 LEU
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 304
   random chunks:
   chunk 67 optimal weight:    3.9990
   chunk 269 optimal weight:    6.9990
   chunk 61 optimal weight:    0.7980
   chunk 176 optimal weight:    8.9990
   chunk 220 optimal weight:    2.9990
   chunk 277 optimal weight:    1.9990
   chunk 78 optimal weight:    8.9990
   chunk 155 optimal weight:    0.9990
   chunk 105 optimal weight:    0.9980
   chunk 8 optimal weight:    1.9990
   chunk 121 optimal weight:    0.9990
   overall best weight:    1.1586

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

Flipped N/Q/H residues before XYZ refinement:
** B 143 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
C 931 ASN
C1136 GLN
** F  31 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 = 0.5485 r_free = 0.5485 target = 0.308100 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.5117 r_free = 0.5117 target = 0.263002 restraints weight = 86440.504|
|-----------------------------------------------------------------------------|
r_work (start): 0.5143 rms_B_bonded: 2.98
r_work: 0.4968 rms_B_bonded: 3.08 restraints_weight: 0.5000
r_work (final): 0.4968
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.5067
moved from start:          0.2170

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.010   0.826  24678  Z= 0.722
  Angle     :  0.583  30.646  33339  Z= 0.303
  Chirality :  0.042   0.159   3774
  Planarity :  0.004   0.058   4348
  Dihedral  :  4.521  62.188   3378
  Min Nonbonded Distance : 1.971

Molprobity Statistics.
  All-atom Clashscore : 5.84
  Ramachandran Plot:
    Outliers :  0.26 %
    Allowed  :  7.16 %
    Favored  : 92.58 %
  Rotamer:
    Outliers :  2.98 %
    Allowed  : 22.50 %
    Favored  : 74.52 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 1.54 %
    Cis-general     : 0.07 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -1.13 (0.15), residues: 3059
  helix:  0.52 (0.17), residues: 957
  sheet:  0.26 (0.29), residues: 324
  loop : -1.75 (0.15), residues: 1778

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.010   0.001   TRP B 199 
 HIS   0.005   0.001   HIS C 507 
 PHE   0.015   0.001   PHE C  40 
 TYR   0.037   0.002   TYR D  70 
 ARG   0.005   0.000   ARG F  25 

