Starting phenix.real_space_refine (version: dev) on Mon May 16 20:15:52 2022 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6ybq_10771/05_2022/6ybq_10771_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6ybq_10771/05_2022/6ybq_10771.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=1.96 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6ybq_10771/05_2022/6ybq_10771.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6ybq_10771/05_2022/6ybq_10771.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6ybq_10771/05_2022/6ybq_10771_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6ybq_10771/05_2022/6ybq_10771_updated.pdb" } resolution = 1.96 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs ------------------------------------------------------------------------------- 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= 0.017 sd= 0.182 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 Convert atoms to be neutral Process input model Symmetric amino acids flipped Residue "A PHE 89": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 189": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F PHE 347": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J PHE 666": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.10s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-4597/modules/chem_data/mon_lib" Total number of atoms: 34092 Number of models: 1 Model: "" Number of chains: 36 Chain: "A" Number of atoms: 3902 Number of conformers: 1 Conformer: "" Number of residues, atoms: 506, 3902 Classifications: {'peptide': 506} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 21, 'TRANS': 484} Chain: "B" Number of atoms: 3902 Number of conformers: 1 Conformer: "" Number of residues, atoms: 506, 3902 Classifications: {'peptide': 506} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 21, 'TRANS': 484} Chain: "C" Number of atoms: 3902 Number of conformers: 1 Conformer: "" Number of residues, atoms: 506, 3902 Classifications: {'peptide': 506} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 21, 'TRANS': 484} Chain: "D" Number of atoms: 3902 Number of conformers: 1 Conformer: "" Number of residues, atoms: 506, 3902 Classifications: {'peptide': 506} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 21, 'TRANS': 484} Chain: "E" Number of atoms: 3902 Number of conformers: 1 Conformer: "" Number of residues, atoms: 506, 3902 Classifications: {'peptide': 506} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 21, 'TRANS': 484} Chain: "F" Number of atoms: 3902 Number of conformers: 1 Conformer: "" Number of residues, atoms: 506, 3902 Classifications: {'peptide': 506} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 21, 'TRANS': 484} Chain: "G" Number of atoms: 1565 Number of conformers: 1 Conformer: "" Number of residues, atoms: 208, 1565 Classifications: {'peptide': 208} Link IDs: {'PTRANS': 11, 'TRANS': 196} Chain: "H" Number of atoms: 1581 Number of conformers: 1 Conformer: "" Number of residues, atoms: 210, 1581 Classifications: {'peptide': 210} Link IDs: {'PTRANS': 12, 'TRANS': 197} Chain: "I" Number of atoms: 1549 Number of conformers: 1 Conformer: "" Number of residues, atoms: 206, 1549 Classifications: {'peptide': 206} Link IDs: {'PTRANS': 11, 'TRANS': 194} Chain: "J" Number of atoms: 1581 Number of conformers: 1 Conformer: "" Number of residues, atoms: 210, 1581 Classifications: {'peptide': 210} Link IDs: {'PTRANS': 12, 'TRANS': 197} Chain: "K" Number of atoms: 1574 Number of conformers: 1 Conformer: "" Number of residues, atoms: 209, 1574 Classifications: {'peptide': 209} Link IDs: {'PTRANS': 12, 'TRANS': 196} Chain: "L" Number of atoms: 1581 Number of conformers: 1 Conformer: "" Number of residues, atoms: 210, 1581 Classifications: {'peptide': 210} Link IDs: {'PTRANS': 12, 'TRANS': 197} Chain: "A" Number of atoms: 48 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 48 Unusual residues: {'COA': 1} Classifications: {'undetermined': 1} Chain: "B" Number of atoms: 48 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 48 Unusual residues: {'COA': 1} Classifications: {'undetermined': 1} Chain: "C" Number of atoms: 48 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 48 Unusual residues: {'COA': 1} Classifications: {'undetermined': 1} Chain: "D" Number of atoms: 48 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 48 Unusual residues: {'COA': 1} Classifications: {'undetermined': 1} Chain: "E" Number of atoms: 48 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 48 Unusual residues: {'COA': 1} Classifications: {'undetermined': 1} Chain: "F" Number of atoms: 48 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 48 Unusual residues: {'COA': 1} Classifications: {'undetermined': 1} Chain: "G" Number of atoms: 15 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 15 Unusual residues: {'BTI': 1} Classifications: {'undetermined': 1} Chain: "H" Number of atoms: 15 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 15 Unusual residues: {'BTI': 1} Classifications: {'undetermined': 1} Chain: "I" Number of atoms: 15 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 15 Unusual residues: {'BTI': 1} Classifications: {'undetermined': 1} Chain: "J" Number of atoms: 15 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 15 Unusual residues: {'BTI': 1} Classifications: {'undetermined': 1} Chain: "K" Number of atoms: 15 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 15 Unusual residues: {'BTI': 1} Classifications: {'undetermined': 1} Chain: "L" Number of atoms: 15 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 15 Unusual residues: {'BTI': 1} Classifications: {'undetermined': 1} Chain: "A" Number of atoms: 138 Number of conformers: 1 Conformer: "" Number of residues, atoms: 138, 138 Classifications: {'water': 138} Link IDs: {None: 137} Chain: "B" Number of atoms: 145 Number of conformers: 1 Conformer: "" Number of residues, atoms: 145, 145 Classifications: {'water': 145} Link IDs: {None: 144} Chain: "C" Number of atoms: 134 Number of conformers: 1 Conformer: "" Number of residues, atoms: 134, 134 Classifications: {'water': 134} Link IDs: {None: 133} Chain: "D" Number of atoms: 144 Number of conformers: 1 Conformer: "" Number of residues, atoms: 144, 144 Classifications: {'water': 144} Link IDs: {None: 143} Chain: "E" Number of atoms: 126 Number of conformers: 1 Conformer: "" Number of residues, atoms: 126, 126 Classifications: {'water': 126} Link IDs: {None: 125} Chain: "F" Number of atoms: 128 Number of conformers: 1 Conformer: "" Number of residues, atoms: 128, 128 Classifications: {'water': 128} Link IDs: {None: 127} Chain: "G" Number of atoms: 8 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 8 Classifications: {'water': 8} Link IDs: {None: 7} Chain: "H" Number of atoms: 11 Number of conformers: 1 Conformer: "" Number of residues, atoms: 11, 11 Classifications: {'water': 11} Link IDs: {None: 10} Chain: "I" Number of atoms: 8 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 8 Classifications: {'water': 8} Link IDs: {None: 7} Chain: "J" Number of atoms: 11 Number of conformers: 1 Conformer: "" Number of residues, atoms: 11, 11 Classifications: {'water': 11} Link IDs: {None: 10} Chain: "K" Number of atoms: 8 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 8 Classifications: {'water': 8} Link IDs: {None: 7} Chain: "L" Number of atoms: 10 Number of conformers: 1 Conformer: "" Number of residues, atoms: 10, 10 Classifications: {'water': 10} Link IDs: {None: 9} Time building chain proxies: 19.20, per 1000 atoms: 0.56 Number of scatterers: 34092 At special positions: 0 Unit cell: (158.323, 149.811, 162.579, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 150 16.00 P 18 15.00 O 7110 8.00 N 5897 7.00 C 20917 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=6, symmetry=0 Number of additional bonds: simple=6, symmetry=0 Coordination: Other bonds: Time building additional restraints: 14.02 Conformation dependent library (CDL) restraints added in 5.1 seconds 8530 Ramachandran restraints generated. 