Starting phenix.real_space_refine (version: dev) on Thu Dec 22 11:26:58 2022 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5n61_3593/12_2022/5n61_3593.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5n61_3593/12_2022/5n61_3593.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.4 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5n61_3593/12_2022/5n61_3593.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5n61_3593/12_2022/5n61_3593.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5n61_3593/12_2022/5n61_3593.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5n61_3593/12_2022/5n61_3593.pdb" } resolution = 3.4 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= 0.000 sd= 0.012 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Convert atoms to be neutral Process input model Symmetric amino acids flipped Residue "A ARG 347": "NH1" <-> "NH2" Residue "B ARG 211": "NH1" <-> "NH2" Residue "B ARG 237": "NH1" <-> "NH2" Residue "B ARG 1063": "NH1" <-> "NH2" Residue "B ARG 1091": "NH1" <-> "NH2" Residue "P ARG 181": "NH1" <-> "NH2" Residue "P GLU 201": "OE1" <-> "OE2" Residue "P GLU 237": "OE1" <-> "OE2" Residue "P ARG 256": "NH1" <-> "NH2" Residue "P GLU 266": "OE1" <-> "OE2" Residue "P GLU 275": "OE1" <-> "OE2" Residue "P ARG 280": "NH1" <-> "NH2" Residue "P GLU 290": "OE1" <-> "OE2" Residue "P GLU 356": "OE1" <-> "OE2" Residue "P ARG 407": "NH1" <-> "NH2" Residue "P ARG 419": "NH1" <-> "NH2" Residue "P GLU 428": "OE1" <-> "OE2" Residue "P ARG 472": "NH1" <-> "NH2" Residue "P ARG 484": "NH1" <-> "NH2" Residue "P GLU 499": "OE1" <-> "OE2" Residue "P GLU 509": "OE1" <-> "OE2" Residue "P ARG 542": "NH1" <-> "NH2" Residue "P GLU 546": "OE1" <-> "OE2" Residue "P TYR 548": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "P GLU 573": "OE1" <-> "OE2" Residue "P GLU 587": "OE1" <-> "OE2" Residue "P ARG 603": "NH1" <-> "NH2" Residue "P GLU 706": "OE1" <-> "OE2" Residue "P ARG 762": "NH1" <-> "NH2" Residue "Q ARG 6": "NH1" <-> "NH2" Residue "Q ARG 18": "NH1" <-> "NH2" Residue "Q ARG 21": "NH1" <-> "NH2" Residue "Q ARG 26": "NH1" <-> "NH2" Residue "Q ARG 27": "NH1" <-> "NH2" Residue "Q GLU 99": "OE1" <-> "OE2" Residue "Q ARG 114": "NH1" <-> "NH2" Residue "Q ARG 117": "NH1" <-> "NH2" Residue "Q GLU 151": "OE1" <-> "OE2" Residue "Q GLU 241": "OE1" <-> "OE2" Residue "Q GLU 278": "OE1" <-> "OE2" Residue "Q ARG 293": "NH1" <-> "NH2" Residue "Q ARG 305": "NH1" <-> "NH2" Residue "Q GLU 336": "OE1" <-> "OE2" Residue "Q ARG 350": "NH1" <-> "NH2" Residue "Q GLU 373": "OE1" <-> "OE2" Residue "Q GLU 376": "OE1" <-> "OE2" Residue "Q GLU 382": "OE1" <-> "OE2" Residue "Q ARG 411": "NH1" <-> "NH2" Residue "Q ARG 478": "NH1" <-> "NH2" Residue "Q GLU 496": "OE1" <-> "OE2" Residue "Q ARG 504": "NH1" <-> "NH2" Residue "R GLU 3": "OE1" <-> "OE2" Residue "R ARG 17": "NH1" <-> "NH2" Residue "R ARG 30": "NH1" <-> "NH2" Residue "R ARG 33": "NH1" <-> "NH2" Residue "R GLU 81": "OE1" <-> "OE2" Residue "R ARG 82": "NH1" <-> "NH2" Residue "R GLU 166": "OE1" <-> "OE2" Residue "R GLU 204": "OE1" <-> "OE2" Residue "R ARG 209": "NH1" <-> "NH2" Residue "R ARG 291": "NH1" <-> "NH2" Residue "R ARG 302": "NH1" <-> "NH2" Residue "R PHE 308": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.14s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-4807/modules/chem_data/mon_lib" Total number of atoms: 48547 Number of models: 1 Model: "" Number of chains: 27 Chain: "A" Number of atoms: 11526 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1459, 11526 Classifications: {'peptide': 1459} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'CIS': 1, 'PCIS': 5, 'PTRANS': 54, 'TRANS': 1398} Chain breaks: 5 Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 3 Unresolved non-hydrogen dihedrals: 1 Unresolved non-hydrogen chiralities: 1 Chain: "B" Number of atoms: 9350 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1177, 9350 Classifications: {'peptide': 1177} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 58, 'TRANS': 1117} Chain breaks: 2 Chain: "C" Number of atoms: 2423 Number of conformers: 1 Conformer: "" Number of residues, atoms: 305, 2423 Classifications: {'peptide': 305} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 19, 'TRANS': 285} Chain: "D" Number of atoms: 431 Number of conformers: 1 Conformer: "" Number of residues, atoms: 54, 431 Classifications: {'peptide': 54} Link IDs: {'PTRANS': 2, 'TRANS': 51} Chain breaks: 1 Chain: "E" Number of atoms: 1735 Number of conformers: 1 Conformer: "" Number of residues, atoms: 212, 1735 Classifications: {'peptide': 212} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 11, 'TRANS': 199} Chain: "F" Number of atoms: 823 Number of conformers: 1 Conformer: "" Number of residues, atoms: 100, 823 Classifications: {'peptide': 100} Link IDs: {'PTRANS': 6, 'TRANS': 93} Chain: "G" Number of atoms: 1526 Number of conformers: 1 Conformer: "" Number of residues, atoms: 193, 1526 Classifications: {'peptide': 193} Link IDs: {'CIS': 1, 'PTRANS': 11, 'TRANS': 180} Chain breaks: 1 Chain: "H" Number of atoms: 1052 Number of conformers: 1 Conformer: "" Number of residues, atoms: 131, 1052 Classifications: {'peptide': 131} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 4, 'TRANS': 126} Chain breaks: 1 Chain: "I" Number of atoms: 466 Number of conformers: 1 Conformer: "" Number of residues, atoms: 63, 466 Classifications: {'peptide': 63} Link IDs: {'PTRANS': 3, 'TRANS': 59} Chain: "J" Number of atoms: 569 Number of conformers: 1 Conformer: "" Number of residues, atoms: 69, 569 Classifications: {'peptide': 69} Link IDs: {'PTRANS': 2, 'TRANS': 66} Chain: "K" Number of atoms: 793 Number of conformers: 1 Conformer: "" Number of residues, atoms: 101, 793 Classifications: {'peptide': 101} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 3, 'TRANS': 97} Chain: "L" Number of atoms: 352 Number of conformers: 1 Conformer: "" Number of residues, atoms: 44, 352 Classifications: {'peptide': 44} Modifications used: {'COO': 1} Link IDs: {'TRANS': 43} Chain: "M" Number of atoms: 856 Number of conformers: 1 Conformer: "" Number of residues, atoms: 108, 856 Classifications: {'peptide': 108} Link IDs: {'PTRANS': 5, 'TRANS': 102} Chain: "N" Number of atoms: 1029 Number of conformers: 1 Conformer: "" Number of residues, atoms: 129, 1029 Classifications: {'peptide': 129} Link IDs: {'PTRANS': 9, 'TRANS': 119} Chain breaks: 3 Chain: "O" Number of atoms: 3811 Number of conformers: 1 Conformer: "" Number of residues, atoms: 463, 3811 Classifications: {'peptide': 463} Incomplete info: {'truncation_to_alanine': 5} Link IDs: {'PTRANS': 13, 'TRANS': 449} Chain breaks: 2 Unresolved non-hydrogen bonds: 23 Unresolved non-hydrogen angles: 28 Unresolved non-hydrogen dihedrals: 20 Planarities with less than four sites: {'PHE:plan': 1, 'ASN:plan1': 2, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 17 Chain: "P" Number of atoms: 4764 Number of conformers: 1 Conformer: "" Number of residues, atoms: 587, 4764 Classifications: {'peptide': 587} Link IDs: {'PCIS': 1, 'PTRANS': 16, 'TRANS': 569} Chain breaks: 6 Chain: "Q" Number of atoms: 3254 Number of conformers: 1 Conformer: "" Number of residues, atoms: 389, 3254 Classifications: {'peptide': 389} Link IDs: {'PCIS': 2, 'PTRANS': 14, 'TRANS': 372} Chain breaks: 5 Chain: "R" Number of atoms: 2535 Number of conformers: 1 Conformer: "" Number of residues, atoms: 303, 2535 Classifications: {'peptide': 303} Link IDs: {'PCIS': 1, 'PTRANS': 10, 'TRANS': 291} Chain breaks: 5 Chain: "S" Number of atoms: 108 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 108 Classifications: {'RNA': 5} Modifications used: {'rna2p_pyr': 1, 'rna3p_pur': 3, 'rna3p_pyr': 1} Link IDs: {'rna2p': 1, 'rna3p': 3} Chain: "T" Number of atoms: 641 Number of conformers: 1 Conformer: "" Number of residues, atoms: 41, 641 Classifications: {'DNA': 41} Modifications used: {'5*END': 1} Link IDs: {'rna3p': 40} Chain breaks: 1 Unresolved non-hydrogen bonds: 220 Unresolved non-hydrogen angles: 350 Unresolved non-hydrogen dihedrals: 150 Unresolved non-hydrogen chiralities: 20 Planarities with less than four sites: {' DG:plan': 5, ' DG:plan2': 5, ' DC:plan2': 5, ' DA:plan2': 5, ' DC:plan': 5, ' DT:plan': 5, ' DA:plan': 5} Unresolved non-hydrogen planarities: 220 Chain: "U" Number of atoms: 490 Number of conformers: 1 Conformer: "" Number of residues, atoms: 33, 490 Classifications: {'DNA': 33} Link IDs: {'rna3p': 32} Chain breaks: 1 Unresolved non-hydrogen bonds: 220 Unresolved non-hydrogen angles: 350 Unresolved non-hydrogen dihedrals: 150 Unresolved non-hydrogen chiralities: 20 Planarities with less than four sites: {' DG:plan': 5, ' DG:plan2': 5, ' DC:plan2': 5, ' DA:plan2': 5, ' DC:plan': 5, ' DT:plan': 5, ' DA:plan': 5} Unresolved non-hydrogen planarities: 220 Chain: "A" Number of atoms: 3 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 3 Unusual residues: {' MG': 1, ' ZN': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "B" Number of atoms: 6 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 6 Unusual residues: {' ZN': 1, 'SO4': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "I" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} Chain: "J" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} Chain: "L" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} Chain: "Q" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 461 SG CYS A 62 77.501 60.829 57.409 1.00100.00 S ATOM 480 SG CYS A 65 75.619 61.718 57.750 1.00100.00 S ATOM 535 SG CYS A 72 75.853 62.596 58.955 1.00100.00 S ATOM 781 SG CYS A 102 72.738 19.661 87.145 1.00100.00 S ATOM 806 SG CYS A 105 71.040 18.688 87.645 1.00100.00 S ATOM 1589 SG CYS A 233 70.383 19.147 88.793 1.00100.00 S ATOM 1611 SG CYS A 236 72.304 16.866 88.318 1.00100.00 S ATOM 20169 SG CYS B1104 61.817 51.057 61.345 1.00100.00 S ATOM 20195 SG CYS B1107 64.162 50.833 63.048 1.00100.00 S ATOM 20342 SG CYS B1128 65.298 51.632 61.415 1.00100.00 S ATOM 20370 SG CYS B1131 63.002 47.717 61.130 1.00100.00 S ATOM 28929 SG CYS I 10 116.641 41.363 140.394 1.00100.00 S ATOM 28951 SG CYS I 13 116.373 41.307 137.691 1.00100.00 S ATOM 29071 SG CYS I 30 116.154 39.926 136.827 1.00100.00 S ATOM 29092 SG CYS I 33 118.149 40.606 138.489 1.00100.00 S ATOM 29386 SG CYS J 7 77.060 120.445 98.918 1.00100.00 S ATOM 29409 SG CYS J 10 74.866 122.916 100.100 1.00100.00 S ATOM 29689 SG CYS J 45 75.542 120.844 100.045 1.00100.00 S ATOM 29695 SG CYS J 46 77.144 123.456 99.329 1.00100.00 S ATOM 30737 SG CYS L 31 113.002 102.587 80.326 1.00100.00 S ATOM 30757 SG CYS L 34 115.110 105.191 80.415 1.00100.00 S ATOM 30861 SG CYS L 48 115.642 103.186 77.901 1.00100.00 S ATOM 30884 SG CYS L 51 117.269 103.111 82.137 1.00100.00 S ATOM 41568 SG CYS Q 10 72.512 83.509 50.555 1.00100.00 S ATOM 41601 SG CYS Q 15 71.967 86.380 48.453 1.00100.00 S ATOM 41721 SG CYS Q 29 71.844 85.218 53.015 1.00100.00 S Time building chain proxies: 26.40, per 1000 atoms: 0.54 Number of scatterers: 48547 At special positions: 0 Unit cell: (210.18, 159.33, 180.8, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 7 Type Number sf(0) Zn 7 29.99 S 229 16.00 P 78 15.00 Mg 1 11.99 O 9260 8.00 N 8294 7.00 C 30678 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 Atom "ATOM 47952 O4' DC T 41 .*. O " rejected from bonding due to valence issues. Atom "ATOM 48205 O4' DA U 16 .*. O " rejected from bonding due to valence issues. Atom "ATOM 47974 O4' DT T 43 .*. O " rejected from bonding due to valence issues. Atom "ATOM 47971 O5' DT T 43 .*. O " rejected from bonding due to valence issues. Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 20.56 Conformation dependent library (CDL) restraints added in 6.5 seconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN A3001 " pdb="ZN ZN A3001 " - pdb=" NE2 HIS A 75 " pdb="ZN ZN A3001 " - pdb=" SG CYS A 72 " pdb="ZN ZN A3001 " - pdb=" SG CYS A 62 " pdb="ZN ZN A3001 " - pdb=" SG CYS A 65 " pdb=" ZN A3002 " pdb="ZN ZN A3002 " - pdb=" SG CYS A 233 " pdb="ZN ZN A3002 " - pdb=" SG CYS A 102 " pdb="ZN ZN A3002 " - pdb=" SG CYS A 236 " pdb="ZN ZN A3002 " - pdb=" SG CYS A 105 " pdb=" ZN B1302 " pdb="ZN ZN B1302 " - pdb=" SG CYS B1128 " pdb="ZN ZN B1302 " - pdb=" SG CYS B1131 " pdb="ZN ZN B1302 " - pdb=" SG CYS B1107 " pdb="ZN ZN B1302 " - pdb=" SG CYS B1104 " pdb=" ZN I3001 " pdb="ZN ZN I3001 " - pdb=" SG CYS I 33 " pdb="ZN ZN I3001 " - pdb=" SG CYS I 10 " pdb="ZN ZN I3001 " - pdb=" SG CYS I 30 " pdb="ZN ZN I3001 " - pdb=" SG CYS I 13 " pdb=" ZN J3001 " pdb="ZN ZN J3001 " - pdb=" SG CYS J 10 " pdb="ZN ZN J3001 " - pdb=" SG CYS J 7 " pdb="ZN ZN J3001 " - pdb=" SG CYS J 46 " pdb="ZN ZN J3001 " - pdb=" SG CYS J 45 " pdb=" ZN L3001 " pdb="ZN ZN L3001 " - pdb=" SG CYS L 48 " pdb="ZN ZN L3001 " - pdb=" SG CYS L 31 " pdb="ZN ZN L3001 " - pdb=" SG CYS L 34 " pdb="ZN ZN L3001 " - pdb=" SG CYS L 51 " pdb=" ZN Q1001 " pdb="ZN ZN Q1001 " - pdb=" SG CYS Q 10 " pdb="ZN ZN Q1001 " - pdb=" SG CYS Q 15 " pdb="ZN ZN Q1001 " - pdb=" SG CYS Q 29 " pdb="ZN ZN Q1001 " - pdb=" ND1 HIS Q 33 " Number of angles added : 36 11574 Ramachandran restraints generated. 5787 Oldfield, 0 Emsley, 5787 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 11174 Finding SS restraints... Secondary structure from input PDB file: 218 helices and 59 sheets defined 44.3% alpha, 15.6% beta 10 base pairs and 25 stacking pairs defined. Time for finding SS restraints: 13.36 Creating SS restraints... Processing helix chain 'A' and resid 20 through 28 Processing helix chain 'A' and resid 51 through 55 Processing helix chain 'A' and resid 91 through 100 Processing helix chain 'A' and resid 111 through 127 removed outlier: 4.283A pdb=" N TYR A 118 " --> pdb=" O GLU A 114 " (cutoff:3.500A) removed outlier: 3.518A pdb=" N ARG A 123 " --> pdb=" O ALA A 119 " (cutoff:3.500A) removed outlier: 3.636A pdb=" N TYR A 127 " --> pdb=" O ARG A 123 " (cutoff:3.500A) Processing helix chain 'A' and resid 129 through 138 removed outlier: 3.858A pdb=" N SER A 133 " --> pdb=" O LEU A 129 " (cutoff:3.500A) removed outlier: 3.744A pdb=" N TYR A 134 " --> pdb=" O ILE A 130 " (cutoff:3.500A) removed outlier: 3.753A pdb=" N ASP A 137 " --> pdb=" O SER A 133 " (cutoff:3.500A) removed outlier: 3.787A pdb=" N GLU A 138 " --> pdb=" O TYR A 134 " (cutoff:3.500A) Processing helix chain 'A' and resid 175 through 199 removed outlier: 3.568A pdb=" N ASP A 199 " --> pdb=" O LYS A 195 " (cutoff:3.500A) Processing helix chain 'A' and resid 209 through 230 removed outlier: 3.670A pdb=" N ARG A 230 " --> pdb=" O LYS A 226 " (cutoff:3.500A) Processing helix chain 'A' and resid 257 through 268 Processing helix chain 'A' and resid 316 through 339 removed outlier: 6.007A pdb=" N CYS A 333 " --> pdb=" O ARG A 329 " (cutoff:3.500A) removed outlier: 5.882A pdb=" N VAL A 334 " --> pdb=" O LYS A 330 " (cutoff:3.500A) removed outlier: 4.175A pdb=" N TYR A 337 " --> pdb=" O CYS A 333 " (cutoff:3.500A) Processing helix chain 'A' and resid 352 through 357 removed outlier: 4.061A pdb=" N PHE A 356 " --> pdb=" O ALA A 352 " (cutoff:3.500A) removed outlier: 3.884A pdb=" N MET A 357 " --> pdb=" O ASP A 353 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 352 through 357' Processing helix chain 'A' and resid 364 through 369 removed outlier: 3.755A pdb=" N LEU A 369 " --> pdb=" O ARG A 366 " (cutoff:3.500A) Processing helix chain 'A' and resid 380 through 406 removed outlier: 3.585A pdb=" N VAL A 389 " --> pdb=" O LEU A 385 " (cutoff:3.500A) Processing helix chain 'A' and resid 412 through 439 removed outlier: 3.708A pdb=" N ARG A 417 " --> pdb=" O LEU A 413 " (cutoff:3.500A) removed outlier: 3.662A pdb=" N ILE A 419 " --> pdb=" O ASP A 415 " (cutoff:3.500A) removed outlier: 3.995A pdb=" N SER A 421 " --> pdb=" O ARG A 417 " (cutoff:3.500A) removed outlier: 4.007A pdb=" N ARG A 422 " --> pdb=" O VAL A 418 " (cutoff:3.500A) removed outlier: 4.046A pdb=" N MET A 424 " --> pdb=" O PHE A 420 " (cutoff:3.500A) removed outlier: 3.643A pdb=" N ASN A 425 " --> pdb=" O SER A 421 " (cutoff:3.500A) removed outlier: 4.579A pdb=" N VAL A 428 " --> pdb=" O MET A 424 " (cutoff:3.500A) removed outlier: 3.563A pdb=" N THR A 429 " --> pdb=" O ASN A 425 " (cutoff:3.500A) Processing helix chain 'A' and resid 455 through 461 Processing helix chain 'A' and resid 462 through 465 removed outlier: 3.669A pdb=" N GLY A 465 " --> pdb=" O LYS A 462 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 462 through 465' Processing helix chain 'A' and resid 498 through 505 Processing helix chain 'A' and resid 515 through 526 removed outlier: 4.086A pdb=" N GLN A 521 " --> pdb=" O ALA A 517 " (cutoff:3.500A) removed outlier: 3.913A pdb=" N GLY A 526 " --> pdb=" O ALA A 522 " (cutoff:3.500A) Processing helix chain 'A' and resid 550 through 562 removed outlier: 3.802A pdb=" N LEU A 557 " --> pdb=" O GLN A 553 " (cutoff:3.500A) removed outlier: 4.597A pdb=" N LEU A 562 " --> pdb=" O ALA A 558 " (cutoff:3.500A) Processing helix chain 'A' and resid 596 through 598 No H-bonds generated for 'chain 'A' and resid 596 through 598' Processing helix chain 'A' and resid 620 through 625 Processing helix chain 'A' and resid 640 through 650 Processing helix chain 'A' and resid 671 through 682 Processing helix chain 'A' and resid 688 through 700 Processing helix chain 'A' and resid 728 through 740 removed outlier: 3.549A pdb=" N ILE A 732 " --> pdb=" O GLY A 728 " (cutoff:3.500A) Processing helix chain 'A' and resid 756 through 760 Processing helix chain 'A' and resid 782 through 787 Processing helix chain 'A' and resid 792 through 802 Processing helix chain 'A' and resid 802 through 825 removed outlier: 3.603A pdb=" N GLY A 814 " --> pdb=" O LEU A 810 " (cutoff:3.500A) Processing helix chain 'A' and resid 829 through 834 Processing helix chain 'A' and resid 836 through 849 removed outlier: 3.524A pdb=" N THR A 849 " --> pdb=" O ASP A 845 " (cutoff:3.500A) Processing helix chain 'A' and resid 852 through 862 Processing helix chain 'A' and resid 872 through 885 Processing helix chain 'A' and resid 885 through 912 Processing helix chain 'A' and resid 923 through 932 Processing helix chain 'A' and resid 936 through 945 Processing helix chain 'A' and resid 991 through 1028 removed outlier: 3.817A pdb=" N SER A1014 " --> pdb=" O ALA A1010 " (cutoff:3.500A) removed outlier: 3.731A pdb=" N SER A1016 " --> pdb=" O LYS A1012 " (cutoff:3.500A) removed outlier: 3.667A pdb=" N GLY A1017 " --> pdb=" O THR A1013 " (cutoff:3.500A) removed outlier: 3.653A pdb=" N ARG A1021 " --> pdb=" O GLY A1017 " (cutoff:3.500A) removed outlier: 3.630A pdb=" N CYS A1022 " --> pdb=" O TYR A1018 " (cutoff:3.500A) Processing helix chain 'A' and resid 1056 through 1064 removed outlier: 4.663A pdb=" N SER A1061 " --> pdb=" O THR A1058 " (cutoff:3.500A) removed outlier: 4.842A pdb=" N HIS A1062 " --> pdb=" O LYS A1059 " (cutoff:3.500A) removed outlier: 3.843A pdb=" N THR A1064 " --> pdb=" O SER A1061 " (cutoff:3.500A) Processing helix chain 'A' and resid 1065 through 1071 Processing helix chain 'A' and resid 1072 through 1081 removed outlier: 3.591A pdb=" N LYS A1078 " --> pdb=" O TYR A1074 " (cutoff:3.500A) Processing helix chain 'A' and resid 1081 through 1086 removed outlier: 4.422A pdb=" N LEU A1085 " --> pdb=" O ASN A1081 " (cutoff:3.500A) Processing helix chain 'A' and resid 1091 through 1108 removed outlier: 3.812A pdb=" N LEU A1095 " --> pdb=" O VAL A1091 " (cutoff:3.500A) removed outlier: 3.906A pdb=" N TYR A1104 " --> pdb=" O LYS A1100 " (cutoff:3.500A) Processing helix chain 'A' and resid 1122 through 1127 removed outlier: 4.116A pdb=" N LYS A1126 " --> pdb=" O PRO A1122 " (cutoff:3.500A) Processing helix chain 'A' and resid 1137 through 1151 Processing helix chain 'A' and resid 1151 through 1158 removed outlier: 3.947A pdb=" N PHE A1155 " --> pdb=" O ASN A1151 " (cutoff:3.500A) removed outlier: 3.670A pdb=" N LYS A1156 " --> pdb=" O SER A1152 " (cutoff:3.500A) Processing helix chain 'A' and resid 1162 through 1177 Processing helix chain 'A' and resid 1184 through 1200 Proline residue: A1196 - end of helix removed outlier: 3.553A pdb=" N GLN A1199 " --> pdb=" O GLU A1195 " (cutoff:3.500A) removed outlier: 3.591A pdb=" N MET A1200 " --> pdb=" O PRO A1196 " (cutoff:3.500A) Processing helix chain 'A' and resid 1217 through 1227 Processing helix chain 'A' and resid 1247 through 1258 Processing helix chain 'A' and resid 1263 through 1266 No H-bonds generated for 'chain 'A' and resid 1263 through 1266' Processing helix chain 'A' and resid 1298 through 1306 Processing helix chain 'A' and resid 1309 through 1319 Processing helix chain 'A' and resid 1319 through 1336 removed outlier: 3.795A pdb=" N ALA A1328 " --> pdb=" O LEU A1324 " (cutoff:3.500A) removed outlier: 3.582A pdb=" N ILE A1329 " --> pdb=" O LEU A1325 " (cutoff:3.500A) Processing helix chain 'A' and resid 1442 through 1454 removed outlier: 3.558A pdb=" N ARG A1446 " --> pdb=" O VAL A1442 " (cutoff:3.500A) removed outlier: 3.624A pdb=" N HIS A1454 " --> pdb=" O ILE A1450 " (cutoff:3.500A) Processing helix chain 'A' and resid 1484 through 1496 removed outlier: 3.797A pdb=" N ILE A1488 " --> pdb=" O LEU A1484 " (cutoff:3.500A) Processing helix chain 'A' and resid 1512 through 1516 removed outlier: 3.897A pdb=" N GLY A1515 " --> pdb=" O PRO A1512 " (cutoff:3.500A) Processing helix chain 'A' and resid 1525 through 1531 removed outlier: 3.528A pdb=" N MET A1529 " --> pdb=" O ASN A1525 " (cutoff:3.500A) Processing helix chain 'A' and resid 1537 through 1541 Processing helix chain 'A' and resid 1545 through 1573 removed outlier: 7.381A pdb=" N VAL A1555 " --> pdb=" O LYS A1551 " (cutoff:3.500A) removed outlier: 8.963A pdb=" N GLU A1556 " --> pdb=" O THR A1552 " (cutoff:3.500A) removed outlier: 4.417A pdb=" N ALA A1557 " --> pdb=" O TYR A1553 " (cutoff:3.500A) Processing helix chain 'A' and resid 1578 through 1590 removed outlier: 3.834A pdb=" N LEU A1582 " --> pdb=" O SER A1578 " (cutoff:3.500A) Processing helix chain 'A' and resid 1599 through 1604 Processing helix chain 'A' and resid 1608 through 1616 removed outlier: 3.731A pdb=" N LYS A1612 " --> pdb=" O SER A1608 " (cutoff:3.500A) removed outlier: 3.905A pdb=" N GLU A1616 " --> pdb=" O LYS A1612 " (cutoff:3.500A) Processing helix chain 'A' and resid 1617 through 1628 removed outlier: 3.627A pdb=" N PHE A1621 " --> pdb=" O THR A1617 " (cutoff:3.500A) Processing helix chain 'A' and resid 1636 through 1644 Processing helix chain 'B' and resid 17 through 27 Processing helix chain 'B' and resid 35 through 54 removed outlier: 3.548A pdb=" N GLN B 39 " --> pdb=" O PHE B 35 " (cutoff:3.500A) removed outlier: 3.773A pdb=" N VAL B 42 " --> pdb=" O LEU B 38 " (cutoff:3.500A) Proline residue: B 44 - end of helix removed outlier: 4.311A pdb=" N THR B 53 " --> pdb=" O PHE B 49 " (cutoff:3.500A) Processing helix chain 'B' and resid 58 through 69 removed outlier: 4.260A pdb=" N ASN B 62 " --> pdb=" O GLY B 58 " (cutoff:3.500A) removed outlier: 3.571A pdb=" N GLY B 69 " --> pdb=" O VAL B 65 " (cutoff:3.500A) Processing helix chain 'B' and resid 122 through 129 removed outlier: 3.532A pdb=" N SER B 126 " --> pdb=" O TYR B 122 " (cutoff:3.500A) Processing helix chain 'B' and resid 176 through 183 Processing helix chain 'B' and resid 219 through 225 removed outlier: 4.137A pdb=" N ALA B 223 " --> pdb=" O ARG B 219 " (cutoff:3.500A) Processing helix chain 'B' and resid 273 through 281 Processing helix chain 'B' and resid 284 through 294 Processing helix chain 'B' and resid 295 through 299 removed outlier: 4.533A pdb=" N LYS B 298 " --> pdb=" O ASN B 295 " (cutoff:3.500A) Processing helix