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

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

  6118 Ramachandran restraints generated.
    3059 Oldfield, 0 Emsley, 3059 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  6118 Ramachandran restraints generated.
    3059 Oldfield, 0 Emsley, 3059 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Residue LYS   19 is missing expected H atoms. Skipping.
Residue LYS   65 is missing expected H atoms. Skipping.
Evaluate side-chains
  282 residues out of total 2658 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 79
    poor density    : 203
  time to evaluate  : 2.893 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: B   24 VAL cc_start: 0.6108 (OUTLIER) cc_final: 0.5665 (t)
REVERT: B  169 ILE cc_start: 0.7410 (OUTLIER) cc_final: 0.7191 (mt)
REVERT: C   31 GLU cc_start: 0.6717 (OUTLIER) cc_final: 0.3914 (pm20)
REVERT: C   40 PHE cc_start: 0.5918 (OUTLIER) cc_final: 0.5359 (t80)
REVERT: C  274 LYS cc_start: 0.6697 (mmmt) cc_final: 0.5991 (mmmt)
REVERT: C  403 HIS cc_start: 0.6244 (OUTLIER) cc_final: 0.5655 (t-90)
REVERT: C  660 THR cc_start: 0.4842 (OUTLIER) cc_final: 0.4505 (p)
REVERT: C 1015 THR cc_start: 0.5397 (OUTLIER) cc_final: 0.4886 (t)
REVERT: C 1074 ARG cc_start: 0.5352 (mtm-85) cc_final: 0.4281 (ttt90)
REVERT: D   19 LYS cc_start: 0.6827 (ptpt) cc_final: 0.6081 (mmtm)
REVERT: D  539 VAL cc_start: 0.3784 (p) cc_final: 0.3548 (p)
REVERT: D  684 MET cc_start: 0.5094 (OUTLIER) cc_final: 0.4830 (mtm)
REVERT: D  843 LEU cc_start: 0.5893 (OUTLIER) cc_final: 0.5592 (mm)
REVERT: D  866 GLU cc_start: 0.0607 (pm20) cc_final: -0.0204 (pm20)
REVERT: F   44 HIS cc_start: 0.2539 (OUTLIER) cc_final: 0.1164 (m90)
REVERT: L   14 MET cc_start: 0.0034 (ppp) cc_final: -0.0302 (ppp)
REVERT: H   75 MET cc_start: 0.2833 (mmt) cc_final: 0.1676 (ppp)
  outliers start: 79
  outliers final: 58
  residues processed: 269
  average time/residue: 0.6423
  time to fit residues: 277.6044
Evaluate side-chains
  265 residues out of total 2658 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 68
    poor density    : 197
  time to evaluate  : 2.845 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   45 LEU
Chi-restraints excluded: chain A residue   47 SER
Chi-restraints excluded: chain A residue  136 PHE
Chi-restraints excluded: chain A residue  197 ASP
Chi-restraints excluded: chain A residue  224 PHE
Chi-restraints excluded: chain B residue   10 GLU
Chi-restraints excluded: chain B residue   24 VAL
Chi-restraints excluded: chain B residue   25 VAL
Chi-restraints excluded: chain B residue   45 LEU
Chi-restraints excluded: chain B residue   47 SER
Chi-restraints excluded: chain B residue   62 LEU
Chi-restraints excluded: chain B residue  129 THR
Chi-restraints excluded: chain B residue  141 THR
Chi-restraints excluded: chain B residue  169 ILE
Chi-restraints excluded: chain B residue  183 THR
Chi-restraints excluded: chain B residue  195 THR
Chi-restraints excluded: chain C residue   13 GLN
Chi-restraints excluded: chain C residue   31 GLU
Chi-restraints excluded: chain C residue   40 PHE
Chi-restraints excluded: chain C residue  124 THR
Chi-restraints excluded: chain C residue  127 ILE
Chi-restraints excluded: chain C residue  131 GLU
Chi-restraints excluded: chain C residue  136 SER
Chi-restraints excluded: chain C residue  403 HIS
Chi-restraints excluded: chain C residue  407 ARG
Chi-restraints excluded: chain C residue  414 GLU
Chi-restraints excluded: chain C residue  510 HIS
Chi-restraints excluded: chain C residue  511 TYR
Chi-restraints excluded: chain C residue  570 ASP
Chi-restraints excluded: chain C residue  623 THR
Chi-restraints excluded: chain C residue  644 GLN
Chi-restraints excluded: chain C residue  660 THR
Chi-restraints excluded: chain C residue  681 ILE
Chi-restraints excluded: chain C residue  708 ASP
Chi-restraints excluded: chain C residue  713 LEU
Chi-restraints excluded: chain C residue  764 MET
Chi-restraints excluded: chain C residue  792 ILE
Chi-restraints excluded: chain C residue  965 ARG
Chi-restraints excluded: chain C residue 1015 THR
Chi-restraints excluded: chain C residue 1043 MET
Chi-restraints excluded: chain C residue 1094 GLU
Chi-restraints excluded: chain C residue 1142 VAL
Chi-restraints excluded: chain D residue   62 CYS
Chi-restraints excluded: chain D residue  349 HIS
Chi-restraints excluded: chain D residue  419 HIS
Chi-restraints excluded: chain D residue  528 ASN
Chi-restraints excluded: chain D residue  533 LEU
Chi-restraints excluded: chain D residue  588 GLU
Chi-restraints excluded: chain D residue  631 PHE
Chi-restraints excluded: chain D residue  634 THR
Chi-restraints excluded: chain D residue  657 THR
Chi-restraints excluded: chain D residue  666 LEU
Chi-restraints excluded: chain D residue  684 MET
Chi-restraints excluded: chain D residue  787 LEU
Chi-restraints excluded: chain D residue  796 ASP
Chi-restraints excluded: chain D residue  843 LEU
Chi-restraints excluded: chain D residue  871 ASP
Chi-restraints excluded: chain D residue  892 CYS
Chi-restraints excluded: chain D residue  953 LEU
Chi-restraints excluded: chain D residue 1038 THR
Chi-restraints excluded: chain D residue 1070 MET
Chi-restraints excluded: chain D residue 1138 SER
Chi-restraints excluded: chain F residue   44 HIS
Chi-restraints excluded: chain L residue   64 ILE
Chi-restraints excluded: chain L residue   71 LEU
Chi-restraints excluded: chain E residue   45 GLU
Chi-restraints excluded: chain E residue   50 VAL
Chi-restraints excluded: chain H residue   38 LEU
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 304
   random chunks:
   chunk 125 optimal weight:    2.9990
   chunk 171 optimal weight:    0.0570
   chunk 299 optimal weight:    5.9990
   chunk 275 optimal weight:    2.9990
   chunk 118 optimal weight:    1.9990
   chunk 15 optimal weight:    2.9990
   chunk 163 optimal weight:    5.9990
   chunk 207 optimal weight:    5.9990
   chunk 272 optimal weight:    1.9990
   chunk 289 optimal weight:    1.9990
   chunk 140 optimal weight:    1.9990
   overall best weight:    1.6106

