Starting phenix.real_space_refine on Sat Feb 24 22:24:39 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7e94_31028/02_2024/7e94_31028_neut.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7e94_31028/02_2024/7e94_31028.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.67 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7e94_31028/02_2024/7e94_31028.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7e94_31028/02_2024/7e94_31028.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7e94_31028/02_2024/7e94_31028_neut.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7e94_31028/02_2024/7e94_31028_neut.pdb" } resolution = 4.67 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= 0.000 sd= 0.001 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 173 5.16 5 C 29352 2.51 5 N 8032 2.21 5 O 8748 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A GLU 53": "OE1" <-> "OE2" Residue "A ARG 139": "NH1" <-> "NH2" Residue "A GLU 143": "OE1" <-> "OE2" Residue "B ARG 61": "NH1" <-> "NH2" Residue "B ARG 122": "NH1" <-> "NH2" Residue "B GLU 207": "OE1" <-> "OE2" Residue "B TYR 231": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 242": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ARG 74": "NH1" <-> "NH2" Residue "C ARG 79": "NH1" <-> "NH2" Residue "C ARG 169": "NH1" <-> "NH2" Residue "D ARG 143": "NH1" <-> "NH2" Residue "E GLU 109": "OE1" <-> "OE2" Residue "F ARG 8": "NH1" <-> "NH2" Residue "F GLU 23": "OE1" <-> "OE2" Residue "F ARG 47": "NH1" <-> "NH2" Residue "F GLU 129": "OE1" <-> "OE2" Residue "F ARG 169": "NH1" <-> "NH2" Residue "F GLU 187": "OE1" <-> "OE2" Residue "G ARG 44": "NH1" <-> "NH2" Residue "G ARG 97": "NH1" <-> "NH2" Residue "G TYR 165": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G ARG 171": "NH1" <-> "NH2" Residue "G GLU 208": "OE1" <-> "OE2" Residue "G GLU 225": "OE1" <-> "OE2" Residue "G ARG 263": "NH1" <-> "NH2" Residue "G ARG 277": "NH1" <-> "NH2" Residue "H GLU 19": "OE1" <-> "OE2" Residue "H GLU 49": "OE1" <-> "OE2" Residue "H ARG 131": "NH1" <-> "NH2" Residue "H GLU 136": "OE1" <-> "OE2" Residue "I ARG 816": "NH1" <-> "NH2" Residue "J GLU 519": "OE1" <-> "OE2" Residue "J ARG 555": "NH1" <-> "NH2" Residue "J ARG 600": "NH1" <-> "NH2" Residue "J GLU 627": "OE1" <-> "OE2" Residue "J PHE 652": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J ARG 655": "NH1" <-> "NH2" Residue "J ARG 661": "NH1" <-> "NH2" Residue "J ARG 734": "NH1" <-> "NH2" Residue "J GLU 776": "OE1" <-> "OE2" Residue "J ARG 779": "NH1" <-> "NH2" Residue "J ARG 820": "NH1" <-> "NH2" Residue "J ARG 821": "NH1" <-> "NH2" Residue "J GLU 967": "OE1" <-> "OE2" Residue "J ARG 993": "NH1" <-> "NH2" Residue "J GLU 1014": "OE1" <-> "OE2" Residue "J ARG 1027": "NH1" <-> "NH2" Residue "J ARG 1035": "NH1" <-> "NH2" Residue "J GLU 1065": "OE1" <-> "OE2" Residue "J ARG 1097": "NH1" <-> "NH2" Residue "J GLU 1186": "OE1" <-> "OE2" Residue "J ARG 1229": "NH1" <-> "NH2" Residue "J GLU 1262": "OE1" <-> "OE2" Residue "K ARG 430": "NH1" <-> "NH2" Residue "L ARG 139": "NH1" <-> "NH2" Residue "M ARG 61": "NH1" <-> "NH2" Residue "M ARG 162": "NH1" <-> "NH2" Residue "N ARG 79": "NH1" <-> "NH2" Residue "N GLU 175": "OE1" <-> "OE2" Residue "O ARG 19": "NH1" <-> "NH2" Residue "O GLU 20": "OE1" <-> "OE2" Residue "O ARG 133": "NH1" <-> "NH2" Residue "O ARG 143": "NH1" <-> "NH2" Residue "O GLU 150": "OE1" <-> "OE2" Residue "Q ARG 79": "NH1" <-> "NH2" Residue "Q ARG 182": "NH1" <-> "NH2" Residue "R ARG 44": "NH1" <-> "NH2" Residue "R ARG 97": "NH1" <-> "NH2" Residue "R ARG 171": "NH1" <-> "NH2" Residue "R ARG 277": "NH1" <-> "NH2" Residue "S GLU 139": "OE1" <-> "OE2" Residue "T ARG 793": "NH1" <-> "NH2" Residue "T GLU 803": "OE1" <-> "OE2" Residue "T ARG 816": "NH1" <-> "NH2" Residue "T GLU 833": "OE1" <-> "OE2" Residue "T GLU 864": "OE1" <-> "OE2" Residue "U GLU 459": "OE1" <-> "OE2" Residue "U ARG 487": "NH1" <-> "NH2" Residue "U ARG 535": "NH1" <-> "NH2" Residue "U ARG 555": "NH1" <-> "NH2" Residue "U ARG 600": "NH1" <-> "NH2" Residue "U ARG 734": "NH1" <-> "NH2" Residue "U PHE 757": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "U ARG 779": "NH1" <-> "NH2" Residue "U ARG 820": "NH1" <-> "NH2" Residue "U ARG 821": "NH1" <-> "NH2" Residue "U GLU 996": "OE1" <-> "OE2" Residue "U ARG 1027": "NH1" <-> "NH2" Residue "U GLU 1029": "OE1" <-> "OE2" Residue "U GLU 1112": "OE1" <-> "OE2" Residue "U PHE 1121": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "U GLU 1179": "OE1" <-> "OE2" Residue "U TYR 1233": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "V PHE 524": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "V GLU 547": "OE1" <-> "OE2" Time to flip residues: 0.14s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5238/modules/chem_data/mon_lib" Total number of atoms: 46305 Number of models: 1 Model: "" Number of chains: 22 Chain: "A" Number of atoms: 1160 Number of conformers: 1 Conformer: "" Number of residues, atoms: 144, 1160 Classifications: {'peptide': 144} Link IDs: {'PTRANS': 5, 'TRANS': 138} Chain: "B" Number of atoms: 1630 Number of conformers: 1 Conformer: "" Number of residues, atoms: 202, 1630 Classifications: {'peptide': 202} Incomplete info: {'truncation_to_alanine': 7} Link IDs: {'PTRANS': 6, 'TRANS': 195} Chain breaks: 2 Unresolved non-hydrogen bonds: 25 Unresolved non-hydrogen angles: 30 Unresolved non-hydrogen dihedrals: 20 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLU:plan': 2, 'ARG:plan': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 16 Chain: "C" Number of atoms: 1482 Number of conformers: 1 Conformer: "" Number of residues, atoms: 184, 1482 Classifications: {'peptide': 184} Link IDs: {'PTRANS': 5, 'TRANS': 178} Chain: "D" Number of atoms: 1235 Number of conformers: 1 Conformer: "" Number of residues, atoms: 151, 1235 Classifications: {'peptide': 151} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'PTRANS': 2, 'TRANS': 148} Chain breaks: 1 Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 4 Planarities with less than four sites: {'ASN:plan1': 1} Unresolved non-hydrogen planarities: 3 Chain: "E" Number of atoms: 1308 Number of conformers: 1 Conformer: "" Number of residues, atoms: 162, 1308 Classifications: {'peptide': 162} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 6, 'TRANS': 155} Chain breaks: 3 Chain: "F" Number of atoms: 1470 Number of conformers: 1 Conformer: "" Number of residues, atoms: 182, 1470 Classifications: {'peptide': 182} Link IDs: {'PTRANS': 5, 'TRANS': 176} Chain: "G" Number of atoms: 1646 Number of conformers: 1 Conformer: "" Number of residues, atoms: 204, 1646 Classifications: {'peptide': 204} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 6, 'TRANS': 197} Chain breaks: 1 Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 1 Unresolved non-hydrogen dihedrals: 1 Chain: "H" Number of atoms: 1180 Number of conformers: 1 Conformer: "" Number of residues, atoms: 147, 1180 Classifications: {'peptide': 147} Incomplete info: {'truncation_to_alanine': 6} Link IDs: {'PTRANS': 8, 'TRANS': 138} Chain breaks: 1 Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 19 Unresolved non-hydrogen angles: 25 Unresolved non-hydrogen dihedrals: 14 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 1, 'ASN:plan1': 2} Unresolved non-hydrogen planarities: 14 Chain: "I" Number of atoms: 4195 Number of conformers: 1 Conformer: "" Number of residues, atoms: 788, 4195 Classifications: {'peptide': 788} Incomplete info: {'truncation_to_alanine': 651} Link IDs: {'PTRANS': 16, 'TRANS': 771} Chain breaks: 2 Unresolved chain link angles: 13 Unresolved non-hydrogen bonds: 2346 Unresolved non-hydrogen angles: 2989 Unresolved non-hydrogen dihedrals: 1940 Unresolved non-hydrogen chiralities: 228 Planarities with less than four sites: {'GLN:plan1': 30, 'ARG:plan': 24, 'TYR:plan': 22, 'ASN:plan1': 41, 'TRP:plan': 8, 'HIS:plan': 9, 'PHE:plan': 42, 'GLU:plan': 61, 'ASP:plan': 38} Unresolved non-hydrogen planarities: 1244 Chain: "J" Number of atoms: 6326 Number of conformers: 1 Conformer: "" Number of residues, atoms: 872, 6326 Classifications: {'peptide': 872} Incomplete info: {'truncation_to_alanine': 252} Link IDs: {'PTRANS': 37, 'TRANS': 834} Chain breaks: 5 Unresolved chain link angles: 9 Unresolved non-hydrogen bonds: 864 Unresolved non-hydrogen angles: 1104 Unresolved non-hydrogen dihedrals: 718 Unresolved non-hydrogen chiralities: 88 Planarities with less than four sites: {'GLN:plan1': 9, 'HIS:plan': 3, 'TYR:plan': 12, 'ASN:plan1': 16, 'TRP:plan': 3, 'ASP:plan': 18, 'PHE:plan': 11, 'GLU:plan': 11, 'ARG:plan': 10} Unresolved non-hydrogen planarities: 424 Chain: "K" Number of atoms: 1649 Number of conformers: 1 Conformer: "" Number of residues, atoms: 251, 1649 Classifications: {'peptide': 251} Incomplete info: {'truncation_to_alanine': 114} Link IDs: {'PTRANS': 11, 'TRANS': 239} Chain breaks: 3 Unresolved chain link angles: 8 Unresolved non-hydrogen bonds: 393 Unresolved non-hydrogen angles: 503 Unresolved non-hydrogen dihedrals: 328 Unresolved non-hydrogen chiralities: 41 Planarities with less than four sites: {'GLN:plan1': 5, 'ARG:plan': 4, 'TYR:plan': 4, 'ASN:plan1': 6, 'TRP:plan': 1, 'HIS:plan': 4, 'PHE:plan': 5, 'GLU:plan': 7, 'ASP:plan': 4} Unresolved non-hydrogen planarities: 185 Chain: "L" Number of atoms: 1206 Number of conformers: 1 Conformer: "" Number of residues, atoms: 150, 1206 Classifications: {'peptide': 150} Link IDs: {'PTRANS': 5, 'TRANS': 144} Chain: "M" Number of atoms: 1459 Number of conformers: 1 Conformer: "" Number of residues, atoms: 195, 1459 Classifications: {'peptide': 195} Incomplete info: {'truncation_to_alanine': 39} Link IDs: {'PTRANS': 6, 'TRANS': 188} Chain breaks: 2 Unresolved non-hydrogen bonds: 147 Unresolved non-hydrogen angles: 186 Unresolved non-hydrogen dihedrals: 119 Unresolved non-hydrogen chiralities: 11 Planarities with less than four sites: {'GLN:plan1': 1, 'ARG:plan': 3, 'TYR:plan': 1, 'ASN:plan1': 2, 'HIS:plan': 4, 'GLU:plan': 8, 'ASP:plan': 3} Unresolved non-hydrogen planarities: 93 Chain: "N" Number of atoms: 1482 Number of conformers: 1 Conformer: "" Number of residues, atoms: 184, 1482 Classifications: {'peptide': 184} Link IDs: {'PTRANS': 5, 'TRANS': 178} Chain: "O" Number of atoms: 1235 Number of conformers: 1 Conformer: "" Number of residues, atoms: 151, 1235 Classifications: {'peptide': 151} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'PTRANS': 2, 'TRANS': 148} Chain breaks: 1 Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 4 Planarities with less than four sites: {'ASN:plan1': 1} Unresolved non-hydrogen planarities: 3 Chain: "P" Number of atoms: 1297 Number of conformers: 1 Conformer: "" Number of residues, atoms: 161, 1297 Classifications: {'peptide': 161} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 6, 'TRANS': 154} Chain breaks: 3 Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 2 Planarities with less than four sites: {'ASN:plan1': 1} Unresolved non-hydrogen planarities: 3 Chain: "Q" Number of atoms: 1470 Number of conformers: 1 Conformer: "" Number of residues, atoms: 182, 1470 Classifications: {'peptide': 182} Link IDs: {'PTRANS': 5, 'TRANS': 176} Chain: "R" Number of atoms: 1617 Number of conformers: 1 Conformer: "" Number of residues, atoms: 204, 1617 Classifications: {'peptide': 204} Incomplete info: {'truncation_to_alanine': 13} Link IDs: {'PCIS': 1, 'PTRANS': 5, 'TRANS': 197} Chain breaks: 1 Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 31 Unresolved non-hydrogen angles: 40 Unresolved non-hydrogen dihedrals: 23 Unresolved non-hydrogen chiralities: 6 Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 1} Unresolved non-hydrogen planarities: 8 Chain: "S" Number of atoms: 1173 Number of conformers: 1 Conformer: "" Number of residues, atoms: 146, 1173 Classifications: {'peptide': 146} Incomplete info: {'truncation_to_alanine': 6} Link IDs: {'PTRANS': 8, 'TRANS': 137} Chain breaks: 1 Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 19 Unresolved non-hydrogen angles: 25 Unresolved non-hydrogen dihedrals: 14 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 1, 'ASN:plan1': 2} Unresolved non-hydrogen planarities: 14 Chain: "T" Number of atoms: 4258 Number of conformers: 1 Conformer: "" Number of residues, atoms: 799, 4258 Classifications: {'peptide': 799} Incomplete info: {'truncation_to_alanine': 660} Link IDs: {'PTRANS': 17, 'TRANS': 781} Chain breaks: 3 Unresolved chain link angles: 14 Unresolved non-hydrogen bonds: 2381 Unresolved non-hydrogen angles: 3030 Unresolved non-hydrogen dihedrals: 1971 Unresolved non-hydrogen chiralities: 227 Planarities with less than four sites: {'GLN:plan1': 29, 'ARG:plan': 25, 'TYR:plan': 24, 'ASN:plan1': 43, 'TRP:plan': 7, 'HIS:plan': 9, 'PHE:plan': 43, 'GLU:plan': 62, 'ASP:plan': 38} Unresolved non-hydrogen planarities: 1266 Chain: "U" Number of atoms: 6259 Number of conformers: 1 Conformer: "" Number of residues, atoms: 873, 6259 Classifications: {'peptide': 873} Incomplete info: {'truncation_to_alanine': 277} Link IDs: {'PTRANS': 37, 'TRANS': 835} Chain breaks: 5 Unresolved chain link angles: 10 Unresolved non-hydrogen bonds: 942 Unresolved non-hydrogen angles: 1202 Unresolved non-hydrogen dihedrals: 780 Unresolved non-hydrogen chiralities: 99 Planarities with less than four sites: {'GLN:plan1': 10, 'HIS:plan': 3, 'TYR:plan': 13, 'ASN:plan1': 15, 'TRP:plan': 3, 'ASP:plan': 20, 'PHE:plan': 11, 'GLU:plan': 11, 'ARG:plan': 13} Unresolved non-hydrogen planarities: 453 Chain: "V" Number of atoms: 1568 Number of conformers: 1 Conformer: "" Number of residues, atoms: 251, 1568 Classifications: {'peptide': 251} Incomplete info: {'truncation_to_alanine': 142} Link IDs: {'PTRANS': 11, 'TRANS': 239} Chain breaks: 3 Unresolved chain link angles: 8 Unresolved non-hydrogen bonds: 474 Unresolved non-hydrogen angles: 602 Unresolved non-hydrogen dihedrals: 391 Unresolved non-hydrogen chiralities: 51 Planarities with less than four sites: {'GLN:plan1': 6, 'ARG:plan': 5, 'TYR:plan': 4, 'ASN:plan1': 10, 'TRP:plan': 1, 'HIS:plan': 4, 'PHE:plan': 5, 'GLU:plan': 8, 'ASP:plan': 5} Unresolved non-hydrogen planarities: 213 Time building chain proxies: 24.16, per 1000 atoms: 0.52 Number of scatterers: 46305 At special positions: 0 Unit cell: (290.206, 273.841, 184.379, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 173 16.00 O 8748 8.00 N 8032 7.00 C 29352 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 17.76 Conformation dependent library (CDL) restraints added in 9.3 seconds 12930 Ramachandran restraints generated. 