4265 Oldfield, 0 Emsley, 4265 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 7774 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 168 helices and 40 sheets defined 36.1% alpha, 18.5% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 3.77 Creating SS restraints... Processing helix chain 'A' and resid 6 through 17 removed outlier: 3.789A pdb=" N LEU A 17 " --> pdb=" O ALA A 13 " (cutoff:3.500A) Processing helix chain 'A' and resid 21 through 29 Processing helix chain 'A' and resid 35 through 42 Processing helix chain 'A' and resid 64 through 66 No H-bonds generated for 'chain 'A' and resid 64 through 66' Processing helix chain 'A' and resid 96 through 98 No H-bonds generated for 'chain 'A' and resid 96 through 98' Processing helix chain 'A' and resid 102 through 118 removed outlier: 3.554A pdb=" N VAL A 111 " --> pdb=" O LYS A 107 " (cutoff:3.500A) Processing helix chain 'A' and resid 133 through 153 removed outlier: 6.964A pdb=" N VAL A 137 " --> pdb=" O GLN A 134 " (cutoff:3.500A) removed outlier: 3.877A pdb=" N ALA A 138 " --> pdb=" O GLU A 135 " (cutoff:3.500A) Processing helix chain 'A' and resid 169 through 177 Proline residue: A 175 - end of helix Processing helix chain 'A' and resid 195 through 202 Processing helix chain 'A' and resid 208 through 212 Processing helix chain 'A' and resid 214 through 219 Processing helix chain 'A' and resid 231 through 244 removed outlier: 3.656A pdb=" N PHE A 244 " --> pdb=" O ARG A 240 " (cutoff:3.500A) Processing helix chain 'A' and resid 267 through 271 Processing helix chain 'A' and resid 283 through 290 Processing helix chain 'A' and resid 292 through 294 No H-bonds generated for 'chain 'A' and resid 292 through 294' Processing helix chain 'A' and resid 329 through 331 No H-bonds generated for 'chain 'A' and resid 329 through 331' Processing helix chain 'A' and resid 335 through 350 removed outlier: 3.582A pdb=" N PHE A 344 " --> pdb=" O LYS A 340 " (cutoff:3.500A) Processing helix chain 'A' and resid 368 through 372 Processing helix chain 'A' and resid 375 through 388 removed outlier: 4.068A pdb=" N LEU A 382 " --> pdb=" O HIS A 378 " (cutoff:3.500A) removed outlier: 3.610A pdb=" N LEU A 383 " --> pdb=" O GLY A 379 " (cutoff:3.500A) Processing helix chain 'A' and resid 403 through 408 removed outlier: 3.554A pdb=" N ILE A 407 " --> pdb=" O GLY A 403 " (cutoff:3.500A) Processing helix chain 'A' and resid 412 through 414 No H-bonds generated for 'chain 'A' and resid 412 through 414' Processing helix chain 'A' and resid 432 through 439 Processing helix chain 'A' and resid 441 through 443 No H-bonds generated for 'chain 'A' and resid 441 through 443' Processing helix chain 'A' and resid 447 through 461 Processing helix chain 'A' and resid 465 through 469 Processing helix chain 'A' and resid 479 through 495 removed outlier: 5.038A pdb=" N ARG A 483 " --> pdb=" O HIS A 480 " (cutoff:3.500A) removed outlier: 3.797A pdb=" N ALA A 487 " --> pdb=" O LYS A 484 " (cutoff:3.500A) removed outlier: 3.758A pdb=" N LEU A 490 " --> pdb=" O ALA A 487 " (cutoff:3.500A) removed outlier: 3.995A pdb=" N THR A 495 " --> pdb=" O MET A 492 " (cutoff:3.500A) Processing helix chain 'B' and resid 6 through 17 removed outlier: 3.923A pdb=" N LEU B 17 " --> pdb=" O ALA B 13 " (cutoff:3.500A) Processing helix chain 'B' and resid 21 through 30 Processing helix chain 'B' and resid 35 through 42 Processing helix chain 'B' and resid 64 through 66 No H-bonds generated for 'chain 'B' and resid 64 through 66' Processing helix chain 'B' and resid 96 through 98 No H-bonds generated for 'chain 'B' and resid 96 through 98' Processing helix chain 'B' and resid 102 through 118 Processing helix chain 'B' and resid 133 through 153 removed outlier: 6.993A pdb=" N VAL B 137 " --> pdb=" O GLN B 134 " (cutoff:3.500A) removed outlier: 3.739A pdb=" N ALA B 138 " --> pdb=" O GLU B 135 " (cutoff:3.500A) removed outlier: 3.640A pdb=" N ARG B 148 " --> pdb=" O GLU B 145 " (cutoff:3.500A) Processing helix chain 'B' and resid 169 through 177 removed outlier: 3.713A pdb=" N TYR B 173 " --> pdb=" O GLY B 170 " (cutoff:3.500A) removed outlier: 3.687A pdb=" N SER B 174 " --> pdb=" O ASP B 171 " (cutoff:3.500A) Proline residue: B 175 - end of helix Processing helix chain 'B' and resid 195 through 202 Processing helix chain 'B' and resid 208 through 212 Processing helix chain 'B' and resid 214 through 219 Processing helix chain 'B' and resid 231 through 242 Processing helix chain 'B' and resid 267 through 271 Processing helix chain 'B' and resid 283 through 290 Processing helix chain 'B' and resid 292 through 294 No H-bonds generated for 'chain 'B' and resid 292 through 294' Processing helix chain 'B' and resid 329 through 331 No H-bonds generated for 'chain 'B' and resid 329 through 331' Processing helix chain 'B' and resid 335 through 350 removed outlier: 3.570A pdb=" N PHE B 344 " --> pdb=" O LYS B 340 " (cutoff:3.500A) Processing helix chain 'B' and resid 368 through 372 Processing helix chain 'B' and resid 375 through 388 removed outlier: 3.670A pdb=" N ALA B 380 " --> pdb=" O ILE B 376 " (cutoff:3.500A) removed outlier: 4.099A pdb=" N LEU B 382 " --> pdb=" O HIS B 378 " (cutoff:3.500A) removed outlier: 3.787A pdb=" N LEU B 383 " --> pdb=" O GLY B 379 " (cutoff:3.500A) Processing helix chain 'B' and resid 403 through 408 Processing helix chain 'B' and resid 412 through 414 No H-bonds generated for 'chain 'B' and resid 412 through 414' Processing helix chain 'B' and resid 432 through 439 Processing helix chain 'B' and resid 448 through 461 Processing helix chain 'B' and resid 465 through 469 Processing helix chain 'B' and resid 479 through 495 removed outlier: 5.190A pdb=" N ARG B 483 " --> pdb=" O HIS B 480 " (cutoff:3.500A) removed outlier: 3.879A pdb=" N ALA B 487 " --> pdb=" O LYS B 484 " (cutoff:3.500A) removed outlier: 3.783A pdb=" N LEU B 490 " --> pdb=" O ALA B 487 " (cutoff:3.500A) removed outlier: 3.724A pdb=" N ARG B 494 " --> pdb=" O GLY B 491 " (cutoff:3.500A) removed outlier: 4.176A pdb=" N THR B 495 " --> pdb=" O MET B 492 " (cutoff:3.500A) Processing helix chain 'C' and resid 6 through 17 removed outlier: 3.981A pdb=" N LEU C 17 " --> pdb=" O ALA C 13 " (cutoff:3.500A) Processing helix chain 'C' and resid 21 through 29 Processing helix chain 'C' and resid 35 through 42 Processing helix chain 'C' and resid 64 through 66 No H-bonds generated for 'chain 'C' and resid 64 through 66' Processing helix chain 'C' and resid 96 through 98 No H-bonds generated for 'chain 'C' and resid 96 through 98' Processing helix chain 'C' and resid 102 through 118 Processing helix chain 'C' and resid 133 through 153 removed outlier: 7.064A pdb=" N VAL C 137 " --> pdb=" O GLN C 134 " (cutoff:3.500A) removed outlier: 3.656A pdb=" N ALA C 138 " --> pdb=" O GLU C 135 " (cutoff:3.500A) removed outlier: 3.764A pdb=" N ARG C 148 " --> pdb=" O GLU C 145 " (cutoff:3.500A) Processing helix chain 'C' and resid 169 through 177 removed outlier: 3.603A pdb=" N SER C 174 " --> pdb=" O ASP C 171 " (cutoff:3.500A) Proline residue: C 175 - end of helix Processing helix chain 'C' and resid 195 through 202 Processing helix chain 'C' and resid 208 through 212 Processing helix chain 'C' and resid 214 through 219 Processing helix chain 'C' and resid 231 through 243 removed outlier: 3.651A pdb=" N ASP C 243 " --> pdb=" O ARG C 239 " (cutoff:3.500A) Processing helix chain 'C' and resid 267 through 271 Processing helix chain 'C' and resid 283 through 290 Processing helix chain 'C' and resid 292 through 294 No H-bonds generated for 'chain 'C' and resid 292 through 294' Processing helix chain 'C' and resid 329 through 331 No H-bonds generated for 'chain 'C' and resid 329 through 331' Processing helix chain 'C' and resid 335 through 350 Processing helix chain 'C' and resid 368 through 373 Processing helix chain 'C' and resid 375 through 388 removed outlier: 4.032A pdb=" N LEU C 382 " --> pdb=" O HIS C 378 " (cutoff:3.500A) removed outlier: 3.652A pdb=" N LEU C 383 " --> pdb=" O GLY C 379 " (cutoff:3.500A) Processing helix chain 'C' and resid 403 through 408 removed outlier: 3.519A pdb=" N ILE C 407 " --> pdb=" O GLY C 403 " (cutoff:3.500A) Processing helix chain 'C' and resid 412 through 414 No H-bonds generated for 'chain 'C' and resid 412 through 414' Processing helix chain 'C' and resid 432 through 439 Processing helix chain 'C' and resid 441 through 443 No H-bonds generated for 'chain 'C' and resid 441 through 443' Processing helix chain 'C' and resid 448 through 461 Processing helix chain 'C' and resid 465 through 470 Processing helix chain 'C' and resid 479 through 495 removed outlier: 5.051A pdb=" N ARG C 483 " --> pdb=" O HIS C 480 " (cutoff:3.500A) removed outlier: 3.712A pdb=" N ALA C 487 " --> pdb=" O LYS C 484 " (cutoff:3.500A) removed outlier: 3.805A pdb=" N LEU C 490 " --> pdb=" O ALA C 487 " (cutoff:3.500A) removed outlier: 4.038A pdb=" N THR C 495 " --> pdb=" O MET C 492 " (cutoff:3.500A) Processing helix chain 'D' and resid 6 through 17 removed outlier: 3.997A pdb=" N LEU D 17 " --> pdb=" O ALA D 13 " (cutoff:3.500A) Processing helix chain 'D' and resid 21 through 29 Processing helix chain 'D' and resid 35 through 42 Processing helix chain 'D' and resid 61 through 66 removed outlier: 5.906A pdb=" N GLU D 65 " --> pdb=" O PHE D 62 " (cutoff:3.500A) Processing helix chain 'D' and resid 96 through 98 No H-bonds generated for 'chain 'D' and resid 96 through 98' Processing helix chain 'D' and resid 102 through 118 removed outlier: 3.565A pdb=" N VAL D 111 " --> pdb=" O LYS D 107 " (cutoff:3.500A) Processing helix chain 'D' and resid 133 through 153 removed outlier: 6.884A pdb=" N VAL D 137 " --> pdb=" O GLN D 134 " (cutoff:3.500A) removed outlier: 3.738A pdb=" N ALA D 138 " --> pdb=" O GLU D 135 " (cutoff:3.500A) removed outlier: 3.787A pdb=" N ARG D 148 " --> pdb=" O GLU D 145 " (cutoff:3.500A) Processing helix chain 'D' and resid 169 through 177 removed outlier: 3.886A pdb=" N SER D 174 " --> pdb=" O ASP D 171 " (cutoff:3.500A) Proline residue: D 175 - end of helix Processing helix chain 'D' and resid 195 through 202 Processing helix chain 'D' and resid 208 through 212 