Starting phenix.real_space_refine on Sun Oct 13 16:58:15 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8hqz_34955/10_2024/8hqz_34955.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8hqz_34955/10_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_34955/10_2024/8hqz_34955.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8hqz_34955/10_2024/8hqz_34955.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8hqz_34955/10_2024/8hqz_34955.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8hqz_34955/10_2024/8hqz_34955.cif" } 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. Time to flip 9 residue(s): 0.15s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5477/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: 29.18, per 1000 atoms: 0.44 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 - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 13.10 Conformation dependent library (CDL) restraints added in 6.7 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: 8.37 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: 7.606A 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: 5.940A 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: 6.926A 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: 32.80 Time building geometry restraints manager: 15.36 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: 9552 1.45 - 1.57: 36556 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: 0.00 - 1.73: 86516 1.73 - 3.46: 4947 3.46 - 5.20: 419 5.20 - 6.93: 29 6.93 - 8.66: 6 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: 6767 0.046 - 0.092: 3079 0.092 - 0.138: 600 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: 39917 2.99 - 3.63: 95019 3.63 - 4.26: 147051 4.26 - 4.90: 245050 Nonbonded interactions: 527076 Sorted by model distance: nonbonded pdb=" NH2 ARG K 126 " pdb=" OD1 ASP Z 13 " model vdw 1.714 3.120 nonbonded pdb=" OD1 ASP Q 13 " pdb=" NH2 ARG 2 126 " model vdw 1.714 3.120 nonbonded pdb=" NH2 ARG T 126 " pdb=" OD1 ASP F 13 " model vdw 1.714 3.120 nonbonded pdb=" OE1 GLU 2 14 " pdb=" N GLY 2 137 " model vdw 2.258 3.120 nonbonded pdb=" OE1 GLU T 14 " pdb=" N GLY T 137 " model vdw 2.258 3.120 ... (remaining 527071 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = (chain '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: 3.130 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.080 Extract box with map and model: 2.160 Check model and map are aligned: 0.440 Set scattering table: 0.500 Process input model: 127.990 Find NCS groups from input model: 2.090 Set up NCS constraints: 0.370 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.210 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 138.990 ------------------------------------------------------------------------------- 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 : 6.096 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: 0.8289 (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: 0.7255 (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: 0.8318 (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: 0.7978 (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: 0.9266 (mtm) cc_final: 0.9043 (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: 0.7893 (mpp) REVERT: Z 41 LEU cc_start: 0.9354 (tp) cc_final: 0.9031 (tp) 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: 0.8195 (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: 0.6739 time to fit residues: 615.2873 Evaluate side-chains 389 residues out of total 7395 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 385 time to evaluate : 6.004 ------------------------------------------------------------------------------- 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: 2.9990 chunk 625 optimal weight: 4.9990 chunk 346 optimal weight: 1.9990 chunk 213 optimal weight: 0.9980 chunk 421 optimal weight: 5.9990 chunk 334 optimal weight: 3.9990 chunk 646 optimal weight: 4.9990 chunk 250 optimal weight: 8.9990 chunk 393 optimal weight: 0.9990 chunk 481 optimal weight: 6.9990 chunk 749 optimal weight: 4.9990 overall best weight: 2.1988 ------------------------------------------------------------------------------- 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 p 31 GLN 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 P 152 ASN U 20 HIS U 31 GLN V 14 ASN V 200 GLN V 597 GLN V 631 GLN V 770 ASN X 25 ASN Y 45 HIS 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: 0.8028 moved from start: 0.1540 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.058 67635 Z= 0.245 Angle : 0.601 8.648 91917 Z= 0.330 Chirality : 0.047 0.172 10497 Planarity : 0.004 0.079 11952 Dihedral : 6.270 47.610 9243 Min Nonbonded Distance : 2.288 Molprobity Statistics. All-atom Clashscore : 2.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.01 % Favored : 97.99 % Rotamer: Outliers : 0.55 % Allowed : 3.69 % Favored : 95.75 % 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: -0.53 (0.09), residues: 8400 helix: 0.08 (0.15), residues: 1104 sheet: -0.15 (0.09), residues: 2907 loop : -0.51 (0.09), residues: 4389 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 0.015 0.002 PHE R 125 TYR 0.020 0.002 TYR L 118 ARG 0.008 0.001 ARG T 115 *********************** 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 514 residues out of total 7395 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 41 poor density : 473 time to evaluate : 6.081 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: A 140 ILE cc_start: 0.8690 (mt) cc_final: 0.8373 (tt) REVERT: A 527 MET cc_start: 0.9295 (mtm) cc_final: 0.9048 (mtm) REVERT: A 682 ASP cc_start: 0.9203 (p0) cc_final: 0.8944 (p0) REVERT: A 695 GLU cc_start: 0.8233 (tt0) cc_final: 0.7724 (tm-30) REVERT: H 1 MET cc_start: 0.8268 (pmm) cc_final: 0.8018 (pmm) REVERT: H 18 GLU cc_start: 0.8660 (tt0) cc_final: 0.8375 (tt0) REVERT: H 61 GLU cc_start: 0.8940 (pm20) cc_final: 0.8532 (pm20) REVERT: H 105 LYS cc_start: 0.8719 (tppt) cc_final: 0.8395 (tppt) REVERT: I 18 GLU cc_start: 0.8383 (tm-30) cc_final: 0.8164 (tm-30) REVERT: I 40 GLU cc_start: 0.8750 (pt0) cc_final: 0.7777 (pm20) REVERT: I 71 GLU cc_start: 0.8848 (tp30) cc_final: 0.8463 (tp30) REVERT: I 78 TYR cc_start: 0.8897 (m-80) cc_final: 0.8620 (m-10) REVERT: I 87 GLU cc_start: 0.9049 (mm-30) cc_final: 0.8847 (mm-30) REVERT: I 122 LYS cc_start: 0.7972 (mttt) cc_final: 0.7631 (mtmm) REVERT: L 104 MET cc_start: 0.8910 (mmt) cc_final: 0.8435 (mmm) REVERT: L 161 GLN cc_start: 0.8872 (tt0) cc_final: 0.8229 (tt0) REVERT: L 165 MET cc_start: 0.7621 (OUTLIER) cc_final: 0.6422 (mmm) REVERT: L 192 GLN cc_start: 0.8173 (mm110) cc_final: 0.7659 (mm-40) REVERT: R 108 TYR cc_start: 0.8554 (m-80) cc_final: 0.8122 (m-80) REVERT: S 25 MET cc_start: 0.7920 (mmm) cc_final: 0.7367 (mmm) REVERT: T 25 MET cc_start: 0.8123 (pmm) cc_final: 0.7457 (pmm) REVERT: T 73 GLN cc_start: 0.8702 (tp-100) cc_final: 0.8132 (mm110) REVERT: T 90 GLU cc_start: 0.8792 (mm-30) cc_final: 0.8319 (mm-30) REVERT: T 95 GLU cc_start: 0.8199 (tp30) cc_final: 0.7708 (tm-30) REVERT: T 113 MET cc_start: 0.8648 (OUTLIER) cc_final: 0.8445 (ttm) REVERT: e 43 GLU cc_start: 0.8582 (pm20) cc_final: 0.8376 (pt0) REVERT: f 25 TYR cc_start: 0.7644 (t80) cc_final: 0.7433 (t80) REVERT: f 38 SER cc_start: 0.8855 (m) cc_final: 0.8157 (p) REVERT: f 43 GLU cc_start: 0.8757 (mm-30) cc_final: 0.8452 (mm-30) REVERT: k 158 ASP cc_start: 0.8477 (m-30) cc_final: 0.8258 (m-30) REVERT: k 161 GLU cc_start: 0.8829 (mm-30) cc_final: 0.8487 (mm-30) REVERT: p 166 ARG cc_start: 0.8476 (ptp90) cc_final: 0.7950 (ptp90) REVERT: p 277 MET cc_start: 0.8381 (mmm) cc_final: 0.7852 (mmm) REVERT: B 527 MET cc_start: 0.9193 (mtm) cc_final: 0.8970 (mtm) REVERT: C 56 GLU cc_start: 0.7934 (pm20) cc_final: 0.7676 (pm20) REVERT: C 61 GLU cc_start: 0.8598 (pm20) cc_final: 0.8018 (pm20) REVERT: C 71 GLU cc_start: 0.8694 (tp30) cc_final: 0.8065 (tp30) REVERT: D 12 LEU cc_start: 0.8591 (mt) cc_final: 0.8302 (mt) REVERT: D 18 GLU cc_start: 0.8328 (tm-30) cc_final: 0.7652 (tm-30) REVERT: D 40 GLU cc_start: 0.8965 (pt0) cc_final: 0.8201 (pm20) REVERT: D 71 GLU cc_start: 0.8678 (tp30) cc_final: 0.8441 (tp30) REVERT: D 122 LYS cc_start: 0.7992 (mttt) cc_final: 0.7782 (mtpp) REVERT: D 164 GLU cc_start: 0.8414 (mp0) cc_final: 0.8046 (mp0) REVERT: E 104 MET cc_start: 0.9041 (mmt) cc_final: 0.8517 (mmm) REVERT: E 161 GLN cc_start: 0.8890 (tt0) cc_final: 0.8268 (tt0) REVERT: E 190 GLN cc_start: 0.8896 (mt0) cc_final: 0.8587 (mt0) REVERT: E 192 GLN cc_start: 0.8335 (mm110) cc_final: 0.7533 (mm110) REVERT: E 218 MET cc_start: 0.8181 (mtt) cc_final: 0.7888 (mtt) REVERT: G 18 TYR cc_start: 0.8899 (t80) cc_final: 0.8646 (t80) REVERT: G 32 TYR cc_start: 0.7747 (t80) cc_final: 0.7477 (t80) REVERT: G 59 GLU cc_start: 0.8486 (tp30) cc_final: 0.8031 (tm-30) REVERT: J 36 GLU cc_start: 0.8682 (pp20) cc_final: 0.8363 (pp20) REVERT: J 41 LEU cc_start: 0.9305 (tp) cc_final: 0.8821 (tp) REVERT: J 113 MET cc_start: 0.8580 (ptm) cc_final: 0.8105 (ptm) REVERT: K 25 MET cc_start: 0.7961 (pmm) cc_final: 0.7330 (pmm) REVERT: K 41 LEU cc_start: 0.9146 (mt) cc_final: 0.8758 (mp) REVERT: K 73 GLN cc_start: 0.8707 (tp-100) cc_final: 0.8223 (mm-40) REVERT: K 90 GLU cc_start: 0.8838 (mm-30) cc_final: 0.8299 (mm-30) REVERT: K 95 GLU cc_start: 0.8306 (tp30) cc_final: 0.7794 (tm-30) REVERT: O 38 SER cc_start: 0.8919 (m) cc_final: 0.8488 (p) REVERT: O 43 GLU cc_start: 0.8852 (mm-30) cc_final: 0.8528 (mm-30) REVERT: U 277 MET cc_start: 0.8363 (mmm) cc_final: 0.7785 (mmm) REVERT: U 282 ASP cc_start: 0.7987 (m-30) cc_final: 0.7777 (m-30) REVERT: V 140 ILE cc_start: 0.8637 (mt) cc_final: 0.8340 (tt) REVERT: V 892 MET cc_start: 0.9464 (tpp) cc_final: 0.9176 (tmm) REVERT: W 61 GLU cc_start: 0.8620 (pm20) cc_final: 0.8160 (pm20) REVERT: W 71 GLU cc_start: 0.8604 (tp30) cc_final: 0.7957 (tp30) REVERT: W 105 LYS cc_start: 0.8628 (tppt) cc_final: 0.8094 (tppt) REVERT: W 164 GLU cc_start: 0.7538 (mp0) cc_final: 0.6809 (mp0) REVERT: X 18 GLU cc_start: 0.8265 (tm-30) cc_final: 0.7988 (tm-30) REVERT: X 40 GLU cc_start: 0.8738 (pt0) cc_final: 0.8110 (pm20) REVERT: X 56 GLU cc_start: 0.7449 (tp30) cc_final: 0.7204 (tp30) REVERT: X 71 GLU cc_start: 0.8797 (tp30) cc_final: 0.8475 (tp30) REVERT: X 87 GLU cc_start: 0.8955 (mm-30) cc_final: 0.8587 (mm-30) REVERT: Y 104 MET cc_start: 0.9044 (mmt) cc_final: 0.8825 (mmm) REVERT: Y 120 GLU cc_start: 0.8110 (OUTLIER) cc_final: 0.7728 (tp30) REVERT: Y 161 GLN cc_start: 0.8892 (tt0) cc_final: 0.8153 (tt0) REVERT: Y 190 GLN cc_start: 0.8689 (mt0) cc_final: 0.8365 (mt0) REVERT: Y 192 GLN cc_start: 0.8381 (mm110) cc_final: 0.7591 (mm110) REVERT: Z 41 LEU cc_start: 0.9284 (tp) cc_final: 0.8842 (tp) REVERT: Z 94 LYS cc_start: 0.9085 (mmmt) cc_final: 0.8854 (mmmt) REVERT: 0 18 TYR cc_start: 0.8931 (t80) cc_final: 0.8689 (t80) REVERT: 0 32 TYR cc_start: 0.7854 (t80) cc_final: 0.7641 (t80) REVERT: 0 36 GLU cc_start: 0.8111 (mt-10) cc_final: 0.7818 (mm-30) REVERT: 0 59 GLU cc_start: 0.8426 (tp30) cc_final: 0.8012 (tm-30) REVERT: 0 129 GLU cc_start: 0.8344 (pm20) cc_final: 0.7888 (pm20) REVERT: 1 25 MET cc_start: 0.7840 (mmm) cc_final: 0.7411 (mmm) REVERT: 1 128 MET cc_start: 0.8797 (OUTLIER) cc_final: 0.8405 (mtp) REVERT: 2 18 TYR cc_start: 0.8945 (t80) cc_final: 0.8558 (t80) REVERT: 2 25 MET cc_start: 0.8200 (pmm) cc_final: 0.7721 (pmm) REVERT: 2 95 GLU cc_start: 0.8140 (tp30) cc_final: 0.7723 (tm-30) REVERT: 3 10 GLN cc_start: 0.8471 (OUTLIER) cc_final: 0.7885 (pm20) REVERT: 5 11 GLN cc_start: 0.8581 (tt0) cc_final: 0.8279 (tt0) REVERT: 5 38 SER cc_start: 0.9138 (m) cc_final: 0.8455 (t) outliers start: 41 outliers final: 18 residues processed: 483 average time/residue: 0.6309 time to fit residues: 526.2878 Evaluate side-chains 425 residues out of total 7395 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 402 time to evaluate : 6.076 ------------------------------------------------------------------------------- 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 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 Y residue 120 GLU 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: 0.3980 chunk 232 optimal weight: 6.9990 chunk 623 optimal weight: 3.9990 chunk 510 optimal weight: 3.9990 chunk 206 optimal weight: 0.5980 chunk 750 optimal weight: 5.9990 chunk 810 optimal weight: 8.9990 chunk 668 optimal weight: 6.9990 chunk 744 optimal weight: 0.6980 chunk 255 optimal weight: 3.9990 chunk 602 optimal weight: 4.9990 overall best weight: 1.9384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 631 GLN S 57 ASN p 118 ASN B 591 ASN B 631 GLN J 57 ASN U 118 ASN V 446 HIS V 591 ASN V 631 GLN 1 57 ASN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8048 moved from start: 0.2112 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= 0.213 Angle : 0.538 9.921 91917 Z= 0.292 Chirality : 0.045 0.153 10497 Planarity : 0.004 0.061 11952 Dihedral : 5.319 22.862 9228 Min Nonbonded Distance : 2.449 Molprobity Statistics. All-atom Clashscore : 2.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.30 % Favored : 97.70 % Rotamer: Outliers : 0.97 % Allowed : 4.92 % Favored : 94.10 % 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: -0.28 (0.09), residues: 8400 helix: 0.45 (0.16), residues: 1107 sheet: -0.00 (0.09), residues: 2868 loop : -0.38 (0.09), residues: 4425 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP V 156 HIS 0.004 0.001 HIS V 66 PHE 0.019 0.001 PHE 6 148 TYR 0.021 0.001 TYR J 18 ARG 0.007 0.001 ARG W 201 *********************** 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 497 residues out of total 7395 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 72 poor density : 425 time to evaluate : 6.104 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 140 ILE cc_start: 0.8662 (mt) cc_final: 0.8445 (tt) REVERT: A 682 ASP cc_start: 0.9190 (p0) cc_final: 0.8934 (p0) REVERT: A 892 MET cc_start: 0.9274 (tpp) cc_final: 0.8855 (tmm) REVERT: H 18 GLU cc_start: 0.8621 (tt0) cc_final: 0.8416 (tm-30) REVERT: H 56 GLU cc_start: 0.8209 (pm20) cc_final: 0.7947 (pm20) REVERT: H 61 GLU cc_start: 0.8810 (pm20) cc_final: 0.8152 (pm20) REVERT: H 105 LYS cc_start: 0.8754 (tppt) cc_final: 0.8440 (tppt) REVERT: I 11 GLU cc_start: 0.8623 (pm20) cc_final: 0.8345 (pm20) REVERT: I 12 LEU cc_start: 0.8602 (mt) cc_final: 0.7901 (mp) REVERT: I 18 GLU cc_start: 0.8493 (tm-30) cc_final: 0.7763 (tm-30) REVERT: I 40 GLU cc_start: 0.8734 (pt0) cc_final: 0.7925 (pm20) REVERT: I 71 GLU cc_start: 0.8898 (tp30) cc_final: 0.8527 (tp30) REVERT: I 78 TYR cc_start: 0.8871 (m-80) cc_final: 0.8540 (m-10) REVERT: I 87 GLU cc_start: 0.9177 (mm-30) cc_final: 0.8869 (mm-30) REVERT: I 122 LYS cc_start: 0.8409 (mttt) cc_final: 0.8031 (mtmm) REVERT: L 104 MET cc_start: 0.8848 (mmt) cc_final: 0.8414 (mmm) REVERT: L 161 GLN cc_start: 0.8804 (tt0) cc_final: 0.8126 (tt0) REVERT: L 192 GLN cc_start: 0.8154 (mm110) cc_final: 0.7737 (mm110) REVERT: Q 113 MET cc_start: 0.8250 (tmm) cc_final: 0.7786 (tmm) REVERT: R 108 TYR cc_start: 0.8428 (m-80) cc_final: 0.7977 (m-80) REVERT: S 25 MET cc_start: 0.7632 (mmm) cc_final: 0.7346 (mmm) REVERT: T 25 MET cc_start: 0.8170 (pmm) cc_final: 0.7324 (pmm) REVERT: T 36 GLU cc_start: 0.8990 (pm20) cc_final: 0.8576 (mp0) REVERT: T 73 GLN cc_start: 0.8700 (tp-100) cc_final: 0.8147 (mm110) REVERT: T 90 GLU cc_start: 0.8806 (mm-30) cc_final: 0.8324 (mm-30) REVERT: T 95 GLU cc_start: 0.8179 (tp30) cc_final: 0.7674 (tm-30) REVERT: T 113 MET cc_start: 0.8609 (OUTLIER) cc_final: 0.8360 (ttm) REVERT: d 43 GLU cc_start: 0.8438 (mt-10) cc_final: 0.8074 (mt-10) REVERT: f 10 GLN cc_start: 0.8392 (pt0) cc_final: 0.8179 (pt0) REVERT: f 25 TYR cc_start: 0.7564 (t80) cc_final: 0.7362 (t80) REVERT: k 148 PHE cc_start: 0.8467 (t80) cc_final: 0.7946 (t80) REVERT: k 158 ASP cc_start: 0.8509 (m-30) cc_final: 0.8258 (m-30) REVERT: p 118 ASN cc_start: 0.8195 (OUTLIER) cc_final: 0.7991 (p0) REVERT: p 166 ARG cc_start: 0.8474 (ptp90) cc_final: 0.7978 (ptp90) REVERT: p 277 MET cc_start: 0.8377 (mmm) cc_final: 0.7826 (mmm) REVERT: B 527 MET cc_start: 0.9202 (mtm) cc_final: 0.8976 (mtm) REVERT: C 1 MET cc_start: 0.8163 (pmm) cc_final: 0.7904 (pmm) REVERT: C 30 ARG cc_start: 0.9029 (ttm-80) cc_final: 0.8796 (ttm-80) REVERT: C 40 GLU cc_start: 0.7910 (mt-10) cc_final: 0.7617 (mt-10) REVERT: C 56 GLU cc_start: 0.8022 (pm20) cc_final: 0.7797 (pm20) REVERT: C 61 GLU cc_start: 0.8715 (pm20) cc_final: 0.7994 (pm20) REVERT: C 71 GLU cc_start: 0.8672 (tp30) cc_final: 0.7945 (tp30) REVERT: D 18 GLU cc_start: 0.8410 (tm-30) cc_final: 0.8049 (tp30) REVERT: D 40 GLU cc_start: 0.9013 (pt0) cc_final: 0.8238 (pm20) REVERT: D 56 GLU cc_start: 0.7558 (tp30) cc_final: 0.7353 (tp30) REVERT: D 71 GLU cc_start: 0.8718 (tp30) cc_final: 0.8477 (tp30) REVERT: D 122 LYS cc_start: 0.8206 (mttt) cc_final: 0.7897 (mtmm) REVERT: D 164 GLU cc_start: 0.8611 (mp0) cc_final: 0.8197 (mp0) REVERT: E 104 MET cc_start: 0.9097 (mmt) cc_final: 0.8583 (mmm) REVERT: E 161 GLN cc_start: 0.8858 (tt0) cc_final: 0.8243 (tt0) REVERT: E 190 GLN cc_start: 0.8845 (mt0) cc_final: 0.8513 (mt0) REVERT: E 192 GLN cc_start: 0.8343 (mm110) cc_final: 0.7583 (mm110) REVERT: E 243 GLU cc_start: 0.8041 (mp0) cc_final: 0.7811 (mp0) REVERT: G 18 TYR cc_start: 0.8958 (t80) cc_final: 0.8682 (t80) REVERT: G 32 TYR cc_start: 0.7800 (t80) cc_final: 0.7517 (t80) REVERT: G 59 GLU cc_start: 0.8479 (tp30) cc_final: 0.8115 (tm-30) REVERT: J 25 MET cc_start: 0.8026 (tpp) cc_final: 0.7590 (tpp) REVERT: J 36 GLU cc_start: 0.8598 (pp20) cc_final: 0.8166 (pp20) REVERT: J 41 LEU cc_start: 0.9355 (tp) cc_final: 0.8851 (tp) REVERT: J 113 MET cc_start: 0.8611 (ptm) cc_final: 0.8152 (ptm) REVERT: K 25 MET cc_start: 0.8197 (pmm) cc_final: 0.7456 (pmm) REVERT: K 73 GLN cc_start: 0.8655 (tp-100) cc_final: 0.8118 (mm-40) REVERT: K 90 GLU cc_start: 0.8921 (mm-30) cc_final: 0.8390 (mm-30) REVERT: K 95 GLU cc_start: 0.8283 (tp30) cc_final: 0.7777 (tm-30) REVERT: K 129 GLU cc_start: 0.8514 (pm20) cc_final: 0.8263 (pm20) REVERT: O 38 SER cc_start: 0.9060 (m) cc_final: 0.8593 (t) REVERT: P 152 ASN cc_start: 0.8411 (m-40) cc_final: 0.8104 (m-40) REVERT: V 140 ILE cc_start: 0.8723 (mt) cc_final: 0.8501 (tt) REVERT: V 581 ASP cc_start: 0.8838 (t0) cc_final: 0.7568 (p0) REVERT: W 30 ARG cc_start: 0.8967 (ttm-80) cc_final: 0.8560 (ttm-80) REVERT: W 61 GLU cc_start: 0.8681 (pm20) cc_final: 0.8102 (pm20) REVERT: W 71 GLU cc_start: 0.8622 (tp30) cc_final: 0.7954 (tp30) REVERT: W 164 GLU cc_start: 0.7886 (mp0) cc_final: 0.7085 (mp0) REVERT: X 12 LEU cc_start: 0.8469 (mt) cc_final: 0.8196 (mp) REVERT: X 18 GLU cc_start: 0.8361 (tm-30) cc_final: 0.8007 (tm-30) REVERT: X 32 GLU cc_start: 0.7809 (tp30) cc_final: 0.7215 (tp30) REVERT: X 40 GLU cc_start: 0.8740 (pt0) cc_final: 0.8207 (pm20) REVERT: X 56 GLU cc_start: 0.7489 (tp30) cc_final: 0.7267 (tp30) REVERT: X 71 GLU cc_start: 0.8794 (tp30) cc_final: 0.8476 (tp30) REVERT: X 164 GLU cc_start: 0.8629 (mp0) cc_final: 0.8300 (mp0) REVERT: Y 104 MET cc_start: 0.9014 (mmt) cc_final: 0.8726 (mmm) REVERT: Y 120 GLU cc_start: 0.8090 (OUTLIER) cc_final: 0.7659 (tp30) REVERT: Y 161 GLN cc_start: 0.8868 (tt0) cc_final: 0.8329 (tt0) REVERT: Y 190 GLN cc_start: 0.8759 (mt0) cc_final: 0.8387 (mt0) REVERT: Y 192 GLN cc_start: 0.8406 (mm110) cc_final: 0.7658 (mm110) REVERT: Z 41 LEU cc_start: 0.9324 (tp) cc_final: 0.8981 (tp) REVERT: Z 113 MET cc_start: 0.8513 (tmm) cc_final: 0.8141 (tmm) REVERT: 0 25 MET cc_start: 0.7845 (mtm) cc_final: 0.7495 (mtm) REVERT: 0 32 TYR cc_start: 0.7836 (t80) cc_final: 0.7614 (t80) REVERT: 0 36 GLU cc_start: 0.8341 (mt-10) cc_final: 0.7991 (mm-30) REVERT: 0 59 GLU cc_start: 0.8412 (tp30) cc_final: 0.8022 (tm-30) REVERT: 0 128 MET cc_start: 0.8060 (OUTLIER) cc_final: 0.7838 (ttm) REVERT: 0 129 GLU cc_start: 0.8500 (pm20) cc_final: 0.7828 (pm20) REVERT: 1 4 GLU cc_start: 0.8191 (pm20) cc_final: 0.7773 (pm20) REVERT: 1 25 MET cc_start: 0.7566 (mmm) cc_final: 0.7232 (mmm) REVERT: 1 128 MET cc_start: 0.8907 (OUTLIER) cc_final: 0.8564 (mtp) REVERT: 2 18 TYR cc_start: 0.8995 (t80) cc_final: 0.8591 (t80) REVERT: 2 25 MET cc_start: 0.8378 (pmm) cc_final: 0.7945 (pmm) REVERT: 2 90 GLU cc_start: 0.8766 (mm-30) cc_final: 0.8346 (mm-30) REVERT: 2 95 GLU cc_start: 0.8110 (tp30) cc_final: 0.7688 (tm-30) REVERT: 6 166 GLU cc_start: 0.8825 (tp30) cc_final: 0.8586 (tp30) outliers start: 72 outliers final: 31 residues processed: 462 average time/residue: 0.6276 time to fit residues: 500.9687 Evaluate side-chains 436 residues out of total 7395 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 36 poor density : 400 time to evaluate : 6.128 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 547 SER 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 T residue 113 MET Chi-restraints excluded: chain T residue 128 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 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 116 CYS Chi-restraints excluded: chain F residue 128 MET 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 W residue 18 GLU Chi-restraints excluded: chain Y residue 116 CYS Chi-restraints excluded: chain Y residue 120 GLU 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 128 MET 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 171 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: 20.0000 chunk 564 optimal weight: 0.0980 chunk 389 optimal weight: 1.9990 chunk 83 optimal weight: 10.0000 chunk 358 optimal weight: 3.9990 chunk 503 optimal weight: 3.9990 chunk 753 optimal weight: 2.9990 chunk 797 optimal weight: 6.9990 chunk 393 optimal weight: 0.9990 chunk 713 optimal weight: 0.9980 chunk 214 optimal weight: 0.3980 overall best weight: 0.8984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: S 57 ASN k 152 ASN p 355 ASN B 631 GLN J 57 ASN M 10 GLN ** P 176 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** U 355 ASN 1 57 ASN 3 10 GLN 7 355 ASN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8034 moved from start: 0.2421 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.040 67635 Z= 0.135 Angle : 0.493 9.474 91917 Z= 0.265 Chirality : 0.044 0.150 10497 Planarity : 0.003 0.043 11952 Dihedral : 4.857 20.627 9228 Min Nonbonded Distance : 2.422 Molprobity Statistics. All-atom Clashscore : 2.