Starting phenix.real_space_refine on Sat Jan 20 05:54:31 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8hqz_34955/01_2024/8hqz_34955.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8hqz_34955/01_2024/8hqz_34955.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.8 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8hqz_34955/01_2024/8hqz_34955.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8hqz_34955/01_2024/8hqz_34955.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8hqz_34955/01_2024/8hqz_34955.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8hqz_34955/01_2024/8hqz_34955.pdb" } resolution = 3.8 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= 0.001 sd= 1.012 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 147 5.16 5 C 41910 2.51 5 N 11004 2.21 5 O 13320 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A PHE 99": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 773": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "T GLU 129": "OE1" <-> "OE2" Residue "B PHE 99": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 773": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K GLU 129": "OE1" <-> "OE2" Residue "V PHE 99": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "V TYR 773": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "2 GLU 129": "OE1" <-> "OE2" Time to flip residues: 0.16s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-1.21-5211/modules/chem_data/mon_lib" Total number of atoms: 66381 Number of models: 1 Model: "" Number of chains: 39 Chain: "A" Number of atoms: 7438 Number of conformers: 1 Conformer: "" Number of residues, atoms: 930, 7438 Classifications: {'peptide': 930} Link IDs: {'PTRANS': 33, 'TRANS': 896} Chain breaks: 2 Chain: "H" Number of atoms: 1600 Number of conformers: 1 Conformer: "" Number of residues, atoms: 204, 1600 Classifications: {'peptide': 204} Link IDs: {'PCIS': 1, 'PTRANS': 13, 'TRANS': 189} Chain: "I" Number of atoms: 1600 Number of conformers: 1 Conformer: "" Number of residues, atoms: 204, 1600 Classifications: {'peptide': 204} Link IDs: {'PCIS': 1, 'PTRANS': 13, 'TRANS': 189} Chain: "L" Number of atoms: 2400 Number of conformers: 1 Conformer: "" Number of residues, atoms: 296, 2400 Classifications: {'peptide': 296} Link IDs: {'PTRANS': 11, 'TRANS': 284} Chain: "Q" Number of atoms: 1069 Number of conformers: 1 Conformer: "" Number of residues, atoms: 139, 1069 Classifications: {'peptide': 139} Link IDs: {'PCIS': 1, 'PTRANS': 4, 'TRANS': 133} Chain: "R" Number of atoms: 1069 Number of conformers: 1 Conformer: "" Number of residues, atoms: 139, 1069 Classifications: {'peptide': 139} Link IDs: {'PTRANS': 5, 'TRANS': 133} Chain: "S" Number of atoms: 1069 Number of conformers: 1 Conformer: "" Number of residues, atoms: 139, 1069 Classifications: {'peptide': 139} Link IDs: {'PCIS': 1, 'PTRANS': 4, 'TRANS': 133} Chain: "T" Number of atoms: 1056 Number of conformers: 1 Conformer: "" Number of residues, atoms: 137, 1056 Classifications: {'peptide': 137} Link IDs: {'PCIS': 1, 'PTRANS': 4, 'TRANS': 131} Chain: "d" Number of atoms: 338 Number of conformers: 1 Conformer: "" Number of residues, atoms: 46, 338 Classifications: {'peptide': 46} Link IDs: {'PTRANS': 1, 'TRANS': 44} Chain: "e" Number of atoms: 343 Number of conformers: 1 Conformer: "" Number of residues, atoms: 47, 343 Classifications: {'peptide': 47} Link IDs: {'PTRANS': 1, 'TRANS': 45} Chain: "f" Number of atoms: 336 Number of conformers: 1 Conformer: "" Number of residues, atoms: 47, 336 Classifications: {'peptide': 47} Link IDs: {'PTRANS': 1, 'TRANS': 45} Chain: "k" Number of atoms: 257 Number of conformers: 1 Conformer: "" Number of residues, atoms: 36, 257 Classifications: {'peptide': 36} Link IDs: {'TRANS': 35} Chain: "p" Number of atoms: 3552 Number of conformers: 1 Conformer: "" Number of residues, atoms: 466, 3552 Classifications: {'peptide': 466} Link IDs: {'PCIS': 1, 'PTRANS': 16, 'TRANS': 448} Chain: "B" Number of atoms: 7438 Number of conformers: 1 Conformer: "" Number of residues, atoms: 930, 7438 Classifications: {'peptide': 930} Link IDs: {'PTRANS': 33, 'TRANS': 896} Chain breaks: 2 Chain: "C" Number of atoms: 1600 Number of conformers: 1 Conformer: "" Number of residues, atoms: 204, 1600 Classifications: {'peptide': 204} Link IDs: {'PCIS': 1, 'PTRANS': 13, 'TRANS': 189} Chain: "D" Number of atoms: 1600 Number of conformers: 1 Conformer: "" Number of residues, atoms: 204, 1600 Classifications: {'peptide': 204} Link IDs: {'PCIS': 1, 'PTRANS': 13, 'TRANS': 189} Chain: "E" Number of atoms: 2400 Number of conformers: 1 Conformer: "" Number of residues, atoms: 296, 2400 Classifications: {'peptide': 296} Link IDs: {'PTRANS': 11, 'TRANS': 284} Chain: "F" Number of atoms: 1069 Number of conformers: 1 Conformer: "" Number of residues, atoms: 139, 1069 Classifications: {'peptide': 139} Link IDs: {'PCIS': 1, 'PTRANS': 4, 'TRANS': 133} Chain: "G" Number of atoms: 1069 Number of conformers: 1 Conformer: "" Number of residues, atoms: 139, 1069 Classifications: {'peptide': 139} Link IDs: {'PTRANS': 5, 'TRANS': 133} Chain: "J" Number of atoms: 1069 Number of conformers: 1 Conformer: "" Number of residues, atoms: 139, 1069 Classifications: {'peptide': 139} Link IDs: {'PCIS': 1, 'PTRANS': 4, 'TRANS': 133} Chain: "K" Number of atoms: 1056 Number of conformers: 1 Conformer: "" Number of residues, atoms: 137, 1056 Classifications: {'peptide': 137} Link IDs: {'PCIS': 1, 'PTRANS': 4, 'TRANS': 131} Chain: "M" Number of atoms: 338 Number of conformers: 1 Conformer: "" Number of residues, atoms: 46, 338 Classifications: {'peptide': 46} Link IDs: {'PTRANS': 1, 'TRANS': 44} Chain: "N" Number of atoms: 343 Number of conformers: 1 Conformer: "" Number of residues, atoms: 47, 343 Classifications: {'peptide': 47} Link IDs: {'PTRANS': 1, 'TRANS': 45} Chain: "O" Number of atoms: 336 Number of conformers: 1 Conformer: "" Number of residues, atoms: 47, 336 Classifications: {'peptide': 47} Link IDs: {'PTRANS': 1, 'TRANS': 45} Chain: "P" Number of atoms: 257 Number of conformers: 1 Conformer: "" Number of residues, atoms: 36, 257 Classifications: {'peptide': 36} Link IDs: {'TRANS': 35} Chain: "U" Number of atoms: 3552 Number of conformers: 1 Conformer: "" Number of residues, atoms: 466, 3552 Classifications: {'peptide': 466} Link IDs: {'PCIS': 1, 'PTRANS': 16, 'TRANS': 448} Chain: "V" Number of atoms: 7438 Number of conformers: 1 Conformer: "" Number of residues, atoms: 930, 7438 Classifications: {'peptide': 930} Link IDs: {'PTRANS': 33, 'TRANS': 896} Chain breaks: 2 Chain: "W" Number of atoms: 1600 Number of conformers: 1 Conformer: "" Number of residues, atoms: 204, 1600 Classifications: {'peptide': 204} Link IDs: {'PCIS': 1, 'PTRANS': 13, 'TRANS': 189} Chain: "X" Number of atoms: 1600 Number of conformers: 1 Conformer: "" Number of residues, atoms: 204, 1600 Classifications: {'peptide': 204} Link IDs: {'PCIS': 1, 'PTRANS': 13, 'TRANS': 189} Chain: "Y" Number of atoms: 2400 Number of conformers: 1 Conformer: "" Number of residues, atoms: 296, 2400 Classifications: {'peptide': 296} Link IDs: {'PTRANS': 11, 'TRANS': 284} Chain: "Z" Number of atoms: 1069 Number of conformers: 1 Conformer: "" Number of residues, atoms: 139, 1069 Classifications: {'peptide': 139} Link IDs: {'PCIS': 1, 'PTRANS': 4, 'TRANS': 133} Chain: "0" Number of atoms: 1069 Number of conformers: 1 Conformer: "" Number of residues, atoms: 139, 1069 Classifications: {'peptide': 139} Link IDs: {'PTRANS': 5, 'TRANS': 133} Chain: "1" Number of atoms: 1069 Number of conformers: 1 Conformer: "" Number of residues, atoms: 139, 1069 Classifications: {'peptide': 139} Link IDs: {'PCIS': 1, 'PTRANS': 4, 'TRANS': 133} Chain: "2" Number of atoms: 1056 Number of conformers: 1 Conformer: "" Number of residues, atoms: 137, 1056 Classifications: {'peptide': 137} Link IDs: {'PCIS': 1, 'PTRANS': 4, 'TRANS': 131} Chain: "3" Number of atoms: 338 Number of conformers: 1 Conformer: "" Number of residues, atoms: 46, 338 Classifications: {'peptide': 46} Link IDs: {'PTRANS': 1, 'TRANS': 44} Chain: "4" Number of atoms: 343 Number of conformers: 1 Conformer: "" Number of residues, atoms: 47, 343 Classifications: {'peptide': 47} Link IDs: {'PTRANS': 1, 'TRANS': 45} Chain: "5" Number of atoms: 336 Number of conformers: 1 Conformer: "" Number of residues, atoms: 47, 336 Classifications: {'peptide': 47} Link IDs: {'PTRANS': 1, 'TRANS': 45} Chain: "6" Number of atoms: 257 Number of conformers: 1 Conformer: "" Number of residues, atoms: 36, 257 Classifications: {'peptide': 36} Link IDs: {'TRANS': 35} Chain: "7" Number of atoms: 3552 Number of conformers: 1 Conformer: "" Number of residues, atoms: 466, 3552 Classifications: {'peptide': 466} Link IDs: {'PCIS': 1, 'PTRANS': 16, 'TRANS': 448} Time building chain proxies: 26.15, per 1000 atoms: 0.39 Number of scatterers: 66381 At special positions: 0 Unit cell: (191.8, 189, 296.8, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 147 16.00 O 13320 8.00 N 11004 7.00 C 41910 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=3, symmetry=0 Simple disulfide: pdb=" SG CYS A 316 " - pdb=" SG CYS A 327 " distance=2.02 Simple disulfide: pdb=" SG CYS B 316 " - pdb=" SG CYS B 327 " distance=2.02 Simple disulfide: pdb=" SG CYS V 316 " - pdb=" SG CYS V 327 " distance=2.02 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 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: 20.13 Conformation dependent library (CDL) restraints added in 8.7 seconds 16800 Ramachandran restraints generated. 8400 Oldfield, 0 Emsley, 8400 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 15846 Finding SS restraints... Secondary structure from input PDB file: 186 helices and 120 sheets defined 17.8% alpha, 27.6% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 5.74 Creating SS restraints... Processing helix chain 'A' and resid 5 through 15 removed outlier: 3.530A pdb=" N ARG A 9 " --> pdb=" O LEU A 5 " (cutoff:3.500A) Processing helix chain 'A' and resid 85 through 94 Processing helix chain 'A' and resid 174 through 180 Processing helix chain 'A' and resid 196 through 202 Processing helix chain 'A' and resid 207 through 216 removed outlier: 3.684A pdb=" N ILE A 212 " --> pdb=" O ALA A 208 " (cutoff:3.500A) removed outlier: 4.367A pdb=" N SER A 213 " --> pdb=" O ASN A 209 " (cutoff:3.500A) Processing helix chain 'A' and resid 217 through 219 No H-bonds generated for 'chain 'A' and resid 217 through 219' Processing helix chain 'A' and resid 241 through 249 Processing helix chain 'A' and resid 259 through 263 Processing helix chain 'A' and resid 318 through 325 Processing helix chain 'A' and resid 338 through 344 removed outlier: 3.821A pdb=" N ALA A 342 " --> pdb=" O MET A 338 " (cutoff:3.500A) Processing helix chain 'A' and resid 380 through 388 Processing helix chain 'A' and resid 392 through 399 Processing helix chain 'A' and resid 401 through 405 Processing helix chain 'A' and resid 459 through 470 Processing helix chain 'A' and resid 478 through 482 Processing helix chain 'A' and resid 483 through 495 removed outlier: 4.011A pdb=" N GLN A 489 " --> pdb=" O GLN A 485 " (cutoff:3.500A) Processing helix chain 'A' and resid 502 through 506 Processing helix chain 'A' and resid 508 through 513 Processing helix chain 'A' and resid 536 through 547 Processing helix chain 'A' and resid 576 through 578 No H-bonds generated for 'chain 'A' and resid 576 through 578' Processing helix chain 'A' and resid 587 through 592 removed outlier: 3.603A pdb=" N ASN A 591 " --> pdb=" O THR A 587 " (cutoff:3.500A) Processing helix chain 'A' and resid 603 through 606 Processing helix chain 'A' and resid 616 through 623 Processing helix chain 'A' and resid 639 through 655 removed outlier: 3.642A pdb=" N ARG A 655 " --> pdb=" O LEU A 651 " (cutoff:3.500A) Processing helix chain 'A' and resid 665 through 669 Processing helix chain 'A' and resid 682 through 685 Processing helix chain 'A' and resid 713 through 717 Processing helix chain 'A' and resid 724 through 728 removed outlier: 3.633A pdb=" N ASN A 727 " --> pdb=" O ASN A 724 " (cutoff:3.500A) removed outlier: 3.912A pdb=" N ASP A 728 " --> pdb=" O SER A 725 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 724 through 728' Processing helix chain 'A' and resid 871 through 875 Processing helix chain 'A' and resid 907 through 918 Processing helix chain 'H' and resid 12 through 16 removed outlier: 4.064A pdb=" N GLY H 16 " --> pdb=" O SER H 13 " (cutoff:3.500A) Processing helix chain 'H' and resid 58 through 76 Processing helix chain 'H' and resid 83 through 88 Processing helix chain 'H' and resid 94 through 98 Processing helix chain 'I' and resid 9 through 16 removed outlier: 3.789A pdb=" N SER I 13 " --> pdb=" O PRO I 10 " (cutoff:3.500A) removed outlier: 5.826A pdb=" N GLY I 14 " --> pdb=" O GLU I 11 " (cutoff:3.500A) Processing helix chain 'I' and resid 58 through 76 removed outlier: 3.624A pdb=" N GLU I 71 " --> pdb=" O ALA I 67 " (cutoff:3.500A) Processing helix chain 'I' and resid 83 through 87 Processing helix chain 'I' and resid 94 through 98 Processing helix chain 'I' and resid 179 through 183 removed outlier: 3.503A pdb=" N PHE I 183 " --> pdb=" O GLY I 180 " (cutoff:3.500A) Processing helix chain 'L' and resid 5 through 9 Processing helix chain 'L' and resid 75 through 83 removed outlier: 4.046A pdb=" N PHE L 79 " --> pdb=" O GLU L 75 " (cutoff:3.500A) Processing helix chain 'L' and resid 200 through 204 removed outlier: 3.517A pdb=" N ILE L 204 " --> pdb=" O VAL L 201 " (cutoff:3.500A) Processing helix chain 'Q' and resid 71 through 73 No H-bonds generated for 'chain 'Q' and resid 71 through 73' Processing helix chain 'Q' and resid 81 through 92 Processing helix chain 'R' and resid 81 through 92 removed outlier: 3.647A pdb=" N GLU R 90 " --> pdb=" O THR R 86 " (cutoff:3.500A) removed outlier: 3.915A pdb=" N LYS R 91 " --> pdb=" O ASN R 87 " (cutoff:3.500A) Processing helix chain 'S' and resid 2 through 6 removed outlier: 3.857A pdb=" N ASN S 5 " --> pdb=" O SER S 2 " (cutoff:3.500A) removed outlier: 3.787A pdb=" N ARG S 6 " --> pdb=" O THR S 3 " (cutoff:3.500A) No H-bonds generated for 'chain 'S' and resid 2 through 6' Processing helix chain 'S' and resid 70 through 73 Processing helix chain 'S' and resid 81 through 92 Processing helix chain 'T' and resid 81 through 92 removed outlier: 3.626A pdb=" N LYS T 91 " --> pdb=" O ASN T 87 " (cutoff:3.500A) Processing helix chain 'd' and resid 40 through 50 Processing helix chain 'e' and resid 42 through 52 removed outlier: 3.741A pdb=" N ALA e 46 " --> pdb=" O GLY e 42 " (cutoff:3.500A) Processing helix chain 'f' and resid 41 through 54 removed outlier: 4.009A pdb=" N THR f 45 " --> pdb=" O ALA f 41 " (cutoff:3.500A) Processing helix chain 'k' and resid 143 through 152 Processing helix chain 'k' and resid 152 through 168 removed outlier: 3.961A pdb=" N LEU k 156 " --> pdb=" O ASN k 152 " (cutoff:3.500A) Processing helix chain 'k' and resid 171 through 177 Processing helix chain 'p' and resid 5 through 9 Processing helix chain 'p' and resid 91 through 98 removed outlier: 3.528A pdb=" N TRP p 95 " --> pdb=" O ASP p 91 " (cutoff:3.500A) Processing helix chain 'p' and resid 192 through 200 removed outlier: 4.008A pdb=" N GLN p 200 " --> pdb=" O TYR p 196 " (cutoff:3.500A) Processing helix chain 'p' and resid 205 through 209 removed outlier: 3.566A pdb=" N LEU p 208 " --> pdb=" O LYS p 205 " (cutoff:3.500A) Processing helix chain 'p' and resid 275 through 285 Processing helix chain 'p' and resid 360 through 369 Processing helix chain 'p' and resid 388 through 390 No H-bonds generated for 'chain 'p' and resid 388 through 390' Processing helix chain 'B' and resid 5 through 15 removed outlier: 3.530A pdb=" N ARG B 9 " --> pdb=" O LEU B 5 " (cutoff:3.500A) Processing helix chain 'B' and resid 85 through 94 Processing helix chain 'B' and resid 174 through 180 Processing helix chain 'B' and resid 196 through 202 Processing helix chain 'B' and resid 207 through 216 removed outlier: 3.683A pdb=" N ILE B 212 " --> pdb=" O ALA B 208 " (cutoff:3.500A) removed outlier: 4.367A pdb=" N SER B 213 " --> pdb=" O ASN B 209 " (cutoff:3.500A) Processing helix chain 'B' and resid 217 through 219 No H-bonds generated for 'chain 'B' and resid 217 through 219' Processing helix chain 'B' and resid 241 through 249 Processing helix chain 'B' and resid 259 through 263 Processing helix chain 