Processing helix chain 'D' and resid 214 through 219 Processing helix chain 'D' and resid 231 through 244 removed outlier: 3.637A pdb=" N ASP D 243 " --> pdb=" O ARG D 239 " (cutoff:3.500A) removed outlier: 3.906A pdb=" N PHE D 244 " --> pdb=" O ARG D 240 " (cutoff:3.500A) Processing helix chain 'D' and resid 267 through 271 Processing helix chain 'D' and resid 283 through 290 Processing helix chain 'D' and resid 292 through 294 No H-bonds generated for 'chain 'D' and resid 292 through 294' Processing helix chain 'D' and resid 329 through 331 No H-bonds generated for 'chain 'D' and resid 329 through 331' Processing helix chain 'D' and resid 335 through 350 removed outlier: 3.552A pdb=" N PHE D 344 " --> pdb=" O LYS D 340 " (cutoff:3.500A) Processing helix chain 'D' and resid 368 through 373 Processing helix chain 'D' and resid 375 through 388 removed outlier: 3.679A pdb=" N ALA D 380 " --> pdb=" O ILE D 376 " (cutoff:3.500A) removed outlier: 4.062A pdb=" N LEU D 382 " --> pdb=" O HIS D 378 " (cutoff:3.500A) removed outlier: 3.734A pdb=" N LEU D 383 " --> pdb=" O GLY D 379 " (cutoff:3.500A) Processing helix chain 'D' and resid 403 through 408 removed outlier: 3.503A pdb=" N ILE D 407 " --> pdb=" O GLY D 403 " (cutoff:3.500A) Processing helix chain 'D' and resid 432 through 439 Processing helix chain 'D' and resid 441 through 443 No H-bonds generated for 'chain 'D' and resid 441 through 443' Processing helix chain 'D' and resid 448 through 461 Processing helix chain 'D' and resid 465 through 469 Processing helix chain 'D' and resid 479 through 495 removed outlier: 5.195A pdb=" N ARG D 483 " --> pdb=" O HIS D 480 " (cutoff:3.500A) removed outlier: 3.955A pdb=" N ALA D 487 " --> pdb=" O LYS D 484 " (cutoff:3.500A) removed outlier: 3.732A pdb=" N LEU D 490 " --> pdb=" O ALA D 487 " (cutoff:3.500A) removed outlier: 3.721A pdb=" N ARG D 494 " --> pdb=" O GLY D 491 " (cutoff:3.500A) removed outlier: 4.031A pdb=" N THR D 495 " --> pdb=" O MET D 492 " (cutoff:3.500A) Processing helix chain 'E' and resid 6 through 17 removed outlier: 3.843A pdb=" N LEU E 17 " --> pdb=" O ALA E 13 " (cutoff:3.500A) Processing helix chain 'E' and resid 21 through 29 Processing helix chain 'E' and resid 35 through 42 Processing helix chain 'E' and resid 96 through 98 No H-bonds generated for 'chain 'E' and resid 96 through 98' Processing helix chain 'E' and resid 102 through 118 removed outlier: 3.572A pdb=" N VAL E 111 " --> pdb=" O LYS E 107 " (cutoff:3.500A) Processing helix chain 'E' and resid 133 through 153 removed outlier: 6.794A pdb=" N VAL E 137 " --> pdb=" O GLN E 134 " (cutoff:3.500A) removed outlier: 3.653A pdb=" N ALA E 138 " --> pdb=" O GLU E 135 " (cutoff:3.500A) removed outlier: 3.763A pdb=" N ARG E 148 " --> pdb=" O GLU E 145 " (cutoff:3.500A) Processing helix chain 'E' and resid 169 through 177 Proline residue: E 175 - end of helix Processing helix chain 'E' and resid 195 through 202 Processing helix chain 'E' and resid 208 through 212 Processing helix chain 'E' and resid 214 through 219 Processing helix chain 'E' and resid 231 through 244 removed outlier: 3.651A pdb=" N PHE E 244 " --> pdb=" O ARG E 240 " (cutoff:3.500A) Processing helix chain 'E' and resid 267 through 271 Processing helix chain 'E' and resid 283 through 290 Processing helix chain 'E' and resid 292 through 294 No H-bonds generated for 'chain 'E' and resid 292 through 294' Processing helix chain 'E' and resid 329 through 331 No H-bonds generated for 'chain 'E' and resid 329 through 331' Processing helix chain 'E' and resid 335 through 350 removed outlier: 3.559A pdb=" N PHE E 344 " --> pdb=" O LYS E 340 " (cutoff:3.500A) Processing helix chain 'E' and resid 368 through 372 Processing helix chain 'E' and resid 375 through 388 removed outlier: 4.199A pdb=" N LEU E 382 " --> pdb=" O HIS E 378 " (cutoff:3.500A) removed outlier: 3.755A pdb=" N LEU E 383 " --> pdb=" O GLY E 379 " (cutoff:3.500A) Processing helix chain 'E' and resid 403 through 408 removed outlier: 3.533A pdb=" N ILE E 407 " --> pdb=" O GLY E 403 " (cutoff:3.500A) Processing helix chain 'E' and resid 412 through 414 No H-bonds generated for 'chain 'E' and resid 412 through 414' Processing helix chain 'E' and resid 432 through 439 Processing helix chain 'E' and resid 448 through 461 Processing helix chain 'E' and resid 465 through 470 Processing helix chain 'E' and resid 479 through 495 removed outlier: 5.350A pdb=" N ARG E 483 " --> pdb=" O HIS E 480 " (cutoff:3.500A) removed outlier: 3.903A pdb=" N ALA E 487 " --> pdb=" O LYS E 484 " (cutoff:3.500A) removed outlier: 3.757A pdb=" N LEU E 490 " --> pdb=" O ALA E 487 " (cutoff:3.500A) removed outlier: 3.710A pdb=" N ARG E 494 " --> pdb=" O GLY E 491 " (cutoff:3.500A) removed outlier: 4.095A pdb=" N THR E 495 " --> pdb=" O MET E 492 " (cutoff:3.500A) Processing helix chain 'F' and resid 6 through 17 removed outlier: 3.989A pdb=" N LEU F 17 " --> pdb=" O ALA F 13 " (cutoff:3.500A) Processing helix chain 'F' and resid 21 through 29 Processing helix chain 'F' and resid 35 through 42 Processing helix chain 'F' and resid 64 through 66 No H-bonds generated for 'chain 'F' and resid 64 through 66' Processing helix chain 'F' and resid 96 through 98 No H-bonds generated for 'chain 'F' and resid 96 through 98' Processing helix chain 'F' and resid 102 through 118 Processing helix chain 'F' and resid 133 through 153 removed outlier: 6.707A pdb=" N VAL F 137 " --> pdb=" O GLN F 134 " (cutoff:3.500A) Processing helix chain 'F' and resid 169 through 177 Proline residue: F 175 - end of helix Processing helix chain 'F' and resid 195 through 202 Processing helix chain 'F' and resid 208 through 212 Processing helix chain 'F' and resid 214 through 219 Processing helix chain 'F' and resid 231 through 244 removed outlier: 3.618A pdb=" N ASP F 243 " --> pdb=" O ARG F 239 " (cutoff:3.500A) removed outlier: 3.951A pdb=" N PHE F 244 " --> pdb=" O ARG F 240 " (cutoff:3.500A) Processing helix chain 'F' and resid 267 through 271 Processing helix chain 'F' and resid 283 through 290 Processing helix chain 'F' and resid 292 through 294 No H-bonds generated for 'chain 'F' and resid 292 through 294' Processing helix chain 'F' and resid 329 through 331 No H-bonds generated for 'chain 'F' and resid 329 through 331' Processing helix chain 'F' and resid 335 through 350 removed outlier: 3.561A pdb=" N PHE F 344 " --> pdb=" O LYS F 340 " (cutoff:3.500A) Processing helix chain 'F' and resid 368 through 372 Processing helix chain 'F' and resid 375 through 388 removed outlier: 4.038A pdb=" N LEU F 382 " --> pdb=" O HIS F 378 " (cutoff:3.500A) removed outlier: 3.650A pdb=" N LEU F 383 " --> pdb=" O GLY F 379 " (cutoff:3.500A) Processing helix chain 'F' and resid 403 through 408 removed outlier: 3.641A pdb=" N ILE F 407 " --> pdb=" O GLY F 403 " (cutoff:3.500A) Processing helix chain 'F' and resid 412 through 414 No H-bonds generated for 'chain 'F' and resid 412 through 414' Processing helix chain 'F' and resid 432 through 439 Processing helix chain 'F' and resid 441 through 443 No H-bonds generated for 'chain 'F' and resid 441 through 443' Processing helix chain 'F' and resid 448 through 461 Processing helix chain 'F' and resid 465 through 469 Processing helix chain 'F' and resid 479 through 495 removed outlier: 5.279A pdb=" N ARG F 483 " --> pdb=" O HIS F 480 " (cutoff:3.500A) removed outlier: 3.763A pdb=" N ALA F 487 " --> pdb=" O LYS F 484 " (cutoff:3.500A) removed outlier: 3.721A pdb=" N LEU F 490 " --> pdb=" O ALA F 487 " (cutoff:3.500A) removed outlier: 4.049A pdb=" N THR F 495 " --> pdb=" O MET F 492 " (cutoff:3.500A) Processing helix chain 'G' and resid 462 through 484 removed outlier: 3.952A pdb=" N GLY G 484 " --> pdb=" O ILE G 480 " (cutoff:3.500A) Processing helix chain 'G' and resid 580 through 588 removed outlier: 3.640A pdb=" N LEU G 588 " --> pdb=" O GLU G 584 " (cutoff:3.500A) Processing helix chain 'H' and resid 462 through 484 removed outlier: 3.989A pdb=" N GLY H 484 " --> pdb=" O ILE H 480 " (cutoff:3.500A) Processing helix chain 'H' and resid 492 through 494 No H-bonds generated for 'chain 'H' and resid 492 through 494' Processing helix chain 'H' and resid 580 through 588 removed outlier: 3.730A pdb=" N LEU H 588 " --> pdb=" O GLU H 584 " (cutoff:3.500A) Processing helix chain 'I' and resid 462 through 484 removed outlier: 3.956A pdb=" N GLY I 484 " --> pdb=" O ILE I 480 " (cutoff:3.500A) Processing helix chain 'I' and resid 492 through 494 No H-bonds generated for 'chain 'I' and resid 492 through 494' Processing helix chain 'I' and resid 580 through 588 removed outlier: 3.794A pdb=" N LEU I 588 " --> pdb=" O GLU I 584 " (cutoff:3.500A) Processing helix chain 'J' and resid 461 through 484 Processing helix chain 'J' and resid 492 through 494 No H-bonds generated for 'chain 'J' and resid 492 through 494' Processing helix chain 'J' and resid 580 through 588 removed outlier: 3.805A pdb=" N LEU J 588 " --> pdb=" O GLU J 584 " (cutoff:3.500A) Processing helix chain 'K' and resid 461 through 484 removed outlier: 3.649A pdb=" N HIS K 465 " --> pdb=" O PRO K 462 " (cutoff:3.500A) Processing