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.86 % Favored : 98.14 % Rotamer: Outliers : 0.85 % Allowed : 5.75 % Favored : 93.40 % 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: -0.11 (0.09), residues: 8400 helix: 0.66 (0.16), residues: 1113 sheet: 0.10 (0.09), residues: 2907 loop : -0.28 (0.09), residues: 4380 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 946 HIS 0.005 0.001 HIS p 113 PHE 0.011 0.001 PHE 6 148 TYR 0.019 0.001 TYR E 118 ARG 0.007 0.000 ARG W 201 *********************** 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 494 residues out of total 7395 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 63 poor density : 431 time to evaluate : 6.084 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: A 1 MET cc_start: 0.8027 (tmm) cc_final: 0.7826 (tmm) REVERT: A 140 ILE cc_start: 0.8671 (mt) cc_final: 0.8289 (tt) REVERT: A 682 ASP cc_start: 0.9183 (p0) cc_final: 0.8900 (p0) REVERT: A 892 MET cc_start: 0.9238 (tpp) cc_final: 0.8927 (tmm) REVERT: H 56 GLU cc_start: 0.8177 (pm20) cc_final: 0.7938 (pm20) REVERT: H 61 GLU cc_start: 0.8812 (pm20) cc_final: 0.8143 (pm20) REVERT: H 66 ASP cc_start: 0.9019 (t0) cc_final: 0.8740 (m-30) REVERT: H 105 LYS cc_start: 0.8706 (tppt) cc_final: 0.8326 (tppt) REVERT: I 18 GLU cc_start: 0.8466 (tm-30) cc_final: 0.7646 (tm-30) REVERT: I 40 GLU cc_start: 0.8706 (pt0) cc_final: 0.7957 (pm20) REVERT: I 71 GLU cc_start: 0.8944 (tp30) cc_final: 0.8596 (tp30) REVERT: I 78 TYR cc_start: 0.8877 (m-80) cc_final: 0.8563 (m-10) REVERT: I 87 GLU cc_start: 0.9138 (mm-30) cc_final: 0.8922 (mm-30) REVERT: I 111 MET cc_start: 0.7850 (OUTLIER) cc_final: 0.7306 (ptm) REVERT: I 122 LYS cc_start: 0.8442 (mttt) cc_final: 0.8088 (mtmm) REVERT: L 104 MET cc_start: 0.8843 (mmt) cc_final: 0.8413 (mmm) REVERT: L 161 GLN cc_start: 0.8713 (tt0) cc_final: 0.7959 (tt0) REVERT: L 171 ILE cc_start: 0.7905 (OUTLIER) cc_final: 0.7643 (tt) REVERT: L 192 GLN cc_start: 0.8009 (mm110) cc_final: 0.7763 (mm110) REVERT: Q 109 TYR cc_start: 0.9334 (p90) cc_final: 0.8916 (p90) REVERT: R 59 GLU cc_start: 0.8291 (tp30) cc_final: 0.7908 (tm-30) REVERT: R 108 TYR cc_start: 0.8295 (m-80) cc_final: 0.7865 (m-80) REVERT: R 129 GLU cc_start: 0.8461 (pm20) cc_final: 0.8060 (pm20) REVERT: S 25 MET cc_start: 0.7618 (mmm) cc_final: 0.7261 (mmm) REVERT: S 36 GLU cc_start: 0.8726 (pm20) cc_final: 0.8484 (pm20) REVERT: T 25 MET cc_start: 0.8160 (pmm) cc_final: 0.7166 (pmm) REVERT: T 36 GLU cc_start: 0.9033 (pm20) cc_final: 0.8622 (mp0) REVERT: T 73 GLN cc_start: 0.8683 (tp-100) cc_final: 0.8118 (mm110) REVERT: T 90 GLU cc_start: 0.8865 (mm-30) cc_final: 0.8349 (mm-30) REVERT: T 95 GLU cc_start: 0.8171 (tp30) cc_final: 0.7653 (tm-30) REVERT: T 113 MET cc_start: 0.8548 (OUTLIER) cc_final: 0.8324 (ttm) REVERT: f 10 GLN cc_start: 0.8334 (pt0) cc_final: 0.8041 (pt0) REVERT: k 148 PHE cc_start: 0.8419 (t80) cc_final: 0.7915 (t80) REVERT: k 158 ASP cc_start: 0.8547 (m-30) cc_final: 0.8270 (m-30) REVERT: p 118 ASN cc_start: 0.8726 (OUTLIER) cc_final: 0.8472 (p0) REVERT: p 166 ARG cc_start: 0.8431 (ptp90) cc_final: 0.7952 (ptp90) REVERT: p 277 MET cc_start: 0.8307 (mmm) cc_final: 0.7730 (mmm) REVERT: B 527 MET cc_start: 0.9164 (mtm) cc_final: 0.8961 (mtm) REVERT: C 18 GLU cc_start: 0.9003 (OUTLIER) cc_final: 0.8409 (tp30) REVERT: C 30 ARG cc_start: 0.8923 (ttm-80) cc_final: 0.8631 (ttm-80) REVERT: C 56 GLU cc_start: 0.8141 (pm20) cc_final: 0.7902 (pm20) REVERT: C 61 GLU cc_start: 0.8862 (pm20) cc_final: 0.8134 (pm20) REVERT: C 71 GLU cc_start: 0.8689 (tp30) cc_final: 0.7917 (tp30) REVERT: C 164 GLU cc_start: 0.8306 (mp0) cc_final: 0.7742 (mp0) REVERT: D 18 GLU cc_start: 0.8370 (tm-30) cc_final: 0.8007 (tp30) REVERT: D 40 GLU cc_start: 0.8992 (pt0) cc_final: 0.8263 (pm20) REVERT: D 71 GLU cc_start: 0.8767 (tp30) cc_final: 0.8529 (tp30) REVERT: D 122 LYS cc_start: 0.8225 (mttt) cc_final: 0.8020 (mtmm) REVERT: D 164 GLU cc_start: 0.8618 (mp0) cc_final: 0.8213 (mp0) REVERT: E 104 MET cc_start: 0.9057 (mmt) cc_final: 0.8653 (mmm) REVERT: E 120 GLU cc_start: 0.8225 (mt-10) cc_final: 0.7880 (mm-30) REVERT: E 161 GLN cc_start: 0.8771 (tt0) cc_final: 0.8146 (tt0) REVERT: E 171 ILE cc_start: 0.7979 (OUTLIER) cc_final: 0.7759 (tt) REVERT: E 192 GLN cc_start: 0.8300 (mm110) cc_final: 0.7792 (mm110) REVERT: E 243 GLU cc_start: 0.8074 (mp0) cc_final: 0.7808 (mp0) REVERT: G 18 TYR cc_start: 0.8920 (t80) cc_final: 0.8635 (t80) REVERT: G 32 TYR cc_start: 0.7712 (t80) cc_final: 0.7499 (t80) REVERT: G 59 GLU cc_start: 0.8361 (tp30) cc_final: 0.7865 (tm-30) REVERT: J 36 GLU cc_start: 0.8673 (pp20) cc_final: 0.8404 (tm-30) REVERT: J 41 LEU cc_start: 0.9363 (tp) cc_final: 0.8842 (tp) REVERT: K 25 MET cc_start: 0.8216 (pmm) cc_final: 0.7374 (pmm) REVERT: K 73 GLN cc_start: 0.8633 (tp-100) cc_final: 0.8035 (mm110) REVERT: K 90 GLU cc_start: 0.8891 (mm-30) cc_final: 0.8376 (mm-30) REVERT: K 95 GLU cc_start: 0.8229 (tp30) cc_final: 0.7722 (tm-30) REVERT: O 38 SER cc_start: 0.9084 (m) cc_final: 0.8622 (t) REVERT: V 140 ILE cc_start: 0.8799 (mt) cc_final: 0.8303 (tt) REVERT: V 581 ASP cc_start: 0.8863 (t0) cc_final: 0.7568 (p0) REVERT: V 798 MET cc_start: 0.9072 (mtp) cc_final: 0.8805 (mtt) REVERT: W 18 GLU cc_start: 0.9057 (OUTLIER) cc_final: 0.8438 (tp30) REVERT: W 30 ARG cc_start: 0.8956 (ttm-80) cc_final: 0.8528 (ttm-80) REVERT: W 61 GLU cc_start: 0.8711 (pm20) cc_final: 0.7972 (pm20) REVERT: W 66 ASP cc_start: 0.8716 (m-30) cc_final: 0.8448 (m-30) REVERT: W 71 GLU cc_start: 0.8607 (tp30) cc_final: 0.7895 (tp30) REVERT: W 125 ASP cc_start: 0.8736 (m-30) cc_final: 0.8289 (t70) REVERT: W 164 GLU cc_start: 0.7898 (mp0) cc_final: 0.7143 (mp0) REVERT: X 18 GLU cc_start: 0.8410 (tm-30) cc_final: 0.8040 (tm-30) REVERT: X 40 GLU cc_start: 0.8755 (pt0) cc_final: 0.8268 (pm20) REVERT: X 56 GLU cc_start: 0.7510 (tp30) cc_final: 0.7275 (tp30) REVERT: X 71 GLU cc_start: 0.8789 (tp30) cc_final: 0.8433 (tp30) REVERT: X 164 GLU cc_start: 0.8547 (mp0) cc_final: 0.8236 (mp0) REVERT: Y 104 MET cc_start: 0.8973 (mmt) cc_final: 0.8765 (mmm) REVERT: Y 192 GLN cc_start: 0.8377 (mm110) cc_final: 0.7800 (mm110) REVERT: Z 25 MET cc_start: 0.8318 (mpp) cc_final: 0.8105 (mpp) REVERT: Z 113 MET cc_start: 0.8553 (tmm) cc_final: 0.7879 (tmm) REVERT: Z 125 PHE cc_start: 0.7696 (OUTLIER) cc_final: 0.6403 (p90) REVERT: 0 25 MET cc_start: 0.7903 (mtm) cc_final: 0.7620 (mtm) REVERT: 0 32 TYR cc_start: 0.7855 (t80) cc_final: 0.7627 (t80) REVERT: 0 36 GLU cc_start: 0.8337 (mt-10) cc_final: 0.7982 (mm-30) REVERT: 0 59 GLU cc_start: 0.8418 (tp30) cc_final: 0.8000 (tm-30) REVERT: 0 129 GLU cc_start: 0.8581 (pm20) cc_final: 0.7783 (pm20) REVERT: 1 25 MET cc_start: 0.7650 (mmm) cc_final: 0.7379 (mmm) REVERT: 1 128 MET cc_start: 0.8955 (OUTLIER) cc_final: 0.8583 (mtp) REVERT: 2 18 TYR cc_start: 0.9001 (t80) cc_final: 0.8620 (t80) REVERT: 2 25 MET cc_start: 0.8397 (pmm) cc_final: 0.7952 (pmm) REVERT: 2 95 GLU cc_start: 0.8106 (tp30) cc_final: 0.7667 (tm-30) REVERT: 2 140 GLN cc_start: 0.8081 (mp10) cc_final: 0.7658 (mp10) REVERT: 7 277 MET cc_start: 0.8524 (mmm) cc_final: 0.8028 (mmm) outliers start: 63 outliers final: 26 residues processed: 469 average time/residue: 0.6234 time to fit residues: 505.8276 Evaluate side-chains 428 residues out of total 7395 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 35 poor density : 393 time to evaluate : 6.114 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 40 LEU Chi-restraints excluded: chain L residue 120 GLU Chi-restraints excluded: chain L residue 137 ILE 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 C residue 18 GLU Chi-restraints excluded: chain D residue 175 THR Chi-restraints excluded: chain E residue 40 LEU Chi-restraints excluded: chain E residue 137 ILE Chi-restraints excluded: chain E residue 171 ILE Chi-restraints excluded: chain E residue 217 GLU Chi-restraints excluded: chain E residue 218 MET Chi-restraints excluded: chain F residue 112 LEU Chi-restraints excluded: chain F residue 114 THR Chi-restraints excluded: chain J residue 122 VAL Chi-restraints excluded: chain N residue 44 LEU Chi-restraints excluded: chain W residue 18 GLU Chi-restraints excluded: chain Z residue 125 PHE 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 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: 5.9990 chunk 452 optimal weight: 3.9990 chunk 11 optimal weight: 4.9990 chunk 593 optimal weight: 9.9990 chunk 329 optimal weight: 5.9990 chunk 680 optimal weight: 4.9990 chunk 551 optimal weight: 3.9990 chunk 0 optimal weight: 10.0000 chunk 407 optimal weight: 9.9990 chunk 715 optimal weight: 3.9990 chunk 201 optimal weight: 6.9990 overall best weight: 4.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 161 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 631 GLN S 57 ASN ** k 176 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 161 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 631 GLN D 9 ASN J 57 ASN M 10 GLN ** P 176 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 113 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** U 318 HIS ** V 161 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** V 800 GLN 5 11 GLN ** 6 176 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8112 moved from start: 0.2593 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.083 67635 Z= 0.426 Angle : 0.619 11.263 91917 Z= 0.327 Chirality : 0.047 0.175 10497 Planarity : 0.004 0.048 11952 Dihedral : 5.148 22.009 9228 Min Nonbonded Distance : 2.434 Molprobity Statistics. All-atom Clashscore : 3.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.29 % Favored : 96.71 % Rotamer: Outliers : 1.30 % Allowed : 6.75 % Favored : 91.95 % 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: -0.44 (0.09), residues: 8400 helix: 0.52 (0.16), residues: 1110 sheet: -0.11 (0.09), residues: 2829 loop : -0.54 (0.09), residues: 4461 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.002 TRP p 417 HIS 0.008 0.002 HIS B 207 PHE 0.024 0.002 PHE Y 119 TYR 0.028 0.002 TYR I 62 ARG 0.008 0.001 ARG W 201 *********************** 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 473 residues out of total 7395 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 96 poor density : 377 time to evaluate : 6.175 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: A 140 ILE cc_start: 0.8761 (mt) cc_final: 0.8250 (tt) REVERT: A 682 ASP cc_start: 0.9204 (p0) cc_final: 0.8905 (p0) REVERT: H 56 GLU cc_start: 0.8288 (pm20) cc_final: 0.8047 (pm20) REVERT: H 61 GLU cc_start: 0.8962 (pm20) cc_final: 0.8278 (pm20) REVERT: I 18 GLU cc_start: 0.8629 (tm-30) cc_final: 0.8344 (tm-30) REVERT: I 40 GLU cc_start: 0.8905 (pt0) cc_final: 0.8112 (pm20) REVERT: I 62 TYR cc_start: 0.8651 (t80) cc_final: 0.8383 (t80) REVERT: I 71 GLU cc_start: 0.8970 (tp30) cc_final: 0.8645 (tp30) REVERT: I 78 TYR cc_start: 0.8960 (m-80) cc_final: 0.8675 (m-10) REVERT: I 87 GLU cc_start: 0.9179 (mm-30) cc_final: 0.8910 (mm-30) REVERT: I 122 LYS cc_start: 0.8554 (mttt) cc_final: 0.8186 (mtmm) REVERT: L 104 MET cc_start: 0.8818 (mmt) cc_final: 0.8391 (mmm) REVERT: L 171 ILE cc_start: 0.8068 (OUTLIER) cc_final: 0.7773 (mt) REVERT: L 190 GLN cc_start: 0.8922 (mt0) cc_final: 0.8721 (mt0) REVERT: L 192 GLN cc_start: 0.8284 (mm110) cc_final: 0.7897 (mm110) REVERT: R 59 GLU cc_start: 0.8373 (tp30) cc_final: 0.8126 (tp30) REVERT: R 108 TYR cc_start: 0.8548 (m-80) cc_final: 0.8073 (m-80) REVERT: S 25 MET cc_start: 0.7704 (mmm) cc_final: 0.7413 (mmm) REVERT: S 36 GLU cc_start: 0.8779 (pm20) cc_final: 0.8535 (pm20) REVERT: S 128 MET cc_start: 0.9072 (mtp) cc_final: 0.8780 (mtp) REVERT: T 25 MET cc_start: 0.8247 (pmm) cc_final: 0.7195 (pmm) REVERT: T 73 GLN cc_start: 0.8683 (tp-100) cc_final: 0.8123 (mm110) REVERT: T 90 GLU cc_start: 0.8919 (mm-30) cc_final: 0.8408 (mm-30) REVERT: T 95 GLU cc_start: 0.8211 (tp30) cc_final: 0.7652 (tm-30) REVERT: T 113 MET cc_start: 0.8613 (OUTLIER) cc_final: 0.8356 (ttm) REVERT: k 158 ASP cc_start: 0.8516 (m-30) cc_final: 0.8231 (m-30) REVERT: p 277 MET cc_start: 0.8345 (mmm) cc_final: 0.7746 (mmm) REVERT: B 527 MET cc_start: 0.9317 (mtm) cc_final: 0.9075 (mtm) REVERT: C 18 GLU cc_start: 0.9031 (tt0) cc_final: 0.8451 (tp30) REVERT: C 30 ARG cc_start: 0.9042 (ttm-80) cc_final: 0.8234 (ttm-80) REVERT: C 46 GLN cc_start: 0.8373 (tm-30) cc_final: 0.8100 (tm-30) REVERT: C 56 GLU cc_start: 0.8315 (pm20) cc_final: 0.8053 (pm20) REVERT: C 61 GLU cc_start: 0.9091 (pm20) cc_final: 0.8452 (pm20) REVERT: C 66 ASP cc_start: 0.8946 (t0) cc_final: 0.8565 (t0) REVERT: C 71 GLU cc_start: 0.8853 (tp30) cc_final: 0.8072 (tp30) REVERT: C 125 ASP cc_start: 0.8626 (m-30) cc_final: 0.8297 (m-30) REVERT: D 1 MET cc_start: 0.8937 (tpp) cc_final: 0.8559 (tpp) REVERT: D 18 GLU cc_start: 0.8623 (tm-30) cc_final: 0.8076 (tp30) REVERT: D 40 GLU cc_start: 0.9001 (pt0) cc_final: 0.8335 (pm20) REVERT: D 71 GLU cc_start: 0.8827 (tp30) cc_final: 0.8564 (tp30) REVERT: D 122 LYS cc_start: 0.8347 (mttt) cc_final: 0.8107 (mtmm) REVERT: D 164 GLU cc_start: 0.8691 (mp0) cc_final: 0.8239 (mp0) REVERT: E 104 MET cc_start: 0.9084 (mmt) cc_final: 0.8637 (mmm) REVERT: E 161 GLN cc_start: 0.9012 (tt0) cc_final: 0.8385 (tt0) REVERT: E 171 ILE cc_start: 0.8010 (OUTLIER) cc_final: 0.7653 (tt) REVERT: E 190 GLN cc_start: 0.8778 (mt0) cc_final: 0.8530 (mt0) REVERT: E 192 GLN cc_start: 0.8465 (mm110) cc_final: 0.8061 (mm110) REVERT: G 18 TYR cc_start: 0.8923 (t80) cc_final: 0.8720 (t80) REVERT: G 32 TYR cc_start: 0.7812 (t80) cc_final: 0.7544 (t80) REVERT: G 59 GLU cc_start: 0.8406 (tp30) cc_final: 0.8065 (tm-30) REVERT: J 36 GLU cc_start: 0.8706 (pp20) cc_final: 0.8389 (tm-30) REVERT: J 41 LEU cc_start: 0.9400 (tp) cc_final: 0.8941 (tp) REVERT: K 25 MET cc_start: 0.8170 (pmm) cc_final: 0.7255 (pmm) REVERT: K 90 GLU cc_start: 0.8952 (mm-30) cc_final: 0.8411 (mm-30) REVERT: K 95 GLU cc_start: 0.8309 (tp30) cc_final: 0.7756 (tm-30) REVERT: O 38 SER cc_start: 0.9182 (m) cc_final: 0.8712 (t) REVERT: U 277 MET cc_start: 0.8457 (mmm) cc_final: 0.8033 (tpp) REVERT: V 140 ILE cc_start: 0.8632 (mt) cc_final: 0.8040 (tt) REVERT: W 18 GLU cc_start: 0.9147 (OUTLIER) cc_final: 0.8473 (tp30) REVERT: W 30 ARG cc_start: 0.9001 (ttm-80) cc_final: 0.8542 (ttm-80) REVERT: W 61 GLU cc_start: 0.8784 (pm20) cc_final: 0.8208 (pm20) REVERT: W 71 GLU cc_start: 0.8626 (tp30) cc_final: 0.7906 (tp30) REVERT: W 164 GLU cc_start: 0.8128 (mp0) cc_final: 0.7115 (mp0) REVERT: X 12 LEU cc_start: 0.8598 (mt) cc_final: 0.8311 (mp) REVERT: X 18 GLU cc_start: 0.8644 (tm-30) cc_final: 0.8260 (tm-30) REVERT: X 40 GLU cc_start: 0.8748 (pt0) cc_final: 0.8339 (pm20) REVERT: X 56 GLU cc_start: 0.7509 (tp30) cc_final: 0.7278 (tp30) REVERT: X 71 GLU cc_start: 0.8883 (tp30) cc_final: 0.8508 (tp30) REVERT: X 164 GLU cc_start: 0.8653 (mp0) cc_final: 0.8170 (mp0) REVERT: Y 40 LEU cc_start: 0.8248 (OUTLIER) cc_final: 0.7915 (tt) REVERT: Y 104 MET cc_start: 0.9004 (mmt) cc_final: 0.8775 (mmm) REVERT: Y 171 ILE cc_start: 0.8203 (OUTLIER) cc_final: 0.7899 (mt) REVERT: Y 190 GLN cc_start: 0.8744 (mt0) cc_final: 0.8463 (mt0) REVERT: Y 192 GLN cc_start: 0.8370 (mm110) cc_final: 0.8052 (mm110) REVERT: Z 25 MET cc_start: 0.8276 (mpp) cc_final: 0.7582 (mpp) REVERT: Z 41 LEU cc_start: 0.9447 (OUTLIER) cc_final: 0.9151 (mm) REVERT: Z 113 MET cc_start: 0.8599 (tmm) cc_final: 0.8264 (tmm) REVERT: 0 25 MET cc_start: 0.7880 (mtm) cc_final: 0.7516 (mtm) REVERT: 0 32 TYR cc_start: 0.7999 (t80) cc_final: 0.7708 (t80) REVERT: 0 36 GLU cc_start: 0.8363 (mt-10) cc_final: 0.8019 (mm-30) REVERT: 0 59 GLU cc_start: 0.8444 (tp30) cc_final: 0.8020 (tm-30) REVERT: 0 129 GLU cc_start: 0.8669 (pm20) cc_final: 0.8102 (pm20) REVERT: 1 25 MET cc_start: 0.7510 (mmm) cc_final: 0.7191 (mmm) REVERT: 1 57 ASN cc_start: 0.9223 (t0) cc_final: 0.8955 (t0) REVERT: 1 128 MET cc_start: 0.9052 (OUTLIER) cc_final: 0.8637 (mtp) REVERT: 2 18 TYR cc_start: 0.9044 (t80) cc_final: 0.8600 (t80) REVERT: 2 25 MET cc_start: 0.8535 (pmm) cc_final: 0.8101 (pmm) REVERT: 2 95 GLU cc_start: 0.8159 (tp30) cc_final: 0.7693 (tm-30) REVERT: 2 129 GLU cc_start: 0.8325 (pm20) cc_final: 0.8096 (pm20) REVERT: 2 140 GLN cc_start: 0.8227 (mp10) cc_final: 0.7870 (mp10) outliers start: 96 outliers final: 52 residues processed: 443 average time/residue: 0.6356 time to fit residues: 489.5920 Evaluate side-chains 426 residues out of total 7395 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 60 poor density : 366 time to evaluate : 6.060 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 104 VAL Chi-restraints excluded: chain H residue 60 ASP Chi-restraints excluded: chain I residue 61 GLU Chi-restraints excluded: chain I residue 70 LEU Chi-restraints excluded: chain I residue 111 MET Chi-restraints excluded: chain I residue 175 THR Chi-restraints excluded: chain L residue 11 VAL Chi-restraints excluded: chain L residue 40 LEU 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 171 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 Q residue 118 ILE Chi-restraints excluded: chain R residue 113 MET Chi-restraints excluded: chain T residue 22 MET Chi-restraints excluded: chain T residue 113 MET Chi-restraints excluded: chain T residue 128 MET Chi-restraints excluded: chain k residue 164 LEU 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 12 LEU Chi-restraints excluded: chain D residue 70 LEU Chi-restraints excluded: chain D residue 175 THR Chi-restraints excluded: chain E residue 40 LEU Chi-restraints excluded: chain E residue 116 CYS Chi-restraints excluded: chain E residue 137 ILE Chi-restraints excluded: chain E residue 171 ILE Chi-restraints excluded: chain E residue 217 GLU Chi-restraints excluded: chain E residue 218 MET Chi-restraints excluded: chain F residue 112 LEU Chi-restraints excluded: chain F residue 128 MET Chi-restraints excluded: chain J residue 7 VAL Chi-restraints excluded: chain J residue 122 VAL Chi-restraints excluded: chain N residue 40 THR Chi-restraints excluded: chain O residue 45 THR Chi-restraints excluded: chain P residue 164 LEU 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 40 LEU Chi-restraints excluded: chain Y residue 116 CYS Chi-restraints excluded: chain Y residue 171 ILE Chi-restraints excluded: chain Y residue 236 MET Chi-restraints excluded: chain Z residue 41 LEU Chi-restraints excluded: chain 0 residue 128 MET 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 12 VAL Chi-restraints excluded: chain 2 residue 128 MET Chi-restraints excluded: chain 3 residue 10 GLN Chi-restraints excluded: chain 4 residue 45 THR Chi-restraints excluded: chain 5 residue 45 THR Chi-restraints excluded: chain 7 residue 120 MET 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: 20.0000 chunk 718 optimal weight: 4.9990 chunk 157 optimal weight: 9.9990 chunk 468 optimal weight: 2.9990 chunk 196 optimal weight: 0.0060 chunk 798 optimal weight: 0.0980 chunk 662 optimal weight: 7.9990 chunk 369 optimal weight: 0.8980 chunk 66 optimal weight: 5.9990 chunk 264 optimal weight: 0.5980 chunk 419 optimal weight: 2.9990 overall best weight: 0.9198 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 591 ASN A 597 GLN S 57 ASN k 152 ASN ** k 176 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** p 87 GLN B 597 GLN J 57 ASN ** P 176 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 113 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** V 631 GLN ** 6 176 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 7 87 GLN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8067 moved from start: 0.2792 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.036 67635 Z= 0.134 Angle : 0.498 10.786 91917 Z= 0.265 Chirality : 0.044 0.150 10497 Planarity : 0.003 0.045 11952 Dihedral : 4.693 21.093 9228 Min Nonbonded Distance : 2.473 Molprobity Statistics. All-atom Clashscore : 3.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.85 % Favored : 98.15 % Rotamer: Outliers : 0.97 % Allowed : 7.76 % Favored : 91.26 % 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: -0.21 (0.09), residues: 8400 helix: 0.82 (0.16), residues: 1095 sheet: -0.05 (0.09), residues: 2922 loop : -0.36 (0.09), residues: 4383 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP p 417 HIS 0.004 0.001 HIS U 318 PHE 0.012 0.001 PHE V 421 TYR 0.019 0.001 TYR I 62 ARG 0.008 0.000 ARG P 146 *********************** REFINEMENT MACRO_CYCLE 6 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 471 residues out of total 7395 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 72 poor density : 399 time to evaluate : 6.191 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: A 1 MET cc_start: 0.7673 (tmm) cc_final: 0.7368 (tmm) REVERT: A 140 ILE cc_start: 0.8693 (mt) cc_final: 0.8304 (tt) REVERT: A 682 ASP cc_start: 0.9178 (p0) cc_final: 0.8891 (p0) REVERT: H 1 MET cc_start: 0.7956 (pmm) cc_final: 0.7721 (pmm) REVERT: H 56 GLU cc_start: 0.8265 (pm20) cc_final: 0.8016 (pm20) REVERT: H 61 GLU cc_start: 0.8880 (pm20) cc_final: 0.8153 (pm20) REVERT: H 66 ASP cc_start: 0.9011 (t0) cc_final: 0.8709 (m-30) REVERT: H 164 GLU cc_start: 0.8269 (mp0) cc_final: 0.7645 (mp0) REVERT: I 11 GLU cc_start: 0.8703 (pm20) cc_final: 0.8439 (pm20) REVERT: I 12 LEU cc_start: 0.8512 (mt) cc_final: 0.8052 (mp) REVERT: I 18 GLU cc_start: 0.8470 (tm-30) cc_final: 0.8144 (tm-30) REVERT: I 40 GLU cc_start: 0.8843 (pt0) cc_final: 0.8101 (pm20) REVERT: I 46 GLN cc_start: 0.8729 (tm-30) cc_final: 0.8509 (tm-30) REVERT: I 71 GLU cc_start: 0.8965 (tp30) cc_final: 0.8646 (tp30) REVERT: I 78 TYR cc_start: 0.8934 (m-80) cc_final: 0.8639 (m-10) REVERT: I 87 GLU cc_start: 0.9150 (mm-30) cc_final: 0.8857 (mm-30) REVERT: I 111 MET cc_start: 0.7790 (OUTLIER) cc_final: 0.7269 (ptm) REVERT: I 122 LYS cc_start: 0.8553 (mttt) cc_final: 0.8177 (mtmm) REVERT: L 104 MET cc_start: 0.8832 (mmt) cc_final: 0.8416 (mmm) REVERT: L 161 GLN cc_start: 0.8819 (tt0) cc_final: 0.8184 (tt0) REVERT: L 171 ILE cc_start: 0.7983 (OUTLIER) cc_final: 0.7720 (tt) REVERT: L 192 GLN cc_start: 0.8155 (mm110) cc_final: 0.7707 (mm110) REVERT: Q 113 MET cc_start: 0.8304 (tmm) cc_final: 0.7994 (tmm) REVERT: R 59 GLU cc_start: 0.8411 (tp30) cc_final: 0.7979 (tm-30) REVERT: R 108 TYR cc_start: 0.8308 (m-80) cc_final: 0.7880 (m-80) REVERT: R 129 GLU cc_start: 0.8680 (pm20) cc_final: 0.8050 (pm20) REVERT: S 36 GLU cc_start: 0.8771 (pm20) cc_final: 0.8338 (tm-30) REVERT: S 128 MET cc_start: 0.9068 (mtp) cc_final: 0.8769 (mtp) REVERT: T 25 MET cc_start: 0.8154 (pmm) cc_final: 0.7112 (pmm) REVERT: T 36 GLU cc_start: 0.8937 (pm20) cc_final: 0.8709 (mp0) REVERT: T 90 