chain 'B' and resid 300 through 314 removed outlier: 3.661A pdb=" N LEU B 308 " --> pdb=" O ASP B 304 " (cutoff:3.500A) removed outlier: 3.550A pdb=" N LEU B 309 " --> pdb=" O ARG B 305 " (cutoff:3.500A) Processing helix chain 'B' and resid 322 through 339 removed outlier: 5.070A pdb=" N VAL B 336 " --> pdb=" O ASP B 332 " (cutoff:3.500A) removed outlier: 4.387A pdb=" N VAL B 337 " --> pdb=" O LYS B 333 " (cutoff:3.500A) Processing helix chain 'B' and resid 345 through 358 Processing helix chain 'B' and resid 359 through 363 Processing helix chain 'B' and resid 366 through 386 removed outlier: 3.690A pdb=" N ARG B 372 " --> pdb=" O GLN B 368 " (cutoff:3.500A) Processing helix chain 'B' and resid 396 through 400 Processing helix chain 'B' and resid 404 through 434 Processing helix chain 'B' and resid 442 through 453 Processing helix chain 'B' and resid 456 through 468 removed outlier: 4.086A pdb=" N LYS B 460 " --> pdb=" O ASN B 456 " (cutoff:3.500A) Processing helix chain 'B' and resid 492 through 501 removed outlier: 3.692A pdb=" N PHE B 496 " --> pdb=" O ASN B 492 " (cutoff:3.500A) removed outlier: 4.220A pdb=" N PHE B 500 " --> pdb=" O PHE B 496 " (cutoff:3.500A) removed outlier: 3.591A pdb=" N ARG B 501 " --> pdb=" O ILE B 497 " (cutoff:3.500A) Processing helix chain 'B' and resid 506 through 511 removed outlier: 3.511A pdb=" N ALA B 510 " --> pdb=" O GLY B 506 " (cutoff:3.500A) Processing helix chain 'B' and resid 515 through 519 Processing helix chain 'B' and resid 521 through 525 Processing helix chain 'B' and resid 559 through 568 removed outlier: 4.711A pdb=" N SER B 563 " --> pdb=" O SER B 559 " (cutoff:3.500A) Processing helix chain 'B' and resid 597 through 615 Processing helix chain 'B' and resid 665 through 670 removed outlier: 3.581A pdb=" N VAL B 670 " --> pdb=" O PRO B 666 " (cutoff:3.500A) Processing helix chain 'B' and resid 677 through 681 Processing helix chain 'B' and resid 692 through 697 Processing helix chain 'B' and resid 698 through 704 Processing helix chain 'B' and resid 711 through 723 removed outlier: 3.595A pdb=" N GLN B 720 " --> pdb=" O MET B 716 " (cutoff:3.500A) Processing helix chain 'B' and resid 732 through 736 Processing helix chain 'B' and resid 754 through 760 removed outlier: 4.074A pdb=" N ASP B 758 " --> pdb=" O ALA B 754 " (cutoff:3.500A) Processing helix chain 'B' and resid 761 through 765 Processing helix chain 'B' and resid 791 through 796 Processing helix chain 'B' and resid 835 through 840 removed outlier: 4.016A pdb=" N LYS B 839 " --> pdb=" O GLU B 835 " (cutoff:3.500A) Processing helix chain 'B' and resid 932 through 936 Processing helix chain 'B' and resid 960 through 976 Processing helix chain 'B' and resid 991 through 1004 Processing helix chain 'B' and resid 1039 through 1043 Processing helix chain 'B' and resid 1072 through 1083 Processing helix chain 'B' and resid 1084 through 1095 Processing helix chain 'B' and resid 1135 through 1140 removed outlier: 3.967A pdb=" N LYS B1139 " --> pdb=" O PHE B1135 " (cutoff:3.500A) removed outlier: 3.655A pdb=" N LYS B1140 " --> pdb=" O GLU B1136 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 1135 through 1140' Processing helix chain 'B' and resid 1179 through 1192 removed outlier: 4.048A pdb=" N LYS B1183 " --> pdb=" O PRO B1179 " (cutoff:3.500A) Processing helix chain 'C' and resid 32 through 40 removed outlier: 3.689A pdb=" N ASP C 39 " --> pdb=" O LYS C 35 " (cutoff:3.500A) Processing helix chain 'C' and resid 60 through 73 removed outlier: 3.689A pdb=" N ALA C 66 " --> pdb=" O SER C 62 " (cutoff:3.500A) removed outlier: 4.137A pdb=" N MET C 71 " --> pdb=" O PHE C 67 " (cutoff:3.500A) removed outlier: 3.559A pdb=" N ILE C 72 " --> pdb=" O ARG C 68 " (cutoff:3.500A) Processing helix chain 'C' and resid 93 through 103 Processing helix chain 'C' and resid 109 through 113 Processing helix chain 'C' and resid 121 through 126 removed outlier: 3.674A pdb=" N PHE C 126 " --> pdb=" O ASP C 122 " (cutoff:3.500A) Processing helix chain 'C' and resid 152 through 156 Processing helix chain 'C' and resid 165 through 167 No H-bonds generated for 'chain 'C' and resid 165 through 167' Processing helix chain 'C' and resid 174 through 179 Processing helix chain 'C' and resid 241 through 250 removed outlier: 3.658A pdb=" N ARG C 245 " --> pdb=" O GLY C 241 " (cutoff:3.500A) Processing helix chain 'C' and resid 278 through 281 Processing helix chain 'C' and resid 282 through 287 removed outlier: 4.091A pdb=" N ASP C 287 " --> pdb=" O GLU C 283 " (cutoff:3.500A) Processing helix chain 'C' and resid 309 through 331 Processing helix chain 'D' and resid 32 through 47 Processing helix chain 'D' and resid 81 through 96 removed outlier: 3.825A pdb=" N GLN D 88 " --> pdb=" O SER D 84 " (cutoff:3.500A) removed outlier: 3.689A pdb=" N PHE D 96 " --> pdb=" O ILE D 92 " (cutoff:3.500A) Processing helix chain 'E' and resid 5 through 26 removed outlier: 3.561A pdb=" N LYS E 20 " --> pdb=" O PHE E 16 " (cutoff:3.500A) Processing helix chain 'E' and resid 31 through 36 Processing helix chain 'E' and resid 38 through 47 Processing helix chain 'E' and resid 54 through 59 Processing helix chain 'E' and resid 65 through 72 Processing helix chain 'E' and resid 89 through 104 Processing helix chain 'E' and resid 117 through 123 Processing helix chain 'E' and resid 138 through 141 Processing helix chain 'E' and resid 157 through 169 Processing helix chain 'E' and resid 171 through 175 removed outlier: 3.622A pdb=" N LEU E 175 " --> pdb=" O GLU E 172 " (cutoff:3.500A) Processing helix chain 'E' and resid 182 through 189 Processing helix chain 'F' and resid 56 through 72 Processing helix chain 'F' and resid 86 through 103 removed outlier: 3.558A pdb=" N ALA F 91 " --> pdb=" O LYS F 87 " (cutoff:3.500A) Processing helix chain 'F' and resid 116 through 127 removed outlier: 3.787A pdb=" N GLU F 127 " --> pdb=" O LYS F 123 " (cutoff:3.500A) Processing helix chain 'G' and resid 50 through 55 removed outlier: 4.236A pdb=" N GLU G 55 " --> pdb=" O MET G 52 " (cutoff:3.500A) Processing helix chain 'G' and resid 56 through 65 Processing helix chain 'G' and resid 65 through 70 removed outlier: 3.711A pdb=" N LEU G 69 " --> pdb=" O HIS G 65 " (cutoff:3.500A) Processing helix chain 'H' and resid 88 through 93 Processing helix chain 'H' and resid 129 through 133 Processing helix chain 'I' and resid 59 through 64 Processing helix chain 'J' and resid 16 through 27 removed outlier: 4.514A pdb=" N SER J 20 " --> pdb=" O ASP J 16 " (cutoff:3.500A) Processing helix chain 'J' and resid 31 through 40 removed outlier: 3.753A pdb=" N ALA J 35 " --> pdb=" O ASP J 31 " (cutoff:3.500A) removed outlier: 3.544A pdb=" N LEU J 36 " --> pdb=" O GLU J 32 " (cutoff:3.500A) Processing helix chain 'J' and resid 43 through 52 removed outlier: 3.872A pdb=" N MET J 49 " --> pdb=" O CYS J 45 " (cutoff:3.500A) removed outlier: 4.058A pdb=" N ILE J 50 " --> pdb=" O CYS J 46 " (cutoff:3.500A) Processing helix chain 'J' and resid 56 through 62 Processing helix chain 'K' and resid 69 through 82 removed outlier: 3.520A pdb=" N TYR K 78 " --> pdb=" O ASN K 74 " (cutoff:3.500A) Processing helix chain 'K' and resid 112 through 142 Processing helix chain 'M' and resid 67 through 72 removed outlier: 3.718A pdb=" N GLN M 71 " --> pdb=" O ASP M 67 " (cutoff:3.500A) removed outlier: 3.527A pdb=" N ALA M 72 " --> pdb=" O SER M 68 " (cutoff:3.500A) No H-bonds generated for 'chain 'M' and resid 67 through 72' Processing helix chain 'M' and resid 103 through 107 removed outlier: 3.796A pdb=" N ASN M 107 " --> pdb=" O LYS M 103 " (cutoff:3.500A) No H-bonds generated for 'chain 'M' and resid 103 through 107' Processing helix chain 'N' and resid 149 through 154 Processing helix chain 'O' and resid 49 through 65 Processing helix chain 'O' and resid 68 through 79 Processing helix chain 'O' and resid 89 through 103 removed outlier: 3.788A pdb=" N ASN O 103 " --> pdb=" O ILE O 99 " (cutoff:3.500A) Processing helix chain 'O' and resid 109 through 122 removed outlier: 4.307A pdb=" N PHE O 114 " --> pdb=" O SER O 110 " (cutoff:3.500A) removed outlier: 4.345A pdb=" N LEU O 115 " --> pdb=" O ARG O 111 " (cutoff:3.500A) Processing helix chain 'O' and resid 124 through 128 Processing helix chain 'O' and resid 129 through 147 Processing helix chain 'O' and resid 150 through 161 Processing helix chain 'O' and resid 162 through 164 No H-bonds generated for 'chain 'O' and resid 162 through 164' Processing helix chain 'O' and resid 165 through 183 removed outlier: 3.561A pdb=" N THR O 169 " --> pdb=" O PRO O 165 " (cutoff:3.500A) removed outlier: 5.028A pdb=" N CYS O 171 " --> pdb=" O LYS O 167 " (cutoff:3.500A) removed outlier: 5.061A pdb=" N HIS O 172 " --> pdb=" O GLN O 168 " (cutoff:3.500A) removed outlier: 3.582A pdb=" N TYR O 178 " --> pdb=" O ASP O 174 " (cutoff:3.500A) removed outlier: 4.111A pdb=" N ARG O 181 " --> pdb=" O LYS O 177 " (cutoff:3.500A) Processing helix chain 'O' and resid 185 through 197 removed outlier: 4.388A pdb=" N PHE O 189 " --> pdb=" O SER O 185 " (cutoff:3.500A) Processing helix chain 'O' and resid 204 through 222 removed outlier: 3.562A pdb=" N LEU O 208 " --> pdb=" O THR O 204 " (cutoff:3.500A) removed outlier: 3.557A pdb=" N GLY O 220 " --> pdb=" O LEU O 216 " (cutoff:3.500A) removed outlier: 3.946A pdb=" N TYR O 221 " --> pdb=" O LYS O 217 " (cutoff:3.500A) Processing helix chain 'O' and resid 227 through 246 removed outlier: 3.947A pdb=" N GLU O 243 " --> pdb=" O SER O 239 " (cutoff:3.500A) removed outlier: 3.542A pdb=" N LEU O 244 " --> pdb=" O ILE O 240 " (cutoff:3.500A) removed outlier: 3.638A pdb=" N GLN O 245 " --> pdb=" O ASP O 241 " (cutoff:3.500A) removed outlier: 3.974A pdb=" N ASN O 246 " --> pdb=" O VAL O 242 " (cutoff:3.500A) Processing helix chain 'O' and resid 325 through 347 Processing helix chain 'O' and resid 356 through 371 Processing helix chain 'O' and resid 382 through 390 removed outlier: 3.532A pdb=" N PHE O 386 " --> pdb=" O GLN O 382 " (cutoff:3.500A) Processing helix chain 'O' and resid 392 through 409 removed outlier: 3.787A pdb=" N THR O 402 " --> pdb=" O SER O 398 " (cutoff:3.500A) Processing helix chain 'O' and resid 413 through 429 removed outlier: 3.602A pdb=" N ILE O 428 " --> pdb=" O LEU O 424 " (cutoff:3.500A) removed outlier: 4.385A pdb=" N ALA O 429 " --> pdb=" O GLY O 425 " (cutoff:3.500A) Processing helix chain 'O' and resid 435 through 456 removed outlier: 3.746A pdb=" N ILE O 439 " --> pdb=" O SER O 435 " (cutoff:3.500A) removed outlier: 3.658A pdb=" N ILE O 440 " --> pdb=" O ARG O 436 " (cutoff:3.500A) removed outlier: 3.989A pdb=" N PHE O 441 " --> pdb=" O THR O 437 " (cutoff:3.500A) removed outlier: 4.706A pdb=" N VAL O 442 " --> pdb=" O GLN O 438 " (cutoff:3.500A) removed outlier: 4.142A pdb=" N GLU O 456 " --> pdb=" O ARG O 452 " (cutoff:3.500A) Processing helix chain 'O' and resid 457 through 462 removed outlier: 3.520A pdb=" N ASP O 462 " --> pdb=" O GLU O 458 " (cutoff:3.500A) Processing helix chain 'O' and resid 466 through 469 removed outlier: 3.657A pdb=" N ARG O 469 " --> pdb=" O GLY O 466 " (cutoff:3.500A) No H-bonds generated for 'chain 'O' and resid 466 through 469' Processing helix chain 'O' and resid 470 through 490 removed outlier: 3.601A pdb=" N TYR O 474 " --> pdb=" O PHE O 470 " (cutoff:3.500A) removed outlier: 4.220A pdb=" N CYS O 485 " --> pdb=" O CYS O 481 " (cutoff:3.500A) removed outlier: 4.414A pdb=" N PHE O 486 " --> pdb=" O TYR O 482 " (cutoff:3.500A) removed outlier: 3.803A pdb=" N ARG O 487 " --> pdb=" O ILE O 483 " (cutoff:3.500A) removed outlier: 3.715A pdb=" N HIS O 488 " --> pdb=" O PHE O 484 " (cutoff:3.500A) removed outlier: 3.905A pdb=" N ASN O 489 " --> pdb=" O CYS O 485 " (cutoff:3.500A) Processing helix chain 