helix chain 'K' and resid 492 through 494 No H-bonds generated for 'chain 'K' and resid 492 through 494' Processing helix chain 'K' and resid 580 through 588 removed outlier: 3.766A pdb=" N LEU K 588 " --> pdb=" O GLU K 584 " (cutoff:3.500A) Processing helix chain 'L' and resid 462 through 484 removed outlier: 4.108A pdb=" N GLY L 484 " --> pdb=" O ILE L 480 " (cutoff:3.500A) Processing helix chain 'L' and resid 580 through 588 removed outlier: 3.798A pdb=" N LEU L 588 " --> pdb=" O GLU L 584 " (cutoff:3.500A) Processing sheet with id= A, first strand: chain 'A' and resid 49 through 51 removed outlier: 4.491A pdb=" N THR A 76 " --> pdb=" O PHE A 51 " (cutoff:3.500A) removed outlier: 8.401A pdb=" N PHE A 89 " --> pdb=" O PRO A 121 " (cutoff:3.500A) removed outlier: 6.515A pdb=" N ILE A 123 " --> pdb=" O PHE A 89 " (cutoff:3.500A) removed outlier: 8.352A pdb=" N LYS A 91 " --> pdb=" O ILE A 123 " (cutoff:3.500A) removed outlier: 7.518A pdb=" N ILE A 125 " --> pdb=" O LYS A 91 " (cutoff:3.500A) removed outlier: 6.298A pdb=" N PHE A 180 " --> pdb=" O SER A 161 " (cutoff:3.500A) removed outlier: 7.619A pdb=" N ILE A 163 " --> pdb=" O PHE A 180 " (cutoff:3.500A) removed outlier: 6.655A pdb=" N PHE A 182 " --> pdb=" O ILE A 163 " (cutoff:3.500A) removed outlier: 6.759A pdb=" N GLY A 226 " --> pdb=" O MET A 183 " (cutoff:3.500A) Processing sheet with id= B, first strand: chain 'A' and resid 166 through 168 removed outlier: 6.356A pdb=" N TYR A 189 " --> pdb=" O CYS A 167 " (cutoff:3.500A) No H-bonds generated for sheet with id= B Processing sheet with id= C, first strand: chain 'A' and resid 296 through 298 removed outlier: 6.550A pdb=" N LEU A 418 " --> pdb=" O THR A 395 " (cutoff:3.500A) removed outlier: 8.025A pdb=" N ILE A 397 " --> pdb=" O LEU A 418 " (cutoff:3.500A) removed outlier: 7.043A pdb=" N TYR A 420 " --> pdb=" O ILE A 397 " (cutoff:3.500A) removed outlier: 6.709A pdb=" N GLU A 475 " --> pdb=" O ALA A 421 " (cutoff:3.500A) Processing sheet with id= D, first strand: chain 'A' and resid 400 through 402 removed outlier: 6.246A pdb=" N GLN A 426 " --> pdb=" O ALA A 401 " (cutoff:3.500A) No H-bonds generated for sheet with id= D Processing sheet with id= E, first strand: chain 'B' and resid 49 through 51 removed outlier: 4.474A pdb=" N THR B 76 " --> pdb=" O PHE B 51 " (cutoff:3.500A) removed outlier: 8.473A pdb=" N PHE B 89 " --> pdb=" O PRO B 121 " (cutoff:3.500A) removed outlier: 6.554A pdb=" N ILE B 123 " --> pdb=" O PHE B 89 " (cutoff:3.500A) removed outlier: 8.254A pdb=" N LYS B 91 " --> pdb=" O ILE B 123 " (cutoff:3.500A) removed outlier: 7.502A pdb=" N ILE B 125 " --> pdb=" O LYS B 91 " (cutoff:3.500A) removed outlier: 6.316A pdb=" N PHE B 180 " --> pdb=" O SER B 161 " (cutoff:3.500A) removed outlier: 7.565A pdb=" N ILE B 163 " --> pdb=" O PHE B 180 " (cutoff:3.500A) removed outlier: 6.628A pdb=" N PHE B 182 " --> pdb=" O ILE B 163 " (cutoff:3.500A) removed outlier: 6.538A pdb=" N GLY B 226 " --> pdb=" O MET B 183 " (cutoff:3.500A) Processing sheet with id= F, first strand: chain 'B' and resid 166 through 168 removed outlier: 6.414A pdb=" N TYR B 189 " --> pdb=" O CYS B 167 " (cutoff:3.500A) No H-bonds generated for sheet with id= F Processing sheet with id= G, first strand: chain 'B' and resid 307 through 314 removed outlier: 7.899A pdb=" N VAL B 322 " --> pdb=" O PRO B 354 " (cutoff:3.500A) removed outlier: 6.379A pdb=" N VAL B 356 " --> pdb=" O VAL B 322 " (cutoff:3.500A) removed outlier: 8.404A pdb=" N ASN B 324 " --> pdb=" O VAL B 356 " (cutoff:3.500A) removed outlier: 7.141A pdb=" N PHE B 358 " --> pdb=" O ASN B 324 " (cutoff:3.500A) removed outlier: 6.596A pdb=" N LEU B 418 " --> pdb=" O THR B 395 " (cutoff:3.500A) removed outlier: 8.112A pdb=" N ILE B 397 " --> pdb=" O LEU B 418 " (cutoff:3.500A) removed outlier: 7.083A pdb=" N TYR B 420 " --> pdb=" O ILE B 397 " (cutoff:3.500A) Processing sheet with id= H, first strand: chain 'C' and resid 49 through 51 removed outlier: 4.536A pdb=" N THR C 76 " --> pdb=" O PHE C 51 " (cutoff:3.500A) removed outlier: 8.455A pdb=" N PHE C 89 " --> pdb=" O PRO C 121 " (cutoff:3.500A) removed outlier: 6.580A pdb=" N ILE C 123 " --> pdb=" O PHE C 89 " (cutoff:3.500A) removed outlier: 8.314A pdb=" N LYS C 91 " --> pdb=" O ILE C 123 " (cutoff:3.500A) removed outlier: 7.408A pdb=" N ILE C 125 " --> pdb=" O LYS C 91 " (cutoff:3.500A) removed outlier: 6.289A pdb=" N PHE C 180 " --> pdb=" O SER C 161 " (cutoff:3.500A) removed outlier: 7.588A pdb=" N ILE C 163 " --> pdb=" O PHE C 180 " (cutoff:3.500A) removed outlier: 6.649A pdb=" N PHE C 182 " --> pdb=" O ILE C 163 " (cutoff:3.500A) removed outlier: 6.640A pdb=" N GLY C 226 " --> pdb=" O MET C 183 " (cutoff:3.500A) Processing sheet with id= I, first strand: chain 'C' and resid 166 through 168 removed outlier: 6.249A pdb=" N TYR C 189 " --> pdb=" O CYS C 167 " (cutoff:3.500A) No H-bonds generated for sheet with id= I Processing sheet with id= J, first strand: chain 'C' and resid 297 through 299 removed outlier: 4.499A pdb=" N THR C 309 " --> pdb=" O ILE C 299 " (cutoff:3.500A) removed outlier: 6.613A pdb=" N LEU C 418 " --> pdb=" O THR C 395 " (cutoff:3.500A) removed outlier: 8.157A pdb=" N ILE C 397 " --> pdb=" O LEU C 418 " (cutoff:3.500A) removed outlier: 7.137A pdb=" N TYR C 420 " --> pdb=" O ILE C 397 " (cutoff:3.500A) Processing sheet with id= K, first strand: chain 'C' and resid 400 through 402 removed outlier: 6.221A pdb=" N GLN C 426 " --> pdb=" O ALA C 401 " (cutoff:3.500A) No H-bonds generated for sheet with id= K Processing sheet with id= L, first strand: chain 'D' and resid 49 through 51 removed outlier: 4.661A pdb=" N THR D 76 " --> pdb=" O PHE D 51 " (cutoff:3.500A) removed outlier: 8.483A pdb=" N PHE D 89 " --> pdb=" O PRO D 121 " (cutoff:3.500A) removed outlier: 6.617A pdb=" N ILE D 123 " --> pdb=" O PHE D 89 " (cutoff:3.500A) removed outlier: 8.322A pdb=" N LYS D 91 " --> pdb=" O ILE D 123 " (cutoff:3.500A) removed outlier: 7.423A pdb=" N ILE D 125 " --> pdb=" O LYS D 91 " (cutoff:3.500A) removed outlier: 6.329A pdb=" N PHE D 180 " --> pdb=" O SER D 161 " (cutoff:3.500A) removed outlier: 7.601A pdb=" N ILE D 163 " --> pdb=" O PHE D 180 " (cutoff:3.500A) removed outlier: 6.682A pdb=" N PHE D 182 " --> pdb=" O ILE D 163 " (cutoff:3.500A) removed outlier: 6.673A pdb=" N GLY D 226 " --> pdb=" O MET D 183 " (cutoff:3.500A) Processing sheet with id= M, first strand: chain 'D' and resid 166 through 168 removed outlier: 6.383A pdb=" N TYR D 189 " --> pdb=" O CYS D 167 " (cutoff:3.500A) No H-bonds generated for sheet with id= M Processing sheet with id= N, first strand: chain 'D' and resid 296 through 298 removed outlier: 6.674A pdb=" N LEU D 418 " --> pdb=" O THR D 395 " (cutoff:3.500A) removed outlier: 8.104A pdb=" N ILE D 397 " --> pdb=" O LEU D 418 " (cutoff:3.500A) removed outlier: 7.083A pdb=" N TYR D 420 " --> pdb=" O ILE D 397 " (cutoff:3.500A) Processing sheet with id= O, first strand: chain 'D' and resid 400 through 402 removed outlier: 6.227A pdb=" N GLN D 426 " --> pdb=" O ALA D 401 " (cutoff:3.500A) No H-bonds generated for sheet with id= O Processing sheet with id= P, first strand: chain 'E' and resid 49 through 51 removed outlier: 4.531A pdb=" N THR E 76 " --> pdb=" O PHE E 51 " (cutoff:3.500A) removed outlier: 8.471A pdb=" N PHE E 89 " --> pdb=" O PRO E 121 " (cutoff:3.500A) removed outlier: 6.515A pdb=" N ILE E 123 " --> pdb=" O PHE E 89 " (cutoff:3.500A) removed outlier: 8.250A pdb=" N LYS E 91 " --> pdb=" O ILE E 123 " (cutoff:3.500A) removed outlier: 7.504A pdb=" N ILE E 125 " --> pdb=" O LYS E 91 " (cutoff:3.500A) removed outlier: 6.198A pdb=" N PHE E 180 " --> pdb=" O SER E 161 " (cutoff:3.500A) removed outlier: 7.488A pdb=" N ILE E 163 " --> pdb=" O PHE E 180 " (cutoff:3.500A) removed outlier: 6.651A pdb=" N PHE E 182 " --> pdb=" O ILE E 163 " (cutoff:3.500A) removed outlier: 6.667A pdb=" N GLY E 226 " --> pdb=" O MET E 183 " (cutoff:3.500A) Processing sheet with id= Q, first strand: chain 'E' and resid 166 through 168 removed outlier: 6.256A pdb=" N TYR E 189 " --> pdb=" O CYS E 167 " (cutoff:3.500A) No H-bonds generated for sheet with id= Q Processing sheet with id= R, first strand: chain 'E' and resid 307 through 314 removed outlier: 6.663A pdb=" N LEU E 418 " --> pdb=" O THR E 395 " (cutoff:3.500A) removed outlier: 8.135A pdb=" N ILE E 397 " --> pdb=" O LEU E 418 " (cutoff:3.500A) removed outlier: 7.118A pdb=" N TYR E 420 " --> pdb=" O ILE E 397 " (cutoff:3.500A) removed outlier: 6.595A pdb=" N GLU E 475 " --> pdb=" O ALA E 421 " (cutoff:3.500A) Processing sheet with id= S, first strand: chain 'F' and resid 49 through 51 removed outlier: 4.518A pdb=" N THR F 76 " --> pdb=" O PHE F 51 " (cutoff:3.500A) removed outlier: 8.456A pdb=" N PHE F 89 " --> pdb=" O PRO F 121 " (cutoff:3.500A) removed outlier: 6.550A pdb=" N ILE F 123 " --> pdb=" O PHE F 89 " (cutoff:3.500A) removed outlier: 8.257A pdb=" N LYS F 91 " --> pdb=" O ILE F 123 " (cutoff:3.500A) removed outlier: 7.515A pdb=" N ILE F 125 " --> pdb=" O LYS F 91 " (cutoff:3.500A) removed outlier: 6.315A pdb=" N PHE F 180 " --> pdb=" O