'B' and resid 318 through 325 Processing helix chain 'B' and resid 338 through 344 removed outlier: 3.821A pdb=" N ALA B 342 " --> pdb=" O MET B 338 " (cutoff:3.500A) Processing helix chain 'B' and resid 380 through 388 Processing helix chain 'B' and resid 392 through 399 Processing helix chain 'B' and resid 401 through 405 Processing helix chain 'B' and resid 459 through 470 Processing helix chain 'B' and resid 478 through 482 Processing helix chain 'B' and resid 483 through 495 removed outlier: 4.011A pdb=" N GLN B 489 " --> pdb=" O GLN B 485 " (cutoff:3.500A) Processing helix chain 'B' and resid 502 through 506 Processing helix chain 'B' and resid 508 through 513 Processing helix chain 'B' and resid 536 through 547 Processing helix chain 'B' and resid 576 through 578 No H-bonds generated for 'chain 'B' and resid 576 through 578' Processing helix chain 'B' and resid 587 through 592 removed outlier: 3.603A pdb=" N ASN B 591 " --> pdb=" O THR B 587 " (cutoff:3.500A) Processing helix chain 'B' and resid 603 through 606 Processing helix chain 'B' and resid 616 through 623 Processing helix chain 'B' and resid 639 through 655 removed outlier: 3.642A pdb=" N ARG B 655 " --> pdb=" O LEU B 651 " (cutoff:3.500A) Processing helix chain 'B' and resid 665 through 669 Processing helix chain 'B' and resid 682 through 685 Processing helix chain 'B' and resid 713 through 717 Processing helix chain 'B' and resid 724 through 728 removed outlier: 3.634A pdb=" N ASN B 727 " --> pdb=" O ASN B 724 " (cutoff:3.500A) removed outlier: 3.911A pdb=" N ASP B 728 " --> pdb=" O SER B 725 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 724 through 728' Processing helix chain 'B' and resid 871 through 875 Processing helix chain 'B' and resid 907 through 918 Processing helix chain 'C' and resid 12 through 16 removed outlier: 4.063A pdb=" N GLY C 16 " --> pdb=" O SER C 13 " (cutoff:3.500A) Processing helix chain 'C' and resid 58 through 76 Processing helix chain 'C' and resid 83 through 88 Processing helix chain 'C' and resid 94 through 98 Processing helix chain 'D' and resid 9 through 16 removed outlier: 3.788A pdb=" N SER D 13 " --> pdb=" O PRO D 10 " (cutoff:3.500A) removed outlier: 5.826A pdb=" N GLY D 14 " --> pdb=" O GLU D 11 " (cutoff:3.500A) Processing helix chain 'D' and resid 58 through 76 removed outlier: 3.624A pdb=" N GLU D 71 " --> pdb=" O ALA D 67 " (cutoff:3.500A) Processing helix chain 'D' and resid 83 through 87 Processing helix chain 'D' and resid 94 through 98 Processing helix chain 'D' and resid 179 through 183 removed outlier: 3.503A pdb=" N PHE D 183 " --> pdb=" O GLY D 180 " (cutoff:3.500A) Processing helix chain 'E' and resid 5 through 9 Processing helix chain 'E' and resid 75 through 83 removed outlier: 4.047A pdb=" N PHE E 79 " --> pdb=" O GLU E 75 " (cutoff:3.500A) Processing helix chain 'E' and resid 200 through 204 removed outlier: 3.517A pdb=" N ILE E 204 " --> pdb=" O VAL E 201 " (cutoff:3.500A) Processing helix chain 'F' and resid 71 through 73 No H-bonds generated for 'chain 'F' and resid 71 through 73' Processing helix chain 'F' and resid 81 through 92 Processing helix chain 'G' and resid 81 through 92 removed outlier: 3.647A pdb=" N GLU G 90 " --> pdb=" O THR G 86 " (cutoff:3.500A) removed outlier: 3.914A pdb=" N LYS G 91 " --> pdb=" O ASN G 87 " (cutoff:3.500A) Processing helix chain 'J' and resid 2 through 6 removed outlier: 3.857A pdb=" N ASN J 5 " --> pdb=" O SER J 2 " (cutoff:3.500A) removed outlier: 3.787A pdb=" N ARG J 6 " --> pdb=" O THR J 3 " (cutoff:3.500A) No H-bonds generated for 'chain 'J' and resid 2 through 6' Processing helix chain 'J' and resid 70 through 73 Processing helix chain 'J' and resid 81 through 92 Processing helix chain 'K' and resid 81 through 92 removed outlier: 3.626A pdb=" N LYS K 91 " --> pdb=" O ASN K 87 " (cutoff:3.500A) Processing helix chain 'M' and resid 40 through 50 Processing helix chain 'N' and resid 42 through 52 removed outlier: 3.741A pdb=" N ALA N 46 " --> pdb=" O GLY N 42 " (cutoff:3.500A) Processing helix chain 'O' and resid 41 through 54 removed outlier: 4.010A pdb=" N THR O 45 " --> pdb=" O ALA O 41 " (cutoff:3.500A) Processing helix chain 'P' and resid 143 through 152 Processing helix chain 'P' and resid 152 through 168 removed outlier: 3.961A pdb=" N LEU P 156 " --> pdb=" O ASN P 152 " (cutoff:3.500A) Processing helix chain 'P' and resid 171 through 177 Processing helix chain 'U' and resid 5 through 9 Processing helix chain 'U' and resid 91 through 98 removed outlier: 3.528A pdb=" N TRP U 95 " --> pdb=" O ASP U 91 " (cutoff:3.500A) Processing helix chain 'U' and resid 192 through 200 removed outlier: 4.008A pdb=" N GLN U 200 " --> pdb=" O TYR U 196 " (cutoff:3.500A) Processing helix chain 'U' and resid 205 through 209 removed outlier: 3.566A pdb=" N LEU U 208 " --> pdb=" O LYS U 205 " (cutoff:3.500A) Processing helix chain 'U' and resid 275 through 285 Processing helix chain 'U' and resid 360 through 369 Processing helix chain 'U' and resid 388 through 390 No H-bonds generated for 'chain 'U' and resid 388 through 390' Processing helix chain 'V' and resid 5 through 15 removed outlier: 3.530A pdb=" N ARG V 9 " --> pdb=" O LEU V 5 " (cutoff:3.500A) Processing helix chain 'V' and resid 85 through 94 Processing helix chain 'V' and resid 174 through 180 Processing helix chain 'V' and resid 196 through 202 Processing helix chain 'V' and resid 207 through 216 removed outlier: 3.683A pdb=" N ILE V 212 " --> pdb=" O ALA V 208 " (cutoff:3.500A) removed outlier: 4.367A pdb=" N SER V 213 " --> pdb=" O ASN V 209 " (cutoff:3.500A) Processing helix chain 'V' and resid 217 through 219 No H-bonds generated for 'chain 'V' and resid 217 through 219' Processing helix chain 'V' and resid 241 through 249 Processing helix chain 'V' and resid 259 through 263 Processing helix chain 'V' and resid 318 through 325 Processing helix chain 'V' and resid 338 through 344 removed outlier: 3.822A pdb=" N ALA V 342 " --> pdb=" O MET V 338 " (cutoff:3.500A) Processing helix chain 'V' and resid 380 through 388 Processing helix chain 'V' and resid 392 through 399 Processing helix chain 'V' and resid 401 through 405 Processing helix chain 'V' and resid 459 through 470 Processing helix chain 'V' and resid 478 through 482 Processing helix chain 'V' and resid 483 through 495 removed outlier: 4.011A pdb=" N GLN V 489 " --> pdb=" O GLN V 485 " (cutoff:3.500A) Processing helix chain 'V' and resid 502 through 506 Processing helix chain 'V' and resid 508 through 513 Processing helix chain 'V' and resid 536 through 547 Processing helix chain 'V' and resid 576 through 578 No H-bonds generated for 'chain 'V' and resid 576 through 578' Processing helix chain 'V' and resid 587 through 592 removed outlier: 3.603A pdb=" N ASN V 591 " --> pdb=" O THR V 587 " (cutoff:3.500A) Processing helix chain 'V' and resid 603 through 606 Processing helix chain 'V' and resid 616 through 623 Processing helix chain 'V' and resid 639 through 655 removed outlier: 3.642A pdb=" N ARG V 655 " --> pdb=" O LEU V 651 " (cutoff:3.500A) Processing helix chain 'V' and resid 665 through 669 Processing helix chain 'V' and resid 682 through 685 Processing helix chain 'V' and resid 713 through 717 Processing helix chain 'V' and resid 724 through 728 removed outlier: 3.633A pdb=" N ASN V 727 " --> pdb=" O ASN V 724 " (cutoff:3.500A) removed outlier: 3.911A pdb=" N ASP V 728 " --> pdb=" O SER V 725 " (cutoff:3.500A) No H-bonds generated for 'chain 'V' and resid 724 through 728' Processing helix chain 'V' and resid 871 through 875 Processing helix chain 'V' and resid 907 through 918 Processing helix chain 'W' and resid 12 through 16 removed outlier: 4.063A pdb=" N GLY W 16 " --> pdb=" O SER W 13 " (cutoff:3.500A) Processing helix chain 'W' and resid 58 through 76 Processing helix chain 'W' and resid 83 through 88 Processing helix chain 'W' and resid 94 through 98 Processing helix chain 'X' and resid 9 through 16 removed outlier: 3.789A pdb=" N SER X 13 " --> pdb=" O PRO X 10 " (cutoff:3.500A) removed outlier: 5.826A pdb=" N GLY X 14 " --> pdb=" O GLU X 11 " (cutoff:3.500A) Processing helix chain 'X' and resid 58 through 76 removed outlier: 3.624A pdb=" N GLU X 71 " --> pdb=" O ALA X 67 " (cutoff:3.500A) Processing helix chain 'X' and resid 83 through 87 Processing helix chain 'X' and resid 94 through 98 Processing helix chain 'X' and resid 179 through 183 removed outlier: 3.503A pdb=" N PHE X 183 " --> pdb=" O GLY X 180 " (cutoff:3.500A) Processing helix chain 'Y' and resid 5 through 9 Processing helix chain 'Y' and resid 75 through 83 removed outlier: 4.047A pdb=" N PHE Y 79 " --> pdb=" O GLU Y 75 " (cutoff:3.500A) Processing helix chain 'Y' and resid 200 through 204 removed outlier: 3.517A pdb=" N ILE Y 204 " --> pdb=" O VAL Y 201 " (cutoff:3.500A) Processing helix chain 'Z' and resid 71 through 73 No H-bonds generated for 'chain 'Z' and resid 71 through 73' Processing helix chain 'Z' and resid 81 through 92 Processing helix chain '0' and resid 81 through 92 removed outlier: 3.647A pdb=" N GLU 0 90 " --> pdb=" O THR 0 86 " (cutoff:3.500A) removed outlier: 3.914A pdb=" N LYS 0 91 " --> pdb=" O ASN 0 87 " (cutoff:3.500A) Processing helix chain '1' and resid 2 through 6 removed outlier: 3.856A pdb=" N ASN 1 5 " --> pdb=" O SER 1 2 " (cutoff:3.500A) removed outlier: 3.787A pdb=" N ARG 1 6 " --> pdb=" O THR 1 3 " (cutoff:3.500A) No H-bonds generated for 'chain '1' and resid 2 through 6' Processing helix chain '1' and resid 70 through 73 Processing helix chain '1' and resid 81 through 92 Processing helix chain '2' and resid 81 through 92 removed outlier: 3.626A pdb=" N LYS 2 91 " --> pdb=" O ASN 2 87 " (cutoff:3.500A) Processing helix chain '3' and resid 40 through 50 Processing helix chain '4' and resid 42 through 52 removed outlier: 3.741A pdb=" N ALA 4 46 " --> pdb=" O GLY 4 42 " (cutoff:3.500A) Processing helix chain '5' and resid 41 through 54 removed outlier: 4.010A pdb=" N THR 5 45 " --> pdb=" O ALA 5 41 " (cutoff:3.500A) Processing helix chain '6' and resid 143 through 152 Processing helix chain '6' and resid 152 through 168 removed outlier: 3.961A pdb=" N LEU 6 156 " --> pdb=" O ASN 6 152 " (cutoff:3.500A) Processing helix chain '6' and resid 171 through 177 Processing helix chain '7' and resid 5 through 9 Processing helix chain '7' and resid 91 through 98 removed outlier: 3.528A pdb=" N TRP 7 95 " --> pdb=" O ASP 7 91 " (cutoff:3.500A) Processing helix chain '7' and resid 192 through 200 removed outlier: 4.008A pdb=" N GLN 7 200 " --> pdb=" O TYR 7 196 " (cutoff:3.500A) Processing helix chain '7' and resid 205 through 209 removed outlier: 3.566A pdb=" N LEU 7 208 " --> pdb=" O LYS 7 205 " (cutoff:3.500A) Processing helix chain '7' and resid 275 through 285 Processing helix chain '7' and resid 360 through 369 Processing helix chain '7' and resid 388 through 390 No H-bonds generated for 'chain '7' and resid 388 through 390' Processing sheet with id= 1, first strand: chain 'A' and resid 17 through 27 WARNING: can't find start of bonding for strands! previous: chain 'A' and resid 38 through 42 current: chain 'A' and resid 53 through 57 WARNING: can't find start of bonding for strands! previous: chain 'A' and resid 53 through 57 current: chain 'A' and resid 77 through 82 WARNING: can't find start of bonding for strands! previous: chain 'A' and resid 77 through 82 current: chain 'A' and resid 128 through 143 removed outlier: 5.241A pdb=" N ILE A 135 " --> pdb=" O SER A 159 " (cutoff:3.500A) removed outlier: 5.940A pdb=" N SER A 159 " --> pdb=" O ILE A 135 " (cutoff:3.500A) removed outlier: 3.618A pdb=" N GLY A 137 " --> pdb=" O ASN A 157 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'A' and resid 151 through 159 current: chain 'I' and resid 38 through 42 Processing sheet with id= 2, first strand: chain 'A' and resid 66 through 69 WARNING: can't find start of bonding for strands! previous: chain 'A' and resid 66 through 69 current: chain 'A' and resid 659 through 664 WARNING: can't find start of bonding for strands! previous: chain 'A' and resid 659 through 664 current: chain 'A' and resid 686 through 698 removed outlier: 6.652A pdb=" N THR A 707 " --> pdb=" O ASP A 694 " (cutoff:3.500A) removed outlier: 4.732A pdb=" N VAL A 696 " --> pdb=" O ASN A 705 " (cutoff:3.500A) removed outlier: 7.022A pdb=" N ASN A 705 " --> pdb=" O VAL A 696 " (cutoff:3.500A) Processing sheet with id= 3, first strand: chain 'A' and resid 181 through 184 Processing sheet with id= 4, first strand: chain 'A' and resid 226 through 228 Processing sheet with id= 5, first strand: chain 'A' and resid 265 through 267 Processing sheet with id= 6, first strand: chain 'A' and resid 270 through 274 removed outlier: 5.977A pdb=" N GLN A 438 " --> pdb=" O PHE A 304 " (cutoff:3.500A) removed outlier: 5.387A pdb=" N PHE A 304 " --> pdb=" O GLN A 438 " (cutoff:3.500A) removed outlier: 8.140A pdb=" N LYS A 440 " --> pdb=" O ASP A 302 " (cutoff:3.500A) removed outlier: 5.675A pdb=" N ASP A 302 " --> pdb=" O LYS A 440 " (cutoff:3.500A) Processing sheet with id= 7, first strand: chain 'A' and resid 276 through 282 removed outlier: 6.409A pdb=" N VAL A 293 " --> pdb=" O ILE A 278 " (cutoff:3.500A) removed outlier: 4.374A pdb=" N ALA A 280 " --> pdb=" O TYR A 291 " (cutoff:3.500A) removed outlier: 6.871A pdb=" N TYR A 291 " --> pdb=" O ALA A 280 " (cutoff:3.500A) removed outlier: 4.507A pdb=" N THR A 282 " --> pdb=" O ILE A 289 " (cutoff:3.500A) removed outlier: 7.181A pdb=" N ILE A 289 " --> pdb=" O THR A 282 " (cutoff:3.500A) removed outlier: 6.748A pdb=" N ALA A 415 " --> pdb=" O PHE A 296 " (cutoff:3.500A) Processing sheet with id= 8, first strand: chain 'A' and resid 315 through 316 Processing sheet with id= 9, first strand: chain 'A' and resid 552 through 553 Processing sheet with id= 10, first strand: chain 'A' and resid 609 through 615 removed outlier: 6.797A pdb=" N SER A 595 " --> pdb=" O LEU A 630 " (cutoff:3.500A) removed outlier: 8.161A pdb=" N LEU A 632 " --> pdb=" O SER A 595 " (cutoff:3.500A) removed outlier: 6.463A pdb=" N GLN A 597 " --> pdb=" O LEU A 632 " (cutoff:3.500A) Processing sheet with id= 11, first strand: chain 'A' and resid 740 through 746 removed outlier: 4.385A pdb=" N PHE A 742 " --> pdb=" O SER A 762 " (cutoff:3.500A) removed outlier: 6.761A pdb=" N SER A 762 " --> pdb=" O PHE A 742 " (cutoff:3.500A) removed outlier: 4.677A pdb=" N TYR A 744 " --> pdb=" O GLU A 760 " (cutoff:3.500A) removed outlier: 6.823A pdb=" N GLU A 760 " --> pdb=" O TYR A 744 " (cutoff:3.500A) Processing sheet with id= 12, first strand: chain 'A' and resid 785 through 788 removed outlier: 3.850A pdb=" N TYR A 773 " --> pdb=" O VAL A 817 " (cutoff:3.500A) Processing sheet with id= 13, first strand: chain 'A' and resid 838 through 839 Processing sheet with id= 14, first strand: chain 'A' and resid 843 through 847 removed outlier: 6.068A pdb=" N ASN A 844 " --> pdb=" O ASP A 868 " (cutoff:3.500A) removed outlier: 4.537A pdb=" N ASP A 868 " --> pdb=" O ASN A 844 " (cutoff:3.500A) Processing sheet with id= 15, first strand: chain 'A' and resid 892 through 898 removed outlier: 6.579A pdb=" N ILE A 885 " --> pdb=" O LEU A 893 " (cutoff:3.500A) removed outlier: 4.450A pdb=" N SER A 895 " --> pdb=" O LEU A 883 " (cutoff:3.500A) removed outlier: 6.764A pdb=" N LEU A 883 " --> pdb=" O SER A 895 " (cutoff:3.500A) removed outlier: 4.525A pdb=" N ARG A 897 " --> pdb=" O TYR A 881 " (cutoff:3.500A) removed outlier: 6.653A pdb=" N TYR A 881 " --> pdb=" O ARG A 897 " (cutoff:3.500A) Processing sheet with id= 16, first strand: chain 'H' and resid 19 through 25 removed outlier: 6.031A pdb=" N TRP H 48 " --> pdb=" O GLU H 202 " (cutoff:3.500A) Processing sheet with id= 17, first strand: chain 'H' and resid 28 through 32 removed outlier: 3.567A pdb=" N ILE H 29 " --> pdb=" O VAL H 41 " (cutoff:3.500A) Processing sheet with id= 18, first strand: chain 'H' and resid 108 through 112 removed outlier: 7.081A pdb=" N SER H 147 " --> pdb=" O ARG H 143 " (cutoff:3.500A) removed outlier: 4.915A pdb=" N ARG H 143 " --> pdb=" O SER H 147 " (cutoff:3.500A) removed outlier: 6.832A pdb=" N SER H 149 " --> pdb=" O PHE H 141 " (cutoff:3.500A) removed outlier: 4.542A pdb=" N PHE H 141 " --> pdb=" O SER H 149 " (cutoff:3.500A) removed outlier: 6.661A pdb=" N ASN H 151 " --> pdb=" O THR H 139 " (cutoff:3.500A) Processing sheet with id= 19, first