6465 Oldfield, 0 Emsley, 6465 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 12674 Finding SS restraints... Secondary structure from input PDB file: 169 helices and 67 sheets defined 33.3% alpha, 10.7% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 5.10 Creating SS restraints... Processing helix chain 'A' and resid 33 through 46 removed outlier: 4.222A pdb=" N LEU A 39 " --> pdb=" O LYS A 35 " (cutoff:3.500A) removed outlier: 3.663A pdb=" N LEU A 44 " --> pdb=" O SER A 40 " (cutoff:3.500A) removed outlier: 3.733A pdb=" N ASP A 45 " --> pdb=" O ASN A 41 " (cutoff:3.500A) Processing helix chain 'A' and resid 100 through 120 removed outlier: 3.995A pdb=" N ALA A 104 " --> pdb=" O ASP A 100 " (cutoff:3.500A) removed outlier: 3.713A pdb=" N ILE A 115 " --> pdb=" O THR A 111 " (cutoff:3.500A) Processing helix chain 'A' and resid 131 through 145 Processing helix chain 'B' and resid 42 through 51 Processing helix chain 'B' and resid 51 through 62 Processing helix chain 'B' and resid 100 through 110 Processing helix chain 'B' and resid 112 through 139 removed outlier: 4.145A pdb=" N ARG B 122 " --> pdb=" O LYS B 118 " (cutoff:3.500A) Processing helix chain 'B' and resid 140 through 142 No H-bonds generated for 'chain 'B' and resid 140 through 142' Processing helix chain 'B' and resid 152 through 170 removed outlier: 4.097A pdb=" N ILE B 156 " --> pdb=" O ASP B 152 " (cutoff:3.500A) removed outlier: 3.548A pdb=" N PHE B 159 " --> pdb=" O LEU B 155 " (cutoff:3.500A) removed outlier: 3.585A pdb=" N CYS B 161 " --> pdb=" O MET B 157 " (cutoff:3.500A) removed outlier: 4.062A pdb=" N ARG B 162 " --> pdb=" O LYS B 158 " (cutoff:3.500A) removed outlier: 4.855A pdb=" N TRP B 165 " --> pdb=" O CYS B 161 " (cutoff:3.500A) removed outlier: 4.539A pdb=" N LYS B 166 " --> pdb=" O ARG B 162 " (cutoff:3.500A) Processing helix chain 'B' and resid 191 through 195 Processing helix chain 'B' and resid 203 through 212 removed outlier: 3.895A pdb=" N LYS B 209 " --> pdb=" O ASN B 205 " (cutoff:3.500A) Processing helix chain 'B' and resid 215 through 228 Processing helix chain 'C' and resid 9 through 17 Processing helix chain 'C' and resid 18 through 20 No H-bonds generated for 'chain 'C' and resid 18 through 20' Processing helix chain 'C' and resid 30 through 45 removed outlier: 3.979A pdb=" N TYR C 34 " --> pdb=" O PHE C 30 " (cutoff:3.500A) Processing helix chain 'C' and resid 50 through 75 removed outlier: 5.016A pdb=" N GLU C 69 " --> pdb=" O CYS C 65 " (cutoff:3.500A) removed outlier: 4.659A pdb=" N ASP C 70 " --> pdb=" O ARG C 66 " (cutoff:3.500A) Processing helix chain 'C' and resid 84 through 100 removed outlier: 4.037A pdb=" N SER C 91 " --> pdb=" O SER C 87 " (cutoff:3.500A) removed outlier: 5.911A pdb=" N PHE C 95 " --> pdb=" O SER C 91 " (cutoff:3.500A) removed outlier: 5.577A pdb=" N LYS C 96 " --> pdb=" O LYS C 92 " (cutoff:3.500A) Processing helix chain 'C' and resid 141 through 151 removed outlier: 3.824A pdb=" N CYS C 145 " --> pdb=" O SER C 141 " (cutoff:3.500A) Processing helix chain 'C' and resid 152 through 155 removed outlier: 3.576A pdb=" N VAL C 155 " --> pdb=" O LEU C 152 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 152 through 155' Processing helix chain 'D' and resid 40 through 58 Processing helix chain 'D' and resid 99 through 110 Processing helix chain 'D' and resid 110 through 115 Processing helix chain 'D' and resid 144 through 154 Processing helix chain 'E' and resid 31 through 50 removed outlier: 3.975A pdb=" N ILE E 35 " --> pdb=" O ASN E 31 " (cutoff:3.500A) removed outlier: 3.911A pdb=" N ALA E 45 " --> pdb=" O HIS E 41 " (cutoff:3.500A) removed outlier: 3.746A pdb=" N LEU E 50 " --> pdb=" O ILE E 46 " (cutoff:3.500A) Processing helix chain 'E' and resid 170 through 190 Processing helix chain 'E' and resid 204 through 219 removed outlier: 4.044A pdb=" N ASP E 208 " --> pdb=" O SER E 204 " (cutoff:3.500A) removed outlier: 3.785A pdb=" N GLU E 209 " --> pdb=" O ASN E 205 " (cutoff:3.500A) removed outlier: 3.838A pdb=" N LYS E 213 " --> pdb=" O GLU E 209 " (cutoff:3.500A) removed outlier: 3.801A pdb=" N MET E 214 " --> pdb=" O LYS E 210 " (cutoff:3.500A) Processing helix chain 'F' and resid 9 through 19 removed outlier: 5.073A pdb=" N GLU F 15 " --> pdb=" O LYS F 11 " (cutoff:3.500A) removed outlier: 3.789A pdb=" N GLU F 16 " --> pdb=" O ALA F 12 " (cutoff:3.500A) Processing helix chain 'F' and resid 27 through 45 removed outlier: 3.580A pdb=" N TYR F 45 " --> pdb=" O LEU F 41 " (cutoff:3.500A) Processing helix chain 'F' and resid 48 through 75 removed outlier: 4.078A pdb=" N VAL F 52 " --> pdb=" O ASP F 48 " (cutoff:3.500A) removed outlier: 4.009A pdb=" N ASN F 53 " --> pdb=" O PHE F 49 " (cutoff:3.500A) removed outlier: 3.860A pdb=" N ASP F 54 " --> pdb=" O ASN F 50 " (cutoff:3.500A) removed outlier: 3.963A pdb=" N ASN F 62 " --> pdb=" O SER F 58 " (cutoff:3.500A) removed outlier: 4.082A pdb=" N ARG F 66 " --> pdb=" O ASN F 62 " (cutoff:3.500A) removed outlier: 5.253A pdb=" N GLU F 69 " --> pdb=" O CYS F 65 " (cutoff:3.500A) removed outlier: 3.966A pdb=" N ASP F 70 " --> pdb=" O ARG F 66 " (cutoff:3.500A) removed outlier: 3.663A pdb=" N ALA F 73 " --> pdb=" O GLU F 69 " (cutoff:3.500A) Processing helix chain 'F' and resid 82 through 93 Processing helix chain 'F' and resid 93 through 98 removed outlier: 3.713A pdb=" N PHE F 98 " --> pdb=" O ALA F 94 " (cutoff:3.500A) Processing helix chain 'F' and resid 142 through 155 removed outlier: 3.750A pdb=" N GLY F 146 " --> pdb=" O ASN F 142 " (cutoff:3.500A) removed outlier: 4.495A pdb=" N LEU F 152 " --> pdb=" O LEU F 148 " (cutoff:3.500A) Processing helix chain 'G' and resid 59 through 76 Processing helix chain 'G' and resid 79 through 108 removed outlier: 3.641A pdb=" N PHE G 83 " --> pdb=" O THR G 79 " (cutoff:3.500A) removed outlier: 3.707A pdb=" N ILE G 94 " --> pdb=" O TYR G 90 " (cutoff:3.500A) removed outlier: 4.350A pdb=" N ARG G 97 " --> pdb=" O ASN G 93 " (cutoff:3.500A) removed outlier: 4.957A pdb=" N GLU G 100 " --> pdb=" O ILE G 96 " (cutoff:3.500A) removed outlier: 3.772A pdb=" N LEU G 101 " --> pdb=" O ARG G 97 " (cutoff:3.500A) removed outlier: 3.634A pdb=" N SER G 108 " --> pdb=" O PHE G 104 " (cutoff:3.500A) Processing helix chain 'G' and resid 175 through 192 removed outlier: 4.068A pdb=" N ILE G 179 " --> pdb=" O LYS G 175 " (cutoff:3.500A) removed outlier: 3.533A pdb=" N LEU G 180 " --> pdb=" O ILE G 176 " (cutoff:3.500A) removed outlier: 4.274A pdb=" N GLN G 181 " --> pdb=" O LEU G 177 " (cutoff:3.500A) removed outlier: 5.046A pdb=" N TRP G 188 " --> pdb=" O HIS G 184 " (cutoff:3.500A) removed outlier: 3.903A pdb=" N SER G 189 " --> pdb=" O GLY G 185 " (cutoff:3.500A) Processing helix chain 'G' and resid 227 through 229 No H-bonds generated for 'chain 'G' and resid 227 through 229' Processing helix chain 'G' and resid 230 through 242 removed outlier: 4.165A pdb=" N CYS G 234 " --> pdb=" O GLU G 230 " (cutoff:3.500A) Processing helix chain 'G' and resid 243 through 245 No H-bonds generated for 'chain 'G' and resid 243 through 245' Processing helix chain 'G' and resid 271 through 281 removed outlier: 3.932A pdb=" N LEU G 275 " --> pdb=" O ASP G 271 " (cutoff:3.500A) removed outlier: 4.060A pdb=" N ARG G 277 " --> pdb=" O GLN G 273 " (cutoff:3.500A) Processing helix chain 'H' and resid 31 through 52 removed outlier: 4.213A pdb=" N GLU H 35 " --> pdb=" O GLN H 31 " (cutoff:3.500A) removed outlier: 4.834A pdb=" N ASN H 37 " --> pdb=" O LEU H 33 " (cutoff:3.500A) Proline residue: H 38 - end of helix removed outlier: 3.572A pdb=" N LEU H 41 " --> pdb=" O ASN H 37 " (cutoff:3.500A) removed outlier: 4.023A pdb=" N ASP H 46 " --> pdb=" O HIS H 42 " (cutoff:3.500A) removed outlier: 4.104A pdb=" N ILE H 47 " --> pdb=" O ALA H 43 " (cutoff:3.500A) Processing helix chain 'H' and resid 123 through 125 No H-bonds generated for 'chain 'H' and resid 123 through 125' Processing helix chain 'H' and resid 126 through 146 removed outlier: 3.791A pdb=" N ARG H 131 " --> pdb=" O ASP H 127 " (cutoff:3.500A) removed outlier: 4.697A pdb=" N SER H 132 " --> pdb=" O ASN H 128 " (cutoff:3.500A) Processing helix chain 'H' and resid 158 through 172 removed outlier: 3.610A pdb=" N ASP H 162 " --> pdb=" O SER H 158 " (cutoff:3.500A) Processing helix chain 'I' and resid 251 through 269 Processing helix chain 'I' and resid 276 through 292 removed outlier: 3.702A pdb=" N TYR I 280 " --> pdb=" O GLN I 276 " (cutoff:3.500A) Processing helix chain 'I' and resid 297 through 317 removed outlier: 3.725A pdb=" N PHE I 309 " --> pdb=" O LEU I 305 " (cutoff:3.500A) Processing helix chain 'I' and resid 321 through 339 removed outlier: 4.003A pdb=" N SER I 336 " --> pdb=" O THR I 332 " (cutoff:3.500A) Processing helix chain 'I' and resid 346 through 369 removed outlier: 3.590A pdb=" N GLU I 350 " --> pdb=" O PRO I 346 " (cutoff:3.500A) removed outlier: 3.600A pdb=" N ILE I 351 " --> pdb=" O LEU I 347 " (cutoff:3.500A) Processing helix chain 'I' and resid 400 through 420 removed outlier: 4.010A pdb=" N GLU I 404 " --> pdb=" O THR I 400 " (cutoff:3.500A) removed outlier: 3.769A pdb=" N ASN I 405 " --> pdb=" O VAL I 401 " (cutoff:3.500A) Processing helix chain 'I' and resid 424 through 441 removed outlier: 3.635A pdb=" N VAL I 428 " --> pdb=" O ARG I 424 " (cutoff:3.500A) Processing helix chain 'I' and resid 447 through 452 Processing helix chain 'I' and resid 452 through 459 Processing helix chain 'I' and resid 466 through 481 removed outlier: 3.687A pdb=" N GLN I 473 " --> pdb=" O LEU I 469 " (cutoff:3.500A) Processing helix chain 'I' and resid 497 through 509 removed outlier: 3.896A pdb=" N PHE I 505 " --> pdb=" O LEU I 501 " (cutoff:3.500A) Processing helix chain 'I' and resid 512 through 514 No H-bonds generated for 'chain 'I' and resid 512 through 514' Processing helix chain 'I' and resid 515 through 529 removed outlier: 3.865A pdb=" N GLU I 519 " --> pdb=" O ASN I 515 " (cutoff:3.500A) Processing helix chain 'I' and resid 628 through 632 removed outlier: 4.145A pdb=" N GLY I 631 " --> pdb=" O ILE I 628 " (cutoff:3.500A) Processing helix chain 'I' and resid 862 through 875 removed outlier: 3.973A pdb=" N LEU I 875 " --> pdb=" O THR I 871 " (cutoff:3.500A) Processing helix chain 'I' and resid 880 through 885 removed outlier: 4.061A pdb=" N ILE I 884 " --> pdb=" O VAL I 880 " (cutoff:3.500A) Processing helix chain 'I' and resid 889 through 898 Processing helix chain 'I' and resid 921 through 930 removed outlier: 4.205A pdb=" N LYS I 925 " --> pdb=" O ILE I 921 " (cutoff:3.500A) removed outlier: 3.843A pdb=" N ILE I 930 " --> pdb=" O THR I 926 " (cutoff:3.500A) Processing helix chain 'I' and resid 933 through 938 Processing helix chain 'I' and resid 938 through 948 removed outlier: 3.897A pdb=" N LEU I 944 " --> pdb=" O LEU I 940 " (cutoff:3.500A) Processing helix chain 'I' and resid 957 through 962 Processing helix chain 'J' and resid 266 through 288 removed outlier: 3.523A pdb=" N ARG J 288 " --> pdb=" O LEU J 284 " (cutoff:3.500A) Processing helix chain 'J' and resid 289 through 293 removed outlier: 3.787A pdb=" N ALA J 292 " --> pdb=" O TYR J 289 " (cutoff:3.500A) removed outlier: 3.898A pdb=" N LEU J 293 " --> pdb=" O VAL J 290 " (cutoff:3.500A) No H-bonds generated for 'chain 'J' and resid 289 through 293' Processing helix chain 'J' and resid 307 through 327 Processing helix chain 'J' and resid 380 through 397 removed outlier: 4.265A pdb=" N ALA J 384 " --> pdb=" O ILE J 380 " (cutoff:3.500A) removed outlier: 3.987A pdb=" N MET J 385 " --> pdb=" O SER J 381 " (cutoff:3.500A) Proline residue: J 388 - end of helix Processing helix chain 'J' and resid 402 through 417 Proline residue: J 410 - end of helix Processing helix chain 'J' and resid 426 through 442 Proline residue: J 436 - end of helix removed outlier: 4.117A pdb=" N VAL J 439 " --> pdb=" O ALA J 435 " (cutoff:3.500A) Processing helix chain 'J' and resid 459 through 476 removed outlier: 4.532A pdb=" N LEU J 465 " --> pdb=" O SER J 461 " (cutoff:3.500A) removed outlier: 3.700A pdb=" N ASN J 467 " --> pdb=" O ASP J 463 " (cutoff:3.500A) removed outlier: 4.258A pdb=" N LEU J 476 " --> pdb=" O GLN J 472 " (cutoff:3.500A) Processing helix chain 'J' and resid 487 through 495 removed outlier: 3.844A pdb=" N TYR J 491 " --> pdb=" O ARG J 487 " (cutoff:3.500A) Processing helix chain 