SER F 161 " (cutoff:3.500A) removed outlier: 7.583A pdb=" N ILE F 163 " --> pdb=" O PHE F 180 " (cutoff:3.500A) removed outlier: 6.636A pdb=" N PHE F 182 " --> pdb=" O ILE F 163 " (cutoff:3.500A) removed outlier: 6.609A pdb=" N GLY F 226 " --> pdb=" O MET F 183 " (cutoff:3.500A) Processing sheet with id= T, first strand: chain 'F' and resid 166 through 168 removed outlier: 6.231A pdb=" N TYR F 189 " --> pdb=" O CYS F 167 " (cutoff:3.500A) No H-bonds generated for sheet with id= T Processing sheet with id= U, first strand: chain 'F' and resid 297 through 299 removed outlier: 4.526A pdb=" N THR F 309 " --> pdb=" O ILE F 299 " (cutoff:3.500A) removed outlier: 6.637A pdb=" N LEU F 418 " --> pdb=" O THR F 395 " (cutoff:3.500A) removed outlier: 8.139A pdb=" N ILE F 397 " --> pdb=" O LEU F 418 " (cutoff:3.500A) removed outlier: 7.085A pdb=" N TYR F 420 " --> pdb=" O ILE F 397 " (cutoff:3.500A) removed outlier: 6.603A pdb=" N GLU F 475 " --> pdb=" O ALA F 421 " (cutoff:3.500A) Processing sheet with id= V, first strand: chain 'F' and resid 400 through 402 removed outlier: 6.325A pdb=" N GLN F 426 " --> pdb=" O ALA F 401 " (cutoff:3.500A) No H-bonds generated for sheet with id= V Processing sheet with id= W, first strand: chain 'G' and resid 509 through 513 Processing sheet with id= X, first strand: chain 'G' and resid 600 through 602 Processing sheet with id= Y, first strand: chain 'G' and resid 608 through 612 removed outlier: 6.561A pdb=" N ILE G 628 " --> pdb=" O LYS G 610 " (cutoff:3.500A) removed outlier: 4.975A pdb=" N ILE G 612 " --> pdb=" O LEU G 626 " (cutoff:3.500A) removed outlier: 7.952A pdb=" N LEU G 626 " --> pdb=" O ILE G 612 " (cutoff:3.500A) removed outlier: 6.863A pdb=" N LEU G 638 " --> pdb=" O LEU G 626 " (cutoff:3.500A) Processing sheet with id= Z, first strand: chain 'H' and resid 509 through 513 Processing sheet with id= AA, first strand: chain 'H' and resid 600 through 603 removed outlier: 3.812A pdb=" N LEU H 664 " --> pdb=" O LEU H 601 " (cutoff:3.500A) removed outlier: 6.340A pdb=" N CYS H 603 " --> pdb=" O VAL H 662 " (cutoff:3.500A) removed outlier: 6.859A pdb=" N VAL H 662 " --> pdb=" O CYS H 603 " (cutoff:3.500A) Processing sheet with id= AB, first strand: chain 'H' and resid 608 through 612 removed outlier: 6.605A pdb=" N ILE H 628 " --> pdb=" O LYS H 610 " (cutoff:3.500A) removed outlier: 4.984A pdb=" N ILE H 612 " --> pdb=" O LEU H 626 " (cutoff:3.500A) removed outlier: 8.371A pdb=" N LEU H 626 " --> pdb=" O ILE H 612 " (cutoff:3.500A) removed outlier: 6.842A pdb=" N LEU H 638 " --> pdb=" O LEU H 626 " (cutoff:3.500A) Processing sheet with id= AC, first strand: chain 'I' and resid 509 through 513 Processing sheet with id= AD, first strand: chain 'I' and resid 600 through 602 removed outlier: 3.745A pdb=" N LEU I 664 " --> pdb=" O LEU I 601 " (cutoff:3.500A) Processing sheet with id= AE, first strand: chain 'I' and resid 608 through 612 removed outlier: 6.642A pdb=" N ILE I 628 " --> pdb=" O LYS I 610 " (cutoff:3.500A) removed outlier: 4.729A pdb=" N ILE I 612 " --> pdb=" O LEU I 626 " (cutoff:3.500A) removed outlier: 8.064A pdb=" N LEU I 626 " --> pdb=" O ILE I 612 " (cutoff:3.500A) removed outlier: 6.916A pdb=" N LEU I 638 " --> pdb=" O LEU I 626 " (cutoff:3.500A) removed outlier: 4.403A pdb=" N ILE I 628 " --> pdb=" O ASN I 636 " (cutoff:3.500A) removed outlier: 6.252A pdb=" N ASN I 636 " --> pdb=" O ILE I 628 " (cutoff:3.500A) Processing sheet with id= AF, first strand: chain 'J' and resid 509 through 513 Processing sheet with id= AG, first strand: chain 'J' and resid 600 through 602 removed outlier: 3.879A pdb=" N LEU J 664 " --> pdb=" O LEU J 601 " (cutoff:3.500A) Processing sheet with id= AH, first strand: chain 'J' and resid 608 through 612 removed outlier: 6.650A pdb=" N ILE J 628 " --> pdb=" O LYS J 610 " (cutoff:3.500A) removed outlier: 4.772A pdb=" N ILE J 612 " --> pdb=" O LEU J 626 " (cutoff:3.500A) removed outlier: 8.166A pdb=" N LEU J 626 " --> pdb=" O ILE J 612 " (cutoff:3.500A) removed outlier: 6.958A pdb=" N LEU J 638 " --> pdb=" O LEU J 626 " (cutoff:3.500A) removed outlier: 4.349A pdb=" N ILE J 628 " --> pdb=" O ASN J 636 " (cutoff:3.500A) removed outlier: 6.331A pdb=" N ASN J 636 " --> pdb=" O ILE J 628 " (cutoff:3.500A) removed outlier: 4.758A pdb=" N GLU J 630 " --> pdb=" O MET J 634 " (cutoff:3.500A) removed outlier: 6.392A pdb=" N MET J 634 " --> pdb=" O GLU J 630 " (cutoff:3.500A) Processing sheet with id= AI, first strand: chain 'K' and resid 509 through 513 Processing sheet with id= AJ, first strand: chain 'K' and resid 601 through 603 removed outlier: 3.896A pdb=" N LEU K 664 " --> pdb=" O LEU K 601 " (cutoff:3.500A) removed outlier: 6.439A pdb=" N CYS K 603 " --> pdb=" O VAL K 662 " (cutoff:3.500A) removed outlier: 6.774A pdb=" N VAL K 662 " --> pdb=" O CYS K 603 " (cutoff:3.500A) Processing sheet with id= AK, first strand: chain 'K' and resid 608 through 612 removed outlier: 6.638A pdb=" N ILE K 628 " --> pdb=" O LYS K 610 " (cutoff:3.500A) removed outlier: 4.942A pdb=" N ILE K 612 " --> pdb=" O LEU K 626 " (cutoff:3.500A) removed outlier: 8.122A pdb=" N LEU K 626 " --> pdb=" O ILE K 612 " (cutoff:3.500A) removed outlier: 6.963A pdb=" N LEU K 638 " --> pdb=" O LEU K 626 " (cutoff:3.500A) removed outlier: 4.421A pdb=" N ILE K 628 " --> pdb=" O ASN K 636 " (cutoff:3.500A) removed outlier: 6.180A pdb=" N ASN K 636 " --> pdb=" O ILE K 628 " (cutoff:3.500A) Processing sheet with id= AL, first strand: chain 'L' and resid 508 through 513 Processing sheet with id= AM, first strand: chain 'L' and resid 600 through 603 removed outlier: 3.682A pdb=" N LEU L 664 " --> pdb=" O LEU L 601 " (cutoff:3.500A) removed outlier: 6.383A pdb=" N CYS L 603 " --> pdb=" O VAL L 662 " (cutoff:3.500A) removed outlier: 6.825A pdb=" N VAL L 662 " --> pdb=" O CYS L 603 " (cutoff:3.500A) Processing sheet with id= AN, first strand: chain 'L' and resid 608 through 612 removed outlier: 6.573A pdb=" N ILE L 628 " --> pdb=" O LYS L 610 " (cutoff:3.500A) removed outlier: 4.849A pdb=" N ILE L 612 " --> pdb=" O LEU L 626 " (cutoff:3.500A) removed outlier: 8.226A pdb=" N LEU L 626 " --> pdb=" O ILE L 612 " (cutoff:3.500A) removed outlier: 6.882A pdb=" N LEU L 638 " --> pdb=" O LEU L 626 " (cutoff:3.500A) removed outlier: 4.324A pdb=" N ILE L 628 " --> pdb=" O ASN L 636 " (cutoff:3.500A) removed outlier: 6.224A pdb=" N ASN L 636 " --> pdb=" O ILE L 628 " (cutoff:3.500A) removed outlier: 4.691A pdb=" N GLU L 630 " --> pdb=" O MET L 634 " (cutoff:3.500A) removed outlier: 6.402A pdb=" N MET L 634 " --> pdb=" O GLU L 630 " (cutoff:3.500A) 1265 hydrogen bonds defined for protein. 2985 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: 14.57 Time building geometry restraints manager: 14.90 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.19 - 1.74: 33541 1.74 - 2.28: 276 2.28 - 2.82: 0 2.82 - 3.37: 0 3.37 - 3.91: 12 Bond restraints: 33829 Sorted by residual: bond pdb="AO5* COA C 601 " pdb="AP1 COA C 601 " ideal model delta sigma weight residual 1.610 3.912 -2.302 2.00e-02 2.50e+03 1.32e+04 bond pdb="AO5* COA D 601 " pdb="AP1 COA D 601 " ideal model delta sigma weight residual 1.610 3.830 -2.220 2.00e-02 2.50e+03 1.23e+04 bond pdb="AO5* COA E 601 " pdb="AP1 COA E 601 " ideal model delta sigma weight residual 1.610 3.823 -2.213 2.00e-02 2.50e+03 1.22e+04 bond pdb="AO5* COA A 601 " pdb="AP1 COA A 601 " ideal model delta sigma weight residual 1.610 3.811 -2.201 2.00e-02 2.50e+03 1.21e+04 bond pdb="AO5* COA B 601 " pdb="AP1 COA B 601 " ideal model delta sigma weight residual 1.610 3.795 -2.185 2.00e-02 2.50e+03 1.19e+04 ... (remaining 33824 not shown) Histogram of bond angle deviations from ideal: 20.50 - 45.32: 11 45.32 - 70.14: 6 70.14 - 94.95: 10 94.95 - 119.77: 29426 119.77 - 144.59: 16299 Bond angle restraints: 45752 Sorted by residual: angle pdb="AO3 COA C 601 " pdb="AP1 COA C 601 " pdb="AO5* COA C 601 " ideal model delta sigma weight residual 102.60 20.50 82.10 3.00e+00 1.11e-01 7.49e+02 angle pdb="AO3 COA B 601 " pdb="AP1 COA B 601 " pdb="AO5* COA B 601 " ideal model delta sigma weight residual 102.60 21.27 81.33 3.00e+00 1.11e-01 7.35e+02 angle pdb="AO3 COA D 601 " pdb="AP1 COA D 601 " pdb="AO5* COA D 601 " ideal model delta sigma weight residual 102.60 21.77 80.83 3.00e+00 1.11e-01 7.26e+02 angle pdb="AO3 COA E 601 " pdb="AP1 COA E 601 " pdb="AO5* COA E 601 " ideal model delta sigma weight residual 102.60 21.97 80.63 3.00e+00 1.11e-01 7.22e+02 angle pdb="AO3 COA F 601 " pdb="AP1 COA F 601 " pdb="AO5* COA F 601 " ideal model delta sigma weight residual 102.60 25.85 76.75 3.00e+00 1.11e-01 6.55e+02 ... (remaining 45747 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.81: 20034 35.81 - 71.62: 303 71.62 - 107.43: 54 107.43 - 143.24: 14 143.24 - 179.05: 7 Dihedral angle restraints: 20412 sinusoidal: 8301 harmonic: 12111 Sorted by residual: dihedral pdb="AO3 COA F 601 " pdb="AO6 COA F 601 " pdb="AP2 COA F 601 " pdb="PC12 COA F 601 " ideal model delta sinusoidal sigma weight residual 278.38 99.33 179.05 1 2.00e+01 2.50e-03 4.80e+01 dihedral pdb="AO3 COA D 601 " pdb="AO6 COA D 601 " pdb="AP2 