strand: chain 'H' and resid 184 through 187 removed outlier: 3.902A pdb=" N VAL I 20 " --> pdb=" O LEU H 187 " (cutoff:3.500A) removed outlier: 4.265A pdb=" N SER I 19 " --> pdb=" O SER I 53 " (cutoff:3.500A) removed outlier: 3.633A pdb=" N SER I 53 " --> pdb=" O SER I 19 " (cutoff:3.500A) removed outlier: 6.141A pdb=" N TRP I 48 " --> pdb=" O GLU I 202 " (cutoff:3.500A) Processing sheet with id= 20, first strand: chain 'I' and resid 91 through 92 Processing sheet with id= 21, first strand: chain 'I' and resid 108 through 112 removed outlier: 7.070A pdb=" N SER I 147 " --> pdb=" O ARG I 143 " (cutoff:3.500A) removed outlier: 4.726A pdb=" N ARG I 143 " --> pdb=" O SER I 147 " (cutoff:3.500A) removed outlier: 6.713A pdb=" N SER I 149 " --> pdb=" O PHE I 141 " (cutoff:3.500A) removed outlier: 4.450A pdb=" N PHE I 141 " --> pdb=" O SER I 149 " (cutoff:3.500A) removed outlier: 6.634A pdb=" N ASN I 151 " --> pdb=" O THR I 139 " (cutoff:3.500A) Processing sheet with id= 22, first strand: chain 'I' and resid 186 through 188 removed outlier: 3.725A pdb=" N THR I 186 " --> pdb=" O SER I 194 " (cutoff:3.500A) removed outlier: 3.670A pdb=" N THR I 192 " --> pdb=" O ASN I 188 " (cutoff:3.500A) Processing sheet with id= 23, first strand: chain 'L' and resid 10 through 15 WARNING: can't find start of bonding for strands! previous: chain 'L' and resid 18 through 21 current: chain 'L' and resid 61 through 68 WARNING: can't find start of bonding for strands! previous: chain 'L' and resid 61 through 68 current: chain 'L' and resid 90 through 92 WARNING: can't find start of bonding for strands! previous: chain 'L' and resid 90 through 92 current: chain 'L' and resid 116 through 130 removed outlier: 5.283A pdb=" N VAL L 124 " --> pdb=" O GLU L 143 " (cutoff:3.500A) removed outlier: 6.242A pdb=" N GLU L 143 " --> pdb=" O VAL L 124 " (cutoff:3.500A) removed outlier: 4.448A pdb=" N SER L 130 " --> pdb=" O ILE L 137 " (cutoff:3.500A) removed outlier: 4.625A pdb=" N ILE L 137 " --> pdb=" O SER L 130 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'L' and resid 137 through 144 current: chain 'L' and resid 177 through 178 WARNING: can't find start of bonding for strands! previous: chain 'L' and resid 177 through 178 current: chain 'L' and resid 213 through 227 WARNING: can't find start of bonding for strands! previous: chain 'L' and resid 213 through 227 current: chain 'L' and resid 255 through 269 Processing sheet with id= 24, first strand: chain 'L' and resid 34 through 39 removed outlier: 3.669A pdb=" N ALA L 57 " --> pdb=" O GLU L 35 " (cutoff:3.500A) removed outlier: 6.525A pdb=" N PHE L 37 " --> pdb=" O ILE L 55 " (cutoff:3.500A) removed outlier: 5.476A pdb=" N ILE L 55 " --> pdb=" O PHE L 37 " (cutoff:3.500A) removed outlier: 7.391A pdb=" N THR L 39 " --> pdb=" O SER L 53 " (cutoff:3.500A) removed outlier: 5.214A pdb=" N SER L 53 " --> pdb=" O THR L 39 " (cutoff:3.500A) Processing sheet with id= 25, first strand: chain 'Q' and resid 10 through 13 removed outlier: 6.326A pdb=" N ILE Q 10 " --> pdb=" O TYR Q 133 " (cutoff:3.500A) removed outlier: 7.190A pdb=" N SER Q 135 " --> pdb=" O ILE Q 10 " (cutoff:3.500A) removed outlier: 6.909A pdb=" N VAL Q 12 " --> pdb=" O SER Q 135 " (cutoff:3.500A) removed outlier: 5.789A pdb=" N ILE Q 134 " --> pdb=" O PHE Q 105 " (cutoff:3.500A) removed outlier: 5.401A pdb=" N PHE Q 105 " --> pdb=" O ILE Q 134 " (cutoff:3.500A) removed outlier: 6.902A pdb=" N ILE Q 50 " --> pdb=" O LEU Q 61 " (cutoff:3.500A) Processing sheet with id= 26, first strand: chain 'Q' and resid 18 through 28 WARNING: can't find start of bonding for strands! previous: chain 'Q' and resid 35 through 38 current: chain 'Q' and resid 75 through 80 WARNING: can't find start of bonding for strands! previous: chain 'Q' and resid 75 through 80 current: chain 'f' and resid 22 through 32 Processing sheet with id= 27, first strand: chain 'Q' and resid 44 through 46 Processing sheet with id= 28, first strand: chain 'R' and resid 10 through 13 removed outlier: 6.820A pdb=" N SER R 124 " --> pdb=" O ARG R 115 " (cutoff:3.500A) removed outlier: 7.606A pdb=" N ARG R 115 " --> pdb=" O SER R 124 " (cutoff:3.500A) removed outlier: 5.561A pdb=" N ARG R 126 " --> pdb=" O MET R 113 " (cutoff:3.500A) removed outlier: 6.750A pdb=" N MET R 113 " --> pdb=" O ARG R 126 " (cutoff:3.500A) removed outlier: 3.673A pdb=" N MET R 128 " --> pdb=" O ILE R 111 " (cutoff:3.500A) removed outlier: 5.594A pdb=" N ILE R 134 " --> pdb=" O PHE R 105 " (cutoff:3.500A) removed outlier: 5.419A pdb=" N PHE R 105 " --> pdb=" O ILE R 134 " (cutoff:3.500A) removed outlier: 3.776A pdb=" N ASP R 110 " --> pdb=" O THR R 49 " (cutoff:3.500A) removed outlier: 3.648A pdb=" N THR R 49 " --> pdb=" O ASP R 110 " (cutoff:3.500A) removed outlier: 7.421A pdb=" N GLY R 48 " --> pdb=" O SER R 63 " (cutoff:3.500A) removed outlier: 4.923A pdb=" N SER R 63 " --> pdb=" O GLY R 48 " (cutoff:3.500A) removed outlier: 6.926A pdb=" N ILE R 50 " --> pdb=" O LEU R 61 " (cutoff:3.500A) Processing sheet with id= 29, first strand: chain 'R' and resid 18 through 28 WARNING: can't find start of bonding for strands! previous: chain 'R' and resid 35 through 38 current: chain 'R' and resid 75 through 80 WARNING: can't find start of bonding for strands! previous: chain 'R' and resid 75 through 80 current: chain 'e' and resid 29 through 32 Processing sheet with id= 30, first strand: chain 'S' and resid 11 through 13 removed outlier: 6.695A pdb=" N VAL S 12 " --> pdb=" O SER S 135 " (cutoff:3.500A) removed outlier: 6.671A pdb=" N SER S 124 " --> pdb=" O THR S 114 " (cutoff:3.500A) removed outlier: 6.682A pdb=" N THR S 114 " --> pdb=" O SER S 124 " (cutoff:3.500A) removed outlier: 6.556A pdb=" N ARG S 126 " --> pdb=" O LEU S 112 " (cutoff:3.500A) removed outlier: 6.449A pdb=" N LEU S 112 " --> pdb=" O ARG S 126 " (cutoff:3.500A) removed outlier: 6.961A pdb=" N MET S 128 " --> pdb=" O ASP S 110 " (cutoff:3.500A) removed outlier: 4.726A pdb=" N ASP S 110 " --> pdb=" O MET S 128 " (cutoff:3.500A) removed outlier: 7.070A pdb=" N GLY S 130 " --> pdb=" O TYR S 108 " (cutoff:3.500A) removed outlier: 4.852A pdb=" N TYR S 108 " --> pdb=" O GLY S 130 " (cutoff:3.500A) removed outlier: 6.665A pdb=" N VAL S 132 " --> pdb=" O ALA S 106 " (cutoff:3.500A) removed outlier: 3.632A pdb=" N THR S 49 " --> pdb=" O ASP S 110 " (cutoff:3.500A) removed outlier: 7.863A pdb=" N GLY S 48 " --> pdb=" O SER S 63 " (cutoff:3.500A) removed outlier: 5.324A pdb=" N SER S 63 " --> pdb=" O GLY S 48 " (cutoff:3.500A) removed outlier: 6.926A pdb=" N ILE S 50 " --> pdb=" O LEU S 61 " (cutoff:3.500A) Processing sheet with id= 31, first strand: chain 'S' and resid 18 through 28 WARNING: can't find start of bonding for strands! previous: chain 'S' and resid 35 through 38 current: chain 'S' and resid 75 through 80 WARNING: can't find start of bonding for strands! previous: chain 'S' and resid 75 through 80 current: chain 'e' and resid 21 through 24 Processing sheet with id= 32, first strand: chain 'T' and resid 10 through 13 removed outlier: 7.118A pdb=" N SER T 124 " --> pdb=" O THR T 114 " (cutoff:3.500A) removed outlier: 7.215A pdb=" N THR T 114 " --> pdb=" O SER T 124 " (cutoff:3.500A) removed outlier: 6.947A pdb=" N ARG T 126 " --> pdb=" O LEU T 112 " (cutoff:3.500A) removed outlier: 6.862A pdb=" N LEU T 112 " --> pdb=" O ARG T 126 " (cutoff:3.500A) removed outlier: 7.142A pdb=" N MET T 128 " --> pdb=" O ASP T 110 " (cutoff:3.500A) removed outlier: 4.869A pdb=" N ASP T 110 " --> pdb=" O MET T 128 " (cutoff:3.500A) removed outlier: 7.068A pdb=" N GLY T 130 " --> pdb=" O TYR T 108 " (cutoff:3.500A) removed outlier: 4.811A pdb=" N TYR T 108 " --> pdb=" O GLY T 130 " (cutoff:3.500A) removed outlier: 7.046A pdb=" N VAL T 132 " --> pdb=" O ALA T 106 " (cutoff:3.500A) removed outlier: 3.537A pdb=" N ASP T 110 " --> pdb=" O THR T 49 " (cutoff:3.500A) removed outlier: 3.515A pdb=" N THR T 49 " --> pdb=" O ASP T 110 " (cutoff:3.500A) Processing sheet with id= 33, first strand: chain 'T' and resid 18 through 28 WARNING: can't find start of bonding for strands! previous: chain 'T' and resid 35 through 38 current: chain 'T' and resid 75 through 80 Processing sheet with id= 34, first strand: chain 'd' and resid 35 through 36 removed outlier: 6.714A pdb=" N SER d 35 " --> pdb=" O ILE e 36 " (cutoff:3.500A) No H-bonds generated for sheet with id= 34 Processing sheet with id= 35, first strand: chain 'p' and resid 10 through 14 removed outlier: 4.412A pdb=" N ILE p 11 " --> pdb=" O ILE p 28 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'p' and resid 25 through 28 current: chain 'p' and resid 68 through 75 WARNING: can't find start of bonding for strands! previous: chain 'p' and resid 68 through 75 current: chain 'p' and resid 119 through 122 WARNING: can't find start of bonding for strands! previous: chain 'p' and resid 119 through 122 current: chain 'p' and resid 143 through 157 removed outlier: 3.887A pdb=" N GLN p 175 " --> pdb=" O ASP p 148 " (cutoff:3.500A) removed outlier: 6.500A pdb=" N CYS p 150 " --> pdb=" O GLY p 173 " (cutoff:3.500A) removed outlier: 6.433A pdb=" N GLY p 173 " --> pdb=" O CYS p 150 " (cutoff:3.500A) removed outlier: 6.838A pdb=" N ILE p 152 " --> pdb=" O GLY p 171 " (cutoff:3.500A) removed outlier: 6.381A pdb=" N GLY p 171 " --> pdb=" O ILE p 152 " (cutoff:3.500A) removed outlier: 6.616A pdb=" N GLN p 154 " --> pdb=" O TRP p 169 " (cutoff:3.500A) removed outlier: 4.561A pdb=" N TRP p 169 " --> pdb=" O GLN p 154 " (cutoff:3.500A) removed outlier: 6.849A pdb=" N GLU p 156 " --> pdb=" O VAL p 167 " (cutoff:3.500A) removed outlier: 4.778A pdb=" N VAL p 167 " --> pdb=" O GLU p 156 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'p' and resid 166 through 177 current: chain 'p' and resid 260 through 268 WARNING: can't find start of bonding for strands! previous: chain 'p' and resid 260 through 268 current: chain 'p' and resid 307 through 319 WARNING: can't find start of bonding for strands! previous: chain 'p' and resid 307 through 319 current: chain 'p' and resid 331 through 337 Processing sheet with id= 36, first strand: chain 'p' and resid 40 through 46 removed outlier: 6.219A pdb=" N THR p 43 " --> pdb=" O ASN p 62 " (cutoff:3.500A) removed outlier: 5.405A pdb=" N ASN p 62 " --> pdb=" O THR p 43 " (cutoff:3.500A) removed outlier: 6.967A pdb=" N ILE p 45 " --> pdb=" O ARG p 60 " (cutoff:3.500A) removed outlier: 5.123A pdb=" N ARG p 60 " --> pdb=" O ILE p 45 " (cutoff:3.500A) Processing sheet with id= 37, first strand: chain 'p' and resid 79 through 80 Processing sheet with id= 38, first strand: chain 'p' and resid 238 through 240 removed outlier: 3.919A pdb=" N GLY p 253 " --> pdb=" O LEU p 240 " (cutoff:3.500A) Processing sheet with id= 39, first strand: chain 'p' and resid 381 through 386 Processing sheet with id= 40, first strand: chain 'p' and resid 392 through 394 removed outlier: 6.529A pdb=" N ILE p 445 " --> pdb=" O SER p 420 " (cutoff:3.500A) Processing sheet with id= 41, first strand: chain 'B' and resid 17 through 27 WARNING: can't find start of bonding for strands! previous: chain 'B' and resid 38 through 42 current: chain 'B' and resid 53 through 57 WARNING: can't find start of bonding for strands! previous: chain 'B' and resid 53 through 57 current: chain 'B' and resid 77 through 82 WARNING: can't find start of bonding for strands! previous: chain 'B' and resid 77 through 82 current: chain 'B' and resid 128 through 143 removed outlier: 5.242A pdb=" N ILE B 135 " --> pdb=" O SER B 159 " (cutoff:3.500A) removed outlier: 5.941A pdb=" N SER B 159 " --> pdb=" O ILE B 135 " (cutoff:3.500A) removed outlier: 3.618A pdb=" N GLY B 137 " --> pdb=" O ASN B 157 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'B' and resid 151 through 159 current: chain 'D' and resid 38 through 42 Processing sheet with id= 42, first strand: chain 'B' and resid 66 through 69 WARNING: can't find start of bonding for strands! previous: chain 'B' and resid 66 through 69 current: chain 'B' and resid 659 through 664 WARNING: can't find start of bonding for strands! previous: chain 'B' and resid 659 through 664 current: chain 'B' and resid 686 through 698 removed outlier: 6.652A pdb=" N THR B 707 " --> pdb=" O ASP B 694 " (cutoff:3.500A) removed outlier: 4.731A pdb=" N VAL B 696 " --> pdb=" O ASN B 705 " (cutoff:3.500A) removed outlier: 7.022A pdb=" N ASN B 705 " --> pdb=" O VAL B 696 " (cutoff:3.500A) Processing sheet with id= 43, first strand: chain 'B' and resid 181 through 184 Processing sheet with id= 44, first strand: chain 'B' and resid 226 through 228 Processing sheet with id= 45, first strand: chain 'B' and resid 265 through 267 Processing sheet with id= 46, first strand: chain 'B' and resid 270 through 274 removed outlier: 5.977A pdb=" N GLN B 438 " --> pdb=" O PHE B 304 " (cutoff:3.500A) removed outlier: 5.387A pdb=" N PHE B 304 " --> pdb=" O GLN B 438 " (cutoff:3.500A) removed outlier: 8.140A pdb=" N LYS B 440 " --> pdb=" O ASP B 302 " (cutoff:3.500A) removed outlier: 5.675A pdb=" N ASP B 302 " --> pdb=" O LYS B 440 " (cutoff:3.500A) Processing sheet with id= 47, first strand: chain 'B' and resid 276 through 282 removed outlier: 6.409A pdb=" N VAL B 293 " --> pdb=" O ILE B 278 " (cutoff:3.500A) removed outlier: 4.374A pdb=" N ALA B 280 " --> pdb=" O TYR B 291 " (cutoff:3.500A) removed outlier: 6.871A pdb=" N TYR B 291 " --> pdb=" O ALA B 280 " (cutoff:3.500A) removed outlier: 4.507A pdb=" N THR B 282 " --> pdb=" O ILE B 289 " (cutoff:3.500A) removed outlier: 7.181A pdb=" N ILE B 289 " --> pdb=" O THR B 282 " (cutoff:3.500A) removed outlier: 6.748A pdb=" N ALA B 415 " --> pdb=" O PHE B 296 " (cutoff:3.500A) Processing sheet with id= 48, first strand: chain 'B' and resid 315 through 316 Processing sheet with id= 49, first strand: chain 'B' and resid 552 through 553 Processing sheet with id= 50, first strand: chain 'B' and resid 609 through 615 removed outlier: 6.797A pdb=" N SER B 595 " --> pdb=" O LEU B 630 " (cutoff:3.500A) removed outlier: 8.162A pdb=" N LEU B 632 " --> pdb=" O SER B 595 " (cutoff:3.500A) removed outlier: 6.462A pdb=" N GLN B 597 " --> pdb=" O LEU B 632 " (cutoff:3.500A) Processing sheet with id= 51, first strand: chain 'B' and resid 740 through 746 removed outlier: 4.385A pdb=" N PHE B 742 " --> pdb=" O SER B 762 " (cutoff:3.500A) removed outlier: 6.760A pdb=" N SER B 762 " --> pdb=" O PHE B 742 " (cutoff:3.500A) removed outlier: 4.677A pdb=" N TYR B 744 " --> pdb=" O GLU B 760 " (cutoff:3.500A) removed outlier: 6.823A pdb=" N GLU B 760 " --> pdb=" O TYR B 744 " (cutoff:3.500A) Processing sheet with id= 52, first strand: chain 'B' and resid 785 through 788 removed outlier: 3.850A pdb=" N TYR B 773 " --> pdb=" O VAL B 817 " (cutoff:3.500A) Processing sheet with id= 53, first strand: chain 'B' and resid 838 through 839 Processing sheet with id= 54, first strand: chain 'B' and resid 843 through 847 removed outlier: 6.069A pdb=" N ASN B 844 " --> pdb=" O ASP B 868 " (cutoff:3.500A) removed outlier: 4.537A pdb=" N ASP B 868 " --> pdb=" O ASN B 844 " (cutoff:3.500A) Processing sheet with id= 55, first strand: chain 'B' and resid 892 through 898 removed outlier: 6.579A pdb=" N ILE B 885 " --> pdb=" O LEU B 893 " (cutoff:3.500A) removed outlier: 4.449A pdb=" N SER B 895 " --> pdb=" O LEU B 883 " (cutoff:3.500A) removed outlier: 6.763A pdb=" N LEU B 883 " --> pdb=" O SER B 895 " (cutoff:3.500A) removed outlier: 4.525A pdb=" N ARG B 897 " --> pdb=" O TYR B 881 " (cutoff:3.500A) removed outlier: 6.652A pdb=" N TYR B 881 " --> pdb=" O ARG B 897 " (cutoff:3.500A) Processing sheet with id= 56, first strand: chain 'C' and resid 19 through 25 removed outlier: 6.031A pdb=" N TRP C 48 " --> pdb=" O GLU C 202 " (cutoff:3.500A) Processing sheet with id= 57, first strand: chain 'C' and resid 28 through 32 removed outlier: 3.567A pdb=" N ILE C 29 " --> pdb=" O VAL C 41 " (cutoff:3.500A) Processing sheet with id= 58, first strand: chain 'C' and resid 108 through 112 removed outlier: 7.081A pdb=" N SER C 147 " --> pdb=" O ARG C 143 " (cutoff:3.500A) removed outlier: 4.915A pdb=" N ARG C 143 " --> pdb=" O SER C 147 " (cutoff:3.500A) removed outlier: 6.832A pdb=" N SER C 149 " --> pdb=" O PHE C 141 " (cutoff:3.500A) removed outlier: 4.542A pdb=" N PHE C 141 " --> pdb=" O SER C 149 " (cutoff:3.500A) removed outlier: 6.661A pdb=" N ASN C 151 " --> pdb=" O THR C 139 " (cutoff:3.500A) Processing sheet with id= 59, first strand: chain 'C' and resid 184 through 187 removed outlier: 3.902A pdb=" N VAL D 20 " --> pdb=" O LEU C 187 " (cutoff:3.500A) removed outlier: 4.264A pdb=" N SER D 19 " --> pdb=" O SER D 53 " (cutoff:3.500A) removed outlier: 3.633A pdb=" N SER D 53 " --> pdb=" O SER D 19 " (cutoff:3.500A) removed outlier: 6.141A pdb=" N TRP D 48 " --> pdb=" O GLU D 202 " (cutoff:3.500A) Processing sheet with id= 60, first strand: chain 'D' and resid 91 through 92 Processing sheet with id= 61, first strand: chain 'D' and resid 108 through 112 removed outlier: 7.070A pdb=" N SER D 147 " --> pdb=" O ARG D 143 " (cutoff:3.500A) removed outlier: 4.727A pdb=" N ARG D 143 " --> pdb=" O SER D 147 " (cutoff:3.500A) removed outlier: 6.713A pdb=" N SER D 149 " --> pdb=" O PHE D 141 " (cutoff:3.500A) removed outlier: 4.450A pdb=" N PHE D 141 " --> pdb=" O SER D 149 " (cutoff:3.500A) removed outlier: 6.634A pdb=" N ASN D 151 " --> pdb=" O THR D 139 " (cutoff:3.500A) Processing sheet with id= 62, first strand: chain 'D' and resid 186 through 188 removed outlier: 3.725A pdb=" N THR D 186 " --> pdb=" O SER D 194 " (cutoff:3.500A) removed outlier: 3.670A pdb=" N THR D 192 " --> pdb=" O ASN D 188 " (cutoff:3.500A) Processing sheet with id= 63, first strand: chain 'E' and resid 10 through 15 WARNING: can't find start of bonding for strands! previous: chain 'E' and resid 18 through 21 current: chain 'E' and resid 61 through 68 WARNING: can't find start of bonding for strands! previous: chain 'E' and resid 61 through 68 current: chain 'E' and resid 90 through 92 WARNING: can't find start of bonding for strands! previous: chain 'E' and resid 90 through 92 current: chain 'E' and resid 116 through 130 removed outlier: 5.283A pdb=" N VAL E 124 " --> pdb=" O GLU E 143 " (cutoff:3.500A) removed outlier: 6.242A pdb=" N GLU E 143 " --> pdb=" O VAL E 124 " (cutoff:3.500A) removed outlier: 4.449A pdb=" N SER E 130 " --> pdb=" O ILE E 137 " (cutoff:3.500A) removed outlier: 4.625A pdb=" N ILE E 137 " --> pdb=" O SER E 130 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'E' and resid 137 through 144 current: chain 'E' and resid 177 through 178 WARNING: can't find start of bonding for strands! previous: chain 'E' and resid 177 through 178 current: chain 'E' and resid 213 through 227 WARNING: can't find start of bonding for strands! previous: chain 'E' and resid 213 through 227 current: chain 'E' and resid 255 through 269 Processing sheet with id= 64, first strand: chain 'E' and resid 34 through 39 removed outlier: 3.669A pdb=" N ALA E 57 " --> pdb=" O GLU E 35 " (cutoff:3.500A) removed outlier: 6.525A pdb=" N PHE E 37 " --> pdb=" O ILE E 55 " (cutoff:3.500A) removed outlier: 5.476A pdb=" N ILE E 55 " --> pdb=" O PHE E 37 " (cutoff:3.500A) removed outlier: 7.391A pdb=" N THR E 39 " --> pdb=" O SER E 53 " (cutoff:3.500A) removed outlier: 5.214A pdb=" N SER E 53 " --> pdb=" O THR E 39 " (cutoff:3.500A) Processing sheet with id= 65, first strand: chain 'F' and resid 10 through 13 removed outlier: 6.326A pdb=" N ILE F 10 " --> pdb=" O TYR F 133 " (cutoff:3.500A) removed outlier: 7.191A pdb=" N SER F 135 " --> pdb=" O ILE F 10 " (cutoff:3.500A) removed outlier: 6.909A pdb=" N VAL F 12 " --> pdb=" O SER F 135 " (cutoff:3.500A) removed outlier: 5.789A pdb=" N ILE F 134 " --> pdb=" O PHE F 105 " (cutoff:3.500A) removed outlier: 5.400A pdb=" N PHE F 105 " --> pdb=" O ILE F 134 " (cutoff:3.500A) removed outlier: 6.902A pdb=" N ILE F 50 " --> pdb=" O LEU F 61 " (cutoff:3.500A) Processing sheet with id= 66, first strand: chain 'F' and resid 18 through 28 WARNING: can't find start of bonding for strands! previous: chain 'F' and resid 35 through 38 current: chain 'F' and resid 75 through 80 WARNING: can't find start of bonding for strands! previous: chain 'F' and resid 75 through 80 current: chain 'O' and resid 22 through 32 Processing sheet with id= 67, first strand: chain 'F' and resid 44 through 46 Processing sheet with id= 68, first strand: chain 'G' and resid 10 through 13 removed outlier: 6.821A pdb=" N SER G 124 " --> pdb=" O ARG G 115 " (cutoff:3.500A) removed outlier: 7.607A pdb=" N ARG G 115 " --> pdb=" O SER G 124 " (cutoff:3.500A) removed outlier: 5.561A pdb=" N ARG G 126 " --> pdb=" O MET G 113 " (cutoff:3.500A) removed outlier: 6.751A pdb=" N MET G 113 " --> pdb=" O ARG G 126 " (cutoff:3.500A) removed outlier: 3.672A pdb=" N MET G 128 " --> pdb=" O ILE G 111 " (cutoff:3.500A) removed outlier: 5.594A pdb=" N ILE G 134 " --> pdb=" O PHE G 105 " (cutoff:3.500A) removed outlier: 5.418A pdb=" N PHE G 105 " --> pdb=" O ILE G 134 " (cutoff:3.500A) removed outlier: 3.776A pdb=" N ASP G 110 " --> pdb=" O THR G 49 " (cutoff:3.500A) removed outlier: 3.647A pdb=" N THR G 49 " --> pdb=" O ASP G 110 " (cutoff:3.500A) removed outlier: 7.421A pdb=" N GLY G 48 " --> pdb=" O SER G 63 " (cutoff:3.500A) removed outlier: 4.923A pdb=" N SER G 63 " --> pdb=" O GLY G 48 " (cutoff:3.500A) removed outlier: 6.926A pdb=" N ILE G 50 " --> pdb=" O LEU G 61 " (cutoff:3.500A) Processing sheet with id= 69, first strand: chain 'G' and resid 18 through 28 WARNING: can't find start of bonding for strands! previous: chain 'G' and resid 35 through 38 current: chain 'G' and resid 75 through 80 WARNING: can't find start of bonding for strands! previous: chain 'G' and resid 75 through 80 current: chain 'N' and resid 29 through 32 Processing sheet with id= 70, first strand: chain 'J' and resid 11 through 13 removed outlier: 6.695A pdb=" N VAL J 12 " --> pdb=" O SER J 135 " (cutoff:3.500A) removed outlier: 6.670A pdb=" N SER J 124 " --> pdb=" O THR J 114 " (cutoff:3.500A) removed outlier: 6.681A pdb=" N THR J 114 " --> pdb=" O SER J 124 " (cutoff:3.500A) removed outlier: 6.556A pdb=" N ARG J 126 " --> pdb=" O LEU J 112 " (cutoff:3.500A) removed outlier: 6.449A pdb=" N LEU J 112 " --> pdb=" O ARG J 126 " (cutoff:3.500A) removed outlier: 6.961A pdb=" N MET J 128 " --> pdb=" O ASP J 110 " (cutoff:3.500A) removed outlier: 4.726A pdb=" N ASP J 110 " --> pdb=" O MET J 128 " (cutoff:3.500A) removed outlier: 7.070A pdb=" N GLY J 130 " --> pdb=" O TYR J 108 " (cutoff:3.500A) removed outlier: 4.853A pdb=" N TYR J 108 " --> pdb=" O GLY J 130 " (cutoff:3.500A) removed outlier: 6.666A pdb=" N VAL J 132 " --> pdb=" O ALA J 106 " (cutoff:3.500A) removed outlier: 3.632A pdb=" N THR J 49 " --> pdb=" O ASP J 110 " (cutoff:3.500A) removed outlier: 7.863A pdb=" N GLY J 48 " --> pdb=" O SER J 63 " (cutoff:3.500A) removed outlier: 5.324A pdb=" N SER J 63 " --> pdb=" O GLY J 48 " (cutoff:3.500A) removed outlier: 6.927A pdb=" N ILE J 50 " --> pdb=" O LEU J 61 " (cutoff:3.500A) Processing sheet with id= 71, first strand: chain 'J' and resid 18 through 28 WARNING: can't find start of bonding for strands! previous: chain 'J' and resid 35 through 38 current: chain 'J' and resid 75 through 80 WARNING: can't find start of bonding for strands! previous: chain 'J' and resid 75 through 80 current: chain 'N' and resid 21 through 24 Processing sheet with id= 72, first strand: chain 'K' and resid 10 through 13 removed outlier: 7.118A pdb=" N SER K 124 " --> pdb=" O THR K 114 " (cutoff:3.500A) removed outlier: 7.214A pdb=" N THR K 114 " --> pdb=" O SER K 124 " (cutoff:3.500A) removed outlier: 6.948A pdb=" N ARG K 126 " --> pdb=" O LEU K 112 " (cutoff:3.500A) removed outlier: 6.862A pdb=" N LEU K 112 " --> pdb=" O ARG K 126 " (cutoff:3.500A) removed outlier: 7.142A pdb=" N MET K 128 " --> pdb=" O ASP K 110 " (cutoff:3.500A) removed outlier: 4.869A pdb=" N ASP K 110 " --> pdb=" O MET K 128 " (cutoff:3.500A) removed outlier: 7.068A pdb=" N GLY K 130 " --> pdb=" O TYR K 108 " (cutoff:3.500A) removed outlier: 4.811A pdb=" N TYR K 108 " --> pdb=" O GLY K 130 " (cutoff:3.500A) removed outlier: 7.046A pdb=" N VAL K 132 " --> pdb=" O ALA K 106 " (cutoff:3.500A) removed outlier: 3.537A pdb=" N ASP K 110 " --> pdb=" O THR K 49 " (cutoff:3.500A) removed outlier: 3.515A pdb=" N THR K 49 " --> pdb=" O ASP K 110 " (cutoff:3.500A) Processing sheet with id= 73, first strand: chain 'K' and resid 18 through 28 WARNING: can't find start of bonding for strands! previous: chain 'K' and resid 35 through 38 current: chain 'K' and resid 75 through 80 Processing sheet with id= 74, first strand: chain 'M' and resid 35 through 36 removed outlier: 6.714A pdb=" N SER M 35 " --> pdb=" O ILE N 36 " (cutoff:3.500A) No H-bonds generated for sheet with id= 74 Processing sheet with id= 75, first strand: chain 'U' and resid 10 through 14 removed outlier: 4.412A pdb=" N ILE U 11 " --> pdb=" O ILE U 28 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'U' and resid 25 through 28 current: chain 'U' and resid 68 through 75 WARNING: can't find start of bonding for strands! previous: chain 'U' and resid 68 through 75 current: chain 'U' and resid 119 through 122 WARNING: can't find start of bonding for strands! previous: chain 'U' and resid 119 through 122 current: chain 'U' and resid 143 through 157 removed outlier: 3.887A pdb=" N GLN U 175 " --> pdb=" O ASP U 148 " (cutoff:3.500A) removed outlier: 6.500A pdb=" N CYS U 150 " --> pdb=" O GLY U 173 " (cutoff:3.500A) removed outlier: 6.434A pdb=" N GLY U 173 " --> pdb=" O CYS U 150 " (cutoff:3.500A) removed outlier: 6.837A pdb=" N ILE U 152 " --> pdb=" O GLY U 171 " (cutoff:3.500A) removed outlier: 6.381A pdb=" N GLY U 171 " --> pdb=" O ILE U 152 " (cutoff:3.500A) removed outlier: 6.616A pdb=" N GLN U 154 " --> pdb=" O TRP U 169 " (cutoff:3.500A) removed outlier: 4.561A pdb=" N TRP U 169 " --> pdb=" O GLN U 154 " (cutoff:3.500A) removed outlier: 6.849A pdb=" N GLU U 156 " --> pdb=" O VAL U 167 " (cutoff:3.500A) removed outlier: 4.778A pdb=" N VAL U 167 " --> pdb=" O GLU U 156 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'U' and resid 166 through 177 current: chain 'U' and resid 260 through 268 WARNING: can't find start of bonding for strands! previous: chain 'U' and resid 260 through 268 current: chain 'U' and resid 307 through 319 WARNING: can't find start of bonding for strands! previous: chain 'U' and resid 307 through 319 current: chain 'U' and resid 331 through 337 Processing sheet with id= 76, first strand: chain 'U' and resid 40 through 46 removed outlier: 6.219A pdb=" N THR U 43 " --> pdb=" O ASN U 62 " (cutoff:3.500A) removed outlier: 5.404A pdb=" N ASN U 62 " --> pdb=" O THR U 43 " (cutoff:3.500A) removed outlier: 6.967A pdb=" N ILE U 45 " --> pdb=" O ARG U 60 " (cutoff:3.500A) removed outlier: 5.123A pdb=" N ARG U 60 " --> pdb=" O ILE U 45 " (cutoff:3.500A) Processing sheet with id= 77, first strand: chain 'U' and resid 79 through 80 Processing sheet with id= 78, first strand: chain 'U' and resid 238 through 240 removed outlier: 3.918A pdb=" N GLY U 253 " --> pdb=" O LEU U 240 " (cutoff:3.500A) Processing sheet with id= 79, first strand: chain 'U' and resid 381 through 386 Processing sheet with id= 80, first strand: chain 'U' and resid 392 through 394 removed outlier: 6.529A pdb=" N ILE U 445 " --> pdb=" O SER U 420 " (cutoff:3.500A) Processing sheet with id= 81, first strand: chain 'V' and resid 17 through 27 WARNING: can't find start of bonding for strands! previous: chain 'V' and resid 38 through 42 current: chain 'V' and resid 53 through 57 WARNING: can't find start of bonding for strands! previous: chain 'V' and resid 53 through 57 current: chain 'V' and resid 77 through 82 WARNING: can't find start of bonding for strands! previous: chain 'V' and resid 77 through 82 current: chain 'V' and resid 128 through 143 removed outlier: 5.242A pdb=" N ILE V 135 " --> pdb=" O SER V 159 " (cutoff:3.500A) removed outlier: 5.941A pdb=" N SER V 159 " --> pdb=" O ILE V 135 " (cutoff:3.500A) removed outlier: 3.618A pdb=" N GLY V 137 " --> pdb=" O ASN V 157 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'V' and resid 151 through 159 current: chain 'X' and resid 38 through 42 Processing sheet with id= 82, first strand: chain 'V' and resid 66 through 69 WARNING: can't find start of bonding for strands! previous: chain 'V' and resid 66 through 69 current: chain 'V' and resid 659 through 664 WARNING: can't find start of bonding for strands! previous: chain 'V' and resid 659 through 664 current: chain 'V' and resid 686 through 698 removed outlier: 6.652A pdb=" N THR V 707 " --> pdb=" O ASP V 694 " (cutoff:3.500A) removed outlier: 4.731A pdb=" N VAL V 696 " --> pdb=" O ASN V 705 " (cutoff:3.500A) removed outlier: 7.022A pdb=" N ASN V 705 " --> pdb=" O VAL V 696 " (cutoff:3.500A) Processing sheet with id= 83, first strand: chain 'V' and resid 181 through 184 Processing sheet with id= 84, first strand: chain 'V' and resid 226 through 228 Processing sheet with id= 85, first strand: chain 'V' and resid 265 through 267 Processing sheet with id= 86, first strand: chain 'V' and resid 270 through 274 removed outlier: 5.977A pdb=" N GLN V 438 " --> pdb=" O PHE V 304 " (cutoff:3.500A) removed outlier: 5.387A pdb=" N PHE V 304 " --> pdb=" O GLN V 438 " (cutoff:3.500A) removed outlier: 8.140A pdb=" N LYS V 440 " --> pdb=" O ASP V 302 " (cutoff:3.500A) removed outlier: 5.675A pdb=" N ASP V 302 " --> pdb=" O LYS V 440 " (cutoff:3.500A) Processing sheet with id= 87, first strand: chain 'V' and resid 276 through 282 removed outlier: 6.409A pdb=" N VAL V 293 " --> pdb=" O ILE V 278 " (cutoff:3.500A) removed outlier: 4.374A pdb=" N ALA V 280 " --> pdb=" O TYR V 291 " (cutoff:3.500A) removed outlier: 6.871A pdb=" N TYR V 291 " --> pdb=" O ALA V 280 " (cutoff:3.500A) removed outlier: 4.506A pdb=" N THR V 282 " --> pdb=" O ILE V 289 " (cutoff:3.500A) removed outlier: 7.181A pdb=" N ILE V 289 " --> pdb=" O THR V 282 " (cutoff:3.500A) removed outlier: 6.748A pdb=" N ALA V 415 " --> pdb=" O PHE V 296 " (cutoff:3.500A) Processing sheet with id= 88, first strand: chain 'V' and resid 315 through 316 Processing sheet with id= 89, first strand: chain 'V' and resid 552 through 553 Processing sheet with id= 90, first strand: chain 'V' and resid 609 through 615 removed outlier: 6.797A pdb=" N SER V 595 " --> pdb=" O LEU V 630 " (cutoff:3.500A) removed outlier: 8.162A pdb=" N LEU V 632 " --> pdb=" O SER V 595 " (cutoff:3.500A) removed outlier: 6.463A pdb=" N GLN V 597 " --> pdb=" O LEU V 632 " (cutoff:3.500A) Processing sheet with id= 91, first strand: chain 'V' and resid 740 through 746 removed outlier: 4.385A pdb=" N PHE V 742 " --> pdb=" O SER V 762 " (cutoff:3.500A) removed outlier: 6.760A pdb=" N SER V 762 " --> pdb=" O PHE V 742 " (cutoff:3.500A) removed outlier: 4.677A pdb=" N TYR V 744 " --> pdb=" O GLU V 760 " (cutoff:3.500A) removed outlier: 6.823A pdb=" N GLU V 760 " --> pdb=" O TYR V 744 " (cutoff:3.500A) Processing sheet with id= 92, first strand: chain 'V' and resid 785 through 788 removed outlier: 3.850A pdb=" N TYR V 773 " --> pdb=" O VAL V 817 " (cutoff:3.500A) Processing sheet with id= 93, first strand: chain 'V' and resid 838 through 839 Processing sheet with id= 94, first strand: chain 'V' and resid 843 through 847 removed outlier: 6.068A pdb=" N ASN V 844 " --> pdb=" O ASP V 868 " (cutoff:3.500A) removed outlier: 4.537A pdb=" N ASP V 868 " --> pdb=" O ASN V 844 " (cutoff:3.500A) Processing sheet with id= 95, first strand: chain 'V' and resid 892 through 898 removed outlier: 6.580A pdb=" N ILE V 885 " --> pdb=" O LEU V 893 " (cutoff:3.500A) removed outlier: 4.449A pdb=" N SER V 895 " --> pdb=" O LEU V 883 " (cutoff:3.500A) removed outlier: 6.764A pdb=" N LEU V 883 " --> pdb=" O SER V 895 " (cutoff:3.500A) removed outlier: 4.525A pdb=" N ARG V 897 " --> pdb=" O TYR V 881 " (cutoff:3.500A) removed outlier: 6.653A pdb=" N TYR V 881 " --> pdb=" O ARG V 897 " (cutoff:3.500A) Processing sheet with id= 96, first strand: chain 'W' and resid 19 through 25 removed outlier: 6.031A pdb=" N TRP W 48 " --> pdb=" O GLU W 202 " (cutoff:3.500A) Processing sheet with id= 97, first strand: chain 'W' and resid 28 through 32 removed outlier: 3.568A pdb=" N ILE W 29 " --> pdb=" O VAL W 41 " (cutoff:3.500A) Processing sheet with id= 98, first strand: chain 'W' and resid 108 through 112 removed outlier: 7.080A pdb=" N SER W 147 " --> pdb=" O ARG W 143 " (cutoff:3.500A) removed outlier: 4.914A pdb=" N ARG W 143 " --> pdb=" O SER W 147 " (cutoff:3.500A) removed outlier: 6.832A pdb=" N SER W 149 " --> pdb=" O PHE W 141 " (cutoff:3.500A) removed outlier: 4.542A pdb=" N PHE W 141 " --> pdb=" O SER W 149 " (cutoff:3.500A) removed outlier: 