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

Flipped N/Q/H residues before XYZ refinement:
** B 143 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
C 406 ASN
** C 931 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** F  31 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 = 0.5458 r_free = 0.5458 target = 0.302882 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 53)----------------|
| r_work = 0.5122 r_free = 0.5122 target = 0.261015 restraints weight = 87054.690|
|-----------------------------------------------------------------------------|
r_work (start): 0.5143 rms_B_bonded: 3.44
r_work: 0.4934 rms_B_bonded: 3.08 restraints_weight: 0.5000
r_work (final): 0.4934
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.5164
moved from start:          0.2571

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.010   0.828  24678  Z= 0.738
  Angle     :  0.626  30.840  33339  Z= 0.328
  Chirality :  0.043   0.162   3774
  Planarity :  0.005   0.064   4348
  Dihedral  :  4.813  64.424   3378
  Min Nonbonded Distance : 1.970

Molprobity Statistics.
  All-atom Clashscore : 7.24
  Ramachandran Plot:
    Outliers :  0.23 %
    Allowed  :  7.98 %
    Favored  : 91.79 %
  Rotamer:
    Outliers :  3.35 %
    Allowed  : 22.69 %
    Favored  : 73.95 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 1.54 %
    Cis-general     : 0.07 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -1.42 (0.15), residues: 3059
  helix:  0.23 (0.17), residues: 959
  sheet:  0.17 (0.29), residues: 317
  loop : -1.91 (0.14), residues: 1783

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.012   0.001   TRP B 199 
 HIS   0.006   0.001   HIS C 507 
 PHE   0.018   0.002   PHE C  40 
 TYR   0.038   0.002   TYR D  70 
 ARG   0.006   0.000   ARG B  30 

