Starting phenix.real_space_refine (version: 1.21rc1) on Sun Aug 13 00:48:22 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8pkp_17751/08_2023/8pkp_17751.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8pkp_17751/08_2023/8pkp_17751.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.2 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8pkp_17751/08_2023/8pkp_17751.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8pkp_17751/08_2023/8pkp_17751.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8pkp_17751/08_2023/8pkp_17751.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8pkp_17751/08_2023/8pkp_17751.pdb" } resolution = 3.2 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.002 sd= 0.083 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians Zn 1 6.06 5 S 404 5.16 5 C 41346 2.51 5 N 11036 2.21 5 O 11904 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A GLU 1436": "OE1" <-> "OE2" Residue "A GLU 1635": "OE1" <-> "OE2" Residue "A GLU 1729": "OE1" <-> "OE2" Residue "K GLU 422": "OE1" <-> "OE2" Residue "L ARG 46": "NH1" <-> "NH2" Residue "M GLU 35": "OE1" <-> "OE2" Residue "P GLU 649": "OE1" <-> "OE2" Residue "Q GLU 155": "OE1" <-> "OE2" Residue "Q GLU 229": "OE1" <-> "OE2" Residue "Q GLU 524": "OE1" <-> "OE2" Residue "U GLU 133": "OE1" <-> "OE2" Residue "V PHE 94": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "V GLU 288": "OE1" <-> "OE2" Residue "V GLU 377": "OE1" <-> "OE2" Residue "W GLU 20": "OE1" <-> "OE2" Residue "Z GLU 110": "OE1" <-> "OE2" Residue "Z ARG 438": "NH1" <-> "NH2" Residue "I GLU 163": "OE1" <-> "OE2" Residue "N GLU 77": "OE1" <-> "OE2" Residue "N GLU 680": "OE1" <-> "OE2" Time to flip residues: 0.15s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5044/modules/chem_data/mon_lib" Total number of atoms: 64691 Number of models: 1 Model: "" Number of chains: 20 Chain: "A" Number of atoms: 12311 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1580, 12311 Classifications: {'peptide': 1580} Incomplete info: {'truncation_to_alanine': 34} Link IDs: {'PCIS': 1, 'PTRANS': 89, 'TRANS': 1489} Chain breaks: 16 Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 134 Unresolved non-hydrogen angles: 169 Unresolved non-hydrogen dihedrals: 104 Unresolved non-hydrogen chiralities: 5 Planarities with less than four sites: {'ASP:plan': 5, 'ASN:plan1': 5, 'HIS:plan': 1, 'PHE:plan': 1, 'GLU:plan': 9, 'ARG:plan': 6} Unresolved non-hydrogen planarities: 107 Chain: "D" Number of atoms: 458 Number of conformers: 1 Conformer: "" Number of residues, atoms: 56, 458 Classifications: {'peptide': 56} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 5, 'TRANS': 50} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 4 Chain: "G" Number of atoms: 226 Number of conformers: 1 Conformer: "" Number of residues, atoms: 27, 226 Classifications: {'peptide': 27} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'PTRANS': 1, 'TRANS': 25} Unresolved non-hydrogen bonds: 11 Unresolved non-hydrogen angles: 13 Unresolved non-hydrogen dihedrals: 9 Planarities with less than four sites: {'GLU:plan': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 7 Chain: "H" Number of atoms: 459 Number of conformers: 1 Conformer: "" Number of residues, atoms: 57, 459 Classifications: {'peptide': 57} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 2, 'TRANS': 54} Unresolved non-hydrogen bonds: 10 Unresolved non-hydrogen angles: 12 Unresolved non-hydrogen dihedrals: 8 Planarities with less than four sites: {'GLU:plan': 1, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 9 Chain: "J" Number of atoms: 3601 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 476, 3593 Classifications: {'peptide': 476} Incomplete info: {'truncation_to_alanine': 67} Link IDs: {'PTRANS': 15, 'TRANS': 460} Chain breaks: 2 Unresolved chain link angles: 3 Unresolved non-hydrogen bonds: 251 Unresolved non-hydrogen angles: 317 Unresolved non-hydrogen dihedrals: 209 Unresolved non-hydrogen chiralities: 23 Planarities with less than four sites: {'GLN:plan1': 5, 'HIS:plan': 2, 'TYR:plan': 2, 'ASN:plan1': 5, 'TRP:plan': 1, 'ASP:plan': 3, 'PHE:plan': 2, 'GLU:plan': 6, 'ARG:plan': 2} Unresolved non-hydrogen planarities: 123 Conformer: "B" Number of residues, atoms: 476, 3593 Classifications: {'peptide': 476} Incomplete info: {'truncation_to_alanine': 67} Link IDs: {'PTRANS': 15, 'TRANS': 460} Chain breaks: 2 Unresolved chain link angles: 3 Unresolved non-hydrogen bonds: 251 Unresolved non-hydrogen angles: 317 Unresolved non-hydrogen dihedrals: 209 Unresolved non-hydrogen chiralities: 23 Planarities with less than four sites: {'GLN:plan1': 5, 'HIS:plan': 2, 'TYR:plan': 2, 'ASN:plan1': 5, 'TRP:plan': 1, 'ASP:plan': 3, 'PHE:plan': 2, 'GLU:plan': 6, 'ARG:plan': 2} Unresolved non-hydrogen planarities: 123 bond proxies already assigned to first conformer: 3666 Chain: "K" Number of atoms: 4134 Number of conformers: 1 Conformer: "" Number of residues, atoms: 512, 4134 Classifications: {'peptide': 512} Incomplete info: {'truncation_to_alanine': 7} Link IDs: {'PTRANS': 14, 'TRANS': 497} Chain breaks: 2 Unresolved non-hydrogen bonds: 29 Unresolved non-hydrogen angles: 36 Unresolved non-hydrogen dihedrals: 25 Planarities with less than four sites: {'TYR:plan': 1, 'GLU:plan': 2, 'ARG:plan': 1, 'ASN:plan1': 1} Unresolved non-hydrogen planarities: 23 Chain: "L" Number of atoms: 1446 Number of conformers: 1 Conformer: "" Number of residues, atoms: 179, 1446 Classifications: {'peptide': 179} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PCIS': 1, 'PTRANS': 11, 'TRANS': 166} Chain breaks: 1 Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 4 Chain: "M" Number of atoms: 478 Number of conformers: 1 Conformer: "" Number of residues, atoms: 58, 478 Classifications: {'peptide': 58} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 3, 'TRANS': 54} Chain breaks: 1 Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 4 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLU:plan': 1} Unresolved non-hydrogen planarities: 4 Chain: "O" Number of atoms: 5404 Number of conformers: 1 Conformer: "" Number of residues, atoms: 683, 5404 Classifications: {'peptide': 683} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 5} Link IDs: {'PTRANS': 18, 'TRANS': 664} Chain breaks: 3 Unresolved non-hydrogen bonds: 17 Unresolved non-hydrogen angles: 20 Unresolved non-hydrogen dihedrals: 14 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLU:plan': 2} Unresolved non-hydrogen planarities: 8 Chain: "P" Number of atoms: 3883 Number of conformers: 1 Conformer: "" Number of residues, atoms: 484, 3883 Classifications: {'peptide': 484} Incomplete info: {'truncation_to_alanine': 4} Link IDs: {'PTRANS': 15, 'TRANS': 468} Chain breaks: 1 Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 17 Unresolved non-hydrogen angles: 22 Unresolved non-hydrogen dihedrals: 15 Planarities with less than four sites: {'GLN:plan1': 1, 'PHE:plan': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 13 Chain: "Q" Number of atoms: 4049 Number of conformers: 1 Conformer: "" Number of residues, atoms: 504, 4049 Classifications: {'peptide': 504} Incomplete info: {'truncation_to_alanine': 12} Link IDs: {'PTRANS': 14, 'TRANS': 489} Chain breaks: 1 Unresolved non-hydrogen bonds: 40 Unresolved non-hydrogen angles: 48 Unresolved non-hydrogen dihedrals: 32 Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 3, 'ASN:plan1': 1, 'ASP:plan': 1, 'ARG:plan': 2} Unresolved non-hydrogen planarities: 32 Chain: "U" Number of atoms: 4221 Number of conformers: 1 Conformer: "" Number of residues, atoms: 521, 4221 Classifications: {'peptide': 521} Incomplete info: {'truncation_to_alanine': 22} Link IDs: {'PTRANS': 12, 'TRANS': 508} Chain breaks: 1 Unresolved non-hydrogen bonds: 81 Unresolved non-hydrogen angles: 98 Unresolved non-hydrogen dihedrals: 66 Unresolved non-hydrogen chiralities: 6 Planarities with less than four sites: {'GLN:plan1': 2, 'ASN:plan1': 1, 'ASP:plan': 2, 'PHE:plan': 1, 'GLU:plan': 2, 'ARG:plan': 2} Unresolved non-hydrogen planarities: 41 Chain: "V" Number of atoms: 4393 Number of conformers: 1 Conformer: "" Number of residues, atoms: 534, 4393 Classifications: {'peptide': 534} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'PTRANS': 13, 'TRANS': 520} Unresolved non-hydrogen bonds: 7 Unresolved non-hydrogen angles: 9 Unresolved non-hydrogen dihedrals: 5 Planarities with less than four sites: {'ASN:plan1': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 6 Chain: "W" Number of atoms: 217 Number of conformers: 1 Conformer: "" Number of residues, atoms: 25, 217 Classifications: {'peptide': 25} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 1, 'TRANS': 23} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 2 Planarities with less than four sites: {'ASP:plan': 1} Unresolved non-hydrogen planarities: 3 Chain: "Y" Number of atoms: 3907 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 499, 3899 Classifications: {'peptide': 499} Incomplete info: {'truncation_to_alanine': 7} Link IDs: {'PTRANS': 15, 'TRANS': 483} Chain breaks: 1 Unresolved non-hydrogen bonds: 27 Unresolved non-hydrogen angles: 32 Unresolved non-hydrogen dihedrals: 22 Planarities with less than four sites: {'GLU:plan': 4, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 19 Conformer: "B" Number of residues, atoms: 499, 3899 Classifications: {'peptide': 499} Incomplete info: {'truncation_to_alanine': 7} Link IDs: {'PTRANS': 15, 'TRANS': 483} Chain breaks: 1 Unresolved non-hydrogen bonds: 27 Unresolved non-hydrogen angles: 32 Unresolved non-hydrogen dihedrals: 22 Planarities with less than four sites: {'GLU:plan': 4, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 19 bond proxies already assigned to first conformer: 3950 Chain: "Z" Number of atoms: 3807 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 486, 3799 Classifications: {'peptide': 486} Incomplete info: {'truncation_to_alanine': 6} Link IDs: {'PTRANS': 15, 'TRANS': 470} Chain breaks: 1 Unresolved non-hydrogen bonds: 17 Unresolved non-hydrogen angles: 21 Unresolved non-hydrogen dihedrals: 13 Planarities with less than four sites: {'GLU:plan': 3, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 15 Conformer: "B" Number of residues, atoms: 486, 3799 Classifications: {'peptide': 486} Incomplete info: {'truncation_to_alanine': 6} Link IDs: {'PTRANS': 15, 'TRANS': 470} Chain breaks: 1 Unresolved non-hydrogen bonds: 17 Unresolved non-hydrogen angles: 21 Unresolved non-hydrogen dihedrals: 13 Planarities with less than four sites: {'GLU:plan': 3, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 15 bond proxies already assigned to first conformer: 3850 Chain: "I" Number of atoms: 5722 Number of conformers: 1 Conformer: "" Number of residues, atoms: 718, 5722 Classifications: {'peptide': 718} Incomplete info: {'truncation_to_alanine': 12} Link IDs: {'PCIS': 1, 'PTRANS': 21, 'TRANS': 695} Chain breaks: 3 Unresolved non-hydrogen bonds: 47 Unresolved non-hydrogen angles: 54 Unresolved non-hydrogen dihedrals: 40 Planarities with less than four sites: {'GLU:plan': 3, 'ARG:plan': 2, 'ASP:plan': 2} Unresolved non-hydrogen planarities: 28 Chain: "N" Number of atoms: 5294 Number of conformers: 1 Conformer: "" Number of residues, atoms: 652, 5294 Classifications: {'peptide': 652} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PCIS': 1, 'PTRANS': 32, 'TRANS': 618} Chain breaks: 3 Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 7 Unresolved non-hydrogen dihedrals: 5 Planarities with less than four sites: {'ARG:plan': 1} Unresolved non-hydrogen planarities: 5 Chain: "C" Number of atoms: 680 Number of conformers: 1 Conformer: "" Number of residues, atoms: 84, 680 Classifications: {'peptide': 84} Link IDs: {'PTRANS': 4, 'TRANS': 79} Chain: "N" 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 60268 SG CYS N 221 81.433 15.729 185.297 1.00163.03 S ATOM 60283 SG CYS N 224 78.913 15.301 188.018 1.00154.94 S ATOM 60336 SG CYS N 231 79.215 12.577 185.377 1.00152.84 S ATOM 60356 SG CYS N 233 77.694 15.785 184.375 1.00132.25 S Time building chain proxies: 29.16, per 1000 atoms: 0.45 Number of scatterers: 64691 At special positions: 0 Unit cell: (172.27, 202.23, 241.82, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) Zn 1 29.99 S 404 16.00 O 11904 8.00 N 11036 7.00 C 41346 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=2, symmetry=0 Simple disulfide: pdb=" SG CYS A 129 " - pdb=" SG CYS A 152 " distance=2.03 Simple disulfide: pdb=" SG CYS P 673 " - pdb=" SG CYS P 705 " distance=2.01 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 19.66 Conformation dependent library (CDL) restraints added in 8.1 seconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN N 901 " pdb="ZN ZN N 901 " - pdb=" SG CYS N 231 " pdb="ZN ZN N 901 " - pdb=" SG CYS N 233 " pdb="ZN ZN N 901 " - pdb=" SG CYS N 224 " pdb="ZN ZN N 901 " - pdb=" SG CYS N 221 " Number of angles added : 6 16056 Ramachandran restraints generated. 