6.661A pdb=" N ASN W 151 " --> pdb=" O THR W 139 " (cutoff:3.500A) Processing sheet with id= 99, first strand: chain 'W' and resid 184 through 187 removed outlier: 3.902A pdb=" N VAL X 20 " --> pdb=" O LEU W 187 " (cutoff:3.500A) removed outlier: 4.265A pdb=" N SER X 19 " --> pdb=" O SER X 53 " (cutoff:3.500A) removed outlier: 3.633A pdb=" N SER X 53 " --> pdb=" O SER X 19 " (cutoff:3.500A) removed outlier: 6.141A pdb=" N TRP X 48 " --> pdb=" O GLU X 202 " (cutoff:3.500A) Processing sheet with id=100, first strand: chain 'X' and resid 91 through 92 Processing sheet with id=101, first strand: chain 'X' and resid 108 through 112 removed outlier: 7.070A pdb=" N SER X 147 " --> pdb=" O ARG X 143 " (cutoff:3.500A) removed outlier: 4.726A pdb=" N ARG X 143 " --> pdb=" O SER X 147 " (cutoff:3.500A) removed outlier: 6.713A pdb=" N SER X 149 " --> pdb=" O PHE X 141 " (cutoff:3.500A) removed outlier: 4.451A pdb=" N PHE X 141 " --> pdb=" O SER X 149 " (cutoff:3.500A) removed outlier: 6.635A pdb=" N ASN X 151 " --> pdb=" O THR X 139 " (cutoff:3.500A) Processing sheet with id=102, first strand: chain 'X' and resid 186 through 188 removed outlier: 3.725A pdb=" N THR X 186 " --> pdb=" O SER X 194 " (cutoff:3.500A) removed outlier: 3.670A pdb=" N THR X 192 " --> pdb=" O ASN X 188 " (cutoff:3.500A) Processing sheet with id=103, first strand: chain 'Y' and resid 10 through 15 WARNING: can't find start of bonding for strands! previous: chain 'Y' and resid 18 through 21 current: chain 'Y' and resid 61 through 68 WARNING: can't find start of bonding for strands! previous: chain 'Y' and resid 61 through 68 current: chain 'Y' and resid 90 through 92 WARNING: can't find start of bonding for strands! previous: chain 'Y' and resid 90 through 92 current: chain 'Y' and resid 116 through 130 removed outlier: 5.283A pdb=" N VAL Y 124 " --> pdb=" O GLU Y 143 " (cutoff:3.500A) removed outlier: 6.242A pdb=" N GLU Y 143 " --> pdb=" O VAL Y 124 " (cutoff:3.500A) removed outlier: 4.449A pdb=" N SER Y 130 " --> pdb=" O ILE Y 137 " (cutoff:3.500A) removed outlier: 4.625A pdb=" N ILE Y 137 " --> pdb=" O SER Y 130 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'Y' and resid 137 through 144 current: chain 'Y' and resid 177 through 178 WARNING: can't find start of bonding for strands! previous: chain 'Y' and resid 177 through 178 current: chain 'Y' and resid 213 through 227 WARNING: can't find start of bonding for strands! previous: chain 'Y' and resid 213 through 227 current: chain 'Y' and resid 255 through 269 Processing sheet with id=104, first strand: chain 'Y' and resid 34 through 39 removed outlier: 3.670A pdb=" N ALA Y 57 " --> pdb=" O GLU Y 35 " (cutoff:3.500A) removed outlier: 6.526A pdb=" N PHE Y 37 " --> pdb=" O ILE Y 55 " (cutoff:3.500A) removed outlier: 5.476A pdb=" N ILE Y 55 " --> pdb=" O PHE Y 37 " (cutoff:3.500A) removed outlier: 7.391A pdb=" N THR Y 39 " --> pdb=" O SER Y 53 " (cutoff:3.500A) removed outlier: 5.214A pdb=" N SER Y 53 " --> pdb=" O THR Y 39 " (cutoff:3.500A) Processing sheet with id=105, first strand: chain 'Z' and resid 10 through 13 removed outlier: 6.326A pdb=" N ILE Z 10 " --> pdb=" O TYR Z 133 " (cutoff:3.500A) removed outlier: 7.191A pdb=" N SER Z 135 " --> pdb=" O ILE Z 10 " (cutoff:3.500A) removed outlier: 6.909A pdb=" N VAL Z 12 " --> pdb=" O SER Z 135 " (cutoff:3.500A) removed outlier: 5.789A pdb=" N ILE Z 134 " --> pdb=" O PHE Z 105 " (cutoff:3.500A) removed outlier: 5.401A pdb=" N PHE Z 105 " --> pdb=" O ILE Z 134 " (cutoff:3.500A) removed outlier: 6.902A pdb=" N ILE Z 50 " --> pdb=" O LEU Z 61 " (cutoff:3.500A) Processing sheet with id=106, first strand: chain 'Z' and resid 18 through 28 WARNING: can't find start of bonding for strands! previous: chain 'Z' and resid 35 through 38 current: chain 'Z' and resid 75 through 80 WARNING: can't find start of bonding for strands! previous: chain 'Z' and resid 75 through 80 current: chain '5' and resid 22 through 32 Processing sheet with id=107, first strand: chain 'Z' and resid 44 through 46 Processing sheet with id=108, first strand: chain '0' and resid 10 through 13 removed outlier: 6.820A pdb=" N SER 0 124 " --> pdb=" O ARG 0 115 " (cutoff:3.500A) removed outlier: 7.606A pdb=" N ARG 0 115 " --> pdb=" O SER 0 124 " (cutoff:3.500A) removed outlier: 5.561A pdb=" N ARG 0 126 " --> pdb=" O MET 0 113 " (cutoff:3.500A) removed outlier: 6.750A pdb=" N MET 0 113 " --> pdb=" O ARG 0 126 " (cutoff:3.500A) removed outlier: 3.672A pdb=" N MET 0 128 " --> pdb=" O ILE 0 111 " (cutoff:3.500A) removed outlier: 5.594A pdb=" N ILE 0 134 " --> pdb=" O PHE 0 105 " (cutoff:3.500A) removed outlier: 5.418A pdb=" N PHE 0 105 " --> pdb=" O ILE 0 134 " (cutoff:3.500A) removed outlier: 3.776A pdb=" N ASP 0 110 " --> pdb=" O THR 0 49 " (cutoff:3.500A) removed outlier: 3.647A pdb=" N THR 0 49 " --> pdb=" O ASP 0 110 " (cutoff:3.500A) removed outlier: 7.421A pdb=" N GLY 0 48 " --> pdb=" O SER 0 63 " (cutoff:3.500A) removed outlier: 4.923A pdb=" N SER 0 63 " --> pdb=" O GLY 0 48 " (cutoff:3.500A) removed outlier: 6.925A pdb=" N ILE 0 50 " --> pdb=" O LEU 0 61 " (cutoff:3.500A) Processing sheet with id=109, first strand: chain '0' and resid 18 through 28 WARNING: can't find start of bonding for strands! previous: chain '0' and resid 35 through 38 current: chain '0' and resid 75 through 80 WARNING: can't find start of bonding for strands! previous: chain '0' and resid 75 through 80 current: chain '4' and resid 29 through 32 Processing sheet with id=110, first strand: chain '1' and resid 11 through 13 removed outlier: 6.696A pdb=" N VAL 1 12 " --> pdb=" O SER 1 135 " (cutoff:3.500A) removed outlier: 6.670A pdb=" N SER 1 124 " --> pdb=" O THR 1 114 " (cutoff:3.500A) removed outlier: 6.681A pdb=" N THR 1 114 " --> pdb=" O SER 1 124 " (cutoff:3.500A) removed outlier: 6.556A pdb=" N ARG 1 126 " --> pdb=" O LEU 1 112 " (cutoff:3.500A) removed outlier: 6.449A pdb=" N LEU 1 112 " --> pdb=" O ARG 1 126 " (cutoff:3.500A) removed outlier: 6.961A pdb=" N MET 1 128 " --> pdb=" O ASP 1 110 " (cutoff:3.500A) removed outlier: 4.726A pdb=" N ASP 1 110 " --> pdb=" O MET 1 128 " (cutoff:3.500A) removed outlier: 7.070A pdb=" N GLY 1 130 " --> pdb=" O TYR 1 108 " (cutoff:3.500A) removed outlier: 4.853A pdb=" N TYR 1 108 " --> pdb=" O GLY 1 130 " (cutoff:3.500A) removed outlier: 6.665A pdb=" N VAL 1 132 " --> pdb=" O ALA 1 106 " (cutoff:3.500A) removed outlier: 3.632A pdb=" N THR 1 49 " --> pdb=" O ASP 1 110 " (cutoff:3.500A) removed outlier: 7.862A pdb=" N GLY 1 48 " --> pdb=" O SER 1 63 " (cutoff:3.500A) removed outlier: 5.325A pdb=" N SER 1 63 " --> pdb=" O GLY 1 48 " (cutoff:3.500A) removed outlier: 6.926A pdb=" N ILE 1 50 " --> pdb=" O LEU 1 61 " (cutoff:3.500A) Processing sheet with id=111, first strand: chain '1' and resid 18 through 28 WARNING: can't find start of bonding for strands! previous: chain '1' and resid 35 through 38 current: chain '1' and resid 75 through 80 WARNING: can't find start of bonding for strands! previous: chain '1' and resid 75 through 80 current: chain '4' and resid 21 through 24 Processing sheet with id=112, first strand: chain '2' and resid 10 through 13 removed outlier: 7.118A pdb=" N SER 2 124 " --> pdb=" O THR 2 114 " (cutoff:3.500A) removed outlier: 7.215A pdb=" N THR 2 114 " --> pdb=" O SER 2 124 " (cutoff:3.500A) removed outlier: 6.948A pdb=" N ARG 2 126 " --> pdb=" O LEU 2 112 " (cutoff:3.500A) removed outlier: 6.862A pdb=" N LEU 2 112 " --> pdb=" O ARG 2 126 " (cutoff:3.500A) removed outlier: 7.142A pdb=" N MET 2 128 " --> pdb=" O ASP 2 110 " (cutoff:3.500A) removed outlier: 4.869A pdb=" N ASP 2 110 " --> pdb=" O MET 2 128 " (cutoff:3.500A) removed outlier: 7.069A pdb=" N GLY 2 130 " --> pdb=" O TYR 2 108 " (cutoff:3.500A) removed outlier: 4.811A pdb=" N TYR 2 108 " --> pdb=" O GLY 2 130 " (cutoff:3.500A) removed outlier: 7.046A pdb=" N VAL 2 132 " --> pdb=" O ALA 2 106 " (cutoff:3.500A) removed outlier: 3.537A pdb=" N ASP 2 110 " --> pdb=" O THR 2 49 " (cutoff:3.500A) removed outlier: 3.514A pdb=" N THR 2 49 " --> pdb=" O ASP 2 110 " (cutoff:3.500A) Processing sheet with id=113, first strand: chain '2' and resid 18 through 28 WARNING: can't find start of bonding for strands! previous: chain '2' and resid 35 through 38 current: chain '2' and resid 75 through 80 Processing sheet with id=114, first strand: chain '3' and resid 35 through 36 removed outlier: 6.714A pdb=" N SER 3 35 " --> pdb=" O ILE 4 36 " (cutoff:3.500A) No H-bonds generated for sheet with id=114 Processing sheet with id=115, first strand: chain '7' and resid 10 through 14 removed outlier: 4.412A pdb=" N ILE 7 11 " --> pdb=" O ILE 7 28 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain '7' and resid 25 through 28 current: chain '7' and resid 68 through 75 WARNING: can't find start of bonding for strands! previous: chain '7' and resid 68 through 75 current: chain '7' and resid 119 through 122 WARNING: can't find start of bonding for strands! previous: chain '7' and resid 119 through 122 current: chain '7' and resid 143 through 157 removed outlier: 3.886A pdb=" N GLN 7 175 " --> pdb=" O ASP 7 148 " (cutoff:3.500A) removed outlier: 6.499A pdb=" N CYS 7 150 " --> pdb=" O GLY 7 173 " (cutoff:3.500A) removed outlier: 6.433A pdb=" N GLY 7 173 " --> pdb=" O CYS 7 150 " (cutoff:3.500A) removed outlier: 6.837A pdb=" N ILE 7 152 " --> pdb=" O GLY 7 171 " (cutoff:3.500A) removed outlier: 6.381A pdb=" N GLY 7 171 " --> pdb=" O ILE 7 152 " (cutoff:3.500A) removed outlier: 6.616A pdb=" N GLN 7 154 " --> pdb=" O TRP 7 169 " (cutoff:3.500A) removed outlier: 4.561A pdb=" N TRP 7 169 " --> pdb=" O GLN 7 154 " (cutoff:3.500A) removed outlier: 6.849A pdb=" N GLU 7 156 " --> pdb=" O VAL 7 167 " (cutoff:3.500A) removed outlier: 4.778A pdb=" N VAL 7 167 " --> pdb=" O GLU 7 156 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain '7' and resid 166 through 177 current: chain '7' and resid 260 through 268 WARNING: can't find start of bonding for strands! previous: chain '7' and resid 260 through 268 current: chain '7' and resid 307 through 319 WARNING: can't find start of bonding for strands! previous: chain '7' and resid 307 through 319 current: chain '7' and resid 331 through 337 Processing sheet with id=116, first strand: chain '7' and resid 40 through 46 removed outlier: 6.219A pdb=" N THR 7 43 " --> pdb=" O ASN 7 62 " (cutoff:3.500A) removed outlier: 5.405A pdb=" N ASN 7 62 " --> pdb=" O THR 7 43 " (cutoff:3.500A) removed outlier: 6.967A pdb=" N ILE 7 45 " --> pdb=" O ARG 7 60 " (cutoff:3.500A) removed outlier: 5.123A pdb=" N ARG 7 60 " --> pdb=" O ILE 7 45 " (cutoff:3.500A) Processing sheet with id=117, first strand: chain '7' and resid 79 through 80 Processing sheet with id=118, first strand: chain '7' and resid 238 through 240 removed outlier: 3.919A pdb=" N GLY 7 253 " --> pdb=" O LEU 7 240 " (cutoff:3.500A) Processing sheet with id=119, first strand: chain '7' and resid 381 through 386 Processing sheet with id=120, first strand: chain '7' and resid 392 through 394 removed outlier: 6.529A pdb=" N ILE 7 445 " --> pdb=" O SER 7 420 " (cutoff:3.500A) 1659 hydrogen bonds defined for protein. 4302 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: 28.36 Time building geometry restraints manager: 22.23 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.33: 21254 1.33 - 1.45: 9551 1.45 - 1.57: 36557 1.57 - 1.69: 0 1.69 - 1.80: 273 Bond restraints: 67635 Sorted by residual: bond pdb=" N LEU V 518 " pdb=" CA LEU V 518 " ideal model delta sigma weight residual 1.458 1.489 -0.032 1.28e-02 6.10e+03 6.10e+00 bond pdb=" N LEU B 518 " pdb=" CA LEU B 518 " ideal model delta sigma weight residual 1.458 1.489 -0.031 1.28e-02 6.10e+03 6.01e+00 bond pdb=" N LEU A 518 " pdb=" CA LEU A 518 " ideal model delta sigma weight residual 1.458 1.489 -0.031 1.28e-02 6.10e+03 5.97e+00 bond pdb=" N ARG X 90 " pdb=" CA ARG X 90 " ideal model delta sigma weight residual 1.456 1.486 -0.030 1.31e-02 5.83e+03 5.07e+00 bond pdb=" N ARG D 90 " pdb=" CA ARG D 90 " ideal model delta sigma weight residual 1.456 1.486 -0.029 1.31e-02 5.83e+03 4.92e+00 ... (remaining 67630 not shown) Histogram of bond angle deviations from ideal: 98.51 - 105.63: 1340 105.63 - 112.75: 35879 112.75 - 119.87: 22788 119.87 - 126.99: 31345 126.99 - 134.11: 565 Bond angle restraints: 91917 Sorted by residual: angle pdb=" CA ILE A 524 " pdb=" C ILE A 524 " pdb=" O ILE A 524 " ideal model delta sigma weight residual 121.05 116.46 4.59 1.04e+00 9.25e-01 1.95e+01 angle pdb=" CA ILE B 524 " pdb=" C ILE B 524 " pdb=" O ILE B 524 " ideal model delta sigma weight residual 121.05 116.48 4.57 1.04e+00 9.25e-01 1.93e+01 angle pdb=" CA ILE V 524 " pdb=" C ILE V 524 " pdb=" O ILE V 524 " ideal model delta sigma weight residual 121.05 116.49 4.56 1.04e+00 9.25e-01 1.92e+01 angle pdb=" CA ALA V 519 " pdb=" C ALA V 519 " pdb=" O ALA V 519 " ideal model delta sigma weight residual 121.56 117.08 4.48 1.09e+00 8.42e-01 1.69e+01 angle pdb=" CA ALA B 519 " pdb=" C ALA B 519 " pdb=" O ALA B 519 " ideal model delta sigma weight residual 121.56 117.08 4.48 1.09e+00 8.42e-01 1.69e+01 ... (remaining 91912 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.60: 37683 17.60 - 35.21: 2352 35.21 - 52.81: 345 52.81 - 70.42: 123 70.42 - 88.02: 60 Dihedral angle restraints: 40563 sinusoidal: 15843 harmonic: 24720 Sorted by residual: dihedral pdb=" CD ARG X 201 " pdb=" NE ARG X 201 " pdb=" CZ ARG X 201 " pdb=" NH1 ARG X 201 " ideal model delta sinusoidal sigma weight residual 0.00 68.74 -68.74 1 1.00e+01 1.00e-02 6.12e+01 dihedral pdb=" CD ARG D 201 " pdb=" NE ARG D 201 " pdb=" CZ ARG D 201 " pdb=" NH1 ARG D 201 " ideal model delta sinusoidal sigma weight residual 0.00 68.72 -68.72 1 1.00e+01 1.00e-02 6.12e+01 dihedral pdb=" CD ARG I 201 " pdb=" NE ARG I 201 " pdb=" CZ ARG I 201 " pdb=" NH1 ARG I 201 " ideal model delta sinusoidal sigma weight residual 0.00 68.70 -68.70 1 1.00e+01 1.00e-02 6.11e+01 ... (remaining 40560 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.046: 6768 0.046 - 0.092: 3080 0.092 - 0.138: 598 0.138 - 0.185: 46 0.185 - 0.231: 5 Chirality restraints: 10497 Sorted by residual: chirality pdb=" CA GLU B 520 " pdb=" N GLU B 520 " pdb=" C GLU B 520 " pdb=" CB GLU B 520 " both_signs ideal model delta sigma weight residual False 2.51 2.74 -0.23 2.00e-01 2.50e+01 1.33e+00 chirality pdb=" CA GLU V 520 " pdb=" N GLU V 520 " pdb=" C GLU V 520 " pdb=" CB GLU V 520 " both_signs ideal model delta sigma weight residual False 2.51 2.74 -0.23 2.00e-01 2.50e+01 1.31e+00 chirality pdb=" CA GLU A 520 " pdb=" N GLU A 520 " pdb=" C GLU A 520 " pdb=" CB GLU A 520 " both_signs ideal model delta sigma weight residual False 2.51 2.74 -0.23 2.00e-01 2.50e+01 1.30e+00 ... (remaining 10494 not shown) Planarity restraints: 11952 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CD ARG L 42 " -1.036 9.50e-02 1.11e+02 4.64e-01 1.30e+02 pdb=" NE ARG L 42 " 0.060 2.00e-02 2.50e+03 pdb=" CZ ARG L 42 " 0.017 2.00e-02 2.50e+03 pdb=" NH1 ARG L 42 " -0.007 2.00e-02 2.50e+03 pdb=" NH2 ARG L 42 " -0.024 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CD ARG Y 42 " -1.036 9.50e-02 1.11e+02 4.64e-01 1.30e+02 pdb=" NE ARG Y 42 " 0.060 2.00e-02 2.50e+03 pdb=" CZ ARG Y 42 " 0.017 2.00e-02 2.50e+03 pdb=" NH1 ARG Y 42 " -0.007 2.00e-02 2.50e+03 pdb=" NH2 ARG Y 42 " -0.024 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CD ARG E 42 " -1.035 9.50e-02 1.11e+02 4.64e-01 1.30e+02 pdb=" NE ARG E 42 " 0.060 2.00e-02 2.50e+03 pdb=" CZ ARG E 42 " 0.017 2.00e-02 2.50e+03 pdb=" NH1 ARG E 42 " -0.007 2.00e-02 2.50e+03 pdb=" NH2 ARG E 42 " -0.024 2.00e-02 2.50e+03 ... (remaining 11949 not shown) Histogram of nonbonded interaction distances: 1.71 - 2.35: 39 2.35 - 2.99: 39916 2.99 - 3.63: 95019 3.63 - 4.26: 147053 4.26 - 4.90: 245048 Nonbonded interactions: 527075 Sorted by model distance: nonbonded pdb=" NH2 ARG K 126 " pdb=" OD1 ASP Z 13 " model vdw 1.714 2.520 nonbonded pdb=" OD1 ASP Q 13 " pdb=" NH2 ARG 2 126 " model vdw 1.714 2.520 nonbonded pdb=" NH2 ARG T 126 " pdb=" OD1 ASP F 13 " model vdw 1.714 2.520 nonbonded pdb=" OE1 GLU 2 14 " pdb=" N GLY 2 137 " model vdw 2.258 2.520 nonbonded pdb=" OE1 GLU T 14 " pdb=" N GLY T 137 " model vdw 2.258 2.520 ... (remaining 527070 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = (chain '0' and resid 4 through 140) selection = (chain '1' and resid 4 through 140) selection = chain '2' selection = (chain 'F' and resid 4 through 140) selection = (chain 'G' and resid 4 through 140) selection = (chain 'J' and resid 4 through 140) selection = chain 'K' selection = (chain 'Q' and resid 4 through 140) selection = (chain 'R' and resid 4 through 140) selection = (chain 'S' and resid 4 through 140) selection = chain 'T' selection = (chain 'Z' and resid 4 through 140) } ncs_group { reference = (chain '3' and resid 8 through 51) selection = (chain '4' and resid 8 through 51) selection = (chain '5' and resid 8 through 51) selection = (chain 'M' and resid 8 through 51) selection = (chain 'N' and resid 8 through 51) selection = (chain 'O' and resid 8 through 51) selection = (chain 'd' and resid 8 through 51) selection = (chain 'e' and resid 8 through 51) selection = (chain 'f' and resid 8 through 51) } ncs_group { reference = chain '6' selection = chain 'P' selection = chain 'k' } ncs_group { reference = chain '7' selection = chain 'U' selection = chain 'p' } ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'V' } ncs_group { reference = chain 'C' selection = chain 'D' selection = chain 'H' selection = chain 'I' selection = chain 'W' selection = chain 'X' } ncs_group { reference = chain 'E' selection = chain 'L' selection = chain 'Y' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 3.020 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: 0.070 Extract box with map and model: 15.040 Check model and map are aligned: 0.740 Set scattering table: 0.460 Process input model: 138.020 Find NCS groups from input model: 3.260 Set up NCS constraints: 0.510 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: 0.020 Load rotamer database and sin/cos tables:2.560 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 163.700 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7976 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 0.067 67635 Z= 0.633 Angle : 0.853 8.659 91917 Z= 0.502 Chirality : 0.050 0.231 10497 Planarity : 0.017 0.464 11952 Dihedral : 12.876 88.019 24708 Min Nonbonded Distance : 1.714 Molprobity Statistics. All-atom Clashscore : 3.