COA D 601 " pdb="PC12 COA D 601 " ideal model delta sinusoidal sigma weight residual 278.38 99.60 178.78 1 2.00e+01 2.50e-03 4.80e+01 dihedral pdb="AO3 COA E 601 " pdb="AO6 COA E 601 " pdb="AP2 COA E 601 " pdb="PC12 COA E 601 " ideal model delta sinusoidal sigma weight residual -81.62 93.04 -174.66 1 2.00e+01 2.50e-03 4.79e+01 ... (remaining 20409 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.209: 5096 0.209 - 0.418: 12 0.418 - 0.627: 1 0.627 - 0.836: 0 0.836 - 1.045: 2 Chirality restraints: 5111 Sorted by residual: chirality pdb=" C2 BTI J 701 " pdb=" C4 BTI J 701 " pdb=" C7 BTI J 701 " pdb=" S1 BTI J 701 " both_signs ideal model delta sigma weight residual False 3.11 2.06 1.04 2.00e-01 2.50e+01 2.73e+01 chirality pdb="AC2* COA F 601 " pdb="AC1* COA F 601 " pdb="AC3* COA F 601 " pdb="AO2* COA F 601 " both_signs ideal model delta sigma weight residual False -2.47 -1.50 -0.98 2.00e-01 2.50e+01 2.38e+01 chirality pdb=" C2 BTI I 701 " pdb=" C4 BTI I 701 " pdb=" C7 BTI I 701 " pdb=" S1 BTI I 701 " both_signs ideal model delta sigma weight residual False 3.11 3.55 -0.45 2.00e-01 2.50e+01 5.03e+00 ... (remaining 5108 not shown) Planarity restraints: 6000 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C3 BTI H 701 " -0.038 2.00e-02 2.50e+03 9.61e-02 1.38e+02 pdb=" C4 BTI H 701 " 0.018 2.00e-02 2.50e+03 pdb=" C5 BTI H 701 " 0.123 2.00e-02 2.50e+03 pdb=" N2 BTI H 701 " -0.070 2.00e-02 2.50e+03 pdb=" N3 BTI H 701 " -0.145 2.00e-02 2.50e+03 pdb=" O3 BTI H 701 " 0.112 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C3 BTI G 701 " -0.019 2.00e-02 2.50e+03 8.66e-02 1.12e+02 pdb=" C4 BTI G 701 " 0.122 2.00e-02 2.50e+03 pdb=" C5 BTI G 701 " -0.121 2.00e-02 2.50e+03 pdb=" N2 BTI G 701 " -0.082 2.00e-02 2.50e+03 pdb=" N3 BTI G 701 " 0.092 2.00e-02 2.50e+03 pdb=" O3 BTI G 701 " 0.008 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C3 BTI K 701 " -0.032 2.00e-02 2.50e+03 7.88e-02 9.32e+01 pdb=" C4 BTI K 701 " -0.021 2.00e-02 2.50e+03 pdb=" C5 BTI K 701 " 0.118 2.00e-02 2.50e+03 pdb=" N2 BTI K 701 " -0.020 2.00e-02 2.50e+03 pdb=" N3 BTI K 701 " -0.124 2.00e-02 2.50e+03 pdb=" O3 BTI K 701 " 0.079 2.00e-02 2.50e+03 ... (remaining 5997 not shown) Histogram of nonbonded interaction distances: 1.55 - 2.22: 19 2.22 - 2.89: 13095 2.89 - 3.56: 47594 3.56 - 4.23: 82394 4.23 - 4.90: 139373 Nonbonded interactions: 282475 Sorted by model distance: nonbonded pdb="AO6 COA B 601 " pdb="AP1 COA B 601 " model vdw 1.550 2.720 nonbonded pdb="AO6 COA C 601 " pdb="AP1 COA C 601 " model vdw 1.572 2.720 nonbonded pdb="AO5* COA F 601 " pdb="AP2 COA F 601 " model vdw 1.575 2.720 nonbonded pdb="AO5* COA E 601 " pdb="AP2 COA E 601 " model vdw 1.580 2.720 nonbonded pdb="AO5* COA A 601 " pdb="AP2 COA A 601 " model vdw 1.583 2.720 ... (remaining 282470 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' selection = chain 'D' selection = chain 'E' selection = chain 'F' } ncs_group { reference = (chain 'G' and (resid 461 through 666 or resid 701)) selection = (chain 'H' and (resid 461 through 666 or resid 701)) selection = chain 'I' selection = (chain 'J' and (resid 461 through 666 or resid 701)) selection = (chain 'K' and (resid 461 through 666 or resid 701)) selection = (chain 'L' and (resid 461 through 666 or resid 701)) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians P 18 5.49 5 S 150 5.16 5 C 20917 2.51 5 N 5897 2.21 5 O 7110 1.98 5 sf(0) = scattering factor at diffraction angle 0. 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 individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 4.780 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.000 Extract box with map and model: 10.720 Check model and map are aligned: 0.490 Convert atoms to be neutral: 0.290 Process input model: 89.780 Find NCS groups from input model: 2.690 Set up NCS constraints: 0.260 Set refine NCS operators: 0.000 Set scattering table: 0.020 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:13.790 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 122.830 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8708 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 : 0.039 2.302 33829 Z= 2.633 Angle : 1.578 82.098 45752 Z= 0.621 Chirality : 0.054 1.045 5111 Planarity : 0.006 0.096 6000 Dihedral : 15.054 179.045 12638 Min Nonbonded Distance : 1.550 Molprobity Statistics. All-atom Clashscore : 4.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.70 % Favored : 97.30 % Rotamer Outliers : 0.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -1.94 (0.11), residues: 4265 helix: -1.47 (0.11), residues: 1529 sheet: 0.22 (0.16), residues: 803 loop : -1.72 (0.11), residues: 1933 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8530 Ramachandran restraints generated. 4265 Oldfield, 0 Emsley, 4265 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8530 Ramachandran restraints generated. 4265 Oldfield, 0 Emsley, 4265 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** WARNING: vdw radius undefined for: (HS1 HS); setting to: 1.0 Evaluate side-chains 556 residues out of total 3431 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 556 time to evaluate : 4.278 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 556 average time/residue: 1.9772 time to fit residues: 1259.9698 Evaluate side-chains 458 residues out of total 3431 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 458 time to evaluate : 3.712 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 5.1399 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 423 random chunks: chunk 357 optimal weight: 20.0000 chunk 320 optimal weight: 20.0000 chunk 177 optimal weight: 0.9990 chunk 109 optimal weight: 8.9990 chunk 216 optimal weight: 8.9990 chunk 171 optimal weight: 2.9990 chunk 331 optimal weight: 10.0000 chunk 128 optimal weight: 0.2980 chunk 201 optimal weight: 0.9990 chunk 246 optimal weight: 2.9990 chunk 384 optimal weight: 3.9990 overall best weight: 1.6588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 14 GLN A 57 HIS A 112 GLN B 57 HIS C 57 HIS C 67 GLN C 112 GLN D 56 GLN D 57 HIS D 112 GLN E 57 HIS E 112 GLN F 57 HIS F 112 GLN G 479 ASN G 551 GLN G 611 GLN G 618 GLN H 556 GLN I 551 GLN I 556 GLN I 562 ASN I 600 GLN J 508 GLN J 562 ASN J 636 ASN K 508 GLN K 511 ASN K 562 ASN K 567 GLN K 611 GLN K 618 GLN L 562 ASN ** L 568 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** L 618 GLN L 636 ASN Total number of N/Q/H flips: 35 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8748 moved from start: 0.1333 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.043 33829 Z= 0.186 Angle : 0.760 37.808 45752 Z= 0.362 Chirality : 0.047 0.215 5111 Planarity : 0.005 0.043 6000 Dihedral : 10.072 159.187 4811 Min Nonbonded Distance : 2.033 Molprobity Statistics. All-atom Clashscore : 4.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.58 % Favored : 97.42 % Rotamer Outliers : 0.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -0.65 (0.12), residues: 4265 helix: -0.17 (0.12), residues: 1529 sheet: 1.04 (0.18), residues: 700 loop : -1.14 (0.12), residues: 2036 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8530 Ramachandran restraints generated. 4265 Oldfield, 0 Emsley, 4265 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8530 Ramachandran restraints generated. 4265 Oldfield, 0 Emsley, 4265 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** WARNING: vdw radius undefined for: (HS1 HS); setting to: 1.0 Evaluate side-chains 503 residues out of total 3431 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 478 time to evaluate : 4.279 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 25 outliers final: 12 residues processed: 486 average time/residue: 1.9483 time to fit residues: 1095.3210 Evaluate side-chains 458 residues out of total 3431 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 446 time to evaluate : 4.311 Switching outliers to nearest non-outliers outliers start: 12 outliers final: 4 residues processed: 8 average time/residue: 1.1987 time to fit residues: 17.1480 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 423 random chunks: chunk 213 optimal weight: 10.0000 chunk 119 optimal weight: 9.9990 chunk 319 optimal weight: 10.0000 chunk 261 optimal weight: 0.6980 chunk 105 optimal weight: 4.9990 chunk 384 optimal weight: 0.8980 chunk 415 optimal weight: 0.0470 chunk 342 optimal weight: 6.9990 chunk 381 optimal weight: 0.5980 chunk 131 optimal weight: 3.9990 chunk 308 optimal weight: 9.9990 overall best weight: 1.2480 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 263 ASN C 263 ASN E 67 GLN G 562 ASN G 567 GLN H 562 ASN J 511 ASN L 479 ASN ** L 568 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8733 moved from start: 0.1595 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.040 33829 Z= 0.158 Angle : 0.638 30.372 45752 Z= 0.319 Chirality : 0.045 0.201 5111 Planarity : 0.004 0.038 6000 Dihedral : 8.930 145.667 4811 Min Nonbonded Distance : 2.080 Molprobity Statistics. All-atom Clashscore : 4.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.53 % Favored : 97.47 % Rotamer Outliers : 0.