'J' and resid 506 through 525 Processing helix chain 'J' and resid 526 through 543 Processing helix chain 'J' and resid 551 through 565 removed outlier: 3.713A pdb=" N ARG J 555 " --> pdb=" O HIS J 551 " (cutoff:3.500A) removed outlier: 3.925A pdb=" N LEU J 565 " --> pdb=" O ILE J 561 " (cutoff:3.500A) Processing helix chain 'J' and resid 585 through 602 removed outlier: 3.987A pdb=" N LEU J 594 " --> pdb=" O LYS J 590 " (cutoff:3.500A) removed outlier: 3.847A pdb=" N LYS J 597 " --> pdb=" O GLN J 593 " (cutoff:3.500A) Processing helix chain 'J' and resid 604 through 616 removed outlier: 3.744A pdb=" N VAL J 608 " --> pdb=" O ASP J 604 " (cutoff:3.500A) Processing helix chain 'J' and resid 617 through 619 No H-bonds generated for 'chain 'J' and resid 617 through 619' Processing helix chain 'J' and resid 627 through 635 removed outlier: 3.855A pdb=" N LEU J 631 " --> pdb=" O GLU J 627 " (cutoff:3.500A) Processing helix chain 'J' and resid 636 through 641 Processing helix chain 'J' and resid 897 through 909 Proline residue: J 903 - end of helix Processing helix chain 'J' and resid 1016 through 1028 removed outlier: 3.812A pdb=" N GLU J1020 " --> pdb=" O VAL J1016 " (cutoff:3.500A) removed outlier: 4.419A pdb=" N TYR J1021 " --> pdb=" O ASP J1017 " (cutoff:3.500A) removed outlier: 3.778A pdb=" N ALA J1028 " --> pdb=" O SER J1024 " (cutoff:3.500A) Processing helix chain 'J' and resid 1110 through 1129 removed outlier: 3.648A pdb=" N THR J1114 " --> pdb=" O ASN J1110 " (cutoff:3.500A) removed outlier: 3.993A pdb=" N ARG J1124 " --> pdb=" O LYS J1120 " (cutoff:3.500A) removed outlier: 3.739A pdb=" N SER J1129 " --> pdb=" O GLU J1125 " (cutoff:3.500A) Processing helix chain 'J' and resid 1157 through 1165 removed outlier: 3.520A pdb=" N VAL J1161 " --> pdb=" O ASP J1157 " (cutoff:3.500A) Processing helix chain 'J' and resid 1166 through 1169 Processing helix chain 'K' and resid 237 through 249 removed outlier: 4.081A pdb=" N PHE K 247 " --> pdb=" O LEU K 243 " (cutoff:3.500A) Processing helix chain 'K' and resid 483 through 499 Processing helix chain 'L' and resid 32 through 46 removed outlier: 3.959A pdb=" N VAL L 38 " --> pdb=" O LEU L 34 " (cutoff:3.500A) Processing helix chain 'L' and resid 98 through 121 removed outlier: 3.929A pdb=" N CYS L 121 " --> pdb=" O ILE L 117 " (cutoff:3.500A) Processing helix chain 'L' and resid 132 through 142 Processing helix chain 'M' and resid 41 through 61 removed outlier: 3.869A pdb=" N TYR M 45 " --> pdb=" O SER M 41 " (cutoff:3.500A) removed outlier: 5.381A pdb=" N VAL M 53 " --> pdb=" O LEU M 49 " (cutoff:3.500A) Proline residue: M 54 - end of helix Processing helix chain 'M' and resid 101 through 110 removed outlier: 3.658A pdb=" N HIS M 106 " --> pdb=" O HIS M 102 " (cutoff:3.500A) removed outlier: 3.740A pdb=" N GLU M 107 " --> pdb=" O ASN M 103 " (cutoff:3.500A) removed outlier: 4.285A pdb=" N LYS M 110 " --> pdb=" O HIS M 106 " (cutoff:3.500A) Processing helix chain 'M' and resid 118 through 133 removed outlier: 4.045A pdb=" N ARG M 122 " --> pdb=" O LYS M 118 " (cutoff:3.500A) removed outlier: 4.162A pdb=" N GLY M 127 " --> pdb=" O LEU M 123 " (cutoff:3.500A) removed outlier: 4.058A pdb=" N PHE M 128 " --> pdb=" O ARG M 124 " (cutoff:3.500A) removed outlier: 3.995A pdb=" N GLN M 129 " --> pdb=" O ASN M 125 " (cutoff:3.500A) removed outlier: 3.650A pdb=" N ILE M 130 " --> pdb=" O ILE M 126 " (cutoff:3.500A) removed outlier: 3.614A pdb=" N LYS M 133 " --> pdb=" O GLN M 129 " (cutoff:3.500A) Processing helix chain 'M' and resid 134 through 140 removed outlier: 3.827A pdb=" N ILE M 139 " --> pdb=" O SER M 135 " (cutoff:3.500A) removed outlier: 3.541A pdb=" N PHE M 140 " --> pdb=" O GLU M 136 " (cutoff:3.500A) Processing helix chain 'M' and resid 156 through 161 Processing helix chain 'M' and resid 163 through 168 Processing helix chain 'M' and resid 206 through 211 removed outlier: 3.991A pdb=" N MET M 210 " --> pdb=" O GLU M 206 " (cutoff:3.500A) removed outlier: 3.509A pdb=" N ILE M 211 " --> pdb=" O GLU M 207 " (cutoff:3.500A) No H-bonds generated for 'chain 'M' and resid 206 through 211' Processing helix chain 'M' and resid 213 through 215 No H-bonds generated for 'chain 'M' and resid 213 through 215' Processing helix chain 'M' and resid 216 through 230 removed outlier: 4.017A pdb=" N GLY M 220 " --> pdb=" O GLU M 216 " (cutoff:3.500A) removed outlier: 3.830A pdb=" N ILE M 221 " --> pdb=" O ILE M 217 " (cutoff:3.500A) removed outlier: 3.895A pdb=" N ILE M 222 " --> pdb=" O PRO M 218 " (cutoff:3.500A) removed outlier: 3.515A pdb=" N LEU M 226 " --> pdb=" O ILE M 222 " (cutoff:3.500A) Processing helix chain 'N' and resid 9 through 21 removed outlier: 4.846A pdb=" N GLY N 14 " --> pdb=" O LEU N 10 " (cutoff:3.500A) removed outlier: 4.748A pdb=" N GLU N 15 " --> pdb=" O LYS N 11 " (cutoff:3.500A) Processing helix chain 'N' and resid 26 through 45 removed outlier: 3.601A pdb=" N PHE N 30 " --> pdb=" O ASN N 26 " (cutoff:3.500A) removed outlier: 3.962A pdb=" N ILE N 37 " --> pdb=" O THR N 33 " (cutoff:3.500A) Processing helix chain 'N' and resid 49 through 75 removed outlier: 3.824A pdb=" N ASN N 53 " --> pdb=" O PHE N 49 " (cutoff:3.500A) removed outlier: 4.057A pdb=" N ASP N 54 " --> pdb=" O ASN N 50 " (cutoff:3.500A) removed outlier: 4.869A pdb=" N HIS N 55 " --> pdb=" O LYS N 51 " (cutoff:3.500A) removed outlier: 4.706A pdb=" N ARG N 66 " --> pdb=" O ASN N 62 " (cutoff:3.500A) removed outlier: 5.340A pdb=" N GLU N 69 " --> pdb=" O CYS N 65 " (cutoff:3.500A) removed outlier: 4.370A pdb=" N ASP N 70 " --> pdb=" O ARG N 66 " (cutoff:3.500A) Processing helix chain 'N' and resid 83 through 97 removed outlier: 3.895A pdb=" N GLU N 88 " --> pdb=" O VAL N 84 " (cutoff:3.500A) removed outlier: 4.563A pdb=" N ALA N 94 " --> pdb=" O LEU N 90 " (cutoff:3.500A) removed outlier: 5.850A pdb=" N PHE N 95 " --> pdb=" O SER N 91 " (cutoff:3.500A) Processing helix chain 'N' and resid 141 through 153 removed outlier: 3.594A pdb=" N CYS N 145 " --> pdb=" O SER N 141 " (cutoff:3.500A) Processing helix chain 'O' and resid 37 through 57 removed outlier: 4.105A pdb=" N LYS O 42 " --> pdb=" O GLU O 38 " (cutoff:3.500A) removed outlier: 3.550A pdb=" N MET O 47 " --> pdb=" O LEU O 43 " (cutoff:3.500A) removed outlier: 3.546A pdb=" N SER O 50 " --> pdb=" O GLY O 46 " (cutoff:3.500A) removed outlier: 3.706A pdb=" N THR O 55 " --> pdb=" O LEU O 51 " (cutoff:3.500A) Processing helix chain 'O' and resid 101 through 109 Processing helix chain 'O' and resid 142 through 154 removed outlier: 3.727A pdb=" N ILE O 146 " --> pdb=" O ASN O 142 " (cutoff:3.500A) removed outlier: 3.867A pdb=" N SER O 147 " --> pdb=" O ARG O 143 " (cutoff:3.500A) Processing helix chain 'P' and resid 29 through 47 removed outlier: 3.804A pdb=" N TYR P 33 " --> pdb=" O ASN P 29 " (cutoff:3.500A) removed outlier: 3.551A pdb=" N ILE P 46 " --> pdb=" O GLY P 42 " (cutoff:3.500A) Processing helix chain 'P' and resid 170 through 190 removed outlier: 3.652A pdb=" N ALA P 175 " --> pdb=" O ALA P 171 " (cutoff:3.500A) removed outlier: 3.928A pdb=" N LEU P 179 " --> pdb=" O ALA P 175 " (cutoff:3.500A) removed outlier: 4.024A pdb=" N LYS P 181 " --> pdb=" O ASN P 177 " (cutoff:3.500A) removed outlier: 3.544A pdb=" N TYR P 183 " --> pdb=" O LEU P 179 " (cutoff:3.500A) Processing helix chain 'P' and resid 204 through 216 removed outlier: 3.766A pdb=" N LYS P 210 " --> pdb=" O LEU P 206 " (cutoff:3.500A) removed outlier: 4.108A pdb=" N MET P 214 " --> pdb=" O LYS P 210 " (cutoff:3.500A) removed outlier: 3.859A pdb=" N GLU P 216 " --> pdb=" O LYS P 212 " (cutoff:3.500A) Processing helix chain 'Q' and resid 9 through 18 removed outlier: 3.902A pdb=" N GLU Q 15 " --> pdb=" O LYS Q 11 " (cutoff:3.500A) Processing helix chain 'Q' and resid 26 through 45 removed outlier: 4.054A pdb=" N PHE Q 30 " --> pdb=" O ASN Q 26 " (cutoff:3.500A) Processing helix chain 'Q' and resid 48 through 75 removed outlier: 3.952A pdb=" N ILE Q 63 " --> pdb=" O MET Q 59 " (cutoff:3.500A) removed outlier: 4.567A pdb=" N ARG Q 66 " --> pdb=" O ASN Q 62 " (cutoff:3.500A) removed outlier: 4.436A pdb=" N ILE Q 68 " --> pdb=" O GLY Q 64 " (cutoff:3.500A) removed outlier: 5.514A pdb=" N GLU Q 69 " --> pdb=" O CYS Q 65 " (cutoff:3.500A) removed outlier: 4.404A pdb=" N ASP Q 70 " --> pdb=" O ARG Q 66 " (cutoff:3.500A) Processing helix chain 'Q' and resid 84 through 99 removed outlier: 4.451A pdb=" N LYS Q 96 " --> pdb=" O LYS Q 92 " (cutoff:3.500A) removed outlier: 3.903A pdb=" N PHE Q 98 " --> pdb=" O ALA Q 94 " (cutoff:3.500A) Processing helix chain 'Q' and resid 131 through 136 removed outlier: 3.816A pdb=" N MET Q 135 " --> pdb=" O MET Q 132 " (cutoff:3.500A) removed outlier: 4.237A pdb=" N LYS Q 136 " --> pdb=" O ASP Q 133 " (cutoff:3.500A) Processing helix chain 'Q' and resid 142 through 154 removed outlier: 3.688A pdb=" N LYS Q 149 " --> pdb=" O CYS Q 145 " (cutoff:3.500A) Processing helix chain 'R' and resid 59 through 77 Processing helix chain 'R' and resid 79 through 107 removed outlier: 3.747A pdb=" N PHE R 83 " --> pdb=" O THR R 79 " (cutoff:3.500A) removed outlier: 5.367A pdb=" N TYR R 90 " --> pdb=" O LYS R 86 " (cutoff:3.500A) removed outlier: 4.185A pdb=" N GLY R 91 " --> pdb=" O LEU R 87 " (cutoff:3.500A) removed outlier: 4.782A pdb=" N ILE R 96 " --> pdb=" O HIS R 92 " (cutoff:3.500A) removed outlier: 4.701A pdb=" N ARG R 97 " --> pdb=" O ASN R 93 " (cutoff:3.500A) removed outlier: 3.624A pdb=" N LEU R 101 " --> pdb=" O ARG R 97 " (cutoff:3.500A) Processing helix chain 'R' and resid 178 through 187 removed outlier: 3.579A pdb=" N HIS R 184 " --> pdb=" O LEU R 180 " (cutoff:3.500A) Processing helix chain 'R' and resid 187 through 192 Processing helix chain 'R' and resid 227 through 229 No H-bonds generated for 'chain 'R' and resid 227 through 229' Processing helix chain 'R' and resid 230 through 242 removed outlier: 3.782A pdb=" N CYS R 234 " --> pdb=" O GLU R 230 " (cutoff:3.500A) removed outlier: 3.576A pdb=" N GLY R 235 " --> pdb=" O TYR R 231 " (cutoff:3.500A) Processing helix chain 'R' and resid 271 through 279 removed outlier: 3.537A pdb=" N LEU R 275 " --> pdb=" O ASP R 271 " (cutoff:3.500A) Processing helix chain 'S' and resid 37 through 53 removed outlier: 4.410A pdb=" N TRP S 53 " --> pdb=" O GLU S 49 " (cutoff:3.500A) Processing helix chain 'S' and resid 130 through 146 removed outlier: 3.527A pdb=" N TYR S 134 " --> pdb=" O MET S 130 " (cutoff:3.500A) removed outlier: 3.599A pdb=" N GLN S 135 " --> pdb=" O ARG S 131 " (cutoff:3.500A) removed outlier: 4.719A pdb=" N GLU S 136 " --> pdb=" O SER S 132 " (cutoff:3.500A) removed outlier: 4.553A pdb=" N GLU S 139 " --> pdb=" O GLN S 135 " (cutoff:3.500A) removed outlier: 4.567A pdb=" N LEU S 140 " --> pdb=" O GLU S 136 " (cutoff:3.500A) Processing helix chain 'S' and resid 160 through 169 removed outlier: 4.007A pdb=" N ARG S 166 " --> pdb=" O ASP S 162 " (cutoff:3.500A) removed outlier: 3.877A pdb=" N THR S 167 " --> pdb=" O SER S 163 " (cutoff:3.500A) Processing helix chain 'T' and resid 255 through 269 removed outlier: 3.665A pdb=" N SER T 259 " --> pdb=" O SER T 255 " (cutoff:3.500A) Processing helix chain 'T' and resid 276 through 289 removed outlier: 3.895A pdb=" N PHE T 282 " --> pdb=" O HIS T 278 " (cutoff:3.500A) Processing helix chain 'T' and resid 296 through 314 Processing helix chain 'T' and resid 322 through 333 Processing helix chain 'T' and resid 334 through 337 Processing helix chain 'T' and resid 348 through 367 Processing helix chain 'T' and resid 399 through 409 Processing helix chain 'T' and resid 409 through 417 removed outlier: 3.939A pdb=" N SER T 415 " --> pdb=" O LYS T 411 " (cutoff:3.500A) removed outlier: 4.115A pdb=" N LEU T 416 " --> pdb=" O GLU T 412 " (cutoff:3.500A) removed outlier: 3.937A pdb=" N PHE T 417 " --> pdb=" O ILE T 413 " (cutoff:3.500A) Processing helix chain 'T' and resid 418 through 421 removed outlier: 3.804A pdb=" N GLU T 421 " --> pdb=" O ASN T 418 " (cutoff:3.500A) No H-bonds generated for 'chain 'T' and resid 418 through 421' Processing helix chain 'T' and resid 456 through 460 removed outlier: 3.633A pdb=" N TYR T 459 " --> pdb=" O TYR T 456 " (cutoff:3.500A) removed outlier: 3.734A pdb=" N THR T 460 " --> pdb=" O GLU T 457 " (cutoff:3.500A) No H-bonds generated for 'chain 'T' and resid 456 through 460' Processing helix chain 'T' and resid 467 through 472 Processing helix chain 'T' and resid 476 through 481 removed outlier: 4.515A pdb=" N HIS T 481 " --> pdb=" O ASP T 477 " (cutoff:3.500A) Processing helix chain 'T' and resid 517 through 526 removed outlier: 4.413A pdb=" N LYS T 523 " --> pdb=" O GLU T 519 " (cutoff:3.500A) removed outlier: 4.956A pdb=" N LYS T 524 " --> pdb=" O ILE T 520 " (cutoff:3.500A) Processing helix chain 'T' and resid 862 through 866 Processing helix chain 'T' and resid 867 through 869 No H-bonds generated for 'chain 'T' and resid 867 through 869' Processing helix chain 'T' and resid 886 through 888 No H-bonds generated for 'chain 'T' and resid 886 through 888' Processing helix chain 'T' and resid 889 through 894 Processing helix chain 'T' and resid 896 through 900 removed outlier: 3.635A pdb=" N LYS T 899 " --> pdb=" O GLU T 896 " (cutoff:3.500A) Processing helix chain 'T' and resid 921 through 924 removed outlier: 4.056A pdb=" N ASN T 924 " --> pdb=" O ILE T 921 " (cutoff:3.500A) No H-bonds generated for 'chain 'T' and resid 921 through 924' Processing helix chain 'T' and