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.70 % Favored : 96.30 % Rotamer: Outliers : 0.08 % Allowed : 0.49 % Favored : 99.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.36 % Cis-general : 0.00 % 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: -1.21 (0.08), residues: 8400 helix: -1.45 (0.13), residues: 1116 sheet: -0.30 (0.09), residues: 2772 loop : -0.89 (0.09), residues: 4512 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.035 0.005 TRP E 195 HIS 0.010 0.003 HIS B 207 PHE 0.026 0.003 PHE T 125 TYR 0.054 0.006 TYR e 28 ARG 0.026 0.003 ARG B 700 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 16800 Ramachandran restraints generated. 8400 Oldfield, 0 Emsley, 8400 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 16800 Ramachandran restraints generated. 8400 Oldfield, 0 Emsley, 8400 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 551 residues out of total 7395 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 545 time to evaluate : 5.875 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: A 140 ILE cc_start: 0.8499 (mt) cc_final: 0.8109 (tt) REVERT: A 695 GLU cc_start: 0.8443 (tt0) cc_final: 0.7782 (tm-30) REVERT: H 18 GLU cc_start: 0.8771 (tt0) cc_final: 0.8494 (tt0) REVERT: I 12 LEU cc_start: 0.8698 (mt) cc_final: 0.8392 (mt) REVERT: I 71 GLU cc_start: 0.8733 (tp30) cc_final: 0.8500 (tp30) REVERT: I 114 GLN cc_start: 0.9120 (tt0) cc_final: 0.8820 (mt0) REVERT: L 104 MET cc_start: 0.9005 (mmt) cc_final: 0.8612 (mmm) REVERT: L 161 GLN cc_start: 0.9047 (tt0) cc_final: 0.8605 (tt0) REVERT: L 191 GLN cc_start: 0.9049 (tt0) cc_final: 0.8453 (tt0) REVERT: L 192 GLN cc_start: 0.8185 (mm110) cc_final: 0.7829 (mm110) REVERT: Q 95 GLU cc_start: 0.8979 (tp30) cc_final: 0.8018 (tp30) REVERT: R 34 PRO cc_start: 0.8598 (Cg_endo) cc_final: 0.7880 (Cg_exo) REVERT: R 36 GLU cc_start: 0.8009 (mt-10) cc_final: 0.7641 (mp0) REVERT: R 108 TYR cc_start: 0.8699 (m-80) cc_final: 0.8176 (m-80) REVERT: R 113 MET cc_start: 0.7715 (ttp) cc_final: 0.7407 (ttm) REVERT: S 25 MET cc_start: 0.7693 (mmm) cc_final: 0.6774 (mmm) REVERT: T 25 MET cc_start: 0.7809 (pmm) cc_final: 0.7431 (pmm) REVERT: T 73 GLN cc_start: 0.8596 (tp-100) cc_final: 0.8290 (mm-40) REVERT: T 90 GLU cc_start: 0.8795 (mm-30) cc_final: 0.8339 (mm-30) REVERT: T 95 GLU cc_start: 0.8174 (tp30) cc_final: 0.7680 (tm-30) REVERT: d 43 GLU cc_start: 0.8010 (mt-10) cc_final: 0.7575 (mt-10) REVERT: f 38 SER cc_start: 0.8716 (m) cc_final: 0.8037 (p) REVERT: k 158 ASP cc_start: 0.8684 (m-30) cc_final: 0.8354 (m-30) REVERT: p 277 MET cc_start: 0.8394 (mmm) cc_final: 0.7948 (mmm) REVERT: B 140 ILE cc_start: 0.8470 (mt) cc_final: 0.8159 (tt) REVERT: B 527 MET cc_start: 0.9268 (mtm) cc_final: 0.9011 (mtm) REVERT: B 639 ASN cc_start: 0.7296 (t0) cc_final: 0.7010 (t0) REVERT: C 71 GLU cc_start: 0.8423 (tp30) cc_final: 0.8033 (tp30) REVERT: D 12 LEU cc_start: 0.8612 (mt) cc_final: 0.8329 (mt) REVERT: D 18 GLU cc_start: 0.8093 (tm-30) cc_final: 0.7560 (tm-30) REVERT: D 71 GLU cc_start: 0.8453 (tp30) cc_final: 0.8100 (tp30) REVERT: D 78 TYR cc_start: 0.9000 (m-80) cc_final: 0.8714 (m-80) REVERT: D 164 GLU cc_start: 0.8320 (mp0) cc_final: 0.7988 (mp0) REVERT: D 201 ARG cc_start: 0.8868 (OUTLIER) cc_final: 0.7868 (ttm-80) REVERT: E 104 MET cc_start: 0.9073 (mmt) cc_final: 0.8540 (mmm) REVERT: E 116 CYS cc_start: 0.8934 (m) cc_final: 0.8700 (m) REVERT: E 161 GLN cc_start: 0.8918 (tt0) cc_final: 0.8563 (tt0) REVERT: E 192 GLN cc_start: 0.8203 (mm110) cc_final: 0.7932 (mm110) REVERT: E 218 MET cc_start: 0.8088 (mtt) cc_final: 0.7561 (mtt) REVERT: F 95 GLU cc_start: 0.8883 (tp30) cc_final: 0.7960 (tp30) REVERT: G 18 TYR cc_start: 0.8881 (t80) cc_final: 0.8597 (t80) REVERT: G 32 TYR cc_start: 0.7656 (t80) cc_final: 0.7369 (t80) REVERT: G 34 PRO cc_start: 0.8615 (Cg_endo) cc_final: 0.7888 (Cg_exo) REVERT: G 36 GLU cc_start: 0.7650 (mt-10) cc_final: 0.7448 (mp0) REVERT: J 25 MET cc_start: 0.8160 (mmm) cc_final: 0.6521 (mmm) REVERT: J 41 LEU cc_start: 0.9246 (tp) cc_final: 0.8818 (tp) REVERT: K 25 MET cc_start: 0.7561 (pmm) cc_final: 0.7254 (pmm) REVERT: K 73 GLN cc_start: 0.8755 (tp-100) cc_final: 0.8327 (mm-40) REVERT: K 90 GLU cc_start: 0.8842 (mm-30) cc_final: 0.8319 (mm-30) REVERT: K 95 GLU cc_start: 0.8209 (tp30) cc_final: 0.7722 (tm-30) REVERT: O 11 GLN cc_start: 0.8429 (tt0) cc_final: 0.8184 (tt0) REVERT: O 38 SER cc_start: 0.8697 (m) cc_final: 0.8173 (p) REVERT: P 152 ASN cc_start: 0.8403 (m110) cc_final: 0.7979 (m-40) REVERT: P 158 ASP cc_start: 0.8528 (m-30) cc_final: 0.8287 (m-30) REVERT: P 166 GLU cc_start: 0.8580 (tp30) cc_final: 0.8355 (tp30) REVERT: U 277 MET cc_start: 0.8426 (mmm) cc_final: 0.7938 (mmm) REVERT: V 140 ILE cc_start: 0.8563 (mt) cc_final: 0.8156 (tt) REVERT: V 527 MET cc_start: 0.9265 (mtm) cc_final: 0.9042 (mtp) REVERT: W 71 GLU cc_start: 0.8355 (tp30) cc_final: 0.7938 (tp30) REVERT: W 164 GLU cc_start: 0.7450 (mp0) cc_final: 0.6931 (mp0) REVERT: X 12 LEU cc_start: 0.8692 (mt) cc_final: 0.8322 (mt) REVERT: X 71 GLU cc_start: 0.8568 (tp30) cc_final: 0.8203 (tp30) REVERT: X 87 GLU cc_start: 0.8996 (mm-30) cc_final: 0.8611 (mm-30) REVERT: X 164 GLU cc_start: 0.8424 (mp0) cc_final: 0.8031 (mp0) REVERT: Y 104 MET cc_start: 0.9047 (mmt) cc_final: 0.8823 (mmm) REVERT: Y 161 GLN cc_start: 0.9037 (tt0) cc_final: 0.8568 (tt0) REVERT: Y 192 GLN cc_start: 0.8193 (mm110) cc_final: 0.7887 (mm110) REVERT: Z 25 MET cc_start: 0.8101 (mtt) cc_final: 0.7892 (mpp) REVERT: Z 41 LEU cc_start: 0.9354 (tp) cc_final: 0.9030 (tp) REVERT: Z 95 GLU cc_start: 0.8926 (tp30) cc_final: 0.7964 (tp30) REVERT: 0 18 TYR cc_start: 0.8992 (t80) cc_final: 0.8722 (t80) REVERT: 0 32 TYR cc_start: 0.7815 (t80) cc_final: 0.7502 (t80) REVERT: 1 25 MET cc_start: 0.7609 (mmm) cc_final: 0.6920 (mmm) REVERT: 2 18 TYR cc_start: 0.8846 (t80) cc_final: 0.8551 (t80) REVERT: 2 25 MET cc_start: 0.7747 (pmm) cc_final: 0.7457 (pmm) REVERT: 2 73 GLN cc_start: 0.8560 (tp-100) cc_final: 0.8175 (mm-40) REVERT: 2 95 GLU cc_start: 0.8125 (tp30) cc_final: 0.7722 (tm-30) REVERT: 2 129 GLU cc_start: 0.8003 (OUTLIER) cc_final: 0.7718 (mt-10) REVERT: 5 11 GLN cc_start: 0.8705 (tt0) cc_final: 0.8446 (tt0) REVERT: 5 38 SER cc_start: 0.8902 (m) cc_final: 0.8196 (p) REVERT: 6 158 ASP cc_start: 0.8602 (m-30) cc_final: 0.8369 (m-30) outliers start: 6 outliers final: 2 residues processed: 548 average time/residue: 0.6968 time to fit residues: 641.8997 Evaluate side-chains 389 residues out of total 7395 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 385 time to evaluate : 5.651 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain I residue 201 ARG Chi-restraints excluded: chain D residue 201 ARG Chi-restraints excluded: chain X residue 201 ARG Chi-restraints excluded: chain 2 residue 129 GLU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 825 random chunks: chunk 696 optimal weight: 1.9990 chunk 625 optimal weight: 3.9990 chunk 346 optimal weight: 0.9990 chunk 213 optimal weight: 2.9990 chunk 421 optimal weight: 4.9990 chunk 334 optimal weight: 2.9990 chunk 646 optimal weight: 3.9990 chunk 250 optimal weight: 3.9990 chunk 393 optimal weight: 0.9990 chunk 481 optimal weight: 7.9990 chunk 749 optimal weight: 7.9990 overall best weight: 1.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 14 ASN A 200 GLN A 446 HIS A 597 GLN A 631 GLN A 770 ASN I 25 ASN L 45 HIS L 106 ASN S 57 ASN p 20 HIS B 14 ASN B 200 GLN B 446 HIS B 597 GLN B 631 GLN B 770 ASN D 25 ASN E 45 HIS E 106 ASN J 57 ASN ** M 10 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** P 152 ASN U 20 HIS V 14 ASN V 200 GLN V 446 HIS V 597 GLN V 631 GLN V 770 ASN X 25 ASN Y 45 HIS Y 98 ASN Y 106 ASN 1 57 ASN 7 20 HIS Total number of N/Q/H flips: 35 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8004 moved from start: 0.1482 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.055 67635 Z= 0.221 Angle : 0.581 9.281 91917 Z= 0.318 Chirality : 0.046 0.170 10497 Planarity : 0.004 0.073 11952 Dihedral : 6.157 47.196 9243 Min Nonbonded Distance : 2.175 Molprobity Statistics. All-atom Clashscore : 3.43 Ramachandran Plot: Outliers : 0.02 % Allowed : 1.99 % Favored : 97.99 % Rotamer: Outliers : 0.57 % Allowed : 3.66 % Favored : 95.77 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.36 % Cis-general : 0.00 % 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: -0.48 (0.09), residues: 8400 helix: 0.08 (0.15), residues: 1116 sheet: -0.08 (0.09), residues: 2856 loop : -0.49 (0.09), residues: 4428 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP A 156 HIS 0.007 0.001 HIS U 20 PHE 0.016 0.002 PHE 0 125 TYR 0.018 0.001 TYR Z 133 ARG 0.006 0.001 ARG E 42 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 16800 Ramachandran restraints generated. 8400 Oldfield, 0 Emsley, 8400 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 16800 Ramachandran restraints generated. 8400 Oldfield, 0 Emsley, 8400 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 506 residues out of total 7395 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 42 poor density : 464 time to evaluate : 5.854 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: A 140 ILE cc_start: 0.8507 (mt) cc_final: 0.8165 (tt) REVERT: A 527 MET cc_start: 0.9273 (mtm) cc_final: 0.9022 (mtm) REVERT: A 695 GLU cc_start: 0.8246 (tt0) cc_final: 0.7743 (tm-30) REVERT: A 892 MET cc_start: 0.9329 (tpp) cc_final: 0.8893 (tmm) REVERT: H 18 GLU cc_start: 0.8635 (tt0) cc_final: 0.8372 (tt0) REVERT: H 105 LYS cc_start: 0.8776 (tppt) cc_final: 0.8441 (tppt) REVERT: I 18 GLU cc_start: 0.8354 (tm-30) cc_final: 0.8152 (tm-30) REVERT: I 40 GLU cc_start: 0.8600 (pt0) cc_final: 0.7747 (pm20) REVERT: I 46 GLN cc_start: 0.8712 (tm-30) cc_final: 0.8381 (tm-30) REVERT: I 71 GLU cc_start: 0.8707 (tp30) cc_final: 0.8376 (tp30) REVERT: I 78 TYR cc_start: 0.8883 (m-80) cc_final: 0.8625 (m-10) REVERT: I 87 GLU cc_start: 0.9048 (mm-30) cc_final: 0.8845 (mm-30) REVERT: I 122 LYS cc_start: 0.7663 (mttt) cc_final: 0.7352 (mtmm) REVERT: L 104 MET cc_start: 0.8877 (mmt) cc_final: 0.8393 (mmm) REVERT: L 161 GLN cc_start: 0.8865 (tt0) cc_final: 0.8205 (tt0) REVERT: L 165 MET cc_start: 0.7634 (OUTLIER) cc_final: 0.6455 (mmm) REVERT: L 192 GLN cc_start: 0.8238 (mm110) cc_final: 0.7733 (mm-40) REVERT: R 108 TYR cc_start: 0.8553 (m-80) cc_final: 0.8134 (m-80) REVERT: S 25 MET cc_start: 0.7962 (mmm) cc_final: 0.7373 (mmm) REVERT: T 25 MET cc_start: 0.8092 (pmm) cc_final: 0.7537 (pmm) REVERT: T 73 GLN cc_start: 0.8682 (tp-100) cc_final: 0.8110 (mm110) REVERT: T 90 GLU cc_start: 0.8790 (mm-30) cc_final: 0.8320 (mm-30) REVERT: T 95 GLU cc_start: 0.8215 (tp30) cc_final: 0.7716 (tm-30) REVERT: T 113 MET cc_start: 0.8616 (OUTLIER) cc_final: 0.8372 (ttm) REVERT: d 43 GLU cc_start: 0.8002 (mt-10) cc_final: 0.7509 (mt-10) REVERT: f 25 TYR cc_start: 0.7643 (t80) cc_final: 0.7428 (t80) REVERT: f 43 GLU cc_start: 0.8751 (mm-30) cc_final: 0.8550 (mm-30) REVERT: k 158 ASP cc_start: 0.8461 (m-30) cc_final: 0.8243 (m-30) REVERT: p 277 MET cc_start: 0.8372 (mmm) cc_final: 0.7841 (mmm) REVERT: B 527 MET cc_start: 0.9181 (mtm) cc_final: 0.8936 (mtm) REVERT: C 30 ARG cc_start: 0.8902 (ttm-80) cc_final: 0.8109 (ttm-80) REVERT: C 56 GLU cc_start: 0.8124 (pm20) cc_final: 0.7871 (pm20) REVERT: C 61 GLU cc_start: 0.8587 (pm20) cc_final: 0.8131 (pm20) REVERT: C 71 GLU cc_start: 0.8510 (tp30) cc_final: 0.8006 (tp30) REVERT: D 12 LEU cc_start: 0.8593 (mt) cc_final: 0.8384 (mt) REVERT: D 18 GLU cc_start: 0.8227 (tm-30) cc_final: 0.7607 (tm-30) REVERT: D 40 GLU cc_start: 0.8815 (pt0) cc_final: 0.8057 (pm20) REVERT: D 71 GLU cc_start: 0.8540 (tp30) cc_final: 0.8309 (tp30) REVERT: D 164 GLU cc_start: 0.8269 (mp0) cc_final: 0.7803 (mp0) REVERT: E 104 MET cc_start: 0.9046 (mmt) cc_final: 0.8526 (mmm) REVERT: E 161 GLN cc_start: 0.8731 (tt0) cc_final: 0.8023 (tt0) REVERT: E 190 GLN cc_start: 0.8898 (mt0) cc_final: 0.8544 (mt0) REVERT: E 192 GLN cc_start: 0.8291 (mm110) cc_final: 0.7500 (mm110) REVERT: E 218 MET cc_start: 0.8134 (mtt) cc_final: 0.7702 (mtt) REVERT: G 18 TYR cc_start: 0.8865 (t80) cc_final: 0.8627 (t80) REVERT: G 32 TYR cc_start: 0.7733 (t80) cc_final: 0.7474 (t80) REVERT: G 59 GLU cc_start: 0.8568 (tp30) cc_final: 0.8368 (tp30) REVERT: J 25 MET cc_start: 0.8187 (mmm) cc_final: 0.7908 (tpp) REVERT: J 36 GLU cc_start: 0.8695 (pp20) cc_final: 0.8388 (pp20) REVERT: J 41 LEU cc_start: 0.9304 (tp) cc_final: 0.8827 (tp) REVERT: J 113 MET cc_start: 0.8636 (ptm) cc_final: 0.8131 (ptm) REVERT: K 25 MET cc_start: 0.7925 (pmm) cc_final: 0.7373 (pmm) REVERT: K 73 GLN cc_start: 0.8690 (tp-100) cc_final: 0.8199 (mm-40) REVERT: K 90 GLU cc_start: 0.8843 (mm-30) cc_final: 0.8301 (mm-30) REVERT: K 95 GLU cc_start: 0.8323 (tp30) cc_final: 0.7809 (tm-30) REVERT: K 129 GLU cc_start: 0.8006 (mp0) cc_final: 0.7754 (pm20) REVERT: O 38 SER cc_start: 0.8993 (m) cc_final: 0.8478 (t) REVERT: U 277 MET cc_start: 0.8360 (mmm) cc_final: 0.7777 (mmm) REVERT: U 282 ASP cc_start: 0.7819 (m-30) cc_final: 0.7601 (m-30) REVERT: V 140 ILE cc_start: 0.8585 (mt) cc_final: 0.8281 (tt) REVERT: V 892 MET cc_start: 0.9480 (tpp) cc_final: 0.9192 (tmm) REVERT: W 71 GLU cc_start: 0.8355 (tp30) cc_final: 0.7793 (tp30) REVERT: W 105 LYS cc_start: 0.8629 (tppt) cc_final: 0.8411 (tppt) REVERT: W 164 GLU cc_start: 0.7467 (mp0) cc_final: 0.6925 (mp0) REVERT: X 18 GLU cc_start: 0.8208 (tm-30) cc_final: 0.7914 (tm-30) REVERT: X 40 GLU cc_start: 0.8513 (pt0) cc_final: 0.7991 (pm20) REVERT: X 56 GLU cc_start: 0.7459 (tp30) cc_final: 0.7208 (tp30) REVERT: X 71 GLU cc_start: 0.8634 (tp30) cc_final: 0.8364 (tp30) REVERT: X 87 GLU cc_start: 0.8954 (mm-30) cc_final: 0.8588 (mm-30) REVERT: X 164 GLU cc_start: 0.8295 (mp0) cc_final: 0.7818 (mp0) REVERT: Y 104 MET cc_start: 0.9042 (mmt) cc_final: 0.8798 (mmm) REVERT: Y 161 GLN cc_start: 0.8846 (tt0) cc_final: 0.8080 (tt0) REVERT: Y 190 GLN cc_start: 0.8647 (mt0) cc_final: 0.8339 (mt0) REVERT: Y 192 GLN cc_start: 0.8272 (mm110) cc_final: 0.7523 (mm110) REVERT: Z 41 LEU cc_start: 0.9349 (tp) cc_final: 0.8900 (tp) REVERT: Z 94 LYS cc_start: 0.9069 (mmmt) cc_final: 0.8834 (mmmt) REVERT: 0 18 TYR cc_start: 0.8903 (t80) cc_final: 0.8658 (t80) REVERT: 0 32 TYR cc_start: 0.7844 (t80) cc_final: 0.7636 (t80) REVERT: 0 36 GLU cc_start: 0.8107 (mt-10) cc_final: 0.7825 (mm-30) REVERT: 0 59 GLU cc_start: 0.8433 (tp30) cc_final: 