GLU cc_start: 0.8872 (mm-30) cc_final: 0.8360 (mm-30) REVERT: T 95 GLU cc_start: 0.8169 (tp30) cc_final: 0.7618 (tm-30) REVERT: T 113 MET cc_start: 0.8527 (OUTLIER) cc_final: 0.8290 (ttm) REVERT: k 158 ASP cc_start: 0.8519 (m-30) cc_final: 0.8231 (m-30) REVERT: p 277 MET cc_start: 0.8268 (mmm) cc_final: 0.7669 (mmm) REVERT: B 494 LEU cc_start: 0.8162 (OUTLIER) cc_final: 0.7761 (tt) REVERT: C 18 GLU cc_start: 0.9007 (OUTLIER) cc_final: 0.8452 (tp30) REVERT: C 40 GLU cc_start: 0.7923 (mt-10) cc_final: 0.7611 (mt-10) REVERT: C 46 GLN cc_start: 0.8325 (tm-30) cc_final: 0.8101 (tm-30) REVERT: C 61 GLU cc_start: 0.9043 (pm20) cc_final: 0.8639 (mp0) REVERT: C 71 GLU cc_start: 0.8785 (tp30) cc_final: 0.7989 (tp30) REVERT: C 164 GLU cc_start: 0.8428 (mp0) cc_final: 0.7793 (mp0) REVERT: D 18 GLU cc_start: 0.8523 (tm-30) cc_final: 0.7977 (tp30) REVERT: D 40 GLU cc_start: 0.8978 (pt0) cc_final: 0.8337 (pm20) REVERT: D 56 GLU cc_start: 0.7945 (tp30) cc_final: 0.7551 (tp30) REVERT: D 71 GLU cc_start: 0.8911 (tp30) cc_final: 0.8654 (tp30) REVERT: D 122 LYS cc_start: 0.8357 (mttt) cc_final: 0.8135 (mtmm) REVERT: D 164 GLU cc_start: 0.8597 (mp0) cc_final: 0.8186 (mp0) REVERT: E 104 MET cc_start: 0.9086 (mmt) cc_final: 0.8671 (mmm) REVERT: E 120 GLU cc_start: 0.8357 (OUTLIER) cc_final: 0.8048 (mm-30) REVERT: E 161 GLN cc_start: 0.8940 (tt0) cc_final: 0.8325 (tt0) REVERT: E 171 ILE cc_start: 0.7979 (OUTLIER) cc_final: 0.7754 (tt) REVERT: E 190 GLN cc_start: 0.8690 (mt0) cc_final: 0.8422 (mt0) REVERT: E 192 GLN cc_start: 0.8363 (mm110) cc_final: 0.7966 (mm110) REVERT: F 25 MET cc_start: 0.8310 (mpp) cc_final: 0.7205 (mpp) REVERT: G 18 TYR cc_start: 0.8858 (t80) cc_final: 0.8536 (t80) REVERT: G 32 TYR cc_start: 0.7863 (t80) cc_final: 0.7583 (t80) REVERT: G 59 GLU cc_start: 0.8296 (tp30) cc_final: 0.7827 (tm-30) REVERT: J 36 GLU cc_start: 0.8700 (pp20) cc_final: 0.8308 (tm-30) REVERT: J 41 LEU cc_start: 0.9398 (tp) cc_final: 0.8901 (tp) REVERT: K 25 MET cc_start: 0.8226 (pmm) cc_final: 0.7410 (pmm) REVERT: K 90 GLU cc_start: 0.8906 (mm-30) cc_final: 0.8390 (mm-30) REVERT: K 95 GLU cc_start: 0.8254 (tp30) cc_final: 0.7668 (tm-30) REVERT: K 134 ILE cc_start: 0.7670 (OUTLIER) cc_final: 0.7435 (tt) REVERT: O 38 SER cc_start: 0.9152 (m) cc_final: 0.8651 (t) REVERT: V 140 ILE cc_start: 0.8794 (mt) cc_final: 0.8423 (tt) REVERT: V 581 ASP cc_start: 0.8986 (t0) cc_final: 0.7694 (p0) REVERT: W 18 GLU cc_start: 0.9080 (OUTLIER) cc_final: 0.8475 (tm-30) REVERT: W 30 ARG cc_start: 0.8920 (ttm-80) cc_final: 0.8565 (ttm-80) REVERT: W 46 GLN cc_start: 0.8427 (tm-30) cc_final: 0.8189 (pp30) REVERT: W 61 GLU cc_start: 0.8659 (pm20) cc_final: 0.8074 (pm20) REVERT: W 71 GLU cc_start: 0.8607 (tp30) cc_final: 0.7869 (tp30) REVERT: W 125 ASP cc_start: 0.8735 (m-30) cc_final: 0.8416 (m-30) REVERT: W 164 GLU cc_start: 0.8069 (mp0) cc_final: 0.7159 (mp0) REVERT: X 18 GLU cc_start: 0.8606 (tm-30) cc_final: 0.8180 (tm-30) REVERT: X 40 GLU cc_start: 0.8827 (pt0) cc_final: 0.8394 (pm20) REVERT: X 56 GLU cc_start: 0.7543 (tp30) cc_final: 0.7274 (tp30) REVERT: X 71 GLU cc_start: 0.8818 (tp30) cc_final: 0.8414 (tp30) REVERT: X 164 GLU cc_start: 0.8591 (mp0) cc_final: 0.8201 (mp0) REVERT: Y 40 LEU cc_start: 0.8238 (OUTLIER) cc_final: 0.7887 (tt) REVERT: Y 104 MET cc_start: 0.8941 (mmt) cc_final: 0.8731 (mmm) REVERT: Y 161 GLN cc_start: 0.8961 (tt0) cc_final: 0.8328 (tt0) REVERT: Y 190 GLN cc_start: 0.8721 (mt0) cc_final: 0.8323 (mt0) REVERT: Y 192 GLN cc_start: 0.8267 (mm110) cc_final: 0.7850 (mm110) REVERT: Z 25 MET cc_start: 0.8174 (mpp) cc_final: 0.7728 (mpp) REVERT: Z 113 MET cc_start: 0.8665 (tmm) cc_final: 0.8056 (tmm) REVERT: 0 25 MET cc_start: 0.7766 (mtm) cc_final: 0.7438 (mtm) REVERT: 0 32 TYR cc_start: 0.7917 (t80) cc_final: 0.7662 (t80) REVERT: 0 36 GLU cc_start: 0.8326 (mt-10) cc_final: 0.7998 (mm-30) REVERT: 0 59 GLU cc_start: 0.8452 (tp30) cc_final: 0.8020 (tm-30) REVERT: 0 128 MET cc_start: 0.7912 (OUTLIER) cc_final: 0.7696 (ptp) REVERT: 0 129 GLU cc_start: 0.8686 (pm20) cc_final: 0.8028 (pm20) REVERT: 1 25 MET cc_start: 0.7623 (mmm) cc_final: 0.7345 (mmm) REVERT: 1 57 ASN cc_start: 0.9180 (t0) cc_final: 0.8902 (t0) REVERT: 1 128 MET cc_start: 0.8971 (OUTLIER) cc_final: 0.8588 (mtp) REVERT: 2 18 TYR cc_start: 0.9008 (t80) cc_final: 0.8566 (t80) REVERT: 2 25 MET cc_start: 0.8480 (pmm) cc_final: 0.8088 (pmm) REVERT: 2 95 GLU cc_start: 0.8150 (tp30) cc_final: 0.7656 (tm-30) REVERT: 2 140 GLN cc_start: 0.8200 (mp10) cc_final: 0.7893 (mp10) REVERT: 7 277 MET cc_start: 0.8541 (mmm) cc_final: 0.8035 (mmm) outliers start: 72 outliers final: 39 residues processed: 448 average time/residue: 0.6322 time to fit residues: 492.0943 Evaluate side-chains 431 residues out of total 7395 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 51 poor density : 380 time to evaluate : 6.339 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 597 GLN Chi-restraints excluded: chain I residue 111 MET Chi-restraints excluded: chain I residue 175 THR Chi-restraints excluded: chain L residue 32 THR Chi-restraints excluded: chain L residue 40 LEU Chi-restraints excluded: chain L residue 120 GLU Chi-restraints excluded: chain L residue 137 ILE Chi-restraints excluded: chain L residue 171 ILE Chi-restraints excluded: chain L residue 218 MET Chi-restraints excluded: chain Q residue 94 LYS Chi-restraints excluded: chain Q residue 112 LEU Chi-restraints excluded: chain Q residue 118 ILE 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 B residue 48 VAL Chi-restraints excluded: chain B residue 382 VAL Chi-restraints excluded: chain B residue 494 LEU Chi-restraints excluded: chain B residue 530 ILE Chi-restraints excluded: chain C residue 18 GLU Chi-restraints excluded: chain D residue 175 THR Chi-restraints excluded: chain E residue 40 LEU Chi-restraints excluded: chain E residue 120 GLU Chi-restraints excluded: chain E residue 171 ILE Chi-restraints excluded: chain E residue 217 GLU Chi-restraints excluded: chain E residue 218 MET Chi-restraints excluded: chain F residue 112 LEU Chi-restraints excluded: chain F residue 114 THR Chi-restraints excluded: chain F residue 128 MET Chi-restraints excluded: chain J residue 7 VAL Chi-restraints excluded: chain J residue 122 VAL Chi-restraints excluded: chain J residue 138 VAL Chi-restraints excluded: chain K residue 134 ILE Chi-restraints excluded: chain V residue 104 VAL Chi-restraints excluded: chain W residue 18 GLU Chi-restraints excluded: chain W residue 70 LEU Chi-restraints excluded: chain Y residue 40 LEU Chi-restraints excluded: chain Y residue 171 ILE Chi-restraints excluded: chain Y residue 236 MET Chi-restraints excluded: chain Z residue 114 THR Chi-restraints excluded: chain 0 residue 128 MET 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 12 VAL Chi-restraints excluded: chain 2 residue 128 MET Chi-restraints excluded: chain 4 residue 43 GLU Chi-restraints excluded: chain 4 residue 45 THR Chi-restraints excluded: chain 7 residue 285 ARG Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 825 random chunks: chunk 769 optimal weight: 2.9990 chunk 89 optimal weight: 7.9990 chunk 454 optimal weight: 9.9990 chunk 582 optimal weight: 9.9990 chunk 451 optimal weight: 2.9990 chunk 671 optimal weight: 0.7980 chunk 445 optimal weight: 2.9990 chunk 795 optimal weight: 7.9990 chunk 497 optimal weight: 0.7980 chunk 484 optimal weight: 2.9990 chunk 367 optimal weight: 10.0000 overall best weight: 2.1186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 161 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** S 57 ASN p 113 HIS ** B 161 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 597 GLN J 57 ASN ** P 176 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** U 87 GLN ** U 113 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 6 176 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8086 moved from start: 0.2900 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 : 0.514 10.961 91917 Z= 0.272 Chirality : 0.044 0.169 10497 Planarity : 0.003 0.047 11952 Dihedral : 4.619 20.700 9228 Min Nonbonded Distance : 2.452 Molprobity Statistics. All-atom Clashscore : 3.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.42 % Favored : 97.58 % Rotamer: Outliers : 1.14 % Allowed : 8.22 % Favored : 90.64 % 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: -0.28 (0.09), residues: 8400 helix: 0.86 (0.16), residues: 1098 sheet: -0.13 (0.09), residues: 2937 loop : -0.41 (0.09), residues: 4365 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP B 369 HIS 0.004 0.001 HIS U 318 PHE 0.013 0.001 PHE A 421 TYR 0.021 0.001 TYR D 62 ARG 0.009 0.000 ARG W 201 *********************** REFINEMENT MACRO_CYCLE 7 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: 84 poor density : 380 time to evaluate : 6.098 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 140 ILE cc_start: 0.8693 (mt) cc_final: 0.8297 (tt) REVERT: A 682 ASP cc_start: 0.9191 (p0) cc_final: 0.8883 (p0) REVERT: H 56 GLU cc_start: 0.8364 (pm20) cc_final: 0.8132 (pm20) REVERT: H 61 GLU cc_start: 0.8926 (pm20) cc_final: 0.8175 (pm20) REVERT: H 164 GLU cc_start: 0.8368 (mp0) cc_final: 0.7746 (mp0) REVERT: I 11 GLU cc_start: 0.8715 (pm20) cc_final: 0.8430 (pm20) REVERT: I 12 LEU cc_start: 0.8554 (mt) cc_final: 0.7953 (mp) REVERT: I 18 GLU cc_start: 0.8660 (tm-30) cc_final: 0.8320 (tm-30) REVERT: I 40 GLU cc_start: 0.8869 (pt0) cc_final: 0.8140 (pm20) REVERT: I 62 TYR cc_start: 0.8683 (t80) cc_final: 0.8406 (t80) REVERT: I 71 GLU cc_start: 0.8958 (tp30) cc_final: 0.8635 (tp30) REVERT: I 78 TYR cc_start: 0.8949 (m-80) cc_final: 0.8651 (m-10) REVERT: I 87 GLU cc_start: 0.9155 (mm-30) cc_final: 0.8852 (mm-30) REVERT: I 111 MET cc_start: 0.7802 (OUTLIER) cc_final: 0.7308 (ptm) REVERT: I 122 LYS cc_start: 0.8591 (mttt) cc_final: 0.8241 (mtmm) REVERT: L 104 MET cc_start: 0.8843 (mmt) cc_final: 0.8420 (mmm) REVERT: L 161 GLN cc_start: 0.8862 (tt0) cc_final: 0.8186 (tt0) REVERT: L 165 MET cc_start: 0.7095 (mtp) cc_final: 0.6881 (mtp) REVERT: L 171 ILE cc_start: 0.8011 (OUTLIER) cc_final: 0.7727 (mt) REVERT: L 192 GLN cc_start: 0.8239 (mm110) cc_final: 0.7955 (mm110) REVERT: Q 113 MET cc_start: 0.8436 (tmm) cc_final: 0.8068 (tmm) REVERT: R 108 TYR cc_start: 0.8340 (m-80) cc_final: 0.7953 (m-80) REVERT: R 129 GLU cc_start: 0.8671 (pm20) cc_final: 0.8037 (pm20) REVERT: S 36 GLU cc_start: 0.8790 (pm20) cc_final: 0.8346 (tm-30) REVERT: S 128 MET cc_start: 0.9109 (mtp) cc_final: 0.8808 (mtp) REVERT: T 25 MET cc_start: 0.8297 (pmm) cc_final: 0.7156 (pmm) REVERT: T 36 GLU cc_start: 0.8962 (pm20) cc_final: 0.8712 (mp0) REVERT: T 90 GLU cc_start: 0.8899 (mm-30) cc_final: 0.8391 (mm-30) REVERT: T 95 GLU cc_start: 0.8198 (tp30) cc_final: 0.7646 (tm-30) REVERT: T 113 MET cc_start: 0.8575 (OUTLIER) cc_final: 0.8308 (ttm) REVERT: k 158 ASP cc_start: 0.8512 (m-30) cc_final: 0.8225 (m-30) REVERT: p 166 ARG cc_start: 0.8536 (ptp90) cc_final: 0.8031 (ptp90) REVERT: p 277 MET cc_start: 0.8298 (mmm) cc_final: 0.7904 (mmm) REVERT: B 494 LEU cc_start: 0.8268 (OUTLIER) cc_final: 0.7812 (tt) REVERT: C 18 GLU cc_start: 0.8989 (tt0) cc_final: 0.8463 (tp30) REVERT: C 46 GLN cc_start: 0.8381 (tm-30) cc_final: 0.8135 (tm-30) REVERT: C 61 GLU cc_start: 0.9088 (pm20) cc_final: 0.8654 (mp0) REVERT: C 66 ASP cc_start: 0.8951 (t0) cc_final: 0.8422 (t0) REVERT: C 71 GLU cc_start: 0.8865 (tp30) cc_final: 0.8068 (tp30) REVERT: C 125 ASP cc_start: 0.8587 (m-30) cc_final: 0.8278 (m-30) REVERT: C 164 GLU cc_start: 0.8479 (mp0) cc_final: 0.7818 (mp0) REVERT: D 18 GLU cc_start: 0.8560 (tm-30) cc_final: 0.7999 (tp30) REVERT: D 40 GLU cc_start: 0.8970 (pt0) cc_final: 0.8360 (pm20) REVERT: D 56 GLU cc_start: 0.7945 (tp30) cc_final: 0.7618 (tp30) REVERT: D 71 GLU cc_start: 0.8879 (tp30) cc_final: 0.8675 (tp30) REVERT: D 122 LYS cc_start: 0.8370 (mttt) cc_final: 0.8165 (mtmm) REVERT: D 164 GLU cc_start: 0.8651 (mp0) cc_final: 0.8212 (mp0) REVERT: E 104 MET cc_start: 0.9066 (mmt) cc_final: 0.8658 (mmm) REVERT: E 161 GLN cc_start: 0.8967 (tt0) cc_final: 0.8350 (tt0) REVERT: E 171 ILE cc_start: 0.7994 (OUTLIER) cc_final: 0.7730 (tt) REVERT: E 192 GLN cc_start: 0.8419 (mm110) cc_final: 0.8091 (mm110) REVERT: F 25 MET cc_start: 0.8354 (mpp) cc_final: 0.7837 (mpp) REVERT: G 18 TYR cc_start: 0.8888 (t80) cc_final: 0.8582 (t80) REVERT: G 32 TYR cc_start: 0.7795 (t80) cc_final: 0.7521 (t80) REVERT: G 59 GLU cc_start: 0.8221 (tp30) cc_final: 0.7815 (tm-30) REVERT: J 36 GLU cc_start: 0.8669 (pp20) cc_final: 0.8207 (tm-30) REVERT: J 41 LEU cc_start: 0.9388 (tp) cc_final: 0.8917 (tp) REVERT: K 25 MET cc_start: 0.8188 (pmm) cc_final: 0.7261 (pmm) REVERT: K 36 GLU cc_start: 0.8372 (mp0) cc_final: 0.8111 (mp0) REVERT: K 90 GLU cc_start: 0.8936 (mm-30) cc_final: 0.8393 (mm-30) REVERT: K 95 GLU cc_start: 0.8261 (tp30) cc_final: 0.7661 (tm-30) REVERT: K 134 ILE cc_start: 0.7700 (OUTLIER) cc_final: 0.7444 (tt) REVERT: O 38 SER cc_start: 0.9178 (m) cc_final: 0.8719 (t) REVERT: U 277 MET cc_start: 0.8272 (mmm) cc_final: 0.7828 (tpp) REVERT: V 140 ILE cc_start: 0.8792 (mt) cc_final: 0.8416 (tt) REVERT: W 18 GLU cc_start: 0.9087 (OUTLIER) cc_final: 0.8500 (tp30) REVERT: W 30 ARG cc_start: 0.8978 (ttm-80) cc_final: 0.8572 (ttm-80) REVERT: W 61 GLU cc_start: 0.8747 (pm20) cc_final: 0.8107 (pm20) REVERT: W 164 GLU cc_start: 0.8155 (mp0) cc_final: 0.7211 (mp0) REVERT: X 18 GLU cc_start: 0.8644 (tm-30) cc_final: 0.8204 (tm-30) REVERT: X 40 GLU cc_start: 0.8827 (pt0) cc_final: 0.8409 (pm20) REVERT: X 56 GLU cc_start: 0.7522 (tp30) cc_final: 0.7259 (tp30) REVERT: X 71 GLU cc_start: 0.8881 (tp30) cc_final: 0.8485 (tp30) REVERT: X 164 GLU cc_start: 0.8631 (mp0) cc_final: 0.8235 (mp0) REVERT: Y 40 LEU cc_start: 0.8261 (OUTLIER) cc_final: 0.7927 (tt) REVERT: Y 104 MET cc_start: 0.8935 (mmt) cc_final: 0.8721 (mmm) REVERT: Y 161 GLN cc_start: 0.8957 (tt0) cc_final: 0.8370 (tt0) REVERT: Y 190 GLN cc_start: 0.8739 (mt0) cc_final: 0.8463 (mt0) REVERT: Y 192 GLN cc_start: 0.8340 (mm110) cc_final: 0.7974 (mm110) REVERT: Z 25 MET cc_start: 0.8263 (mpp) cc_final: 0.7611 (mpp) REVERT: Z 113 MET cc_start: 0.8608 (tmm) cc_final: 0.7925 (tmm) REVERT: 0 25 MET cc_start: 0.7765 (mtm) cc_final: 0.7468 (mtm) REVERT: 0 32 TYR cc_start: 0.7948 (t80) cc_final: 0.7676 (t80) REVERT: 0 36 GLU cc_start: 0.8330 (mt-10) cc_final: 0.7838 (mm-30) REVERT: 0 59 GLU cc_start: 0.8416 (tp30) cc_final: 0.7976 (tm-30) REVERT: 0 128 MET cc_start: 0.7907 (OUTLIER) cc_final: 0.7652 (ptp) REVERT: 0 129 GLU cc_start: 0.8709 (pm20) cc_final: 0.8046 (pm20) REVERT: 1 25 MET cc_start: 0.7460 (mmm) cc_final: 0.7188 (mmm) REVERT: 1 128 MET cc_start: 0.8977 (OUTLIER) cc_final: 0.8599 (mtp) REVERT: 2 18 TYR cc_start: 0.9030 (t80) cc_final: 0.8598 (t80) REVERT: 2 25 MET cc_start: 0.8499 (pmm) cc_final: 0.8122 (pmm) REVERT: 2 95 GLU cc_start: 0.8141 (tp30) cc_final: 0.7648 (tm-30) REVERT: 2 98 LYS cc_start: 0.8560 (tptm) cc_final: 0.8248 (ttmm) REVERT: 2 140 GLN cc_start: 0.8201 (mp10) cc_final: 0.7906 (mp10) outliers start: 84 outliers final: 57 residues processed: 441 average time/residue: 0.6170 time to fit residues: 472.9829 Evaluate side-chains 435 residues out of total 7395 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 67 poor density : 368 time to evaluate : 6.355 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 29 ILE 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 11 VAL Chi-restraints excluded: chain L residue 32 THR Chi-restraints excluded: chain L residue 40 LEU 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 171 ILE Chi-restraints excluded: chain L residue 218 MET Chi-restraints excluded: chain Q residue 112 LEU Chi-restraints excluded: chain Q residue 118 ILE Chi-restraints excluded: chain R residue 113 MET Chi-restraints excluded: chain S residue 138 VAL Chi-restraints excluded: chain T residue 113 MET Chi-restraints excluded: chain T residue 128 MET Chi-restraints excluded: chain e residue 40 THR Chi-restraints excluded: chain k residue 174 LEU Chi-restraints excluded: chain p residue 39 ASP Chi-restraints excluded: chain B residue 48 VAL Chi-restraints excluded: chain B residue 382 VAL Chi-restraints excluded: chain B residue 494 LEU Chi-restraints excluded: chain B residue 530 ILE Chi-restraints excluded: chain B residue 555 LEU Chi-restraints excluded: chain C residue 1 MET Chi-restraints excluded: chain D residue 175 THR Chi-restraints excluded: chain E residue 40 LEU Chi-restraints excluded: chain E residue 137 ILE Chi-restraints excluded: chain E residue 152 THR Chi-restraints excluded: chain E residue 171 ILE Chi-restraints excluded: chain E residue 217 GLU Chi-restraints excluded: chain E residue 218 MET Chi-restraints excluded: chain F residue 112 LEU Chi-restraints excluded: chain F residue 114 THR Chi-restraints excluded: chain F residue 128 MET Chi-restraints excluded: chain J residue 7 VAL Chi-restraints excluded: chain J residue 122 VAL Chi-restraints excluded: chain J residue 138 VAL Chi-restraints excluded: chain K residue 134 ILE Chi-restraints excluded: chain K residue 136 ASP Chi-restraints excluded: chain N residue 40 THR Chi-restraints excluded: chain O residue 45 THR Chi-restraints excluded: chain U residue 401 MET Chi-restraints excluded: chain V residue 104 VAL 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 Y residue 40 LEU Chi-restraints excluded: chain Y residue 171 ILE Chi-restraints excluded: chain Y residue 236 MET Chi-restraints excluded: chain Z residue 114 THR Chi-restraints excluded: chain 0 residue 128 MET 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 1 residue 138 VAL Chi-restraints excluded: chain 2 residue 12 VAL Chi-restraints excluded: chain 2 residue 128 MET Chi-restraints excluded: chain 3 residue 7 ILE Chi-restraints excluded: chain 4 residue 43 GLU Chi-restraints excluded: chain 4 residue 45 THR Chi-restraints excluded: chain 5 residue 32 LEU Chi-restraints excluded: chain 7 residue 120 MET Chi-restraints excluded: chain 7 residue 180 ASP Chi-restraints excluded: chain 7 residue 285 ARG Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 825 random chunks: chunk 491 optimal weight: 6.9990 chunk 317 optimal weight: 5.9990 chunk 474 optimal weight: 9.9990 chunk 239 optimal weight: 0.0070 chunk 156 optimal weight: 7.9990 chunk 154 optimal weight: 0.0070 chunk 505 optimal weight: 3.9990 chunk 541 optimal weight: 20.0000 chunk 393 optimal weight: 0.5980 chunk 74 optimal weight: 0.8980 chunk 625 optimal weight: 7.9990 overall best weight: 1.1018 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 597 GLN S 57 ASN k 152 ASN B 597 GLN J 57 ASN ** P 176 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 113 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 6 176 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8065 moved from start: 0.3081 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.038 67635 Z= 0.144 Angle : 0.493 11.700 91917 Z= 0.260 Chirality : 0.044 0.166 10497 Planarity : 0.003 0.047 11952 Dihedral : 4.334 19.958 9228 Min Nonbonded Distance : 2.440 Molprobity Statistics. All-atom Clashscore : 3.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.89 % Favored : 98.11 % Rotamer: Outliers : 1.07 % Allowed : 8.59 % Favored : 90.34 % 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: -0.11 (0.09), residues: 8400 helix: 1.06 (0.16), residues: 1080 sheet: -0.04 (0.09), residues: 2910 loop : -0.28 (0.09), residues: 4410 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP V 946 HIS 0.004 0.001 HIS U 318 PHE 0.015 0.001 PHE k 148 TYR 0.017 0.001 TYR I 62 ARG 0.008 0.000 ARG P 146 *********************** REFINEMENT MACRO_CYCLE 8 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 476 residues out of total 7395 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 79 poor density : 397 time to evaluate : 6.323 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 1 MET cc_start: 0.7753 (tmm) cc_final: 0.7452 (tmm) REVERT: A 140 ILE cc_start: 0.8652 (mt) cc_final: 0.8288 (tt) REVERT: A 682 ASP cc_start: 0.9182 (p0) cc_final: 0.8878 (p0) REVERT: H 61 GLU cc_start: 0.8904 (pm20) cc_final: 0.8122 (pm20) REVERT: H 66 ASP cc_start: 0.8972 (t0) cc_final: 0.8659 (m-30) REVERT: H 164 GLU cc_start: 0.8336 (mp0) cc_final: 0.7721 (mp0) REVERT: I 11 GLU cc_start: 0.8725 (pm20) cc_final: 0.8443 (pm20) REVERT: I 12 LEU cc_start: 0.8458 (mt) cc_final: 0.7954 (mp) REVERT: I 40 GLU cc_start: 0.8845 (pt0) cc_final: 0.8144 (pm20) REVERT: I 71 GLU cc_start: 0.8982 (tp30) cc_final: 0.8681 (tp30) REVERT: I 78 TYR cc_start: 0.8916 (m-80) cc_final: 0.8614 (m-10) REVERT: I 111 MET cc_start: 0.7752 (OUTLIER) cc_final: 0.7445 (ptm) REVERT: I 122 LYS cc_start: 0.8595 (mttt) cc_final: 0.8170 (mtmm) REVERT: L 104 MET cc_start: 0.8821 (mmt) cc_final: 0.8344 (mmm) REVERT: L 161 GLN cc_start: 0.8782 (tt0) cc_final: 0.8123 (tt0) REVERT: L 171 ILE cc_start: 0.7935 (OUTLIER) cc_final: 0.7633 (tt) REVERT: L 192 GLN cc_start: 0.8250 (mm110) cc_final: 0.7883 (mm110) REVERT: R 59 GLU cc_start: 0.8254 (tp30) cc_final: 0.7895 (tm-30) REVERT: R 108 TYR cc_start: 0.8093 (m-80) cc_final: 0.7625 (m-80) REVERT: S 36 GLU cc_start: 0.8806 (pm20) cc_final: 0.8352 (tm-30) REVERT: T 25 MET cc_start: 0.8154 (pmm) cc_final: 0.7105 (pmm) REVERT: T 36 GLU cc_start: 0.8981 (pm20) cc_final: 0.8559 (mp0) REVERT: T 90 GLU cc_start: 0.8900 (mm-30) cc_final: 0.8444 (mm-30) REVERT: T 95 GLU cc_start: 0.8199 (tp30) cc_final: 0.7663 (tm-30) REVERT: T 113 MET cc_start: 0.8535 (OUTLIER) cc_final: 0.8311 (ttm) REVERT: T 129 GLU cc_start: 0.8146 (pm20) cc_final: 0.7902 (pm20) REVERT: d 43 GLU cc_start: 0.8545 (mt-10) cc_final: 0.8219 (mt-10) REVERT: k 158 ASP cc_start: 0.8538 (m-30) cc_final: 0.8248 (m-30) REVERT: p 166 ARG cc_start: 0.8484 (ptp90) cc_final: 0.7982 (ptp90) REVERT: p 277 MET cc_start: 0.8231 (mmm) cc_final: 0.7746 (mmm) REVERT: B 494 LEU cc_start: 0.8207 (OUTLIER) cc_final: 0.7794 (tt) REVERT: B 597 GLN cc_start: 0.8819 (OUTLIER) cc_final: 0.8482 (pp30) REVERT: C 61 GLU cc_start: 0.9074 (pm20) cc_final: 0.8631 (mp0) REVERT: C 71 GLU cc_start: 0.8819 (tp30) cc_final: 0.8022 (tp30) REVERT: C 164 GLU cc_start: 0.8429 (mp0) cc_final: 0.7767 (mp0) REVERT: D 18 GLU cc_start: 0.8559 (tm-30) cc_final: 0.7980 (tp30) REVERT: D 40 GLU cc_start: 0.8907 (pt0) cc_final: 0.8372 (pm20) REVERT: D 56 GLU cc_start: 0.7953 (tp30) cc_final: 0.7608 (tp30) REVERT: D 71 GLU cc_start: 0.8901 (tp30) cc_final: 