resid 925 through 930 removed outlier: 4.216A pdb=" N LYS T 929 " --> pdb=" O LYS T 925 " (cutoff:3.500A) removed outlier: 3.650A pdb=" N ILE T 930 " --> pdb=" O THR T 926 " (cutoff:3.500A) No H-bonds generated for 'chain 'T' and resid 925 through 930' Processing helix chain 'T' and resid 933 through 938 Processing helix chain 'T' and resid 939 through 947 Processing helix chain 'U' and resid 267 through 286 Processing helix chain 'U' and resid 310 through 328 Processing helix chain 'U' and resid 381 through 395 removed outlier: 3.818A pdb=" N MET U 385 " --> pdb=" O SER U 381 " (cutoff:3.500A) Proline residue: U 388 - end of helix Processing helix chain 'U' and resid 407 through 416 Processing helix chain 'U' and resid 426 through 441 Proline residue: U 436 - end of helix Processing helix chain 'U' and resid 459 through 475 removed outlier: 4.402A pdb=" N LEU U 465 " --> pdb=" O SER U 461 " (cutoff:3.500A) Processing helix chain 'U' and resid 476 through 478 No H-bonds generated for 'chain 'U' and resid 476 through 478' Processing helix chain 'U' and resid 506 through 524 removed outlier: 3.612A pdb=" N GLN U 510 " --> pdb=" O GLN U 506 " (cutoff:3.500A) removed outlier: 3.753A pdb=" N TYR U 521 " --> pdb=" O MET U 517 " (cutoff:3.500A) Processing helix chain 'U' and resid 526 through 544 removed outlier: 3.752A pdb=" N GLN U 530 " --> pdb=" O TYR U 526 " (cutoff:3.500A) Processing helix chain 'U' and resid 553 through 563 Processing helix chain 'U' and resid 584 through 603 Processing helix chain 'U' and resid 604 through 619 Processing helix chain 'U' and resid 636 through 641 Processing helix chain 'U' and resid 897 through 905 Proline residue: U 903 - end of helix Processing helix chain 'U' and resid 920 through 924 removed outlier: 3.631A pdb=" N LEU U 924 " --> pdb=" O LEU U 921 " (cutoff:3.500A) Processing helix chain 'U' and resid 1016 through 1026 Processing helix chain 'U' and resid 1112 through 1129 removed outlier: 3.683A pdb=" N ARG U1118 " --> pdb=" O THR U1114 " (cutoff:3.500A) Processing helix chain 'U' and resid 1158 through 1163 removed outlier: 3.756A pdb=" N TYR U1162 " --> pdb=" O HIS U1158 " (cutoff:3.500A) Processing helix chain 'U' and resid 1197 through 1201 removed outlier: 3.557A pdb=" N CYS U1200 " --> pdb=" O THR U1197 " (cutoff:3.500A) removed outlier: 3.588A pdb=" N ARG U1201 " --> pdb=" O SER U1198 " (cutoff:3.500A) No H-bonds generated for 'chain 'U' and resid 1197 through 1201' Processing helix chain 'V' and resid 237 through 249 removed outlier: 4.939A pdb=" N LEU V 243 " --> pdb=" O ALA V 239 " (cutoff:3.500A) removed outlier: 3.761A pdb=" N THR V 244 " --> pdb=" O SER V 240 " (cutoff:3.500A) removed outlier: 3.658A pdb=" N PHE V 247 " --> pdb=" O LEU V 243 " (cutoff:3.500A) Processing helix chain 'V' and resid 483 through 500 removed outlier: 3.717A pdb=" N LEU V 489 " --> pdb=" O ASN V 485 " (cutoff:3.500A) removed outlier: 3.581A pdb=" N ALA V 497 " --> pdb=" O TYR V 493 " (cutoff:3.500A) removed outlier: 3.605A pdb=" N GLY V 499 " --> pdb=" O LYS V 495 " (cutoff:3.500A) removed outlier: 4.824A pdb=" N ILE V 500 " --> pdb=" O ILE V 496 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 17 through 21 removed outlier: 3.725A pdb=" N LEU A 19 " --> pdb=" O LEU A 10 " (cutoff:3.500A) removed outlier: 3.823A pdb=" N PHE A 7 " --> pdb=" O GLY A 89 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'B' and resid 39 through 41 Processing sheet with id=AA3, first strand: chain 'B' and resid 89 through 91 removed outlier: 3.660A pdb=" N VAL B 96 " --> pdb=" O LYS B 89 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 175 through 178 removed outlier: 3.639A pdb=" N ASN B 175 " --> pdb=" O LEU B 187 " (cutoff:3.500A) removed outlier: 3.752A pdb=" N PHE B 184 " --> pdb=" O VAL B 262 " (cutoff:3.500A) removed outlier: 3.836A pdb=" N VAL B 262 " --> pdb=" O PHE B 184 " (cutoff:3.500A) removed outlier: 4.189A pdb=" N PHE B 260 " --> pdb=" O LEU B 186 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'C' and resid 104 through 106 removed outlier: 3.718A pdb=" N PHE C 115 " --> pdb=" O VAL C 178 " (cutoff:3.500A) removed outlier: 3.609A pdb=" N VAL C 178 " --> pdb=" O PHE C 115 " (cutoff:3.500A) removed outlier: 3.567A pdb=" N ILE C 176 " --> pdb=" O LEU C 117 " (cutoff:3.500A) removed outlier: 7.012A pdb=" N GLU C 175 " --> pdb=" O VAL C 164 " (cutoff:3.500A) removed outlier: 3.680A pdb=" N ASP C 160 " --> pdb=" O LYS C 179 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'D' and resid 17 through 20 removed outlier: 3.761A pdb=" N PHE D 17 " --> pdb=" O ILE D 8 " (cutoff:3.500A) removed outlier: 4.518A pdb=" N SER D 5 " --> pdb=" O LEU D 91 " (cutoff:3.500A) removed outlier: 3.773A pdb=" N LEU D 91 " --> pdb=" O SER D 5 " (cutoff:3.500A) removed outlier: 3.528A pdb=" N TRP D 7 " --> pdb=" O VAL D 89 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N VAL D 89 " --> pdb=" O TRP D 7 " (cutoff:3.500A) removed outlier: 5.089A pdb=" N ARG D 68 " --> pdb=" O THR D 79 " (cutoff:3.500A) removed outlier: 7.252A pdb=" N ILE D 67 " --> pdb=" O THR E 124 " (cutoff:3.500A) removed outlier: 6.656A pdb=" N THR E 124 " --> pdb=" O ILE D 67 " (cutoff:3.500A) removed outlier: 6.888A pdb=" N SER D 69 " --> pdb=" O LEU E 122 " (cutoff:3.500A) removed outlier: 4.849A pdb=" N LEU E 122 " --> pdb=" O SER D 69 " (cutoff:3.500A) removed outlier: 6.777A pdb=" N SER D 71 " --> pdb=" O ARG E 120 " (cutoff:3.500A) removed outlier: 5.496A pdb=" N ARG E 120 " --> pdb=" O ILE E 131 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'F' and resid 24 through 26 Processing sheet with id=AA8, first strand: chain 'F' and resid 104 through 106 removed outlier: 3.558A pdb=" N ASN F 104 " --> pdb=" O ILE F 118 " (cutoff:3.500A) removed outlier: 4.226A pdb=" N THR F 174 " --> pdb=" O LEU F 119 " (cutoff:3.500A) removed outlier: 7.225A pdb=" N GLU F 175 " --> pdb=" O VAL F 164 " (cutoff:3.500A) removed outlier: 3.617A pdb=" N VAL F 164 " --> pdb=" O GLU F 175 " (cutoff:3.500A) removed outlier: 3.713A pdb=" N TRP F 162 " --> pdb=" O LYS F 177 " (cutoff:3.500A) removed outlier: 3.576A pdb=" N LYS F 179 " --> pdb=" O ASP F 160 " (cutoff:3.500A) removed outlier: 7.162A pdb=" N ASP F 158 " --> pdb=" O ASN F 181 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'G' and resid 34 through 36 removed outlier: 3.645A pdb=" N THR H 21 " --> pdb=" O GLU G 35 " (cutoff:3.500A) removed outlier: 3.516A pdb=" N TYR H 16 " --> pdb=" O ILE H 7 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'G' and resid 198 through 201 removed outlier: 3.691A pdb=" N TYR G 209 " --> pdb=" O ILE G 268 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'H' and resid 88 through 94 removed outlier: 5.389A pdb=" N GLY H 90 " --> pdb=" O ALA H 102 " (cutoff:3.500A) removed outlier: 3.901A pdb=" N ALA H 102 " --> pdb=" O GLY H 90 " (cutoff:3.500A) removed outlier: 7.253A pdb=" N ILE H 100 " --> pdb=" O VAL H 92 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'I' and resid 562 through 565 Processing sheet with id=AB4, first strand: chain 'I' and resid 593 through 594 removed outlier: 4.009A pdb=" N VAL I 593 " --> pdb=" O ILE I 609 " (cutoff:3.500A) removed outlier: 3.881A pdb=" N ILE I 609 " --> pdb=" O VAL I 593 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB4 Processing sheet with id=AB5, first strand: chain 'I' and resid 674 through 675 removed outlier: 3.542A pdb=" N GLU I 728 " --> pdb=" O VAL I 689 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'I' and resid 722 through 723 Processing sheet with id=AB7, first strand: chain 'I' and resid 769 through 777 Processing sheet with id=AB8, first strand: chain 'I' and resid 819 through 820 removed outlier: 3.609A pdb=" N TYR I 819 " --> pdb=" O SER I 802 " (cutoff:3.500A) removed outlier: 5.858A pdb=" N LEU I 799 " --> pdb=" O ASN I 860 " (cutoff:3.500A) removed outlier: 6.471A pdb=" N ASN I 860 " --> pdb=" O LEU I 799 " (cutoff:3.500A) removed outlier: 3.845A pdb=" N SER I 801 " --> pdb=" O ARG I 858 " (cutoff:3.500A) removed outlier: 3.561A pdb=" N ASN I 854 " --> pdb=" O SER I 805 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'I' and resid 988 through 992 removed outlier: 3.699A pdb=" N ASP I1031 " --> pdb=" O GLN I 992 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'I' and resid 1014 through 1016 removed outlier: 6.812A pdb=" N THR I1014 " --> pdb=" O GLU I1062 " (cutoff:3.500A) removed outlier: 3.901A pdb=" N GLU I1062 " --> pdb=" O THR I1014 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'J' and resid 772 through 773 removed outlier: 4.636A pdb=" N ASP J 751 " --> pdb=" O VAL J 773 " (cutoff:3.500A) removed outlier: 5.569A pdb=" N SER J 755 " --> pdb=" O SER J 804 " (cutoff:3.500A) removed outlier: 4.746A pdb=" N SER J 804 " --> pdb=" O SER J 755 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'J' and resid 860 through 861 Processing sheet with id=AC4, first strand: chain 'J' and resid 929 through 930 removed outlier: 6.805A pdb=" N ARG J 930 " --> pdb=" O MET J 970 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'J' and resid 1000 through 1004 removed outlier: 3.862A pdb=" N LEU J1042 " --> pdb=" O ILE J1076 " (cutoff:3.500A) removed outlier: 3.779A pdb=" N PHE J1044 " --> pdb=" O SER J1074 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'J' and resid 1134 through 1135 Processing sheet with id=AC7, first strand: chain 'J' and resid 1171 through 1177 removed outlier: 3.751A pdb=" N GLN J1174 " --> pdb=" O ILE J1193 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'J' and resid 1181 through 1182 removed outlier: 3.702A pdb=" N TYR J1261 " --> pdb=" O LEU J1286 " (cutoff:3.500A) removed outlier: 3.566A pdb=" N GLU J1262 " --> pdb=" O PHE J1216 " (cutoff:3.500A) removed outlier: 3.663A pdb=" N PHE J1216 " --> pdb=" O GLU J1262 " (cutoff:3.500A) removed outlier: 3.724A pdb=" N SER J1264 " --> pdb=" O VAL J1214 " (cutoff:3.500A) removed outlier: 3.680A pdb=" N VAL J1214 " --> pdb=" O SER J1264 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'K' and resid 215 through 223 removed outlier: 3.732A pdb=" N LYS K 223 " --> pdb=" O CYS K 227 " (cutoff:3.500A) removed outlier: 4.112A pdb=" N CYS K 227 " --> pdb=" O LYS K 223 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'K' and resid 284 through 285 removed outlier: 3.872A pdb=" N VAL K 285 " --> pdb=" O LYS K 258 " (cutoff:3.500A) removed outlier: 3.805A pdb=" N LYS K 258 " --> pdb=" O VAL K 285 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'K' and resid 306 through 311 Processing sheet with id=AD3, first strand: chain 'K' and resid 403 through 404 removed outlier: 3.644A pdb=" N PHE K 427 " --> pdb=" O PHE K 524 " (cutoff:3.500A) removed outlier: 3.510A pdb=" N PHE K 524 " --> pdb=" O PHE K 427 " (cutoff:3.500A) removed outlier: 3.541A pdb=" N ALA K 520 " --> pdb=" O LEU K 431 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'K' and resid 419 through 421 removed outlier: 6.114A pdb=" N LYS K 420 " --> pdb=" O VAL K 557 " (cutoff:3.500A) removed outlier: 3.736A pdb=" N SER K 556 " --> pdb=" O TYR K 532 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'K' and resid 507 through 508 removed outlier: 3.836A pdb=" N GLU K 547 " --> pdb=" O ASP K 542 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'L' and resid 17 through 21 removed outlier: 4.563A pdb=" N ILE L 86 " --> pdb=" O MET L 77 " (cutoff:3.500A) removed outlier: 3.588A pdb=" N MET L 77 " --> pdb=" O ILE L 86 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'L' and resid 72 through 74 Processing sheet with id=AD8, first strand: chain 'M' and resid 177 through 179 removed outlier: 3.721A pdb=" N THR M 183 " --> pdb=" O ASN M 179 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'M' and resid 187 through 188 removed outlier: 3.571A pdb=" N SER M 259 " --> pdb=" O CYS M 238 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'N' and resid 104 through 106 removed outlier: 3.678A pdb=" N LEU N 117 " --> pdb=" O ILE N 176 " (cutoff:3.500A) removed outlier: 3.695A pdb=" N ILE N 176 " --> pdb=" O LEU N 117 " (cutoff:3.500A) removed outlier: 6.485A pdb=" N GLU N 175 " --> pdb=" O VAL N 164 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'O' and resid 3 through 9 removed outlier: 3.955A pdb=" N SER O 5 " --> pdb=" O LEU O 91 " (cutoff:3.500A) removed outlier: 5.195A pdb=" N ARG O 68 " --> pdb=" O THR O 79 " (cutoff:3.500A) removed outlier: 8.040A pdb=" N GLU P 4 " --> pdb=" O ASN P 20 " (cutoff:3.500A) removed outlier: 4.858A pdb=" N ASN P 20 " --> pdb=" O GLU P 4 " (cutoff:3.500A) removed outlier: 6.968A pdb=" N ILE P 6 " --> pdb=" O GLN P 18 " (cutoff:3.500A) removed outlier: 4.451A pdb=" N GLN P 18 " --> pdb=" O ILE P 6 " (cutoff:3.500A) removed outlier: 6.604A pdb=" N VAL P 8 " --> pdb=" O ILE P 16 " (cutoff:3.500A) removed outlier: 4.176A pdb=" N GLY P 14 " --> pdb=" O ASN P 10 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'Q' and resid 24 through 25 Processing sheet with id=AE4, first strand: chain 'Q' and resid 161 through 165 removed outlier: 6.987A pdb=" N GLU Q 175 " --> pdb=" O VAL Q 164 " (cutoff:3.500A) Processing sheet with id=AE5, first strand: chain 'R' and resid 209 through 213 Processing sheet with id=AE6, first strand: chain 'S' and resid 14 through 20 removed outlier: 3.529A pdb=" N ILE S 8 " --> pdb=" O LYS S 110 " (cutoff:3.500A) removed outlier: 4.429A pdb=" N MET S 113 " --> pdb=" O THR S 101 " (cutoff:3.500A) removed outlier: 4.123A pdb=" N THR S 101 " --> pdb=" O MET S 113 " (cutoff:3.500A) removed outlier: 3.767A pdb=" N ASP S 93 " --> pdb=" O ILE S 100 " (cutoff:3.500A) removed outlier: 6.449A pdb=" N ALA S 102 " --> pdb=" O LYS S 91 " (cutoff:3.500A) removed outlier: 5.942A pdb=" N LYS S 91 " --> pdb=" O ALA S 102 " (cutoff:3.500A) removed outlier: 8.557A pdb=" N ILE S 104 " --> pdb=" O LEU S 89 " (cutoff:3.500A) removed outlier: 7.049A pdb=" N LEU S 89 " --> pdb=" O ILE S 104 " (cutoff:3.500A) Processing sheet with id=AE7, first strand: chain 'T' and resid 563 through 565 removed outlier: 3.805A pdb=" N MET T 580 " --> pdb=" O SER T 621 " (cutoff:3.500A) removed outlier: 3.760A pdb=" N LEU T 582 " --> pdb=" O GLU T 619 " (cutoff:3.500A) Processing sheet with id=AE8, first strand: chain 'T' and resid 674 through 677 Processing sheet with id=AE9, first strand: chain 'T' and resid 742 through 745 Processing sheet with id=AF1, first strand: chain 'T' and resid 769 through 772 removed outlier: 3.714A pdb=" N ILE T 781 " --> pdb=" O LYS T 778 " (cutoff:3.500A) Processing sheet with id=AF2, first strand: chain 'T' and resid 769 through 772 removed outlier: 4.012A pdb=" N PHE T 782 " --> pdb=" O ILE T 841 " (cutoff:3.500A) Processing sheet with id=AF3, first strand: chain 'T' and resid 819 through 820 removed outlier: 4.943A pdb=" N LEU T 799 " --> pdb=" O ASN T 860 " (cutoff:3.500A) removed outlier: 7.209A pdb=" N ASN T 860 " --> pdb=" O LEU T 799 " (cutoff:3.500A) removed outlier: 4.425A pdb=" N SER T 801 " --> pdb=" O ARG T 858 " (cutoff:3.500A) removed outlier: 4.303A pdb=" N ASN T 854 " --> pdb=" O SER T 805 " (cutoff:3.500A) Processing sheet with id=AF4, first strand: chain 'T' and resid 983 through 984 removed outlier: 8.265A pdb=" N GLU T 983 " --> pdb=" O VAL T1078 " (cutoff:3.500A) No H-bonds generated for sheet with id=AF4 Processing sheet with id=AF5, first strand: chain 'T' and resid 987 through 992 Processing sheet with id=AF6, first strand: chain 'U' and resid 753 through 757 removed outlier: 3.659A pdb=" N SER U 804 " --> pdb=" O ILE U 754 " (cutoff:3.500A) removed outlier: 4.963A pdb=" N GLU U 756 " --> pdb=" O LYS U 802 " (cutoff:3.500A) removed outlier: 7.394A pdb=" N LYS U 802 " --> pdb=" O GLU U 756 " (cutoff:3.500A) Processing sheet with id=AF7, first strand: chain 'U' and resid 860 through 861 removed outlier: 3.569A pdb=" N ASN U 861 " --> pdb=" O THR U 990 " (cutoff:3.500A) No H-bonds generated for sheet with id=AF7 Processing sheet with id=AF8, first strand: chain 'U' and resid 967 through 970 Processing sheet with id=AF9, first strand: chain 'U' and resid 995 through 996 Processing sheet with id=AG1, first strand: chain 'U' and resid 995 through 996 Processing sheet with id=AG2, first strand: chain 'U' and resid 1055 through 1057 removed outlier: 3.635A pdb=" N ASN U1134 " --> pdb=" O ASN U1055 " (cutoff:3.500A) Processing sheet with id=AG3, first strand: chain 'U' and resid 1172 through 1177 Processing sheet with id=AG4, first strand: chain 'U' and resid 1181 through 1182 removed outlier: 3.502A pdb=" N VAL U1182 " --> pdb=" O SER U1287 " (cutoff:3.500A) Processing sheet with id=AG5, first strand: chain 'U' and resid 1208 through 1209 Processing sheet with id=AG6, first strand: chain 'U' and resid 1231 through 1232 Processing sheet with id=AG7, first strand: chain 'V' and resid 217 through 221 Processing sheet with id=AG8, first strand: chain 'V' and resid 283 through 284 Processing sheet with id=AG9, first strand: chain 'V' and resid 267 through 268 removed outlier: 4.318A pdb=" N LYS V 306 " --> pdb=" O LEU V 268 " (cutoff:3.500A) Processing sheet with id=AH1, first strand: chain 'V' and resid 310 through 311 Processing sheet with id=AH2, first strand: chain 'V' and resid 411 through 414 Processing sheet with id=AH3, first strand: chain 'V' and resid 420 through 421 removed outlier: 5.909A pdb=" N LYS V 420 " --> pdb=" O VAL V 557 " (cutoff:3.500A) No H-bonds generated for sheet with id=AH3 Processing sheet with id=AH4, first strand: chain 'V' and resid 444 through 446 1716 hydrogen bonds defined for protein. 4893 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: 18.24 Time building geometry restraints manager: 19.15 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.34: 13811 1.34 - 1.46: 10447 1.46 - 1.58: 22479 1.58 - 1.71: 2 1.71 - 1.83: 274 Bond restraints: 47013 Sorted by residual: bond pdb=" C GLY J 769 " pdb=" N PRO J 770 " ideal model delta sigma weight residual 1.334 1.377 -0.043 8.40e-03 1.42e+04 2.67e+01 bond pdb=" N PHE R 215 " pdb=" CA PHE R 215 " ideal model delta sigma weight residual 1.463 1.421 0.041 9.30e-03 1.16e+04 1.97e+01 bond pdb=" N ILE E 67 " pdb=" CA ILE E 67 " ideal model delta sigma weight residual 1.457 1.497 -0.040 9.00e-03 1.23e+04 1.93e+01 bond pdb=" N GLY T 372 " pdb=" CA GLY T 372 " ideal model delta sigma weight residual 1.443 1.475 -0.032 8.60e-03 1.35e+04 1.36e+01 bond pdb=" CA ARG F 169 " pdb=" C ARG F 169 " ideal model delta sigma weight residual 1.523 1.580 -0.056 1.56e-02 4.11e+03 1.30e+01 ... (remaining 47008 not shown) Histogram of bond angle deviations from ideal: 86.99 - 97.77: 12 97.77 - 108.55: 2769 108.55 - 119.33: 36343 119.33 - 130.11: 24645 130.11 - 140.89: 226 Bond angle restraints: 63995 Sorted by residual: angle pdb=" N PRO T 346 " pdb=" CA PRO T 346 " pdb=" CB PRO T 346 " ideal model delta sigma weight residual 102.28 110.17 -7.89 7.50e-01 1.78e+00 1.11e+02 angle pdb=" N VAL F 155 " pdb=" CA VAL F 155 " pdb=" C VAL F 155 " ideal model delta sigma weight residual 112.17 103.14 9.03 9.50e-01 1.11e+00 9.03e+01 angle pdb=" N PRO T 976 " pdb=" CA PRO T 976 " pdb=" CB PRO T 976 " ideal model delta sigma weight residual 103.25 112.84 -9.59 1.05e+00 9.07e-01 8.34e+01 angle pdb=" N PRO T1076 " pdb=" CA PRO T1076 " pdb=" CB PRO T1076 " ideal model delta sigma weight residual 103.25 112.03 -8.78 1.05e+00 9.07e-01 6.99e+01 angle pdb=" N PRO I 639 " pdb=" CA PRO I 639 " pdb=" CB PRO I 639 " ideal model delta sigma weight residual 103.25 111.99 -8.74 1.05e+00 9.07e-01 6.93e+01 ... (remaining 63990 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 18.12: 25571 18.12 - 36.24: 2236 36.24 - 54.36: 321 54.36 - 72.48: 87 72.48 - 90.60: 27 Dihedral angle restraints: 28242 sinusoidal: 8852 harmonic: 19390 Sorted by residual: dihedral pdb=" CA ILE R 41 " pdb=" C ILE R 41 " pdb=" N PRO R 42 " pdb=" CA PRO R 42 " ideal model delta harmonic sigma weight residual 0.00 -34.96 34.96 0 5.00e+00 4.00e-02 4.89e+01 dihedral pdb=" CA SER L 132 " pdb=" C SER L 132 " pdb=" N ILE L 133 " pdb=" CA ILE L 133 " ideal model delta harmonic sigma weight residual 180.00 150.13 29.87 0 5.00e+00 4.00e-02 3.57e+01 dihedral pdb=" CA ARG T1051 " pdb=" C ARG T1051 " pdb=" N CYS T1052 " pdb=" CA CYS T1052 " ideal model delta harmonic sigma weight residual -180.00 -150.28 -29.72 0 5.00e+00 4.00e-02 3.53e+01 ... (remaining 28239 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.121: 6817 0.121 - 0.241: 702 0.241 - 0.362: 88 0.362 - 0.482: 18 0.482 - 0.603: 5 Chirality restraints: 7630 Sorted by residual: chirality pdb=" CB VAL Q 155 " pdb=" CA VAL Q 155 " pdb=" CG1 VAL Q 155 " pdb=" CG2 VAL Q 155 " both_signs ideal model delta sigma weight residual False -2.63 -2.03 -0.60 2.00e-01 2.50e+01 9.08e+00 chirality pdb=" CB ILE P 172 " pdb=" CA ILE P 172 " pdb=" CG1 ILE P 172 " pdb=" CG2 ILE P 172 " both_signs ideal model delta sigma weight residual False 2.64 2.11 0.54 2.00e-01 2.50e+01 7.28e+00 chirality pdb=" CB ILE P 70 " pdb=" CA ILE P 70 " pdb=" CG1 ILE P 70 " pdb=" CG2 ILE P 70 " both_signs ideal model delta sigma weight residual False 2.64 2.11 0.54 2.00e-01 2.50e+01 7.26e+00 ... (remaining 7627 not shown) Planarity restraints: 8350 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ILE P 67 " -0.077 5.00e-02 4.00e+02 1.17e-01 2.20e+01 pdb=" N PRO P 68 " 0.203 5.00e-02 4.00e+02 pdb=" CA PRO P 68 " -0.065 5.00e-02 4.00e+02 pdb=" CD PRO P 68 " -0.061 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA ASN U 660 " 0.022 2.00e-02 2.50e+03 4.40e-02 1.94e+01 pdb=" C ASN U 660 " -0.076 2.00e-02 2.50e+03 pdb=" O ASN U 660 " 0.029 2.00e-02 2.50e+03 pdb=" N ARG U 661 " 0.025 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C GLU B 212 " 0.069 5.00e-02 4.00e+02 1.03e-01 1.71e+01 pdb=" N PRO B 213 " -0.179 5.00e-02 4.00e+02 pdb=" CA PRO B 213 " 0.053 5.00e-02 4.00e+02 pdb=" CD PRO B 213 " 0.057 5.00e-02 4.00e+02 ... (remaining 8347 not shown) Histogram of nonbonded interaction distances: 1.40 - 2.10: 13 2.10 - 2.80: 12452 2.80 - 3.50: 62436 3.50 - 4.20: 99446 4.20 - 4.90: 166627 Nonbonded interactions: 340974 Sorted by model distance: nonbonded pdb=" O ARG R 44 " pdb=" N TYR R 46 " model vdw 1.403 2.520 nonbonded pdb=" CZ3 TRP J 906 " pdb=" O ILE J1095 " model vdw 1.563 3.340 nonbonded pdb=" SD MET A 77 " pdb=" CD2 PHE A 109 " model vdw 1.622 3.700 nonbonded pdb=" CG2 ILE L 79 " pdb=" OE1 GLN L 81 " model vdw 1.675 3.460 nonbonded pdb=" ND2 ASN J 737 " pdb=" CA LEU J 785 " model vdw 1.714 3.550 ... (remaining 340969 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = chain 'A' selection = (chain 'L' and resid 3 through 146) } ncs_group { reference = (chain 'B' and ((resid 34 through 37 and (name N or name CA or name C or name O \ or name CB )) or resid 38 through 61 or (resid 62 and (name N or name CA or name \ C or name O or name CB )) or (resid 87 through 114 and (name N or name CA or na \ me C or name O or name CB )) or resid 115 through 263)) selection = chain 'M' } ncs_group { reference = (chain 'C' and resid 8 through 189) selection = chain 'F' selection = (chain 'N' and resid 8 through 189) selection = chain 'Q' } ncs_group { reference = chain 'D' selection = chain 'O' } ncs_group { reference = (chain 'E' and (resid 2 through 55 or (resid 65 and (name N or name CA or name C \ or name O or name CB )) or resid 66 through 219)) selection = chain 'P' } ncs_group { reference = (chain 'G' and ((resid 25 through 26 and (name N or name CA or name C or name O \ or name CB )) or resid 27 or (resid 28 through 39 and (name N or name CA or name \ C or name O or name CB )) or resid 40 through 282)) selection = chain 'R' } ncs_group { reference = (chain 'H' and (resid 2 through 58 or resid 85 through 173)) selection = chain 'S' } ncs_group { reference = (chain 'I' and (resid 250 through 484 or resid 492 through 1084)) selection = (chain 'T' and (resid 250 through 371 or resid 399 through 463 or (resid 464 thr \ ough 467 and (name N or name CA or name C or name O or name CB )) or resid 468 t \ hrough 1084)) } ncs_group { reference = (chain 'J' and (resid 266 through 632 or (resid 633 and (name N or name CA or na \ me C or name O or name CB )) or resid 634 through 979 or (resid 980 through 993 \ and (name N or name CA or name C or name O or name CB )) or resid 994 through 11 \ 37 or (resid 1138 through 1144 and (name N or name CA or name C or name O or nam \ e CB )) or resid 1145 or (resid 1146 through 1148 and (name N or name CA or name \ C or name O or name CB )) or resid 1149 through 1289)) selection = (chain 'U' and (resid 266 through 328 or resid 378 through 568 or resid 583 thro \ ugh 655 or (resid 656 and (name N or name CA or name C or name O or name CB )) o \ r resid 657 through 1289)) } ncs_group { reference = (chain 'K' and (resid 212 through 337 or (resid 401 through 406 and (name N or n \ ame CA or name C or name O or name CB )) or resid 407 or (resid 408 through 411 \ and (name N or name CA or name C or name O or name CB )) or resid 412 or (resid \ 413 and (name N or name CA or name C or name O or name CB )) or resid 414 or (re \ sid 415 through 419 and (name N or name CA or name C or name O or name CB )) or \ resid 420 through 421 or (resid 422 through 423 and (name N or name CA or name C \ or name O or name CB )) or resid 424 or (resid 425 through 426 and (name N or n \ ame CA or name C or name O or name CB )) or resid 427 or (resid 428 and (name N \ or name CA or name C or name O or name CB )) or resid 429 or (resid 430 through \ 433 and (name N or name CA or name C or name O or name CB )) or resid 434 throug \ h 437 or (resid 438 and (name N or name CA or name C or name O or name CB )) or \ resid 439 through 440 or (resid 441 through 442 and (name N or name CA or name C \ or name O or name CB )) or resid 443 through 559)) selection = chain 'V' } 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=0.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 5.550 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.040 Extract box with map and model: 24.900 Check model and map are aligned: 0.670 Set scattering table: 0.420 Process input model: 118.540 Find NCS groups from input model: 3.500 Set up NCS constraints: 0.240 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:2.610 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 156.480 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5335 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 : 0.008 0.094 47013 Z= 0.513 Angle : 1.467 23.714 63995 Z= 0.823 Chirality : 0.079 0.603 7630 Planarity : 0.008 0.117 8350 Dihedral : 14.816 90.603 15568 Min Nonbonded Distance : 1.403 Molprobity Statistics. All-atom Clashscore : 10.80 Ramachandran Plot: Outliers : 1.01 % Allowed : 12.44 % Favored : 86.56 % Rotamer: Outliers : 1.04 % Allowed : 1.63 % Favored : 97.33 % Cbeta Deviations : 0.11 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.47 % 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: -5.01 (0.08), residues: 6465 helix: -2.99 (0.08), residues: 2052 sheet: -2.65 (0.15), residues: 1099 loop : -3.88 (0.08), residues: 3314 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.060 0.003 TRP C 162 HIS 0.012 0.002 HIS S 172 PHE 0.058 0.004 PHE T 784 TYR 0.052 0.004 TYR V 447 ARG 0.025 0.002 ARG B 87 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 12930 Ramachandran restraints generated. 6465 Oldfield, 0 Emsley, 6465 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 12930 Ramachandran restraints generated. 6465 Oldfield, 0 Emsley, 6465 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 557 residues out of total 6105 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 41 poor density : 516 time to evaluate : 6.173 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash 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: B 139 ILE cc_start: 0.7938 (OUTLIER) cc_final: 0.7538 (tp) REVERT: B 157 MET cc_start: 0.6687 (mmp) cc_final: 0.6027 (tpp) REVERT: B 210 MET cc_start: 0.4619 (mmp) cc_final: 0.4295 (mmp) REVERT: J 482 SER cc_start: 0.7589 (OUTLIER) cc_final: 0.7271 (p) REVERT: J 1054 LEU cc_start: 0.8126 (mt) cc_final: 0.7850 (mp) REVERT: M 184 PHE cc_start: 0.3490 (OUTLIER) cc_final: 0.3088 (m-10) REVERT: N 132 MET cc_start: 0.7158 (mpp) cc_final: 0.6875 (mpp) REVERT: T 785 LYS cc_start: 0.8139 (ttpt) cc_final: 0.7821 (tptt) REVERT: U 661 ARG cc_start: 0.5908 (OUTLIER) cc_final: 0.4660 (tpp80) REVERT: U 732 THR cc_start: 0.8149 (OUTLIER) cc_final: 0.7712 (p) REVERT: U 1150 ASN cc_start: 0.8712 (m-40) cc_final: 0.8054 (p0) REVERT: V 503 LEU cc_start: 0.8729 (mt) cc_final: 0.8503 (mm) REVERT: V 538 LEU cc_start: 0.8486 (tp) cc_final: 0.7771 (tt) outliers start: 41 outliers final: 16 residues processed: 554 average time/residue: 0.6356 time to fit residues: 562.0161 Evaluate side-chains 314 residues out of total 6105 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 293 time to evaluate : 5.429 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 651 random chunks: chunk 549 optimal weight: 10.0000 chunk 493 optimal weight: 30.0000 chunk 273 optimal weight: 1.9990 chunk 168 optimal weight: 3.9990 chunk 332 optimal weight: 2.9990 chunk 263 optimal weight: 5.9990 chunk 510 optimal weight: 7.9990 chunk 197 optimal weight: 3.9990 chunk 310 optimal weight: 20.0000 chunk 379 optimal weight: 0.6980 chunk 591 optimal weight: 10.0000 overall best weight: 2.7388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 50 ASN ** B 103 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 40 GLN D 104 GLN ** D 135 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 142 ASN ** E 133 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 37 ASN ** H 42 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 129 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 135 GLN ** J1012 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 46 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 43 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 117 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 133 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 243 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** R 257 GLN ** S 129 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** U1006 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** U1174 GLN ** U1278 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5553 moved from start: 0.2701 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.070 47013 Z= 0.269 Angle : 0.737 12.533 63995 Z= 0.396 Chirality : 0.046 0.311 7630 Planarity : 0.005 0.072 8350 Dihedral : 6.443 37.885 6899 Min Nonbonded Distance : 2.029 Molprobity Statistics. All-atom Clashscore : 16.86 Ramachandran Plot: Outliers : 0.29 % Allowed : 9.96 % Favored : 89.74 % Rotamer: Outliers : 0.28 % Allowed : 7.56 % Favored : 92.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.47 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % 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: -3.85 (0.09), residues: 6465 helix: -1.27 (0.10), residues: 2128 sheet: -2.46 (0.15), residues: 1098 loop : -3.59 (0.09), residues: 3239 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.002 TRP U 584 HIS 0.006 0.001 HIS N 55 PHE 0.034 0.002 PHE Q 30 TYR 0.024 0.002 TYR U 648 ARG 0.008 0.001 ARG F 66 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 12930 Ramachandran restraints generated. 6465 Oldfield, 0 Emsley, 6465 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 12930 Ramachandran restraints generated. 6465 Oldfield, 0 Emsley, 6465 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 330 residues out of total 6105 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 319 time to evaluate : 5.988 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 157 MET cc_start: 0.7293 (mmp) cc_final: 0.6698 (tpt) REVERT: B 210 MET cc_start: 0.5157 (mmp) cc_final: 0.4836 (mmp) REVERT: E 1 MET cc_start: 0.2777 (mmp) cc_final: 0.1661 (mmm) REVERT: G 169 MET cc_start: 0.7395 (ptt) cc_final: 0.6529 (ptt) REVERT: J 1054 LEU cc_start: 0.8436 (mt) cc_final: 0.8150 (mp) REVERT: N 132 MET cc_start: 0.7230 (mpp) cc_final: 0.6992 (mpp) REVERT: S 146 MET cc_start: 0.5982 (mmp) cc_final: 0.5632 (mmp) REVERT: U 505 MET cc_start: 0.1318 (pmm) cc_final: -0.1132 (ptt) REVERT: U 1023 MET cc_start: 0.8745 (mmp) cc_final: 0.8282 (mmm) outliers start: 11 outliers final: 2 residues processed: 328 average time/residue: 0.6161 time to fit residues: 331.8050 Evaluate side-chains 246 residues out of total 6105 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 244 time to evaluate : 5.698 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 651 random chunks: chunk 328 optimal weight: 10.0000 chunk 183 optimal weight: 2.9990 chunk 492 optimal weight: 40.0000 chunk 402 optimal weight: 0.8980 chunk 163 optimal weight: 40.0000 chunk 592 optimal weight: 20.0000 chunk 639 optimal weight: 10.0000 chunk 527 optimal weight: 0.0170 chunk 587 optimal weight: 0.9980 chunk 201 optimal weight: 8.9990 chunk 475 optimal weight: 6.9990 overall best weight: 2.3822 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 103 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 129 GLN ** C 55 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 135 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 133 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 43 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 55 HIS H 42 HIS H 135 GLN J 510 GLN J 895 ASN J 899 GLN J1209 ASN ** M 46 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 50 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 43 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 117 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** O 142 ASN ** P 133 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 100 ASN R 93 ASN ** R 243 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** R 257 GLN S 42 HIS S 129 ASN ** U 772 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5620 moved from start: 0.3500 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.076 47013 Z= 0.224 Angle : 0.676 11.188 63995 Z= 0.358 Chirality : 0.046 0.419 7630 Planarity : 0.004 0.058 8350 Dihedral : 5.817 26.127 6899 Min Nonbonded Distance : 2.090 Molprobity Statistics. All-atom Clashscore : 16.14 Ramachandran Plot: Outliers : 0.25 % Allowed : 10.80 % Favored : 88.96 % Rotamer: Outliers : 0.13 % Allowed : 6.16 % Favored : 93.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.47 % 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: -3.29 (0.10), residues: 6465 helix: -0.45 (0.11), residues: 2143 sheet: -2.29 (0.15), residues: 1099 loop : -3.49 (0.10), residues: 3223 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.041 0.002 TRP J 584 HIS 0.008 0.001 HIS S 42 PHE 0.026 0.002 PHE U1121 TYR 0.020 0.002 TYR J 491 ARG 0.021 0.001 ARG U 555 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 12930 Ramachandran restraints generated. 6465 Oldfield, 0 Emsley, 6465 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 12930 Ramachandran restraints generated. 6465 Oldfield, 0 Emsley, 6465 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 299 residues out of total 6105 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 294 time to evaluate : 6.004 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: B 157 MET cc_start: 0.7240 (mmp) cc_final: 0.6704 (mmt) REVERT: B 210 MET cc_start: 0.5365 (mmp) cc_final: 0.5155 (mmp) REVERT: G 40 TYR cc_start: 0.7434 (p90) cc_final: 0.6966 (p90) REVERT: G 169 MET cc_start: 0.7641 (ptt) cc_final: 0.5346 (mtt) REVERT: J 894 MET cc_start: 0.7990 (mtm) cc_final: 0.7752 (mtt) REVERT: J 1054 LEU cc_start: 0.8320 (mt) cc_final: 0.8019 (mp) REVERT: J 1160 MET cc_start: 0.8907 (mmp) cc_final: 0.8421 (mmm) REVERT: N 132 MET cc_start: 0.7228 (mpp) cc_final: 0.6992 (mpp) REVERT: P 203 ARG cc_start: 0.5770 (pmt170) cc_final: 0.5516 (pmt170) REVERT: Q 13 MET cc_start: 0.7706 (tpp) cc_final: 0.6603 (ttt) REVERT: Q 135 MET cc_start: 0.6017 (mmp) cc_final: 0.5499 (mmm) REVERT: U 505 MET cc_start: 0.1860 (pmm) cc_final: -0.0501 (ptt) REVERT: U 593 GLN cc_start: 0.6100 (mt0) cc_final: 0.5032 (mt0) REVERT: U 1023 MET cc_start: 0.8874 (mmp) cc_final: 0.8433 (mmm) outliers start: 5 outliers final: 0 residues processed: 299 average time/residue: 0.6423 time to fit residues: 322.0371 Evaluate side-chains 229 residues out of total 6105 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 229 time to evaluate : 6.116 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 651 random chunks: chunk 585 optimal weight: 7.9990 chunk 445 optimal weight: 0.8980 chunk 307 optimal weight: 9.9990 chunk 65 optimal weight: 0.1980 chunk 282 optimal weight: 1.9990 chunk 397 optimal weight: 9.9990 chunk 594 optimal weight: 40.0000 chunk 629 optimal weight: 1.9990 chunk 310 optimal weight: 30.0000 chunk 563 optimal weight: 6.9990 chunk 169 optimal weight: 50.0000 overall best weight: 2.4186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 62 GLN ** B 103 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 167 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 135 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 133 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 43 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 854 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 749 GLN J 899 GLN ** J1012 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 46 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 50 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 43 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** N 62 ASN N 181 ASN O 117 ASN ** P 133 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 20 ASN Q 100 ASN Q 110 HIS ** R 243 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 129 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 628 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** U1204 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** U1205 ASN U1272 ASN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5690 moved from start: 0.4222 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.063 47013 Z= 0.226 Angle : 0.650 10.355 63995 Z= 0.346 Chirality : 0.045 0.198 7630 Planarity : 0.004 0.060 8350 Dihedral : 5.521 26.962 6899 Min Nonbonded Distance : 2.048 Molprobity Statistics. All-atom Clashscore : 17.22 Ramachandran Plot: Outliers : 0.28 % Allowed : 10.35 % Favored : 89.37 % Rotamer: Outliers : 0.10 % Allowed : 5.57 % Favored : 94.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.47 % 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: -2.92 (0.10), residues: 6465 helix: 0.06 (0.11), residues: 2117 sheet: -2.15 (0.15), residues: 1100 loop : -3.38 (0.10), residues: 3248 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.039 0.002 TRP J 584 HIS 0.022 0.001 HIS S 42 PHE 0.024 0.002 PHE V 414 TYR 0.018 0.002 TYR J 491 ARG 0.008 0.001 ARG P 203 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 12930 Ramachandran restraints generated. 6465 Oldfield, 0 Emsley, 6465 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 12930 Ramachandran restraints generated. 