0.8015 (tm-30) REVERT: 0 129 GLU cc_start: 0.8405 (pm20) cc_final: 0.8038 (pm20) REVERT: 1 25 MET cc_start: 0.7813 (mmm) cc_final: 0.7363 (mmm) REVERT: 1 128 MET cc_start: 0.8757 (OUTLIER) cc_final: 0.8342 (mtp) REVERT: 2 18 TYR cc_start: 0.8939 (t80) cc_final: 0.8547 (t80) REVERT: 2 25 MET cc_start: 0.8252 (pmm) cc_final: 0.7886 (pmm) REVERT: 2 95 GLU cc_start: 0.8147 (tp30) cc_final: 0.7735 (tm-30) REVERT: 6 161 GLU cc_start: 0.8853 (mm-30) cc_final: 0.8633 (mm-30) outliers start: 42 outliers final: 22 residues processed: 476 average time/residue: 0.6463 time to fit residues: 532.4535 Evaluate side-chains 426 residues out of total 7395 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 401 time to evaluate : 5.806 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 32 GLU Chi-restraints excluded: chain I residue 61 GLU Chi-restraints excluded: chain I residue 111 MET Chi-restraints excluded: chain I residue 175 THR Chi-restraints excluded: chain L residue 165 MET Chi-restraints excluded: chain L residue 218 MET Chi-restraints excluded: chain Q residue 22 MET Chi-restraints excluded: chain Q residue 90 GLU Chi-restraints excluded: chain S residue 9 ASP Chi-restraints excluded: chain T residue 113 MET Chi-restraints excluded: chain e residue 44 LEU Chi-restraints excluded: chain p residue 39 ASP Chi-restraints excluded: chain p residue 93 MET Chi-restraints excluded: chain D residue 175 THR Chi-restraints excluded: chain N residue 44 LEU Chi-restraints excluded: chain O residue 45 THR Chi-restraints excluded: chain P residue 164 LEU Chi-restraints excluded: chain 0 residue 128 MET Chi-restraints excluded: chain 1 residue 128 MET Chi-restraints excluded: chain 2 residue 128 MET Chi-restraints excluded: chain 3 residue 10 GLN Chi-restraints excluded: chain 4 residue 44 LEU Chi-restraints excluded: chain 5 residue 45 THR Chi-restraints excluded: chain 6 residue 171 LEU Chi-restraints excluded: chain 7 residue 285 ARG Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 825 random chunks: chunk 416 optimal weight: 0.0040 chunk 232 optimal weight: 7.9990 chunk 623 optimal weight: 10.0000 chunk 510 optimal weight: 7.9990 chunk 206 optimal weight: 9.9990 chunk 750 optimal weight: 6.9990 chunk 810 optimal weight: 9.9990 chunk 668 optimal weight: 6.9990 chunk 744 optimal weight: 0.8980 chunk 255 optimal weight: 1.9990 chunk 602 optimal weight: 6.9990 overall best weight: 3.3798 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** H 199 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** S 57 ASN p 118 ASN J 57 ASN ** U 118 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Y 98 ASN Y 106 ASN 1 57 ASN 5 11 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8074 moved from start: 0.2104 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.084 67635 Z= 0.339 Angle : 0.588 10.318 91917 Z= 0.316 Chirality : 0.046 0.162 10497 Planarity : 0.004 0.054 11952 Dihedral : 5.493 25.350 9228 Min Nonbonded Distance : 2.091 Molprobity Statistics. All-atom Clashscore : 4.83 Ramachandran Plot: Outliers : 0.02 % Allowed : 2.92 % Favored : 97.06 % Rotamer: Outliers : 1.05 % Allowed : 5.50 % Favored : 93.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.36 % Cis-general : 0.00 % 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: -0.50 (0.09), residues: 8400 helix: 0.31 (0.16), residues: 1110 sheet: -0.13 (0.09), residues: 2877 loop : -0.55 (0.09), residues: 4413 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP V 156 HIS 0.006 0.001 HIS B 207 PHE 0.023 0.002 PHE Y 119 TYR 0.023 0.002 TYR Y 118 ARG 0.006 0.001 ARG Q 47 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 16800 Ramachandran restraints generated. 8400 Oldfield, 0 Emsley, 8400 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 16800 Ramachandran restraints generated. 8400 Oldfield, 0 Emsley, 8400 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 478 residues out of total 7395 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 78 poor density : 400 time to evaluate : 5.875 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: A 140 ILE cc_start: 0.8527 (mt) cc_final: 0.8115 (tt) REVERT: A 553 ASN cc_start: 0.7694 (OUTLIER) cc_final: 0.7261 (p0) REVERT: H 56 GLU cc_start: 0.8249 (pm20) cc_final: 0.7967 (pm20) REVERT: I 12 LEU cc_start: 0.8754 (mt) cc_final: 0.8482 (mp) REVERT: I 40 GLU cc_start: 0.8710 (pt0) cc_final: 0.7987 (pm20) REVERT: I 56 GLU cc_start: 0.7765 (tp30) cc_final: 0.7478 (tp30) REVERT: I 71 GLU cc_start: 0.8887 (tp30) cc_final: 0.8600 (tp30) REVERT: I 78 TYR cc_start: 0.8931 (m-80) cc_final: 0.8657 (m-10) REVERT: I 87 GLU cc_start: 0.9195 (mm-30) cc_final: 0.8896 (mm-30) REVERT: I 122 LYS cc_start: 0.8171 (mttt) cc_final: 0.7832 (mtmm) REVERT: L 104 MET cc_start: 0.8836 (mmt) cc_final: 0.8386 (mmm) REVERT: L 161 GLN cc_start: 0.9010 (tt0) cc_final: 0.8306 (tt0) REVERT: L 192 GLN cc_start: 0.8329 (mm110) cc_final: 0.7958 (mm110) REVERT: R 108 TYR cc_start: 0.8570 (m-80) cc_final: 0.8107 (m-80) REVERT: S 25 MET cc_start: 0.7562 (mmm) cc_final: 0.7271 (mmm) REVERT: S 128 MET cc_start: 0.9031 (mtp) cc_final: 0.8636 (mtp) REVERT: T 25 MET cc_start: 0.8143 (pmm) cc_final: 0.7469 (pmm) REVERT: T 73 GLN cc_start: 0.8669 (tp-100) cc_final: 0.8113 (mm110) REVERT: T 90 GLU cc_start: 0.8826 (mm-30) cc_final: 0.8348 (mm-30) REVERT: T 95 GLU cc_start: 0.8210 (tp30) cc_final: 0.7679 (tm-30) REVERT: T 113 MET cc_start: 0.8551 (OUTLIER) cc_final: 0.8282 (ttm) REVERT: d 43 GLU cc_start: 0.8298 (mt-10) cc_final: 0.7786 (mt-10) REVERT: e 43 GLU cc_start: 0.8631 (pm20) cc_final: 0.8262 (pt0) REVERT: f 25 TYR cc_start: 0.7651 (t80) cc_final: 0.7397 (t80) REVERT: p 60 ARG cc_start: 0.8165 (OUTLIER) cc_final: 0.7828 (ptt-90) REVERT: p 118 ASN cc_start: 0.8608 (OUTLIER) cc_final: 0.8240 (p0) REVERT: p 277 MET cc_start: 0.8391 (mmm) cc_final: 0.7761 (mmm) REVERT: B 494 LEU cc_start: 0.8448 (OUTLIER) cc_final: 0.8245 (tt) REVERT: B 527 MET cc_start: 0.9262 (mtm) cc_final: 0.8981 (mtm) REVERT: C 46 GLN cc_start: 0.8215 (tm-30) cc_final: 0.7940 (tm-30) REVERT: C 61 GLU cc_start: 0.8681 (pm20) cc_final: 0.8130 (pm20) REVERT: C 71 GLU cc_start: 0.8617 (tp30) cc_final: 0.7970 (tp30) REVERT: D 18 GLU cc_start: 0.8436 (tm-30) cc_final: 0.7672 (tm-30) REVERT: D 40 GLU cc_start: 0.8923 (pt0) cc_final: 0.8232 (pm20) REVERT: D 164 GLU cc_start: 0.8496 (mp0) cc_final: 0.7909 (mp0) REVERT: E 104 MET cc_start: 0.9055 (mmt) cc_final: 0.8498 (mmm) REVERT: E 120 GLU cc_start: 0.8052 (OUTLIER) cc_final: 0.7595 (tp30) REVERT: E 161 GLN cc_start: 0.9023 (tt0) cc_final: 0.8384 (tt0) REVERT: E 165 MET cc_start: 0.7118 (mtm) cc_final: 0.6499 (mmt) REVERT: E 183 ILE cc_start: 0.8758 (mt) cc_final: 0.8525 (mt) REVERT: E 190 GLN cc_start: 0.8904 (mt0) cc_final: 0.8500 (mt0) REVERT: E 192 GLN cc_start: 0.8628 (mm110) cc_final: 0.7937 (mm110) REVERT: E 218 MET cc_start: 0.8266 (mtt) cc_final: 0.8021 (mtt) REVERT: G 32 TYR cc_start: 0.7833 (t80) cc_final: 0.7568 (t80) REVERT: G 59 GLU cc_start: 0.8416 (tp30) cc_final: 0.8091 (tm-30) REVERT: J 25 MET cc_start: 0.8059 (mmm) cc_final: 0.7696 (tpp) REVERT: J 36 GLU cc_start: 0.8819 (pp20) cc_final: 0.8291 (pp20) REVERT: J 41 LEU cc_start: 0.9360 (tp) cc_final: 0.8890 (tp) REVERT: J 113 MET cc_start: 0.8716 (ptm) cc_final: 0.8180 (ptm) REVERT: K 25 MET cc_start: 0.8046 (pmm) cc_final: 0.7310 (pmm) REVERT: K 90 GLU cc_start: 0.8989 (mm-30) cc_final: 0.8454 (mm-30) REVERT: K 95 GLU cc_start: 0.8320 (tp30) cc_final: 0.7803 (tm-30) REVERT: K 129 GLU cc_start: 0.8065 (mp0) cc_final: 0.7722 (pm20) REVERT: O 38 SER cc_start: 0.8847 (m) cc_final: 0.8315 (p) REVERT: U 277 MET cc_start: 0.8364 (mmm) cc_final: 0.7954 (tpp) REVERT: V 140 ILE cc_start: 0.8658 (mt) cc_final: 0.8220 (tt) REVERT: V 553 ASN cc_start: 0.7579 (OUTLIER) cc_final: 0.7225 (p0) REVERT: V 798 MET cc_start: 0.9105 (mtp) cc_final: 0.8837 (mtt) REVERT: W 1 MET cc_start: 0.8042 (pmm) cc_final: 0.7785 (pmm) REVERT: W 18 GLU cc_start: 0.9154 (OUTLIER) cc_final: 0.8470 (tp30) REVERT: W 30 ARG cc_start: 0.8809 (ttm-80) cc_final: 0.8503 (ttm-80) REVERT: W 71 GLU cc_start: 0.8569 (tp30) cc_final: 0.7957 (tp30) REVERT: W 125 ASP cc_start: 0.8481 (m-30) cc_final: 0.8257 (t70) REVERT: W 164 GLU cc_start: 0.7757 (mp0) cc_final: 0.7068 (mp0) REVERT: X 18 GLU cc_start: 0.8440 (tm-30) cc_final: 0.8098 (tm-30) REVERT: X 32 GLU cc_start: 0.8078 (mm-30) cc_final: 0.7538 (tp30) REVERT: X 40 GLU cc_start: 0.8634 (pt0) cc_final: 0.8192 (pm20) REVERT: X 56 GLU cc_start: 0.7375 (tp30) cc_final: 0.7136 (tp30) REVERT: X 71 GLU cc_start: 0.8782 (tp30) cc_final: 0.8458 (tp30) REVERT: Y 104 MET cc_start: 0.8988 (mmt) cc_final: 0.8683 (mmm) REVERT: Y 161 GLN cc_start: 0.9049 (tt0) cc_final: 0.8495 (tt0) REVERT: Y 165 MET cc_start: 0.7048 (mtm) cc_final: 0.6313 (mmt) REVERT: Y 192 GLN cc_start: 0.8403 (mm110) cc_final: 0.7959 (mm110) REVERT: Z 41 LEU cc_start: 0.9396 (tp) cc_final: 0.9019 (mp) REVERT: Z 94 LYS cc_start: 0.9012 (mmmt) cc_final: 0.8811 (mmmt) REVERT: Z 113 MET cc_start: 0.8408 (tmm) cc_final: 0.7946 (tmm) REVERT: 0 25 MET cc_start: 0.7765 (mtm) cc_final: 0.7471 (mtm) REVERT: 0 32 TYR cc_start: 0.7952 (t80) cc_final: 0.7694 (t80) REVERT: 0 36 GLU cc_start: 0.8318 (mt-10) cc_final: 0.7988 (mm-30) REVERT: 0 59 GLU cc_start: 0.8453 (tp30) cc_final: 0.8111 (tm-30) REVERT: 0 129 GLU cc_start: 0.8628 (pm20) cc_final: 0.8233 (pm20) REVERT: 1 25 MET cc_start: 0.7770 (mmm) cc_final: 0.7360 (mmm) REVERT: 1 128 MET cc_start: 0.9012 (OUTLIER) cc_final: 0.8581 (mtp) REVERT: 2 18 TYR cc_start: 0.9017 (t80) cc_final: 0.8555 (t80) REVERT: 2 25 MET cc_start: 0.8398 (pmm) cc_final: 0.8067 (pmm) REVERT: 2 90 GLU cc_start: 0.8818 (mm-30) cc_final: 0.8411 (mm-30) REVERT: 2 95 GLU cc_start: 0.8140 (tp30) cc_final: 0.7711 (tm-30) REVERT: 3 10 GLN cc_start: 0.8587 (OUTLIER) cc_final: 0.8021 (pm20) REVERT: 6 166 GLU cc_start: 0.8913 (tp30) cc_final: 0.8645 (tp30) outliers start: 78 outliers final: 41 residues processed: 444 average time/residue: 0.6213 time to fit residues: 478.6653 Evaluate side-chains 418 residues out of total 7395 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 51 poor density : 367 time to evaluate : 5.675 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 494 LEU Chi-restraints excluded: chain A residue 547 SER Chi-restraints excluded: chain A residue 553 ASN Chi-restraints excluded: chain H residue 32 GLU Chi-restraints excluded: chain I residue 61 GLU Chi-restraints excluded: chain I residue 111 MET Chi-restraints excluded: chain I residue 175 THR Chi-restraints excluded: chain L residue 116 CYS Chi-restraints excluded: chain L residue 137 ILE Chi-restraints excluded: chain L residue 218 MET Chi-restraints excluded: chain Q residue 22 MET Chi-restraints excluded: chain Q residue 112 LEU Chi-restraints excluded: chain R residue 113 MET Chi-restraints excluded: chain S residue 9 ASP Chi-restraints excluded: chain T residue 113 MET Chi-restraints excluded: chain T residue 128 MET Chi-restraints excluded: chain e residue 44 LEU Chi-restraints excluded: chain k residue 153 SER Chi-restraints excluded: chain p residue 39 ASP Chi-restraints excluded: chain p residue 60 ARG Chi-restraints excluded: chain p residue 93 MET Chi-restraints excluded: chain p residue 118 ASN Chi-restraints excluded: chain B residue 494 LEU Chi-restraints excluded: chain B residue 530 ILE Chi-restraints excluded: chain D residue 175 THR Chi-restraints excluded: chain E residue 116 CYS Chi-restraints excluded: chain E residue 120 GLU Chi-restraints excluded: chain E residue 137 ILE Chi-restraints excluded: chain E residue 217 GLU Chi-restraints excluded: chain F residue 128 MET Chi-restraints excluded: chain G residue 90 GLU Chi-restraints excluded: chain J residue 122 VAL Chi-restraints excluded: chain K residue 128 MET Chi-restraints excluded: chain N residue 44 LEU Chi-restraints excluded: chain O residue 45 THR Chi-restraints excluded: chain P residue 164 LEU Chi-restraints excluded: chain V residue 553 ASN Chi-restraints excluded: chain W residue 18 GLU Chi-restraints excluded: chain Y residue 116 CYS Chi-restraints excluded: chain Y residue 272 ASP Chi-restraints excluded: chain 0 residue 128 MET Chi-restraints excluded: chain 1 residue 122 VAL Chi-restraints excluded: chain 1 residue 128 MET Chi-restraints excluded: chain 2 residue 12 VAL Chi-restraints excluded: chain 2 residue 128 MET Chi-restraints excluded: chain 3 residue 10 GLN Chi-restraints excluded: chain 4 residue 44 LEU Chi-restraints excluded: chain 4 residue 45 THR Chi-restraints excluded: chain 5 residue 45 THR Chi-restraints excluded: chain 6 residue 164 LEU Chi-restraints excluded: chain 7 residue 285 ARG Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 825 random chunks: chunk 741 optimal weight: 0.7980 chunk 564 optimal weight: 9.9990 chunk 389 optimal weight: 7.9990 chunk 83 optimal weight: 0.0470 chunk 358 optimal weight: 2.9990 chunk 503 optimal weight: 8.9990 chunk 753 optimal weight: 4.9990 chunk 797 optimal weight: 0.3980 chunk 393 optimal weight: 0.6980 chunk 713 optimal weight: 8.9990 chunk 214 optimal weight: 0.2980 overall best weight: 0.4478 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** H 199 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** S 57 ASN J 57 ASN ** M 10 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 1 57 ASN 3 10 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8024 moved from start: 0.2417 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.042 67635 Z= 0.118 Angle : 0.479 11.090 91917 Z= 0.258 Chirality : 0.044 0.150 10497 Planarity : 0.003 0.042 11952 Dihedral : 4.794 20.793 9228 Min Nonbonded Distance : 2.072 Molprobity Statistics. All-atom Clashscore : 4.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.82 % Favored : 98.18 % Rotamer: Outliers : 0.77 % Allowed : 6.25 % Favored : 92.98 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.36 % Cis-general : 0.00 % 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: -0.12 (0.09), residues: 8400 helix: 0.75 (0.16), residues: 1092 sheet: 0.10 (0.09), residues: 2925 loop : -0.32 (0.09), residues: 4383 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 946 HIS 0.004 0.001 HIS p 113 PHE 0.017 0.001 PHE k 148 TYR 0.015 0.001 TYR C 62 ARG 0.007 0.000 ARG C 30 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 16800 Ramachandran restraints generated. 8400 Oldfield, 0 Emsley, 8400 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 16800 Ramachandran restraints generated. 