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

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

  6118 Ramachandran restraints generated.
    3059 Oldfield, 0 Emsley, 3059 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  6118 Ramachandran restraints generated.
    3059 Oldfield, 0 Emsley, 3059 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Residue LYS   19 is missing expected H atoms. Skipping.
Residue LYS   65 is missing expected H atoms. Skipping.
Evaluate side-chains
  287 residues out of total 2658 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 89
    poor density    : 198
  time to evaluate  : 2.886 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: B   24 VAL cc_start: 0.6263 (OUTLIER) cc_final: 0.5835 (t)
REVERT: B  169 ILE cc_start: 0.7434 (OUTLIER) cc_final: 0.7195 (mt)
REVERT: C   31 GLU cc_start: 0.6803 (OUTLIER) cc_final: 0.4136 (pm20)
REVERT: C   40 PHE cc_start: 0.5789 (OUTLIER) cc_final: 0.5115 (t80)
REVERT: C  274 LYS cc_start: 0.6846 (mmmt) cc_final: 0.6165 (mmmt)
REVERT: C  403 HIS cc_start: 0.6322 (OUTLIER) cc_final: 0.5701 (t-90)
REVERT: C  660 THR cc_start: 0.5174 (OUTLIER) cc_final: 0.4851 (p)
REVERT: C  907 GLN cc_start: 0.3447 (pt0) cc_final: 0.2780 (pp30)
REVERT: C 1015 THR cc_start: 0.5591 (OUTLIER) cc_final: 0.5071 (t)
REVERT: C 1074 ARG cc_start: 0.5548 (mtm-85) cc_final: 0.4365 (ttt90)
REVERT: D   19 LYS cc_start: 0.6817 (ptpt) cc_final: 0.6064 (mmtm)
REVERT: D  539 VAL cc_start: 0.3728 (p) cc_final: 0.3484 (p)
REVERT: D  843 LEU cc_start: 0.6248 (OUTLIER) cc_final: 0.5925 (mm)
REVERT: F   22 VAL cc_start: 0.6532 (t) cc_final: 0.6222 (t)
REVERT: F   44 HIS cc_start: 0.2720 (OUTLIER) cc_final: 0.1291 (m90)
REVERT: L   14 MET cc_start: 0.0143 (ppp) cc_final: -0.0216 (ppp)
REVERT: H   75 MET cc_start: 0.2704 (mmt) cc_final: 0.1418 (ppp)
  outliers start: 89
  outliers final: 61
  residues processed: 272
  average time/residue: 0.6153
  time to fit residues: 267.4537
Evaluate side-chains
  265 residues out of total 2658 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 70
    poor density    : 195
  time to evaluate  : 2.837 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   47 SER
Chi-restraints excluded: chain A residue   66 SER
Chi-restraints excluded: chain A residue  130 LEU
Chi-restraints excluded: chain A residue  136 PHE
Chi-restraints excluded: chain A residue  197 ASP
Chi-restraints excluded: chain A residue  224 PHE
Chi-restraints excluded: chain B residue   24 VAL
Chi-restraints excluded: chain B residue   25 VAL
Chi-restraints excluded: chain B residue   45 LEU
Chi-restraints excluded: chain B residue   47 SER
Chi-restraints excluded: chain B residue   74 ASP
Chi-restraints excluded: chain B residue  129 THR
Chi-restraints excluded: chain B residue  141 THR
Chi-restraints excluded: chain B residue  169 ILE
Chi-restraints excluded: chain B residue  183 THR
Chi-restraints excluded: chain B residue  195 THR
Chi-restraints excluded: chain C residue   31 GLU
Chi-restraints excluded: chain C residue   40 PHE
Chi-restraints excluded: chain C residue  124 THR
Chi-restraints excluded: chain C residue  127 ILE
Chi-restraints excluded: chain C residue  131 GLU
Chi-restraints excluded: chain C residue  136 SER
Chi-restraints excluded: chain C residue  403 HIS
Chi-restraints excluded: chain C residue  407 ARG
Chi-restraints excluded: chain C residue  414 GLU
Chi-restraints excluded: chain C residue  510 HIS
Chi-restraints excluded: chain C residue  511 TYR
Chi-restraints excluded: chain C residue  570 ASP
Chi-restraints excluded: chain C residue  613 VAL
Chi-restraints excluded: chain C residue  623 THR
Chi-restraints excluded: chain C residue  644 GLN
Chi-restraints excluded: chain C residue  654 GLU
Chi-restraints excluded: chain C residue  660 THR
Chi-restraints excluded: chain C residue  681 ILE
Chi-restraints excluded: chain C residue  708 ASP
Chi-restraints excluded: chain C residue  713 LEU
Chi-restraints excluded: chain C residue  764 MET
Chi-restraints excluded: chain C residue  792 ILE
Chi-restraints excluded: chain C residue  965 ARG
Chi-restraints excluded: chain C residue 1015 THR
Chi-restraints excluded: chain C residue 1043 MET
Chi-restraints excluded: chain C residue 1094 GLU
Chi-restraints excluded: chain C residue 1142 VAL
Chi-restraints excluded: chain D residue   62 CYS
Chi-restraints excluded: chain D residue  176 HIS
Chi-restraints excluded: chain D residue  419 HIS
Chi-restraints excluded: chain D residue  528 ASN
Chi-restraints excluded: chain D residue  533 LEU
Chi-restraints excluded: chain D residue  588 GLU
Chi-restraints excluded: chain D residue  631 PHE
Chi-restraints excluded: chain D residue  634 THR
Chi-restraints excluded: chain D residue  637 SER
Chi-restraints excluded: chain D residue  657 THR
Chi-restraints excluded: chain D residue  666 LEU
Chi-restraints excluded: chain D residue  787 LEU
Chi-restraints excluded: chain D residue  796 ASP
Chi-restraints excluded: chain D residue  843 LEU
Chi-restraints excluded: chain D residue  871 ASP
Chi-restraints excluded: chain D residue  892 CYS
Chi-restraints excluded: chain D residue  953 LEU
Chi-restraints excluded: chain D residue 1038 THR
Chi-restraints excluded: chain D residue 1070 MET
Chi-restraints excluded: chain D residue 1138 SER
Chi-restraints excluded: chain F residue   44 HIS
Chi-restraints excluded: chain F residue   58 LEU
Chi-restraints excluded: chain L residue   64 ILE
Chi-restraints excluded: chain L residue   71 LEU
Chi-restraints excluded: chain E residue   45 GLU
Chi-restraints excluded: chain E residue   50 VAL
Chi-restraints excluded: chain H residue   38 LEU
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 304
   random chunks:
   chunk 235 optimal weight:    3.9990
   chunk 165 optimal weight:    5.9990
   chunk 150 optimal weight:    1.9990
   chunk 74 optimal weight:    9.9990
   chunk 153 optimal weight:    0.9990
   chunk 177 optimal weight:    3.9990
   chunk 47 optimal weight:    2.9990
   chunk 48 optimal weight:    0.8980
   chunk 221 optimal weight:    0.2980
   chunk 272 optimal weight:    0.1980
   chunk 111 optimal weight:    2.9990
   overall best weight:    0.8784