6465 Oldfield, 0 Emsley, 6465 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 285 residues out of total 6105 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 281 time to evaluate : 5.950 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: B 157 MET cc_start: 0.7103 (mmp) cc_final: 0.6628 (mmt) REVERT: B 210 MET cc_start: 0.5477 (mmp) cc_final: 0.5058 (mmp) REVERT: G 40 TYR cc_start: 0.7662 (p90) cc_final: 0.7166 (p90) REVERT: G 169 MET cc_start: 0.7741 (ptt) cc_final: 0.5704 (mtt) REVERT: H 130 MET cc_start: 0.2105 (tmm) cc_final: 0.1585 (ppp) REVERT: J 1054 LEU cc_start: 0.8279 (mt) cc_final: 0.8012 (mp) REVERT: J 1160 MET cc_start: 0.8776 (mmp) cc_final: 0.8381 (mmm) REVERT: N 132 MET cc_start: 0.7252 (mpp) cc_final: 0.7002 (mpp) REVERT: P 214 MET cc_start: 0.1184 (tpt) cc_final: 0.0924 (tpt) REVERT: Q 13 MET cc_start: 0.7913 (tpp) cc_final: 0.6869 (ttt) REVERT: S 113 MET cc_start: 0.1270 (tmm) cc_final: 0.0803 (tmm) REVERT: S 128 ASN cc_start: 0.7332 (t0) cc_final: 0.7117 (m-40) REVERT: U 538 MET cc_start: -0.4657 (ttt) cc_final: -0.5916 (mtp) REVERT: U 593 GLN cc_start: 0.5529 (mt0) cc_final: 0.4809 (mp10) REVERT: U 1023 MET cc_start: 0.9092 (mmp) cc_final: 0.8514 (mmm) REVERT: U 1160 MET cc_start: 0.8050 (ptt) cc_final: 0.7766 (ptt) outliers start: 4 outliers final: 2 residues processed: 284 average time/residue: 0.6026 time to fit residues: 290.6369 Evaluate side-chains 232 residues out of total 6105 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 230 time to evaluate : 5.649 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 651 random chunks: chunk 524 optimal weight: 30.0000 chunk 357 optimal weight: 9.9990 chunk 9 optimal weight: 7.9990 chunk 468 optimal weight: 7.9990 chunk 259 optimal weight: 2.9990 chunk 536 optimal weight: 1.9990 chunk 434 optimal weight: 10.0000 chunk 0 optimal weight: 30.0000 chunk 321 optimal weight: 0.6980 chunk 564 optimal weight: 1.9990 chunk 158 optimal weight: 0.0980 overall best weight: 1.5586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 103 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 167 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 41 HIS ** E 133 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 43 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 854 ASN ** J1012 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J1209 ASN L 31 ASN ** M 46 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 50 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** N 55 HIS O 14 ASN Q 100 ASN R 257 GLN S 129 ASN T 789 ASN U 495 ASN ** U1204 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5682 moved from start: 0.4483 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.057 47013 Z= 0.178 Angle : 0.620 11.198 63995 Z= 0.325 Chirality : 0.045 0.258 7630 Planarity : 0.004 0.057 8350 Dihedral : 5.284 27.120 6899 Min Nonbonded Distance : 2.062 Molprobity Statistics. All-atom Clashscore : 15.45 Ramachandran Plot: Outliers : 0.25 % Allowed : 10.47 % Favored : 89.28 % Rotamer: Outliers : 0.05 % Allowed : 3.46 % Favored : 96.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.47 % 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: -2.65 (0.10), residues: 6465 helix: 0.32 (0.12), residues: 2118 sheet: -2.00 (0.15), residues: 1121 loop : -3.25 (0.10), residues: 3226 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP J 584 HIS 0.012 0.001 HIS S 42 PHE 0.028 0.001 PHE C 127 TYR 0.020 0.001 TYR U 607 ARG 0.012 0.001 ARG A 118 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 12930 Ramachandran restraints generated. 6465 Oldfield, 0 Emsley, 6465 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 12930 Ramachandran restraints generated. 6465 Oldfield, 0 Emsley, 6465 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 287 residues out of total 6105 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 285 time to evaluate : 5.729 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: B 157 MET cc_start: 0.7086 (mmp) cc_final: 0.6612 (mmt) REVERT: B 210 MET cc_start: 0.5551 (mmp) cc_final: 0.5136 (mmp) REVERT: C 59 MET cc_start: 0.8610 (mtt) cc_final: 0.8367 (mtt) REVERT: G 40 TYR cc_start: 0.7613 (p90) cc_final: 0.7108 (p90) REVERT: G 169 MET cc_start: 0.7260 (ptt) cc_final: 0.5469 (mtt) REVERT: J 894 MET cc_start: 0.7751 (mtm) cc_final: 0.7245 (mtt) REVERT: J 1054 LEU cc_start: 0.8210 (mt) cc_final: 0.7934 (mp) REVERT: J 1160 MET cc_start: 0.8764 (mmp) cc_final: 0.8396 (mmm) REVERT: N 132 MET cc_start: 0.7401 (mpp) cc_final: 0.7136 (mpp) REVERT: P 214 MET cc_start: 0.1086 (tpt) cc_final: 0.0856 (tpt) REVERT: Q 13 MET cc_start: 0.7935 (tpp) cc_final: 0.6863 (ttt) REVERT: S 113 MET cc_start: 0.1775 (tmm) cc_final: 0.1386 (tmm) REVERT: S 128 ASN cc_start: 0.7357 (t0) cc_final: 0.7133 (m-40) REVERT: S 130 MET cc_start: 0.4490 (tpt) cc_final: 0.4081 (mmm) REVERT: U 505 MET cc_start: 0.1851 (pmm) cc_final: -0.0484 (ptt) REVERT: U 538 MET cc_start: -0.4825 (ttt) cc_final: -0.5818 (mtp) REVERT: U 1023 MET cc_start: 0.9116 (mmp) cc_final: 0.8490 (mmm) outliers start: 2 outliers final: 1 residues processed: 286 average time/residue: 0.5841 time to fit residues: 284.3996 Evaluate side-chains 230 residues out of total 6105 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 229 time to evaluate : 5.656 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 651 random chunks: chunk 211 optimal weight: 40.0000 chunk 566 optimal weight: 9.9990 chunk 124 optimal weight: 8.9990 chunk 369 optimal weight: 9.9990 chunk 155 optimal weight: 40.0000 chunk 629 optimal weight: 2.9990 chunk 522 optimal weight: 20.0000 chunk 291 optimal weight: 0.6980 chunk 52 optimal weight: 2.9990 chunk 208 optimal weight: 20.0000 chunk 330 optimal weight: 0.7980 overall best weight: 3.2986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 103 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 167 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 53 ASN ** D 104 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 23 ASN ** E 133 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 43 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 184 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 172 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** J1012 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J1209 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 409 ASN K 544 ASN ** L 41 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** O 104 GLN O 130 ASN Q 20 ASN Q 100 ASN ** R 243 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** S 129 ASN U 495 ASN U 899 GLN ** U1278 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5833 moved from start: 0.5484 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.063 47013 Z= 0.272 Angle : 0.705 11.204 63995 Z= 0.375 Chirality : 0.046 0.224 7630 Planarity : 0.004 0.059 8350 Dihedral : 5.549 31.342 6899 Min Nonbonded Distance : 2.012 Molprobity Statistics. All-atom Clashscore : 22.84 Ramachandran Plot: Outliers : 0.26 % Allowed : 11.88 % Favored : 87.86 % Rotamer: Outliers : 0.05 % Allowed : 4.33 % Favored : 95.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.47 % 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: -2.73 (0.10), residues: 6465 helix: 0.25 (0.11), residues: 2141 sheet: -2.06 (0.15), residues: 1140 loop : -3.31 (0.10), residues: 3184 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.002 TRP J 649 HIS 0.019 0.002 HIS S 42 PHE 0.025 0.002 PHE G 83 TYR 0.024 0.002 TYR J 514 ARG 0.022 0.001 ARG F 66 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 12930 Ramachandran restraints generated. 6465 Oldfield, 0 Emsley, 6465 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 12930 Ramachandran restraints generated. 6465 Oldfield, 0 Emsley, 6465 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 262 residues out of total 6105 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 260 time to evaluate : 5.839 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: B 157 MET cc_start: 0.7123 (mmp) cc_final: 0.6681 (tpt) REVERT: C 59 MET cc_start: 0.8675 (mtt) cc_final: 0.8428 (mtt) REVERT: G 40 TYR cc_start: 0.7621 (p90) cc_final: 0.6988 (p90) REVERT: J 894 MET cc_start: 0.7737 (mtm) cc_final: 0.7483 (mtm) REVERT: J 1160 MET cc_start: 0.8855 (mmp) cc_final: 0.8445 (mmp) REVERT: N 84 VAL cc_start: 0.8579 (t) cc_final: 0.8304 (m) REVERT: N 132 MET cc_start: 0.7450 (mpp) cc_final: 0.7215 (mpp) REVERT: P 214 MET cc_start: 0.1348 (tpt) cc_final: 0.1119 (tpt) REVERT: Q 13 MET cc_start: 0.8042 (tpp) cc_final: 0.7168 (ttt) REVERT: Q 135 MET cc_start: 0.6201 (mmp) cc_final: 0.5579 (mmp) REVERT: S 130 MET cc_start: 0.4778 (tpt) cc_final: 0.3968 (mmm) REVERT: U 505 MET cc_start: 0.2041 (pmm) cc_final: 0.1510 (ptp) REVERT: U 538 MET cc_start: -0.4642 (ttt) cc_final: -0.5362 (ptt) REVERT: U 1023 MET cc_start: 0.9315 (mmp) cc_final: 0.8737 (mmm) outliers start: 2 outliers final: 1 residues processed: 261 average time/residue: 0.6111 time to fit residues: 269.9601 Evaluate side-chains 216 residues out of total 6105 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 215 time to evaluate : 5.799 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 651 random chunks: chunk 607 optimal weight: 0.7980 chunk 70 optimal weight: 0.9980 chunk 358 optimal weight: 7.9990 chunk 459 optimal weight: 7.9990 chunk 356 optimal weight: 6.9990 chunk 530 optimal weight: 50.0000 chunk 351 optimal weight: 4.9990 chunk 627 optimal weight: 0.1980 chunk 392 optimal weight: 20.0000 chunk 382 optimal weight: 0.4980 chunk 289 optimal weight: 0.0970 overall best weight: 0.5178 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 62 GLN ** B 103 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 167 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 133 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 43 GLN F 53 ASN G 30 GLN J 510 GLN ** J1012 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J1209 ASN ** M 46 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 100 ASN Q 107 ASN ** R 243 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** R 257 GLN S 129 ASN U 495 ASN U 603 ASN ** U1204 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5731 moved from start: 0.5416 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.057 47013 Z= 0.165 Angle : 0.623 11.478 63995 Z= 0.324 Chirality : 0.045 0.205 7630 Planarity : 0.004 0.049 8350 Dihedral : 5.143 30.300 6899 Min Nonbonded Distance : 2.063 Molprobity Statistics. All-atom Clashscore : 14.68 Ramachandran Plot: Outliers : 0.25 % Allowed : 9.22 % Favored : 90.53 % Rotamer: Outliers : 0.00 % Allowed : 2.04 % Favored : 97.96 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.47 % 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: -2.41 (0.10), residues: 6465 helix: 0.59 (0.12), residues: 2130 sheet: -1.93 (0.15), residues: 1145 loop : -3.15 (0.10), residues: 3190 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.044 0.001 TRP U1122 HIS 0.008 0.001 HIS V 490 PHE 0.025 0.001 PHE M 148 TYR 0.022 0.001 TYR J 491 ARG 0.008 0.000 ARG U1118 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 12930 Ramachandran restraints generated. 6465 Oldfield, 0 Emsley, 6465 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 12930 Ramachandran restraints generated. 6465 Oldfield, 0 Emsley, 6465 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 278 residues out of total 6105 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 278 time to evaluate : 6.261 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: B 157 MET cc_start: 0.6995 (mmp) cc_final: 0.6681 (mmt) REVERT: G 40 TYR cc_start: 0.7480 (p90) cc_final: 0.6935 (p90) REVERT: G 169 MET cc_start: 0.7016 (ptt) cc_final: 0.5402 (mtt) REVERT: J 484 MET cc_start: 0.4974 (tpt) cc_final: 0.4403 (mmm) REVERT: J 894 MET cc_start: 0.7612 (mtm) cc_final: 0.7107 (mtt) REVERT: J 1054 LEU cc_start: 0.7951 (mt) cc_final: 0.7719 (mp) REVERT: J 1160 MET cc_start: 0.8828 (mmp) cc_final: 0.8336 (mmm) REVERT: K 429 MET cc_start: 0.7844 (tpp) cc_final: 0.7163 (ttt) REVERT: N 84 VAL cc_start: 0.8461 (t) cc_final: 0.8171 (m) REVERT: N 132 MET cc_start: 0.7301 (mpp) cc_final: 0.7055 (mpp) REVERT: P 170 LEU cc_start: 0.8418 (tp) cc_final: 0.8098 (pp) REVERT: P 214 MET cc_start: 0.1722 (tpt) cc_final: 0.1509 (tpt) REVERT: Q 13 MET cc_start: 0.8020 (tpp) cc_final: 0.7104 (ttt) REVERT: Q 135 MET cc_start: 0.6220 (mmp) cc_final: 0.5792 (mmp) REVERT: S 130 MET cc_start: 0.5005 (tpt) cc_final: 0.4252 (mmm) REVERT: U 505 MET cc_start: 0.1602 (pmm) cc_final: 0.0985 (ptp) REVERT: U 538 MET cc_start: -0.4605 (ttt) cc_final: -0.5397 (ptt) REVERT: U 593 GLN cc_start: 0.5390 (mt0) cc_final: 0.4547 (mm110) REVERT: U 1018 TRP cc_start: 0.8344 (p90) cc_final: 0.8112 (p90) REVERT: U 1023 MET cc_start: 0.9290 (mmp) cc_final: 0.8656 (mmm) outliers start: 0 outliers final: 0 residues processed: 278 average time/residue: 0.5712 time to fit residues: 270.8965 Evaluate side-chains 228 residues out of total 6105 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 228 time to evaluate : 6.226 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 651 random chunks: chunk 388 optimal weight: 9.9990 chunk 250 optimal weight: 0.9990 chunk 374 optimal weight: 0.0870 chunk 189 optimal weight: 10.0000 chunk 123 optimal weight: 10.0000 chunk 121 optimal weight: 8.9990 chunk 398 optimal weight: 9.9990 chunk 427 optimal weight: 20.0000 chunk 310 optimal weight: 30.0000 chunk 58 optimal weight: 5.9990 chunk 493 optimal weight: 30.0000 overall best weight: 5.2166 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 103 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 167 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 104 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 133 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 184 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 257 GLN J 510 GLN J 736 GLN ** J1012 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J1046 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J1204 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J1272 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 41 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 243 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 129 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** U 495 ASN ** U1278 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5949 moved from start: 0.6549 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.143 47013 Z= 0.369 Angle : 0.806 16.429 63995 Z= 0.431 Chirality : 0.049 0.343 7630 Planarity : 0.005 0.098 8350 Dihedral : 5.943 33.993 6899 Min Nonbonded Distance : 2.002 Molprobity Statistics. All-atom Clashscore : 28.82 Ramachandran Plot: Outliers : 0.31 % Allowed : 13.32 % Favored : 86.37 % Rotamer: Outliers : 0.03 % Allowed : 1.83 % Favored : 98.14 % Cbeta Deviations : 0.02 % Peptide Plane: Cis-proline : 0.47 % 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: -2.85 (0.10), residues: 6465 helix: 0.09 (0.11), residues: 2182 sheet: -2.13 (0.15), residues: 1146 loop : -3.36 (0.10), residues: 3137 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.029 0.003 TRP J1122 HIS 0.009 0.002 HIS G 184 PHE 0.030 0.003 PHE J1149 TYR 0.035 0.003 TYR V 518 ARG 0.013 0.001 ARG I 793 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 12930 Ramachandran restraints generated. 