8028 Oldfield, 0 Emsley, 8028 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 15564 Finding SS restraints... Secondary structure from input PDB file: 410 helices and 26 sheets defined 70.0% alpha, 5.5% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 4.38 Creating SS restraints... Processing helix chain 'A' and resid 22 through 29 removed outlier: 3.934A pdb=" N ASP A 26 " --> pdb=" O PRO A 22 " (cutoff:3.500A) removed outlier: 3.696A pdb=" N LYS A 29 " --> pdb=" O ARG A 25 " (cutoff:3.500A) Processing helix chain 'A' and resid 143 through 145 No H-bonds generated for 'chain 'A' and resid 143 through 145' Processing helix chain 'A' and resid 346 through 352 removed outlier: 4.248A pdb=" N ARG A 352 " --> pdb=" O ALA A 348 " (cutoff:3.500A) Processing helix chain 'A' and resid 615 through 629 removed outlier: 3.683A pdb=" N ILE A 628 " --> pdb=" O ALA A 624 " (cutoff:3.500A) Processing helix chain 'A' and resid 630 through 646 Processing helix chain 'A' and resid 655 through 669 Processing helix chain 'A' and resid 703 through 713 removed outlier: 4.347A pdb=" N TRP A 707 " --> pdb=" O SER A 703 " (cutoff:3.500A) removed outlier: 3.570A pdb=" N GLU A 708 " --> pdb=" O ASP A 704 " (cutoff:3.500A) Processing helix chain 'A' and resid 713 through 722 Processing helix chain 'A' and resid 755 through 757 No H-bonds generated for 'chain 'A' and resid 755 through 757' Processing helix chain 'A' and resid 758 through 775 removed outlier: 4.032A pdb=" N LEU A 775 " --> pdb=" O GLU A 771 " (cutoff:3.500A) Processing helix chain 'A' and resid 780 through 797 removed outlier: 3.773A pdb=" N CYS A 784 " --> pdb=" O GLY A 780 " (cutoff:3.500A) removed outlier: 3.817A pdb=" N GLU A 788 " --> pdb=" O CYS A 784 " (cutoff:3.500A) removed outlier: 3.977A pdb=" N LEU A 789 " --> pdb=" O SER A 785 " (cutoff:3.500A) Processing helix chain 'A' and resid 799 through 810 removed outlier: 3.803A pdb=" N VAL A 803 " --> pdb=" O LEU A 799 " (cutoff:3.500A) removed outlier: 3.564A pdb=" N ASP A 809 " --> pdb=" O HIS A 805 " (cutoff:3.500A) Processing helix chain 'A' and resid 843 through 852 Processing helix chain 'A' and resid 867 through 882 Processing helix chain 'A' and resid 925 through 938 Processing helix chain 'A' and resid 940 through 946 removed outlier: 3.675A pdb=" N GLU A 945 " --> pdb=" O LEU A 941 " (cutoff:3.500A) removed outlier: 3.900A pdb=" N THR A 946 " --> pdb=" O ARG A 942 " (cutoff:3.500A) Processing helix chain 'A' and resid 948 through 965 Proline residue: A 954 - end of helix Processing helix chain 'A' and resid 971 through 979 Processing helix chain 'A' and resid 980 through 992 Processing helix chain 'A' and resid 1020 through 1028 Processing helix chain 'A' and resid 1032 through 1042 Processing helix chain 'A' and resid 1058 through 1088 removed outlier: 3.531A pdb=" N GLN A1075 " --> pdb=" O LEU A1071 " (cutoff:3.500A) removed outlier: 4.140A pdb=" N ARG A1076 " --> pdb=" O GLN A1072 " (cutoff:3.500A) removed outlier: 3.619A pdb=" N ALA A1079 " --> pdb=" O GLN A1075 " (cutoff:3.500A) Proline residue: A1081 - end of helix Processing helix chain 'A' and resid 1132 through 1146 Processing helix chain 'A' and resid 1154 through 1158 removed outlier: 3.973A pdb=" N TRP A1157 " --> pdb=" O ASP A1154 " (cutoff:3.500A) Processing helix chain 'A' and resid 1165 through 1167 No H-bonds generated for 'chain 'A' and resid 1165 through 1167' Processing helix chain 'A' and resid 1168 through 1182 Processing helix chain 'A' and resid 1184 through 1188 removed outlier: 3.550A pdb=" N LEU A1188 " --> pdb=" O LEU A1185 " (cutoff:3.500A) Processing helix chain 'A' and resid 1192 through 1198 removed outlier: 3.689A pdb=" N TYR A1196 " --> pdb=" O ASN A1192 " (cutoff:3.500A) Processing helix chain 'A' and resid 1201 through 1215 Processing helix chain 'A' and resid 1221 through 1230 removed outlier: 3.526A pdb=" N ILE A1230 " --> pdb=" O ARG A1226 " (cutoff:3.500A) Processing helix chain 'A' and resid 1246 through 1261 Processing helix chain 'A' and resid 1266 through 1278 removed outlier: 4.269A pdb=" N GLY A1278 " --> pdb=" O LEU A1274 " (cutoff:3.500A) Processing helix chain 'A' and resid 1290 through 1307 removed outlier: 3.668A pdb=" N TYR A1294 " --> pdb=" O ASP A1290 " (cutoff:3.500A) Processing helix chain 'A' and resid 1320 through 1331 Processing helix chain 'A' and resid 1359 through 1375 Proline residue: A1365 - end of helix Processing helix chain 'A' and resid 1380 through 1386 removed outlier: 4.134A pdb=" N TRP A1386 " --> pdb=" O SER A1382 " (cutoff:3.500A) Processing helix chain 'A' and resid 1394 through 1398 removed outlier: 3.514A pdb=" N PHE A1398 " --> pdb=" O LEU A1395 " (cutoff:3.500A) Processing helix chain 'A' and resid 1400 through 1415 removed outlier: 3.868A pdb=" N LEU A1405 " --> pdb=" O PRO A1401 " (cutoff:3.500A) removed outlier: 3.943A pdb=" N LEU A1406 " --> pdb=" O GLU A1402 " (cutoff:3.500A) Processing helix chain 'A' and resid 1416 through 1419 Processing helix chain 'A' and resid 1422 through 1429 removed outlier: 3.680A pdb=" N VAL A1426 " --> pdb=" O ASN A1422 " (cutoff:3.500A) removed outlier: 3.591A pdb=" N ASN A1429 " --> pdb=" O TRP A1425 " (cutoff:3.500A) Processing helix chain 'A' and resid 1431 through 1436 Processing helix chain 'A' and resid 1453 through 1476 Processing helix chain 'A' and resid 1481 through 1500 removed outlier: 3.904A pdb=" N SER A1500 " --> pdb=" O MET A1496 " (cutoff:3.500A) Processing helix chain 'A' and resid 1503 through 1508 Processing helix chain 'A' and resid 1508 through 1527 Processing helix chain 'A' and resid 1532 through 1544 Processing helix chain 'A' and resid 1551 through 1566 Processing helix chain 'A' and resid 1567 through 1570 Processing helix chain 'A' and resid 1577 through 1588 removed outlier: 3.544A pdb=" N CYS A1586 " --> pdb=" O ALA A1582 " (cutoff:3.500A) Processing helix chain 'A' and resid 1603 through 1612 removed outlier: 4.350A pdb=" N TYR A1610 " --> pdb=" O ARG A1607 " (cutoff:3.500A) removed outlier: 3.725A pdb=" N VAL A1611 " --> pdb=" O HIS A1608 " (cutoff:3.500A) Processing helix chain 'A' and resid 1659 through 1661 No H-bonds generated for 'chain 'A' and resid 1659 through 1661' Processing helix chain 'A' and resid 1684 through 1693 Processing helix chain 'A' and resid 1726 through 1732 removed outlier: 3.668A pdb=" N ARG A1731 " --> pdb=" O ASN A1727 " (cutoff:3.500A) removed outlier: 3.728A pdb=" N ALA A1732 " --> pdb=" O SER A1728 " (cutoff:3.500A) Processing helix chain 'A' and resid 1744 through 1754 Processing helix chain 'A' and resid 1764 through 1781 removed outlier: 3.605A pdb=" N LEU A1768 " --> pdb=" O LYS A1764 " (cutoff:3.500A) Processing helix chain 'A' and resid 1783 through 1785 No H-bonds generated for 'chain 'A' and resid 1783 through 1785' Processing helix chain 'A' and resid 1786 through 1802 Processing helix chain 'A' and resid 1810 through 1821 Processing helix chain 'A' and resid 1822 through 1827 removed outlier: 6.122A pdb=" N SER A1825 " --> pdb=" O SER A1822 " (cutoff:3.500A) removed outlier: 3.631A pdb=" N GLN A1827 " --> pdb=" O ARG A1824 " (cutoff:3.500A) Processing helix chain 'A' and resid 1843 through 1863 Processing helix chain 'A' and resid 1863 through 1874 removed outlier: 4.200A pdb=" N CYS A1867 " --> pdb=" O GLY A1863 " (cutoff:3.500A) Processing helix chain 'A' and resid 1878 through 1880 No H-bonds generated for 'chain 'A' and resid 1878 through 1880' Processing helix chain 'A' and resid 1881 through 1893 Processing helix chain 'A' and resid 1910 through 1920 removed outlier: 4.122A pdb=" N GLN A1920 " --> pdb=" O PHE A1916 " (cutoff:3.500A) Processing helix chain 'A' and resid 1924 through 1936 removed outlier: 3.606A pdb=" N ARG A1930 " --> pdb=" O ARG A1926 " (cutoff:3.500A) Proline residue: A1933 - end of helix Processing helix chain 'D' and resid 26 through 46 Processing helix chain 'G' and resid 12 through 15 removed outlier: 3.671A pdb=" N ASP G 15 " --> pdb=" O LYS G 12 " (cutoff:3.500A) No H-bonds generated for 'chain 'G' and resid 12 through 15' Processing helix chain 'G' and resid 16 through 27 removed outlier: 3.781A pdb=" N GLU G 20 " --> pdb=" O ILE G 16 " (cutoff:3.500A) removed outlier: 3.687A pdb=" N ILE G 22 " --> pdb=" O GLU G 18 " (cutoff:3.500A) removed outlier: 4.169A pdb=" N ASP G 25 " --> pdb=" O ASN G 21 " (cutoff:3.500A) removed outlier: 3.726A pdb=" N LEU G 26 " --> pdb=" O ILE G 22 " (cutoff:3.500A) removed outlier: 3.731A pdb=" N GLU G 27 " --> pdb=" O ARG G 23 " (cutoff:3.500A) Processing helix chain 'H' and resid 52 through 92 removed outlier: 3.978A pdb=" N VAL H 86 " --> pdb=" O LEU H 82 " (cutoff:3.500A) removed outlier: 4.443A pdb=" N GLU H 87 " --> pdb=" O ALA H 83 " (cutoff:3.500A) removed outlier: 3.871A pdb=" N GLU H 88 " --> pdb=" O GLY H 84 " (cutoff:3.500A) removed outlier: 3.878A pdb=" N GLU H 90 " --> pdb=" O VAL H 86 " (cutoff:3.500A) removed outlier: 3.679A pdb=" N ALA H 91 " --> pdb=" O GLU H 87 " (cutoff:3.500A) removed outlier: 3.550A pdb=" N ASP H 92 " --> pdb=" O GLU H 88 " (cutoff:3.500A) Processing helix chain 'H' and resid 93 through 96 Processing helix chain 'H' and resid 98 through 103 Processing helix chain 'J' and resid 6 through 18 Processing helix chain 'J' and resid 20 through 35 Processing helix chain 'J' and resid 37 through 51 removed outlier: 3.569A pdb=" N SER J 51 " --> pdb=" O CYS J 47 " (cutoff:3.500A) Processing helix chain 'J' and resid 53 through 64 removed outlier: 4.180A pdb=" N ALA J 57 " --> pdb=" O LYS J 53 " (cutoff:3.500A) Processing helix chain 'J' and resid 68 through 82 Processing helix chain 'J' and resid 84 through 94 Processing helix chain 'J' and resid 102 through 111 Processing helix chain 'J' and resid 113 through 128 removed outlier: 3.931A pdb=" N SER J 119 " --> pdb=" O CYS J 115 " (cutoff:3.500A) Processing helix chain 'J' and resid 130 through 145 removed outlier: 3.736A pdb=" N GLY J 134 " --> pdb=" O ARG J 130 " (cutoff:3.500A) removed outlier: 3.738A pdb=" N GLU J 136 " --> pdb=" O ALA J 132 " (cutoff:3.500A) Processing helix chain 'J' and resid 149 through 158 Processing helix chain 'J' and resid 163 through 168 removed outlier: 3.606A pdb=" N PHE J 168 " --> pdb=" O PRO J 164 " (cutoff:3.500A) Processing helix chain 'J' and resid 452 through 478 removed outlier: 4.098A pdb=" N GLY J 461 " --> pdb=" O ALA J 457 " (cutoff:3.500A) removed outlier: 4.918A pdb=" N LEU J 462 " --> pdb=" O ALA J 458 " (cutoff:3.500A) removed outlier: 4.547A pdb=" N LEU J 465 " --> pdb=" O GLY J 461 " (cutoff:3.500A) Processing helix chain 'J' and resid 480 through 490 removed outlier: 3.953A pdb=" N ALA J 484 " --> pdb=" O ASN J 480 " (cutoff:3.500A) Processing helix chain 'J' and resid 492 through 497 Processing helix chain 'J' and resid 498 through 512 Processing helix chain 'J' and resid 514 through 529 removed outlier: 3.634A pdb=" N ALA J 518 " --> pdb=" O GLU J 514 " (cutoff:3.500A) Processing helix chain 'J' and resid 535 through 546 removed outlier: 4.053A pdb=" N TYR J 539 " --> pdb=" O GLY J 535 " (cutoff:3.500A) Processing helix chain 'J' and resid 549 through 563 Processing helix chain 'J' and resid 566 through 579 removed outlier: 4.009A pdb=" N TRP J 570 " --> pdb=" O SER J 566 " (cutoff:3.500A) Processing helix chain 'J' and resid 582 through 597 Processing helix chain 'J' and resid 600 through 615 removed outlier: 3.906A pdb=" N TYR J 604 " --> pdb=" O TYR J 600 " (cutoff:3.500A) removed outlier: 3.566A pdb=" N THR J 605 " --> pdb=" O ALA J 601 " (cutoff:3.500A) removed outlier: 4.043A pdb=" N LEU J 606 " --> pdb=" O TYR J 602 " (cutoff:3.500A) removed outlier: 3.611A pdb=" N LEU J 607 " --> pdb=" O ALA J 603 " (cutoff:3.500A) Processing helix chain 'J' and resid 616 through 631 removed outlier: 3.546A pdb=" N ASN J 631 " --> pdb=" O ALA J 627 " (cutoff:3.500A) Processing helix chain 'J' and resid 634 through 647 Processing helix chain 'J' and resid 650 through 665 removed outlier: 3.819A pdb=" N MET J 656 " --> pdb=" O SER J 652 " (cutoff:3.500A) removed outlier: 3.760A pdb=" N HIS J 657 " --> pdb=" O LEU J 653 " (cutoff:3.500A) Processing helix chain 'J' and resid 669 through 682 removed outlier: 4.249A pdb=" N ILE J 675 " --> pdb=" O LEU J 671 " (cutoff:3.500A) Processing helix chain 'J' and resid 692 through 699 removed outlier: 3.766A pdb=" N ILE J 698 " --> pdb=" O LYS J 694 " (cutoff:3.500A) Processing helix chain 'J' and resid 702 through 716 Processing helix chain 'J' and resid 718 through 733 removed outlier: 3.638A pdb=" N ALA J 722 " --> pdb=" O LYS J 718 " (cutoff:3.500A) removed outlier: 3.952A pdb=" N LEU J 723 " --> pdb=" O TYR J 719 " (cutoff:3.500A) removed outlier: 4.027A pdb=" N GLN J 724 " --> pdb=" O LYS J 720 " (cutoff:3.500A) removed outlier: 3.837A pdb=" N GLN J 731 " --> pdb=" O GLU J 727 " (cutoff:3.500A) removed outlier: 3.914A pdb=" N ILE J 732 " --> pdb=" O GLU J 728 " (cutoff:3.500A) Processing helix chain 'J' and resid 736 through 750 removed outlier: 3.658A pdb=" N TYR J 740 " --> pdb=" O GLU J 736 " (cutoff:3.500A) Processing helix chain 'J' and resid 753 through 767 Processing helix chain 'K' and resid 2 through 16 Processing helix chain 'K' and resid 19 through 33 Processing helix chain 'K' and resid 36 through 50 Processing helix chain 'K' and resid 52 through 62 Processing helix chain 'K' and resid 64 through 69 removed outlier: 4.143A pdb=" N LEU K 68 " --> pdb=" O LYS K 64 " (cutoff:3.500A) removed outlier: 3.521A pdb=" N TYR K 69 " --> pdb=" O LEU K 65 " (cutoff:3.500A) No H-bonds generated for 'chain 'K' and resid 64 through 69' Processing helix chain 'K' and resid 69 through 83 Processing helix chain 'K' and resid 85 through 94 removed outlier: 3.582A pdb=" N ALA K 89 " --> pdb=" O GLU K 85 " (cutoff:3.500A) Processing helix chain 'K' and resid 128 through 143 Processing helix chain 'K' and resid 146 through 160 Processing helix chain 'K' and resid 163 through 171 removed outlier: 3.802A pdb=" N PHE K 167 " --> pdb=" O CYS K 163 " (cutoff:3.500A) Processing helix chain 'K' and resid 177 through 188 removed outlier: 3.501A pdb=" N LEU K 188 " --> pdb=" O LEU K 184 " (cutoff:3.500A) Processing helix chain 'K' and resid 194 through 210 Processing helix chain 'K' and resid 225 through 229 removed outlier: 3.755A pdb=" N GLN K 228 " --> pdb=" O ASP K 225 " (cutoff:3.500A) removed outlier: 3.653A pdb=" N GLU K 229 " --> pdb=" O GLY K 226 " (cutoff:3.500A) No H-bonds generated for 'chain 'K' and resid 225 through 229' Processing helix chain 'K' and resid 230 through 243 Processing helix chain 'K' and resid 246 through 261 Processing helix chain 'K' and resid 267 through 278 Processing helix chain 'K' and resid 280 through 295 Processing helix chain 'K' and resid 298 through 313 removed outlier: 4.174A pdb=" N TRP K 302 " --> pdb=" O ASN K 298 " (cutoff:3.500A) Processing helix chain 'K' and resid 315 through 330 Processing helix chain 'K' and resid 333 through 346 removed outlier: 3.873A pdb=" N TRP K 337 " --> pdb=" O TYR K 333 " (cutoff:3.500A) Processing helix chain 'K' and resid 349 through 364 removed outlier: 3.542A pdb=" N LEU K 363 " --> pdb=" O THR K 359 " (cutoff:3.500A) Processing helix chain 'K' and resid 367 through 380 removed outlier: 4.325A pdb=" N MET K 371 " --> pdb=" O CYS K 367 " (cutoff:3.500A) Processing helix chain 'K' and resid 384 through 398 Processing helix chain 'K' and resid 401 through 416 Processing helix chain 'K' and resid 418 through 435 Processing helix chain 'K' and resid 440 through 443 removed outlier: 3.615A pdb=" N LYS K 443 " --> pdb=" O THR K 440 " (cutoff:3.500A) No H-bonds generated for 'chain 'K' and resid 440 through 443' Processing helix chain 'K' and resid 444 through 458 removed outlier: 3.718A pdb=" N LEU K 448 " --> pdb=" O TRP K 444 " (cutoff:3.500A) Processing helix chain 'K' and resid 460 through 475 Processing helix chain 'K' and resid 478 through 492 Processing helix chain 'K' and resid 494 through 509 removed outlier: 3.645A pdb=" N ASP K 500 " --> pdb=" O GLU K 496 " (cutoff:3.500A) Processing helix chain 'K' and resid 512 through 528 removed outlier: 3.570A pdb=" N VAL K 516 " --> pdb=" O ASP K 512 " (cutoff:3.500A) Processing helix chain 'K' and resid 554 through 559 Processing helix chain 'L' and resid 12 through 19 removed outlier: 3.586A pdb=" N ARG L 18 " --> pdb=" O LYS L 14 " (cutoff:3.500A) removed outlier: 4.254A pdb=" N THR L 19 " --> pdb=" O GLN L 15 " (cutoff:3.500A) Processing helix chain 'L' and resid 41 through 47 removed outlier: 3.652A pdb=" N LEU L 45 " --> pdb=" O