8400 Oldfield, 0 Emsley, 8400 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 465 residues out of total 7395 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 57 poor density : 408 time to evaluate : 6.794 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: A 140 ILE cc_start: 0.8561 (mt) cc_final: 0.8288 (tt) REVERT: H 56 GLU cc_start: 0.8282 (pm20) cc_final: 0.7994 (pm20) REVERT: I 18 GLU cc_start: 0.8367 (tm-30) cc_final: 0.7644 (tm-30) REVERT: I 40 GLU cc_start: 0.8669 (pt0) cc_final: 0.7994 (pm20) REVERT: I 46 GLN cc_start: 0.8658 (tm-30) cc_final: 0.8424 (tm-30) REVERT: I 71 GLU cc_start: 0.8897 (tp30) cc_final: 0.8630 (tp30) REVERT: I 78 TYR cc_start: 0.8877 (m-80) cc_final: 0.8617 (m-10) REVERT: I 87 GLU cc_start: 0.9141 (mm-30) cc_final: 0.8920 (mm-30) REVERT: I 111 MET cc_start: 0.7758 (OUTLIER) cc_final: 0.7527 (ptm) REVERT: I 122 LYS cc_start: 0.8107 (mttt) cc_final: 0.7794 (mtmm) REVERT: L 104 MET cc_start: 0.8827 (mmt) cc_final: 0.8431 (mmm) REVERT: L 161 GLN cc_start: 0.8764 (tt0) cc_final: 0.8063 (tt0) REVERT: L 171 ILE cc_start: 0.8017 (OUTLIER) cc_final: 0.7731 (mt) REVERT: L 192 GLN cc_start: 0.8060 (mm110) cc_final: 0.7704 (mm110) REVERT: Q 113 MET cc_start: 0.8415 (tmm) cc_final: 0.7750 (tmm) REVERT: R 59 GLU cc_start: 0.8300 (tp30) cc_final: 0.7857 (tm-30) REVERT: R 108 TYR cc_start: 0.8322 (m-80) cc_final: 0.7878 (m-80) REVERT: R 129 GLU cc_start: 0.8348 (pm20) cc_final: 0.8144 (pm20) REVERT: S 25 MET cc_start: 0.7574 (mmm) cc_final: 0.7298 (mmm) REVERT: S 128 MET cc_start: 0.9067 (mtp) cc_final: 0.8688 (mtp) REVERT: T 25 MET cc_start: 0.8125 (pmm) cc_final: 0.7346 (pmm) REVERT: T 36 GLU cc_start: 0.8951 (pm20) cc_final: 0.8587 (mp0) REVERT: T 73 GLN cc_start: 0.8723 (tp-100) cc_final: 0.8233 (mm110) REVERT: T 90 GLU cc_start: 0.8849 (mm-30) cc_final: 0.8387 (mm-30) REVERT: T 95 GLU cc_start: 0.8184 (tp30) cc_final: 0.7644 (tm-30) REVERT: T 113 MET cc_start: 0.8508 (OUTLIER) cc_final: 0.8294 (ttm) REVERT: e 43 GLU cc_start: 0.8601 (pm20) cc_final: 0.8291 (pt0) REVERT: f 25 TYR cc_start: 0.7526 (t80) cc_final: 0.7318 (t80) REVERT: p 118 ASN cc_start: 0.8886 (OUTLIER) cc_final: 0.8563 (p0) REVERT: p 277 MET cc_start: 0.8286 (mmm) cc_final: 0.7771 (mmm) REVERT: B 527 MET cc_start: 0.9112 (mtm) cc_final: 0.8892 (mtm) REVERT: C 18 GLU cc_start: 0.8927 (tt0) cc_final: 0.8583 (tp30) REVERT: C 61 GLU cc_start: 0.8728 (pm20) cc_final: 0.8056 (pm20) REVERT: C 71 GLU cc_start: 0.8594 (tp30) cc_final: 0.7901 (tp30) REVERT: D 18 GLU cc_start: 0.8330 (tm-30) cc_final: 0.7977 (tp30) REVERT: D 40 GLU cc_start: 0.8857 (pt0) cc_final: 0.8215 (pm20) REVERT: D 164 GLU cc_start: 0.8342 (mp0) cc_final: 0.8005 (mp0) REVERT: E 104 MET cc_start: 0.9099 (mmt) cc_final: 0.8583 (mmm) REVERT: E 161 GLN cc_start: 0.8848 (tt0) cc_final: 0.8162 (tt0) REVERT: E 165 MET cc_start: 0.6987 (mtm) cc_final: 0.6424 (mmt) REVERT: E 171 ILE cc_start: 0.8024 (OUTLIER) cc_final: 0.7788 (tt) REVERT: E 190 GLN cc_start: 0.8883 (mt0) cc_final: 0.8570 (mt0) REVERT: E 192 GLN cc_start: 0.8413 (mm110) cc_final: 0.7660 (mm110) REVERT: E 218 MET cc_start: 0.8229 (mtt) cc_final: 0.8002 (mtt) REVERT: G 32 TYR cc_start: 0.7729 (t80) cc_final: 0.7524 (t80) REVERT: G 59 GLU cc_start: 0.8357 (tp30) cc_final: 0.7916 (tm-30) REVERT: J 36 GLU cc_start: 0.8751 (pp20) cc_final: 0.8372 (tm-30) REVERT: J 41 LEU cc_start: 0.9362 (tp) cc_final: 0.8856 (tp) REVERT: K 25 MET cc_start: 0.7983 (pmm) cc_final: 0.7118 (pmm) REVERT: K 90 GLU cc_start: 0.8885 (mm-30) cc_final: 0.8368 (mm-30) REVERT: K 95 GLU cc_start: 0.8264 (tp30) cc_final: 0.7710 (tm-30) REVERT: K 128 MET cc_start: 0.8935 (OUTLIER) cc_final: 0.8583 (ptm) REVERT: K 129 GLU cc_start: 0.7931 (mp0) cc_final: 0.7578 (pm20) REVERT: O 38 SER cc_start: 0.8934 (m) cc_final: 0.8450 (t) REVERT: V 140 ILE cc_start: 0.8627 (mt) cc_final: 0.8344 (tt) REVERT: V 798 MET cc_start: 0.9017 (mtp) cc_final: 0.8788 (mtt) REVERT: W 1 MET cc_start: 0.7928 (pmm) cc_final: 0.7706 (pmm) REVERT: W 18 GLU cc_start: 0.9105 (OUTLIER) cc_final: 0.8466 (tp30) REVERT: W 71 GLU cc_start: 0.8498 (tp30) cc_final: 0.7866 (tp30) REVERT: W 164 GLU cc_start: 0.7817 (mp0) cc_final: 0.7128 (mp0) REVERT: X 18 GLU cc_start: 0.8379 (tm-30) cc_final: 0.7972 (tm-30) REVERT: X 32 GLU cc_start: 0.8051 (mm-30) cc_final: 0.7844 (mm-30) REVERT: X 40 GLU cc_start: 0.8648 (pt0) cc_final: 0.8101 (pm20) REVERT: X 56 GLU cc_start: 0.7546 (tp30) cc_final: 0.7250 (tp30) REVERT: X 71 GLU cc_start: 0.8750 (tp30) cc_final: 0.8444 (tp30) REVERT: X 164 GLU cc_start: 0.8319 (mp0) cc_final: 0.7993 (mp0) REVERT: Y 104 MET cc_start: 0.8957 (mmt) cc_final: 0.8743 (mmm) REVERT: Y 161 GLN cc_start: 0.8876 (tt0) cc_final: 0.8126 (tt0) REVERT: Y 190 GLN cc_start: 0.8847 (mt0) cc_final: 0.8456 (mt0) REVERT: Y 192 GLN cc_start: 0.8135 (mm110) cc_final: 0.7702 (mm110) REVERT: Z 41 LEU cc_start: 0.9348 (tp) cc_final: 0.8970 (mp) REVERT: Z 113 MET cc_start: 0.8530 (tmm) cc_final: 0.7805 (tmm) REVERT: Z 125 PHE cc_start: 0.7616 (OUTLIER) cc_final: 0.6281 (p90) REVERT: 0 25 MET cc_start: 0.7774 (mtm) cc_final: 0.7561 (mtm) REVERT: 0 32 TYR cc_start: 0.7871 (t80) cc_final: 0.7644 (t80) REVERT: 0 36 GLU cc_start: 0.8320 (mt-10) cc_final: 0.7995 (mm-30) REVERT: 0 59 GLU cc_start: 0.8443 (tp30) cc_final: 0.8001 (tm-30) REVERT: 0 129 GLU cc_start: 0.8603 (pm20) cc_final: 0.8091 (pm20) REVERT: 1 25 MET cc_start: 0.7822 (mmm) cc_final: 0.7516 (mmm) REVERT: 1 128 MET cc_start: 0.8977 (OUTLIER) cc_final: 0.8565 (mtp) REVERT: 2 18 TYR cc_start: 0.8996 (t80) cc_final: 0.8568 (t80) REVERT: 2 25 MET cc_start: 0.8333 (pmm) cc_final: 0.8015 (pmm) REVERT: 2 95 GLU cc_start: 0.8119 (tp30) cc_final: 0.7667 (tm-30) REVERT: 7 277 MET cc_start: 0.8536 (mmm) cc_final: 0.8034 (mmm) outliers start: 57 outliers final: 24 residues processed: 441 average time/residue: 0.6330 time to fit residues: 489.1358 Evaluate side-chains 412 residues out of total 7395 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 33 poor density : 379 time to evaluate : 5.635 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 92 LEU Chi-restraints excluded: chain I residue 111 MET Chi-restraints excluded: chain I residue 175 THR Chi-restraints excluded: chain L residue 137 ILE Chi-restraints excluded: chain L residue 152 THR Chi-restraints excluded: chain L residue 171 ILE Chi-restraints excluded: chain L residue 218 MET Chi-restraints excluded: chain Q residue 112 LEU Chi-restraints excluded: chain R residue 113 MET Chi-restraints excluded: chain T residue 113 MET Chi-restraints excluded: chain T residue 128 MET Chi-restraints excluded: chain p residue 39 ASP Chi-restraints excluded: chain p residue 93 MET Chi-restraints excluded: chain p residue 118 ASN Chi-restraints excluded: chain B residue 530 ILE Chi-restraints excluded: chain D residue 175 THR Chi-restraints excluded: chain E residue 152 THR Chi-restraints excluded: chain E residue 171 ILE Chi-restraints excluded: chain F residue 84 ASP Chi-restraints excluded: chain G residue 90 GLU Chi-restraints excluded: chain J residue 122 VAL Chi-restraints excluded: chain K residue 128 MET Chi-restraints excluded: chain N residue 44 LEU Chi-restraints excluded: chain W residue 18 GLU Chi-restraints excluded: chain Y residue 152 THR Chi-restraints excluded: chain Y residue 171 ILE Chi-restraints excluded: chain Z residue 125 PHE Chi-restraints excluded: chain 1 residue 57 ASN Chi-restraints excluded: chain 1 residue 122 VAL Chi-restraints excluded: chain 1 residue 128 MET Chi-restraints excluded: chain 2 residue 128 MET Chi-restraints excluded: chain 4 residue 45 THR Chi-restraints excluded: chain 7 residue 285 ARG Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 825 random chunks: chunk 664 optimal weight: 0.8980 chunk 452 optimal weight: 0.8980 chunk 11 optimal weight: 1.9990 chunk 593 optimal weight: 7.9990 chunk 329 optimal weight: 0.9980 chunk 680 optimal weight: 2.9990 chunk 551 optimal weight: 4.9990 chunk 0 optimal weight: 10.0000 chunk 407 optimal weight: 10.0000 chunk 715 optimal weight: 7.9990 chunk 201 optimal weight: 9.9990 overall best weight: 1.5584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** H 199 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** S 57 ASN B 219 GLN J 57 ASN ** M 10 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Y 106 ASN 5 11 GLN 6 165 ASN 7 355 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8043 moved from start: 0.2587 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 67635 Z= 0.171 Angle : 0.473 9.785 91917 Z= 0.252 Chirality : 0.043 0.151 10497 Planarity : 0.003 0.041 11952 Dihedral : 4.595 20.681 9228 Min Nonbonded Distance : 2.093 Molprobity Statistics. All-atom Clashscore : 4.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.04 % Favored : 97.96 % Rotamer: Outliers : 1.01 % Allowed : 6.77 % Favored : 92.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.36 % Cis-general : 0.00 % 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: -0.04 (0.09), residues: 8400 helix: 0.84 (0.16), residues: 1098 sheet: 0.19 (0.09), residues: 2883 loop : -0.32 (0.09), residues: 4419 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP C 48 HIS 0.004 0.001 HIS 7 318 PHE 0.017 0.001 PHE k 148 TYR 0.018 0.001 TYR X 62 ARG 0.004 0.000 ARG C 30 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 16800 Ramachandran restraints generated. 8400 Oldfield, 0 Emsley, 8400 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 16800 Ramachandran restraints generated. 8400 Oldfield, 0 Emsley, 8400 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 464 residues out of total 7395 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 75 poor density : 389 time to evaluate : 5.845 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: A 140 ILE cc_start: 0.8648 (mt) cc_final: 0.8279 (tt) REVERT: H 56 GLU cc_start: 0.8305 (pm20) cc_final: 0.8017 (pm20) REVERT: I 18 GLU cc_start: 0.8491 (tm-30) cc_final: 0.7694 (tm-30) REVERT: I 40 GLU cc_start: 0.8668 (pt0) cc_final: 0.8031 (pm20) REVERT: I 71 GLU cc_start: 0.8887 (tp30) cc_final: 0.8583 (tp30) REVERT: I 78 TYR cc_start: 0.8907 (m-80) cc_final: 0.8615 (m-10) REVERT: I 87 GLU cc_start: 0.9147 (mm-30) cc_final: 0.8885 (mm-30) REVERT: I 122 LYS cc_start: 0.8159 (mttt) cc_final: 0.7858 (mtmm) REVERT: L 104 MET cc_start: 0.8800 (mmt) cc_final: 0.8339 (mmm) REVERT: L 165 MET cc_start: 0.7766 (OUTLIER) cc_final: 0.6582 (mmm) REVERT: L 171 ILE cc_start: 0.8046 (OUTLIER) cc_final: 0.7755 (mt) REVERT: L 192 GLN cc_start: 0.8122 (mm110) cc_final: 0.7791 (mm110) REVERT: Q 113 MET cc_start: 0.8499 (tmm) cc_final: 0.8259 (tmm) REVERT: R 59 GLU cc_start: 0.8358 (tp30) cc_final: 0.7910 (tm-30) REVERT: R 108 TYR cc_start: 0.8442 (m-80) cc_final: 0.8000 (m-80) REVERT: S 25 MET cc_start: 0.7632 (mmm) cc_final: 0.7416 (mmm) REVERT: S 128 MET cc_start: 0.9015 (mtp) cc_final: 0.8718 (mtp) REVERT: T 25 MET cc_start: 0.8178 (pmm) cc_final: 0.7339 (pmm) REVERT: T 36 GLU cc_start: 0.8931 (pm20) cc_final: 0.8553 (mp0) REVERT: T 90 GLU cc_start: 0.8877 (mm-30) cc_final: 0.8414 (mm-30) REVERT: T 95 GLU cc_start: 0.8173 (tp30) cc_final: 0.7641 (tm-30) REVERT: T 113 MET cc_start: 0.8549 (OUTLIER) cc_final: 0.8295 (ttm) REVERT: e 43 GLU cc_start: 0.8749 (pm20) cc_final: 0.8520 (pt0) REVERT: p 277 MET cc_start: 0.8281 (mmm) cc_final: 0.7853 (mmm) REVERT: B 527 MET cc_start: 0.9139 (mtm) cc_final: 0.8734 (mtm) REVERT: C 18 GLU cc_start: 0.8973 (tt0) cc_final: 0.8580 (tp30) REVERT: C 61 GLU cc_start: 0.8784 (pm20) cc_final: 0.8109 (pm20) REVERT: C 66 ASP cc_start: 0.8957 (t0) cc_final: 0.8363 (t0) REVERT: C 71 GLU cc_start: 0.8679 (tp30) cc_final: 0.7945 (tp30) REVERT: C 125 ASP cc_start: 0.8082 (m-30) cc_final: 0.7813 (m-30) REVERT: D 18 GLU cc_start: 0.8451 (tm-30) cc_final: 0.7960 (tp30) REVERT: D 40 GLU cc_start: 0.8848 (pt0) cc_final: 0.8229 (pm20) REVERT: D 164 GLU cc_start: 0.8443 (mp0) cc_final: 0.8004 (mp0) REVERT: E 104 MET cc_start: 0.9110 (mmt) cc_final: 0.8590 (mmm) REVERT: E 161 GLN cc_start: 0.8920 (tt0) cc_final: 0.8245 (tt0) REVERT: E 165 MET cc_start: 0.6999 (mtm) cc_final: 0.6453 (mmt) REVERT: E 171 ILE cc_start: 0.8083 (OUTLIER) cc_final: 0.7834 (tt) REVERT: E 190 GLN cc_start: 0.8918 (mt0) cc_final: 0.8695 (mt0) REVERT: E 192 GLN cc_start: 0.8559 (mm110) cc_final: 0.7907 (mm110) REVERT: E 218 MET cc_start: 0.8268 (mtt) cc_final: 0.8040 (mtt) REVERT: G 32 TYR cc_start: 0.7765 (t80) cc_final: 0.7546 (t80) REVERT: G 59 GLU cc_start: 0.8359 (tp30) cc_final: 0.7948 (tm-30) REVERT: J 36 GLU cc_start: 0.8819 (pp20) cc_final: 0.8334 (tm-30) REVERT: J 41 LEU cc_start: 0.9368 (tp) cc_final: 0.8869 (tp) REVERT: K 25 MET cc_start: 0.8035 (pmm) cc_final: 0.7081 (pmm) REVERT: K 90 GLU cc_start: 0.8913 (mm-30) cc_final: 0.8397 (mm-30) REVERT: K 95 GLU cc_start: 0.8268 (tp30) cc_final: 0.7701 (tm-30) REVERT: O 38 SER cc_start: 0.8940 (m) cc_final: 0.8485 (t) REVERT: V 140 ILE cc_start: 0.8541 (mt) cc_final: 0.8241 (tt) REVERT: V 798 MET cc_start: 0.9004 (mtp) cc_final: 0.8781 (mtt) REVERT: W 18 GLU cc_start: 0.9095 (OUTLIER) cc_final: 0.8381 (tm-30) REVERT: W 61 GLU cc_start: 0.8645 (pm20) cc_final: 0.8061 (pm20) REVERT: W 71 GLU cc_start: 0.8501 (tp30) cc_final: 0.7859 (tp30) REVERT: W 125 ASP cc_start: 0.8424 (m-30) cc_final: 0.8218 (t70) REVERT: W 164 GLU cc_start: 0.7957 (mp0) cc_final: 0.7214 (mp0) REVERT: X 18 GLU cc_start: 0.8440 (tm-30) cc_final: 0.8030 (tm-30) REVERT: X 32 GLU cc_start: 0.8062 (mm-30) cc_final: 0.7554 (tp30) REVERT: X 40 GLU cc_start: 0.8632 (pt0) cc_final: 0.8118 (pm20) REVERT: X 56 GLU cc_start: 0.7533 (tp30) cc_final: 0.7252 (tp30) REVERT: X 71 GLU cc_start: 0.8819 (tp30) cc_final: 0.8468 (tp30) REVERT: X 164 GLU cc_start: 0.8368 (mp0) cc_final: 0.8021 (mp0) REVERT: Y 104 MET cc_start: 0.8946 (mmt) cc_final: 0.8746 (mmm) REVERT: Y 161 GLN cc_start: 0.8957 (tt0) cc_final: 0.8246 (tt0) REVERT: Y 190 GLN cc_start: 0.8784 (mt0) cc_final: 0.8526 (mt0) REVERT: Y 192 GLN cc_start: 0.8232 (mm110) cc_final: 0.7832 (mm110) REVERT: Z 41 LEU cc_start: 0.9307 (tp) cc_final: 0.8885 (mp) REVERT: Z 113 MET cc_start: 0.8594 (tmm) cc_final: 0.8259 (tmm) REVERT: 0 25 MET cc_start: 0.7766 (mtm) cc_final: 0.7501 (mtm) REVERT: 0 32 TYR cc_start: 0.7938 (t80) cc_final: 0.7657 (t80) REVERT: 0 36 GLU cc_start: 0.8428 (mt-10) cc_final: 0.8014 (mm-30) REVERT: 0 59 GLU cc_start: 0.8462 (tp30) cc_final: 0.8039 (tm-30) REVERT: 1 25 MET cc_start: 0.7622 (mmm) cc_final: 0.7304 (mmm) REVERT: 1 32 TYR cc_start: 0.8652 (m-80) cc_final: 0.8414 (m-80) REVERT: 1 128 MET cc_start: 0.9031 (OUTLIER) cc_final: 0.8471 (mtp) REVERT: 2 18 TYR cc_start: 0.9009 (t80) cc_final: 0.8588 (t80) REVERT: 2 25 MET cc_start: 0.8436 (pmm) cc_final: 0.8124 (pmm) REVERT: 2 95 GLU cc_start: 0.8118 (tp30) cc_final: 0.7666 (tm-30) REVERT: 6 166 GLU cc_start: 0.8701 (tp30) cc_final: 0.8450 (tp30) REVERT: 7 277 MET cc_start: 0.8593 (mmm) cc_final: 0.8099 (mmm) outliers start: 75 outliers final: 45 residues processed: 442 average time/residue: 0.6005 time to fit residues: 466.5254 Evaluate side-chains 415 residues out of total 7395 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 51 poor density : 364 time to evaluate : 5.678 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 92 LEU Chi-restraints excluded: chain A residue 104 VAL Chi-restraints excluded: chain A residue 597 GLN Chi-restraints excluded: chain I residue 175 THR Chi-restraints excluded: chain L residue 11 VAL Chi-restraints excluded: chain L residue 116 CYS Chi-restraints excluded: chain L residue 120 GLU Chi-restraints excluded: chain L residue 137 ILE Chi-restraints excluded: chain L residue 152 THR Chi-restraints excluded: chain L residue 165 MET Chi-restraints excluded: chain L residue 171 ILE Chi-restraints excluded: chain L residue 218 MET Chi-restraints excluded: chain Q residue 112 LEU Chi-restraints excluded: chain R residue 113 MET Chi-restraints excluded: chain S residue 7 VAL Chi-restraints excluded: chain T residue 113 MET Chi-restraints excluded: chain T residue 128 MET Chi-restraints excluded: chain p residue 39 ASP Chi-restraints excluded: chain p residue 93 MET Chi-restraints excluded: chain B residue 382 VAL Chi-restraints excluded: chain B residue 530 ILE Chi-restraints excluded: chain D residue 175 THR Chi-restraints excluded: chain E residue 40 LEU Chi-restraints excluded: chain E residue 152 THR Chi-restraints excluded: chain E residue 171 ILE Chi-restraints excluded: chain F residue 84 ASP Chi-restraints excluded: chain F residue 112 LEU Chi-restraints excluded: chain F residue 128 MET Chi-restraints excluded: chain G residue 90 GLU Chi-restraints excluded: chain J residue 7 VAL Chi-restraints excluded: chain J residue 122 VAL Chi-restraints excluded: chain K residue 128 MET Chi-restraints excluded: chain N residue 40 THR Chi-restraints excluded: chain O residue 45 THR Chi-restraints excluded: chain U residue 133 MET Chi-restraints excluded: chain V residue 92 LEU Chi-restraints excluded: chain V residue 587 THR Chi-restraints excluded: chain V residue 597 GLN Chi-restraints excluded: chain W residue 18 GLU Chi-restraints excluded: chain W residue 70 LEU Chi-restraints excluded: chain X residue 70 LEU Chi-restraints excluded: chain Y residue 152 THR Chi-restraints excluded: chain Y residue 171 ILE Chi-restraints excluded: chain Y residue 272 ASP Chi-restraints excluded: chain 1 residue 7 VAL Chi-restraints excluded: chain 1 residue 122 VAL Chi-restraints excluded: chain 1 residue 128 MET Chi-restraints excluded: chain 2 residue 128 MET Chi-restraints excluded: chain 4 residue 45 THR Chi-restraints excluded: chain 6 residue 164 LEU Chi-restraints excluded: chain 7 residue 285 ARG Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 825 random chunks: chunk 268 optimal weight: 30.0000 chunk 718 optimal weight: 4.9990 chunk 157 optimal weight: 3.9990 chunk 468 optimal weight: 0.3980 chunk 196 optimal weight: 0.1980 chunk 798 optimal weight: 7.9990 chunk 662 optimal weight: 10.0000 chunk 369 optimal weight: 3.9990 chunk 66 optimal weight: 0.9980 chunk 264 optimal weight: 7.9990 chunk 419 optimal weight: 3.9990 overall best weight: 1.9184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Sorry: Reduce crashed with command 'molprobity.reduce -quiet -trim -'. Dumping stdin to file 'reduce_failure.pdb'. Return code: -15 Dumping stderr: