Starting phenix.real_space_refine on Sun Feb 18 22:53:10 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6zmt_11301/02_2024/6zmt_11301.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6zmt_11301/02_2024/6zmt_11301.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.0 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6zmt_11301/02_2024/6zmt_11301.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6zmt_11301/02_2024/6zmt_11301.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6zmt_11301/02_2024/6zmt_11301.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6zmt_11301/02_2024/6zmt_11301.pdb" } resolution = 3.0 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.001 sd= 0.010 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: 6 Type Number sf(0) Gaussians Zn 2 6.06 5 P 1569 5.49 5 S 197 5.16 5 C 41992 2.51 5 N 13965 2.21 5 O 18465 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "B GLU 69": "OE1" <-> "OE2" Residue "B PHE 90": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 192": "OE1" <-> "OE2" Residue "C GLU 89": "OE1" <-> "OE2" Residue "D GLU 90": "OE1" <-> "OE2" Residue "D GLU 146": "OE1" <-> "OE2" Residue "D GLU 258": "OE1" <-> "OE2" Residue "E PHE 99": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F GLU 20": "OE1" <-> "OE2" Residue "F GLU 61": "OE1" <-> "OE2" Residue "F GLU 103": "OE1" <-> "OE2" Residue "F ARG 116": "NH1" <-> "NH2" Residue "F ARG 143": "NH1" <-> "NH2" Residue "F GLU 216": "OE1" <-> "OE2" Residue "G GLU 43": "OE1" <-> "OE2" Residue "H GLU 42": "OE1" <-> "OE2" Residue "H GLU 52": "OE1" <-> "OE2" Residue "I GLU 89": "OE1" <-> "OE2" Residue "I GLU 132": "OE1" <-> "OE2" Residue "I GLU 151": "OE1" <-> "OE2" Residue "J GLU 73": "OE1" <-> "OE2" Residue "J PHE 147": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K GLU 123": "OE1" <-> "OE2" Residue "L GLU 31": "OE1" <-> "OE2" Residue "M TYR 70": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "N GLU 142": "OE1" <-> "OE2" Residue "O GLU 66": "OE1" <-> "OE2" Residue "O GLU 71": "OE1" <-> "OE2" Residue "O GLU 125": "OE1" <-> "OE2" Residue "Q GLU 71": "OE1" <-> "OE2" Residue "Q GLU 110": "OE1" <-> "OE2" Residue "S ARG 78": "NH1" <-> "NH2" Residue "S ARG 81": "NH1" <-> "NH2" Residue "S GLU 97": "OE1" <-> "OE2" Residue "U GLU 32": "OE1" <-> "OE2" Residue "V GLU 33": "OE1" <-> "OE2" Residue "Z GLU 64": "OE1" <-> "OE2" Residue "a GLU 75": "OE1" <-> "OE2" Residue "a GLU 90": "OE1" <-> "OE2" Residue "b GLU 13": "OE1" <-> "OE2" Residue "b TYR 31": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "b GLU 75": "OE1" <-> "OE2" Residue "e ARG 31": "NH1" <-> "NH2" Residue "g GLU 110": "OE1" <-> "OE2" Residue "g GLU 125": "OE1" <-> "OE2" Residue "j GLU 49": "OE1" <-> "OE2" Residue "j GLU 223": "OE1" <-> "OE2" Residue "i GLU 159": "OE1" <-> "OE2" Residue "u ARG 73": "NH1" <-> "NH2" Residue "u ARG 93": "NH1" <-> "NH2" Residue "u ARG 128": "NH1" <-> "NH2" Residue "u ARG 132": "NH1" <-> "NH2" Residue "u ARG 139": "NH1" <-> "NH2" Residue "u TYR 185": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "u ARG 204": "NH1" <-> "NH2" Residue "u ARG 214": "NH1" <-> "NH2" Residue "u ARG 249": "NH1" <-> "NH2" Residue "u GLU 264": "OE1" <-> "OE2" Residue "u GLU 265": "OE1" <-> "OE2" Residue "u ARG 287": "NH1" <-> "NH2" Residue "u GLU 465": "OE1" <-> "OE2" Residue "u GLU 473": "OE1" <-> "OE2" Residue "u ARG 492": "NH1" <-> "NH2" Residue "u ARG 499": "NH1" <-> "NH2" Residue "u ARG 537": "NH1" <-> "NH2" Residue "u ARG 599": "NH1" <-> "NH2" Residue "u GLU 613": "OE1" <-> "OE2" Residue "u ARG 624": "NH1" <-> "NH2" Residue "u ARG 642": "NH1" <-> "NH2" Residue "u ARG 720": "NH1" <-> "NH2" Residue "u ARG 732": "NH1" <-> "NH2" Residue "u ARG 737": "NH1" <-> "NH2" Residue "u GLU 743": "OE1" <-> "OE2" Time to flip residues: 0.10s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5238/modules/chem_data/mon_lib" Total number of atoms: 76190 Number of models: 1 Model: "" Number of chains: 37 Chain: "B" Number of atoms: 1624 Number of conformers: 1 Conformer: "" Number of residues, atoms: 206, 1624 Classifications: {'peptide': 206} Link IDs: {'PTRANS': 12, 'TRANS': 193} Chain: "C" Number of atoms: 1729 Number of conformers: 1 Conformer: "" Number of residues, atoms: 213, 1729 Classifications: {'peptide': 213} Link IDs: {'PTRANS': 5, 'TRANS': 207} Chain: "D" Number of atoms: 1682 Number of conformers: 1 Conformer: "" Number of residues, atoms: 218, 1682 Classifications: {'peptide': 218} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 12, 'TRANS': 205} Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 6 Planarities with less than four sites: {'GLU:plan': 2} Unresolved non-hydrogen planarities: 8 Chain: "E" Number of atoms: 2076 Number of conformers: 1 Conformer: "" Number of residues, atoms: 262, 2076 Classifications: {'peptide': 262} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 14, 'TRANS': 247} Chain: "F" Number of atoms: 1748 Number of conformers: 1 Conformer: "" Number of residues, atoms: 225, 1748 Classifications: {'peptide': 225} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 11, 'TRANS': 213} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 5 Unresolved non-hydrogen dihedrals: 3 Planarities with less than four sites: {'GLU:plan': 1} Unresolved non-hydrogen planarities: 4 Chain: "G" Number of atoms: 1862 Number of conformers: 1 Conformer: "" Number of residues, atoms: 230, 1862 Classifications: {'peptide': 230} Link IDs: {'PTRANS': 10, 'TRANS': 219} Chain: "H" Number of atoms: 1501 Number of conformers: 1 Conformer: "" Number of residues, atoms: 186, 1501 Classifications: {'peptide': 186} Link IDs: {'PTRANS': 9, 'TRANS': 176} Chain: "I" Number of atoms: 1682 Number of conformers: 1 Conformer: "" Number of residues, atoms: 205, 1682 Classifications: {'peptide': 205} Link IDs: {'PTRANS': 7, 'TRANS': 197} Chain: "J" Number of atoms: 1499 Number of conformers: 1 Conformer: "" Number of residues, atoms: 180, 1499 Classifications: {'peptide': 180} Link IDs: {'PTRANS': 6, 'TRANS': 173} Chain: "K" Number of atoms: 1495 Number of conformers: 1 Conformer: "" Number of residues, atoms: 189, 1495 Classifications: {'peptide': 189} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 5, 'TRANS': 183} Chain: "L" Number of atoms: 1229 Number of conformers: 1 Conformer: "" Number of residues, atoms: 151, 1229 Classifications: {'peptide': 151} Link IDs: {'PTRANS': 6, 'TRANS': 144} Chain: "M" Number of atoms: 800 Number of conformers: 1 Conformer: "" Number of residues, atoms: 95, 800 Classifications: {'peptide': 95} Link IDs: {'PTRANS': 7, 'TRANS': 87} Chain: "N" Number of atoms: 1202 Number of conformers: 1 Conformer: "" Number of residues, atoms: 149, 1202 Classifications: {'peptide': 149} Link IDs: {'PTRANS': 8, 'TRANS': 140} Chain: "O" Number of atoms: 953 Number of conformers: 1 Conformer: "" Number of residues, atoms: 123, 953 Classifications: {'peptide': 123} Link IDs: {'PTRANS': 2, 'TRANS': 120} Chain: "P" Number of atoms: 897 Number of conformers: 1 Conformer: "" Number of residues, atoms: 122, 897 Classifications: {'peptide': 122} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 6, 'TRANS': 115} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 5 Unresolved non-hydrogen dihedrals: 3 Planarities with less than four sites: {'GLU:plan': 1} Unresolved non-hydrogen planarities: 4 Chain: "Q" Number of atoms: 984 Number of conformers: 1 Conformer: "" Number of residues, atoms: 120, 984 Classifications: {'peptide': 120} Link IDs: {'PTRANS': 7, 'TRANS': 112} Chain: "R" Number of atoms: 1109 Number of conformers: 1 Conformer: "" Number of residues, atoms: 139, 1109 Classifications: {'peptide': 139} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 5, 'TRANS': 133} Chain: "S" Number of atoms: 1050 Number of conformers: 1 Conformer: "" Number of residues, atoms: 130, 1050 Classifications: {'peptide': 130} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 6, 'TRANS': 123} Chain breaks: 1 Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 3 Unresolved non-hydrogen dihedrals: 1 Unresolved non-hydrogen chiralities: 1 Chain: "T" Number of atoms: 1184 Number of conformers: 1 Conformer: "" Number of residues, atoms: 143, 1184 Classifications: {'peptide': 143} Link IDs: {'PTRANS': 3, 'TRANS': 139} Chain: "U" Number of atoms: 1122 Number of conformers: 1 Conformer: "" Number of residues, atoms: 144, 1122 Classifications: {'peptide': 144} Link IDs: {'PTRANS': 4, 'TRANS': 139} Chain: "V" Number of atoms: 803 Number of conformers: 1 Conformer: "" Number of residues, atoms: 101, 803 Classifications: {'peptide': 101} Link IDs: {'PTRANS': 5, 'TRANS': 95} Chain: "W" Number of atoms: 1034 Number of conformers: 1 Conformer: "" Number of residues, atoms: 129, 1034 Classifications: {'peptide': 129} Modifications used: {'COO': 1} Link IDs: {'PCIS': 2, 'PTRANS': 1, 'TRANS': 125} Chain: "X" Number of atoms: 1098 Number of conformers: 1 Conformer: "" Number of residues, atoms: 141, 1098 Classifications: {'peptide': 141} Link IDs: {'PTRANS': 5, 'TRANS': 135} Chain: "Y" Number of atoms: 1014 Number of conformers: 1 Conformer: "" Number of residues, atoms: 124, 1014 Classifications: {'peptide': 124} Link IDs: {'PTRANS': 4, 'TRANS': 119} Chain: "Z" Number of atoms: 625 Number of conformers: 1 Conformer: "" Number of residues, atoms: 82, 625 Classifications: {'peptide': 82} Link IDs: {'PTRANS': 1, 'TRANS': 80} Chain: "a" Number of atoms: 574 Number of conformers: 1 Conformer: "" Number of residues, atoms: 72, 574 Classifications: {'peptide': 72} Link IDs: {'PTRANS': 2, 'TRANS': 69} Chain: "b" Number of atoms: 640 Number of conformers: 1 Conformer: "" Number of residues, atoms: 82, 640 Classifications: {'peptide': 82} Link IDs: {'PTRANS': 5, 'TRANS': 76} Chain: "d" Number of atoms: 479 Number of conformers: 1 Conformer: "" Number of residues, atoms: 61, 479 Classifications: {'peptide': 61} Link IDs: {'PTRANS': 1, 'TRANS': 59} Chain: "e" Number of atoms: 430 Number of conformers: 1 Conformer: "" Number of residues, atoms: 56, 430 Classifications: {'peptide': 56} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'PTRANS': 3, 'TRANS': 52} Unresolved non-hydrogen bonds: 13 Unresolved non-hydrogen angles: 16 Unresolved non-hydrogen dihedrals: 12 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'PHE:plan': 1} Unresolved non-hydrogen planarities: 6 Chain: "f" Number of atoms: 455 Number of conformers: 1 Conformer: "" Number of residues, atoms: 54, 455 Classifications: {'peptide': 54} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 52} Chain: "g" Number of atoms: 477 Number of conformers: 1 Conformer: "" Number of residues, atoms: 64, 477 Classifications: {'peptide': 64} Incomplete info: {'truncation_to_alanine': 11} Link IDs: {'PTRANS': 2, 'TRANS': 61} Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 42 Unresolved non-hydrogen angles: 49 Unresolved non-hydrogen dihedrals: 38 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'ARG:plan': 1, 'ASN:plan1': 1, 'HIS:plan': 1} Unresolved non-hydrogen planarities: 13 Chain: "j" Number of atoms: 2440 Number of conformers: 1 Conformer: "" Number of residues, atoms: 314, 2440 Classifications: {'peptide': 314} Link IDs: {'PTRANS': 10, 'TRANS': 303} Chain: "2" Number of atoms: 33498 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1569, 33498 Classifications: {'RNA': 1569} Modifications used: {'rna2p_pur': 120, 'rna2p_pyr': 104, 'rna3p_pur': 711, 'rna3p_pyr': 634} Link IDs: {'rna2p': 224, 'rna3p': 1344} Chain breaks: 13 Chain: "i" Number of atoms: 239 Number of conformers: 1 Conformer: "" Number of residues, atoms: 29, 239 Classifications: {'peptide': 29} Link IDs: {'PTRANS': 1, 'TRANS': 27} Chain: "u" Number of atoms: 4954 Number of conformers: 1 Conformer: "" Number of residues, atoms: 615, 4954 Classifications: {'peptide': 615} Incomplete info: {'truncation_to_alanine': 6} Link IDs: {'PCIS': 1, 'PTRANS': 40, 'TRANS': 573} Chain breaks: 3 Unresolved non-hydrogen bonds: 23 Unresolved non-hydrogen angles: 29 Unresolved non-hydrogen dihedrals: 17 Planarities with less than four sites: {'GLU:plan': 5, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 23 Chain: "f" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} Chain: "g" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 34287 SG CYS f 21 161.066 158.479 70.276 1.00 49.65 S ATOM 34311 SG CYS f 24 158.696 156.023 69.097 1.00 47.12 S ATOM 34458 SG CYS f 42 158.055 156.471 72.720 1.00 43.18 S ATOM 34881 SG CYS g 126 188.977 149.998 31.689 1.00 78.56 S Time building chain proxies: 29.79, per 1000 atoms: 0.39 Number of scatterers: 76190 At special positions: 0 Unit cell: (220.272, 250.983, 204.387, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) Zn 2 29.99 S 197 16.00 P 1569 15.00 O 18465 8.00 N 13965 7.00 C 41992 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: 29.14 Conformation dependent library (CDL) restraints added in 6.4 seconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN f 201 " pdb="ZN ZN f 201 " - pdb=" SG CYS f 24 " pdb="ZN ZN f 201 " - pdb=" SG CYS f 42 " pdb="ZN ZN f 201 " - pdb=" SG CYS f 21 " pdb=" ZN g 500 " pdb="ZN ZN g 500 " - pdb=" SG CYS g 126 " 10556 Ramachandran restraints generated. 5278 Oldfield, 0 Emsley, 5278 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 9938 Finding SS restraints... Secondary structure from input PDB file: 175 helices and 64 sheets defined 33.1% alpha, 18.8% beta 489 base pairs and 884 stacking pairs defined. Time for finding SS restraints: 23.67 Creating SS restraints... Processing helix chain 'B' and resid 11 through 22 removed outlier: 3.554A pdb=" N VAL B 15 " --> pdb=" O LYS B 11 " (cutoff:3.500A) Processing helix chain 'B' and resid 34 through 36 No H-bonds generated for 'chain 'B' and resid 34 through 36' Processing helix chain 'B' and resid 43 through 45 No H-bonds generated for 'chain 'B' and resid 43 through 45' Processing helix chain 'B' and resid 50 through 67 Processing helix chain 'B' and resid 70 through 72 No H-bonds generated for 'chain 'B' and resid 70 through 72' Processing helix chain 'B' and resid 80 through 82 No H-bonds generated for 'chain 'B' and resid 80 through 82' Processing helix chain 'B' and resid 83 through 94 removed outlier: 3.646A pdb=" N LEU B 88 " --> pdb=" O GLN B 84 " (cutoff:3.500A) removed outlier: 3.568A pdb=" N ALA B 92 " --> pdb=" O LEU B 88 " (cutoff:3.500A) Processing helix chain 'B' and resid 130 through 136 removed outlier: 3.680A pdb=" N LEU B 134 " --> pdb=" O ASP B 130 " (cutoff:3.500A) Processing helix chain 'B' and resid 137 through 140 removed outlier: 3.675A pdb=" N VAL B 140 " --> pdb=" O ALA B 137 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 137 through 140' Processing helix chain 'B' and resid 167 through 186 removed outlier: 3.632A pdb=" N GLY B 172 " --> pdb=" O ALA B 168 " (cutoff:3.500A) Processing helix chain 'C' and resid 23 through 26 Processing helix chain 'C' and resid 58 through 63 Processing helix chain 'C' and resid 106 through 114 Processing helix chain 'C' and resid 157 through 175 removed outlier: 3.556A pdb=" N ILE C 164 " --> pdb=" O GLN C 160 " (cutoff:3.500A) removed outlier: 3.677A pdb=" N ILE C 171 " --> pdb=" O LYS C 167 " (cutoff:3.500A) removed outlier: 3.519A pdb=" N MET C 172 " --> pdb=" O MET C 168 " (cutoff:3.500A) removed outlier: 4.375A pdb=" N THR C 173 " --> pdb=" O MET C 169 " (cutoff:3.500A) Processing helix chain 'C' and resid 191 through 201 removed outlier: 4.116A pdb=" N GLU C 198 " --> pdb=" O GLY C 194 " (cutoff:3.500A) removed outlier: 3.538A pdb=" N LYS C 199 " --> pdb=" O LYS C 195 " (cutoff:3.500A) Processing helix chain 'C' and resid 202 through 204 No H-bonds generated for 'chain 'C' and resid 202 through 204' Processing helix chain 'C' and resid 224 through 232 removed outlier: 3.564A pdb=" N LEU C 228 " --> pdb=" O GLU C 224 " (cutoff:3.500A) removed outlier: 3.736A pdb=" N GLU C 230 " --> pdb=" O GLY C 226 " (cutoff:3.500A) Processing helix chain 'D' and resid 64 through 72 Processing helix chain 'D' and resid 77 through 84 removed outlier: 4.314A pdb=" N ILE D 81 " --> pdb=" O SER D 77 " (cutoff:3.500A) Processing helix chain 'D' and resid 91 through 98 Processing helix chain 'D' and resid 146 through 161 Processing helix chain 'D' and resid 207 through 218 removed outlier: 3.758A pdb=" N LYS D 212 " --> pdb=" O PRO D 208 " (cutoff:3.500A) removed outlier: 3.826A pdb=" N LEU D 213 " --> pdb=" O VAL D 209 " (cutoff:3.500A) Processing helix chain 'D' and resid 232 through 245 removed outlier: 3.937A pdb=" N THR D 240 " --> pdb=" O PHE D 236 " (cutoff:3.500A) Processing helix chain 'D' and resid 252 through 256 Processing helix chain 'D' and resid 264 through 269 Processing helix chain 'E' and resid 15 through 19 Processing helix chain 'E' and resid 44 through 50 Processing helix chain 'E' and resid 57 through 66 removed outlier: 3.516A pdb=" N VAL E 61 " --> pdb=" O THR E 57 " (cutoff:3.500A) Processing helix chain 'E' and resid 117 through 119 No H-bonds generated for 'chain 'E' and resid 117 through 119' Processing helix chain 'E' and resid 247 through 258 Processing helix chain 'F' and resid 6 through 30 removed outlier: 3.748A pdb=" N GLY F 15 " --> pdb=" O PHE F 11 " (cutoff:3.500A) removed outlier: 3.699A pdb=" N LYS F 18 " --> pdb=" O ASP F 14 " (cutoff:3.500A) Processing helix chain 'F' and resid 54 through 60 removed outlier: 3.517A pdb=" N VAL F 58 " --> pdb=" O ARG F 54 " (cutoff:3.500A) removed outlier: 3.682A pdb=" N LEU F 59 " --> pdb=" O THR F 55 " (cutoff:3.500A) removed outlier: 4.087A pdb=" N GLY F 60 " --> pdb=" O GLN F 56 " (cutoff:3.500A) No H-bonds generated for 'chain 'F' and resid 54 through 60' Processing helix chain 'F' and resid 64 through 77 removed outlier: 3.887A pdb=" N GLU F 68 " --> pdb=" O ARG F 64 " (cutoff:3.500A) removed outlier: 3.686A pdb=" N LEU F 69 " --> pdb=" O ARG F 65 " (cutoff:3.500A) removed outlier: 3.532A pdb=" N PHE F 77 " --> pdb=" O VAL F 73 " (cutoff:3.500A) Processing helix chain 'F' and resid 97 through 103 Processing helix chain 'F' and resid 103 through 111 Processing helix chain 'F' and resid 114 through 130 Processing helix chain 'F' and resid 161 through 165 Processing helix chain 'G' and resid 22 through 26 removed outlier: 3.635A pdb=" N ARG G 25 " --> pdb=" O ARG G 22 " (cutoff:3.500A) removed outlier: 3.728A pdb=" N THR G 26 " --> pdb=" O LYS G 23 " (cutoff:3.500A) No H-bonds generated for 'chain 'G' and resid 22 through 26' Processing helix chain 'G' and resid 39 through 42 removed outlier: 3.808A pdb=" N GLY G 42 " --> pdb=" O ASP G 39 " (cutoff:3.500A) No H-bonds generated for 'chain 'G' and resid 39 through 42' Processing helix chain 'G' and resid 137 through 146 Processing helix chain 'G' and resid 181 through 225 removed outlier: 3.519A pdb=" N ARG G 191 " --> pdb=" O HIS G 187 " (cutoff:3.500A) removed outlier: 3.597A pdb=" N ILE G 192 " --> pdb=" O LYS G 188 " (cutoff:3.500A) removed outlier: 3.519A pdb=" N LYS G 195 " --> pdb=" O ARG G 191 " (cutoff:3.500A) removed outlier: 4.082A pdb=" N LYS G 215 " --> pdb=" O LYS G 211 " (cutoff:3.500A) removed outlier: 3.517A pdb=" N ARG G 216 " --> pdb=" O LEU G 212 " (cutoff:3.500A) removed outlier: 3.857A pdb=" N ALA G 220 " --> pdb=" O ARG G 216 " (cutoff:3.500A) removed outlier: 3.709A pdb=" N LYS G 223 " --> pdb=" O GLU G 219 " (cutoff:3.500A) removed outlier: 4.035A pdb=" N GLN G 225 " --> pdb=" O LYS G 221 " (cutoff:3.500A) Processing helix chain 'G' and resid 225 through 230 removed outlier: 4.073A pdb=" N ALA G 229 " --> pdb=" O GLN G 225 " (cutoff:3.500A) removed outlier: 3.992A pdb=" N LYS G 230 " --> pdb=" O GLU G 226 " (cutoff:3.500A) No H-bonds generated for 'chain 'G' and resid 225 through 230' Processing helix chain 'H' and resid 17 through 33 removed outlier: 3.604A pdb=" N ALA H 26 " --> pdb=" O GLY H 22 " (cutoff:3.500A) Processing helix chain 'H' and resid 36 through 41 Processing helix chain 'H' and resid 65 through 67 No H-bonds generated for 'chain 'H' and resid 65 through 67' Processing helix chain 'H' and resid 68 through 74 removed outlier: 3.659A pdb=" N PHE H 72 " --> pdb=" O GLN H 68 " (cutoff:3.500A) Processing helix chain 'H' and resid 76 through 87 removed outlier: 4.121A pdb=" N ARG H 81 " --> pdb=" O VAL H 77 " (cutoff:3.500A) removed outlier: 4.404A pdb=" N GLU H 82 " --> pdb=" O ARG H 78 " (cutoff:3.500A) removed outlier: 3.617A pdb=" N LYS H 86 " --> pdb=" O GLU H 82 " (cutoff:3.500A) Processing helix chain 'H' and resid 117 through 120 Processing helix chain 'H' and resid 121 through 133 removed outlier: 4.067A pdb=" N GLU H 131 " --> pdb=" O ASP H 127 " (cutoff:3.500A) Processing helix chain 'H' and resid 162 through 167 removed outlier: 3.700A pdb=" N VAL H 166 " --> pdb=" O GLN H 162 " (cutoff:3.500A) Processing helix chain 'H' and resid 169 through 181 removed outlier: 3.641A pdb=" N SER H 174 " --> pdb=" O VAL H 170 " (cutoff:3.500A) removed outlier: 3.809A pdb=" N GLY H 175 " --> pdb=" O GLU H 171 " (cutoff:3.500A) Processing helix chain 'I' and resid 88 through 93 removed outlier: 3.846A pdb=" N ARG I 92 " --> pdb=" O ASN I 88 " (cutoff:3.500A) removed outlier: 3.716A pdb=" N THR I 93 " --> pdb=" O GLU I 89 " (cutoff:3.500A) No H-bonds generated for 'chain 'I' and resid 88 through 93' Processing helix chain 'I' and resid 106 through 118 Processing helix chain 'I' and resid 130 through 138 removed outlier: 3.857A pdb=" N GLU I 134 " --> pdb=" O THR I 130 " (cutoff:3.500A) removed outlier: 4.397A pdb=" N GLU I 135 " --> pdb=" O PRO I 131 " (cutoff:3.500A) removed outlier: 4.362A pdb=" N ILE I 136 " --> pdb=" O GLU I 132 " (cutoff:3.500A) Processing helix chain 'I' and resid 142 through 152 Processing helix chain 'I' and resid 153 through 155 No H-bonds generated for 'chain 'I' and resid 153 through 155' Processing helix chain 'I' and resid 159 through 167 removed outlier: 3.547A pdb=" N GLU I 164 " --> pdb=" O SER I 160 " (cutoff:3.500A) removed outlier: 4.239A pdb=" N GLN I 165 " --> pdb=" O LEU I 161 " (cutoff:3.500A) Processing helix chain 'I' and resid 178 through 183 Processing helix chain 'I' and resid 192 through 206 Processing helix chain 'J' and resid 24 through 36 Processing helix chain 'J' and resid 40 through 61 removed outlier: 3.855A pdb=" N VAL J 46 " --> pdb=" O GLU J 42 " (cutoff:3.500A) removed outlier: 3.548A pdb=" N LEU J 60 " --> pdb=" O ALA J 56 " (cutoff:3.500A) Processing helix chain 'J' and resid 67 through 84 removed outlier: 3.644A pdb=" N ASN J 75 " --> pdb=" O LEU J 71 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N LEU J 78 " --> pdb=" O GLY J 74 " (cutoff:3.500A) removed outlier: 3.543A pdb=" N LEU J 81 " --> pdb=" O LEU J 77 " (cutoff:3.500A) Processing helix chain 'J' and resid 96 through 100 Processing helix chain 'J' and resid 101 through 107 removed outlier: 3.782A pdb=" N PHE J 105 " --> pdb=" O LYS J 101 " (cutoff:3.500A) Processing helix chain 'J' and resid 109 through 117 Processing helix chain 'J' and resid 122 through 132 removed outlier: 3.742A pdb=" N ARG J 127 " --> pdb=" O ILE J 123 " (cutoff:3.500A) removed outlier: 3.677A pdb=" N GLN J 132 " --> pdb=" O VAL J 128 " (cutoff:3.500A) Processing helix chain 'J' and resid 171 through 181 Processing helix chain 'K' and resid 18 through 22 Processing helix chain 'K' and resid 62 through 66 removed outlier: 3.943A pdb=" N CYS K 66 " --> pdb=" O LYS K 63 " (cutoff:3.500A) Processing helix chain 'K' and resid 67 through 75 Processing helix chain 'K' and resid 79 through 83 removed outlier: 3.505A pdb=" N ASN K 83 " --> pdb=" O GLY K 80 " (cutoff:3.500A) Processing helix chain 'K' and resid 89 through 104 removed outlier: 3.848A pdb=" N HIS K 95 " --> pdb=" O ARG K 91 " (cutoff:3.500A) removed outlier: 4.134A pdb=" N GLU K 98 " --> pdb=" O LYS K 94 " (cutoff:3.500A) removed outlier: 5.297A pdb=" N ILE K 99 " --> pdb=" O HIS K 95 " (cutoff:3.500A) Processing helix chain 'K' and resid 107 through 120 removed outlier: 3.945A pdb=" N VAL K 111 " --> pdb=" O ASN K 107 " (cutoff:3.500A) removed outlier: 3.552A pdb=" N LEU K 112 " --> pdb=" O PRO K 108 " (cutoff:3.500A) removed outlier: 3.560A pdb=" N SER K 119 " --> pdb=" O ALA K 115 " (cutoff:3.500A) Processing helix chain 'K' and resid 142 through 161 removed outlier: 3.710A pdb=" N THR K 156 " --> pdb=" O TRP K 152 " (cutoff:3.500A) removed outlier: 3.714A pdb=" N ALA K 158 " --> pdb=" O LEU K 154 " (cutoff:3.500A) removed outlier: 3.990A pdb=" N ARG K 159 " --> pdb=" O CYS K 155 " (cutoff:3.500A) removed outlier: 3.711A pdb=" N GLU K 160 " --> pdb=" O THR K 156 " (cutoff:3.500A) removed outlier: 3.645A pdb=" N ALA K 161 " --> pdb=" O GLY K 157 " (cutoff:3.500A) Processing helix chain 'K' and resid 168 through 182 removed outlier: 3.816A pdb=" N ALA K 174 " --> pdb=" O ALA K 170 " (cutoff:3.500A) removed outlier: 3.744A pdb=" N ASN K 179 " --> pdb=" O ASP K 175 " (cutoff:3.500A) removed outlier: 4.041A pdb=" N ALA K 180 " --> pdb=" O GLU K 176 " (cutoff:3.500A) removed outlier: 3.628A pdb=" N LYS K 182 " --> pdb=" O ILE K 178 " (cutoff:3.500A) Processing helix chain 'K' and resid 187 through 202 removed outlier: 3.661A pdb=" N LYS K 191 " --> pdb=" O SER K 187 " (cutoff:3.500A) removed outlier: 3.704A pdb=" N VAL K 199 " --> pdb=" O GLU K 195 " (cutoff:3.500A) Processing helix chain 'L' and resid 23 through 28 Processing helix chain 'L' and resid 47 through 53 removed outlier: 3.642A pdb=" N ILE L 51 " --> pdb=" O PRO L 47 " (cutoff:3.500A) Processing helix chain 'M' and resid 4 through 9 removed outlier: 4.116A pdb=" N ARG M 8 " --> pdb=" O PRO M 4 " (cutoff:3.500A) removed outlier: 3.612A pdb=" N ILE M 9 " --> pdb=" O LYS M 5 " (cutoff:3.500A) No H-bonds generated for 'chain 'M' and resid 4 through 9' Processing helix chain 'M' and resid 12 through 16 removed outlier: 3.584A pdb=" N PHE M 16 " --> pdb=" O GLU M 13 " (cutoff:3.500A) Processing helix chain 'M' and resid 42 through 56 removed outlier: 4.258A pdb=" N ALA M 48 " --> pdb=" O HIS M 44 " (cutoff:3.500A) removed outlier: 3.594A pdb=" N SER M 54 " --> pdb=" O GLN M 50 " (cutoff:3.500A) removed outlier: 3.571A pdb=" N ARG M 55 " --> pdb=" O SER M 51 " (cutoff:3.500A) Processing helix chain 'M' and resid 74 through 83 removed outlier: 3.596A pdb=" N TYR M 78 " --> pdb=" O GLU M 74 " (cutoff:3.500A) removed outlier: 3.668A pdb=" N ASP M 81 " --> pdb=" O GLN M 77 " (cutoff:3.500A) removed outlier: 3.625A pdb=" N TYR M 82 " --> pdb=" O TYR M 78 " (cutoff:3.500A) Processing helix chain 'M' and resid 91 through 95 removed outlier: 3.645A pdb=" N LEU M 94 " --> pdb=" O PRO M 91 " (cutoff:3.500A) removed outlier: 4.113A pdb=" N ARG M 95 " --> pdb=" O ALA M 92 " (cutoff:3.500A) No H-bonds generated for 'chain 'M' and resid 91 through 95' Processing helix chain 'N' and resid 29 through 42 removed outlier: 3.583A pdb=" N VAL N 33 " --> pdb=" O THR N 29 " (cutoff:3.500A) removed outlier: 3.693A pdb=" N LYS N 42 " --> pdb=" O TYR N 38 " (cutoff:3.500A) Processing helix chain 'N' and resid 46 through 57 removed outlier: 3.604A pdb=" N GLY N 51 " --> pdb=" O PRO N 47 " (cutoff:3.500A) removed outlier: 3.713A pdb=" N VAL N 52 " --> pdb=" O SER N 48 " (cutoff:3.500A) Processing helix chain 'N' and resid 62 through 68 Processing helix chain 'N' and resid 70 through 79 Processing helix chain 'N' and resid 85 through 105 removed outlier: 3.631A pdb=" N LEU N 91 " --> pdb=" O ASP N 87 " (cutoff:3.500A) removed outlier: 3.851A pdb=" N ARG N 104 " --> pdb=" O LYS N 100 " (cutoff:3.500A) Processing helix chain 'N' and resid 108 through 132 removed outlier: 4.556A pdb=" N ARG N 114 " --> pdb=" O ASP N 110 " (cutoff:3.500A) removed outlier: 3.562A pdb=" N ILE N 116 " --> pdb=" O LYS N 112 " (cutoff:3.500A) removed outlier: 3.736A pdb=" N TYR N 128 " --> pdb=" O ARG N 124 " (cutoff:3.500A) Processing helix chain 'O' and resid 18 through 25 removed outlier: 3.888A pdb=" N LEU O 22 " --> pdb=" O LEU O 18 " (cutoff:3.500A) Processing helix chain 'O' and resid 35 through 44 removed outlier: 3.761A pdb=" N LEU O 42 " --> pdb=" O ALA O 38 " (cutoff:3.500A) removed outlier: 3.822A pdb=" N LYS O 44 " --> pdb=" O LYS O 40 " (cutoff:3.500A) Processing helix chain 'O' and resid 58 through 72 removed outlier: 4.132A pdb=" N VAL O 62 " --> pdb=" O GLU O 58 " (cutoff:3.500A) removed outlier: 3.814A pdb=" N LYS O 63 " --> pdb=" O PRO O 59 " (cutoff:3.500A) removed outlier: 3.696A pdb=" N LEU O 68 " --> pdb=" O LEU O 64 " (cutoff:3.500A) removed outlier: 3.644A pdb=" N GLU O 71 " --> pdb=" O ALA O 67 " (cutoff:3.500A) Processing helix chain 'O' and resid 81 through 86 Processing helix chain 'O' and resid 87 through 89 No H-bonds generated for 'chain 'O' and resid 87 through 89' Processing helix chain 'O' and resid 123 through 130 removed outlier: 3.711A pdb=" N CYS O 130 " --> pdb=" O GLU O 126 " (cutoff:3.500A) Processing helix chain 'P' and resid 57 through 62 removed outlier: 3.618A pdb=" N LYS P 61 " --> pdb=" O THR P 57 " (cutoff:3.500A) Processing helix chain 'P' and resid 72 through 81 removed outlier: 3.805A pdb=" N LEU P 76 " --> pdb=" O TYR P 72 " (cutoff:3.500A) removed outlier: 3.981A pdb=" N GLN P 79 " --> pdb=" O MET P 75 " (cutoff:3.500A) removed outlier: 3.644A pdb=" N ASP P 80 " --> pdb=" O LEU P 76 " (cutoff:3.500A) removed outlier: 4.006A pdb=" N VAL P 81 " --> pdb=" O ALA P 77 " (cutoff:3.500A) Processing helix chain 'P' and resid 81 through 89 removed outlier: 3.576A pdb=" N CYS P 85 " --> pdb=" O VAL P 81 " (cutoff:3.500A) removed outlier: 3.649A pdb=" N LYS P 86 " --> pdb=" O ALA P 82 " (cutoff:3.500A) Processing helix chain 'P' and resid 110 through 121 removed outlier: 4.219A pdb=" N SER P 114 " --> pdb=" O PRO P 110 " (cutoff:3.500A) Processing helix chain 'Q' and resid 22 through 27 removed outlier: 3.506A pdb=" N LEU Q 26 " --> pdb=" O LEU Q 22 " (cutoff:3.500A) removed outlier: 4.078A pdb=" N ASP Q 27 " --> pdb=" O ASP Q 23 " (cutoff:3.500A) No H-bonds generated for 'chain 'Q' and resid 22 through 27' Processing helix chain 'Q' and resid 29 through 35 removed outlier: 4.075A pdb=" N GLN Q 35 " --> pdb=" O GLU Q 31 " (cutoff:3.500A) Processing helix chain 'Q' and resid 38 through 48 Processing helix chain 'Q' and resid 50 through 66 removed outlier: 3.885A pdb=" N LEU Q 56 " --> pdb=" O LYS Q 52 " (cutoff:3.500A) Processing helix chain 'Q' and resid 86 through 90 removed outlier: 3.835A pdb=" N VAL Q 90 " --> pdb=" O PRO Q 87 " (cutoff:3.500A) Processing helix chain 'R' and resid 40 through 42 No H-bonds generated for 'chain 'R' and resid 40 through 42' Processing helix chain 'R' and resid 47 through 53 Processing helix chain 'R' and resid 54 through 59 Processing helix chain 'R' and resid 77 through 99 removed outlier: 3.776A pdb=" N GLN R 86 " --> pdb=" O TYR R 82 " (cutoff:3.500A) removed outlier: 3.567A pdb=" N VAL R 93 " --> pdb=" O SER R 89 " (cutoff:3.500A) Processing helix chain 'R' and resid 101 through 116 removed outlier: 3.865A pdb=" N LYS R 105 " --> pdb=" O ASP R 101 " (cutoff:3.500A) removed outlier: 3.621A pdb=" N ILE R 111 " --> pdb=" O GLU R 107 " (cutoff:3.500A) Processing helix chain 'R' and resid 117 through 120 Processing helix chain 'S' and resid 6 through 20 Processing helix chain 'S' and resid 27 through 38 removed outlier: 3.527A pdb=" N ASN S 31 " --> pdb=" O ASP S 27 " (cutoff:3.500A) removed outlier: 3.527A pdb=" N ARG S 33 " --> pdb=" O HIS S 29 " (cutoff:3.500A) removed outlier: 3.650A pdb=" N GLU S 36 " --> pdb=" O LYS S 32 " (cutoff:3.500A) removed outlier: 3.728A pdb=" N GLU S 37 " --> pdb=" O ARG S 33 " (cutoff:3.500A) Processing helix chain 'S' and resid 44 through 62 removed outlier: 3.625A pdb=" N ARG S 60 " --> pdb=" O HIS S 56 " (cutoff:3.500A) removed outlier: 3.935A pdb=" N GLN S 62 " --> pdb=" O MET S 58 " (cutoff:3.500A) Processing helix chain 'S' and resid 70 through 81 removed outlier: 3.749A pdb=" N ARG S 78 " --> pdb=" O GLN S 74 " (cutoff:3.500A) Processing helix chain 'S' and resid 99 through 109 Processing helix chain 'T' and resid 25 through 30 removed outlier: 3.959A pdb=" N ILE T 30 " --> pdb=" O ILE T 26 " (cutoff:3.500A) Processing helix chain 'T' and resid 31 through 33 No H-bonds generated for 'chain 'T' and resid 31 through 33' Processing helix chain 'T' and resid 38 through 48 removed outlier: 3.545A pdb=" N LEU T 45 " --> pdb=" O ALA T 41 " (cutoff:3.500A) Processing helix chain 'T' and resid 55 through 59 removed outlier: 3.772A pdb=" N GLU T 58 " --> pdb=" O ARG T 55 " (cutoff:3.500A) removed outlier: 3.805A pdb=" N LEU T 59 " --> pdb=" O ALA T 56 " (cutoff:3.500A) No H-bonds generated for 'chain 'T' and resid 55 through 59' Processing helix chain 'T' and resid 62 through 73 removed outlier: 4.137A pdb=" N ILE T 68 " --> pdb=" O VAL T 64 " (cutoff:3.500A) Processing helix chain 'T' and resid 74 through 78 removed outlier: 3.854A pdb=" N LYS T 78 " --> pdb=" O ARG T 75 " (cutoff:3.500A) Processing helix chain 'T' and resid 99 through 118 removed outlier: 3.764A pdb=" N ASP T 104 " --> pdb=" O ALA T 100 " (cutoff:3.500A) removed outlier: 4.074A pdb=" N ASN T 105 " --> pdb=" O ASN T 101 " (cutoff:3.500A) removed outlier: 3.730A pdb=" N LEU T 107 " --> pdb=" O LEU T 103 " (cutoff:3.500A) removed outlier: 3.685A pdb=" N ARG T 108 " --> pdb=" O ASP T 104 " (cutoff:3.500A) removed outlier: 3.652A pdb=" N LEU T 114 " --> pdb=" O ASP T 110 " (cutoff:3.500A) Processing helix chain 'T' and resid 121 through 128 removed outlier: 3.676A pdb=" N HIS T 125 " --> pdb=" O ARG T 121 " (cutoff:3.500A) Processing helix chain 'U' and resid 5 through 9 removed outlier: 3.536A pdb=" N VAL U 9 " --> pdb=" O VAL U 6 " (cutoff:3.500A) Processing helix chain 'U' and resid 10 through 26 removed outlier: 3.811A pdb=" N ALA U 20 " --> pdb=" O ARG U 16 " (cutoff:3.500A) removed outlier: 4.024A pdb=" N GLY U 26 " --> pdb=" O LEU U 22 " (cutoff:3.500A) Processing helix chain 'U' and resid 32 through 36 removed outlier: 4.514A pdb=" N ASP U 35 " --> pdb=" O GLU U 32 " (cutoff:3.500A) Processing helix chain 'U' and resid 51 through 67 removed outlier: 3.844A pdb=" N THR U 55 " --> pdb=" O ASN U 51 " (cutoff:3.500A) Processing helix chain 'U' and resid 71 through 77 Processing helix chain 'U' and resid 98 through 110 removed outlier: 4.322A pdb=" N LEU U 104 " --> pdb=" O ALA U 100 " (cutoff:3.500A) removed outlier: 3.527A pdb=" N GLN U 105 " --> pdb=" O ARG U 101 " (cutoff:3.500A) removed outlier: 3.505A pdb=" N ALA U 106 " --> pdb=" O ARG U 102 " (cutoff:3.500A) removed outlier: 3.522A pdb=" N LEU U 110 " --> pdb=" O ALA U 106 " (cutoff:3.500A) Processing helix chain 'U' and resid 124 through 144 removed outlier: 3.826A pdb=" N ASP U 130 " --> pdb=" O GLN U 126 " (cutoff:3.500A) removed outlier: 3.616A pdb=" N ILE U 134 " --> pdb=" O ASP U 130 " (cutoff:3.500A) removed outlier: 4.317A pdb=" N ASN U 142 " --> pdb=" O VAL U 138 " (cutoff:3.500A) removed outlier: 3.657A pdb=" N LYS U 143 " --> pdb=" O ALA U 139 " (cutoff:3.500A) removed outlier: 4.531A pdb=" N LYS U 144 " --> pdb=" O ALA U 140 " (cutoff:3.500A) Processing helix chain 'V' and resid 29 through 46 Processing helix chain 'V' and resid 94 through 103 removed outlier: 3.971A pdb=" N VAL V 98 " --> pdb=" O PRO V 94 " (cutoff:3.500A) removed outlier: 4.174A pdb=" N LYS V 99 " --> pdb=" O SER V 95 " (cutoff:3.500A) removed outlier: 4.296A pdb=" N GLN V 100 " --> pdb=" O GLU V 96 " (cutoff:3.500A) removed outlier: 3.637A pdb=" N ILE V 101 " --> pdb=" O ILE V 97 " (cutoff:3.500A) removed outlier: 3.681A pdb=" N THR V 102 " --> pdb=" O VAL V 98 " (cutoff:3.500A) removed outlier: 3.663A pdb=" N SER V 103 " --> pdb=" O LYS V 99 " (cutoff:3.500A) No H-bonds generated for 'chain 'V' and resid 94 through 103' Processing helix chain 'W' and resid 5 through 20 removed outlier: 3.686A pdb=" N ASP W 9 " --> pdb=" O ASN W 5 " (cutoff:3.500A) removed outlier: 3.506A pdb=" N ALA W 10 " --> pdb=" O VAL W 6 " (cutoff:3.500A) removed outlier: 3.630A pdb=" N GLU W 18 " --> pdb=" O ILE W 14 " (cutoff:3.500A) removed outlier: 3.590A pdb=" N ARG W 20 " --> pdb=" O ASN W 16 " (cutoff:3.500A) Processing helix chain 'W' and resid 31 through 44 removed outlier: 3.515A pdb=" N HIS W 44 " --> pdb=" O VAL W 40 " (cutoff:3.500A) Processing helix chain 'W' and resid 82 through 84 No H-bonds generated for 'chain 'W' and resid 82 through 84' Processing helix chain 'W' and resid 85 through 94 removed outlier: 3.608A pdb=" N TRP W 89 " --> pdb=" O ASP W 85 " (cutoff:3.500A) Processing helix chain 'W' and resid 113 through 119 removed outlier: 3.505A pdb=" N ARG W 117 " --> pdb=" O HIS W 113 " (cutoff:3.500A) Processing helix chain 'X' and resid 9 through 21 Processing helix chain 'X' and resid 24 through 33 removed outlier: 4.687A pdb=" N GLY X 33 " --> pdb=" O LYS X 29 " (cutoff:3.500A) Processing helix chain 'X' and resid 33 through 39 Processing helix chain 'X' and resid 130 through 135 Processing helix chain 'Y' and resid 36 through 48 removed outlier: 3.715A pdb=" N LYS Y 46 " --> pdb=" O GLU Y 42 " (cutoff:3.500A) removed outlier: 3.590A pdb=" N MET Y 47 " --> pdb=" O LYS Y 43 " (cutoff:3.500A) Processing helix chain 'Y' and resid 51 through 53 No H-bonds generated for 'chain 'Y' and resid 51 through 53' Processing helix chain 'Y' and resid 78 through 85 Processing helix chain 'Y' and resid 87 through 92 Processing helix chain 'Y' and resid 93 through 95 No H-bonds generated for 'chain 'Y' and resid 93 through 95' Processing helix chain 'Y' and resid 104 through 114 Processing helix chain 'Y' and resid 118 through 123 removed outlier: 3.621A pdb=" N ALA Y 121 " --> pdb=" O ARG Y 118 " (cutoff:3.500A) removed outlier: 3.572A pdb=" N ALA Y 123 " --> pdb=" O THR Y 120 " (cutoff:3.500A) Processing helix chain 'Z' and resid 56 through 63 removed outlier: 3.507A pdb=" N ARG Z 60 " --> pdb=" O CYS Z 56 " (cutoff:3.500A) Processing helix chain 'Z' and resid 64 through 76 removed outlier: 3.500A pdb=" N ASP Z 76 " --> pdb=" O LEU Z 72 " (cutoff:3.500A) Processing helix chain 'a' and resid 51 through 61 removed outlier: 3.511A pdb=" N ASP a 56 " --> pdb=" O LYS a 52 " (cutoff:3.500A) removed outlier: 3.815A pdb=" N LYS a 57 " --> pdb=" O ALA a 53 " (cutoff:3.500A) removed outlier: 3.685A pdb=" N CYS a 59 " --> pdb=" O TYR a 55 " (cutoff:3.500A) Processing helix chain 'a' and resid 62 through 65 removed outlier: 3.661A pdb=" N TYR a 65 " --> pdb=" O VAL a 62 " (cutoff:3.500A) No H-bonds generated for 'chain 'a' and resid 62 through 65' Processing helix chain 'a' and resid 69 through 77 removed outlier: 3.675A pdb=" N ARG a 76 " --> pdb=" O VAL a 72 " (cutoff:3.500A) removed outlier: 3.583A pdb=" N LEU a 77 " --> pdb=" O VAL a 73 " (cutoff:3.500A) Processing helix chain 'a' and resid 80 through 94 removed outlier: 4.071A pdb=" N LEU a 88 " --> pdb=" O ALA a 84 " (cutoff:3.500A) removed outlier: 4.359A pdb=" N GLN a 89 " --> pdb=" O ARG a 85 " (cutoff:3.500A) removed outlier: 3.781A pdb=" N GLU a 90 " --> pdb=" O ALA a 86 " (cutoff:3.500A) Processing helix chain 'e' and resid 10 through 16 Processing helix chain 'e' and resid 30 through 43 removed outlier: 3.787A pdb=" N ARG e 41 " --> pdb=" O GLN e 37 " (cutoff:3.500A) removed outlier: 3.596A pdb=" N VAL e 43 " --> pdb=" O ASN e 39 " (cutoff:3.500A) Processing helix chain 'f' and resid 40 through 51 removed outlier: 3.673A pdb=" N ARG f 44 " --> pdb=" O ARG f 40 " (cutoff:3.500A) removed outlier: 3.912A pdb=" N GLN f 45 " --> pdb=" O GLN f 41 " (cutoff:3.500A) removed outlier: 3.617A pdb=" N TYR f 46 " --> pdb=" O CYS f 42 " (cutoff:3.500A) removed outlier: 5.299A pdb=" N LYS f 48 " --> pdb=" O ARG f 44 " (cutoff:3.500A) removed outlier: 5.654A pdb=" N ASP f 49 " --> pdb=" O GLN f 45 " (cutoff:3.500A) Processing helix chain 'g' and resid 101 through 105 removed outlier: 3.570A pdb=" N TYR g 105 " --> pdb=" O ALA g 101 " (cutoff:3.500A) No H-bonds generated for 'chain 'g' and resid 101 through 105' Processing helix chain 'g' and resid 123 through 127 removed outlier: 3.537A pdb=" N CYS g 126 " --> pdb=" O SER g 123 " (cutoff:3.500A) Processing helix chain 'j' and resid 276 through 281 removed outlier: 3.628A pdb=" N SER j 279 " --> pdb=" O SER j 276 " (cutoff:3.500A) removed outlier: 4.436A pdb=" N LYS j 280 " --> pdb=" O THR j 277 " (cutoff:3.500A) Processing helix chain 'i' and resid 153 through 161 Processing helix chain 'i' and resid 165 through 178 Processing helix chain 'u' and resid 49 through 72 Processing helix chain 'u' and resid 95 through 104 Processing helix chain 'u' and resid 142 through 150 removed outlier: 4.454A pdb=" N ASP u 148 " --> pdb=" O HIS u 144 " (cutoff:3.500A) Processing helix chain 'u' and resid 167 through 181 removed outlier: 3.814A pdb=" N ALA u 179 " --> pdb=" O SER u 175 " (cutoff:3.500A) Processing helix chain 'u' and resid 202 through 212 Processing helix chain 'u' and resid 225 through 238 Processing helix chain 'u' and resid 244 through 250 removed outlier: 3.521A pdb=" N ARG u 250 " --> pdb=" O PHE u 246 " (cutoff:3.500A) Processing helix chain 'u' and resid 465 through 481 Processing helix chain 'u' and resid 495 through 500 Processing helix chain 'u' and resid 521 through 526 removed outlier: 3.511A pdb=" N TYR u 524 " --> pdb=" O PRO u 521 " (cutoff:3.500A) Processing helix chain 'u' and resid 532 through 545 removed outlier: 3.652A pdb=" N THR u 536 " --> pdb=" O ASN u 532 " (cutoff:3.500A) Processing helix chain 'u' and resid 567 through 576 Processing helix chain 'u' and resid 720 through 726 removed outlier: 3.541A pdb=" N LEU u 724 " --> pdb=" O ARG u 720 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'B' and resid 38 through 41 removed outlier: 6.938A pdb=" N ILE B 48 " --> pdb=" O TYR B 39 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'B' and resid 97 through 100 removed outlier: 6.677A pdb=" N VAL B 74 " --> pdb=" O THR B 97 " (cutoff:3.500A) removed outlier: 7.802A pdb=" N ILE B 99 " --> pdb=" O VAL B 74 " (cutoff:3.500A) removed outlier: 6.245A pdb=" N VAL B 76 " --> pdb=" O ILE B 99 " (cutoff:3.500A) removed outlier: 6.299A pdb=" N SER B 75 " --> pdb=" O VAL B 123 " (cutoff:3.500A) removed outlier: 6.104A pdb=" N LEU B 122 " --> pdb=" O ILE B 145 " (cutoff:3.500A) removed outlier: 8.034A pdb=" N LEU B 147 " --> pdb=" O LEU B 122 " (cutoff:3.500A) removed outlier: 7.505A pdb=" N VAL B 124 " --> pdb=" O LEU B 147 " (cutoff:3.500A) removed outlier: 6.851A pdb=" N THR B 144 " --> pdb=" O ILE B 159 " (cutoff:3.500A) removed outlier: 7.608A pdb=" N ILE B 161 " --> pdb=" O THR B 144 " (cutoff:3.500A) removed outlier: 6.598A pdb=" N ALA B 146 " --> pdb=" O ILE B 161 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA2 Processing sheet with id=AA3, first strand: chain 'C' and resid 43 through 50 removed outlier: 3.764A pdb=" N GLY C 45 " --> pdb=" O VAL C 33 " (cutoff:3.500A) removed outlier: 8.712A pdb=" N CYS C 96 " --> pdb=" O TRP C 30 " (cutoff:3.500A) removed outlier: 7.116A pdb=" N ASP C 32 " --> pdb=" O CYS C 96 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'C' and resid 82 through 87 removed outlier: 6.965A pdb=" N LYS C 83 " --> pdb=" O MET C 103 " (cutoff:3.500A) removed outlier: 5.164A pdb=" N MET C 103 " --> pdb=" O LYS C 83 " (cutoff:3.500A) removed outlier: 6.515A pdb=" N LYS C 85 " --> pdb=" O HIS C 101 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'C' and resid 120 through 128 removed outlier: 3.742A pdb=" N VAL C 125 " --> pdb=" O LEU C 137 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'C' and resid 120 through 128 removed outlier: 3.742A pdb=" N VAL C 125 " --> pdb=" O LEU C 137 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'D' and resid 103 through 115 removed outlier: 5.417A pdb=" N ASP D 104 " --> pdb=" O GLY D 131 " (cutoff:3.500A) removed outlier: 6.973A pdb=" N GLY D 131 " --> pdb=" O ASP D 104 " (cutoff:3.500A) removed outlier: 5.219A pdb=" N VAL D 106 " --> pdb=" O ALA D 129 " (cutoff:3.500A) removed outlier: 6.492A pdb=" N ALA D 129 " --> pdb=" O VAL D 106 " (cutoff:3.500A) removed outlier: 3.877A pdb=" N LYS D 108 " --> pdb=" O PHE D 127 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'D' and resid 184 through 188 removed outlier: 3.550A pdb=" N VAL D 191 " --> pdb=" O CYS D 188 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'E' and resid 42 through 43 Processing sheet with id=AB1, first strand: chain 'E' and resid 75 through 76 removed outlier: 4.215A pdb=" N HIS E 112 " --> pdb=" O ARG E 100 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'E' and resid 146 through 148 removed outlier: 6.145A pdb=" N ILE E 136 " --> pdb=" O VAL E 131 " (cutoff:3.500A) removed outlier: 4.713A pdb=" N VAL E 131 " --> pdb=" O ILE E 136 " (cutoff:3.500A) removed outlier: 6.692A pdb=" N HIS E 138 " --> pdb=" O ILE E 129 " (cutoff:3.500A) removed outlier: 4.527A pdb=" N ILE E 129 " --> pdb=" O HIS E 138 " (cutoff:3.500A) removed outlier: 6.595A pdb=" N VAL E 140 " --> pdb=" O ARG E 127 " (cutoff:3.500A) removed outlier: 4.214A pdb=" N ASP E 171 " --> pdb=" O GLN E 161 " (cutoff:3.500A) removed outlier: 6.300A pdb=" N ASP E 163 " --> pdb=" O ILE E 169 " (cutoff:3.500A) removed outlier: 6.478A pdb=" N ILE E 169 " --> pdb=" O ASP E 163 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'E' and resid 217 through 221 removed outlier: 6.530A pdb=" N VAL E 207 " --> pdb=" O ARG E 198 " (cutoff:3.500A) removed outlier: 4.424A pdb=" N ARG E 198 " --> pdb=" O VAL E 207 " (cutoff:3.500A) removed outlier: 6.691A pdb=" N HIS E 209 " --> pdb=" O THR E 196 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'F' and resid 34 through 40 removed outlier: 3.824A pdb=" N GLY F 36 " --> pdb=" O LEU F 51 " (cutoff:3.500A) removed outlier: 7.047A pdb=" N ILE F 48 " --> pdb=" O TYR F 87 " (cutoff:3.500A) removed outlier: 7.459A pdb=" N GLU F 89 " --> pdb=" O ILE F 48 " (cutoff:3.500A) removed outlier: 6.301A pdb=" N ILE F 50 " --> pdb=" O GLU F 89 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'F' and resid 148 through 155 removed outlier: 3.703A pdb=" N GLY F 133 " --> pdb=" O MET F 189 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'F' and resid 209 through 210 Processing sheet with id=AB7, first strand: chain 'F' and resid 223 through 226 removed outlier: 6.431A pdb=" N VAL j 176 " --> pdb=" O LYS j 185 " (cutoff:3.500A) removed outlier: 4.326A pdb=" N ASN j 187 " --> pdb=" O VAL j 174 " (cutoff:3.500A) removed outlier: 6.446A pdb=" N VAL j 174 " --> pdb=" O ASN j 187 " (cutoff:3.500A) removed outlier: 3.716A pdb=" N CYS j 153 " --> pdb=" O CYS j 168 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'G' and resid 14 through 17 removed outlier: 6.769A pdb=" N LYS G 2 " --> pdb=" O LEU G 109 " (cutoff:3.500A) removed outlier: 7.449A pdb=" N LEU G 111 " --> pdb=" O LYS G 2 " (cutoff:3.500A) removed outlier: 6.203A pdb=" N ASN G 4 " --> pdb=" O LEU G 111 " (cutoff:3.500A) removed outlier: 7.456A pdb=" N ILE G 113 " --> pdb=" O ASN G 4 " (cutoff:3.500A) removed outlier: 7.215A pdb=" N SER G 6 " --> pdb=" O ILE G 113 " (cutoff:3.500A) removed outlier: 8.590A pdb=" N LYS G 115 " --> pdb=" O SER G 6 " (cutoff:3.500A) removed outlier: 3.628A pdb=" N VAL G 108 " --> pdb=" O ASN G 56 " (cutoff:3.500A) removed outlier: 4.028A pdb=" N GLY G 54 " --> pdb=" O ASN G 110 " (cutoff:3.500A) removed outlier: 6.614A pdb=" N VAL G 112 " --> pdb=" O ILE G 52 " (cutoff:3.500A) removed outlier: 5.751A pdb=" N ILE G 52 " --> pdb=" O VAL G 112 " (cutoff:3.500A) removed outlier: 6.150A pdb=" N VAL G 114 " --> pdb=" O VAL G 50 " (cutoff:3.500A) removed outlier: 7.495A pdb=" N VAL G 50 " --> pdb=" O VAL G 114 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'G' and resid 72 through 77 Processing sheet with id=AC1, first strand: chain 'G' and resid 160 through 162 Processing sheet with id=AC2, first strand: chain 'H' and resid 47 through 53 removed outlier: 3.537A pdb=" N ALA H 47 " --> pdb=" O PHE H 63 " (cutoff:3.500A) removed outlier: 3.577A pdb=" N HIS H 91 " --> pdb=" O LYS H 58 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'H' and resid 185 through 188 removed outlier: 3.774A pdb=" N GLY H 141 " --> pdb=" O HIS H 157 " (cutoff:3.500A) removed outlier: 4.555A pdb=" N LYS H 142 " --> pdb=" O ASP W 54 " (cutoff:3.500A) removed outlier: 3.561A pdb=" N PHE W 50 " --> pdb=" O VAL H 146 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'I' and resid 37 through 38 removed outlier: 6.118A pdb=" N LYS I 37 " --> pdb=" O LEU I 60 " (cutoff:3.500A) removed outlier: 6.426A pdb=" N ARG I 42 " --> pdb=" O LEU I 58 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'I' and resid 62 through 67 removed outlier: 7.340A pdb=" N ILE I 78 " --> pdb=" O ASP I 105 " (cutoff:3.500A) removed outlier: 6.534A pdb=" N ASP I 105 " --> pdb=" O ILE I 78 " (cutoff:3.500A) removed outlier: 6.924A pdb=" N ILE I 101 " --> pdb=" O VAL I 82 " (cutoff:3.500A) removed outlier: 9.112A pdb=" N GLY I 187 " --> pdb=" O VAL I 62 " (cutoff:3.500A) removed outlier: 6.914A pdb=" N ASN I 64 " --> pdb=" O GLY I 187 " (cutoff:3.500A) removed outlier: 8.006A pdb=" N VAL I 189 " --> pdb=" O ASN I 64 " (cutoff:3.500A) removed outlier: 7.168A pdb=" N SER I 66 " --> pdb=" O VAL I 189 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'J' and resid 140 through 141 removed outlier: 3.507A pdb=" N ARG J 136 " --> pdb=" O ASP J 158 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'K' and resid 123 through 126 removed outlier: 3.543A pdb=" N GLN K 137 " --> pdb=" O THR K 126 " (cutoff:3.500A) removed outlier: 11.110A pdb=" N ALA K 138 " --> pdb=" O ILE d 43 " (cutoff:3.500A) removed outlier: 6.011A pdb=" N ASN d 45 " --> pdb=" O ALA K 138 " (cutoff:3.500A) removed outlier: 3.590A pdb=" N VAL d 30 " --> pdb=" O ARG d 44 " (cutoff:3.500A) removed outlier: 6.280A pdb=" N CYS d 27 " --> pdb=" O ARG d 20 " (cutoff:3.500A) removed outlier: 4.575A pdb=" N ARG d 20 " --> pdb=" O CYS d 27 " (cutoff:3.500A) removed outlier: 6.715A pdb=" N GLN d 29 " --> pdb=" O LEU d 18 " (cutoff:3.500A) removed outlier: 3.625A pdb=" N LYS d 16 " --> pdb=" O ARG d 31 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'L' and resid 72 through 79 removed outlier: 17.847A pdb=" N ILE L 72 " --> pdb=" O LEU L 93 " (cutoff:3.500A) removed outlier: 15.005A pdb=" N LEU L 93 " --> pdb=" O ILE L 72 " (cutoff:3.500A) removed outlier: 9.069A pdb=" N SER L 74 " --> pdb=" O ASP L 91 " (cutoff:3.500A) removed outlier: 6.208A pdb=" N ASP L 91 " --> pdb=" O SER L 74 " (cutoff:3.500A) removed outlier: 6.834A pdb=" N VAL L 87 " --> pdb=" O THR L 78 " (cutoff:3.500A) removed outlier: 9.944A pdb=" N PHE L 140 " --> pdb=" O ASN L 108 " (cutoff:3.500A) removed outlier: 7.849A pdb=" N SER L 110 " --> pdb=" O PHE L 140 " (cutoff:3.500A) removed outlier: 8.391A pdb=" N VAL L 142 " --> pdb=" O SER L 110 " (cutoff:3.500A) removed outlier: 7.478A pdb=" N HIS L 112 " --> pdb=" O VAL L 142 " (cutoff:3.500A) removed outlier: 8.542A pdb=" N LYS L 144 " --> pdb=" O HIS L 112 " (cutoff:3.500A) removed outlier: 6.480A pdb=" N THR L 127 " --> pdb=" O LEU L 143 " (cutoff:3.500A) removed outlier: 4.697A pdb=" N VAL L 145 " --> pdb=" O ILE L 125 " (cutoff:3.500A) removed outlier: 7.048A pdb=" N ILE L 125 " --> pdb=" O VAL L 145 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'M' and resid 21 through 22 removed outlier: 3.637A pdb=" N TYR M 70 " --> pdb=" O LYS M 59 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'O' and resid 78 through 79 removed outlier: 8.614A pdb=" N VAL O 79 " --> pdb=" O CYS O 50 " (cutoff:3.500A) removed outlier: 6.164A pdb=" N LEU O 52 " --> pdb=" O VAL O 79 " (cutoff:3.500A) removed outlier: 3.602A pdb=" N VAL O 109 " --> pdb=" O VAL O 51 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'O' and resid 93 through 94 removed outlier: 3.663A pdb=" N LYS O 102 " --> pdb=" O LYS O 93 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'P' and resid 44 through 45 removed outlier: 6.528A pdb=" N GLY P 29 " --> pdb=" O HIS P 94 " (cutoff:3.500A) removed outlier: 7.739A pdb=" N LYS P 96 " --> pdb=" O GLY P 29 " (cutoff:3.500A) removed outlier: 6.215A pdb=" N CYS P 31 " --> pdb=" O LYS P 96 " (cutoff:3.500A) removed outlier: 6.019A pdb=" N LEU P 93 " --> pdb=" O ILE P 126 " (cutoff:3.500A) removed outlier: 4.664A pdb=" N ARG P 128 " --> pdb=" O LEU P 93 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'Q' and resid 16 through 17 Processing sheet with id=AD5, first strand: chain 'Q' and resid 76 through 78 removed outlier: 3.528A pdb=" N VAL Q 94 " --> pdb=" O VAL Q 105 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'R' and resid 10 through 15 removed outlier: 3.674A pdb=" N HIS R 24 " --> pdb=" O ARG R 69 " (cutoff:3.500A) removed outlier: 3.941A pdb=" N LEU R 31 " --> pdb=" O VAL R 66 " (cutoff:3.500A) removed outlier: 3.613A pdb=" N VAL R 70 " --> pdb=" O LYS R 33 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'S' and resid 96 through 98 removed outlier: 6.084A pdb=" N ILE S 96 " --> pdb=" O GLN S 118 " (cutoff:3.500A) No H-bonds generated for sheet with id=AD7 Processing sheet with id=AD8, first strand: chain 'T' and resid 12 through 14 Processing sheet with id=AD9, first strand: chain 'U' and resid 81 through 83 Processing sheet with id=AE1, first strand: chain 'U' and resid 113 through 115 Processing sheet with id=AE2, first strand: chain 'V' and resid 50 through 55 removed outlier: 5.206A pdb=" N GLY V 52 " --> pdb=" O ASP V 90 " (cutoff:3.500A) removed outlier: 4.465A pdb=" N ASP V 90 " --> pdb=" O GLY V 52 " (cutoff:3.500A) removed outlier: 3.523A pdb=" N LYS V 59 " --> pdb=" O ILE V 84 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'V' and resid 50 through 55 removed outlier: 5.206A pdb=" N GLY V 52 " --> pdb=" O ASP V 90 " (cutoff:3.500A) removed outlier: 4.465A pdb=" N ASP V 90 " --> pdb=" O GLY V 52 " (cutoff:3.500A) removed outlier: 3.548A pdb=" N ILE V 20 " --> pdb=" O LEU V 91 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'W' and resid 71 through 74 Processing sheet with id=AE5, first strand: chain 'W' and resid 71 through 74 removed outlier: 6.794A pdb=" N VAL W 103 " --> pdb=" O LEU W 126 " (cutoff:3.500A) removed outlier: 4.618A pdb=" N PHE W 128 " --> pdb=" O PHE W 101 " (cutoff:3.500A) removed outlier: 6.906A pdb=" N PHE W 101 " --> pdb=" O PHE W 128 " (cutoff:3.500A) Processing sheet with id=AE6, first strand: chain 'X' and resid 128 through 129 removed outlier: 6.385A pdb=" N LEU X 101 " --> pdb=" O VAL X 123 " (cutoff:3.500A) removed outlier: 4.697A pdb=" N VAL X 125 " --> pdb=" O GLU X 99 " (cutoff:3.500A) removed outlier: 7.177A pdb=" N GLU X 99 " --> pdb=" O VAL X 125 " (cutoff:3.500A) removed outlier: 6.878A pdb=" N ARG X 71 " --> pdb=" O LEU X 52 " (cutoff:3.500A) removed outlier: 5.136A pdb=" N LYS X 54 " --> pdb=" O CYS X 69 " (cutoff:3.500A) removed outlier: 7.087A pdb=" N CYS X 69 " --> pdb=" O LYS X 54 " (cutoff:3.500A) removed outlier: 4.663A pdb=" N GLY X 56 " --> pdb=" O ARG X 67 " (cutoff:3.500A) removed outlier: 6.263A pdb=" N ARG X 67 " --> pdb=" O GLY X 56 " (cutoff:3.500A) removed outlier: 4.607A pdb=" N PHE X 120 " --> pdb=" O THR X 82 " (cutoff:3.500A) Processing sheet with id=AE7, first strand: chain 'Y' and resid 6 through 9 Processing sheet with id=AE8, first strand: chain 'Y' and resid 6 through 9 removed outlier: 7.187A pdb=" N LYS Y 68 " --> pdb=" O THR Y 62 " (cutoff:3.500A) removed outlier: 4.589A pdb=" N THR Y 62 " --> pdb=" O LYS Y 68 " (cutoff:3.500A) removed outlier: 6.310A pdb=" N THR Y 70 " --> pdb=" O PHE Y 60 " (cutoff:3.500A) removed outlier: 4.265A pdb=" N PHE Y 60 " --> pdb=" O THR Y 70 " (cutoff:3.500A) Processing sheet with id=AE9, first strand: chain 'Z' and resid 32 through 39 removed outlier: 4.799A pdb=" N GLN Z 49 " --> pdb=" O GLU Z 38 " (cutoff:3.500A) Processing sheet with id=AF1, first strand: chain 'a' and resid 98 through 102 removed outlier: 7.228A pdb=" N ILE a 108 " --> pdb=" O VAL a 100 " (cutoff:3.500A) Processing sheet with id=AF2, first strand: chain 'b' and resid 43 through 47 Processing sheet with id=AF3, first strand: chain 'b' and resid 54 through 56 removed outlier: 6.711A pdb=" N VAL b 54 " --> pdb=" O LEU b 63 " (cutoff:3.500A) removed outlier: 3.853A pdb=" N THR b 61 " --> pdb=" O CYS b 56 " (cutoff:3.500A) Processing sheet with id=AF4, first strand: chain 'd' and resid 10 through 12 Processing sheet with id=AF5, first strand: chain 'f' and resid 30 through 31 Processing sheet with id=AF6, first strand: chain 'g' and resid 106 through 108 Processing sheet with id=AF7, first strand: chain 'g' and resid 133 through 134 Processing sheet with id=AF8, first strand: chain 'j' and resid 4 through 11 removed outlier: 6.471A pdb=" N MET j 5 " --> pdb=" O THR j 313 " (cutoff:3.500A) removed outlier: 6.952A pdb=" N THR j 313 " --> pdb=" O MET j 5 " (cutoff:3.500A) removed outlier: 5.985A pdb=" N LEU j 7 " --> pdb=" O GLN j 311 " (cutoff:3.500A) removed outlier: 7.068A pdb=" N GLN j 311 " --> pdb=" O LEU j 7 " (cutoff:3.500A) removed outlier: 4.372A pdb=" N GLY j 9 " --> pdb=" O VAL j 309 " (cutoff:3.500A) removed outlier: 4.104A pdb=" N LEU j 306 " --> pdb=" O TYR j 302 " (cutoff:3.500A) Processing sheet with id=AF9, first strand: chain 'j' and resid 21 through 22 removed outlier: 3.527A pdb=" N LEU j 32 " --> pdb=" O ALA j 22 " (cutoff:3.500A) removed outlier: 3.543A pdb=" N SER j 33 " --> pdb=" O ILE j 41 " (cutoff:3.500A) removed outlier: 3.541A pdb=" N ILE j 41 " --> pdb=" O SER j 33 " (cutoff:3.500A) removed outlier: 3.818A pdb=" N ILE j 40 " --> pdb=" O LEU j 59 " (cutoff:3.500A) removed outlier: 5.779A pdb=" N LYS j 44 " --> pdb=" O PRO j 55 " (cutoff:3.500A) Processing sheet with id=AG1, first strand: chain 'j' and resid 66 through 71 removed outlier: 3.762A pdb=" N LEU j 89 " --> pdb=" O ARG j 99 " (cutoff:3.500A) Processing sheet with id=AG2, first strand: chain 'j' and resid 108 through 113 removed outlier: 3.563A pdb=" N VAL j 121 " --> pdb=" O ALA j 112 " (cutoff:3.500A) removed outlier: 4.139A pdb=" N ILE j 129 " --> pdb=" O VAL j 142 " (cutoff:3.500A) Processing sheet with id=AG3, first strand: chain 'j' and resid 195 through 200 removed outlier: 7.008A pdb=" N GLY j 210 " --> pdb=" O ASN j 196 " (cutoff:3.500A) removed outlier: 4.396A pdb=" N VAL j 198 " --> pdb=" O ALA j 208 " (cutoff:3.500A) removed outlier: 6.821A pdb=" N ALA j 208 " --> pdb=" O VAL j 198 " (cutoff:3.500A) removed outlier: 4.431A pdb=" N VAL j 200 " --> pdb=" O LEU j 206 " (cutoff:3.500A) removed outlier: 6.633A pdb=" N LEU j 206 " --> pdb=" O VAL j 200 " (cutoff:3.500A) removed outlier: 4.490A pdb=" N TYR j 228 " --> pdb=" O LEU j 218 " (cutoff:3.500A) removed outlier: 7.055A pdb=" N ASP j 220 " --> pdb=" O HIS j 226 " (cutoff:3.500A) removed outlier: 6.780A pdb=" N HIS j 226 " --> pdb=" O ASP j 220 " (cutoff:3.500A) Processing sheet with id=AG4, first strand: chain 'j' and resid 238 through 241 removed outlier: 3.955A pdb=" N ALA j 238 " --> pdb=" O ALA j 251 " (cutoff:3.500A) removed outlier: 3.603A pdb=" N ILE j 256 " --> pdb=" O LEU j 270 " (cutoff:3.500A) removed outlier: 3.567A pdb=" N LEU j 270 " --> pdb=" O ILE j 256 " (cutoff:3.500A) Processing sheet with id=AG5, first strand: chain 'u' and resid 110 through 112 removed outlier: 4.167A pdb=" N LEU u 124 " --> pdb=" O TRP u 133 " (cutoff:3.500A) removed outlier: 6.000A pdb=" N HIS u 83 " --> pdb=" O PHE u 134 " (cutoff:3.500A) removed outlier: 6.974A pdb=" N THR u 136 " --> pdb=" O HIS u 83 " (cutoff:3.500A) removed outlier: 5.841A pdb=" N VAL u 85 " --> pdb=" O THR u 136 " (cutoff:3.500A) removed outlier: 6.413A pdb=" N GLN u 84 " --> pdb=" O THR u 155 " (cutoff:3.500A) removed outlier: 7.516A pdb=" N LEU u 157 " --> pdb=" O GLN u 84 " (cutoff:3.500A) removed outlier: 6.944A pdb=" N LEU u 86 " --> pdb=" O LEU u 157 " (cutoff:3.500A) removed outlier: 8.037A pdb=" N LEU u 159 " --> pdb=" O LEU u 86 " (cutoff:3.500A) removed outlier: 7.228A pdb=" N VAL u 88 " --> pdb=" O LEU u 159 " (cutoff:3.500A) removed outlier: 6.408A pdb=" N ILE u 156 " --> pdb=" O THR u 186 " (cutoff:3.500A) Processing sheet with id=AG6, first strand: chain 'u' and resid 252 through 253 removed outlier: 3.656A pdb=" N PHE u 582 " --> pdb=" O HIS u 290 " (cutoff:3.500A) Processing sheet with id=AG7, first strand: chain 'u' and resid 257 through 264 removed outlier: 3.915A pdb=" N SER u 263 " --> pdb=" O VAL u 269 " (cutoff:3.500A) removed outlier: 7.985A pdb=" N VAL u 269 " --> pdb=" O SER u 263 " (cutoff:3.500A) removed outlier: 4.480A pdb=" N LEU u 272 " --> pdb=" O VAL u 562 " (cutoff:3.500A) Processing sheet with id=AG8, first strand: chain 'u' and resid 257 through 264 removed outlier: 3.915A pdb=" N SER u 263 " --> pdb=" O VAL u 269 " (cutoff:3.500A) removed outlier: 7.985A pdb=" N VAL u 269 " --> pdb=" O SER u 263 " (cutoff:3.500A) Processing sheet with id=AG9, first strand: chain 'u' and resid 623 through 625 removed outlier: 7.411A pdb=" N VAL u 665 " --> pdb=" O THR u 681 " (cutoff:3.500A) removed outlier: 5.253A pdb=" N THR u 681 " --> pdb=" O VAL u 665 " (cutoff:3.500A) removed outlier: 7.196A pdb=" N LEU u 667 " --> pdb=" O ILE u 679 " (cutoff:3.500A) removed outlier: 3.895A pdb=" N ILE u 679 " --> pdb=" O LEU u 667 " (cutoff:3.500A) removed outlier: 6.497A pdb=" N MET u 675 " --> pdb=" O LYS u 671 " (cutoff:3.500A) Processing sheet with id=AH1, first strand: chain 'u' and resid 637 through 639 removed outlier: 6.206A pdb=" N HIS u 638 " --> pdb=" O ILE u 694 " (cutoff:3.500A) removed outlier: 7.432A pdb=" N ARG u 696 " --> pdb=" O HIS u 638 " (cutoff:3.500A) removed outlier: 3.721A pdb=" N LEU u 699 " --> pdb=" O MET u 767 " (cutoff:3.500A) removed outlier: 4.035A pdb=" N MET u 767 " --> pdb=" O LEU u 699 " (cutoff:3.500A) removed outlier: 3.935A pdb=" N GLY u 701 " --> pdb=" O VAL u 765 " (cutoff:3.500A) removed outlier: 3.668A pdb=" N VAL u 765 " --> pdb=" O GLY u 701 " (cutoff:3.500A) removed outlier: 6.376A pdb=" N LYS u 752 " --> pdb=" O LYS u 742 " (cutoff:3.500A) removed outlier: 3.842A pdb=" N MET u 751 " --> pdb=" O VAL u 713 " (cutoff:3.500A) removed outlier: 3.940A pdb=" N VAL u 713 " --> pdb=" O MET u 751 " (cutoff:3.500A) removed outlier: 3.679A pdb=" N MET u 710 " --> pdb=" O PHE u 707 " (cutoff:3.500A) removed outlier: 6.086A pdb=" N ARG u 714 " --> pdb=" O PRO u 703 " (cutoff:3.500A) 1422 hydrogen bonds defined for protein. 3996 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 1212 hydrogen bonds 1920 hydrogen bond angles 0 basepair planarities 489 basepair parallelities 884 stacking parallelities Total time for adding SS restraints: 55.53 Time building geometry restraints manager: 31.75 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.19 - 1.32: 10125 1.32 - 1.45: 29989 1.45 - 1.57: 37365 1.57 - 1.70: 3123 1.70 - 1.82: 307 Bond restraints: 80909 Sorted by residual: bond pdb=" CA TYR B 204 " pdb=" C TYR B 204 " ideal model delta sigma weight residual 1.526 1.440 0.085 1.30e-02 5.92e+03 4.32e+01 bond pdb=" C ARG I 18 " pdb=" N LYS I 19 " ideal model delta sigma weight residual 1.331 1.223 0.108 2.07e-02 2.33e+03 2.75e+01 bond pdb=" N TYR B 204 " pdb=" CA TYR B 204 " ideal model delta sigma weight residual 1.461 1.410 0.051 1.38e-02 5.25e+03 1.35e+01 bond pdb=" CA ILE S 71 " pdb=" C ILE S 71 " ideal model delta sigma weight residual 1.524 1.478 0.045 1.30e-02 5.92e+03 1.22e+01 bond pdb=" C ILE S 71 " pdb=" O ILE S 71 " ideal model delta sigma weight residual 1.237 1.197 0.040 1.19e-02 7.06e+03 1.11e+01 ... (remaining 80904 not shown) Histogram of bond angle deviations from ideal: 96.36 - 104.73: 7527 104.73 - 113.09: 47372 113.09 - 121.45: 41895 121.45 - 129.82: 18837 129.82 - 138.18: 1107 Bond angle restraints: 116738 Sorted by residual: angle pdb=" C VAL J 137 " pdb=" N ARG J 138 " pdb=" CA ARG J 138 " ideal model delta sigma weight residual 121.54 134.35 -12.81 1.91e+00 2.74e-01 4.50e+01 angle pdb=" C3' G 2 114 " pdb=" O3' G 2 114 " pdb=" P U 2 115 " ideal model delta sigma weight residual 120.20 129.84 -9.64 1.50e+00 4.44e-01 4.13e+01 angle pdb=" C PRO H 65 " pdb=" N VAL H 66 " pdb=" CA VAL H 66 " ideal model delta sigma weight residual 120.24 124.28 -4.04 6.30e-01 2.52e+00 4.11e+01 angle pdb=" C SER S 43 " pdb=" N LYS S 44 " pdb=" CA LYS S 44 " ideal model delta sigma weight residual 120.38 129.51 -9.13 1.46e+00 4.69e-01 3.91e+01 angle pdb=" O3' G 2 114 " pdb=" C3' G 2 114 " pdb=" C2' G 2 114 " ideal model delta sigma weight residual 109.50 118.70 -9.20 1.50e+00 4.44e-01 3.76e+01 ... (remaining 116733 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.98: 46564 35.98 - 71.96: 4196 71.96 - 107.95: 477 107.95 - 143.93: 25 143.93 - 179.91: 36 Dihedral angle restraints: 51298 sinusoidal: 35899 harmonic: 15399 Sorted by residual: dihedral pdb=" CA ASN K 165 " pdb=" C ASN K 165 " pdb=" N ILE K 166 " pdb=" CA ILE K 166 " ideal model delta harmonic sigma weight residual -180.00 -125.27 -54.73 0 5.00e+00 4.00e-02 1.20e+02 dihedral pdb=" CA PRO F 194 " pdb=" C PRO F 194 " pdb=" N THR F 195 " pdb=" CA THR F 195 " ideal model delta harmonic sigma weight residual -180.00 -126.34 -53.66 0 5.00e+00 4.00e-02 1.15e+02 dihedral pdb=" C5' G 21587 " pdb=" C4' G 21587 " pdb=" C3' G 21587 " pdb=" O3' G 21587 " ideal model delta sinusoidal sigma weight residual 147.00 78.42 68.58 1 8.00e+00 1.56e-02 9.52e+01 ... (remaining 51295 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.101: 13360 0.101 - 0.203: 865 0.203 - 0.304: 59 0.304 - 0.405: 22 0.405 - 0.506: 6 Chirality restraints: 14312 Sorted by residual: chirality pdb=" C3' C 21373 " pdb=" C4' C 21373 " pdb=" O3' C 21373 " pdb=" C2' C 21373 " both_signs ideal model delta sigma weight residual False -2.48 -1.97 -0.51 2.00e-01 2.50e+01 6.41e+00 chirality pdb=" C3' C 2 382 " pdb=" C4' C 2 382 " pdb=" O3' C 2 382 " pdb=" C2' C 2 382 " both_signs ideal model delta sigma weight residual False -2.48 -2.02 -0.46 2.00e-01 2.50e+01 5.32e+00 chirality pdb=" C3' G 21587 " pdb=" C4' G 21587 " pdb=" O3' G 21587 " pdb=" C2' G 21587 " both_signs ideal model delta sigma weight residual False -2.74 -2.29 -0.46 2.00e-01 2.50e+01 5.21e+00 ... (remaining 14309 not shown) Planarity restraints: 9006 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C1' G 2 309 " -0.068 2.00e-02 2.50e+03 2.85e-02 2.43e+01 pdb=" N9 G 2 309 " 0.064 2.00e-02 2.50e+03 pdb=" C8 G 2 309 " 0.004 2.00e-02 2.50e+03 pdb=" N7 G 2 309 " 0.001 2.00e-02 2.50e+03 pdb=" C5 G 2 309 " -0.001 2.00e-02 2.50e+03 pdb=" C6 G 2 309 " -0.006 2.00e-02 2.50e+03 pdb=" O6 G 2 309 " -0.022 2.00e-02 2.50e+03 pdb=" N1 G 2 309 " -0.003 2.00e-02 2.50e+03 pdb=" C2 G 2 309 " 0.001 2.00e-02 2.50e+03 pdb=" N2 G 2 309 " -0.000 2.00e-02 2.50e+03 pdb=" N3 G 2 309 " 0.013 2.00e-02 2.50e+03 pdb=" C4 G 2 309 " 0.016 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1' A 2 604 " 0.053 2.00e-02 2.50e+03 2.30e-02 1.45e+01 pdb=" N9 A 2 604 " -0.049 2.00e-02 2.50e+03 pdb=" C8 A 2 604 " -0.004 2.00e-02 2.50e+03 pdb=" N7 A 2 604 " -0.001 2.00e-02 2.50e+03 pdb=" C5 A 2 604 " -0.004 2.00e-02 2.50e+03 pdb=" C6 A 2 604 " 0.005 2.00e-02 2.50e+03 pdb=" N6 A 2 604 " 0.019 2.00e-02 2.50e+03 pdb=" N1 A 2 604 " 0.004 2.00e-02 2.50e+03 pdb=" C2 A 2 604 " -0.004 2.00e-02 2.50e+03 pdb=" N3 A 2 604 " -0.007 2.00e-02 2.50e+03 pdb=" C4 A 2 604 " -0.011 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C ALA E 28 " -0.063 5.00e-02 4.00e+02 9.48e-02 1.44e+01 pdb=" N PRO E 29 " 0.164 5.00e-02 4.00e+02 pdb=" CA PRO E 29 " -0.049 5.00e-02 4.00e+02 pdb=" CD PRO E 29 " -0.052 5.00e-02 4.00e+02 ... (remaining 9003 not shown) Histogram of nonbonded interaction distances: 1.82 - 2.43: 286 2.43 - 3.05: 41050 3.05 - 3.67: 131437 3.67 - 4.28: 203180 4.28 - 4.90: 291067 Nonbonded interactions: 667020 Sorted by model distance: nonbonded pdb=" N VAL S 66 " pdb=" OE1 GLN S 74 " model vdw 1.817 2.520 nonbonded pdb=" OE2 GLU g 125 " pdb="ZN ZN g 500 " model vdw 2.187 2.230 nonbonded pdb=" OP1 U 2 115 " pdb=" O2' C 2 382 " model vdw 2.200 2.440 nonbonded pdb=" O6 G 21722 " pdb=" O2 U 21812 " model vdw 2.213 2.432 nonbonded pdb=" O6 G 21206 " pdb=" O4 U 21692 " model vdw 2.242 2.432 ... (remaining 667015 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 3.900 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.070 Extract box with map and model: 12.120 Check model and map are aligned: 0.860 Set scattering table: 0.510 Process input model: 209.430 Find NCS groups from input model: 1.980 Set up NCS constraints: 0.260 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.020 Load rotamer database and sin/cos tables:11.240 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 240.400 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8048 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 0.138 80909 Z= 0.505 Angle : 0.995 14.903 116738 Z= 0.508 Chirality : 0.056 0.506 14312 Planarity : 0.007 0.095 9006 Dihedral : 22.508 179.910 41360 Min Nonbonded Distance : 1.817 Molprobity Statistics. All-atom Clashscore : 5.46 Ramachandran Plot: Outliers : 0.19 % Allowed : 5.15 % Favored : 94.66 % Rotamer: Outliers : 0.59 % Allowed : 8.84 % Favored : 90.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.31 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.18 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.87 (0.09), residues: 5278 helix: -3.53 (0.08), residues: 1541 sheet: -1.92 (0.15), residues: 1014 loop : -2.16 (0.10), residues: 2723 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.002 TRP N 25 HIS 0.018 0.002 HIS Q 79 PHE 0.037 0.003 PHE X 105 TYR 0.016 0.002 TYR I 21 ARG 0.020 0.001 ARG Y 104 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10556 Ramachandran restraints generated. 5278 Oldfield, 0 Emsley, 5278 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10556 Ramachandran restraints generated. 5278 Oldfield, 0 Emsley, 5278 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 720 residues out of total 4631 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 693 time to evaluate : 4.641 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: E 66 MET cc_start: 0.8160 (mmm) cc_final: 0.7920 (mmm) REVERT: F 157 MET cc_start: 0.8349 (tpp) cc_final: 0.8055 (tpp) REVERT: H 162 GLN cc_start: 0.7603 (mm-40) cc_final: 0.7352 (tp40) REVERT: K 48 TYR cc_start: 0.7364 (m-80) cc_final: 0.7095 (m-10) REVERT: O 12 MET cc_start: -0.1219 (ptt) cc_final: -0.1717 (pp-130) REVERT: S 79 GLU cc_start: 0.8400 (OUTLIER) cc_final: 0.7763 (tp30) REVERT: W 111 MET cc_start: 0.8421 (ptp) cc_final: 0.8203 (ptm) outliers start: 27 outliers final: 9 residues processed: 716 average time/residue: 1.6530 time to fit residues: 1543.4894 Evaluate side-chains 534 residues out of total 4631 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 524 time to evaluate : 4.493 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 205 ARG Chi-restraints excluded: chain D residue 271 ASP Chi-restraints excluded: chain E residue 126 VAL Chi-restraints excluded: chain Q residue 94 VAL Chi-restraints excluded: chain S residue 78 ARG Chi-restraints excluded: chain S residue 79 GLU Chi-restraints excluded: chain S residue 81 ARG Chi-restraints excluded: chain W residue 25 VAL Chi-restraints excluded: chain Y residue 117 VAL Chi-restraints excluded: chain u residue 567 VAL Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 678 random chunks: chunk 572 optimal weight: 5.9990 chunk 513 optimal weight: 5.9990 chunk 285 optimal weight: 5.9990 chunk 175 optimal weight: 0.9980 chunk 346 optimal weight: 0.9990 chunk 274 optimal weight: 0.9990 chunk 531 optimal weight: 40.0000 chunk 205 optimal weight: 20.0000 chunk 323 optimal weight: 50.0000 chunk 395 optimal weight: 6.9990 chunk 615 optimal weight: 3.9990 overall best weight: 2.5988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 99 ASN C 118 GLN ** C 149 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 158 HIS D 272 HIS E 8 HIS E 98 ASN E 179 ASN E 209 HIS F 57 ASN ** F 74 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 101 GLN G 13 GLN G 59 GLN G 70 HIS G 105 ASN G 163 ASN G 197 GLN H 76 GLN H 165 ASN I 165 GLN J 156 HIS K 31 ASN K 179 ASN L 18 GLN ** M 32 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** M 73 ASN N 49 GLN N 58 HIS N 105 ASN ** O 119 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 26 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 32 GLN Q 35 GLN Q 41 GLN R 11 GLN R 86 GLN S 26 ASN T 42 HIS T 72 GLN T 85 ASN V 81 GLN V 92 HIS W 92 ASN X 97 ASN X 127 ASN Y 63 HIS Y 94 HIS Y 106 GLN b 65 GLN ** d 45 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** e 44 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** e 58 ASN f 45 GLN j 20 GLN j 64 HIS i 158 GLN i 162 ASN u 55 HIS ** u 63 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** u 180 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** u 241 GLN ** u 256 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** u 281 GLN u 312 ASN u 356 GLN u 617 HIS Total number of N/Q/H flips: 57 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8007 moved from start: 0.1342 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.058 80909 Z= 0.221 Angle : 0.658 11.000 116738 Z= 0.341 Chirality : 0.041 0.337 14312 Planarity : 0.005 0.070 9006 Dihedral : 23.648 179.000 30413 Min Nonbonded Distance : 2.085 Molprobity Statistics. All-atom Clashscore : 11.03 Ramachandran Plot: Outliers : 0.09 % Allowed : 3.69 % Favored : 96.21 % Rotamer: Outliers : 2.32 % Allowed : 16.17 % Favored : 81.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.31 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.04 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.44 (0.10), residues: 5278 helix: -1.50 (0.11), residues: 1606 sheet: -1.46 (0.15), residues: 982 loop : -1.69 (0.11), residues: 2690 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.001 TRP u 556 HIS 0.009 0.001 HIS T 120 PHE 0.030 0.001 PHE C 138 TYR 0.023 0.001 TYR M 57 ARG 0.012 0.001 ARG Z 45 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10556 Ramachandran restraints generated. 5278 Oldfield, 0 Emsley, 5278 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10556 Ramachandran restraints generated. 5278 Oldfield, 0 Emsley, 5278 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 703 residues out of total 4631 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 107 poor density : 596 time to evaluate : 4.680 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: C 67 PHE cc_start: 0.6715 (m-80) cc_final: 0.6424 (m-80) REVERT: C 217 MET cc_start: 0.7339 (tpt) cc_final: 0.6798 (tpt) REVERT: E 66 MET cc_start: 0.8234 (mmm) cc_final: 0.7946 (mmm) REVERT: F 157 MET cc_start: 0.8273 (tpp) cc_final: 0.7813 (tpp) REVERT: K 48 TYR cc_start: 0.7283 (m-80) cc_final: 0.6979 (m-10) REVERT: R 42 ILE cc_start: 0.6514 (OUTLIER) cc_final: 0.6145 (mp) REVERT: T 126 PHE cc_start: 0.6866 (OUTLIER) cc_final: 0.6659 (t80) REVERT: V 82 MET cc_start: 0.7720 (OUTLIER) cc_final: 0.7070 (ttp) REVERT: W 4 MET cc_start: 0.8341 (OUTLIER) cc_final: 0.8004 (mpp) REVERT: d 18 LEU cc_start: 0.7515 (OUTLIER) cc_final: 0.7298 (mt) REVERT: u 217 HIS cc_start: 0.7077 (OUTLIER) cc_final: 0.5737 (p90) outliers start: 107 outliers final: 40 residues processed: 665 average time/residue: 1.5655 time to fit residues: 1378.8394 Evaluate side-chains 576 residues out of total 4631 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 46 poor density : 530 time to evaluate : 4.559 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 6 ASP Chi-restraints excluded: chain B residue 79 SER Chi-restraints excluded: chain D residue 162 ILE Chi-restraints excluded: chain D residue 260 VAL Chi-restraints excluded: chain D residue 271 ASP Chi-restraints excluded: chain E residue 19 MET Chi-restraints excluded: chain E residue 126 VAL Chi-restraints excluded: chain G residue 197 GLN Chi-restraints excluded: chain H residue 105 THR Chi-restraints excluded: chain H residue 133 LEU Chi-restraints excluded: chain I residue 130 THR Chi-restraints excluded: chain I residue 138 ASN Chi-restraints excluded: chain I residue 146 GLN Chi-restraints excluded: chain K residue 26 ASP Chi-restraints excluded: chain K residue 79 HIS Chi-restraints excluded: chain N residue 32 ASP Chi-restraints excluded: chain N residue 86 GLU Chi-restraints excluded: chain P residue 33 ILE Chi-restraints excluded: chain P residue 54 CYS Chi-restraints excluded: chain P residue 100 THR Chi-restraints excluded: chain Q residue 79 HIS Chi-restraints excluded: chain R residue 12 VAL Chi-restraints excluded: chain R residue 42 ILE Chi-restraints excluded: chain S residue 74 GLN Chi-restraints excluded: chain S residue 85 VAL Chi-restraints excluded: chain S residue 92 ASP Chi-restraints excluded: chain S residue 101 ASP Chi-restraints excluded: chain T residue 92 ASP Chi-restraints excluded: chain T residue 126 PHE Chi-restraints excluded: chain V residue 31 SER Chi-restraints excluded: chain V residue 36 CYS Chi-restraints excluded: chain V residue 82 MET Chi-restraints excluded: chain W residue 4 MET Chi-restraints excluded: chain W residue 25 VAL Chi-restraints excluded: chain X residue 72 VAL Chi-restraints excluded: chain Y residue 50 THR Chi-restraints excluded: chain Y residue 117 VAL Chi-restraints excluded: chain b residue 53 VAL Chi-restraints excluded: chain d residue 18 LEU Chi-restraints excluded: chain d residue 50 VAL Chi-restraints excluded: chain e residue 43 VAL Chi-restraints excluded: chain e residue 46 VAL Chi-restraints excluded: chain j residue 64 HIS Chi-restraints excluded: chain u residue 217 HIS Chi-restraints excluded: chain u residue 567 VAL Chi-restraints excluded: chain u residue 765 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 678 random chunks: chunk 342 optimal weight: 10.0000 chunk 191 optimal weight: 20.0000 chunk 512 optimal weight: 10.0000 chunk 419 optimal weight: 0.0980 chunk 169 optimal weight: 7.9990 chunk 616 optimal weight: 2.9990 chunk 666 optimal weight: 7.9990 chunk 549 optimal weight: 20.0000 chunk 611 optimal weight: 40.0000 chunk 210 optimal weight: 0.9980 chunk 494 optimal weight: 5.9990 overall best weight: 3.6186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 99 ASN ** C 149 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 177 GLN ** F 74 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 226 GLN G 56 ASN G 105 ASN G 163 ASN G 197 GLN H 165 ASN K 82 ASN ** M 32 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** M 42 ASN N 36 GLN ** O 119 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 32 GLN R 11 GLN S 26 ASN T 42 HIS U 126 GLN ** V 81 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** V 92 HIS X 97 ASN a 45 ASN b 65 GLN ** d 45 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** u 63 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** u 180 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** u 256 HIS Total number of N/Q/H flips: 21 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8027 moved from start: 0.1572 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.084 80909 Z= 0.273 Angle : 0.651 9.854 116738 Z= 0.336 Chirality : 0.042 0.354 14312 Planarity : 0.005 0.070 9006 Dihedral : 23.531 179.387 30397 Min Nonbonded Distance : 2.052 Molprobity Statistics. All-atom Clashscore : 10.92 Ramachandran Plot: Outliers : 0.06 % Allowed : 4.62 % Favored : 95.32 % Rotamer: Outliers : 3.26 % Allowed : 18.00 % Favored : 78.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.31 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.04 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.77 (0.11), residues: 5278 helix: -0.61 (0.13), residues: 1597 sheet: -1.17 (0.16), residues: 994 loop : -1.48 (0.11), residues: 2687 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP j 43 HIS 0.016 0.001 HIS j 64 PHE 0.021 0.002 PHE U 21 TYR 0.032 0.002 TYR K 188 ARG 0.011 0.000 ARG d 31 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10556 Ramachandran restraints generated. 5278 Oldfield, 0 Emsley, 5278 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10556 Ramachandran restraints generated. 5278 Oldfield, 0 Emsley, 5278 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 704 residues out of total 4631 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 150 poor density : 554 time to evaluate : 4.594 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: C 217 MET cc_start: 0.7258 (tpt) cc_final: 0.6858 (tpt) REVERT: E 66 MET cc_start: 0.8263 (mmm) cc_final: 0.8025 (mmm) REVERT: F 157 MET cc_start: 0.8249 (tpp) cc_final: 0.8030 (tpp) REVERT: K 48 TYR cc_start: 0.7185 (m-80) cc_final: 0.6845 (m-10) REVERT: L 124 ASP cc_start: 0.7319 (OUTLIER) cc_final: 0.6772 (p0) REVERT: L 147 LYS cc_start: 0.8881 (OUTLIER) cc_final: 0.8639 (mtpp) REVERT: O 12 MET cc_start: 0.0208 (pp-130) cc_final: -0.0198 (pp-130) REVERT: P 55 ARG cc_start: 0.7699 (tmt90) cc_final: 0.7200 (ttp80) REVERT: T 126 PHE cc_start: 0.6969 (OUTLIER) cc_final: 0.6726 (t80) REVERT: V 38 ASP cc_start: 0.6886 (m-30) cc_final: 0.6627 (m-30) REVERT: V 82 MET cc_start: 0.7652 (OUTLIER) cc_final: 0.7029 (ttp) REVERT: W 4 MET cc_start: 0.8368 (OUTLIER) cc_final: 0.7880 (mpp) REVERT: X 119 ARG cc_start: 0.7555 (OUTLIER) cc_final: 0.7212 (mmt-90) REVERT: d 18 LEU cc_start: 0.7795 (OUTLIER) cc_final: 0.7586 (mt) REVERT: u 217 HIS cc_start: 0.7110 (OUTLIER) cc_final: 0.5692 (p90) REVERT: u 345 MET cc_start: 0.5371 (pmm) cc_final: 0.3473 (pmm) outliers start: 150 outliers final: 66 residues processed: 656 average time/residue: 1.5060 time to fit residues: 1320.9550 Evaluate side-chains 587 residues out of total 4631 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 74 poor density : 513 time to evaluate : 4.603 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 6 ASP Chi-restraints excluded: chain B residue 79 SER Chi-restraints excluded: chain C residue 29 ASP Chi-restraints excluded: chain C residue 47 THR Chi-restraints excluded: chain D residue 162 ILE Chi-restraints excluded: chain D residue 202 THR Chi-restraints excluded: chain D residue 240 THR Chi-restraints excluded: chain D residue 260 VAL Chi-restraints excluded: chain E residue 19 MET Chi-restraints excluded: chain E residue 126 VAL Chi-restraints excluded: chain E residue 173 ILE Chi-restraints excluded: chain E residue 251 GLU Chi-restraints excluded: chain G residue 126 ASP Chi-restraints excluded: chain G residue 181 THR Chi-restraints excluded: chain G residue 197 GLN Chi-restraints excluded: chain H residue 105 THR Chi-restraints excluded: chain H residue 133 LEU Chi-restraints excluded: chain I residue 130 THR Chi-restraints excluded: chain I residue 138 ASN Chi-restraints excluded: chain I residue 146 GLN Chi-restraints excluded: chain J residue 100 LEU Chi-restraints excluded: chain J residue 161 LEU Chi-restraints excluded: chain K residue 26 ASP Chi-restraints excluded: chain K residue 79 HIS Chi-restraints excluded: chain L residue 46 THR Chi-restraints excluded: chain L residue 66 VAL Chi-restraints excluded: chain L residue 76 VAL Chi-restraints excluded: chain L residue 85 THR Chi-restraints excluded: chain L residue 124 ASP Chi-restraints excluded: chain L residue 147 LYS Chi-restraints excluded: chain N residue 32 ASP Chi-restraints excluded: chain P residue 33 ILE Chi-restraints excluded: chain P residue 56 VAL Chi-restraints excluded: chain P residue 100 THR Chi-restraints excluded: chain Q residue 79 HIS Chi-restraints excluded: chain R residue 12 VAL Chi-restraints excluded: chain S residue 85 VAL Chi-restraints excluded: chain S residue 92 ASP Chi-restraints excluded: chain S residue 101 ASP Chi-restraints excluded: chain S residue 130 THR Chi-restraints excluded: chain T residue 89 ASP Chi-restraints excluded: chain T residue 92 ASP Chi-restraints excluded: chain T residue 126 PHE Chi-restraints excluded: chain U residue 48 TYR Chi-restraints excluded: chain V residue 31 SER Chi-restraints excluded: chain V residue 36 CYS Chi-restraints excluded: chain V residue 82 MET Chi-restraints excluded: chain W residue 4 MET Chi-restraints excluded: chain W residue 6 VAL Chi-restraints excluded: chain W residue 25 VAL Chi-restraints excluded: chain X residue 72 VAL Chi-restraints excluded: chain X residue 105 PHE Chi-restraints excluded: chain X residue 119 ARG Chi-restraints excluded: chain Y residue 51 THR Chi-restraints excluded: chain Y residue 117 VAL Chi-restraints excluded: chain b residue 53 VAL Chi-restraints excluded: chain b residue 63 LEU Chi-restraints excluded: chain d residue 14 VAL Chi-restraints excluded: chain d residue 18 LEU Chi-restraints excluded: chain d residue 50 VAL Chi-restraints excluded: chain e residue 43 VAL Chi-restraints excluded: chain e residue 46 VAL Chi-restraints excluded: chain j residue 69 VAL Chi-restraints excluded: chain j residue 153 CYS Chi-restraints excluded: chain j residue 174 VAL Chi-restraints excluded: chain j residue 199 THR Chi-restraints excluded: chain i residue 166 SER Chi-restraints excluded: chain u residue 184 THR Chi-restraints excluded: chain u residue 217 HIS Chi-restraints excluded: chain u residue 362 ASP Chi-restraints excluded: chain u residue 567 VAL Chi-restraints excluded: chain u residue 597 VAL Chi-restraints excluded: chain u residue 598 VAL Chi-restraints excluded: chain u residue 653 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 678 random chunks: chunk 609 optimal weight: 10.0000 chunk 463 optimal weight: 6.9990 chunk 320 optimal weight: 20.0000 chunk 68 optimal weight: 5.9990 chunk 294 optimal weight: 9.9990 chunk 414 optimal weight: 6.9990 chunk 619 optimal weight: 7.9990 chunk 655 optimal weight: 9.9990 chunk 323 optimal weight: 6.9990 chunk 586 optimal weight: 10.0000 chunk 176 optimal weight: 3.9990 overall best weight: 6.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 99 ASN G 197 GLN I 167 GLN ** M 32 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** M 42 ASN ** O 119 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 79 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** R 11 GLN S 26 ASN ** S 118 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** T 42 HIS ** U 126 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** V 28 ASN ** V 81 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** V 85 HIS V 92 HIS X 97 ASN X 127 ASN b 65 GLN ** e 44 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** j 159 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** j 191 HIS j 237 ASN i 165 HIS u 63 GLN ** u 180 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** u 239 GLN Total number of N/Q/H flips: 18 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8066 moved from start: 0.1726 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.126 80909 Z= 0.428 Angle : 0.722 9.965 116738 Z= 0.368 Chirality : 0.046 0.388 14312 Planarity : 0.005 0.075 9006 Dihedral : 23.546 179.685 30395 Min Nonbonded Distance : 2.055 Molprobity Statistics. All-atom Clashscore : 12.53 Ramachandran Plot: Outliers : 0.08 % Allowed : 5.04 % Favored : 94.88 % Rotamer: Outliers : 3.76 % Allowed : 19.67 % Favored : 76.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.31 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.08 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.54 (0.11), residues: 5278 helix: -0.31 (0.13), residues: 1604 sheet: -1.10 (0.16), residues: 1008 loop : -1.39 (0.12), residues: 2666 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP J 7 HIS 0.011 0.001 HIS Q 79 PHE 0.034 0.002 PHE F 79 TYR 0.038 0.002 TYR j 246 ARG 0.012 0.001 ARG H 41 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10556 Ramachandran restraints generated. 5278 Oldfield, 0 Emsley, 5278 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10556 Ramachandran restraints generated. 5278 Oldfield, 0 Emsley, 5278 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 701 residues out of total 4631 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 173 poor density : 528 time to evaluate : 4.637 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 198 MET cc_start: 0.8149 (tmm) cc_final: 0.7888 (tmt) REVERT: B 205 ARG cc_start: 0.7824 (OUTLIER) cc_final: 0.7582 (ptm160) REVERT: C 103 MET cc_start: 0.7993 (tmm) cc_final: 0.7410 (tmm) REVERT: C 217 MET cc_start: 0.7388 (tpt) cc_final: 0.6937 (tpt) REVERT: D 221 ASP cc_start: 0.8448 (OUTLIER) cc_final: 0.8183 (p0) REVERT: E 38 LEU cc_start: 0.8512 (OUTLIER) cc_final: 0.8256 (pp) REVERT: E 66 MET cc_start: 0.8311 (mmm) cc_final: 0.8043 (mmm) REVERT: E 230 LYS cc_start: 0.9007 (OUTLIER) cc_final: 0.8594 (ttpp) REVERT: K 48 TYR cc_start: 0.7301 (m-80) cc_final: 0.6996 (m-10) REVERT: L 124 ASP cc_start: 0.7533 (OUTLIER) cc_final: 0.6868 (p0) REVERT: L 147 LYS cc_start: 0.8898 (OUTLIER) cc_final: 0.8648 (mtpp) REVERT: M 21 MET cc_start: 0.6283 (OUTLIER) cc_final: 0.5968 (ttm) REVERT: O 12 MET cc_start: 0.0191 (pp-130) cc_final: -0.0107 (pp-130) REVERT: P 128 ARG cc_start: 0.7210 (mmt90) cc_final: 0.6826 (mtt90) REVERT: Q 93 MET cc_start: 0.6190 (mmp) cc_final: 0.5963 (mmp) REVERT: T 126 PHE cc_start: 0.7022 (OUTLIER) cc_final: 0.6730 (t80) REVERT: U 74 SER cc_start: 0.8600 (m) cc_final: 0.8113 (p) REVERT: U 134 ILE cc_start: 0.7582 (OUTLIER) cc_final: 0.7235 (tt) REVERT: V 82 MET cc_start: 0.7622 (OUTLIER) cc_final: 0.6990 (ttp) REVERT: W 4 MET cc_start: 0.8456 (OUTLIER) cc_final: 0.8056 (mpp) REVERT: X 119 ARG cc_start: 0.7614 (OUTLIER) cc_final: 0.7242 (mmt-90) REVERT: Y 74 MET cc_start: 0.7775 (OUTLIER) cc_final: 0.7169 (mpp) REVERT: u 217 HIS cc_start: 0.7260 (OUTLIER) cc_final: 0.5754 (p90) outliers start: 173 outliers final: 93 residues processed: 641 average time/residue: 1.4670 time to fit residues: 1264.0443 Evaluate side-chains 612 residues out of total 4631 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 107 poor density : 505 time to evaluate : 4.572 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 6 ASP Chi-restraints excluded: chain B residue 79 SER Chi-restraints excluded: chain B residue 82 THR Chi-restraints excluded: chain B residue 205 ARG Chi-restraints excluded: chain C residue 29 ASP Chi-restraints excluded: chain C residue 47 THR Chi-restraints excluded: chain C residue 106 THR Chi-restraints excluded: chain D residue 132 ASP Chi-restraints excluded: chain D residue 160 LEU Chi-restraints excluded: chain D residue 162 ILE Chi-restraints excluded: chain D residue 202 THR Chi-restraints excluded: chain D residue 215 MET Chi-restraints excluded: chain D residue 221 ASP Chi-restraints excluded: chain D residue 240 THR Chi-restraints excluded: chain D residue 245 SER Chi-restraints excluded: chain D residue 260 VAL Chi-restraints excluded: chain E residue 19 MET Chi-restraints excluded: chain E residue 38 LEU Chi-restraints excluded: chain E residue 126 VAL Chi-restraints excluded: chain E residue 173 ILE Chi-restraints excluded: chain E residue 230 LYS Chi-restraints excluded: chain E residue 251 GLU Chi-restraints excluded: chain F residue 26 THR Chi-restraints excluded: chain F residue 91 VAL Chi-restraints excluded: chain G residue 78 SER Chi-restraints excluded: chain G residue 126 ASP Chi-restraints excluded: chain G residue 181 THR Chi-restraints excluded: chain G residue 197 GLN Chi-restraints excluded: chain H residue 105 THR Chi-restraints excluded: chain H residue 133 LEU Chi-restraints excluded: chain I residue 130 THR Chi-restraints excluded: chain I residue 138 ASN Chi-restraints excluded: chain J residue 100 LEU Chi-restraints excluded: chain J residue 112 THR Chi-restraints excluded: chain J residue 161 LEU Chi-restraints excluded: chain K residue 26 ASP Chi-restraints excluded: chain K residue 79 HIS Chi-restraints excluded: chain L residue 46 THR Chi-restraints excluded: chain L residue 66 VAL Chi-restraints excluded: chain L residue 85 THR Chi-restraints excluded: chain L residue 124 ASP Chi-restraints excluded: chain L residue 147 LYS Chi-restraints excluded: chain M residue 21 MET Chi-restraints excluded: chain M residue 40 VAL Chi-restraints excluded: chain N residue 32 ASP Chi-restraints excluded: chain O residue 123 VAL Chi-restraints excluded: chain P residue 33 ILE Chi-restraints excluded: chain P residue 56 VAL Chi-restraints excluded: chain P residue 100 THR Chi-restraints excluded: chain Q residue 20 VAL Chi-restraints excluded: chain Q residue 79 HIS Chi-restraints excluded: chain R residue 12 VAL Chi-restraints excluded: chain S residue 74 GLN Chi-restraints excluded: chain S residue 85 VAL Chi-restraints excluded: chain S residue 130 THR Chi-restraints excluded: chain T residue 89 ASP Chi-restraints excluded: chain T residue 92 ASP Chi-restraints excluded: chain T residue 126 PHE Chi-restraints excluded: chain U residue 8 ASP Chi-restraints excluded: chain U residue 48 TYR Chi-restraints excluded: chain U residue 55 THR Chi-restraints excluded: chain U residue 134 ILE Chi-restraints excluded: chain V residue 31 SER Chi-restraints excluded: chain V residue 36 CYS Chi-restraints excluded: chain V residue 82 MET Chi-restraints excluded: chain W residue 4 MET Chi-restraints excluded: chain W residue 6 VAL Chi-restraints excluded: chain W residue 25 VAL Chi-restraints excluded: chain W residue 30 CYS Chi-restraints excluded: chain W residue 51 GLU Chi-restraints excluded: chain X residue 72 VAL Chi-restraints excluded: chain X residue 100 VAL Chi-restraints excluded: chain X residue 108 LYS Chi-restraints excluded: chain X residue 119 ARG Chi-restraints excluded: chain Y residue 4 THR Chi-restraints excluded: chain Y residue 13 MET Chi-restraints excluded: chain Y residue 51 THR Chi-restraints excluded: chain Y residue 74 MET Chi-restraints excluded: chain Y residue 117 VAL Chi-restraints excluded: chain Z residue 52 THR Chi-restraints excluded: chain Z residue 66 ASP Chi-restraints excluded: chain a residue 107 VAL Chi-restraints excluded: chain b residue 53 VAL Chi-restraints excluded: chain b residue 55 LEU Chi-restraints excluded: chain b residue 57 VAL Chi-restraints excluded: chain b residue 63 LEU Chi-restraints excluded: chain d residue 50 VAL Chi-restraints excluded: chain d residue 55 VAL Chi-restraints excluded: chain e residue 43 VAL Chi-restraints excluded: chain e residue 46 VAL Chi-restraints excluded: chain g residue 98 VAL Chi-restraints excluded: chain j residue 69 VAL Chi-restraints excluded: chain j residue 153 CYS Chi-restraints excluded: chain j residue 174 VAL Chi-restraints excluded: chain j residue 199 THR Chi-restraints excluded: chain j residue 249 CYS Chi-restraints excluded: chain i residue 166 SER Chi-restraints excluded: chain u residue 169 THR Chi-restraints excluded: chain u residue 184 THR Chi-restraints excluded: chain u residue 217 HIS Chi-restraints excluded: chain u residue 362 ASP Chi-restraints excluded: chain u residue 475 TYR Chi-restraints excluded: chain u residue 567 VAL Chi-restraints excluded: chain u residue 587 HIS Chi-restraints excluded: chain u residue 597 VAL Chi-restraints excluded: chain u residue 598 VAL Chi-restraints excluded: chain u residue 653 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 678 random chunks: chunk 545 optimal weight: 40.0000 chunk 372 optimal weight: 4.9990 chunk 9 optimal weight: 8.9990 chunk 487 optimal weight: 6.9990 chunk 270 optimal weight: 20.0000 chunk 559 optimal weight: 10.0000 chunk 453 optimal weight: 0.6980 chunk 0 optimal weight: 10.0000 chunk 334 optimal weight: 9.9990 chunk 588 optimal weight: 20.0000 chunk 165 optimal weight: 9.9990 overall best weight: 6.3388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 99 ASN ** C 186 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 105 ASN G 197 GLN ** G 227 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 32 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** M 42 ASN ** O 119 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** P 38 ASN Q 53 GLN Q 79 HIS R 24 HIS S 26 ASN ** S 118 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** T 42 HIS ** T 87 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 126 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 81 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** V 92 HIS W 56 HIS X 97 ASN X 127 ASN b 65 GLN e 44 ASN ** j 159 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** u 144 HIS ** u 180 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** u 301 GLN Total number of N/Q/H flips: 18 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8070 moved from start: 0.1853 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.127 80909 Z= 0.435 Angle : 0.724 10.024 116738 Z= 0.369 Chirality : 0.046 0.391 14312 Planarity : 0.005 0.076 9006 Dihedral : 23.550 179.848 30395 Min Nonbonded Distance : 2.056 Molprobity Statistics. All-atom Clashscore : 12.68 Ramachandran Plot: Outliers : 0.08 % Allowed : 5.23 % Favored : 94.69 % Rotamer: Outliers : 3.99 % Allowed : 20.56 % Favored : 75.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.31 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.08 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.43 (0.11), residues: 5278 helix: -0.21 (0.13), residues: 1615 sheet: -1.08 (0.16), residues: 995 loop : -1.31 (0.12), residues: 2668 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP C 30 HIS 0.018 0.001 HIS g 139 PHE 0.030 0.002 PHE F 79 TYR 0.030 0.002 TYR K 188 ARG 0.010 0.001 ARG b 80 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10556 Ramachandran restraints generated. 5278 Oldfield, 0 Emsley, 5278 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10556 Ramachandran restraints generated. 5278 Oldfield, 0 Emsley, 5278 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 711 residues out of total 4631 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 184 poor density : 527 time to evaluate : 4.685 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: C 103 MET cc_start: 0.8051 (tmm) cc_final: 0.7561 (tmm) REVERT: C 217 MET cc_start: 0.7399 (tpt) cc_final: 0.6946 (tpt) REVERT: E 66 MET cc_start: 0.8316 (mmm) cc_final: 0.8041 (mmm) REVERT: E 230 LYS cc_start: 0.9009 (OUTLIER) cc_final: 0.8605 (ttpp) REVERT: G 228 ILE cc_start: 0.6620 (OUTLIER) cc_final: 0.6405 (mm) REVERT: J 172 ARG cc_start: 0.9189 (OUTLIER) cc_final: 0.8870 (ptt180) REVERT: L 124 ASP cc_start: 0.7443 (OUTLIER) cc_final: 0.6793 (p0) REVERT: L 147 LYS cc_start: 0.8904 (OUTLIER) cc_final: 0.8643 (mtpp) REVERT: M 53 LYS cc_start: 0.8392 (OUTLIER) cc_final: 0.8105 (ttmt) REVERT: O 12 MET cc_start: 0.0263 (pp-130) cc_final: -0.0018 (pp-130) REVERT: P 128 ARG cc_start: 0.7237 (mmt90) cc_final: 0.6784 (mtt90) REVERT: T 126 PHE cc_start: 0.7103 (OUTLIER) cc_final: 0.6780 (t80) REVERT: V 82 MET cc_start: 0.7706 (OUTLIER) cc_final: 0.7093 (ttp) REVERT: W 4 MET cc_start: 0.8454 (OUTLIER) cc_final: 0.7988 (mpp) REVERT: X 119 ARG cc_start: 0.7610 (OUTLIER) cc_final: 0.7233 (mmt-90) REVERT: Y 74 MET cc_start: 0.7769 (OUTLIER) cc_final: 0.7163 (mpp) REVERT: g 97 LYS cc_start: 0.1243 (pttt) cc_final: 0.0343 (pttt) REVERT: u 217 HIS cc_start: 0.7223 (OUTLIER) cc_final: 0.5683 (p90) REVERT: u 345 MET cc_start: 0.4778 (pmm) cc_final: 0.4420 (pmm) outliers start: 184 outliers final: 108 residues processed: 658 average time/residue: 1.4829 time to fit residues: 1311.6072 Evaluate side-chains 620 residues out of total 4631 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 120 poor density : 500 time to evaluate : 4.643 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 6 ASP Chi-restraints excluded: chain B residue 79 SER Chi-restraints excluded: chain B residue 82 THR Chi-restraints excluded: chain C residue 29 ASP Chi-restraints excluded: chain C residue 47 THR Chi-restraints excluded: chain C residue 106 THR Chi-restraints excluded: chain C residue 186 ASN Chi-restraints excluded: chain D residue 63 VAL Chi-restraints excluded: chain D residue 160 LEU Chi-restraints excluded: chain D residue 162 ILE Chi-restraints excluded: chain D residue 190 SER Chi-restraints excluded: chain D residue 202 THR Chi-restraints excluded: chain D residue 215 MET Chi-restraints excluded: chain D residue 240 THR Chi-restraints excluded: chain D residue 260 VAL Chi-restraints excluded: chain E residue 19 MET Chi-restraints excluded: chain E residue 42 LEU Chi-restraints excluded: chain E residue 126 VAL Chi-restraints excluded: chain E residue 173 ILE Chi-restraints excluded: chain E residue 230 LYS Chi-restraints excluded: chain E residue 233 LYS Chi-restraints excluded: chain F residue 26 THR Chi-restraints excluded: chain F residue 91 VAL Chi-restraints excluded: chain G residue 78 SER Chi-restraints excluded: chain G residue 89 THR Chi-restraints excluded: chain G residue 126 ASP Chi-restraints excluded: chain G residue 127 THR Chi-restraints excluded: chain G residue 181 THR Chi-restraints excluded: chain G residue 197 GLN Chi-restraints excluded: chain G residue 228 ILE Chi-restraints excluded: chain H residue 105 THR Chi-restraints excluded: chain H residue 133 LEU Chi-restraints excluded: chain I residue 130 THR Chi-restraints excluded: chain I residue 138 ASN Chi-restraints excluded: chain J residue 100 LEU Chi-restraints excluded: chain J residue 112 THR Chi-restraints excluded: chain J residue 161 LEU Chi-restraints excluded: chain J residue 172 ARG Chi-restraints excluded: chain K residue 26 ASP Chi-restraints excluded: chain K residue 79 HIS Chi-restraints excluded: chain L residue 33 LEU Chi-restraints excluded: chain L residue 46 THR Chi-restraints excluded: chain L residue 66 VAL Chi-restraints excluded: chain L residue 76 VAL Chi-restraints excluded: chain L residue 85 THR Chi-restraints excluded: chain L residue 124 ASP Chi-restraints excluded: chain L residue 147 LYS Chi-restraints excluded: chain M residue 53 LYS Chi-restraints excluded: chain M residue 58 VAL Chi-restraints excluded: chain N residue 32 ASP Chi-restraints excluded: chain N residue 87 ASP Chi-restraints excluded: chain O residue 123 VAL Chi-restraints excluded: chain P residue 31 CYS Chi-restraints excluded: chain P residue 33 ILE Chi-restraints excluded: chain P residue 56 VAL Chi-restraints excluded: chain P residue 100 THR Chi-restraints excluded: chain Q residue 20 VAL Chi-restraints excluded: chain Q residue 79 HIS Chi-restraints excluded: chain R residue 12 VAL Chi-restraints excluded: chain R residue 22 VAL Chi-restraints excluded: chain S residue 73 LEU Chi-restraints excluded: chain S residue 74 GLN Chi-restraints excluded: chain S residue 85 VAL Chi-restraints excluded: chain S residue 101 ASP Chi-restraints excluded: chain S residue 130 THR Chi-restraints excluded: chain T residue 89 ASP Chi-restraints excluded: chain T residue 92 ASP Chi-restraints excluded: chain T residue 126 PHE Chi-restraints excluded: chain U residue 8 ASP Chi-restraints excluded: chain U residue 48 TYR Chi-restraints excluded: chain U residue 55 THR Chi-restraints excluded: chain V residue 31 SER Chi-restraints excluded: chain V residue 36 CYS Chi-restraints excluded: chain V residue 82 MET Chi-restraints excluded: chain W residue 4 MET Chi-restraints excluded: chain W residue 6 VAL Chi-restraints excluded: chain W residue 25 VAL Chi-restraints excluded: chain W residue 30 CYS Chi-restraints excluded: chain W residue 121 THR Chi-restraints excluded: chain X residue 72 VAL Chi-restraints excluded: chain X residue 108 LYS Chi-restraints excluded: chain X residue 119 ARG Chi-restraints excluded: chain Y residue 4 THR Chi-restraints excluded: chain Y residue 13 MET Chi-restraints excluded: chain Y residue 51 THR Chi-restraints excluded: chain Y residue 74 MET Chi-restraints excluded: chain Y residue 117 VAL Chi-restraints excluded: chain Z residue 52 THR Chi-restraints excluded: chain Z residue 66 ASP Chi-restraints excluded: chain a residue 107 VAL Chi-restraints excluded: chain b residue 53 VAL Chi-restraints excluded: chain b residue 55 LEU Chi-restraints excluded: chain b residue 63 LEU Chi-restraints excluded: chain d residue 42 ILE Chi-restraints excluded: chain d residue 50 VAL Chi-restraints excluded: chain d residue 55 VAL Chi-restraints excluded: chain d residue 58 LEU Chi-restraints excluded: chain e residue 22 GLN Chi-restraints excluded: chain e residue 43 VAL Chi-restraints excluded: chain e residue 46 VAL Chi-restraints excluded: chain g residue 102 VAL Chi-restraints excluded: chain j residue 97 THR Chi-restraints excluded: chain j residue 153 CYS Chi-restraints excluded: chain j residue 174 VAL Chi-restraints