GLY L 41 " (cutoff:3.500A) Processing helix chain 'L' and resid 146 through 148 No H-bonds generated for 'chain 'L' and resid 146 through 148' Processing helix chain 'L' and resid 175 through 180 Processing helix chain 'M' and resid 8 through 15 Processing helix chain 'M' and resid 16 through 22 Processing helix chain 'M' and resid 49 through 55 removed outlier: 3.867A pdb=" N MET M 55 " --> pdb=" O LYS M 51 " (cutoff:3.500A) Processing helix chain 'O' and resid 31 through 45 Processing helix chain 'O' and resid 53 through 70 removed outlier: 4.071A pdb=" N ARG O 57 " --> pdb=" O SER O 53 " (cutoff:3.500A) removed outlier: 3.783A pdb=" N GLN O 62 " --> pdb=" O ARG O 58 " (cutoff:3.500A) removed outlier: 3.889A pdb=" N LEU O 63 " --> pdb=" O ARG O 59 " (cutoff:3.500A) removed outlier: 4.104A pdb=" N LEU O 65 " --> pdb=" O ASN O 61 " (cutoff:3.500A) Proline residue: O 66 - end of helix removed outlier: 3.520A pdb=" N GLN O 69 " --> pdb=" O LEU O 65 " (cutoff:3.500A) Processing helix chain 'O' and resid 74 through 86 Processing helix chain 'O' and resid 86 through 103 Processing helix chain 'O' and resid 104 through 116 removed outlier: 4.233A pdb=" N MET O 108 " --> pdb=" O GLU O 104 " (cutoff:3.500A) removed outlier: 3.613A pdb=" N GLU O 109 " --> pdb=" O LEU O 105 " (cutoff:3.500A) removed outlier: 3.791A pdb=" N SER O 116 " --> pdb=" O PHE O 112 " (cutoff:3.500A) Processing helix chain 'O' and resid 117 through 119 No H-bonds generated for 'chain 'O' and resid 117 through 119' Processing helix chain 'O' and resid 130 through 146 removed outlier: 3.841A pdb=" N LEU O 146 " --> pdb=" O ALA O 142 " (cutoff:3.500A) Processing helix chain 'O' and resid 147 through 168 Processing helix chain 'O' and resid 208 through 226 Processing helix chain 'O' and resid 232 through 247 Processing helix chain 'O' and resid 250 through 264 removed outlier: 3.954A pdb=" N HIS O 254 " --> pdb=" O PHE O 250 " (cutoff:3.500A) removed outlier: 3.523A pdb=" N TYR O 255 " --> pdb=" O ALA O 251 " (cutoff:3.500A) removed outlier: 3.563A pdb=" N VAL O 264 " --> pdb=" O ASN O 260 " (cutoff:3.500A) Processing helix chain 'O' and resid 267 through 280 removed outlier: 3.833A pdb=" N SER O 273 " --> pdb=" O SER O 269 " (cutoff:3.500A) removed outlier: 3.609A pdb=" N LEU O 274 " --> pdb=" O SER O 270 " (cutoff:3.500A) Processing helix chain 'O' and resid 288 through 292 Processing helix chain 'O' and resid 297 through 315 removed outlier: 4.404A pdb=" N ARG O 301 " --> pdb=" O GLY O 297 " (cutoff:3.500A) removed outlier: 3.712A pdb=" N TYR O 302 " --> pdb=" O ARG O 298 " (cutoff:3.500A) Processing helix chain 'O' and resid 316 through 335 Processing helix chain 'O' and resid 337 through 355 removed outlier: 3.704A pdb=" N HIS O 342 " --> pdb=" O VAL O 338 " (cutoff:3.500A) removed outlier: 3.815A pdb=" N LYS O 353 " --> pdb=" O VAL O 349 " (cutoff:3.500A) Processing helix chain 'O' and resid 360 through 370 removed outlier: 3.599A pdb=" N HIS O 370 " --> pdb=" O LYS O 366 " (cutoff:3.500A) Processing helix chain 'O' and resid 373 through 390 Processing helix chain 'O' and resid 406 through 412 removed outlier: 3.876A pdb=" N TRP O 410 " --> pdb=" O ASP O 406 " (cutoff:3.500A) removed outlier: 3.869A pdb=" N HIS O 412 " --> pdb=" O LEU O 408 " (cutoff:3.500A) Processing helix chain 'O' and resid 414 through 432 removed outlier: 3.741A pdb=" N ILE O 418 " --> pdb=" O LEU O 414 " (cutoff:3.500A) Processing helix chain 'O' and resid 434 through 447 Processing helix chain 'O' and resid 463 through 480 removed outlier: 3.647A pdb=" N ALA O 467 " --> pdb=" O THR O 463 " (cutoff:3.500A) removed outlier: 3.738A pdb=" N GLN O 480 " --> pdb=" O LEU O 476 " (cutoff:3.500A) Processing helix chain 'O' and resid 482 through 497 Processing helix chain 'O' and resid 504 through 522 removed outlier: 3.707A pdb=" N CYS O 510 " --> pdb=" O LEU O 506 " (cutoff:3.500A) Processing helix chain 'O' and resid 524 through 539 removed outlier: 3.562A pdb=" N THR O 533 " --> pdb=" O ASP O 529 " (cutoff:3.500A) removed outlier: 3.897A pdb=" N GLY O 534 " --> pdb=" O SER O 530 " (cutoff:3.500A) Processing helix chain 'O' and resid 539 through 554 Processing helix chain 'O' and resid 556 through 575 Processing helix chain 'O' and resid 576 through 592 Processing helix chain 'O' and resid 596 through 598 No H-bonds generated for 'chain 'O' and resid 596 through 598' Processing helix chain 'O' and resid 599 through 614 removed outlier: 4.724A pdb=" N MET O 603 " --> pdb=" O ILE O 599 " (cutoff:3.500A) Processing helix chain 'O' and resid 616 through 635 Processing helix chain 'O' and resid 636 through 647 Processing helix chain 'O' and resid 648 through 654 Processing helix chain 'O' and resid 656 through 675 Processing helix chain 'O' and resid 679 through 705 removed outlier: 3.508A pdb=" N GLU O 685 " --> pdb=" O PRO O 681 " (cutoff:3.500A) Processing helix chain 'O' and resid 706 through 725 removed outlier: 3.639A pdb=" N ILE O 710 " --> pdb=" O CYS O 706 " (cutoff:3.500A) Processing helix chain 'O' and resid 726 through 742 removed outlier: 4.531A pdb=" N GLN O 742 " --> pdb=" O ARG O 738 " (cutoff:3.500A) Processing helix chain 'O' and resid 749 through 754 Processing helix chain 'P' and resid 6 through 18 Processing helix chain 'P' and resid 20 through 35 removed outlier: 4.151A pdb=" N ALA P 24 " --> pdb=" O ALA P 20 " (cutoff:3.500A) Processing helix chain 'P' and resid 37 through 51 Processing helix chain 'P' and resid 53 through 63 Processing helix chain 'P' and resid 68 through 82 Processing helix chain 'P' and resid 84 through 93 Processing helix chain 'P' and resid 102 through 111 Processing helix chain 'P' and resid 113 through 128 removed outlier: 3.634A pdb=" N THR P 117 " --> pdb=" O SER P 113 " (cutoff:3.500A) Processing helix chain 'P' and resid 130 through 145 Processing helix chain 'P' and resid 149 through 159 Processing helix chain 'P' and resid 163 through 168 Processing helix chain 'P' and resid 453 through 478 removed outlier: 4.649A pdb=" N GLY P 461 " --> pdb=" O ALA P 457 " (cutoff:3.500A) removed outlier: 5.400A pdb=" N LEU P 462 " --> pdb=" O ALA P 458 " (cutoff:3.500A) Processing helix chain 'P' and resid 480 through 489 Processing helix chain 'P' and resid 492 through 497 Processing helix chain 'P' and resid 498 through 512 Processing helix chain 'P' and resid 514 through 529 Processing helix chain 'P' and resid 535 through 547 removed outlier: 3.528A pdb=" N TYR P 539 " --> pdb=" O GLY P 535 " (cutoff:3.500A) Processing helix chain 'P' and resid 548 through 563 Processing helix chain 'P' and resid 566 through 580 removed outlier: 4.090A pdb=" N TRP P 570 " --> pdb=" O SER P 566 " (cutoff:3.500A) removed outlier: 3.644A pdb=" N PHE P 577 " --> pdb=" O ALA P 573 " (cutoff:3.500A) Processing helix chain 'P' and resid 582 through 597 Processing helix chain 'P' and resid 600 through 614 removed outlier: 3.694A pdb=" N TYR P 604 " --> pdb=" O TYR P 600 " (cutoff:3.500A) Processing helix chain 'P' and resid 616 through 631 removed outlier: 3.885A pdb=" N ALA P 622 " --> pdb=" O ASP P 618 " (cutoff:3.500A) removed outlier: 3.670A pdb=" N CYS P 623 " --> pdb=" O LYS P 619 " (cutoff:3.500A) Processing helix chain 'P' and resid 634 through 648 removed outlier: 3.768A pdb=" N TRP P 638 " --> pdb=" O HIS P 634 " (cutoff:3.500A) Processing helix chain 'P' and resid 650 through 665 removed outlier: 3.625A pdb=" N ILE P 664 " --> pdb=" O LYS P 660 " (cutoff:3.500A) Processing helix chain 'P' and resid 668 through 682 Processing helix chain 'P' and resid 684 through 699 Processing helix chain 'P' and resid 703 through 716 Processing helix chain 'P' and resid 718 through 733 removed outlier: 3.792A pdb=" N GLU P 728 " --> pdb=" O GLN P 724 " (cutoff:3.500A) removed outlier: 4.064A pdb=" N GLN P 731 " --> pdb=" O GLU P 727 " (cutoff:3.500A) removed outlier: 3.582A pdb=" N ILE P 732 " --> pdb=" O GLU P 728 " (cutoff:3.500A) Processing helix chain 'P' and resid 737 through 751 Processing helix chain 'P' and resid 752 through 767 Processing helix chain 'Q' and resid 3 through 16 removed outlier: 3.853A pdb=" N ARG Q 9 " --> pdb=" O ARG Q 5 " (cutoff:3.500A) Processing helix chain 'Q' and resid 18 through 33 Processing helix chain 'Q' and resid 36 through 50 Processing helix chain 'Q' and resid 52 through 63 removed outlier: 4.039A pdb=" N ARG Q 63 " --> pdb=" O ALA Q 59 " (cutoff:3.500A) Processing helix chain 'Q' and resid 64 through 69 Processing helix chain 'Q' and resid 69 through 83 Processing helix chain 'Q' and resid 85 through 94 removed outlier: 3.620A pdb=" N ALA Q 89 " --> pdb=" O GLU Q 85 " (cutoff:3.500A) Processing helix chain 'Q' and resid 126 through 143 removed outlier: 4.203A pdb=" N SER Q 130 " --> pdb=" O SER Q 126 " (cutoff:3.500A) Processing helix chain 'Q' and resid 146 through 160 removed outlier: 3.980A pdb=" N TYR Q 151 " --> pdb=" O THR Q 147 " (cutoff:3.500A) Processing helix chain 'Q' and resid 163 through 172 removed outlier: 3.800A pdb=" N PHE Q 167 " --> pdb=" O CYS Q 163 " (cutoff:3.500A) Processing helix chain 'Q' and resid 177 through 188 Processing helix chain 'Q' and resid 194 through 207 Processing helix chain 'Q' and resid 230 through 244 removed outlier: 4.187A pdb=" N SER Q 236 " --> pdb=" O ASP Q 232 " (cutoff:3.500A) Processing helix chain 'Q' and resid 246 through 261 removed outlier: 3.722A pdb=" N VAL Q 256 " --> pdb=" O LYS Q 252 " (cutoff:3.500A) Processing helix chain 'Q' and resid 267 through 278 Processing helix chain 'Q' and resid 280 through 295 Processing helix chain 'Q' and resid 298 through 313 removed outlier: 4.165A pdb=" N TRP Q 302 " --> pdb=" O ASN Q 298 " (cutoff:3.500A) Processing helix chain 'Q' and resid 315 through 330 Processing helix chain 'Q' and resid 334 through 347 removed outlier: 3.628A pdb=" N ILE Q 338 " --> pdb=" O GLY Q 334 " (cutoff:3.500A) removed outlier: 3.601A pdb=" N GLU Q 347 " --> pdb=" O SER Q 343 " (cutoff:3.500A) Processing helix chain 'Q' and resid 349 through 364 Processing helix chain 'Q' and resid 368 through 381 Processing helix chain 'Q' and resid 383 through 398 Processing helix chain 'Q' and resid 401 through 416 removed outlier: 4.238A pdb=" N GLY Q 409 " --> pdb=" O MET Q 405 " (cutoff:3.500A) Processing helix chain 'Q' and resid 417 through 433 removed outlier: 3.777A pdb=" N ALA Q 421 " --> pdb=" O GLU Q 417 " (cutoff:3.500A) removed outlier: 3.564A pdb=" N LYS Q 431 " --> pdb=" O ASP Q 427 " (cutoff:3.500A) Processing helix chain 'Q' and resid 444 through 458 removed outlier: 3.819A pdb=" N LEU Q 448 " --> pdb=" O TRP Q 444 " (cutoff:3.500A) Processing helix chain 'Q' and resid 460 through 475 Processing helix chain 'Q' and resid 478 through 493 Processing helix chain 'Q' and resid 494 through 510 removed outlier: 4.180A pdb=" N ASP Q 500 " --> pdb=" O GLU Q 496 " (cutoff:3.500A) removed outlier: 3.555A pdb=" N ALA Q 505 " --> pdb=" O TYR Q 501 " (cutoff:3.500A) removed outlier: 3.727A pdb=" N LEU Q 508 " --> pdb=" O THR Q 504 " (cutoff:3.500A) Processing helix chain 'Q' and resid 512 through 530 removed outlier: 3.640A pdb=" N ASP Q 529 " --> pdb=" O MET Q 525 " (cutoff:3.500A) Processing helix chain 'U' and resid 28 through 46 Processing helix chain 'U' and resid 48 through 62 removed outlier: 3.623A pdb=" N SER U 61 " --> pdb=" O GLU U 57 " (cutoff:3.500A) removed outlier: 3.776A pdb=" N LEU U 62 " --> pdb=" O LEU U 58 " (cutoff:3.500A) Processing helix chain 'U' and resid 77 through 83 removed outlier: 3.555A pdb=" N ASP U 83 " --> pdb=" O GLU U 79 " (cutoff:3.500A) Processing helix chain 'U' and resid 83 through 96 Processing helix chain 'U' and resid 98 through 106 removed outlier: 3.654A pdb=" N LEU U 106 " --> pdb=" O ALA U 102 " (cutoff:3.500A) Processing helix chain 'U' and resid 111 through 133 Processing helix chain 'U' and resid 148 through 164 removed outlier: 3.689A pdb=" N GLU U 153 " --> pdb=" O GLU U 149 " (cutoff:3.500A) removed outlier: 3.922A pdb=" N LEU U 154 " --> pdb=" O ALA U 150 " (cutoff:3.500A) Processing helix chain 'U' and resid 169 through 182 removed outlier: 3.792A pdb=" N TYR U 173 " --> pdb=" O GLY U 169 " (cutoff:3.500A) Processing helix chain 'U' and resid 184 through 199 Processing helix chain 'U' and resid 202 through 211 removed outlier: 3.900A pdb=" N TRP U 206 " --> pdb=" O HIS U 202 " (cutoff:3.500A) removed outlier: 3.572A pdb=" N ASN U 211 " --> pdb=" O LEU U 207 " (cutoff:3.500A) Processing helix chain 'U' and resid 215 through 222 removed outlier: 3.969A pdb=" N LEU U 219 " --> pdb=" O ASP U 215 " (cutoff:3.500A) removed outlier: 4.304A pdb=" N LYS U 220 " --> pdb=" O LYS U 216 " (cutoff:3.500A) removed outlier: 3.554A pdb=" N PHE U 221 " --> pdb=" O GLU U 217 " (cutoff:3.500A) Processing helix chain 'U' and resid 228 through 241 removed outlier: 4.529A pdb=" N PHE U 232 " --> pdb=" O TRP U 228 " (cutoff:3.500A) Processing helix chain 'U' and resid 243 through 258 Processing helix chain 'U' and resid 262 through 276 Processing helix chain 'U' and resid 278 through 293 removed outlier: 4.141A pdb=" N ALA U 282 " --> pdb=" O ASP U 278 " (cutoff:3.500A) Processing helix chain 'U' and resid 299 through 311 removed outlier: 3.552A pdb=" N PHE U 303 " --> pdb=" O ASN U 299 " (cutoff:3.500A) removed outlier: 3.544A pdb=" N VAL U 309 " --> pdb=" O ASN U 305 " (cutoff:3.500A) Processing helix chain 'U' and resid 312 through 327 Processing helix chain 'U' and resid 330 through 344 Processing helix chain 'U' and resid 346 through 361 Processing helix chain 'U' and resid 365 through 378 removed outlier: 4.681A pdb=" N THR U 369 " --> pdb=" O LEU U 365 " (cutoff:3.500A) Processing helix chain 'U' and resid 381 through 395 Processing helix chain 'U' and resid 398 through 412 removed outlier: 3.507A pdb=" N LEU U 412 " --> pdb=" O THR U 408 " (cutoff:3.500A) Processing helix chain 'U' and resid 414 through 429 removed outlier: 3.580A pdb=" N LEU U 428 " --> pdb=" O ARG U 424 " (cutoff:3.500A) Processing helix chain 'U' and resid 432 through 446 removed outlier: 4.043A pdb=" N LEU U 436 " --> pdb=" O ASP U 432 " (cutoff:3.500A) Processing helix chain 'U' and resid 449 through 461 removed outlier: 3.518A pdb=" N LYS U 454 " --> pdb=" O VAL U 450 " (cutoff:3.500A) Processing helix chain 'U' and resid 470 through 480 removed outlier: 3.541A pdb=" N GLN U 479 " --> pdb=" O LYS U 475 " (cutoff:3.500A) Processing helix chain 'U' and resid 483 through 500 removed outlier: 3.572A pdb=" N CYS U 500 " --> pdb=" O ASP U 496 " (cutoff:3.500A) Processing helix chain 'U' and resid 508 through 523 removed outlier: 3.550A pdb=" N PHE U 513 " --> pdb=" O GLU U 509 " (cutoff:3.500A) removed outlier: 3.606A pdb=" N ARG U 514 " --> pdb=" O SER U 510 " (cutoff:3.500A) removed outlier: 3.528A pdb=" N TYR U 515 " --> pdb=" O THR U 511 " (cutoff:3.500A) removed outlier: 3.674A pdb=" N TYR U 520 " --> pdb=" O LEU U 516 " (cutoff:3.500A) removed outlier: 3.691A pdb=" N PHE U 521 " --> pdb=" O ALA U 517 " (cutoff:3.500A) removed outlier: 3.539A pdb=" N LYS U 522 " --> pdb=" O GLN U 518 " (cutoff:3.500A) Processing helix chain 'U' and resid 525 through 537 removed outlier: 3.907A pdb=" N THR U 531 " --> pdb=" O ASP U 527 " (cutoff:3.500A) removed outlier: 3.625A pdb=" N LYS U 535 " --> pdb=" O THR U 531 " (cutoff:3.500A) Processing helix chain 'U' and resid 542 through 552 removed outlier: 4.068A pdb=" N GLY U 546 " --> pdb=" O THR U 542 " (cutoff:3.500A) Processing helix chain 'V' and resid 29 through 47 Processing helix chain 'V' and resid 49 through 62 removed outlier: 3.908A pdb=" N SER V 61 " --> pdb=" O GLU V 57 " (cutoff:3.500A) removed outlier: 4.023A pdb=" N LEU V 62 " --> pdb=" O LEU V 58 " (cutoff:3.500A) Processing helix chain 'V' and resid 77 through 83 Processing helix chain 'V' and resid 83 through 96 removed outlier: 3.824A pdb=" N LEU V 89 " --> pdb=" O ASP V 85 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N VAL V 96 " --> pdb=" O ALA V 92 " (cutoff:3.500A) Processing helix chain 'V' and resid 98 through 106 Processing helix chain 'V' and resid 111 through 137 Processing helix chain 'V' and resid 139 through 145 Processing helix chain 'V' and resid 150 through 164 Processing helix chain 'V' and resid 168 through 182 Processing helix chain 'V' and resid 184 through 199 Processing helix chain 'V' and resid 202 through 213 removed outlier: 3.842A pdb=" N TRP V 206 " --> pdb=" O HIS V 202 " (cutoff:3.500A) removed outlier: 3.617A pdb=" N ASN V 211 " --> pdb=" O LEU V 207 " (cutoff:3.500A) Processing helix chain 'V' and resid 215 through 222 removed outlier: 4.185A pdb=" N LEU V 219 " --> pdb=" O ASP V 215 " (cutoff:3.500A) removed outlier: 3.808A pdb=" N LYS V 220 " --> pdb=" O LYS V 216 " (cutoff:3.500A) removed outlier: 3.531A pdb=" N PHE V 221 " --> pdb=" O GLU V 217 " (cutoff:3.500A) Processing helix chain 'V' and resid 227 through 241 removed outlier: 4.243A pdb=" N GLU V 231 " --> pdb=" O THR V 227 " (cutoff:3.500A) removed outlier: 3.738A pdb=" N PHE V 232 " --> pdb=" O TRP V 228 " (cutoff:3.500A) Processing helix chain 'V' and resid 243 through 258 removed outlier: 3.511A pdb=" N GLY V 258 " --> pdb=" O LEU V 254 " (cutoff:3.500A) Processing helix chain 'V' and resid 262 through 276 Processing helix chain 'V' and resid 278 through 293 Processing helix chain 'V' and resid 299 through 311 Processing helix chain 'V' and resid 312 through 327 removed outlier: 3.545A pdb=" N GLU V 325 " --> pdb=" O HIS V 321 " (cutoff:3.500A) Processing helix chain 'V' and resid 330 through 344 Processing helix chain 'V' and resid 346 through 361 removed outlier: 3.557A pdb=" N LYS V 359 " --> pdb=" O GLN V 355 " (cutoff:3.500A) Processing helix chain 'V' and resid 368 through 378 removed outlier: 3.593A pdb=" N MET V 378 " --> pdb=" O GLU V 374 " (cutoff:3.500A) Processing helix chain 'V' and resid 380 through 395 Processing helix chain 'V' and resid 398 through 412 removed outlier: 3.760A pdb=" N LEU V 412 " --> pdb=" O THR V 408 " (cutoff:3.500A) Processing helix chain 'V' and resid 417 through 429 removed outlier: 4.451A pdb=" N TYR V 421 " --> pdb=" O TYR V 417 " (cutoff:3.500A) Processing helix chain 'V' and resid 432 through 446 removed outlier: 3.959A pdb=" N LEU V 436 " --> pdb=" O ASP V 432 " (cutoff:3.500A) Processing helix chain 'V' and resid 448 through 462 Processing helix chain 'V' and resid 468 through 480 Processing helix chain 'V' and resid 482 through 500 removed outlier: 3.529A pdb=" N CYS V 500 " --> pdb=" O ASP V 496 " (cutoff:3.500A) Processing helix chain 'V' and resid 508 through 523 Processing helix chain 'V' and resid 525 through 539 removed outlier: 4.020A pdb=" N LYS V 535 " --> pdb=" O THR V 531 " (cutoff:3.500A) removed outlier: 3.641A pdb=" N ALA V 538 " --> pdb=" O GLN V 534 " (cutoff:3.500A) removed outlier: 4.125A pdb=" N PHE V 539 " --> pdb=" O LYS V 535 " (cutoff:3.500A) Processing helix chain 'V' and resid 542 through 557 removed outlier: 3.787A pdb=" N GLN V 555 " --> pdb=" O ARG V 551 " (cutoff:3.500A) Processing helix chain 'W' and resid 12 through 14 No H-bonds generated for 'chain 'W' and resid 12 through 14' Processing helix chain 'W' and resid 15 through 25 removed outlier: 4.116A pdb=" N PHE W 19 " --> pdb=" O ASP W 15 " (cutoff:3.500A) Processing helix chain 'Y' and resid 3 through 13 Processing helix chain 'Y' and resid 15 through 33 removed outlier: 3.713A pdb=" N LEU Y 21 " --> pdb=" O SER Y 17 " (cutoff:3.500A) removed outlier: 3.662A pdb=" N THR Y 28 " --> pdb=" O SER Y 24 " (cutoff:3.500A) removed outlier: 4.189A pdb=" N ASN Y 33 " --> pdb=" O MET Y 29 " (cutoff:3.500A) Processing helix chain 'Y' and resid 38 through 55 removed outlier: 3.688A pdb=" N HIS Y 55 " --> pdb=" O ASP Y 51 " (cutoff:3.500A) Processing helix chain 'Y' and resid 59 through 76 removed outlier: 4.194A pdb=" N MET Y 68 " --> pdb=" O SER Y 64 " (cutoff:3.500A) Processing helix chain 'Y' and resid 100 through 115 removed outlier: 3.529A pdb=" N VAL Y 104 " --> pdb=" O SER Y 100 " (cutoff:3.500A) Processing helix chain 'Y' and resid 117 through 126 Processing helix chain 'Y' and resid 129 through 133 removed outlier: 3.898A pdb=" N ARG Y 133 " --> pdb=" O SER Y 130 " (cutoff:3.500A) Processing helix chain 'Y' and resid 134 through 149 Processing helix chain 'Y' and resid 150 through 165 removed outlier: 3.563A pdb=" N SER Y 154 " --> pdb=" O GLN Y 150 " (cutoff:3.500A) removed outlier: 3.905A pdb=" N THR Y 156 " --> pdb=" O ARG Y 152 " (cutoff:3.500A) Processing helix chain 'Y' and resid 168 through 177 removed outlier: 3.657A pdb=" N SER Y 177 " --> pdb=" O LEU Y 173 " (cutoff:3.500A) Processing helix chain 'Y' and resid 181 through 190 removed outlier: 3.701A pdb=" N VAL Y 185 " --> pdb=" O LYS Y 181 " (cutoff:3.500A) Processing helix chain 'Y' and resid 200 through 210 removed outlier: 4.629A pdb=" N VAL Y 204 " --> pdb=" O ASP Y 200 " (cutoff:3.500A) Processing helix chain 'Y' and resid 217 through 231 removed outlier: 3.655A pdb=" N LYS Y 230 " --> pdb=" O SER Y 226 " (cutoff:3.500A) Processing helix chain 'Y' and resid 236 through 250 Processing helix chain 'Y' and resid 253 through 267 removed outlier: 3.554A pdb=" N VAL Y 257 " --> pdb=" O ASN Y 253 " (cutoff:3.500A) removed outlier: 4.219A pdb=" N LEU Y 258 " --> pdb=" O LYS Y 254 " (cutoff:3.500A) removed outlier: 3.784A pdb=" N LYS Y 259 " --> pdb=" O ASN Y 255 " (cutoff:3.500A) Processing helix chain 'Y' and resid 273 through 284 removed outlier: 3.775A pdb=" N TYR Y 279 " --> pdb=" O ASP Y 275 " (cutoff:3.500A) Processing helix chain 'Y' and resid 287 through 298 Processing helix chain 'Y' and resid 304 through 318 removed outlier: 4.592A pdb=" N TRP Y 308 " --> pdb=" O HIS Y 304 " (cutoff:3.500A) Processing helix chain 'Y' and resid 320 through 335 removed outlier: 4.150A pdb=" N ALA Y 324 " --> pdb=" O ARG Y 320 " (cutoff:3.500A) removed outlier: 3.849A pdb=" N TYR Y 326 " --> pdb=" O SER Y 322 " (cutoff:3.500A) Processing helix chain 'Y' and resid 338 through 353 Processing helix chain 'Y' and resid 355 through 369 removed outlier: 3.823A pdb=" N ARG Y 367 " --> pdb=" O ARG Y 363 " (cutoff:3.500A) removed outlier: 3.799A pdb=" N LEU Y 368 " --> pdb=" O GLU Y 364 " (cutoff:3.500A) removed outlier: 3.501A pdb=" N ALA Y 369 " --> pdb=" O ALA Y 365 " (cutoff:3.500A) Processing helix chain 'Y' and resid 372 through 386 removed outlier: 4.247A pdb=" N TYR Y 376 " --> pdb=" O ARG Y 372 " (cutoff:3.500A) Processing helix chain 'Y' and resid 388 through 404 Processing helix chain 'Y' and resid 406 through 418 Processing helix chain 'Y' and resid 419 through 422 removed outlier: 6.447A pdb=" N VAL Y 422 " --> pdb=" O GLU Y 419 " (cutoff:3.500A) No H-bonds generated for 'chain 'Y' and resid 419 through 422' Processing helix chain 'Y' and resid 423 through 438 Processing helix chain 'Y' and resid 441 through 454 Processing helix chain 'Y' and resid 457 through 473 removed outlier: 3.773A pdb=" N GLY Y 461 " --> pdb=" O LYS Y 457 " (cutoff:3.500A) removed outlier: 4.495A pdb=" N ASN Y 471 " --> pdb=" O ASN Y 467 " (cutoff:3.500A) removed outlier: 3.599A pdb=" N GLN Y 472 " --> pdb=" O ALA Y 468 " (cutoff:3.500A) Processing helix chain 'Y' and resid 474 through 488 removed outlier: 3.950A pdb=" N ALA Y 487 " --> pdb=" O ASP Y 483 " (cutoff:3.500A) removed outlier: 3.878A pdb=" N VAL Y 488 " --> pdb=" O PHE Y 484 " (cutoff:3.500A) Processing helix chain 'Y' and resid 490 through 505 removed outlier: 3.612A pdb=" N ASP Y 505 " --> pdb=" O ALA Y 501 " (cutoff:3.500A) Processing helix chain 'Y' and resid 508 through 521 removed outlier: 3.587A pdb=" N GLU Y 521 " --> pdb=" O LYS Y 517 " (cutoff:3.500A) Processing helix chain 'Z' and resid 3 through 10 Processing helix chain 'Z' and resid 16 through 33 Processing helix chain 'Z' and resid 38 through 56 removed outlier: 3.682A pdb=" N LEU Z 53 " --> pdb=" O HIS Z 49 " (cutoff:3.500A) Processing helix chain 'Z' and resid 58 through 77 removed outlier: 3.552A pdb=" N SER Z 64 " --> pdb=" O ARG Z 60 " (cutoff:3.500A) removed outlier: 3.613A pdb=" N SER Z 77 " --> pdb=" O LYS Z 73 " (cutoff:3.500A) Processing helix chain 'Z' and resid 100 through 115 Processing helix chain 'Z' and resid 118 through 127 removed outlier: 3.990A pdb=" N GLY Z 127 " --> pdb=" O ALA Z 123 " (cutoff:3.500A) Processing helix chain 'Z' and resid 128 through 133 removed outlier: 5.963A pdb=" N ARG Z 131 " --> pdb=" O ILE Z 128 " (cutoff:3.500A) removed outlier: 3.735A pdb=" N ARG Z 133 " --> pdb=" O SER Z 130 " (cutoff:3.500A) Processing helix chain 'Z' and resid 134 through 149 Processing helix chain 'Z' and resid 151 through 165 Processing helix chain 'Z' and resid 168 through 178 Processing helix chain 'Z' and resid 181 through 188 removed outlier: 3.625A pdb=" N VAL Z 185 " --> pdb=" O LYS Z 181 " (cutoff:3.500A) Processing helix chain 'Z' and resid 189 through 196 Processing helix chain 'Z' and resid 199 through 214 removed outlier: 3.595A pdb=" N PHE Z 211 " --> pdb=" O LYS Z 207 " (cutoff:3.500A) removed outlier: 3.665A pdb=" N HIS Z 213 " --> pdb=" O TYR Z 209 " (cutoff:3.500A) removed outlier: 3.582A pdb=" N THR Z 214 " --> pdb=" O ALA Z 210 " (cutoff:3.500A) Processing helix chain 'Z' and resid 216 through 229 removed outlier: 3.675A pdb=" N CYS Z 225 " --> pdb=" O ILE Z 221 " (cutoff:3.500A) removed outlier: 4.461A pdb=" N SER Z 226 " --> pdb=" O SER Z 222 " (cutoff:3.500A) removed outlier: 4.509A pdb=" N LEU Z 227 " --> pdb=" O THR Z 223 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N GLU Z 228 " --> pdb=" O ILE Z 224 " (cutoff:3.500A) Processing helix chain 'Z' and resid 236 through 250 Processing helix chain 'Z' and resid 253 through 267 removed outlier: 3.718A pdb=" N LEU Z 266 " --> pdb=" O GLN Z 262 " (cutoff:3.500A) Processing helix chain 'Z' and resid 273 through 285 Processing helix chain 'Z' and resid 286 through 301 Processing helix chain 'Z' and resid 304 through 318 removed outlier: 4.595A pdb=" N TRP Z 308 " --> pdb=" O HIS Z 304 " (cutoff:3.500A) Processing helix chain 'Z' and resid 320 through 335 removed outlier: 3.632A pdb=" N ALA Z 324 " --> pdb=" O ARG Z 320 " (cutoff:3.500A) Processing helix chain 'Z' and resid 338 through 353 removed outlier: 3.985A pdb=" N LEU Z 342 " --> pdb=" O SER Z 338 " (cutoff:3.500A) removed outlier: 3.635A pdb=" N LYS Z 345 " --> pdb=" O ALA Z 341 " (cutoff:3.500A) removed outlier: 4.037A pdb=" N ASN Z 351 " --> pdb=" O ALA Z 347 " (cutoff:3.500A) removed outlier: 4.286A pdb=" N MET Z 352 " --> pdb=" O ALA Z 348 " (cutoff:3.500A) removed outlier: 3.730A pdb=" N GLY Z 353 " --> pdb=" O LEU Z 349 " (cutoff:3.500A) Processing helix chain 'Z' and resid 354 through 369 removed outlier: 3.977A pdb=" N ALA Z 358 " --> pdb=" O ARG Z 354 " (cutoff:3.500A) removed outlier: 4.001A pdb=" N ILE Z 360 " --> pdb=" O GLN Z 356 " (cutoff:3.500A) Processing helix chain 'Z' and resid 372 through 385 removed outlier: 3.714A pdb=" N TYR Z 376 " --> pdb=" O ARG Z 372 " (cutoff:3.500A) Processing helix chain 'Z' and resid 389 through 403 removed outlier: 3.760A pdb=" N MET Z 395 " --> pdb=" O GLU Z 391 " (cutoff:3.500A) removed outlier: 4.583A pdb=" N ASN Z 398 " --> pdb=" O VAL Z 394 " (cutoff:3.500A) removed outlier: 4.355A pdb=" N VAL Z 399 " --> pdb=" O MET Z 395 " (cutoff:3.500A) removed outlier: 3.812A pdb=" N TYR Z 400 " --> pdb=" O ALA Z 396 " (cutoff:3.500A) Processing helix chain 'Z' and resid 406 through 417 removed outlier: 3.823A pdb=" N VAL Z 416 " --> pdb=" O LEU Z 412 " (cutoff:3.500A) removed outlier: 3.505A pdb=" N CYS Z 417 " --> pdb=" O LEU Z 413 " (cutoff:3.500A) Processing helix chain 'Z' and resid 418 through 420 No H-bonds generated for 'chain 'Z' and resid 418 through 420' Processing helix chain 'Z' and resid 423 through 438 Processing helix chain 'Z' and resid 441 through 455 removed outlier: 3.797A pdb=" N VAL Z 445 " --> pdb=" O TYR Z 441 " (cutoff:3.500A) Processing helix chain 'Z' and resid 457 through 469 removed outlier: 4.180A pdb=" N GLY Z 461 " --> pdb=" O LYS Z 457 " (cutoff:3.500A) removed outlier: 3.579A pdb=" N ARG Z 466 " --> pdb=" O ILE Z 462 " (cutoff:3.500A) removed outlier: 3.619A pdb=" N ASN Z 467 " --> pdb=" O ALA Z 463 " (cutoff:3.500A) Processing helix chain 'Z' and resid 476 through 489 removed outlier: 3.575A pdb=" N ILE Z 480 " --> pdb=" O VAL Z 476 " (cutoff:3.500A) removed outlier: 3.558A pdb=" N LEU Z 481 " --> pdb=" O LEU Z 477 " (cutoff:3.500A) removed outlier: 4.624A pdb=" N GLY Z 482 " --> pdb=" O HIS Z 478 " (cutoff:3.500A) removed outlier: 4.855A pdb=" N ALA Z 487 " --> pdb=" O ASP Z 483 " (cutoff:3.500A) removed outlier: 3.773A pdb=" N VAL Z 488 " --> pdb=" O PHE Z 484 " (cutoff:3.500A) Processing helix chain 'Z' and resid 493 through 505 removed outlier: 3.556A pdb=" N GLN Z 497 " --> pdb=" O GLU Z 493 " (cutoff:3.500A) removed outlier: 4.090A pdb=" N TYR Z 498 " --> pdb=" O ALA Z 494 " (cutoff:3.500A) Processing helix chain 'I' and resid 50 through 52 No H-bonds generated for 'chain 'I' and resid 50 through 52' Processing helix chain 'I' and resid 122 through 139 removed outlier: 3.681A pdb=" N LEU I 137 " --> pdb=" O ASP I 133 " (cutoff:3.500A) removed outlier: 3.563A pdb=" N LEU I 138 " --> pdb=" O GLU I 134 " (cutoff:3.500A) Processing helix chain 'I' and resid 162 through 169 Processing helix chain 'I' and resid 238 through 244 Processing helix chain 'I' and resid 244 through 294 removed outlier: 3.852A pdb=" N ARG I 250 " --> pdb=" O PRO I 246 " (cutoff:3.500A) removed outlier: 3.541A pdb=" N MET I 251 " --> pdb=" O GLU I 247 " (cutoff:3.500A) removed outlier: 3.904A pdb=" N MET I 283 " --> pdb=" O ILE I 279 " (cutoff:3.500A) removed outlier: 5.445A pdb=" N LYS I 289 " --> pdb=" O SER I 285 " (cutoff:3.500A) removed outlier: 5.647A pdb=" N PHE I 290 " --> pdb=" O ARG I 286 " (cutoff:3.500A) Processing helix chain 'I' and resid 299 through 310 Processing helix chain 'I' and resid 314 through 323 Processing helix chain 'I' and resid 326 through 351 Processing helix chain 'I' and resid 351 through 371 Processing helix chain 'I' and resid 372 through 377 Processing helix chain 'I' and resid 378 through 380 No H-bonds generated for 'chain 'I' and resid 378 through 380' Processing helix chain 'I' and resid 382 through 429 removed outlier: 3.502A pdb=" N ILE I 386 " --> pdb=" O ASP I 382 " (cutoff:3.500A) Processing helix chain 'I' and resid 441 through 456 Processing helix chain 'I' and resid 474 through 478 Processing helix chain 'I' and resid 495 through 504 Processing helix chain 'I' and resid 521 through 546 removed outlier: 3.534A pdb=" N VAL I 525 " --> pdb=" O SER I 521 " (cutoff:3.500A) Proline residue: I 540 - end of helix Processing helix chain 'I' and resid 560 through 564 Processing helix chain 'I' and resid 671 through 675 Processing helix chain 'N' and resid 17 through 32 Processing helix chain 'N' and resid 51 through 66 removed outlier: 3.574A pdb=" N ALA N 57 " --> pdb=" O GLU N 53 " (cutoff:3.500A) removed outlier: 3.510A pdb=" N GLY N 64 " --> pdb=" O GLU N 60 " (cutoff:3.500A) removed outlier: 3.581A pdb=" N HIS N 65 " --> pdb=" O VAL N 61 " (cutoff:3.500A) Processing helix chain 'N' and resid 69 through 86 removed outlier: 4.686A pdb=" N GLU N 73 " --> pdb=" O SER N 69 " (cutoff:3.500A) Processing helix chain 'N' and resid 86 through 100 removed outlier: 3.659A pdb=" N ASN N 100 " --> pdb=" O SER N 96 " (cutoff:3.500A) Processing helix chain 'N' and resid 103 through 138 Proline residue: N 124 - end of helix Processing helix chain 'N' and resid 148 through 162 Processing helix chain 'N' and resid 166 through 189 Processing helix chain 'N' and resid 205 through 218 removed outlier: 3.754A pdb=" N SER N 218 " --> pdb=" O ARG N 214 " (cutoff:3.500A) Processing helix chain 'N' and resid 232 through 250 removed outlier: 3.725A pdb=" N LEU N 237 " --> pdb=" O CYS N 233 " (cutoff:3.500A) removed outlier: 4.641A pdb=" N GLU N 238 " --> pdb=" O ARG N 234 " (cutoff:3.500A) removed outlier: 3.566A pdb=" N LEU N 250 " --> pdb=" O VAL N 246 " (cutoff:3.500A) Processing helix chain 'N' and resid 252 through 257 removed outlier: 3.923A pdb=" N SER N 257 " --> pdb=" O LEU N 253 " (cutoff:3.500A) Processing helix chain 'N' and resid 257 through 278 removed outlier: 3.603A pdb=" N ARG N 278 " --> pdb=" O GLU N 274 " (cutoff:3.500A) Processing helix chain 'N' and resid 285 through 304 removed outlier: 3.610A pdb=" N TRP N 292 " --> pdb=" O GLU N 288 " (cutoff:3.500A) Processing helix chain 'N' and resid 316 through 343 removed outlier: 3.852A pdb=" N THR N 320 " --> pdb=" O GLU N 316 " (cutoff:3.500A) removed outlier: 3.834A pdb=" N LEU N 321 " --> pdb=" O ALA N 317 " (cutoff:3.500A) Processing helix chain 'N' and resid 343 through 350 removed outlier: 3.664A pdb=" N ASP N 350 " --> pdb=" O SER N 346 " (cutoff:3.500A) Processing helix chain 'N' and resid 350 through 366 Proline residue: N 356 - end of helix Processing helix chain 'N' and resid 370 through 386 Processing helix chain 'N' and resid 392 through 411 removed outlier: 3.713A pdb=" N THR N 398 " --> pdb=" O CYS N 394 " (cutoff:3.500A) Processing helix chain 'N' and resid 414 through 421 Processing helix chain 'N' and resid 421 through 431 removed outlier: 3.727A pdb=" N ARG N 429 " --> pdb=" O ARG N 425 " (cutoff:3.500A) removed outlier: 3.621A pdb=" N THR N 430 " --> pdb=" O ARG N 426 " (cutoff:3.500A) Processing helix chain 'N' and resid 433 through 442 Processing helix chain 'N' and resid 476 through 480 removed outlier: 3.653A pdb=" N TRP N 480 " --> pdb=" O PRO N 477 " (cutoff:3.500A) Processing helix chain 'N' and resid 500 through 510 removed outlier: 3.790A pdb=" N LEU N 504 " --> pdb=" O ASP N 500 " (cutoff:3.500A) removed outlier: 4.161A pdb=" N SER N 507 " --> pdb=" O SER N 503 " (cutoff:3.500A) removed outlier: 3.662A pdb=" N ILE N 508 " --> pdb=" O LEU N 504 " (cutoff:3.500A) removed outlier: 3.897A pdb=" N TYR N 509 " --> pdb=" O LEU N 505 " (cutoff:3.500A) Processing helix chain 'N' and resid 511 through 530 removed outlier: 3.640A pdb=" N ILE N 516 " --> pdb=" O LYS N 512 " (cutoff:3.500A) removed outlier: 3.681A pdb=" N HIS N 529 " --> pdb=" O ASP N 525 " (cutoff:3.500A) removed outlier: 3.948A pdb=" N GLN N 530 " --> pdb=" O ARG N 526 " (cutoff:3.500A) Processing helix chain 'N' and resid 534 through 550 removed outlier: 3.680A pdb=" N GLU N 538 " --> pdb=" O SER N 534 " (cutoff:3.500A) removed outlier: 3.914A pdb=" N ARG N 540 " --> pdb=" O GLU N 536 " (cutoff:3.500A) removed outlier: 4.732A pdb=" N ASN N 541 " --> pdb=" O ARG N 537 " (cutoff:3.500A) removed outlier: 3.627A pdb=" N LEU N 547 " --> pdb=" O GLU N 543 " (cutoff:3.500A) removed outlier: 3.765A pdb=" N ARG N 548 " --> pdb=" O LEU N 544 " (cutoff:3.500A) Processing helix chain 'N' and resid 554 through 580 removed outlier: 3.659A pdb=" N GLU N 558 " --> pdb=" O MET N 554 " (cutoff:3.500A) removed outlier: 3.617A pdb=" N VAL N 559 " --> pdb=" O HIS N 555 " (cutoff:3.500A) removed outlier: 3.752A pdb=" N MET N 560 " --> pdb=" O PHE N 556 " (cutoff:3.500A) removed outlier: 3.555A pdb=" N LEU N 561 " --> pdb=" O CYS N 557 " (cutoff:3.500A) removed outlier: 3.695A pdb=" N LYS N 580 " --> pdb=" O GLU N 576 " (cutoff:3.500A) Processing helix chain 'N' and resid 612 through 630 Processing helix chain 'N' and resid 660 through 673 removed outlier: 3.661A pdb=" N ILE N 666 " --> pdb=" O VAL N 662 " (cutoff:3.500A) removed outlier: 3.590A pdb=" N LEU N 667 " --> pdb=" O GLN N 663 " (cutoff:3.500A) removed outlier: 3.859A pdb=" N ASP N 672 " --> pdb=" O LEU N 668 " (cutoff:3.500A) removed outlier: 3.577A pdb=" N GLN N 673 " --> pdb=" O TYR N 669 " (cutoff:3.500A) Processing helix chain 'N' and resid 678 through 686 Processing helix chain 'N' and resid 688 through 703 removed outlier: 3.976A pdb=" N ARG N 693 " --> pdb=" O VAL N 689 " (cutoff:3.500A) removed outlier: 4.834A pdb=" N ARG N 694 " --> pdb=" O ALA N 690 " (cutoff:3.500A) removed outlier: 3.676A pdb=" N ARG N 695 " --> pdb=" O LEU N 691 " (cutoff:3.500A) removed outlier: 3.799A pdb=" N VAL N 698 " --> pdb=" O ARG N 694 " (cutoff:3.500A) removed outlier: 3.738A pdb=" N TRP N 699 " --> pdb=" O ARG N 695 " (cutoff:3.500A) Processing helix chain 'C' and resid 56 through 66 removed outlier: 3.679A pdb=" N ALA C 66 " --> pdb=" O LYS C 62 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 11 through 13 removed outlier: 6.162A pdb=" N ILE A 12 " --> pdb=" O PHE A 510 " (cutoff:3.500A) removed outlier: 3.815A pdb=" N VAL A 504 " --> pdb=" O THR A 501 " (cutoff:3.500A) removed outlier: 6.607A pdb=" N LEU A 499 " --> pdb=" O VAL A 506 " (cutoff:3.500A) removed outlier: 4.538A pdb=" N LYS A 508 " --> pdb=" O LEU A 497 " (cutoff:3.500A) removed outlier: 7.298A pdb=" N LEU A 497 " --> pdb=" O LYS A 508 " (cutoff:3.500A) removed outlier: 3.528A pdb=" N THR A 487 " --> pdb=" O VAL A 482 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 18 through 19 removed outlier: 6.932A pdb=" N ARG A 594 " --> pdb=" O ASP A 589 " (cutoff:3.500A) removed outlier: 6.954A pdb=" N ASP A 589 " --> pdb=" O ARG A 594 " (cutoff:3.500A) removed outlier: 7.046A pdb=" N THR A 596 " --> pdb=" O ILE A 587 " (cutoff:3.500A) removed outlier: 4.642A pdb=" N ILE A 587 " --> pdb=" O THR A 596 " (cutoff:3.500A) removed outlier: 6.665A pdb=" N GLU A 598 " --> pdb=" O HIS A 585 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 72 through 78 Processing sheet with id=AA4, first strand: chain 'A' and resid 125 through 132 Processing sheet with id=AA5, first strand: chain 'A' and resid 177 through 182 removed outlier: 6.642A pdb=" N GLU A 190 " --> pdb=" O ALA A 178 " (cutoff:3.500A) removed outlier: 4.226A pdb=" N VAL A 180 " --> pdb=" O LEU A 188 " (cutoff:3.500A) removed outlier: 6.445A pdb=" N LEU A 188 " --> pdb=" O VAL A 180 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 237 through 238 removed outlier: 3.705A pdb=" N VAL A 224 " --> pdb=" O LEU A 407 " (cutoff:3.500A) removed outlier: 6.600A pdb=" N VAL A 268 " --> pdb=" O LEU A 412 " (cutoff:3.500A) removed outlier: 4.543A pdb=" N THR A 414 " --> pdb=" O HIS A 266 " (cutoff:3.500A) removed outlier: 6.954A pdb=" N HIS A 266 " --> pdb=" O THR A 414 " (cutoff:3.500A) removed outlier: 3.523A pdb=" N VAL A 265 " --> pdb=" O ASP A 260 " (cutoff:3.500A) removed outlier: 6.773A pdb=" N ILE A 255 " --> pdb=" O LEU A 249 " (cutoff:3.500A) removed outlier: 4.615A pdb=" N LEU A 249 " --> pdb=" O ILE A 255 " (cutoff:3.500A) removed outlier: 6.649A pdb=" N MET A 257 " --> pdb=" O VAL A 247 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 429 through 434 removed outlier: 4.005A pdb=" N LYS A 429 " --> pdb=" O LEU A 445 " (cutoff:3.500A) removed outlier: 4.135A pdb=" N LYS A 440 " --> pdb=" O PHE A 457 " (cutoff:3.500A) removed outlier: 3.595A pdb=" N VAL A 455 " --> pdb=" O LEU A 442 " (cutoff:3.500A) removed outlier: 4.847A pdb=" N SER A 470 " --> pdb=" O LYS A 456 " (cutoff:3.500A) removed outlier: 7.371A pdb=" N GLN A 458 " --> pdb=" O PHE A 468 " (cutoff:3.500A) removed outlier: 5.558A pdb=" N PHE A 468 " --> pdb=" O GLN A 458 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 860 through 862 removed outlier: 6.317A pdb=" N TYR A 860 " --> pdb=" O THR A 897 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA8 Processing sheet with id=AA9, first strand: chain 'A' and resid 1047 through 1048 removed outlier: 6.736A pdb=" N VAL A1047 " --> pdb=" O ARG A1110 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'A' and resid 1352 through 1353 removed outlier: 3.662A pdb=" N HIS L 62 " --> pdb=" O VAL L 141 " (cutoff:3.500A) removed outlier: 6.571A pdb=" N LYS L 93 " --> pdb=" O LEU L 142 " (cutoff:3.500A) removed outlier: 6.240A pdb=" N ASN L 144 " --> pdb=" O PRO L 91 " (cutoff:3.500A) removed outlier: 3.941A pdb=" N ARG L 109 " --> pdb=" O VAL L 96 " (cutoff:3.500A) removed outlier: 6.189A pdb=" N VAL L 98 " --> pdb=" O GLU L 107 " (cutoff:3.500A) removed outlier: 5.260A pdb=" N GLU L 107 " --> pdb=" O VAL L 98 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'A' and resid 1572 through 1574 Processing sheet with id=AB3, first strand: chain 'A' and resid 1620 through 1623 Processing sheet with id=AB4, first strand: chain 'A' and resid 1647 through 1652 removed outlier: 4.177A pdb=" N LEU A1633 " --> pdb=" O LYS A1669 " (cutoff:3.500A) removed outlier: 3.703A pdb=" N LYS A1667 " --> pdb=" O GLU A1635 " (cutoff:3.500A) removed outlier: 3.875A pdb=" N GLN A1665 " --> pdb=" O THR A1637 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'L' and resid 54 through 55 Processing sheet with id=AB6, first strand: chain 'L' and resid 73 through 74 Processing sheet with id=AB7, first strand: chain 'L' and resid 119 through 123 removed outlier: 3.512A pdb=" N THR L 76 " --> pdb=" O TYR L 159 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'I' and resid 12 through 15 removed outlier: 6.571A pdb=" N VAL I 743 " --> pdb=" O VAL I 14 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'I' and resid 23 through 28 removed outlier: 6.534A pdb=" N ALA I 38 " --> pdb=" O ILE I 24 " (cutoff:3.500A) removed outlier: 4.298A pdb=" N LEU I 26 " --> pdb=" O ALA I 36 " (cutoff:3.500A) removed outlier: 6.825A pdb=" N ALA I 36 " --> pdb=" O LEU I 26 " (cutoff:3.500A) removed outlier: 5.191A pdb=" N TRP I 28 " --> pdb=" O LEU I 34 " (cutoff:3.500A) removed outlier: 7.154A pdb=" N LEU I 34 " --> pdb=" O TRP I 28 " (cutoff:3.500A) removed outlier: 6.615A pdb=" N VAL I 44 " --> pdb=" O SER I 57 " (cutoff:3.500A) removed outlier: 4.661A pdb=" N SER I 57 " --> pdb=" O VAL I 44 " (cutoff:3.500A) removed outlier: 7.146A pdb=" N LEU I 46 " --> pdb=" O VAL I 55 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'I' and resid 71 through 73 removed outlier: 6.788A pdb=" N ASP I 94 " --> pdb=" O SER I 100 " (cutoff:3.500A) removed outlier: 6.848A pdb=" N SER I 100 " --> pdb=" O ASP I 94 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'I' and resid 110 through 117 removed outlier: 6.260A pdb=" N ILE I 185 " --> pdb=" O ARG I 197 " (cutoff:3.500A) removed outlier: 4.228A pdb=" N ARG I 197 " --> pdb=" O ILE I 185 " (cutoff:3.500A) removed outlier: 6.697A pdb=" N LEU I 187 " --> pdb=" O ILE I 195 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'I' and resid 204 through 210 removed outlier: 5.470A pdb=" N CYS I 205 " --> pdb=" O GLU I 222 " (cutoff:3.500A) removed outlier: 6.100A pdb=" N GLU I 222 " --> pdb=" O CYS I 205 " (cutoff:3.500A) removed outlier: 3.560A pdb=" N TYR I 557 " --> pdb=" O VAL I 231 " (cutoff:3.500A) removed outlier: 6.592A pdb=" N TYR I 233 " --> pdb=" O PRO I 555 " (cutoff:3.500A) removed outlier: 7.932A pdb=" N GLN I 235 " --> pdb=" O CYS I 553 " (cutoff:3.500A) removed outlier: 6.398A pdb=" N CYS I 553 " --> pdb=" O GLN I 235 " (cutoff:3.500A) removed outlier: 8.071A pdb=" N GLU I 237 " --> pdb=" O ALA I 551 " (cutoff:3.500A) removed outlier: 7.287A pdb=" N ALA I 551 " --> pdb=" O GLU I 237 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'I' and resid 574 through 577 removed outlier: 11.868A pdb=" N TYR I 596 " --> pdb=" O PHE I 620 " (cutoff:3.500A) removed outlier: 8.908A pdb=" N PHE I 620 " --> pdb=" O TYR I 596 " (cutoff:3.500A) removed outlier: 4.235A pdb=" N MET I 598 " --> pdb=" O ILE I 618 " (cutoff:3.500A) removed outlier: 6.889A pdb=" N PHE I 707 " --> pdb=" O GLY I 621 " (cutoff:3.500A) removed outlier: 3.993A pdb=" N PHE I 623 " --> pdb=" O PHE I 707 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'I' and resid 638 through 643 removed outlier: 5.794A pdb=" N CYS I 638 " --> pdb=" O LYS I 654 " (cutoff:3.500A) removed outlier: 6.345A pdb=" N LYS I 654 " --> pdb=" O CYS I 638 " (cutoff:3.500A) removed outlier: 3.931A pdb=" N ASP I 640 " --> pdb=" O VAL I 652 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'N' and resid 590 through 592 removed outlier: 3.528A pdb=" N GLY N 590 " --> pdb=" O LYS C 6 " (cutoff:3.500A) removed outlier: 12.130A pdb=" N CYS C 7 " --> pdb=" O GLY N 642 " (cutoff:3.500A) removed outlier: 10.698A pdb=" N GLY N 642 " --> pdb=" O CYS C 7 " (cutoff:3.500A) removed outlier: 9.862A pdb=" N ASN C 9 " --> pdb=" O THR N 640 " (cutoff:3.500A) removed outlier: 8.339A pdb=" N THR N 640 " --> pdb=" O ASN C 9 " (cutoff:3.500A) removed outlier: 4.671A pdb=" N VAL C 11 " --> pdb=" O LYS N 638 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'N' and resid 595 through 597 removed outlier: 7.170A pdb=" N THR N 645 " --> pdb=" O LYS C 6 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N VAL N 657 " --> pdb=" O MET N 646 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'N' and resid 675 through 677 3963 hydrogen bonds defined for protein. 11762 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 22.85 Time building geometry restraints manager: 21.63 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 16283 1.33 - 1.46: 17497 1.46 - 1.59: 31692 1.59 - 1.71: 1 1.71 - 1.84: 610 Bond restraints: 66083 Sorted by residual: bond pdb=" N ILE A1102 " pdb=" CA ILE A1102 " ideal model delta sigma weight residual 1.460 1.492 -0.032 7.30e-03 1.88e+04 1.92e+01 bond pdb=" CB THR Z 134 " pdb=" CG2 THR Z 134 " ideal model delta sigma weight residual 1.521 1.415 0.106 3.30e-02 9.18e+02 1.04e+01 bond pdb=" CB MET Y 108 " pdb=" CG MET Y 108 " ideal model delta sigma weight residual 1.520 1.424 0.096 3.00e-02 1.11e+03 1.03e+01 bond pdb=" N VAL A 87 " pdb=" CA VAL A 87 " ideal model delta sigma weight residual 1.458 1.493 -0.035 1.17e-02 7.31e+03 8.97e+00 bond pdb=" N HIS A 833 " pdb=" CA HIS A 833 " ideal model delta sigma weight residual 1.453 1.488 -0.035 1.16e-02 7.43e+03 8.92e+00 ... (remaining 66078 not shown) Histogram of bond angle deviations from ideal: 92.22 - 100.60: 76 100.60 - 108.98: 3904 108.98 - 117.36: 43305 117.36 - 125.74: 41160 125.74 - 134.12: 1038 Bond angle restraints: 89483 Sorted by residual: angle pdb=" CB ILE O 541 " pdb=" CG1 ILE O 541 " pdb=" CD1 ILE O 541 " ideal model delta sigma weight residual 113.80 105.05 8.75 2.10e+00 2.27e-01 1.74e+01 angle pdb=" N ASP A 86 " pdb=" CA ASP A 86 " pdb=" C ASP A 86 " ideal model delta sigma weight residual 113.28 108.40 4.88 1.22e+00 6.72e-01 1.60e+01 angle pdb=" N PRO A1390 " pdb=" CA PRO A1390 " pdb=" CB PRO A1390 " ideal model delta sigma weight residual 103.25 99.77 3.48 8.80e-01 1.29e+00 1.57e+01 angle pdb=" CG MET U 371 " pdb=" SD MET U 371 " pdb=" CE MET U 371 " ideal model delta sigma weight residual 100.90 92.22 8.68 2.20e+00 2.07e-01 1.56e+01 angle pdb=" CG GLU A1436 " pdb=" CD GLU A1436 " pdb=" OE1 GLU A1436 " ideal model delta sigma weight residual 118.40 109.60 8.80 2.30e+00 1.89e-01 1.46e+01 ... (remaining 89478 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.96: 33737 17.96 - 35.93: 4724 35.93 - 53.89: 1139 53.89 - 71.86: 216 71.86 - 89.82: 80 Dihedral angle restraints: 39896 sinusoidal: 15873 harmonic: 24023 Sorted by residual: dihedral pdb=" CA ARG A 726 " pdb=" C ARG A 726 " pdb=" N SER A 727 " pdb=" CA SER A 727 " ideal model delta harmonic sigma weight residual 180.00 156.91 23.09 0 5.00e+00 4.00e-02 2.13e+01 dihedral pdb=" CA GLN Q 18 " pdb=" C GLN Q 18 " pdb=" N TYR Q 19 " pdb=" CA TYR Q 19 " ideal model delta harmonic sigma weight residual -180.00 -159.49 -20.51 0 5.00e+00 4.00e-02 1.68e+01 dihedral pdb=" CA ALA Y 405 " pdb=" C ALA Y 405 " pdb=" N ASN Y 406 " pdb=" CA ASN Y 406 " ideal model delta harmonic sigma weight residual 180.00 159.58 20.42 0 5.00e+00 4.00e-02 1.67e+01 ... (remaining 39893 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.081: 9316 0.081 - 0.162: 667 0.162 - 0.243: 21 0.243 - 0.324: 4 0.324 - 0.404: 1 Chirality restraints: 10009 Sorted by residual: chirality pdb=" CG LEU Z 26 " pdb=" CB LEU Z 26 " pdb=" CD1 LEU Z 26 " pdb=" CD2 LEU Z 26 " both_signs ideal model delta sigma weight residual False -2.59 -2.19 -0.40 2.00e-01 2.50e+01 4.09e+00 chirality pdb=" CG LEU I 452 " pdb=" CB LEU I 452 " pdb=" CD1 LEU I 452 " pdb=" CD2 LEU I 452 " both_signs ideal model delta sigma weight residual False -2.59 -2.30 -0.29 2.00e-01 2.50e+01 2.09e+00 chirality pdb=" CG LEU Y 232 " pdb=" CB LEU Y 232 " pdb=" CD1 LEU Y 232 " pdb=" CD2 LEU Y 232 " both_signs ideal model delta sigma weight residual False -2.59 -2.33 -0.26 2.00e-01 2.50e+01 1.64e+00 ... (remaining 10006 not shown) Planarity restraints: 11389 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB HIS P 495 " 0.037 2.00e-02 2.50e+03 4.41e-02 2.91e+01 pdb=" CG HIS P 495 " -0.092 2.00e-02 2.50e+03 pdb=" ND1 HIS P 495 " 0.032 2.00e-02 2.50e+03 pdb=" CD2 HIS P 495 " 0.016 2.00e-02 2.50e+03 pdb=" CE1 HIS P 495 " -0.013 2.00e-02 2.50e+03 pdb=" NE2 HIS P 495 " 0.020 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C ASN P 145 " 0.061 5.00e-02 4.00e+02 9.38e-02 1.41e+01 pdb=" N PRO P 146 " -0.162 5.00e-02 4.00e+02 pdb=" CA PRO P 146 " 0.051 5.00e-02 4.00e+02 pdb=" CD PRO P 146 " 0.051 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CB PHE U 416 " 0.027 2.00e-02 2.50e+03 2.81e-02 1.38e+01 pdb=" CG PHE U 416 " -0.064 2.00e-02 2.50e+03 pdb=" CD1 PHE U 416 " 0.022 2.00e-02 2.50e+03 pdb=" CD2 PHE U 416 " 0.009 2.00e-02 2.50e+03 pdb=" CE1 PHE U 416 " -0.007 2.00e-02 2.50e+03 pdb=" CE2 PHE U 416 " 0.005 2.00e-02 2.50e+03 pdb=" CZ PHE U 416 " 0.008 2.00e-02 2.50e+03 ... (remaining 11386 not shown) Histogram of nonbonded interaction distances: 2.19 - 2.73: 5375 2.73 - 3.28: 66792 3.28 - 3.82: 111750 3.82 - 4.36: 129763 4.36 - 4.90: 222638 Nonbonded interactions: 536318 Sorted by model distance: nonbonded pdb=" N GLN O 742 " pdb=" OE1 GLN O 742 " model vdw 2.193 2.520 nonbonded pdb=" OG SER O 130 " pdb=" O LEU I 309 " model vdw 2.198 2.440 nonbonded pdb=" N GLU M 35 " pdb=" OE1 GLU M 35 " model vdw 2.205 2.520 nonbonded pdb=" O LEU N 31 " pdb=" OG SER N 128 " model vdw 2.207 2.440 nonbonded pdb=" OG SER H 57 " pdb=" NH2 ARG Z 323 " model vdw 2.210 2.520 ... (remaining 536313 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = (chain 'G' and resid 1 through 25) selection = (chain 'W' and (resid 1 through 23 or (resid 24 through 25 and (name N or name C \ A or name C or name O or name CB )))) } ncs_group { reference = (chain 'J' and (resid 5 through 170 or (resid 452 and (name N or name CA or name \ C or name O or name CB )) or resid 453 through 632 or resid 634 through 768)) selection = (chain 'P' and (resid 5 through 170 or resid 452 through 580 or (resid 581 and ( \ name N or name CA or name C or name O or name CB )) or resid 582 through 632 or \ resid 634 through 654 or (resid 655 and (name N or name CA or name C or name O o \ r name CB )) or resid 656 through 658 or (resid 659 and (name N or name CA or na \ me C or name O or name CB )) or resid 660 through 664 or (resid 665 and (name N \ or name CA or name C or name O or name CB )) or resid 666 through 670 or (resid \ 671 and (name N or name CA or name C or name O or name CB )) or resid 672 throug \ h 674 or (resid 675 and (name N or name CA or name C or name O or name CB )) or \ resid 676 through 679 or (resid 680 through 682 and (name N or name CA or name C \ or name O or name CB )) or (resid 691 through 702 and (name N or name CA or nam \ e C or name O or name CB )) or resid 703 through 705 or (resid 706 and (name N o \ r name CA or name C or name O or name CB )) or resid 707 through 708 or (resid 7 \ 09 through 713 and (name N or name CA or name C or name O or name CB )) or resid \ 714 through 715 or (resid 716 through 718 and (name N or name CA or name C or n \ ame O or name CB )) or resid 719 or (resid 720 through 722 and (name N or name C \ A or name C or name O or name CB )) or resid 723 or (resid 724 through 736 and ( \ name N or name CA or name C or name O or name CB )) or resid 737 or (resid 738 t \ hrough 743 and (name N or name CA or name C or name O or name CB )) or resid 744 \ or (resid 745 through 749 and (name N or name CA or name C or name O or name CB \ )) or resid 750 through 751 or (resid 752 through 760 and (name N or name CA or \ name C or name O or name CB )) or resid 761 or (resid 762 through 763 and (name \ N or name CA or name C or name O or name CB )) or (resid 764 and (name N or nam \ e CA or name C or name O or name CB or name CG )) or (resid 765 through 768 and \ (name N or name CA or name C or name O or name CB )))) } ncs_group { reference = (chain 'K' and ((resid 2 and (name N or name CA or name C or name O or name CB ) \ ) or resid 3 through 8 or (resid 9 and (name N or name CA or name C or name O or \ name CB )) or resid 10 through 221 or (resid 222 and (name N or name CA or name \ C or name O or name CB )) or resid 223 through 528 or (resid 548 and (name N or \ name CA or name C or name O or name CB )))) selection = (chain 'Q' and (resid 2 through 94 or resid 127 through 436 or (resid 437 throug \ h 438 and (name N or name CA or name C or name O or name CB )) or resid 439 thro \ ugh 529)) } ncs_group { reference = (chain 'U' and (resid 25 through 108 or (resid 109 and (name N or name CA or nam \ e C or name O or name CB )) or resid 110 through 554)) selection = (chain 'V' and (resid 25 through 134 or (resid 135 and (name N or name CA or nam \ e C or name O or name CB )) or (resid 145 and (name N or name CA or name C or na \ me O or name CB )) or resid 146 or (resid 147 and (name N or name CA or name C o \ r name O or name CB )) or resid 148 through 280 or (resid 281 through 282 and (n \ ame N or name CA or name C or name O or name CB )) or resid 283 through 521 or ( \ resid 522 and (name N or name CA or name C or name O or name CB )) or resid 523 \ or (resid 524 and (name N or name CA or name C or name O or name CB )) or resid \ 525 through 536 or (resid 537 through 545 and (name N or name CA or name C or na \ me O or name CB )) or resid 546 or (resid 547 through 554 and (name N or name CA \ or name C or name O or name CB )))) } ncs_group { reference = (chain 'Y' and (resid 2 through 465 or resid 467 through 506)) selection = (chain 'Z' and (resid 2 through 76 or resid 98 through 229 or (resid 230 and (na \ me N or name CA or name C or name O or name CB )) or resid 231 through 465 or re \ sid 467 through 506)) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=0.16 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 2.020 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.050 Extract box with map and model: 13.480 Check model and map are aligned: 0.710 Set scattering table: 0.430 Process input model: 138.420 Find NCS groups from input model: 2.850 Set up NCS constraints: 0.260 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.320 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 160.550 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8123 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 : 0.006 0.116 66083 Z= 0.357 Angle : 0.667 10.434 89483 Z= 0.361 Chirality : 0.044 0.404 10009 Planarity : 0.005 0.122 11389 Dihedral : 17.678 89.820 24326 Min Nonbonded Distance : 2.193 Molprobity Statistics. All-atom Clashscore : 11.76 Ramachandran Plot: Outliers : 0.05 % Allowed : 2.69 % Favored : 97.26 % Rotamer Outliers : 0.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.64 (0.09), residues: 8028 helix: 1.11 (0.07), residues: 5214 sheet: 0.02 (0.25), residues: 481 loop : -0.92 (0.12), residues: 2333 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 16056 Ramachandran restraints generated. 8028 Oldfield, 0 Emsley, 8028 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 16056 Ramachandran restraints generated. 8028 Oldfield, 0 Emsley, 8028 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 668 residues out of total 7133 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 34 poor density : 634 time to evaluate : 5.636 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: 34 outliers final: 9 residues processed: 661 average time/residue: 0.6363 time to fit residues: 708.2136 Evaluate side-chains 449 residues out of total 7133 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 440 time to evaluate : 5.623 Switching outliers to nearest non-outliers outliers start: 9 outliers final: 0 residues processed: 9 average time/residue: 0.4715 time to fit residues: 15.6076 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 804 random chunks: chunk 678 optimal weight: 9.9990 chunk 609 optimal weight: 30.0000 chunk 338 optimal weight: 6.9990 chunk 208 optimal weight: 5.9990 chunk 411 optimal weight: 1.9990 chunk 325 optimal weight: 0.9990 chunk 630 optimal weight: 5.9990 chunk 243 optimal weight: 0.0030 chunk 383 optimal weight: 0.9990 chunk 469 optimal weight: 9.9990 chunk 730 optimal weight: 9.9990 overall best weight: 1.9998 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 124 GLN ** A 266 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A1201 HIS A1268 HIS A1351 GLN A1591 HIS ** A1604 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1627 ASN A1832 ASN ** G 21 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 139 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 583 HIS K 80 HIS K 352 GLN L 5 ASN ** L 60 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 145 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** L 146 GLN ** L 147 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** M 6 GLN M 34 ASN ** O 261 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 332 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 671 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** O 731 ASN P 575 ASN P 599 ASN P 626 ASN P 667 GLN P 674 HIS Q 20 GLN Q 179 GLN ** Q 468 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** U 71 GLN U 107 HIS U 347 HIS U 407 GLN ** U 479 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 145 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Y 31 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Y 255 ASN ** Y 335 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Y 337 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Y 408 GLN Y 507 ASN Z 213 HIS ** Z 262 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Z 333 GLN Z 387 ASN I 301 GLN I 323 ASN I 584 HIS I 668 GLN ** N 235 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** N 373 GLN N 586 GLN N 673 GLN C 58 HIS Total number of N/Q/H flips: 40 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8154 moved from start: 0.1232 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.051 66083 Z= 0.213 Angle : 0.596 11.839 89483 Z= 0.304 Chirality : 0.040 0.204 10009 Planarity : 0.004 0.062 11389 Dihedral : 4.079 22.373 8848 Min Nonbonded Distance : 2.147 Molprobity Statistics. All-atom Clashscore : 13.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.74 % Favored : 97.26 % Rotamer Outliers : 3.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.08 (0.09), residues: 8028 helix: 1.45 (0.07), residues: 5330 sheet: 0.05 (0.25), residues: 473 loop : -0.85 (0.13), residues: 2225 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 16056 Ramachandran restraints generated. 8028 Oldfield, 0 Emsley, 8028 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 16056 Ramachandran restraints generated. 