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

Flipped N/Q/H residues before XYZ refinement:
C 931 ASN
** F  31 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 = 0.5469 r_free = 0.5469 target = 0.304395 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 45)----------------|
| r_work = 0.5103 r_free = 0.5103 target = 0.261837 restraints weight = 86408.819|
|-----------------------------------------------------------------------------|
r_work (start): 0.5135 rms_B_bonded: 3.29
r_work: 0.4958 rms_B_bonded: 3.09 restraints_weight: 0.5000
r_work (final): 0.4958
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.5099
moved from start:          0.2642

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.010   0.825  24678  Z= 0.715
  Angle     :  0.576  30.688  33339  Z= 0.299
  Chirality :  0.041   0.159   3774
  Planarity :  0.004   0.057   4348
  Dihedral  :  4.650  63.762   3378
  Min Nonbonded Distance : 1.970

Molprobity Statistics.
  All-atom Clashscore : 6.19
  Ramachandran Plot:
    Outliers :  0.23 %
    Allowed  :  7.19 %
    Favored  : 92.58 %
  Rotamer:
    Outliers :  2.79 %
    Allowed  : 23.18 %
    Favored  : 74.03 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 1.54 %
    Cis-general     : 0.07 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -1.26 (0.15), residues: 3059
  helix:  0.41 (0.17), residues: 961
  sheet:  0.28 (0.30), residues: 312
  loop : -1.85 (0.14), residues: 1786

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.011   0.001   TRP B 199 
 HIS   0.004   0.001   HIS D 419 
 PHE   0.012   0.001   PHE C  40 
 TYR   0.037   0.001   TYR D  70 
 ARG   0.004   0.000   ARG B  30 