'O' and resid 501 through 511 Processing helix chain 'O' and resid 515 through 520 removed outlier: 4.099A pdb=" N PHE O 519 " --> pdb=" O ASN O 515 " (cutoff:3.500A) removed outlier: 3.811A pdb=" N CYS O 520 " --> pdb=" O PRO O 516 " (cutoff:3.500A) No H-bonds generated for 'chain 'O' and resid 515 through 520' Processing helix chain 'O' and resid 521 through 535 removed outlier: 3.719A pdb=" N LEU O 526 " --> pdb=" O GLU O 522 " (cutoff:3.500A) removed outlier: 3.790A pdb=" N ILE O 531 " --> pdb=" O MET O 527 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N ALA O 532 " --> pdb=" O PHE O 528 " (cutoff:3.500A) removed outlier: 3.747A pdb=" N GLN O 533 " --> pdb=" O ALA O 529 " (cutoff:3.500A) Processing helix chain 'O' and resid 540 through 551 removed outlier: 3.842A pdb=" N GLU O 550 " --> pdb=" O ASN O 546 " (cutoff:3.500A) Processing helix chain 'O' and resid 582 through 591 removed outlier: 3.889A pdb=" N GLN O 589 " --> pdb=" O PHE O 585 " (cutoff:3.500A) removed outlier: 3.616A pdb=" N SER O 590 " --> pdb=" O ILE O 586 " (cutoff:3.500A) removed outlier: 4.075A pdb=" N TYR O 591 " --> pdb=" O ASP O 587 " (cutoff:3.500A) Processing helix chain 'O' and resid 600 through 606 Processing helix chain 'P' and resid 571 through 579 removed outlier: 3.667A pdb=" N SER P 576 " --> pdb=" O PRO P 572 " (cutoff:3.500A) removed outlier: 3.988A pdb=" N LEU P 577 " --> pdb=" O GLU P 573 " (cutoff:3.500A) Processing helix chain 'P' and resid 582 through 613 removed outlier: 4.496A pdb=" N LEU P 592 " --> pdb=" O SER P 588 " (cutoff:3.500A) removed outlier: 3.726A pdb=" N VAL P 593 " --> pdb=" O ILE P 589 " (cutoff:3.500A) removed outlier: 4.116A pdb=" N ASN P 609 " --> pdb=" O SER P 605 " (cutoff:3.500A) removed outlier: 4.133A pdb=" N LEU P 610 " --> pdb=" O ARG P 606 " (cutoff:3.500A) Processing helix chain 'P' and resid 616 through 643 Processing helix chain 'P' and resid 644 through 648 removed outlier: 3.748A pdb=" N GLU P 647 " --> pdb=" O THR P 644 " (cutoff:3.500A) removed outlier: 3.760A pdb=" N SER P 648 " --> pdb=" O LYS P 645 " (cutoff:3.500A) No H-bonds generated for 'chain 'P' and resid 644 through 648' Processing helix chain 'P' and resid 662 through 668 removed outlier: 4.353A pdb=" N SER P 666 " --> pdb=" O LEU P 662 " (cutoff:3.500A) removed outlier: 4.318A pdb=" N ASP P 667 " --> pdb=" O LEU P 663 " (cutoff:3.500A) removed outlier: 4.572A pdb=" N SER P 668 " --> pdb=" O GLU P 664 " (cutoff:3.500A) No H-bonds generated for 'chain 'P' and resid 662 through 668' Processing helix chain 'P' and resid 672 through 686 Processing helix chain 'P' and resid 696 through 705 removed outlier: 4.537A pdb=" N LEU P 702 " --> pdb=" O LYS P 698 " (cutoff:3.500A) removed outlier: 3.802A pdb=" N PHE P 703 " --> pdb=" O LEU P 699 " (cutoff:3.500A) Processing helix chain 'P' and resid 710 through 724 removed outlier: 3.884A pdb=" N PHE P 714 " --> pdb=" O GLY P 710 " (cutoff:3.500A) removed outlier: 3.722A pdb=" N TYR P 715 " --> pdb=" O LEU P 711 " (cutoff:3.500A) Processing helix chain 'P' and resid 728 through 745 Processing helix chain 'P' and resid 754 through 766 removed outlier: 3.602A pdb=" N ASN P 758 " --> pdb=" O GLU P 754 " (cutoff:3.500A) removed outlier: 4.088A pdb=" N ILE P 760 " --> pdb=" O ILE P 756 " (cutoff:3.500A) removed outlier: 3.949A pdb=" N SER P 765 " --> pdb=" O SER P 761 " (cutoff:3.500A) Processing helix chain 'P' and resid 768 through 774 Processing helix chain 'Q' and resid 100 through 124 Processing helix chain 'Q' and resid 127 through 145 removed outlier: 4.239A pdb=" N HIS Q 131 " --> pdb=" O LYS Q 127 " (cutoff:3.500A) Processing helix chain 'Q' and resid 157 through 172 Processing helix chain 'Q' and resid 177 through 187 Processing helix chain 'Q' and resid 226 through 237 Processing helix chain 'Q' and resid 248 through 260 removed outlier: 3.580A pdb=" N LEU Q 252 " --> pdb=" O SER Q 248 " (cutoff:3.500A) Processing helix chain 'Q' and resid 264 through 278 removed outlier: 3.951A pdb=" N PHE Q 268 " --> pdb=" O PRO Q 264 " (cutoff:3.500A) Processing helix chain 'Q' and resid 301 through 321 removed outlier: 3.711A pdb=" N ARG Q 305 " --> pdb=" O HIS Q 301 " (cutoff:3.500A) Processing helix chain 'Q' and resid 329 through 340 Processing helix chain 'Q' and resid 344 through 355 Processing helix chain 'Q' and resid 363 through 368 Processing helix chain 'Q' and resid 370 through 385 Processing helix chain 'Q' and resid 406 through 415 Processing helix chain 'Q' and resid 437 through 449 Processing helix chain 'Q' and resid 471 through 491 removed outlier: 3.866A pdb=" N ALA Q 475 " --> pdb=" O ALA Q 471 " (cutoff:3.500A) Processing helix chain 'Q' and resid 494 through 512 removed outlier: 3.740A pdb=" N ARG Q 512 " --> pdb=" O ALA Q 508 " (cutoff:3.500A) Processing helix chain 'R' and resid 12 through 36 removed outlier: 3.508A pdb=" N ARG R 16 " --> pdb=" O LYS R 12 " (cutoff:3.500A) Processing helix chain 'R' and resid 75 through 84 Processing helix chain 'R' and resid 158 through 168 removed outlier: 3.586A pdb=" N LYS R 164 " --> pdb=" O HIS R 160 " (cutoff:3.500A) removed outlier: 4.369A pdb=" N ILE R 168 " --> pdb=" O LYS R 164 " (cutoff:3.500A) Processing helix chain 'R' and resid 168 through 173 Processing helix chain 'R' and resid 174 through 179 removed outlier: 4.224A pdb=" N LEU R 177 " --> pdb=" O GLU R 174 " (cutoff:3.500A) Processing helix chain 'R' and resid 181 through 193 Processing helix chain 'R' and resid 200 through 205 Processing helix chain 'R' and resid 208 through 226 Processing helix chain 'R' and resid 228 through 242 Processing helix chain 'R' and resid 249 through 257 removed outlier: 3.827A pdb=" N ILE R 253 " --> pdb=" O SER R 249 " (cutoff:3.500A) Processing helix chain 'R' and resid 267 through 278 Processing helix chain 'R' and resid 305 through 322 removed outlier: 3.771A pdb=" N ALA R 309 " --> pdb=" O THR R 305 " (cutoff:3.500A) removed outlier: 4.612A pdb=" N LEU R 317 " --> pdb=" O LEU R 313 " (cutoff:3.500A) Processing helix chain 'R' and resid 346 through 353 Processing helix chain 'R' and resid 361 through 377 Processing helix chain 'R' and resid 402 through 418 removed outlier: 3.989A pdb=" N LYS R 416 " --> pdb=" O ARG R 412 " (cutoff:3.500A) Processing helix chain 'R' and resid 427 through 440 removed outlier: 3.731A pdb=" N ILE R 431 " --> pdb=" O PRO R 427 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 1631 through 1632 removed outlier: 5.161A pdb=" N ILE A 11 " --> pdb=" O GLU B1201 " (cutoff:3.500A) removed outlier: 6.339A pdb=" N GLU B1201 " --> pdb=" O ILE A 11 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 77 through 79 Processing sheet with id=AA3, first strand: chain 'A' and resid 242 through 244 removed outlier: 3.503A pdb=" N LYS A 242 " --> pdb=" O THR A 254 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 371 through 373 Processing sheet with id=AA5, first strand: chain 'A' and resid 475 through 476 removed outlier: 4.147A pdb=" N ILE B1069 " --> pdb=" O VAL A 476 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 1045 through 1046 removed outlier: 5.425A pdb=" N ILE A 495 " --> pdb=" O ARG A 606 " (cutoff:3.500A) removed outlier: 7.487A pdb=" N LEU A 614 " --> pdb=" O ARG A 481 " (cutoff:3.500A) removed outlier: 5.618A pdb=" N VAL A 483 " --> pdb=" O LEU A 614 " (cutoff:3.500A) removed outlier: 7.209A pdb=" N LEU A 616 " --> pdb=" O VAL A 483 " (cutoff:3.500A) removed outlier: 6.161A pdb=" N SER A 485 " --> pdb=" O LEU A 616 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 506 through 510 removed outlier: 3.955A pdb=" N ARG A 579 " --> pdb=" O TYR A 507 " (cutoff:3.500A) removed outlier: 3.596A pdb=" N VAL A 577 " --> pdb=" O GLU A 509 " (cutoff:3.500A) removed outlier: 4.123A pdb=" N GLN A 535 " --> pdb=" O TYR A 578 " (cutoff:3.500A) removed outlier: 5.882A pdb=" N HIS A 580 " --> pdb=" O ALA A 533 " (cutoff:3.500A) removed outlier: 6.406A pdb=" N ALA A 533 " --> pdb=" O HIS A 580 " (cutoff:3.500A) removed outlier: 3.660A pdb=" N LEU A 543 " --> pdb=" O VAL Q 34 " (cutoff:3.500A) removed outlier: 3.545A pdb=" N MET Q 35 " --> pdb=" O ARG Q 27 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 686 through 687 Processing sheet with id=AA9, first strand: chain 'A' and resid 719 through 721 removed outlier: 5.784A pdb=" N ILE A 719 " --> pdb=" O TYR H 98 " (cutoff:3.500A) removed outlier: 6.952A pdb=" N TYR H 98 " --> pdb=" O ILE A 719 " (cutoff:3.500A) removed outlier: 6.514A pdb=" N GLU H 27 " --> pdb=" O SER H 13 " (cutoff:3.500A) removed outlier: 4.490A pdb=" N VAL H 15 " --> pdb=" O ARG H 25 " (cutoff:3.500A) removed outlier: 6.577A pdb=" N ARG H 25 " --> pdb=" O VAL H 15 " (cutoff:3.500A) removed outlier: 5.261A pdb=" N LEU H 122 " --> pdb=" O ASP H 41 " (cutoff:3.500A) removed outlier: 6.697A pdb=" N SER H 117 " --> pdb=" O ALA H 101 " (cutoff:3.500A) removed outlier: 5.698A pdb=" N ALA H 101 " --> pdb=" O SER H 117 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'A' and resid 749 through 751 removed outlier: 6.475A pdb=" N LEU A 770 " --> pdb=" O LEU A 777 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'A' and resid 1031 through 1032 Processing sheet with id=AB3, first strand: chain 'A' and resid 1518 through 1522 Processing sheet with id=AB4, first strand: chain 'A' and resid 1260 through 1262 removed outlier: 6.538A pdb=" N VAL A1261 " --> pdb=" O ILE A1498 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'A' and resid 1457 through 1462 removed outlier: 5.809A pdb=" N ILE A1457 " --> pdb=" O GLU A1475 " (cutoff:3.500A) removed outlier: 6.602A pdb=" N GLU A1475 " --> pdb=" O ILE A1457 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'D' and resid 21 through 24 removed outlier: 3.803A pdb=" N VAL D 21 " --> pdb=" O TYR G 46 " (cutoff:3.500A) removed outlier: 3.894A pdb=" N LYS G 106 " --> pdb=" O PHE G 115 " (cutoff:3.500A) removed outlier: 5.583A pdb=" N VAL A1656 " --> pdb=" O ILE G 107 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'D' and resid 29 through 30 removed outlier: 7.586A pdb=" N TRP G 117 " --> pdb=" O ILE G 89 " (cutoff:3.500A) removed outlier: 5.039A pdb=" N ILE G 89 " --> pdb=" O TRP G 117 " (cutoff:3.500A) removed outlier: 6.531A pdb=" N HIS G 119 " --> pdb=" O LEU G 87 " (cutoff:3.500A) removed outlier: 4.143A pdb=" N LEU G 87 " --> pdb=" O HIS G 119 " (cutoff:3.500A) removed outlier: 6.615A pdb=" N TRP G 125 " --> pdb=" O VAL G 81 " (cutoff:3.500A) removed outlier: 6.051A pdb=" N VAL G 81 " --> pdb=" O TRP G 125 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'B' and resid 71 through 74 removed outlier: 6.763A pdb=" N LYS B 140 " --> pdb=" O GLU B 100 " (cutoff:3.500A) removed outlier: 4.720A pdb=" N VAL B 102 " --> pdb=" O LEU B 138 " (cutoff:3.500A) removed outlier: 6.873A pdb=" N LEU B 138 " --> pdb=" O VAL B 102 " (cutoff:3.500A) removed outlier: 4.525A pdb=" N ILE B 104 " --> pdb=" O LYS B 136 " (cutoff:3.500A) removed outlier: 6.113A pdb=" N LYS B 136 " --> pdb=" O ILE B 104 " (cutoff:3.500A) removed outlier: 5.705A pdb=" N GLY B 135 " --> pdb=" O GLY B 160 " (cutoff:3.500A) removed outlier: 4.424A pdb=" N GLY B 160 " --> pdb=" O GLY B 135 " (cutoff:3.500A) removed outlier: 6.296A pdb=" N LEU B 137 " --> pdb=" O CYS B 158 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'B' and resid 108 through 109 Processing sheet with id=AC1, first strand: chain 'B' and resid 194 through 196 Processing sheet with id=AC2, first strand: chain 'B' and resid 401 through 403 removed outlier: 6.701A pdb=" N MET B 205 " --> pdb=" O HIS B 504 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'B' and resid 215 through 218 removed outlier: 5.371A pdb=" N TYR B 232 " --> pdb=" O TYR B 252 " (cutoff:3.500A) removed outlier: 3.993A pdb=" N TYR B 252 " --> pdb=" O TYR B 232 " (cutoff:3.500A) removed outlier: 6.252A pdb=" N THR B 247 " --> pdb=" O SER B 263 " (cutoff:3.500A) removed outlier: 4.248A pdb=" N SER B 263 " --> pdb=" O THR B 247 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'B' and resid 571 through 572 removed outlier: 6.879A pdb=" N VAL B 586 " --> pdb=" O ILE B 593 " (cutoff:3.500A) removed outlier: 4.784A pdb=" N TRP B 595 " --> pdb=" O CYS B 584 " (cutoff:3.500A) removed outlier: 6.891A pdb=" N CYS B 584 " --> pdb=" O TRP B 595 " (cutoff:3.500A) removed outlier: 5.777A pdb=" N CYS B 585 " --> pdb=" O LEU B 640 " (cutoff:3.500A) removed outlier: 7.505A pdb=" N LEU B 642 " --> pdb=" O CYS B 585 " (cutoff:3.500A) removed outlier: 6.628A pdb=" N GLN B 587 " --> pdb=" O LEU B 642 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'B' and resid 660 through 664 removed outlier: 3.793A pdb=" N LYS B 660 " --> pdb=" O TYR B 655 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'B' and resid 740 through 744 removed outlier: 7.826A pdb=" N THR B 900 " --> pdb=" O LEU B 887 " (cutoff:3.500A) removed outlier: 5.238A pdb=" N LEU B 887 " --> pdb=" O THR B 900 " (cutoff:3.500A) removed outlier: 6.689A pdb=" N SER B 902 " --> pdb=" O VAL B 885 " (cutoff:3.500A) removed outlier: 4.492A pdb=" N VAL B 885 " --> pdb=" O SER B 902 " (cutoff:3.500A) removed outlier: 6.365A pdb=" N LYS B 904 " --> pdb=" O GLU B 883 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'B' and resid 740 through 744 removed outlier: 7.826A pdb=" N THR B 900 " --> pdb=" O LEU B 887 " (cutoff:3.500A) removed outlier: 5.238A pdb=" N LEU B 887 " --> pdb=" O THR B 900 " (cutoff:3.500A) removed outlier: 6.689A pdb=" N SER B 902 " --> pdb=" O VAL B 885 " (cutoff:3.500A) removed outlier: 4.492A pdb=" N VAL B 885 " --> pdb=" O SER B 902 " (cutoff:3.500A) removed outlier: 6.365A pdb=" N LYS B 904 " --> pdb=" O GLU B 883 " (cutoff:3.500A) removed outlier: 5.240A pdb=" N VAL B 885 " --> pdb=" O LYS L 58 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'B' and resid 752 through 753 Processing sheet with id=AC9, first strand: chain 'B' and resid 924 through 926 removed outlier: 3.989A pdb=" N TYR B1027 " --> pdb=" O VAL B 775 " (cutoff:3.500A) removed outlier: 6.558A pdb=" N ILE B 789 " --> pdb=" O TRP B 931 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'B' and resid 924 through 926 Processing sheet with id=AD2, first strand: chain 'B' and resid 823 through 825 Processing sheet with id=AD3, first strand: chain 'B' and resid 938 through 939 Processing sheet with id=AD4, first strand: chain 'B' and resid 1101 through 1104 Processing sheet with id=AD5, first strand: chain 'B' and resid 1113 through 1115 Processing sheet with id=AD6, first strand: chain 'B' and resid 1132 through 1134 Processing sheet with id=AD7, first strand: chain 'C' and resid 41 through 47 removed outlier: 6.769A pdb=" N ASN C 53 " --> pdb=" O SER C 45 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'C' and resid 168 through 170 removed outlier: 4.293A pdb=" N VAL C 133 " --> pdb=" O GLU C 170 " (cutoff:3.500A) removed outlier: 6.782A pdb=" N GLU C 201 " --> pdb=" O ASN C 87 " (cutoff:3.500A) removed outlier: 6.668A pdb=" N ASN C 87 " --> pdb=" O GLU C 201 " (cutoff:3.500A) removed outlier: 7.399A pdb=" N SER C 203 " --> pdb=" O PHE C 85 " (cutoff:3.500A) removed outlier: 5.007A pdb=" N PHE C 85 " --> pdb=" O SER C 203 " (cutoff:3.500A) removed outlier: 6.681A pdb=" N LYS C 205 " --> pdb=" O VAL C 83 " (cutoff:3.500A) removed outlier: 4.738A pdb=" N VAL C 83 " --> pdb=" O LYS C 205 " (cutoff:3.500A) removed outlier: 6.003A pdb=" N HIS C 207 " --> pdb=" O GLU C 81 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'C' and resid 106 through 107 removed outlier: 3.975A pdb=" N VAL C 185 " --> pdb=" O LYS C 107 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'C' and resid 141 through 142 Processing sheet with id=AE2, first strand: chain 'C' and resid 161 through 163 Processing sheet with id=AE3, first strand: chain 'C' and resid 234 through 235 Processing sheet with id=AE4, first strand: chain 'C' and resid 256 through 258 Processing sheet with id=AE5, first strand: chain 'E' and resid 28 through 29 removed outlier: 4.597A pdb=" N ASN E 63 " --> pdb=" O PHE E 29 " (cutoff:3.500A) removed outlier: 6.415A pdb=" N TRP E 79 " --> pdb=" O ILE E 109 " (cutoff:3.500A) removed outlier: 7.708A pdb=" N VAL E 111 " --> pdb=" O TRP E 79 " (cutoff:3.500A) removed outlier: 6.832A pdb=" N GLU E 81 " --> pdb=" O VAL E 111 " (cutoff:3.500A) Processing sheet with id=AE6, first strand: chain 'E' and resid 152 through 155 removed outlier: 3.893A pdb=" N LYS E 152 " --> pdb=" O ILE E 199 " (cutoff:3.500A) Processing sheet with id=AE7, first strand: chain 'G' and resid 132 through 135 removed outlier: 4.933A pdb=" N VAL G 233 " --> pdb=" O THR G 248 " (cutoff:3.500A) removed outlier: 5.341A pdb=" N THR G 248 " --> pdb=" O VAL G 233 " (cutoff:3.500A) Processing sheet with id=AE8, first strand: chain 'G' and resid 167 through 169 Processing sheet with id=AE9, first strand: chain 'I' and resid 3 through 4 Processing sheet with id=AF1, first strand: chain 'I' and resid 27 through 29 Processing sheet with id=AF2, first strand: chain 'K' and resid 47 through 49 Processing sheet with id=AF3, first strand: chain 'M' and resid 11 through 16 removed outlier: 4.788A pdb=" N ILE M 12 " --> pdb=" O ILE M 88 " (cutoff:3.500A) removed outlier: 7.263A pdb=" N LEU M 90 " --> pdb=" O ILE M 12 " (cutoff:3.500A) removed outlier: 5.464A pdb=" N SER M 14 " --> pdb=" O LEU M 90 " (cutoff:3.500A) removed outlier: 7.027A pdb=" N LYS M 92 " --> pdb=" O SER M 14 " (cutoff:3.500A) removed outlier: 6.629A pdb=" N GLN M 16 " --> pdb=" O LYS M 92 " (cutoff:3.500A) Processing sheet with id=AF4, first strand: chain 'N' and resid 30 through 31 removed outlier: 7.039A pdb=" N VAL M 23 " --> pdb=" O LEU M 96 " (cutoff:3.500A) removed outlier: 7.606A pdb=" N SER M 98 " --> pdb=" O VAL M 23 " (cutoff:3.500A) removed outlier: 5.856A pdb=" N SER M 25 " --> pdb=" O SER M 98 " (cutoff:3.500A) removed outlier: 7.385A pdb=" N VAL M 100 " --> pdb=" O SER M 25 " (cutoff:3.500A) removed outlier: 5.587A pdb=" N PHE M 51 " --> pdb=" O THR M 66 " (cutoff:3.500A) removed outlier: 3.661A pdb=" N GLU M 50 " --> pdb=" O LYS M 43 " (cutoff:3.500A) removed outlier: 3.592A pdb=" N THR M 37 " --> pdb=" O GLU M 56 " (cutoff:3.500A) Processing sheet with id=AF5, first strand: chain 'N' and resid 79 through 82 Processing sheet with id=AF6, first strand: chain 'P' and resid 62 through 64 removed outlier: 5.806A pdb=" N GLU P 546 " --> pdb=" O LEU P 541 " (cutoff:3.500A) removed outlier: 4.261A pdb=" N LEU P 541 " --> pdb=" O GLU P 546 " (cutoff:3.500A) removed outlier: 3.678A pdb=" N GLY P 507 " --> pdb=" O LYS P 540 " (cutoff:3.500A) Processing sheet with id=AF7, first strand: chain 'P' and resid 185 through 186 removed outlier: 4.107A pdb=" N GLU R 196 " --> pdb=" O TYR P 186 " (cutoff:3.500A) Processing sheet with id=AF8, first strand: chain 'P' and resid 193 through 197 Processing sheet with id=AF9, first strand: chain 'P' and resid 246 through 250 removed outlier: 3.684A pdb=" N ILE P 274 " --> pdb=" O SER P 289 " (cutoff:3.500A) removed outlier: 3.843A pdb=" N ASP P 283 " --> pdb=" O ARG P 280 " (cutoff:3.500A) Processing sheet with id=AG1, first strand: chain 'P' and resid 300 through 304 removed outlier: 5.071A pdb=" N LEU P 347 " --> pdb=" O ILE P 326 " (cutoff:3.500A) removed outlier: 6.968A pdb=" N ARG P 328 " --> pdb=" O ASP P 345 " (cutoff:3.500A) removed outlier: 5.728A pdb=" N ASP P 345 " --> pdb=" O ARG P 328 " (cutoff:3.500A) Processing sheet with id=AG2, first strand: chain 'P' and resid 361 through 365 Processing sheet with id=AG3, first strand: chain 'P' and resid 404 through 406 removed outlier: 3.815A pdb=" N HIS P 440 " --> pdb=" O ILE P 422 " (cutoff:3.500A) Processing sheet with id=AG4, first strand: chain 'P' and resid 450 through 456 removed outlier: 3.584A pdb=" N SER P 482 " --> pdb=" O GLN P 490 " (cutoff:3.500A) removed outlier: 3.873A pdb=" N GLN P 490 " --> pdb=" O SER P 482 " (cutoff:3.500A) Processing sheet with id=AG5, first strand: chain 'P' and resid 450 through 456 2155 hydrogen bonds defined for protein. 6051 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 22 hydrogen bonds 44 hydrogen bond angles 0 basepair planarities 10 basepair parallelities 25 stacking parallelities Total time for adding SS restraints: 23.19 Time building geometry restraints manager: 22.19 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.17 - 1.49: 29076 1.49 - 1.81: 20525 1.81 - 2.13: 26 2.13 - 2.44: 0 2.44 - 2.76: 1 Bond restraints: 49628 Sorted by residual: bond pdb=" C ARG R 206 " pdb=" N ASN R 207 " ideal model delta sigma weight residual 1.332 2.763 -1.430 1.40e-02 5.10e+03 1.04e+04 bond pdb=" C ASP Q 323 " pdb=" N ARG Q 324 " ideal model delta sigma weight residual 1.331 1.794 -0.462 1.41e-02 5.03e+03 1.08e+03 bond pdb=" CA CYS Q 15 " pdb=" C CYS Q 15 " ideal model delta sigma weight residual 1.524 1.618 -0.094 1.26e-02 6.30e+03 5.54e+01 bond pdb=" C ILE P 247 " pdb=" N PRO P 248 " ideal model delta sigma weight residual 1.334 1.452 -0.118 2.34e-02 1.83e+03 2.53e+01 bond pdb=" C MET B 175 " pdb=" N SER B 176 " ideal model delta sigma weight residual 1.330 1.263 0.067 1.47e-02 4.63e+03 2.07e+01 ... (remaining 49623 not shown) Histogram of bond angle deviations from ideal: 58.44 - 78.26: 1 78.26 - 98.08: 7 98.08 - 117.90: 38188 117.90 - 137.72: 29069 137.72 - 157.54: 3 Bond angle restraints: 67268 Sorted by residual: angle pdb=" CA ASP Q 323 " pdb=" C ASP Q 323 " pdb=" N ARG Q 324 " ideal model delta sigma weight residual 115.14 79.80 35.34 1.22e+00 6.72e-01 8.39e+02 angle pdb=" O ASP Q 323 " pdb=" C ASP Q 323 " pdb=" N ARG Q 324 " ideal model delta sigma weight residual 122.38 157.54 -35.16 1.32e+00 5.74e-01 7.10e+02 angle pdb=" CA ARG R 206 " pdb=" C ARG R 206 " pdb=" N ASN R 207 " ideal model delta sigma weight residual 115.27 86.82 28.45 1.24e+00 6.50e-01 5.26e+02 angle pdb=" O ARG R 206 " pdb=" C ARG R 206 " pdb=" N ASN R 207 " ideal model delta sigma weight residual 122.94 148.60 -25.66 1.12e+00 7.97e-01 5.25e+02 angle pdb=" C ASP Q 323 " pdb=" N ARG Q 324 " pdb=" CA ARG Q 324 " ideal model delta sigma weight residual 122.32 86.50 35.82 1.76e+00 3.23e-01 4.14e+02 ... (remaining 67263 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.67: 27611 17.67 - 35.33: 1582 35.33 - 53.00: 577 53.00 - 70.67: 282 70.67 - 88.33: 53 Dihedral angle restraints: 30105 sinusoidal: 12879 harmonic: 17226 Sorted by residual: dihedral pdb=" CA SER Q 17 " pdb=" C SER Q 17 " pdb=" N ARG Q 18 " pdb=" CA ARG Q 18 " ideal model delta harmonic sigma weight residual -180.00 -99.78 -80.22 0 5.00e+00 4.00e-02 2.57e+02 dihedral pdb=" CA VAL R 294 " pdb=" C VAL R 294 " pdb=" N PRO R 295 " pdb=" CA PRO R 295 " ideal model delta harmonic sigma weight residual -180.00 -106.79 -73.21 0 5.00e+00 4.00e-02 2.14e+02 dihedral pdb=" CA GLY Q 25 " pdb=" C GLY Q 25 " pdb=" N ARG Q 26 " pdb=" CA ARG Q 26 " ideal model delta harmonic sigma weight residual 180.00 111.60 68.40 0 5.00e+00 4.00e-02 1.87e+02 ... (remaining 30102 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.097: 6985 0.097 - 0.194: 536 0.194 - 0.291: 33 0.291 - 0.388: 3 0.388 - 0.485: 1 Chirality restraints: 7558 Sorted by residual: chirality pdb=" CG LEU P 747 " pdb=" CB LEU P 747 " pdb=" CD1 LEU P 747 " pdb=" CD2 LEU P 747 " both_signs ideal model delta sigma weight residual False -2.59 -2.10 -0.49 2.00e-01 2.50e+01 5.89e+00 chirality pdb=" CB ILE P 187 " pdb=" CA ILE P 187 " pdb=" CG1 ILE P 187 " pdb=" CG2 ILE P 187 " both_signs ideal model delta sigma weight residual False 2.64 2.29 0.35 2.00e-01 2.50e+01 3.08e+00 chirality pdb=" CA