6465 Oldfield, 0 Emsley, 6465 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 12930 Ramachandran restraints generated. 6465 Oldfield, 0 Emsley, 6465 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 241 residues out of total 6105 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 240 time to evaluate : 5.756 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: B 157 MET cc_start: 0.6966 (mmp) cc_final: 0.6653 (mmt) REVERT: G 40 TYR cc_start: 0.7529 (p90) cc_final: 0.7029 (p90) REVERT: J 894 MET cc_start: 0.7582 (mtm) cc_final: 0.6956 (mtt) REVERT: J 1160 MET cc_start: 0.8875 (mmp) cc_final: 0.8401 (mmp) REVERT: K 429 MET cc_start: 0.7964 (tpp) cc_final: 0.7333 (ttt) REVERT: N 79 ARG cc_start: 0.3933 (tmm-80) cc_final: 0.3488 (ptp90) REVERT: N 84 VAL cc_start: 0.8601 (t) cc_final: 0.8319 (m) REVERT: P 129 MET cc_start: 0.6087 (ppp) cc_final: 0.5685 (ppp) REVERT: P 170 LEU cc_start: 0.8475 (tp) cc_final: 0.8135 (pp) REVERT: P 214 MET cc_start: 0.2394 (tpt) cc_final: 0.0889 (ptm) REVERT: Q 13 MET cc_start: 0.8290 (tpp) cc_final: 0.7360 (ttt) REVERT: S 126 ASP cc_start: 0.4350 (m-30) cc_final: 0.3944 (t0) REVERT: S 130 MET cc_start: 0.5306 (tpt) cc_final: 0.4034 (tpp) REVERT: U 505 MET cc_start: 0.2584 (pmm) cc_final: 0.2109 (ptp) REVERT: U 538 MET cc_start: -0.4021 (ttt) cc_final: -0.5012 (ptt) REVERT: U 1023 MET cc_start: 0.9443 (mmp) cc_final: 0.8875 (mmm) REVERT: U 1117 MET cc_start: 0.8626 (ppp) cc_final: 0.8421 (ppp) outliers start: 1 outliers final: 0 residues processed: 241 average time/residue: 0.5913 time to fit residues: 246.2785 Evaluate side-chains 202 residues out of total 6105 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 202 time to evaluate : 6.132 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 651 random chunks: chunk 570 optimal weight: 5.9990 chunk 601 optimal weight: 0.9990 chunk 548 optimal weight: 8.9990 chunk 584 optimal weight: 30.0000 chunk 600 optimal weight: 4.9990 chunk 351 optimal weight: 30.0000 chunk 254 optimal weight: 5.9990 chunk 459 optimal weight: 10.0000 chunk 179 optimal weight: 40.0000 chunk 528 optimal weight: 20.0000 chunk 553 optimal weight: 0.0670 overall best weight: 3.6126 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 103 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 167 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 104 GLN ** D 135 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 41 HIS ** E 133 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 26 ASN ** G 184 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** J1012 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J1046 ASN ** J1204 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J1272 ASN ** L 41 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 243 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** R 257 GLN ** S 129 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** U 495 ASN ** U 593 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** U1204 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** U1278 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5921 moved from start: 0.6782 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.058 47013 Z= 0.256 Angle : 0.699 11.447 63995 Z= 0.368 Chirality : 0.046 0.242 7630 Planarity : 0.004 0.063 8350 Dihedral : 5.725 35.466 6899 Min Nonbonded Distance : 2.003 Molprobity Statistics. All-atom Clashscore : 22.36 Ramachandran Plot: Outliers : 0.26 % Allowed : 11.08 % Favored : 88.66 % Rotamer: Outliers : 0.05 % Allowed : 0.92 % Favored : 99.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.47 % 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: -2.68 (0.10), residues: 6465 helix: 0.26 (0.11), residues: 2174 sheet: -2.09 (0.15), residues: 1145 loop : -3.27 (0.10), residues: 3146 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.027 0.002 TRP J 649 HIS 0.008 0.002 HIS G 184 PHE 0.024 0.002 PHE R 66 TYR 0.025 0.002 TYR V 518 ARG 0.019 0.001 ARG K 523 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 12930 Ramachandran restraints generated. 6465 Oldfield, 0 Emsley, 6465 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 12930 Ramachandran restraints generated. 6465 Oldfield, 0 Emsley, 6465 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 238 residues out of total 6105 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 236 time to evaluate : 5.547 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: B 157 MET cc_start: 0.6801 (mmp) cc_final: 0.6578 (mmt) REVERT: J 484 MET cc_start: 0.5851 (tpt) cc_final: 0.4988 (mmm) REVERT: J 1160 MET cc_start: 0.8804 (mmp) cc_final: 0.8344 (mmp) REVERT: K 429 MET cc_start: 0.7977 (tpp) cc_final: 0.7437 (ttt) REVERT: N 79 ARG cc_start: 0.3833 (tmm-80) cc_final: 0.3433 (ptp-170) REVERT: N 84 VAL cc_start: 0.8681 (t) cc_final: 0.8385 (m) REVERT: N 132 MET cc_start: 0.7454 (mpp) cc_final: 0.7247 (mpp) REVERT: P 129 MET cc_start: 0.6279 (ppp) cc_final: 0.5989 (ppp) REVERT: P 170 LEU cc_start: 0.8439 (tp) cc_final: 0.8156 (pp) REVERT: Q 13 MET cc_start: 0.8017 (tpp) cc_final: 0.7451 (ttt) REVERT: U 505 MET cc_start: 0.2976 (pmm) cc_final: 0.2531 (ptp) REVERT: U 538 MET cc_start: -0.4022 (ttt) cc_final: -0.5003 (ptt) REVERT: U 1023 MET cc_start: 0.9447 (mmp) cc_final: 0.8931 (mmm) REVERT: U 1117 MET cc_start: 0.8709 (ppp) cc_final: 0.8463 (ppp) outliers start: 2 outliers final: 0 residues processed: 238 average time/residue: 0.5535 time to fit residues: 226.8272 Evaluate side-chains 202 residues out of total 6105 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 202 time to evaluate : 5.437 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 651 random chunks: chunk 582 optimal weight: 7.9990 chunk 383 optimal weight: 0.5980 chunk 618 optimal weight: 9.9990 chunk 377 optimal weight: 9.9990 chunk 293 optimal weight: 9.9990 chunk 429 optimal weight: 8.9990 chunk 648 optimal weight: 0.9990 chunk 596 optimal weight: 0.7980 chunk 516 optimal weight: 9.9990 chunk 53 optimal weight: 7.9990 chunk 398 optimal weight: 0.0970 overall best weight: 2.0982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 55 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 103 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 167 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 156 GLN D 104 GLN ** E 133 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 184 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 13 ASN ** J1012 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J1204 GLN ** L 41 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 40 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 53 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 243 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** R 257 GLN ** S 129 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** U 495 ASN U 593 GLN ** U1204 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** U1278 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5892 moved from start: 0.6914 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.073 47013 Z= 0.206 Angle : 0.664 13.422 63995 Z= 0.346 Chirality : 0.045 0.216 7630 Planarity : 0.004 0.098 8350 Dihedral : 5.459 30.772 6899 Min Nonbonded Distance : 2.012 Molprobity Statistics. All-atom Clashscore : 20.03 Ramachandran Plot: Outliers : 0.23 % Allowed : 11.93 % Favored : 87.84 % Rotamer: Outliers : 0.03 % Allowed : 0.41 % Favored : 99.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.47 % 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: -2.49 (0.10), residues: 6465 helix: 0.46 (0.12), residues: 2194 sheet: -1.92 (0.15), residues: 1137 loop : -3.24 (0.10), residues: 3134 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.026 0.002 TRP J 649 HIS 0.015 0.001 HIS S 42 PHE 0.024 0.002 PHE E 178 TYR 0.025 0.002 TYR L 46 ARG 0.006 0.001 ARG H 170 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 12930 Ramachandran restraints generated. 6465 Oldfield, 0 Emsley, 6465 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 12930 Ramachandran restraints generated. 6465 Oldfield, 0 Emsley, 6465 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 242 residues out of total 6105 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 241 time to evaluate : 5.823 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: A 55 HIS cc_start: 0.7340 (p-80) cc_final: 0.7115 (p-80) REVERT: H 109 MET cc_start: 0.6977 (mpp) cc_final: 0.6049 (mpp) REVERT: J 484 MET cc_start: 0.5781 (tpt) cc_final: 0.5064 (mmm) REVERT: K 429 MET cc_start: 0.8046 (tpp) cc_final: 0.7419 (ttt) REVERT: N 79 ARG cc_start: 0.3791 (tmm-80) cc_final: 0.3548 (ptp90) REVERT: N 84 VAL cc_start: 0.8806 (t) cc_final: 0.8495 (m) REVERT: P 129 MET cc_start: 0.6127 (ppp) cc_final: 0.5828 (ppp) REVERT: P 170 LEU cc_start: 0.8510 (tp) cc_final: 0.8205 (pp) REVERT: Q 13 MET cc_start: 0.8024 (tpp) cc_final: 0.7401 (ttt) REVERT: U 505 MET cc_start: 0.2985 (pmm) cc_final: 0.2558 (ptp) REVERT: U 538 MET cc_start: -0.4012 (ttt) cc_final: -0.5089 (ptt) REVERT: U 1023 MET cc_start: 0.9448 (mmp) cc_final: 0.8892 (mmm) outliers start: 1 outliers final: 0 residues processed: 242 average time/residue: 0.5907 time to fit residues: 244.5512 Evaluate side-chains 206 residues out of total 6105 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 206 time to evaluate : 5.651 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 651 random chunks: chunk 316 optimal weight: 7.9990 chunk 410 optimal weight: 10.0000 chunk 550 optimal weight: 6.9990 chunk 158 optimal weight: 10.0000 chunk 476 optimal weight: 2.9990 chunk 76 optimal weight: 6.9990 chunk 143 optimal weight: 10.0000 chunk 517 optimal weight: 0.9990 chunk 216 optimal weight: 50.0000 chunk 531 optimal weight: 6.9990 chunk 65 optimal weight: 8.9990 overall best weight: 4.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 55 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 103 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 167 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 104 GLN ** E 133 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 184 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 226 ASN ** G 257 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 13 ASN ** J 588 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J1012 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 41 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 40 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** O 130 ASN R 257 GLN U 495 ASN ** U1278 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** V 490 HIS Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3582 r_free = 0.3582 target = 0.055423 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.3217 r_free = 0.3217 target = 0.037874 restraints weight = 866898.056| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 24)----------------| | r_work = 0.3222 r_free = 0.3222 target = 0.038011 restraints weight = 757929.554| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 41)----------------| | r_work = 0.3228 r_free = 0.3228 target = 0.038255 restraints weight = 685280.019| |-----------------------------------------------------------------------------| r_work (final): 0.3081 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3123 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3123 r_free = 0.3123 target_work(ls_wunit_k1) = 0.037 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 195 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3123 r_free = 0.3123 target_work(ls_wunit_k1) = 0.037 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 201 | |-----------------------------------------------------------------------------| r_final: 0.3123 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6390 moved from start: 0.7653 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.115 47013 Z= 0.354 Angle : 0.789 12.136 63995 Z= 0.420 Chirality : 0.048 0.271 7630 Planarity : 0.005 0.093 8350 Dihedral : 6.037 34.231 6899 Min Nonbonded Distance : 1.980 Molprobity Statistics. All-atom Clashscore : 28.76 Ramachandran Plot: Outliers : 0.23 % Allowed : 14.00 % Favored : 85.77 % Rotamer: Outliers : 0.05 % Allowed : 0.89 % Favored : 99.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.47 % 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: -2.81 (0.10), residues: 6465 helix: 0.08 (0.11), residues: 2197 sheet: -2.06 (0.15), residues: 1110 loop : -3.35 (0.10), residues: 3158 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.034 0.003 TRP J1122 HIS 0.007 0.002 HIS B 102 PHE 0.057 0.002 PHE N 49 TYR 0.033 0.003 TYR J 771 ARG 0.015 0.001 ARG N 47 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 9628.04 seconds wall clock time: 176 minutes 31.46 seconds (10591.46 seconds total)