8028 Oldfield, 0 Emsley, 8028 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 690 residues out of total 7133 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 214 poor density : 476 time to evaluate : 5.648 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 outliers start: 214 outliers final: 67 residues processed: 659 average time/residue: 0.5844 time to fit residues: 671.9490 Evaluate side-chains 483 residues out of total 7133 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 67 poor density : 416 time to evaluate : 5.658 Switching outliers to nearest non-outliers outliers start: 67 outliers final: 0 residues processed: 67 average time/residue: 0.4768 time to fit residues: 67.9322 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 804 random chunks: chunk 405 optimal weight: 9.9990 chunk 226 optimal weight: 0.0980 chunk 607 optimal weight: 6.9990 chunk 497 optimal weight: 6.9990 chunk 201 optimal weight: 10.0000 chunk 731 optimal weight: 20.0000 chunk 790 optimal weight: 7.9990 chunk 651 optimal weight: 20.0000 chunk 725 optimal weight: 0.3980 chunk 249 optimal weight: 10.0000 chunk 586 optimal weight: 8.9990 overall best weight: 4.4986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 266 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A1262 GLN A1351 GLN A1591 HIS ** A1604 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 21 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 69 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 480 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 12 GLN K 16 GLN K 18 GLN K 352 GLN ** L 60 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 145 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 147 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** O 211 GLN O 261 ASN O 306 ASN ** O 332 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 671 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 495 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Q 12 GLN ** Q 468 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** U 355 GLN ** U 479 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 145 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Y 335 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Y 337 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Z 236 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Z 262 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Z 437 GLN I 323 ASN ** N 235 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 266 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8233 moved from start: 0.1753 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.070 66083 Z= 0.338 Angle : 0.626 10.570 89483 Z= 0.318 Chirality : 0.041 0.175 10009 Planarity : 0.004 0.059 11389 Dihedral : 4.138 22.145 8848 Min Nonbonded Distance : 2.094 Molprobity Statistics. All-atom Clashscore : 14.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.02 % Favored : 96.98 % Rotamer Outliers : 2.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.19 (0.09), residues: 8028 helix: 1.56 (0.07), residues: 5348 sheet: -0.05 (0.25), residues: 474 loop : -0.88 (0.13), residues: 2206 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 16056 Ramachandran restraints generated. 8028 Oldfield, 0 Emsley, 8028 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 16056 Ramachandran restraints generated. 8028 Oldfield, 0 Emsley, 8028 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 618 residues out of total 7133 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 190 poor density : 428 time to evaluate : 5.690 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: 190 outliers final: 78 residues processed: 594 average time/residue: 0.5949 time to fit residues: 615.7300 Evaluate side-chains 469 residues out of total 7133 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 78 poor density : 391 time to evaluate : 5.658 Switching outliers to nearest non-outliers outliers start: 78 outliers final: 0 residues processed: 78 average time/residue: 0.4817 time to fit residues: 77.9544 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 804 random chunks: chunk 722 optimal weight: 20.0000 chunk 549 optimal weight: 5.9990 chunk 379 optimal weight: 1.9990 chunk 80 optimal weight: 0.0010 chunk 349 optimal weight: 3.9990 chunk 491 optimal weight: 9.9990 chunk 734 optimal weight: 8.9990 chunk 777 optimal weight: 30.0000 chunk 383 optimal weight: 0.9980 chunk 695 optimal weight: 0.8980 chunk 209 optimal weight: 20.0000 overall best weight: 1.5790 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 18 GLN ** A 266 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A1599 ASN ** A1604 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 21 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 480 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 626 ASN ** L 60 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 147 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 332 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** O 565 GLN ** O 671 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 468 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** U 355 GLN ** U 479 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 145 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Y 335 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Y 337 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Z 49 HIS ** Z 236 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Z 262 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Z 264 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 668 GLN ** N 235 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8183 moved from start: 0.1935 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.046 66083 Z= 0.186 Angle : 0.569 11.600 89483 Z= 0.285 Chirality : 0.039 0.221 10009 Planarity : 0.004 0.083 11389 Dihedral : 4.073 22.711 8848 Min Nonbonded Distance : 2.130 Molprobity Statistics. All-atom Clashscore : 12.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.67 % Favored : 97.33 % Rotamer Outliers : 1.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.35 (0.10), residues: 8028 helix: 1.69 (0.07), residues: 5348 sheet: -0.06 (0.24), residues: 473 loop : -0.83 (0.13), residues: 2207 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 16056 Ramachandran restraints generated. 8028 Oldfield, 0 Emsley, 8028 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 16056 Ramachandran restraints generated. 8028 Oldfield, 0 Emsley, 8028 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 549 residues out of total 7133 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 123 poor density : 426 time to evaluate : 5.671 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 outliers start: 123 outliers final: 43 residues processed: 529 average time/residue: 0.5915 time to fit residues: 548.7152 Evaluate side-chains 438 residues out of total 7133 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 43 poor density : 395 time to evaluate : 5.679 Switching outliers to nearest non-outliers outliers start: 43 outliers final: 0 residues processed: 43 average time/residue: 0.4905 time to fit residues: 47.0985 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 804 random chunks: chunk 647 optimal weight: 10.0000 chunk 441 optimal weight: 6.9990 chunk 11 optimal weight: 0.7980 chunk 578 optimal weight: 20.0000 chunk 320 optimal weight: 0.7980 chunk 663 optimal weight: 0.8980 chunk 537 optimal weight: 6.9990 chunk 0 optimal weight: 10.0000 chunk 396 optimal weight: 0.9980 chunk 697 optimal weight: 0.9980 chunk 196 optimal weight: 8.9990 overall best weight: 0.8980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 266 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A1591 HIS ** A1604 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1661 HIS ** G 21 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 69 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 626 ASN K 86 HIS K 415 ASN ** L 60 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 121 HIS ** L 147 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** O 352 GLN O 606 GLN ** O 671 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 264 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Q 289 HIS ** Q 468 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** U 479 GLN ** Y 335 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Y 337 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Z 150 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Z 236 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Z 262 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Z 264 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 353 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 401 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 235 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** N 555 HIS Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8159 moved from start: 0.2139 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.039 66083 Z= 0.158 Angle : 0.554 10.779 89483 Z= 0.276 Chirality : 0.038 0.235 10009 Planarity : 0.003 0.059 11389 Dihedral : 3.998 21.628 8848 Min Nonbonded Distance : 2.139 Molprobity Statistics. All-atom Clashscore : 12.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.45 % Favored : 97.55 % Rotamer Outliers : 1.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.44 (0.10), residues: 8028 helix: 1.77 (0.07), residues: 5353 sheet: 0.02 (0.24), residues: 474 loop : -0.84 (0.13), residues: 2201 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 16056 Ramachandran restraints generated. 8028 Oldfield, 0 Emsley, 8028 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 16056 Ramachandran restraints generated. 8028 Oldfield, 0 Emsley, 8028 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 532 residues out of total 7133 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 97 poor density : 435 time to evaluate : 5.626 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: 97 outliers final: 22 residues processed: 519 average time/residue: 0.5992 time to fit residues: 542.5257 Evaluate side-chains 419 residues out of total 7133 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 397 time to evaluate : 5.583 Switching outliers to nearest non-outliers outliers start: 22 outliers final: 0 residues processed: 22 average time/residue: 0.5075 time to fit residues: 28.1793 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 804 random chunks: chunk 261 optimal weight: 9.9990 chunk 699 optimal weight: 10.0000 chunk 153 optimal weight: 6.9990 chunk 456 optimal weight: 9.9990 chunk 191 optimal weight: 6.9990 chunk 777 optimal weight: 20.0000 chunk 645 optimal weight: 6.9990 chunk 360 optimal weight: 4.9990 chunk 64 optimal weight: 5.9990 chunk 257 optimal weight: 8.9990 chunk 408 optimal weight: 10.0000 overall best weight: 6.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 162 HIS A 266 HIS ** A 496 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1604 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 21 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 69 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 480 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 626 ASN K 86 HIS ** L 60 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 145 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 147 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 152 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 332 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** O 565 GLN ** O 671 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** O 754 HIS ** P 455 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 490 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 264 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 468 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 145 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** V 202 HIS Y 255 ASN ** Y 303 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Y 335 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Y 337 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Z 264 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 323 ASN ** N 235 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 266 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8287 moved from start: 0.2402 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.007 0.101 66083 Z= 0.465 Angle : 0.696 11.118 89483 Z= 0.351 Chirality : 0.042 0.192 10009 Planarity : 0.004 0.075 11389 Dihedral : 4.181 22.157 8848 Min Nonbonded Distance : 2.059 Molprobity Statistics. All-atom Clashscore : 15.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.30 % Favored : 96.70 % Rotamer Outliers : 2.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.28 (0.09), residues: 8028 helix: 1.65 (0.07), residues: 5347 sheet: -0.13 (0.24), residues: 468 loop : -0.87 (0.13), residues: 2213 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 16056 Ramachandran restraints generated. 8028 Oldfield, 0 Emsley, 8028 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 16056 Ramachandran restraints generated. 8028 Oldfield, 0 Emsley, 8028 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 530 residues out of total 7133 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 141 poor density : 389 time to evaluate : 5.630 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 outliers start: 141 outliers final: 65 residues processed: 499 average time/residue: 0.6091 time to fit residues: 531.6156 Evaluate side-chains 440 residues out of total 7133 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 65 poor density : 375 time to evaluate : 5.592 Switching outliers to nearest non-outliers outliers start: 65 outliers final: 0 residues processed: 65 average time/residue: 0.4891 time to fit residues: 66.9930 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 804 random chunks: chunk 749 optimal weight: 7.9990 chunk 87 optimal weight: 0.9990 chunk 443 optimal weight: 0.9990 chunk 568 optimal weight: 20.0000 chunk 440 optimal weight: 1.9990 chunk 654 optimal weight: 10.0000 chunk 434 optimal weight: 0.7980 chunk 774 optimal weight: 20.0000 chunk 484 optimal weight: 0.8980 chunk 472 optimal weight: 5.9990 chunk 357 optimal weight: 0.9980 overall best weight: 0.9384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 496 ASN A1599 ASN ** A1604 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 32 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 21 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 69 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 626 ASN K 86 HIS ** L 60 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 147 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 152 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** O 261 ASN O 565 GLN ** O 671 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** P 455 GLN ** Q 468 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** Y 335 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Y 337 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Z 150 GLN ** Z 262 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Z 264 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 301 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 353 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 401 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 235 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8185 moved from start: 0.2444 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.045 66083 Z= 0.165 Angle : 0.576 14.376 89483 Z= 0.287 Chirality : 0.039 0.218 10009 Planarity : 0.003 0.058 11389 Dihedral : 4.082 22.851 8848 Min Nonbonded Distance : 2.130 Molprobity Statistics. All-atom Clashscore : 12.