ALA B 786 " pdb=" N ALA B 786 " pdb=" C ALA B 786 " pdb=" CB ALA B 786 " both_signs ideal model delta sigma weight residual False 2.48 2.16 0.32 2.00e-01 2.50e+01 2.61e+00 ... (remaining 7555 not shown) Planarity restraints: 8380 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ASP B 819 " -0.202 5.00e-02 4.00e+02 2.72e-01 1.19e+02 pdb=" N PRO B 820 " 0.459 5.00e-02 4.00e+02 pdb=" CA PRO B 820 " -0.207 5.00e-02 4.00e+02 pdb=" CD PRO B 820 " -0.050 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C GLY Q 7 " 0.136 5.00e-02 4.00e+02 2.12e-01 7.20e+01 pdb=" N PRO Q 8 " -0.365 5.00e-02 4.00e+02 pdb=" CA PRO Q 8 " 0.145 5.00e-02 4.00e+02 pdb=" CD PRO Q 8 " 0.085 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CB TRP Q 20 " 0.079 2.00e-02 2.50e+03 4.26e-02 4.54e+01 pdb=" CG TRP Q 20 " -0.012 2.00e-02 2.50e+03 pdb=" CD1 TRP Q 20 " -0.008 2.00e-02 2.50e+03 pdb=" CD2 TRP Q 20 " -0.052 2.00e-02 2.50e+03 pdb=" NE1 TRP Q 20 " -0.020 2.00e-02 2.50e+03 pdb=" CE2 TRP Q 20 " -0.017 2.00e-02 2.50e+03 pdb=" CE3 TRP Q 20 " -0.060 2.00e-02 2.50e+03 pdb=" CZ2 TRP Q 20 " 0.041 2.00e-02 2.50e+03 pdb=" CZ3 TRP Q 20 " -0.007 2.00e-02 2.50e+03 pdb=" CH2 TRP Q 20 " 0.055 2.00e-02 2.50e+03 ... (remaining 8377 not shown) Histogram of nonbonded interaction distances: 0.34 - 1.25: 45 1.25 - 2.17: 227 2.17 - 3.08: 40351 3.08 - 3.99: 132039 3.99 - 4.90: 244479 Warning: very small nonbonded interaction distances. Nonbonded interactions: 417141 Sorted by model distance: nonbonded pdb=" CE MET B 787 " pdb=" CA VAL B 926 " model vdw 0.343 3.890 nonbonded pdb=" NE ARG R 291 " pdb=" O3' DC T 41 " model vdw 0.430 2.520 nonbonded pdb=" CZ ARG R 291 " pdb=" C3' DC T 41 " model vdw 0.576 3.700 nonbonded pdb=" C SER B 114 " pdb=" C LYS R 281 " model vdw 0.580 3.500 nonbonded pdb=" CG ARG R 291 " pdb=" OP1 DA T 42 " model vdw 0.581 3.440 ... (remaining 417136 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Set scattering table Set to: electron Number of scattering types: 7 Type Number sf(0) Gaussians Zn 7 6.06 5 P 78 5.49 5 Mg 1 5.21 5 S 229 5.16 5 C 30678 2.51 5 N 8294 2.21 5 O 9260 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: 1.710 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: 0.040 Extract box with map and model: 12.270 Check model and map are aligned: 0.740 Convert atoms to be neutral: 0.400 Process input model: 141.200 Find NCS groups from input model: 1.220 Set up NCS constraints: 0.160 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:2.700 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 160.470 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6490 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 : 0.012 1.430 49628 Z= 0.761 Angle : 1.190 66.558 67268 Z= 0.667 Chirality : 0.054 0.485 7558 Planarity : 0.008 0.272 8380 Dihedral : 14.757 88.335 18931 Min Nonbonded Distance : 0.343 Molprobity Statistics. All-atom Clashscore : 36.53 Ramachandran Plot: Outliers : 2.11 % Allowed : 9.09 % Favored : 88.80 % Rotamer Outliers : 7.23 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.00 % Cis-general : 0.04 % Twisted Proline : 2.40 % Twisted General : 0.59 % 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: -4.08 (0.09), residues: 5787 helix: -3.67 (0.07), residues: 2081 sheet: -1.65 (0.16), residues: 795 loop : -2.18 (0.10), residues: 2911 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 11574 Ramachandran restraints generated. 5787 Oldfield, 0 Emsley, 5787 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 11574 Ramachandran restraints generated. 5787 Oldfield, 0 Emsley, 5787 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1437 residues out of total 5302 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 383 poor density : 1054 time to evaluate : 6.111 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 383 outliers final: 76 residues processed: 1387 average time/residue: 0.6352 time to fit residues: 1414.2289 Evaluate side-chains 573 residues out of total 5302 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 76 poor density : 497 time to evaluate : 5.671 Switching outliers to nearest non-outliers revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 76 outliers final: 6 residues processed: 76 average time/residue: 0.5384 time to fit residues: 81.6296 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 587 random chunks: chunk 495 optimal weight: 8.9990 chunk 444 optimal weight: 10.0000 chunk 246 optimal weight: 0.7980 chunk 151 optimal weight: 4.9990 chunk 300 optimal weight: 6.9990 chunk 237 optimal weight: 0.8980 chunk 460 optimal weight: 9.9990 chunk 178 optimal weight: 4.9990 chunk 279 optimal weight: 0.8980 chunk 342 optimal weight: 8.9990 chunk 533 optimal weight: 10.0000 overall best weight: 2.5184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 107 HIS A 378 HIS A 489 ASN A 537 GLN A 559 ASN ** A 592 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 610 ASN A 639 GLN A 880 GLN A 926 GLN A1299 ASN ** A1314 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1447 GLN A1633 GLN B 27 ASN ** B 110 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 267 ASN B 321 GLN B 399 HIS B 504 HIS B 600 GLN B 683 ASN B 724 GLN B 952 HIS B1038 HIS B1171 ASN ** C 58 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 207 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 237 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 297 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 88 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 8 ASN E 114 ASN E 146 HIS G 26 ASN G 32 ASN G 237 HIS H 128 ASN I 44 ASN J 53 HIS K 106 GLN M 75 GLN N 52 GLN N 128 ASN O 173 HIS O 362 ASN ** O 390 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** O 391 GLN O 438 GLN O 472 HIS O 507 GLN P 195 ASN ** P 222 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** P 232 ASN P 554 ASN ** P 665 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 728 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 30 GLN Q 131 HIS Q 145 ASN Q 157 HIS Q 406 GLN Q 434 HIS Q 507 ASN ** R 15 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 75 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 184 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 189 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 207 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 212 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** R 221 HIS ** R 298 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** R 304 HIS R 407 HIS Total number of N/Q/H flips: 55 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6587 moved from start: 0.3564 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.006 0.142 49628 Z= 0.389 Angle : 0.874 26.126 67268 Z= 0.456 Chirality : 0.050 0.483 7558 Planarity : 0.007 0.198 8380 Dihedral : 12.313 73.304 7121 Min Nonbonded Distance : 1.815 Molprobity Statistics. All-atom Clashscore : 20.92 Ramachandran Plot: Outliers : 0.43 % Allowed : 5.48 % Favored : 94.09 % Rotamer Outliers : 3.27 % Cbeta Deviations : 0.02 % Peptide Plane: Cis-proline : 3.60 % Cis-general : 0.04 % Twisted Proline : 3.20 % Twisted General : 0.25 % 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: -2.09 (0.10), residues: 5789 helix: -1.19 (0.10), residues: 2274 sheet: -1.13 (0.17), residues: 777 loop : -1.54 (0.11), residues: 2738 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 11578 Ramachandran restraints generated. 5789 Oldfield, 0 Emsley, 5789 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 11578 Ramachandran restraints generated. 5789 Oldfield, 0 Emsley, 5789 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 778 residues out of total 5302 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 173 poor density : 605 time to evaluate : 5.629 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 173 outliers final: 60 residues processed: 735 average time/residue: 0.5988 time to fit residues: 732.4036 Evaluate side-chains 515 residues out of total 5302 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 60 poor density : 455 time to evaluate : 5.619 Switching outliers to nearest non-outliers outliers start: 60 outliers final: 0 residues processed: 60 average time/residue: 0.4530 time to fit residues: 57.8362 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 587 random chunks: chunk 296 optimal weight: 9.9990 chunk 165 optimal weight: 4.9990 chunk 443 optimal weight: 9.9990 chunk 362 optimal weight: 4.9990 chunk 147 optimal weight: 5.9990 chunk 534 optimal weight: 20.0000 chunk 576 optimal weight: 5.9990 chunk 475 optimal weight: 10.0000 chunk 529 optimal weight: 0.5980 chunk 182 optimal weight: 3.9990 chunk 428 optimal weight: 3.9990 overall best weight: 3.7188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 590 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 592 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 656 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 671 GLN ** A1108 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A1180 ASN A1447 GLN A1560 ASN A1633 GLN ** B 575 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 669 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 720 GLN ** B 735 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B1171 ASN ** C 93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 207 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 88 GLN G 237 HIS H 33 GLN I 27 ASN K 64 GLN N 52 GLN O 342 HIS ** O 390 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** O 438 GLN P 195 ASN ** P 222 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 348 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** P 483 HIS P 642 GLN ** P 665 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** P 701 HIS Q 244 ASN ** R 15 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 184 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** R 189 GLN ** R 207 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 212 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** R 221 HIS R 228 ASN ** R 298 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** R 407 HIS Total number of N/Q/H flips: 24 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6654 moved from start: 0.4436 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.007 0.091 49628 Z= 0.459 Angle : 0.792 17.433 67268 Z= 0.408 Chirality : 0.048 0.591 7558 Planarity : 0.007 0.176 8380 Dihedral : 11.889 72.210 7121 Min Nonbonded Distance : 2.008 Molprobity Statistics. All-atom Clashscore : 19.02 Ramachandran Plot: Outliers : 0.31 % Allowed : 5.93 % Favored : 93.76 % Rotamer Outliers : 2.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.00 % Cis-general : 0.04 % Twisted Proline : 2.00 % Twisted General : 0.18 % 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: -1.45 (0.10), residues: 5789 helix: -0.38 (0.10), residues: 2280 sheet: -1.04 (0.17), residues: 778 loop : -1.36 (0.12), residues: 2731 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 11578 Ramachandran restraints generated. 5789 Oldfield, 0 Emsley, 5789 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 11578 Ramachandran restraints generated. 