0.8646 (tp30) REVERT: D 122 LYS cc_start: 0.8367 (mttt) cc_final: 0.8126 (mtmm) REVERT: D 164 GLU cc_start: 0.8653 (mp0) cc_final: 0.8218 (mp0) REVERT: E 104 MET cc_start: 0.9066 (mmt) cc_final: 0.8674 (mmm) REVERT: E 161 GLN cc_start: 0.8909 (tt0) cc_final: 0.8248 (tt0) REVERT: E 171 ILE cc_start: 0.7988 (OUTLIER) cc_final: 0.7725 (tt) REVERT: E 192 GLN cc_start: 0.8373 (mm110) cc_final: 0.8003 (mm110) REVERT: F 25 MET cc_start: 0.8229 (mpp) cc_final: 0.7314 (mpp) REVERT: G 18 TYR cc_start: 0.8784 (t80) cc_final: 0.8434 (t80) REVERT: G 32 TYR cc_start: 0.7776 (t80) cc_final: 0.7516 (t80) REVERT: G 59 GLU cc_start: 0.8222 (tp30) cc_final: 0.7711 (tm-30) REVERT: J 36 GLU cc_start: 0.8624 (pp20) cc_final: 0.8196 (tm-30) REVERT: J 41 LEU cc_start: 0.9386 (tp) cc_final: 0.8900 (tp) REVERT: K 25 MET cc_start: 0.8218 (pmm) cc_final: 0.7356 (pmm) REVERT: K 36 GLU cc_start: 0.8462 (mp0) cc_final: 0.8196 (mp0) REVERT: K 90 GLU cc_start: 0.8930 (mm-30) cc_final: 0.8477 (mm-30) REVERT: K 95 GLU cc_start: 0.8233 (tp30) cc_final: 0.7629 (tm-30) REVERT: K 134 ILE cc_start: 0.7748 (OUTLIER) cc_final: 0.7508 (tt) REVERT: O 38 SER cc_start: 0.9171 (m) cc_final: 0.8853 (t) REVERT: U 260 GLU cc_start: 0.8476 (mm-30) cc_final: 0.8081 (mm-30) REVERT: V 140 ILE cc_start: 0.8798 (mt) cc_final: 0.8443 (tt) REVERT: V 581 ASP cc_start: 0.8910 (t0) cc_final: 0.7734 (p0) REVERT: V 798 MET cc_start: 0.9123 (mtm) cc_final: 0.8896 (mtp) REVERT: V 892 MET cc_start: 0.9172 (tmm) cc_final: 0.8939 (tmm) REVERT: W 18 GLU cc_start: 0.9050 (OUTLIER) cc_final: 0.8371 (tm-30) REVERT: W 30 ARG cc_start: 0.8953 (ttm-80) cc_final: 0.8616 (ttm-80) REVERT: W 46 GLN cc_start: 0.8412 (tm-30) cc_final: 0.8191 (pp30) REVERT: W 125 ASP cc_start: 0.8771 (m-30) cc_final: 0.8225 (t0) REVERT: W 164 GLU cc_start: 0.8207 (mp0) cc_final: 0.7332 (mp0) REVERT: X 18 GLU cc_start: 0.8648 (tm-30) cc_final: 0.8173 (tm-30) REVERT: X 32 GLU cc_start: 0.7623 (mm-30) cc_final: 0.7148 (tp30) REVERT: X 40 GLU cc_start: 0.8790 (pt0) cc_final: 0.8411 (pm20) REVERT: X 71 GLU cc_start: 0.8835 (tp30) cc_final: 0.8430 (tp30) REVERT: X 164 GLU cc_start: 0.8630 (mp0) cc_final: 0.8238 (mp0) REVERT: Y 40 LEU cc_start: 0.8165 (OUTLIER) cc_final: 0.7843 (tt) REVERT: Y 161 GLN cc_start: 0.8925 (tt0) cc_final: 0.8294 (tt0) REVERT: Y 171 ILE cc_start: 0.8102 (OUTLIER) cc_final: 0.7775 (mt) REVERT: Y 190 GLN cc_start: 0.8717 (mt0) cc_final: 0.8235 (mt0) REVERT: Y 192 GLN cc_start: 0.8244 (mm110) cc_final: 0.7836 (mm110) REVERT: Z 25 MET cc_start: 0.8316 (mpp) cc_final: 0.7696 (mpp) REVERT: Z 113 MET cc_start: 0.8707 (tmm) cc_final: 0.7860 (tmm) REVERT: 0 25 MET cc_start: 0.7687 (mtm) cc_final: 0.7412 (mtm) REVERT: 0 32 TYR cc_start: 0.7957 (t80) cc_final: 0.7663 (t80) REVERT: 0 36 GLU cc_start: 0.8466 (mt-10) cc_final: 0.7953 (mm-30) REVERT: 0 59 GLU cc_start: 0.8469 (tp30) cc_final: 0.7980 (tm-30) REVERT: 0 129 GLU cc_start: 0.8627 (pm20) cc_final: 0.7935 (pm20) REVERT: 1 25 MET cc_start: 0.7440 (mmm) cc_final: 0.7198 (mmm) REVERT: 1 128 MET cc_start: 0.8966 (OUTLIER) cc_final: 0.8405 (mtp) REVERT: 2 18 TYR cc_start: 0.9034 (t80) cc_final: 0.8614 (t80) REVERT: 2 25 MET cc_start: 0.8466 (pmm) cc_final: 0.8109 (pmm) REVERT: 2 95 GLU cc_start: 0.8133 (tp30) cc_final: 0.7666 (tm-30) REVERT: 2 98 LYS cc_start: 0.8573 (tptm) cc_final: 0.8323 (ttmm) REVERT: 2 140 GLN cc_start: 0.8176 (mp10) cc_final: 0.7915 (mp10) REVERT: 3 43 GLU cc_start: 0.8734 (mt-10) cc_final: 0.8250 (pt0) outliers start: 79 outliers final: 52 residues processed: 450 average time/residue: 0.6210 time to fit residues: 485.5126 Evaluate side-chains 438 residues out of total 7395 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 63 poor density : 375 time to evaluate : 6.129 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 48 VAL Chi-restraints excluded: chain A residue 104 VAL Chi-restraints excluded: chain A residue 555 LEU Chi-restraints excluded: chain H residue 29 ILE 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 32 THR Chi-restraints excluded: chain L residue 40 LEU 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 171 ILE Chi-restraints excluded: chain L residue 218 MET Chi-restraints excluded: chain Q residue 112 LEU Chi-restraints excluded: chain Q residue 118 ILE 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 T residue 136 ASP Chi-restraints excluded: chain p residue 39 ASP Chi-restraints excluded: chain p residue 93 MET Chi-restraints excluded: chain B residue 48 VAL Chi-restraints excluded: chain B residue 382 VAL Chi-restraints excluded: chain B residue 494 LEU Chi-restraints excluded: chain B residue 530 ILE Chi-restraints excluded: chain B residue 597 GLN Chi-restraints excluded: chain C residue 18 GLU Chi-restraints excluded: chain D residue 175 THR Chi-restraints excluded: chain E residue 40 LEU Chi-restraints excluded: chain E residue 116 CYS Chi-restraints excluded: chain E residue 152 THR Chi-restraints excluded: chain E residue 171 ILE Chi-restraints excluded: chain E residue 218 MET Chi-restraints excluded: chain F residue 112 LEU Chi-restraints excluded: chain F residue 114 THR Chi-restraints excluded: chain F residue 128 MET Chi-restraints excluded: chain J residue 7 VAL Chi-restraints excluded: chain J residue 122 VAL Chi-restraints excluded: chain J residue 138 VAL Chi-restraints excluded: chain K residue 134 ILE Chi-restraints excluded: chain U residue 133 MET Chi-restraints excluded: chain U residue 401 MET Chi-restraints excluded: chain V residue 104 VAL Chi-restraints excluded: chain V residue 555 LEU 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 Y residue 40 LEU Chi-restraints excluded: chain Y residue 171 ILE Chi-restraints excluded: chain Y residue 236 MET Chi-restraints excluded: chain Z residue 114 THR 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 12 VAL Chi-restraints excluded: chain 2 residue 128 MET Chi-restraints excluded: chain 3 residue 10 GLN Chi-restraints excluded: chain 4 residue 43 GLU Chi-restraints excluded: chain 4 residue 45 THR Chi-restraints excluded: chain 6 residue 171 LEU Chi-restraints excluded: chain 7 residue 180 ASP Chi-restraints excluded: chain 7 residue 285 ARG Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 825 random chunks: chunk 723 optimal weight: 10.0000 chunk 761 optimal weight: 8.9990 chunk 695 optimal weight: 2.9990 chunk 740 optimal weight: 1.9990 chunk 445 optimal weight: 6.9990 chunk 322 optimal weight: 4.9990 chunk 581 optimal weight: 1.9990 chunk 227 optimal weight: 0.9980 chunk 669 optimal weight: 0.8980 chunk 700 optimal weight: 9.9990 chunk 738 optimal weight: 7.9990 overall best weight: 1.7786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 161 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 597 GLN A 631 GLN L 111 ASN S 57 ASN d 10 GLN B 597 GLN J 57 ASN ** P 176 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 113 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 6 176 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8080 moved from start: 0.3140 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 67635 Z= 0.195 Angle : 0.507 12.721 91917 Z= 0.266 Chirality : 0.044 0.164 10497 Planarity : 0.003 0.047 11952 Dihedral : 4.316 19.569 9228 Min Nonbonded Distance : 2.423 Molprobity Statistics. All-atom Clashscore : 3.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.42 % Favored : 97.58 % Rotamer: Outliers : 1.12 % Allowed : 8.61 % Favored : 90.26 % 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: -0.17 (0.09), residues: 8400 helix: 1.00 (0.16), residues: 1098 sheet: -0.05 (0.09), residues: 2892 loop : -0.35 (0.09), residues: 4410 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP B 369 HIS 0.004 0.001 HIS U 318 PHE 0.014 0.001 PHE p 119 TYR 0.026 0.001 TYR X 62 ARG 0.009 0.000 ARG P 146 *********************** REFINEMENT MACRO_CYCLE 9 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 460 residues out of total 7395 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 83 poor density : 377 time to evaluate : 6.246 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 140 ILE cc_start: 0.8597 (mt) cc_final: 0.8203 (tt) REVERT: A 682 ASP cc_start: 0.9180 (p0) cc_final: 0.8877 (p0) REVERT: H 61 GLU cc_start: 0.9053 (pm20) cc_final: 0.8383 (pm20) REVERT: H 164 GLU cc_start: 0.8381 (mp0) cc_final: 0.7753 (mp0) REVERT: I 40 GLU cc_start: 0.8847 (pt0) cc_final: 0.8165 (pm20) REVERT: I 71 GLU cc_start: 0.8944 (tp30) cc_final: 0.8638 (tp30) REVERT: I 78 TYR cc_start: 0.8925 (m-80) cc_final: 0.8628 (m-10) REVERT: I 111 MET cc_start: 0.7765 (OUTLIER) cc_final: 0.7467 (ptm) REVERT: I 122 LYS cc_start: 0.8600 (mttt) cc_final: 0.8079 (mtmm) REVERT: L 104 MET cc_start: 0.8840 (mmt) cc_final: 0.8374 (mmm) REVERT: L 161 GLN cc_start: 0.8833 (tt0) cc_final: 0.8151 (tt0) REVERT: L 171 ILE cc_start: 0.7980 (OUTLIER) cc_final: 0.7682 (tt) REVERT: L 192 GLN cc_start: 0.8312 (mm110) cc_final: 0.7944 (mm110) REVERT: R 59 GLU cc_start: 0.8306 (tp30) cc_final: 0.7938 (tm-30) REVERT: R 108 TYR cc_start: 0.8137 (m-80) cc_final: 0.7632 (m-80) REVERT: S 36 GLU cc_start: 0.8818 (pm20) cc_final: 0.8352 (tm-30) REVERT: T 25 MET cc_start: 0.8147 (pmm) cc_final: 0.7103 (pmm) REVERT: T 36 GLU cc_start: 0.8943 (pm20) cc_final: 0.8592 (mp0) REVERT: T 90 GLU cc_start: 0.8919 (mm-30) cc_final: 0.8423 (mm-30) REVERT: T 95 GLU cc_start: 0.8201 (tp30) cc_final: 0.7657 (tm-30) REVERT: T 113 MET cc_start: 0.8577 (OUTLIER) cc_final: 0.8326 (ttm) REVERT: T 129 GLU cc_start: 0.7909 (pm20) cc_final: 0.7597 (mp0) REVERT: d 43 GLU cc_start: 0.8548 (mt-10) cc_final: 0.8220 (mt-10) REVERT: k 158 ASP cc_start: 0.8536 (m-30) cc_final: 0.8249 (m-30) REVERT: p 166 ARG cc_start: 0.8520 (ptp90) cc_final: 0.7966 (ptp90) REVERT: p 277 MET cc_start: 0.8248 (mmm) cc_final: 0.7845 (mmm) REVERT: B 494 LEU cc_start: 0.8272 (OUTLIER) cc_final: 0.7870 (tt) REVERT: C 18 GLU cc_start: 0.8961 (tt0) cc_final: 0.8525 (tp30) REVERT: C 61 GLU cc_start: 0.9073 (pm20) cc_final: 0.8601 (mp0) REVERT: C 66 ASP cc_start: 0.8956 (t0) cc_final: 0.8428 (t0) REVERT: C 71 GLU cc_start: 0.8841 (tp30) cc_final: 0.8053 (tp30) REVERT: C 164 GLU cc_start: 0.8485 (mp0) cc_final: 0.7803 (mp0) REVERT: D 18 GLU cc_start: 0.8580 (tm-30) cc_final: 0.8013 (tp30) REVERT: D 40 GLU cc_start: 0.8907 (pt0) cc_final: 0.8388 (pm20) REVERT: D 56 GLU cc_start: 0.7976 (tp30) cc_final: 0.7614 (tp30) REVERT: D 71 GLU cc_start: 0.8874 (tp30) cc_final: 0.8615 (tp30) REVERT: D 164 GLU cc_start: 0.8681 (mp0) cc_final: 0.8226 (mp0) REVERT: E 104 MET cc_start: 0.9065 (mmt) cc_final: 0.8674 (mmm) REVERT: E 161 GLN cc_start: 0.8926 (tt0) cc_final: 0.8271 (tt0) REVERT: E 171 ILE cc_start: 0.8012 (OUTLIER) cc_final: 0.7744 (tt) REVERT: E 192 GLN cc_start: 0.8400 (mm110) cc_final: 0.8070 (mm110) REVERT: F 25 MET cc_start: 0.8306 (mpp) cc_final: 0.7246 (mpp) REVERT: G 18 TYR cc_start: 0.8807 (t80) cc_final: 0.8462 (t80) REVERT: G 32 TYR cc_start: 0.7794 (t80) cc_final: 0.7526 (t80) REVERT: G 59 GLU cc_start: 0.8203 (tp30) cc_final: 0.7739 (tm-30) REVERT: J 36 GLU cc_start: 0.8622 (pp20) cc_final: 0.8185 (tm-30) REVERT: J 41 LEU cc_start: 0.9387 (tp) cc_final: 0.8898 (tp) REVERT: K 25 MET cc_start: 