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -0.20 (0.12), residues: 4265 helix: 0.23 (0.13), residues: 1529 sheet: 1.31 (0.18), residues: 700 loop : -0.89 (0.13), residues: 2036 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8530 Ramachandran restraints generated. 4265 Oldfield, 0 Emsley, 4265 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8530 Ramachandran restraints generated. 4265 Oldfield, 0 Emsley, 4265 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** WARNING: vdw radius undefined for: (HS1 HS); setting to: 1.0 Evaluate side-chains 495 residues out of total 3431 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 468 time to evaluate : 4.533 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 27 outliers final: 11 residues processed: 476 average time/residue: 1.9265 time to fit residues: 1056.3135 Evaluate side-chains 472 residues out of total 3431 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 461 time to evaluate : 4.219 Switching outliers to nearest non-outliers outliers start: 11 outliers final: 4 residues processed: 7 average time/residue: 1.0291 time to fit residues: 14.9170 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 423 random chunks: chunk 380 optimal weight: 30.0000 chunk 289 optimal weight: 8.9990 chunk 199 optimal weight: 1.9990 chunk 42 optimal weight: 10.0000 chunk 183 optimal weight: 4.9990 chunk 258 optimal weight: 7.9990 chunk 386 optimal weight: 8.9990 chunk 408 optimal weight: 4.9990 chunk 201 optimal weight: 3.9990 chunk 366 optimal weight: 0.1980 chunk 110 optimal weight: 5.9990 overall best weight: 3.2388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 112 GLN B 263 ASN C 263 ASN G 567 GLN I 556 GLN L 479 ASN L 511 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8784 moved from start: 0.1708 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.046 33829 Z= 0.267 Angle : 0.757 28.447 45752 Z= 0.394 Chirality : 0.050 0.225 5111 Planarity : 0.005 0.046 6000 Dihedral : 9.235 153.025 4811 Min Nonbonded Distance : 2.063 Molprobity Statistics. All-atom Clashscore : 4.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.72 % Favored : 97.28 % Rotamer Outliers : 1.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -0.23 (0.12), residues: 4265 helix: 0.13 (0.13), residues: 1529 sheet: 1.13 (0.17), residues: 754 loop : -0.84 (0.13), residues: 1982 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8530 Ramachandran restraints generated. 4265 Oldfield, 0 Emsley, 4265 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8530 Ramachandran restraints generated. 4265 Oldfield, 0 Emsley, 4265 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** WARNING: vdw radius undefined for: (HS1 HS); setting to: 1.0 Evaluate side-chains 516 residues out of total 3431 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 38 poor density : 478 time to evaluate : 3.952 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 38 outliers final: 17 residues processed: 489 average time/residue: 1.9268 time to fit residues: 1087.8922 Evaluate side-chains 481 residues out of total 3431 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 464 time to evaluate : 3.940 Switching outliers to nearest non-outliers outliers start: 17 outliers final: 7 residues processed: 10 average time/residue: 0.9313 time to fit residues: 17.9983 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 423 random chunks: chunk 340 optimal weight: 20.0000 chunk 232 optimal weight: 7.9990 chunk 5 optimal weight: 0.8980 chunk 304 optimal weight: 9.9990 chunk 168 optimal weight: 0.3980 chunk 348 optimal weight: 9.9990 chunk 282 optimal weight: 0.8980 chunk 0 optimal weight: 10.0000 chunk 208 optimal weight: 4.9990 chunk 366 optimal weight: 10.0000 chunk 103 optimal weight: 3.9990 overall best weight: 2.2384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 263 ASN C 263 ASN G 567 GLN L 479 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8765 moved from start: 0.1749 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.042 33829 Z= 0.208 Angle : 0.687 28.843 45752 Z= 0.353 Chirality : 0.048 0.200 5111 Planarity : 0.005 0.039 6000 Dihedral : 8.964 153.818 4811 Min Nonbonded Distance : 2.093 Molprobity Statistics. All-atom Clashscore : 4.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.39 % Favored : 97.61 % Rotamer Outliers : 0.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -0.09 (0.12), residues: 4265 helix: 0.26 (0.13), residues: 1529 sheet: 1.39 (0.18), residues: 700 loop : -0.79 (0.13), residues: 2036 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8530 Ramachandran restraints generated. 4265 Oldfield, 0 Emsley, 4265 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8530 Ramachandran restraints generated. 4265 Oldfield, 0 Emsley, 4265 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** WARNING: vdw radius undefined for: (HS1 HS); setting to: 1.0 Evaluate side-chains 491 residues out of total 3431 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 463 time to evaluate : 4.420 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 28 outliers final: 13 residues processed: 475 average time/residue: 1.9744 time to fit residues: 1088.3794 Evaluate side-chains 467 residues out of total 3431 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 454 time to evaluate : 4.047 Switching outliers to nearest non-outliers outliers start: 13 outliers final: 7 residues processed: 6 average time/residue: 0.7792 time to fit residues: 11.8932 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 423 random chunks: chunk 137 optimal weight: 4.9990 chunk 368 optimal weight: 5.9990 chunk 80 optimal weight: 8.9990 chunk 240 optimal weight: 3.9990 chunk 100 optimal weight: 6.9990 chunk 409 optimal weight: 10.0000 chunk 339 optimal weight: 50.0000 chunk 189 optimal weight: 5.9990 chunk 34 optimal weight: 2.9990 chunk 135 optimal weight: 5.9990 chunk 214 optimal weight: 0.7980 overall best weight: 3.7588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 263 ASN G 567 GLN I 556 GLN L 479 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8793 moved from start: 0.1794 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.047 33829 Z= 0.296 Angle : 0.789 27.770 45752 Z= 0.414 Chirality : 0.051 0.243 5111 Planarity : 0.006 0.058 6000 Dihedral : 9.265 161.020 4811 Min Nonbonded Distance : 2.037 Molprobity Statistics. All-atom Clashscore : 4.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.72 % Favored : 97.28 % Rotamer Outliers : 1.02 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -0.22 (0.12), residues: 4265 helix: 0.13 (0.13), residues: 1529 sheet: 1.31 (0.17), residues: 712 loop : -0.85 (0.13), residues: 2024 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8530 Ramachandran restraints generated. 4265 Oldfield, 0 Emsley, 4265 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8530 Ramachandran restraints generated. 4265 Oldfield, 0 Emsley, 4265 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** WARNING: vdw radius undefined for: (HS1 HS); setting to: 1.0 Evaluate side-chains 502 residues out of total 3431 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 35 poor density : 467 time to evaluate : 4.356 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 35 outliers final: 21 residues processed: 479 average time/residue: 1.9589 time to fit residues: 1080.5870 Evaluate side-chains 479 residues out of total 3431 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 458 time to evaluate : 3.916 Switching outliers to nearest non-outliers outliers start: 21 outliers final: 8 residues processed: 13 average time/residue: 1.0941 time to fit residues: 23.1114 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 423 random chunks: chunk 394 optimal weight: 0.9990 chunk 46 optimal weight: 3.9990 chunk 233 optimal weight: 0.1980 chunk 298 optimal weight: 6.9990 chunk 231 optimal weight: 4.9990 chunk 344 optimal weight: 1.9990 chunk 228 optimal weight: 1.9990 chunk 407 optimal weight: 9.9990 chunk 255 optimal weight: 10.0000 chunk 248 optimal weight: 5.9990 chunk 188 optimal weight: 5.9990 overall best weight: 1.8388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 263 ASN C 14 GLN G 567 GLN L 479 ASN L 511 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8758 moved from start: 0.1810 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.039 33829 Z= 0.190 Angle : 0.671 29.081 45752 Z= 0.342 Chirality : 0.047 0.194 5111 Planarity : 0.005 0.043 6000 Dihedral : 8.875 159.738 4811 Min Nonbonded Distance : 2.099 Molprobity Statistics. All-atom Clashscore : 4.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.39 % Favored : 97.61 % Rotamer Outliers : 0.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 0.01 (0.12), residues: 4265 helix: 0.34 (0.13), residues: 1526 sheet: 1.45 (0.18), residues: 699 loop : -0.72 (0.13), residues: 2040 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8530 Ramachandran restraints generated. 4265 Oldfield, 0 Emsley, 4265 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8530 Ramachandran restraints generated. 4265 Oldfield, 0 Emsley, 4265 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** WARNING: vdw radius undefined for: (HS1 HS); setting to: 1.0 Evaluate side-chains 486 residues out of total 3431 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 463 time to evaluate : 4.264 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 23 outliers final: 14 residues processed: 475 average time/residue: 1.9228 time to fit residues: 1053.1462 Evaluate side-chains 467 residues out of total 3431 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 453 time to evaluate : 3.994 Switching outliers to nearest non-outliers outliers start: 14 outliers final: 8 residues processed: 6 average time/residue: 1.6281 time to fit residues: 17.4875 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 423 random chunks: chunk 252 optimal weight: 1.9990 chunk 162 optimal weight: 7.9990 chunk 243 optimal weight: 20.0000 chunk 122 optimal weight: 8.9990 chunk 80 optimal weight: 0.9980 chunk 78 optimal weight: 0.8980 chunk 259 optimal weight: 7.9990 chunk 277 optimal weight: 7.9990 chunk 201 optimal weight: 3.9990 chunk 37 optimal weight: 5.9990 chunk 320 optimal weight: 5.9990 overall best weight: 2.7786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 263 ASN G 567 GLN I 511 ASN L 479 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8779 moved from start: 0.1837 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.041 33829 Z= 0.242 Angle : 0.733 28.344 45752 Z= 0.379 Chirality : 0.049 0.224 5111 Planarity : 0.005 0.055 6000 Dihedral : 9.064 164.158 4811 Min Nonbonded Distance : 2.077 Molprobity Statistics. All-atom Clashscore : 4.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.67 % Favored : 97.33 % Rotamer Outliers : 0.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -0.06 (0.12), residues: 4265 helix: 0.25 (0.13), residues: 1526 sheet: 1.43 (0.18), residues: 699 loop : -0.74 (0.13), residues: 2040 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8530 Ramachandran restraints generated. 4265 Oldfield, 0 Emsley, 4265 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8530 Ramachandran restraints generated. 4265 Oldfield, 0 Emsley, 4265 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** WARNING: vdw radius undefined for: (HS1 HS); setting to: 1.0 Evaluate side-chains 485 residues out of total 3431 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 459 time to evaluate : 4.450 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 26 outliers final: 15 residues processed: 472 average time/residue: 2.0310 time to fit residues: 1102.7065 Evaluate side-chains 474 residues out of total 3431 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 459 time to evaluate : 4.051 Switching outliers to nearest non-outliers outliers start: 15 outliers final: 8 residues processed: 7 average time/residue: 1.3034 time to fit residues: 16.5805 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 423 random chunks: chunk 370 optimal weight: 9.9990 chunk 390 optimal weight: 20.0000 chunk 356 optimal weight: 9.9990 chunk 379 optimal weight: 8.9990 chunk 228 optimal weight: 3.9990 chunk 165 optimal weight: 3.9990 chunk 298 optimal weight: 7.9990 chunk 116 optimal weight: 0.5980 chunk 343 optimal weight: 7.9990 chunk 359 optimal weight: 20.0000 chunk 378 optimal weight: 0.7980 overall best weight: 3.4786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: G 567 GLN L 479 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8786 moved from start: 0.1851 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.042 33829 Z= 0.282 Angle : 0.770 27.866 45752 Z= 0.402 Chirality : 0.051 0.237 5111 Planarity : 0.006 0.077 6000 Dihedral : 9.173 166.188 4811 Min Nonbonded Distance : 2.076 Molprobity Statistics. All-atom Clashscore : 4.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.44 % Favored : 97.56 % Rotamer Outliers : 0.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.12 (0.12), residues: 4265 helix: 0.20 (0.13), residues: 1526 sheet: 1.37 (0.17), residues: 711 loop : -0.80 (0.13), residues: 2028 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8530 Ramachandran restraints generated. 4265 Oldfield, 0 Emsley, 4265 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8530 Ramachandran restraints generated. 4265 Oldfield, 0 Emsley, 4265 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** WARNING: vdw radius undefined for: (HS1 HS); setting to: 1.0 Evaluate side-chains 486 residues out of total 3431 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 464 time to evaluate : 3.651 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 22 outliers final: 12 residues processed: 476 average time/residue: 1.9217 time to fit residues: 1056.7801 Evaluate side-chains 472 residues out of total 3431 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 460 time to evaluate : 4.229 Switching outliers to nearest non-outliers outliers start: 12 outliers final: 8 residues processed: 4 average time/residue: 1.2033 time to fit residues: 11.7295 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 423 random chunks: chunk 249 optimal weight: 4.9990 chunk 401 optimal weight: 6.9990 chunk 245 optimal weight: 5.9990 chunk 190 optimal weight: 4.9990 chunk 279 optimal weight: 0.6980 chunk 421 optimal weight: 10.0000 chunk 387 optimal weight: 0.9990 chunk 335 optimal weight: 7.9990 chunk 34 optimal weight: 2.9990 chunk 259 optimal weight: 9.9990 chunk 205 optimal weight: 5.9990 overall best weight: 2.9388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: G 567 GLN L 479 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8779 moved from start: 0.1851 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.044 33829 Z= 0.249 Angle : 0.739 28.533 45752 Z= 0.382 Chirality : 0.049 0.232 5111 Planarity : 0.005 0.082 6000 Dihedral : 9.150 165.827 4811 Min Nonbonded Distance : 2.085 Molprobity Statistics. All-atom Clashscore : 4.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.60 % Favored : 97.40 % Rotamer Outliers : 0.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -0.08 (0.12), residues: 4265 helix: 0.23 (0.13), residues: 1526 sheet: 1.41 (0.18), residues: 699 loop : -0.75 (0.13), residues: 2040 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8530 Ramachandran restraints generated. 4265 Oldfield, 0 Emsley, 4265 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8530 Ramachandran restraints generated. 4265 Oldfield, 0 Emsley, 4265 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** WARNING: vdw radius undefined for: (HS1 HS); setting to: 1.0 Evaluate side-chains 478 residues out of total 3431 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 464 time to evaluate : 4.174 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 14 outliers final: 9 residues processed: 475 average time/residue: 1.9647 time to fit residues: 1075.1754 Evaluate side-chains 471 residues out of total 3431 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 462 time to evaluate : 4.043 Switching outliers to nearest non-outliers outliers start: 9 outliers final: 8 residues processed: 1 average time/residue: 1.8824 time to fit residues: 7.6883 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 423 random chunks: chunk 266 optimal weight: 9.9990 chunk 357 optimal weight: 4.9990 chunk 102 optimal weight: 5.9990 chunk 309 optimal weight: 6.9990 chunk 49 optimal weight: 0.9980 chunk 93 optimal weight: 0.9980 chunk 336 optimal weight: 5.9990 chunk 140 optimal weight: 0.0000 chunk 345 optimal weight: 10.0000 chunk 42 optimal weight: 10.0000 chunk 61 optimal weight: 3.9990 overall best weight: 2.1988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: G 567 GLN L 479 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3952 r_free = 0.3952 target = 0.162170 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3481 r_free = 0.3481 target = 0.124524 restraints weight = 24574.775| |-----------------------------------------------------------------------------| r_work (start): 0.3467 rms_B_bonded: 1.18 r_work: 0.3371 rms_B_bonded: 1.24 restraints_weight: 0.5000 r_work: 0.3277 rms_B_bonded: 1.63 restraints_weight: 0.2500 r_work: 0.3160 rms_B_bonded: 2.54 restraints_weight: 0.1250 r_work: 0.3017 rms_B_bonded: 4.85 restraints_weight: 0.0625 r_work (final): 0.3017 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8910 moved from start: 0.1867 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.039 33829 Z= 0.210 Angle : 0.697 28.884 45752 Z= 0.357 Chirality : 0.048 0.213 5111 Planarity : 0.005 0.042 6000 Dihedral : 9.015 164.919 4811 Min Nonbonded Distance : 2.108 Molprobity Statistics. All-atom Clashscore : 4.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.42 % Favored : 97.58 % Rotamer Outliers : 0.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -0.00 (0.12), residues: 4265 helix: 0.31 (0.13), residues: 1526 sheet: 1.45 (0.18), residues: 699 loop : -0.72 (0.13), residues: 2040 =============================================================================== Job complete usr+sys time: 14438.36 seconds wall clock time: 255 minutes 50.08 seconds (15350.08 seconds total)