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

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

  6118 Ramachandran restraints generated.
    3059 Oldfield, 0 Emsley, 3059 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  6118 Ramachandran restraints generated.
    3059 Oldfield, 0 Emsley, 3059 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Residue LYS   19 is missing expected H atoms. Skipping.
Residue LYS   65 is missing expected H atoms. Skipping.
Evaluate side-chains
  274 residues out of total 2658 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 74
    poor density    : 200
  time to evaluate  : 2.873 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: C   40 PHE cc_start: 0.5768 (OUTLIER) cc_final: 0.4844 (t80)
REVERT: C  274 LYS cc_start: 0.6845 (mmmt) cc_final: 0.6176 (mmmt)
REVERT: C  403 HIS cc_start: 0.6212 (OUTLIER) cc_final: 0.5605 (t-90)
REVERT: C  660 THR cc_start: 0.5106 (OUTLIER) cc_final: 0.4779 (p)
REVERT: C  696 GLU cc_start: 0.4850 (mm-30) cc_final: 0.4631 (mm-30)
REVERT: C  907 GLN cc_start: 0.3421 (pt0) cc_final: 0.2788 (pp30)
REVERT: C 1015 THR cc_start: 0.5492 (OUTLIER) cc_final: 0.4980 (t)
REVERT: C 1074 ARG cc_start: 0.5508 (mtm-85) cc_final: 0.4360 (ttt90)
REVERT: D   19 LYS cc_start: 0.6843 (ptpt) cc_final: 0.6083 (mmtm)
REVERT: D  539 VAL cc_start: 0.3664 (p) cc_final: 0.3418 (p)
REVERT: D  843 LEU cc_start: 0.6145 (OUTLIER) cc_final: 0.5783 (mm)
REVERT: F   22 VAL cc_start: 0.6444 (t) cc_final: 0.6219 (t)
REVERT: F   44 HIS cc_start: 0.2741 (OUTLIER) cc_final: 0.1601 (m170)
REVERT: L   14 MET cc_start: 0.0152 (ppp) cc_final: -0.0198 (ppp)
REVERT: H   75 MET cc_start: 0.2677 (mmt) cc_final: 0.1473 (ppp)
  outliers start: 74
  outliers final: 62
  residues processed: 262
  average time/residue: 0.6312
  time to fit residues: 265.0004
Evaluate side-chains
  266 residues out of total 2658 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 68
    poor density    : 198
  time to evaluate  : 2.835 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   45 LEU
Chi-restraints excluded: chain A residue   47 SER
Chi-restraints excluded: chain A residue   66 SER
Chi-restraints excluded: chain A residue  130 LEU
Chi-restraints excluded: chain A residue  136 PHE
Chi-restraints excluded: chain A residue  197 ASP
Chi-restraints excluded: chain A residue  224 PHE
Chi-restraints excluded: chain B residue   25 VAL
Chi-restraints excluded: chain B residue   45 LEU
Chi-restraints excluded: chain B residue   47 SER
Chi-restraints excluded: chain B residue   74 ASP
Chi-restraints excluded: chain B residue  129 THR
Chi-restraints excluded: chain B residue  141 THR
Chi-restraints excluded: chain B residue  183 THR
Chi-restraints excluded: chain B residue  195 THR
Chi-restraints excluded: chain C residue   40 PHE
Chi-restraints excluded: chain C residue  124 THR
Chi-restraints excluded: chain C residue  127 ILE
Chi-restraints excluded: chain C residue  131 GLU
Chi-restraints excluded: chain C residue  136 SER
Chi-restraints excluded: chain C residue  403 HIS
Chi-restraints excluded: chain C residue  407 ARG
Chi-restraints excluded: chain C residue  414 GLU
Chi-restraints excluded: chain C residue  470 PHE
Chi-restraints excluded: chain C residue  480 LEU
Chi-restraints excluded: chain C residue  510 HIS
Chi-restraints excluded: chain C residue  511 TYR
Chi-restraints excluded: chain C residue  570 ASP
Chi-restraints excluded: chain C residue  613 VAL
Chi-restraints excluded: chain C residue  623 THR
Chi-restraints excluded: chain C residue  644 GLN
Chi-restraints excluded: chain C residue  654 GLU
Chi-restraints excluded: chain C residue  660 THR
Chi-restraints excluded: chain C residue  681 ILE
Chi-restraints excluded: chain C residue  708 ASP
Chi-restraints excluded: chain C residue  713 LEU
Chi-restraints excluded: chain C residue  764 MET
Chi-restraints excluded: chain C residue  792 ILE
Chi-restraints excluded: chain C residue  965 ARG
Chi-restraints excluded: chain C residue 1015 THR
Chi-restraints excluded: chain C residue 1043 MET
Chi-restraints excluded: chain C residue 1094 GLU
Chi-restraints excluded: chain C residue 1142 VAL
Chi-restraints excluded: chain D residue   62 CYS
Chi-restraints excluded: chain D residue  176 HIS
Chi-restraints excluded: chain D residue  419 HIS
Chi-restraints excluded: chain D residue  528 ASN
Chi-restraints excluded: chain D residue  533 LEU
Chi-restraints excluded: chain D residue  546 ASN
Chi-restraints excluded: chain D residue  588 GLU
Chi-restraints excluded: chain D residue  631 PHE
Chi-restraints excluded: chain D residue  634 THR
Chi-restraints excluded: chain D residue  657 THR
Chi-restraints excluded: chain D residue  666 LEU
Chi-restraints excluded: chain D residue  787 LEU
Chi-restraints excluded: chain D residue  796 ASP
Chi-restraints excluded: chain D residue  843 LEU
Chi-restraints excluded: chain D residue  892 CYS
Chi-restraints excluded: chain D residue  953 LEU
Chi-restraints excluded: chain D residue 1038 THR
Chi-restraints excluded: chain D residue 1070 MET
Chi-restraints excluded: chain D residue 1138 SER
Chi-restraints excluded: chain F residue   44 HIS
Chi-restraints excluded: chain L residue   64 ILE
Chi-restraints excluded: chain L residue   71 LEU
Chi-restraints excluded: chain E residue   45 GLU
Chi-restraints excluded: chain E residue   50 VAL
Chi-restraints excluded: chain H residue   38 LEU
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 304
   random chunks:
   chunk 217 optimal weight:    0.6980
   chunk 64 optimal weight:    2.9990
   chunk 45 optimal weight:    2.9990
   chunk 219 optimal weight:    0.9980
   chunk 110 optimal weight:    0.0270
   chunk 289 optimal weight:    2.9990
   chunk 250 optimal weight:    0.9990
   chunk 235 optimal weight:    3.9990
   chunk 4 optimal weight:    1.9990
   chunk 231 optimal weight:    0.1980
   chunk 136 optimal weight:    0.9980
   overall best weight:    0.5838

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

Flipped N/Q/H residues before XYZ refinement:
** F  31 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.5482 r_free = 0.5482 target = 0.306171 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 45)----------------|
| r_work = 0.5142 r_free = 0.5142 target = 0.265128 restraints weight = 86714.383|
|-----------------------------------------------------------------------------|
r_work (start): 0.5167 rms_B_bonded: 3.13
r_work: 0.4971 rms_B_bonded: 3.12 restraints_weight: 0.5000
r_work (final): 0.4971
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.5061
moved from start:          0.2689

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.010   0.824  24678  Z= 0.709
  Angle     :  0.552  30.666  33339  Z= 0.285
  Chirality :  0.041   0.156   3774
  Planarity :  0.004   0.057   4348
  Dihedral  :  4.459  61.667   3378
  Min Nonbonded Distance : 1.970

Molprobity Statistics.
  All-atom Clashscore : 5.37
  Ramachandran Plot:
    Outliers :  0.23 %
    Allowed  :  6.60 %
    Favored  : 93.17 %
  Rotamer:
    Outliers :  2.49 %
    Allowed  : 23.41 %
    Favored  : 74.10 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 1.54 %
    Cis-general     : 0.07 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -1.11 (0.15), residues: 3059
  helix:  0.61 (0.17), residues: 965
  sheet:  0.32 (0.29), residues: 318
  loop : -1.80 (0.14), residues: 1776

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.011   0.001   TRP B 199 
 HIS   0.003   0.001   HIS C 507 
 PHE   0.010   0.001   PHE A 136 
 TYR   0.037   0.001   TYR D  70 
 ARG   0.004   0.000   ARG E  17 

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

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

  6118 Ramachandran restraints generated.
    3059 Oldfield, 0 Emsley, 3059 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  6118 Ramachandran restraints generated.
    3059 Oldfield, 0 Emsley, 3059 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Residue LYS   19 is missing expected H atoms. Skipping.
Residue LYS   65 is missing expected H atoms. Skipping.
Evaluate side-chains
  269 residues out of total 2658 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 66
    poor density    : 203
  time to evaluate  : 2.891 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: C  274 LYS cc_start: 0.6823 (mmmt) cc_final: 0.6154 (mmmt)
REVERT: C  403 HIS cc_start: 0.6186 (OUTLIER) cc_final: 0.5587 (t-90)
REVERT: C  660 THR cc_start: 0.4950 (p) cc_final: 0.4644 (p)
REVERT: C  907 GLN cc_start: 0.3353 (pt0) cc_final: 0.2770 (pp30)
REVERT: C 1015 THR cc_start: 0.5396 (OUTLIER) cc_final: 0.4919 (p)
REVERT: D   19 LYS cc_start: 0.6822 (ptpt) cc_final: 0.6082 (mmtm)
REVERT: D  539 VAL cc_start: 0.3715 (p) cc_final: 0.3472 (p)
REVERT: D  546 ASN cc_start: 0.3448 (OUTLIER) cc_final: 0.3146 (m-40)
REVERT: D  843 LEU cc_start: 0.5928 (OUTLIER) cc_final: 0.5567 (mm)
REVERT: F   44 HIS cc_start: 0.2888 (OUTLIER) cc_final: 0.1796 (m170)
REVERT: L   14 MET cc_start: 0.0080 (ppp) cc_final: -0.0251 (ppp)
REVERT: H   75 MET cc_start: 0.2558 (mmt) cc_final: 0.1446 (ppp)
  outliers start: 66
  outliers final: 59
  residues processed: 261
  average time/residue: 0.6328
  time to fit residues: 265.1376
Evaluate side-chains
  265 residues out of total 2658 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 64
    poor density    : 201
  time to evaluate  : 2.825 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   45 LEU
Chi-restraints excluded: chain A residue   47 SER
Chi-restraints excluded: chain A residue   66 SER
Chi-restraints excluded: chain A residue  136 PHE
Chi-restraints excluded: chain A residue  197 ASP
Chi-restraints excluded: chain A residue  224 PHE
Chi-restraints excluded: chain B residue   25 VAL
Chi-restraints excluded: chain B residue   45 LEU
Chi-restraints excluded: chain B residue   47 SER
Chi-restraints excluded: chain B residue   74 ASP
Chi-restraints excluded: chain B residue  129 THR
Chi-restraints excluded: chain B residue  141 THR
Chi-restraints excluded: chain B residue  183 THR
Chi-restraints excluded: chain B residue  195 THR
Chi-restraints excluded: chain C residue   40 PHE
Chi-restraints excluded: chain C residue  124 THR
Chi-restraints excluded: chain C residue  127 ILE
Chi-restraints excluded: chain C residue  131 GLU
Chi-restraints excluded: chain C residue  136 SER
Chi-restraints excluded: chain C residue  403 HIS
Chi-restraints excluded: chain C residue  407 ARG
Chi-restraints excluded: chain C residue  414 GLU
Chi-restraints excluded: chain C residue  470 PHE
Chi-restraints excluded: chain C residue  480 LEU
Chi-restraints excluded: chain C residue  510 HIS
Chi-restraints excluded: chain C residue  511 TYR
Chi-restraints excluded: chain C residue  570 ASP
Chi-restraints excluded: chain C residue  623 THR
Chi-restraints excluded: chain C residue  644 GLN
Chi-restraints excluded: chain C residue  654 GLU
Chi-restraints excluded: chain C residue  681 ILE
Chi-restraints excluded: chain C residue  708 ASP
Chi-restraints excluded: chain C residue  713 LEU
Chi-restraints excluded: chain C residue  764 MET
Chi-restraints excluded: chain C residue  779 GLU
Chi-restraints excluded: chain C residue  792 ILE
Chi-restraints excluded: chain C residue  965 ARG
Chi-restraints excluded: chain C residue 1015 THR
Chi-restraints excluded: chain C residue 1043 MET
Chi-restraints excluded: chain C residue 1094 GLU
Chi-restraints excluded: chain C residue 1142 VAL
Chi-restraints excluded: chain D residue   62 CYS
Chi-restraints excluded: chain D residue  419 HIS
Chi-restraints excluded: chain D residue  528 ASN
Chi-restraints excluded: chain D residue  546 ASN
Chi-restraints excluded: chain D residue  588 GLU
Chi-restraints excluded: chain D residue  631 PHE
Chi-restraints excluded: chain D residue  637 SER
Chi-restraints excluded: chain D residue  657 THR
Chi-restraints excluded: chain D residue  666 LEU
Chi-restraints excluded: chain D residue  787 LEU
Chi-restraints excluded: chain D residue  796 ASP
Chi-restraints excluded: chain D residue  843 LEU
Chi-restraints excluded: chain D residue  892 CYS
Chi-restraints excluded: chain D residue  953 LEU
Chi-restraints excluded: chain D residue 1038 THR
Chi-restraints excluded: chain D residue 1070 MET
Chi-restraints excluded: chain D residue 1138 SER
Chi-restraints excluded: chain F residue   44 HIS
Chi-restraints excluded: chain L residue   64 ILE
Chi-restraints excluded: chain L residue   71 LEU
Chi-restraints excluded: chain E residue   45 GLU
Chi-restraints excluded: chain E residue   50 VAL
Chi-restraints excluded: chain H residue   38 LEU
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 304
   random chunks:
   chunk 183 optimal weight:    9.9990
   chunk 35 optimal weight:    2.9990
   chunk 150 optimal weight:    2.9990
   chunk 113 optimal weight:    2.9990
   chunk 45 optimal weight:    2.9990
   chunk 258 optimal weight:    2.9990
   chunk 297 optimal weight:    6.9990
   chunk 194 optimal weight:    3.9990
   chunk 131 optimal weight:    4.9990
   chunk 292 optimal weight:    0.9990
   chunk 8 optimal weight:    1.9990
   overall best weight:    2.3990