0.8290 (pmm) cc_final: 0.7429 (pmm) REVERT: K 36 GLU cc_start: 0.8500 (mp0) cc_final: 0.8220 (mp0) REVERT: K 90 GLU cc_start: 0.8948 (mm-30) cc_final: 0.8408 (mm-30) REVERT: K 95 GLU cc_start: 0.8233 (tp30) cc_final: 0.7622 (tm-30) REVERT: K 134 ILE cc_start: 0.7769 (OUTLIER) cc_final: 0.7520 (tt) REVERT: O 38 SER cc_start: 0.9225 (m) cc_final: 0.8931 (p) REVERT: V 140 ILE cc_start: 0.8804 (mt) cc_final: 0.8435 (tt) REVERT: V 798 MET cc_start: 0.9071 (mtm) cc_final: 0.8866 (mtp) REVERT: W 18 GLU cc_start: 0.9048 (OUTLIER) cc_final: 0.8367 (tm-30) REVERT: W 30 ARG cc_start: 0.8976 (ttm-80) cc_final: 0.8624 (ttm-80) REVERT: W 164 GLU cc_start: 0.8263 (mp0) cc_final: 0.7323 (mp0) REVERT: X 1 MET cc_start: 0.8808 (tpp) cc_final: 0.8599 (tpp) REVERT: X 18 GLU cc_start: 0.8598 (tm-30) cc_final: 0.8128 (tm-30) REVERT: X 32 GLU cc_start: 0.7669 (mm-30) cc_final: 0.7193 (tp30) REVERT: X 40 GLU cc_start: 0.8780 (pt0) cc_final: 0.8437 (pm20) REVERT: X 71 GLU cc_start: 0.8859 (tp30) cc_final: 0.8457 (tp30) REVERT: X 164 GLU cc_start: 0.8657 (mp0) cc_final: 0.8255 (mp0) REVERT: Y 40 LEU cc_start: 0.8396 (OUTLIER) cc_final: 0.8099 (tt) REVERT: Y 161 GLN cc_start: 0.8898 (tt0) cc_final: 0.8257 (tt0) REVERT: Y 190 GLN cc_start: 0.8727 (mt0) cc_final: 0.8446 (mt0) REVERT: Y 192 GLN cc_start: 0.8286 (mm110) cc_final: 0.7936 (mm110) REVERT: Z 25 MET cc_start: 0.8114 (mpp) cc_final: 0.7847 (mpp) REVERT: Z 113 MET cc_start: 0.8685 (tmm) cc_final: 0.7828 (tmm) REVERT: 0 25 MET cc_start: 0.7703 (mtm) cc_final: 0.7442 (mtm) REVERT: 0 32 TYR cc_start: 0.7945 (t80) cc_final: 0.7663 (t80) REVERT: 0 36 GLU cc_start: 0.8467 (mt-10) cc_final: 0.7948 (mm-30) REVERT: 0 59 GLU cc_start: 0.8417 (tp30) cc_final: 0.7962 (tm-30) REVERT: 0 129 GLU cc_start: 0.8589 (pm20) cc_final: 0.8046 (pm20) REVERT: 1 25 MET cc_start: 0.7427 (mmm) cc_final: 0.7210 (mmm) REVERT: 1 128 MET cc_start: 0.9026 (OUTLIER) cc_final: 0.8456 (mtp) REVERT: 2 18 TYR cc_start: 0.9017 (t80) cc_final: 0.8589 (t80) REVERT: 2 25 MET cc_start: 0.8450 (pmm) cc_final: 0.8128 (pmm) REVERT: 2 95 GLU cc_start: 0.8142 (tp30) cc_final: 0.7665 (tm-30) REVERT: 2 98 LYS cc_start: 0.8601 (tptm) cc_final: 0.8341 (ttmm) REVERT: 2 140 GLN cc_start: 0.8177 (mp10) cc_final: 0.7906 (mp10) REVERT: 3 43 GLU cc_start: 0.8744 (mt-10) cc_final: 0.8371 (pt0) REVERT: 7 277 MET cc_start: 0.8549 (mmm) cc_final: 0.8111 (mmm) outliers start: 83 outliers final: 61 residues processed: 438 average time/residue: 0.6145 time to fit residues: 470.1378 Evaluate side-chains 437 residues out of total 7395 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 70 poor density : 367 time to evaluate : 6.104 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 48 VAL Chi-restraints excluded: chain A residue 104 VAL Chi-restraints excluded: chain A residue 555 LEU Chi-restraints excluded: chain H residue 29 ILE 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 32 THR Chi-restraints excluded: chain L residue 40 LEU 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 171 ILE Chi-restraints excluded: chain L residue 218 MET Chi-restraints excluded: chain Q residue 112 LEU Chi-restraints excluded: chain Q residue 118 ILE Chi-restraints excluded: chain R residue 113 MET Chi-restraints excluded: chain S residue 138 VAL Chi-restraints excluded: chain T residue 113 MET Chi-restraints excluded: chain T residue 128 MET Chi-restraints excluded: chain T residue 136 ASP Chi-restraints excluded: chain e residue 40 THR Chi-restraints excluded: chain k residue 174 LEU Chi-restraints excluded: chain p residue 39 ASP Chi-restraints excluded: chain p residue 93 MET Chi-restraints excluded: chain B residue 48 VAL Chi-restraints excluded: chain B residue 382 VAL Chi-restraints excluded: chain B residue 494 LEU Chi-restraints excluded: chain B residue 530 ILE Chi-restraints excluded: chain B residue 555 LEU Chi-restraints excluded: chain B residue 597 GLN Chi-restraints excluded: chain C residue 1 MET Chi-restraints excluded: chain D residue 175 THR Chi-restraints excluded: chain E residue 40 LEU Chi-restraints excluded: chain E residue 116 CYS Chi-restraints excluded: chain E residue 137 ILE Chi-restraints excluded: chain E residue 152 THR Chi-restraints excluded: chain E residue 171 ILE Chi-restraints excluded: chain E residue 217 GLU Chi-restraints excluded: chain E residue 218 MET Chi-restraints excluded: chain F residue 112 LEU Chi-restraints excluded: chain F residue 114 THR Chi-restraints excluded: chain F residue 128 MET Chi-restraints excluded: chain J residue 7 VAL Chi-restraints excluded: chain J residue 122 VAL Chi-restraints excluded: chain J residue 138 VAL Chi-restraints excluded: chain K residue 134 ILE Chi-restraints excluded: chain O residue 45 THR Chi-restraints excluded: chain U residue 133 MET Chi-restraints excluded: chain V residue 104 VAL Chi-restraints excluded: chain V residue 555 LEU 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 Y residue 40 LEU Chi-restraints excluded: chain Y residue 171 ILE Chi-restraints excluded: chain Y residue 236 MET Chi-restraints excluded: chain Z residue 114 THR Chi-restraints excluded: chain 0 residue 113 MET 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 1 residue 138 VAL 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 43 GLU Chi-restraints excluded: chain 4 residue 45 THR Chi-restraints excluded: chain 7 residue 180 ASP Chi-restraints excluded: chain 7 residue 285 ARG Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Traceback (most recent call last): File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5477/build/../modules/phenix/phenix/command_line/real_space_refine.py", line 8, in run_program(real_space_refine.Program) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5477/modules/cctbx_project/iotbx/cli_parser.py", line 946, in run_program task.run() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5477/modules/phenix/phenix/programs/real_space_refine.py", line 213, in run log = self.logger) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5477/modules/phenix/phenix/refinement/rsr/wrappers.py", line 58, in __init__ log = log) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5477/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 306, in __init__ self.caller(self.refine_xyz) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5477/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 321, in caller func() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5477/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 702, in refine_xyz self.minimization_no_ncs() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5477/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 766, in minimization_no_ncs log = self.log) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5477/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 51, in __init__ gradients_method = gradients_method) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5477/modules/cctbx_project/mmtbx/refinement/real_space/weight.py", line 87, in __init__ rms_angles_limit = rms_angles_limit) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5477/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 368, in refine rms_angles_limit = rms_angles_limit) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5477/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 235, in __init__ weight = weight) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5477/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 112, in refine states_collector = self.states_accumulator) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5477/modules/cctbx_project/cctbx/maptbx/real_space_refinement_simple.py", line 174, in __init__ exception_handling_params=lbfgs_exception_handling_params) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5477/modules/cctbx_project/scitbx/lbfgs/__init__.py", line 278, in run line_search) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5477/modules/cctbx_project/scitbx/lbfgs/__init__.py", line 131, in run_c_plus_plus f, g = target_evaluator.compute_functional_and_gradients() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5477/modules/cctbx_project/cctbx/maptbx/real_space_refinement_simple.py", line 245, in compute_functional_and_gradients compute_gradients=True) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5477/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1479, in energies_sites flags=flags, sites_cart=sites_cart, site_labels=site_labels) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5477/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1381, in pair_proxies check_bonded_distance_cutoff(sites_frac=sites_frac) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5477/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1262, in check_bonded_distance_cutoff raise RuntimeError(msg) RuntimeError: Bond distance > max_reasonable_bond_distance: 66.6207 > 50: distance: 90 - 95: 32.291 distance: 95 - 96: 27.442 distance: 96 - 97: 13.097 distance: 96 - 99: 22.437 distance: 97 - 98: 25.530 distance: 97 - 106: 29.726 distance: 99 - 100: 27.827 distance: 100 - 101: 36.257 distance: 102 - 103: 8.923 distance: 103 - 104: 20.927 distance: 103 - 105: 22.040 distance: 106 - 107: 41.552 distance: 106 - 169: 46.383 distance: 107 - 108: 38.042 distance: 107 - 110: 34.382 distance: 108 - 109: 28.992 distance: 108 - 114: 33.456 distance: 109 - 166: 32.962 distance: 110 - 111: 43.844 distance: 111 - 112: 47.313 distance: 111 - 113: 49.709 distance: 115 - 116: 59.916 distance: 115 - 118: 38.611 distance: 116 - 117: 46.875 distance: 116 - 123: 15.930 distance: 118 - 119: 13.551 distance: 119 - 120: 23.254 distance: 120 - 121: 38.664 distance: 120 - 122: 40.069 distance: 123 - 124: 19.869 distance: 124 - 125: 7.196 distance: 124 - 127: 42.122 distance: 125 - 126: 62.648 distance: 125 - 131: 41.675 distance: 127 - 128: 38.579 distance: 128 - 129: 19.129 distance: 128 - 130: 45.056 distance: 131 - 132: 26.493 distance: 131 - 137: 41.298 distance: 132 - 133: 24.645 distance: 132 - 135: 36.228 distance: 133 - 134: 25.920 distance: 133 - 138: 39.884 distance: 135 - 136: 26.741 distance: 136 - 137: 28.936 distance: 138 - 139: 24.822 distance: 139 - 140: 10.139 distance: 139 - 142: 24.432 distance: 140 - 141: 12.113 distance: 140 - 146: 17.568 distance: 142 - 143: 10.444 distance: 143 - 144: 33.292 distance: 143 - 145: 25.275 distance: 146 - 147: 15.296 distance: 147 - 148: 22.259 distance: 148 - 149: 14.813 distance: 148 - 150: 14.512 distance: 150 - 151: 5.106 distance: 151 - 152: 16.970 distance: 151 - 154: 17.986 distance: 152 - 153: 21.200 distance: 152 - 159: 20.346 distance: 154 - 155: 11.234 distance: 155 - 156: 18.085 distance: 156 - 157: 15.708 distance: 157 - 158: 25.458 distance: 159 - 160: 5.782 distance: 160 - 161: 11.741 distance: 160 - 163: 20.081 distance: 161 - 162: 10.581 distance: 161 - 166: 11.791 distance: 163 - 164: 27.450 distance: 163 - 165: 22.013 distance: 166 - 167: 26.303 distance: 167 - 168: 18.108 distance: 167 - 170: 15.952 distance: 168 - 169: 16.360 distance: 168 - 174: 19.326 distance: 170 - 171: 37.542 distance: 171 - 172: 21.782 distance: 171 - 173: 31.801