5789 Oldfield, 0 Emsley, 5789 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 630 residues out of total 5302 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 127 poor density : 503 time to evaluate : 5.858 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 127 outliers final: 57 residues processed: 598 average time/residue: 0.5914 time to fit residues: 596.6541 Evaluate side-chains 472 residues out of total 5302 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 57 poor density : 415 time to evaluate : 5.765 Switching outliers to nearest non-outliers outliers start: 57 outliers final: 0 residues processed: 57 average time/residue: 0.4753 time to fit residues: 56.6220 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 587 random chunks: chunk 527 optimal weight: 9.9990 chunk 401 optimal weight: 9.9990 chunk 277 optimal weight: 0.0970 chunk 59 optimal weight: 0.9980 chunk 254 optimal weight: 6.9990 chunk 358 optimal weight: 5.9990 chunk 535 optimal weight: 8.9990 chunk 567 optimal weight: 3.9990 chunk 280 optimal weight: 0.7980 chunk 507 optimal weight: 20.0000 chunk 152 optimal weight: 10.0000 overall best weight: 2.3782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 378 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 537 GLN ** A 592 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 656 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1108 HIS A1180 ASN ** B 669 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 735 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 207 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 323 ASN E 54 GLN G 237 HIS H 33 GLN K 64 GLN K 99 ASN N 52 GLN N 170 HIS ** O 105 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 390 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 222 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** P 228 ASN P 348 HIS P 595 GLN P 665 ASN ** R 15 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** R 212 HIS R 221 HIS ** R 298 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** R 407 HIS Total number of N/Q/H flips: 18 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6641 moved from start: 0.4979 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.091 49628 Z= 0.317 Angle : 0.697 14.089 67268 Z= 0.360 Chirality : 0.045 0.274 7558 Planarity : 0.006 0.166 8380 Dihedral : 11.586 73.882 7121 Min Nonbonded Distance : 1.862 Molprobity Statistics. All-atom Clashscore : 16.92 Ramachandran Plot: Outliers : 0.24 % Allowed : 5.65 % Favored : 94.11 % Rotamer Outliers : 2.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.00 % Cis-general : 0.04 % Twisted Proline : 2.00 % Twisted General : 0.13 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.03 (0.11), residues: 5789 helix: 0.08 (0.10), residues: 2280 sheet: -0.87 (0.17), residues: 789 loop : -1.23 (0.12), residues: 2720 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 11578 Ramachandran restraints generated. 5789 Oldfield, 0 Emsley, 5789 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 11578 Ramachandran restraints generated. 5789 Oldfield, 0 Emsley, 5789 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 604 residues out of total 5302 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 112 poor density : 492 time to evaluate : 5.652 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 112 outliers final: 37 residues processed: 568 average time/residue: 0.5936 time to fit residues: 565.5443 Evaluate side-chains 453 residues out of total 5302 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 37 poor density : 416 time to evaluate : 5.806 Switching outliers to nearest non-outliers outliers start: 37 outliers final: 0 residues processed: 37 average time/residue: 0.4494 time to fit residues: 38.8608 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 587 random chunks: chunk 472 optimal weight: 30.0000 chunk 322 optimal weight: 0.7980 chunk 8 optimal weight: 9.9990 chunk 422 optimal weight: 10.0000 chunk 234 optimal weight: 1.9990 chunk 484 optimal weight: 5.9990 chunk 392 optimal weight: 7.9990 chunk 0 optimal weight: 4.9990 chunk 289 optimal weight: 3.9990 chunk 509 optimal weight: 20.0000 chunk 143 optimal weight: 0.0050 overall best weight: 2.3600 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 378 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 592 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 656 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1108 HIS ** B 669 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 735 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 767 ASN B 912 GLN ** C 93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 207 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 232 GLN ** E 54 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 33 GLN K 64 GLN K 99 ASN N 85 HIS O 105 ASN ** O 390 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** P 232 ASN ** P 390 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** R 25 ASN ** R 207 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** R 221 HIS ** R 298 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6653 moved from start: 0.5310 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.091 49628 Z= 0.318 Angle : 0.680 13.156 67268 Z= 0.351 Chirality : 0.044 0.330 7558 Planarity : 0.005 0.162 8380 Dihedral : 11.417 75.261 7121 Min Nonbonded Distance : 1.906 Molprobity Statistics. All-atom Clashscore : 16.85 Ramachandran Plot: Outliers : 0.24 % Allowed : 5.68 % Favored : 94.07 % Rotamer Outliers : 1.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.40 % Cis-general : 0.04 % Twisted Proline : 1.60 % Twisted General : 0.11 % 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: -0.85 (0.11), residues: 5789 helix: 0.26 (0.10), residues: 2290 sheet: -0.80 (0.17), residues: 810 loop : -1.15 (0.12), residues: 2689 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 11578 Ramachandran restraints generated. 5789 Oldfield, 0 Emsley, 5789 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 11578 Ramachandran restraints generated. 5789 Oldfield, 0 Emsley, 5789 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 548 residues out of total 5302 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 85 poor density : 463 time to evaluate : 5.912 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 85 outliers final: 37 residues processed: 527 average time/residue: 0.5912 time to fit residues: 527.3930 Evaluate side-chains 448 residues out of total 5302 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 37 poor density : 411 time to evaluate : 5.756 Switching outliers to nearest non-outliers outliers start: 37 outliers final: 0 residues processed: 37 average time/residue: 0.4416 time to fit residues: 38.9629 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 587 random chunks: chunk 190 optimal weight: 8.9990 chunk 510 optimal weight: 8.9990 chunk 112 optimal weight: 0.2980 chunk 333 optimal weight: 3.9990 chunk 140 optimal weight: 6.9990 chunk 567 optimal weight: 5.9990 chunk 471 optimal weight: 0.0470 chunk 262 optimal weight: 10.0000 chunk 47 optimal weight: 0.0370 chunk 187 optimal weight: 7.9990 chunk 298 optimal weight: 7.9990 overall best weight: 2.0760 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 378 HIS ** A 592 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 656 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1108 HIS A1299 ASN ** B 422 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 575 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 669 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 735 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 43 ASN ** C 93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 99 HIS ** C 207 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 54 GLN H 33 GLN K 64 GLN K 99 ASN ** O 390 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 390 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 30 GLN Q 449 GLN R 207 ASN R 221 HIS ** R 298 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6650 moved from start: 0.5586 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.090 49628 Z= 0.286 Angle : 0.662 12.497 67268 Z= 0.340 Chirality : 0.044 0.323 7558 Planarity : 0.005 0.160 8380 Dihedral : 11.300 77.274 7121 Min Nonbonded Distance : 1.916 Molprobity Statistics. All-atom Clashscore : 16.03 Ramachandran Plot: Outliers : 0.24 % Allowed : 5.51 % Favored : 94.25 % Rotamer Outliers : 1.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.40 % Cis-general : 0.04 % Twisted Proline : 1.60 % Twisted General : 0.09 % 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: -0.72 (0.11), residues: 5789 helix: 0.39 (0.11), residues: 2302 sheet: -0.76 (0.17), residues: 802 loop : -1.10 (0.12), residues: 2685 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 11578 Ramachandran restraints generated. 5789 Oldfield, 0 Emsley, 5789 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 11578 Ramachandran restraints generated. 5789 Oldfield, 0 Emsley, 5789 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 552 residues out of total 5302 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 82 poor density : 470 time to evaluate : 5.776 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 82 outliers final: 31 residues processed: 529 average time/residue: 0.6104 time to fit residues: 552.4454 Evaluate side-chains 435 residues out of total 5302 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 404 time to evaluate : 5.642 Switching outliers to nearest non-outliers outliers start: 31 outliers final: 0 residues processed: 31 average time/residue: 0.4737 time to fit residues: 34.5763 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 587 random chunks: chunk 547 optimal weight: 20.0000 chunk 64 optimal weight: 2.9990 chunk 323 optimal weight: 5.9990 chunk 414 optimal weight: 10.0000 chunk 321 optimal weight: 0.9990 chunk 478 optimal weight: 0.9990 chunk 317 optimal weight: 0.9990 chunk 565 optimal weight: 5.9990 chunk 354 optimal weight: 0.9980 chunk 344 optimal weight: 9.9990 chunk 261 optimal weight: 0.9990 overall best weight: 0.9988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 592 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 656 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1108 HIS ** B 422 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 669 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 735 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 207 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 101 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 26 ASN K 64 GLN K 99 ASN ** O 390 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 390 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** R 221 HIS ** R 298 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6622 moved from start: 0.5827 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.090 49628 Z= 0.209 Angle : 0.633 14.576 67268 Z= 0.326 Chirality : 0.043 0.478 7558 Planarity : 0.005 0.158 8380 Dihedral : 11.150 77.831 7121 Min Nonbonded Distance : 1.560 Molprobity Statistics. All-atom Clashscore : 15.15 Ramachandran Plot: Outliers : 0.24 % Allowed : 5.39 % Favored : 94.37 % Rotamer Outliers : 0.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.40 % Cis-general : 0.04 % Twisted Proline : 1.60 % Twisted General : 0.04 % 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: -0.52 (0.11), residues: 5789 helix: 0.59 (0.11), residues: 2301 sheet: -0.69 (0.17), residues: 799 loop : -1.01 (0.12), residues: 2689 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 11578 Ramachandran restraints generated. 5789 Oldfield, 0 Emsley, 5789 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 11578 Ramachandran restraints generated. 5789 Oldfield, 0 Emsley, 5789 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 532 residues out of total 5302 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 49 poor density : 483 time to evaluate : 5.977 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 49 outliers final: 28 residues processed: 517 average time/residue: 0.6034 time to fit residues: 533.4395 Evaluate side-chains 439 residues out of total 5302 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 411 time to evaluate : 5.617 Switching outliers to nearest non-outliers outliers start: 28 outliers final: 0 residues processed: 28 average time/residue: 0.4544 time to fit residues: 31.6461 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 587 random chunks: chunk 350 optimal weight: 10.0000 chunk 225 optimal weight: 10.0000 chunk 337 optimal weight: 4.9990 chunk 170 optimal weight: 5.9990 chunk 111 optimal weight: 0.5980 chunk 109 optimal weight: 0.9980 chunk 359 optimal weight: 6.9990 chunk 385 optimal weight: 3.9990 chunk 279 optimal weight: 7.9990 chunk 52 optimal weight: 0.9980 chunk 444 optimal weight: 10.0000 overall best weight: 2.3184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 378 HIS ** A 592 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 656 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1108 HIS ** B 422 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 575 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 669 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 735 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 207 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 26 ASN ** J 23 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 99 ASN ** O 390 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 547 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 390 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** R 221 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6661 moved from start: 0.6001 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.087 49628 Z= 0.307 Angle : 0.664 11.951 67268 Z= 0.342 Chirality : 0.044 0.389 7558 Planarity : 0.005 0.157 8380 Dihedral : 11.141 78.659 7121 Min Nonbonded Distance : 1.717 Molprobity Statistics. All-atom Clashscore : 15.96 Ramachandran Plot: Outliers : 0.24 % Allowed : 5.44 % Favored : 94.32 % Rotamer Outliers : 0.66 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.40 % Cis-general : 0.04 % Twisted Proline : 1.60 % Twisted General : 0.02 % 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: -0.51 (0.11), residues: 5789 helix: 0.62 (0.11), residues: 2297 sheet: -0.72 (0.17), residues: 804 loop : -1.00 (0.12), residues: 2688 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 11578 Ramachandran restraints generated. 5789 Oldfield, 0 Emsley, 5789 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 11578 Ramachandran restraints generated. 5789 Oldfield, 0 Emsley, 5789 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 461 residues out of total 5302 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 35 poor density : 426 time to evaluate : 5.758 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 35 outliers final: 16 residues processed: 448 average time/residue: 0.6089 time to fit residues: 465.9050 Evaluate side-chains 413 residues out of total 5302 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 397 time to evaluate : 5.708 Switching outliers to nearest non-outliers revert: symmetry clash outliers start: 16 outliers final: 1 residues processed: 16 average time/residue: 0.5115 time to fit residues: 22.8341 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 587 random chunks: chunk 514 optimal weight: 6.9990 chunk 542 optimal weight: 6.9990 chunk 494 optimal weight: 8.9990 chunk 527 optimal weight: 30.0000 chunk 541 optimal weight: 8.9990 chunk 317 optimal weight: 7.9990 chunk 229 optimal weight: 4.9990 chunk 414 optimal weight: 9.9990 chunk 161 optimal weight: 1.9990 chunk 476 optimal weight: 2.9990 chunk 498 optimal weight: 30.0000 overall best weight: 4.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 260 GLN ** A 592 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 656 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1108 HIS A1319 ASN ** B 422 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 462 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 575 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 669 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 735 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 755 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 912 GLN B1041 ASN ** B1082 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 207 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** I 27 ASN ** J 23 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 99 ASN ** O 390 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** O 451 ASN ** O 547 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 390 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** P 571 HIS R 221 HIS Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6732 moved from start: 0.6255 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.008 0.103 49628 Z= 0.542 Angle : 0.776 12.551 67268 Z= 0.402 Chirality : 0.048 0.447 7558 Planarity : 0.006 0.158 8380 Dihedral : 11.362 81.681 7121 Min Nonbonded Distance : 1.770 Molprobity Statistics. All-atom Clashscore : 18.42 Ramachandran Plot: Outliers : 0.22 % Allowed : 6.41 % Favored : 93.37 % Rotamer Outliers : 0.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.40 % Cis-general : 0.04 % Twisted Proline : 1.60 % Twisted General : 0.05 % 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: -0.80 (0.11), residues: 5789 helix: 0.33 (0.10), residues: 2283 sheet: -0.70 (0.18), residues: 773 loop : -1.17 (0.12), residues: 2733 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 11578 Ramachandran restraints generated. 5789 Oldfield, 0 Emsley, 5789 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 11578 Ramachandran restraints generated. 5789 Oldfield, 0 Emsley, 5789 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 460 residues out of total 5302 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 44 poor density : 416 time to evaluate : 6.230 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 44 outliers final: 21 residues processed: 441 average time/residue: 0.6072 time to fit residues: 456.4605 Evaluate side-chains 398 residues out of total 5302 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 377 time to evaluate : 5.949 Switching outliers to nearest non-outliers revert: symmetry clash outliers start: 21 outliers final: 1 residues processed: 21 average time/residue: 0.4818 time to fit residues: 26.7183 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 587 random chunks: chunk 525 optimal weight: 5.9990 chunk 346 optimal weight: 0.0980 chunk 557 optimal weight: 8.9990 chunk 340 optimal weight: 3.9990 chunk 264 optimal weight: 2.9990 chunk 387 optimal weight: 6.9990 chunk 584 optimal weight: 20.0000 chunk 538 optimal weight: 20.0000 chunk 465 optimal weight: 5.9990 chunk 48 optimal weight: 3.9990 chunk 359 optimal weight: 0.9990 overall best weight: 2.4188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 378 HIS ** A 592 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 656 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1319 ASN ** B 422 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 575 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 669 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 735 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B1041 ASN ** B1082 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 207 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 23 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 64 GLN K 99 ASN N 52 GLN ** O 390 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** O 451 ASN ** P 390 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** R 221 HIS Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6692 moved from start: 0.6403 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.088 49628 Z= 0.319 Angle : 0.690 16.991 67268 Z= 0.355 Chirality : 0.046 0.643 7558 Planarity : 0.005 0.157 8380 Dihedral : 11.242 81.298 7121 Min Nonbonded Distance : 1.904 Molprobity Statistics. All-atom Clashscore : 16.53 Ramachandran Plot: Outliers : 0.22 % Allowed : 5.74 % Favored : 94.04 % Rotamer Outliers : 0.36 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.40 % Cis-general : 0.04 % Twisted Proline : 1.60 % Twisted General : 0.05 % 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: -0.67 (0.11), residues: 5789 helix: 0.47 (0.11), residues: 2288 sheet: -0.77 (0.17), residues: 800 loop : -1.08 (0.12), residues: 2701 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 11578 Ramachandran restraints generated. 5789 Oldfield, 0 Emsley, 5789 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 11578 Ramachandran restraints generated. 5789 Oldfield, 0 Emsley, 5789 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 441 residues out of total 5302 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 422 time to evaluate : 6.036 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 19 outliers final: 8 residues processed: 434 average time/residue: 0.6181 time to fit residues: 456.9244 Evaluate side-chains 410 residues out of total 5302 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 402 time to evaluate : 5.925 Switching outliers to nearest non-outliers outliers start: 8 outliers final: 0 residues processed: 8 average time/residue: 0.5158 time to fit residues: 15.6545 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 587 random chunks: chunk 285 optimal weight: 4.9990 chunk 369 optimal weight: 1.9990 chunk 496 optimal weight: 9.9990 chunk 142 optimal weight: 7.9990 chunk 429 optimal weight: 10.0000 chunk 68 optimal weight: 0.9990 chunk 129 optimal weight: 0.0570 chunk 466 optimal weight: 8.9990 chunk 195 optimal weight: 0.8980 chunk 478 optimal weight: 10.0000 chunk 59 optimal weight: 0.9980 overall best weight: 0.9902 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 592 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 656 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1062 HIS A1108 HIS ** B 422 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 575 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 669 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 735 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 912 GLN ** C 93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 207 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 38 GLN G 26 ASN ** J 23 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 99 ASN ** O 390 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 547 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 390 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** R 221 HIS Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4249 r_free = 0.4249 target = 0.147034 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3506 r_free = 0.3506 target = 0.101544 restraints weight = 104869.840| |-----------------------------------------------------------------------------| r_work (start): 0.3449 rms_B_bonded: 2.64 r_work: 0.3272 rms_B_bonded: 3.08 restraints_weight: 0.5000 r_work: 0.3112 rms_B_bonded: 4.94 restraints_weight: 0.2500 r_work (final): 0.3112 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8430 moved from start: 0.6543 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.092 49628 Z= 0.209 Angle : 0.653 19.587 67268 Z= 0.334 Chirality : 0.045 0.881 7558 Planarity : 0.005 0.157 8380 Dihedral : 11.095 80.671 7121 Min Nonbonded Distance : 1.983 Molprobity Statistics. All-atom Clashscore : 15.32 Ramachandran Plot: Outliers : 0.21 % Allowed : 5.63 % Favored : 94.16 % Rotamer Outliers : 0.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.40 % Cis-general : 0.04 % Twisted Proline : 1.20 % Twisted General : 0.04 % 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: -0.45 (0.11), residues: 5789 helix: 0.66 (0.11), residues: 2288 sheet: -0.66 (0.17), residues: 808 loop : -0.96 (0.12), residues: 2693 =============================================================================== Job complete usr+sys time: 12594.19 seconds wall clock time: 227 minutes 6.98 seconds (13626.98 seconds total)