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

Flipped N/Q/H residues before XYZ refinement:
** B 143 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** C 931 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** D 677 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** F  31 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.5457 r_free = 0.5457 target = 0.302135 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 90)----------------|
| r_work = 0.5039 r_free = 0.5039 target = 0.253789 restraints weight = 86938.740|
|-----------------------------------------------------------------------------|
r_work (start): 0.5023 rms_B_bonded: 3.32
r_work: 0.4904 rms_B_bonded: 2.92 restraints_weight: 0.5000
r_work: 0.4780 rms_B_bonded: 4.86 restraints_weight: 0.2500
r_work (final): 0.4780
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.5347
moved from start:          0.3067

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.011   0.829  24678  Z= 0.769
  Angle     :  0.693  30.755  33339  Z= 0.367
  Chirality :  0.045   0.166   3774
  Planarity :  0.005   0.057   4348
  Dihedral  :  5.104  66.542   3378
  Min Nonbonded Distance : 1.971

Molprobity Statistics.
  All-atom Clashscore : 9.82
  Ramachandran Plot:
    Outliers :  0.29 %
    Allowed  :  9.15 %
    Favored  : 90.55 %
  Rotamer:
    Outliers :  2.75 %
    Allowed  : 23.22 %
    Favored  : 74.03 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 1.54 %
    Cis-general     : 0.07 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -1.67 (0.15), residues: 3059
  helix:  0.01 (0.17), residues: 969
  sheet:  0.02 (0.29), residues: 330
  loop : -2.08 (0.14), residues: 1760

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.012   0.002   TRP A 199 
 HIS   0.008   0.002   HIS D 419 
 PHE   0.024   0.002   PHE C  40 
 TYR   0.038   0.003   TYR D  70 
 ARG   0.009   0.001   ARG C 965 
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 20791.66 seconds
wall clock time: 354 minutes 24.06 seconds (21264.06 seconds total)