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.40 % Favored : 97.60 % Rotamer Outliers : 0.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.46 (0.10), residues: 8028 helix: 1.80 (0.07), residues: 5365 sheet: -0.10 (0.24), residues: 473 loop : -0.85 (0.13), residues: 2190 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 16056 Ramachandran restraints generated. 8028 Oldfield, 0 Emsley, 8028 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 16056 Ramachandran restraints generated. 8028 Oldfield, 0 Emsley, 8028 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 461 residues out of total 7133 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 42 poor density : 419 time to evaluate : 5.698 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: 42 outliers final: 11 residues processed: 454 average time/residue: 0.6009 time to fit residues: 475.9485 Evaluate side-chains 397 residues out of total 7133 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 386 time to evaluate : 5.626 Switching outliers to nearest non-outliers outliers start: 11 outliers final: 0 residues processed: 11 average time/residue: 0.4727 time to fit residues: 17.4512 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 804 random chunks: chunk 479 optimal weight: 0.9990 chunk 309 optimal weight: 5.9990 chunk 462 optimal weight: 8.9990 chunk 233 optimal weight: 5.9990 chunk 152 optimal weight: 1.9990 chunk 150 optimal weight: 0.9980 chunk 492 optimal weight: 0.8980 chunk 527 optimal weight: 10.0000 chunk 383 optimal weight: 3.9990 chunk 72 optimal weight: 2.9990 chunk 609 optimal weight: 7.9990 overall best weight: 1.5786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A1604 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 21 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 60 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 147 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 152 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 671 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** P 490 HIS ** Q 468 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 145 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Y 335 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Y 337 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Z 262 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Z 264 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 301 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 353 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 401 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 578 ASN ** N 235 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 370 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8193 moved from start: 0.2528 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.042 66083 Z= 0.185 Angle : 0.579 12.759 89483 Z= 0.287 Chirality : 0.039 0.231 10009 Planarity : 0.003 0.056 11389 Dihedral : 4.030 21.989 8848 Min Nonbonded Distance : 2.114 Molprobity Statistics. All-atom Clashscore : 12.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.67 % Favored : 97.33 % Rotamer Outliers : 0.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.49 (0.10), residues: 8028 helix: 1.83 (0.07), residues: 5364 sheet: -0.07 (0.24), residues: 469 loop : -0.85 (0.13), residues: 2195 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 16056 Ramachandran restraints generated. 8028 Oldfield, 0 Emsley, 8028 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 16056 Ramachandran restraints generated. 8028 Oldfield, 0 Emsley, 8028 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 445 residues out of total 7133 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 42 poor density : 403 time to evaluate : 5.955 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 outliers start: 42 outliers final: 18 residues processed: 435 average time/residue: 0.6460 time to fit residues: 491.4724 Evaluate side-chains 406 residues out of total 7133 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 388 time to evaluate : 5.675 Switching outliers to nearest non-outliers outliers start: 18 outliers final: 0 residues processed: 18 average time/residue: 0.5117 time to fit residues: 25.0448 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 804 random chunks: chunk 704 optimal weight: 9.9990 chunk 742 optimal weight: 20.0000 chunk 677 optimal weight: 1.9990 chunk 722 optimal weight: 20.0000 chunk 434 optimal weight: 1.9990 chunk 314 optimal weight: 2.9990 chunk 567 optimal weight: 20.0000 chunk 221 optimal weight: 0.9980 chunk 652 optimal weight: 5.9990 chunk 682 optimal weight: 0.4980 chunk 719 optimal weight: 20.0000 overall best weight: 1.6986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A1604 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 32 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 21 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 60 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 147 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 152 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** O 261 ASN O 645 HIS ** O 671 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 264 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 468 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 145 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Y 335 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Y 337 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Z 236 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Z 262 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Z 264 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 301 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 353 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 401 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 235 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 370 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8190 moved from start: 0.2615 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.046 66083 Z= 0.187 Angle : 0.582 12.243 89483 Z= 0.288 Chirality : 0.039 0.247 10009 Planarity : 0.003 0.055 11389 Dihedral : 4.021 21.780 8848 Min Nonbonded Distance : 2.124 Molprobity Statistics. All-atom Clashscore : 12.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.68 % Favored : 97.32 % Rotamer Outliers : 0.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.54 (0.10), residues: 8028 helix: 1.85 (0.07), residues: 5365 sheet: -0.05 (0.24), residues: 469 loop : -0.82 (0.13), residues: 2194 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 16056 Ramachandran restraints generated. 8028 Oldfield, 0 Emsley, 8028 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 16056 Ramachandran restraints generated. 8028 Oldfield, 0 Emsley, 8028 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 416 residues out of total 7133 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 397 time to evaluate : 5.782 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 outliers start: 19 outliers final: 6 residues processed: 412 average time/residue: 0.6149 time to fit residues: 443.3434 Evaluate side-chains 388 residues out of total 7133 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 382 time to evaluate : 5.709 Switching outliers to nearest non-outliers outliers start: 6 outliers final: 0 residues processed: 6 average time/residue: 0.5081 time to fit residues: 13.3817 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 804 random chunks: chunk 474 optimal weight: 0.0000 chunk 763 optimal weight: 9.9990 chunk 466 optimal weight: 0.3980 chunk 362 optimal weight: 0.9980 chunk 530 optimal weight: 10.0000 chunk 800 optimal weight: 20.0000 chunk 737 optimal weight: 10.0000 chunk 637 optimal weight: 30.0000 chunk 66 optimal weight: 0.8980 chunk 492 optimal weight: 9.9990 chunk 391 optimal weight: 8.9990 overall best weight: 2.2586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A1604 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 21 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 60 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 147 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 152 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** O 261 ASN ** O 332 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 671 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 264 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 468 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 145 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Y 335 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Y 337 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Z 262 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Z 264 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 301 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 353 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 401 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 235 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 370 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** N 673 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8202 moved from start: 0.2674 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.051 66083 Z= 0.212 Angle : 0.593 12.104 89483 Z= 0.294 Chirality : 0.039 0.242 10009 Planarity : 0.003 0.054 11389 Dihedral : 4.017 22.294 8848 Min Nonbonded Distance : 2.106 Molprobity Statistics. All-atom Clashscore : 12.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.73 % Favored : 97.27 % Rotamer Outliers : 0.23 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.57 (0.10), residues: 8028 helix: 1.88 (0.07), residues: 5367 sheet: -0.01 (0.25), residues: 462 loop : -0.82 (0.13), residues: 2199 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 16056 Ramachandran restraints generated. 8028 Oldfield, 0 Emsley, 8028 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 16056 Ramachandran restraints generated. 8028 Oldfield, 0 Emsley, 8028 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 408 residues out of total 7133 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 394 time to evaluate : 5.655 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 outliers start: 14 outliers final: 5 residues processed: 403 average time/residue: 0.6103 time to fit residues: 430.5023 Evaluate side-chains 389 residues out of total 7133 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 384 time to evaluate : 5.650 Switching outliers to nearest non-outliers outliers start: 5 outliers final: 0 residues processed: 5 average time/residue: 0.4844 time to fit residues: 12.2389 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 804 random chunks: chunk 506 optimal weight: 50.0000 chunk 679 optimal weight: 9.9990 chunk 195 optimal weight: 1.9990 chunk 588 optimal weight: 9.9990 chunk 94 optimal weight: 0.9990 chunk 177 optimal weight: 10.0000 chunk 638 optimal weight: 5.9990 chunk 267 optimal weight: 9.9990 chunk 655 optimal weight: 0.0030 chunk 80 optimal weight: 8.9990 chunk 117 optimal weight: 1.9990 overall best weight: 2.1998 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A1604 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 21 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 60 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 147 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 152 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** O 261 ASN ** O 332 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 671 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 264 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 468 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 145 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Y 335 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Y 337 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Z 262 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Z 264 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 301 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 353 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 401 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 235 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 370 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3690 r_free = 0.3690 target = 0.065853 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.3121 r_free = 0.3121 target = 0.045034 restraints weight = 385296.474| |-----------------------------------------------------------------------------| r_work (start): 0.3059 rms_B_bonded: 4.56 r_work (final): 0.3059 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3054 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3054 r_free = 0.3054 target_work(ls_wunit_k1) = 0.043 | | occupancies: max = 1.00 min = 0.16 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3054 r_free = 0.3054 target_work(ls_wunit_k1) = 0.043 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 16 | |-----------------------------------------------------------------------------| r_final: 0.3054 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8553 moved from start: 0.2740 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.054 66083 Z= 0.210 Angle : 0.599 12.638 89483 Z= 0.295 Chirality : 0.039 0.233 10009 Planarity : 0.003 0.053 11389 Dihedral : 4.019 23.907 8848 Min Nonbonded Distance : 2.116 Molprobity Statistics. All-atom Clashscore : 12.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.73 % Favored : 97.27 % Rotamer Outliers : 0.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.55 (0.10), residues: 8028 helix: 1.87 (0.07), residues: 5370 sheet: -0.06 (0.24), residues: 464 loop : -0.83 (0.13), residues: 2194 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 11713.24 seconds wall clock time: 209 minutes 57.60 seconds (12597.60 seconds total)