excluded: chain j residue 199 THR Chi-restraints excluded: chain j residue 249 CYS Chi-restraints excluded: chain j residue 286 CYS Chi-restraints excluded: chain i residue 166 SER Chi-restraints excluded: chain u residue 169 THR Chi-restraints excluded: chain u residue 184 THR Chi-restraints excluded: chain u residue 217 HIS Chi-restraints excluded: chain u residue 362 ASP Chi-restraints excluded: chain u residue 475 TYR Chi-restraints excluded: chain u residue 567 VAL Chi-restraints excluded: chain u residue 587 HIS Chi-restraints excluded: chain u residue 597 VAL Chi-restraints excluded: chain u residue 598 VAL Chi-restraints excluded: chain u residue 608 VAL Chi-restraints excluded: chain u residue 653 THR Chi-restraints excluded: chain u residue 729 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 678 random chunks: chunk 220 optimal weight: 0.4980 chunk 590 optimal weight: 20.0000 chunk 129 optimal weight: 3.9990 chunk 384 optimal weight: 0.9980 chunk 161 optimal weight: 5.9990 chunk 655 optimal weight: 7.9990 chunk 544 optimal weight: 10.0000 chunk 303 optimal weight: 5.9990 chunk 54 optimal weight: 0.9990 chunk 216 optimal weight: 1.9990 chunk 344 optimal weight: 9.9990 overall best weight: 1.6986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 99 ASN ** C 149 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 105 ASN G 197 GLN ** M 32 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 42 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 119 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 79 HIS R 80 GLN S 26 ASN T 42 HIS T 87 GLN U 83 GLN ** U 126 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** U 128 GLN ** V 81 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** V 92 HIS X 97 ASN X 127 ASN ** Z 47 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** b 65 GLN ** e 44 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** f 26 ASN j 143 GLN ** j 159 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** u 144 HIS ** u 180 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** u 617 HIS Total number of N/Q/H flips: 18 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7994 moved from start: 0.2096 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.052 80909 Z= 0.176 Angle : 0.618 12.126 116738 Z= 0.316 Chirality : 0.039 0.311 14312 Planarity : 0.004 0.067 9006 Dihedral : 23.460 179.794 30395 Min Nonbonded Distance : 2.053 Molprobity Statistics. All-atom Clashscore : 11.87 Ramachandran Plot: Outliers : 0.02 % Allowed : 4.24 % Favored : 95.74 % Rotamer: Outliers : 3.32 % Allowed : 21.93 % Favored : 74.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.31 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.04 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.09 (0.11), residues: 5278 helix: 0.15 (0.13), residues: 1606 sheet: -0.88 (0.16), residues: 962 loop : -1.16 (0.12), residues: 2710 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.001 TRP C 30 HIS 0.011 0.001 HIS Q 79 PHE 0.026 0.001 PHE F 79 TYR 0.028 0.001 TYR K 188 ARG 0.012 0.000 ARG d 31 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10556 Ramachandran restraints generated. 5278 Oldfield, 0 Emsley, 5278 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10556 Ramachandran restraints generated. 5278 Oldfield, 0 Emsley, 5278 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 690 residues out of total 4631 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 153 poor density : 537 time to evaluate : 4.756 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: C 103 MET cc_start: 0.8028 (tmm) cc_final: 0.7628 (tmm) REVERT: C 217 MET cc_start: 0.7468 (tpt) cc_final: 0.7229 (tpt) REVERT: E 70 ILE cc_start: 0.8924 (OUTLIER) cc_final: 0.8722 (mp) REVERT: E 199 GLU cc_start: 0.7303 (OUTLIER) cc_final: 0.6898 (pt0) REVERT: J 172 ARG cc_start: 0.9109 (OUTLIER) cc_final: 0.8850 (ptt180) REVERT: L 124 ASP cc_start: 0.7276 (OUTLIER) cc_final: 0.6542 (p0) REVERT: L 147 LYS cc_start: 0.8861 (OUTLIER) cc_final: 0.8537 (mtpp) REVERT: M 16 PHE cc_start: 0.3937 (t80) cc_final: 0.3652 (t80) REVERT: O 12 MET cc_start: 0.0280 (pp-130) cc_final: 0.0063 (pp-130) REVERT: P 128 ARG cc_start: 0.7160 (mmt90) cc_final: 0.6781 (mtt90) REVERT: Q 93 MET cc_start: 0.5856 (mmp) cc_final: 0.5655 (mmp) REVERT: T 126 PHE cc_start: 0.7113 (OUTLIER) cc_final: 0.6788 (t80) REVERT: U 83 GLN cc_start: 0.7526 (tt0) cc_final: 0.7256 (tt0) REVERT: W 4 MET cc_start: 0.8298 (OUTLIER) cc_final: 0.7832 (mpp) REVERT: X 119 ARG cc_start: 0.7498 (OUTLIER) cc_final: 0.7120 (mmt-90) REVERT: u 217 HIS cc_start: 0.7076 (OUTLIER) cc_final: 0.5721 (p90) REVERT: u 345 MET cc_start: 0.4463 (pmm) cc_final: 0.4184 (pmm) outliers start: 153 outliers final: 84 residues processed: 641 average time/residue: 1.4921 time to fit residues: 1283.1913 Evaluate side-chains 586 residues out of total 4631 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 93 poor density : 493 time to evaluate : 4.562 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 6 ASP Chi-restraints excluded: chain B residue 79 SER Chi-restraints excluded: chain B residue 82 THR Chi-restraints excluded: chain C residue 106 THR Chi-restraints excluded: chain D residue 132 ASP Chi-restraints excluded: chain D residue 162 ILE Chi-restraints excluded: chain D residue 245 SER Chi-restraints excluded: chain D residue 260 VAL Chi-restraints excluded: chain E residue 19 MET Chi-restraints excluded: chain E residue 42 LEU Chi-restraints excluded: chain E residue 70 ILE Chi-restraints excluded: chain E residue 126 VAL Chi-restraints excluded: chain E residue 173 ILE Chi-restraints excluded: chain E residue 199 GLU Chi-restraints excluded: chain E residue 251 GLU Chi-restraints excluded: chain F residue 26 THR Chi-restraints excluded: chain F residue 139 SER Chi-restraints excluded: chain G residue 126 ASP Chi-restraints excluded: chain G residue 181 THR Chi-restraints excluded: chain G residue 197 GLN Chi-restraints excluded: chain H residue 35 ASP Chi-restraints excluded: chain H residue 105 THR Chi-restraints excluded: chain H residue 133 LEU Chi-restraints excluded: chain I residue 130 THR Chi-restraints excluded: chain I residue 138 ASN Chi-restraints excluded: chain J residue 161 LEU Chi-restraints excluded: chain J residue 172 ARG Chi-restraints excluded: chain K residue 26 ASP Chi-restraints excluded: chain K residue 79 HIS Chi-restraints excluded: chain L residue 46 THR Chi-restraints excluded: chain L residue 66 VAL Chi-restraints excluded: chain L residue 85 THR Chi-restraints excluded: chain L residue 124 ASP Chi-restraints excluded: chain L residue 147 LYS Chi-restraints excluded: chain M residue 26 ASP Chi-restraints excluded: chain M residue 40 VAL Chi-restraints excluded: chain M residue 58 VAL Chi-restraints excluded: chain N residue 32 ASP Chi-restraints excluded: chain N residue 87 ASP Chi-restraints excluded: chain O residue 123 VAL Chi-restraints excluded: chain P residue 33 ILE Chi-restraints excluded: chain P residue 56 VAL Chi-restraints excluded: chain P residue 100 THR Chi-restraints excluded: chain Q residue 20 VAL Chi-restraints excluded: chain Q residue 79 HIS Chi-restraints excluded: chain Q residue 115 TYR Chi-restraints excluded: chain R residue 12 VAL Chi-restraints excluded: chain S residue 73 LEU Chi-restraints excluded: chain S residue 74 GLN Chi-restraints excluded: chain S residue 85 VAL Chi-restraints excluded: chain S residue 130 THR Chi-restraints excluded: chain T residue 89 ASP Chi-restraints excluded: chain T residue 92 ASP Chi-restraints excluded: chain T residue 126 PHE Chi-restraints excluded: chain U residue 8 ASP Chi-restraints excluded: chain U residue 48 TYR Chi-restraints excluded: chain V residue 31 SER Chi-restraints excluded: chain V residue 36 CYS Chi-restraints excluded: chain W residue 4 MET Chi-restraints excluded: chain W residue 25 VAL Chi-restraints excluded: chain X residue 72 VAL Chi-restraints excluded: chain X residue 100 VAL Chi-restraints excluded: chain X residue 105 PHE Chi-restraints excluded: chain X residue 119 ARG Chi-restraints excluded: chain Y residue 4 THR Chi-restraints excluded: chain Y residue 51 THR Chi-restraints excluded: chain Y residue 117 VAL Chi-restraints excluded: chain a residue 107 VAL Chi-restraints excluded: chain b residue 53 VAL Chi-restraints excluded: chain b residue 55 LEU Chi-restraints excluded: chain b residue 57 VAL Chi-restraints excluded: chain b residue 63 LEU Chi-restraints excluded: chain d residue 17 VAL Chi-restraints excluded: chain d residue 50 VAL Chi-restraints excluded: chain d residue 55 VAL Chi-restraints excluded: chain d residue 58 LEU Chi-restraints excluded: chain e residue 22 GLN Chi-restraints excluded: chain e residue 46 VAL Chi-restraints excluded: chain g residue 102 VAL Chi-restraints excluded: chain j residue 153 CYS Chi-restraints excluded: chain j residue 199 THR Chi-restraints excluded: chain j residue 249 CYS Chi-restraints excluded: chain u residue 169 THR Chi-restraints excluded: chain u residue 217 HIS Chi-restraints excluded: chain u residue 362 ASP Chi-restraints excluded: chain u residue 475 TYR Chi-restraints excluded: chain u residue 583 SER Chi-restraints excluded: chain u residue 587 HIS Chi-restraints excluded: chain u residue 597 VAL Chi-restraints excluded: chain u residue 598 VAL Chi-restraints excluded: chain u residue 608 VAL Chi-restraints excluded: chain u residue 653 THR Chi-restraints excluded: chain u residue 729 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 678 random chunks: chunk 632 optimal weight: 9.9990 chunk 73 optimal weight: 8.9990 chunk 373 optimal weight: 1.9990 chunk 479 optimal weight: 10.0000 chunk 371 optimal weight: 2.9990 chunk 552 optimal weight: 7.9990 chunk 366 optimal weight: 0.0170 chunk 653 optimal weight: 8.9990 chunk 408 optimal weight: 1.9990 chunk 398 optimal weight: 6.9990 chunk 301 optimal weight: 4.9990 overall best weight: 2.4026 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 99 ASN ** C 149 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 197 GLN ** M 32 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 119 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 79 HIS R 80 GLN T 42 HIS ** V 81 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** V 92 HIS X 127 ASN ** Z 47 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** b 65 GLN ** e 44 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** f 26 ASN ** j 159 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** j 226 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** u 144 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** u 180 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** u 595 ASN u 617 HIS Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8003 moved from start: 0.2195 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.112 80909 Z= 0.209 Angle : 0.626 12.925 116738 Z= 0.320 Chirality : 0.039 0.326 14312 Planarity : 0.004 0.066 9006 Dihedral : 23.387 179.876 30394 Min Nonbonded Distance : 2.044 Molprobity Statistics. All-atom Clashscore : 11.79 Ramachandran Plot: Outliers : 0.04 % Allowed : 4.36 % Favored : 95.60 % Rotamer: Outliers : 3.17 % Allowed : 23.21 % Favored : 73.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.31 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.04 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.97 (0.12), residues: 5278 helix: 0.25 (0.13), residues: 1602 sheet: -0.76 (0.16), residues: 971 loop : -1.10 (0.12), residues: 2705 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.026 0.001 TRP C 30 HIS 0.008 0.001 HIS Q 79 PHE 0.029 0.001 PHE U 21 TYR 0.035 0.001 TYR j 246 ARG 0.012 0.000 ARG d 31 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10556 Ramachandran restraints generated. 5278 Oldfield, 0 Emsley, 5278 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10556 Ramachandran restraints generated. 5278 Oldfield, 0 Emsley, 5278 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 669 residues out of total 4631 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 146 poor density : 523 time to evaluate : 4.633 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: C 103 MET cc_start: 0.7943 (tmm) cc_final: 0.7591 (tmm) REVERT: C 217 MET cc_start: 0.7463 (tpt) cc_final: 0.7211 (tpt) REVERT: E 199 GLU cc_start: 0.7321 (OUTLIER) cc_final: 0.6912 (pt0) REVERT: J 172 ARG cc_start: 0.9116 (OUTLIER) cc_final: 0.8839 (ptt180) REVERT: L 124 ASP cc_start: 0.7350 (OUTLIER) cc_final: 0.6575 (p0) REVERT: L 147 LYS cc_start: 0.8860 (OUTLIER) cc_final: 0.8560 (mtpp) REVERT: P 128 ARG cc_start: 0.7260 (mmt90) cc_final: 0.7043 (mtt90) REVERT: Q 93 MET cc_start: 0.6033 (mmp) cc_final: 0.5690 (mmp) REVERT: T 126 PHE cc_start: 0.7093 (OUTLIER) cc_final: 0.6767 (t80) REVERT: U 134 ILE cc_start: 0.7595 (OUTLIER) cc_final: 0.7360 (tt) REVERT: W 4 MET cc_start: 0.8303 (OUTLIER) cc_final: 0.7805 (mpp) REVERT: X 119 ARG cc_start: 0.7523 (OUTLIER) cc_final: 0.7132 (mmt-90) REVERT: u 217 HIS cc_start: 0.7078 (OUTLIER) cc_final: 0.5654 (p90) REVERT: u 345 MET cc_start: 0.4658 (pmm) cc_final: 0.4342 (pmm) outliers start: 146 outliers final: 89 residues processed: 621 average time/residue: 1.4955 time to fit residues: 1252.7868 Evaluate side-chains 590 residues out of total 4631 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 98 poor density : 492 time to evaluate : 4.561 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 6 ASP Chi-restraints excluded: chain B residue 79 SER Chi-restraints excluded: chain B residue 82 THR Chi-restraints excluded: chain B residue 198 MET Chi-restraints excluded: chain C residue 106 THR Chi-restraints excluded: chain D residue 160 LEU Chi-restraints excluded: chain D residue 162 ILE Chi-restraints excluded: chain D residue 202 THR Chi-restraints excluded: chain D residue 245 SER Chi-restraints excluded: chain D residue 260 VAL Chi-restraints excluded: chain D residue 271 ASP Chi-restraints excluded: chain E residue 19 MET Chi-restraints excluded: chain E residue 42 LEU Chi-restraints excluded: chain E residue 126 VAL Chi-restraints excluded: chain E residue 173 ILE Chi-restraints excluded: chain E residue 199 GLU Chi-restraints excluded: chain E residue 233 LYS Chi-restraints excluded: chain E residue 251 GLU Chi-restraints excluded: chain F residue 26 THR Chi-restraints excluded: chain F residue 91 VAL Chi-restraints excluded: chain F residue 139 SER Chi-restraints excluded: chain G residue 89 THR Chi-restraints excluded: chain G residue 126 ASP Chi-restraints excluded: chain H residue 35 ASP Chi-restraints excluded: chain H residue 105 THR Chi-restraints excluded: chain H residue 133 LEU Chi-restraints excluded: chain I residue 130 THR Chi-restraints excluded: chain I residue 138 ASN Chi-restraints excluded: chain J residue 100 LEU Chi-restraints excluded: chain J residue 112 THR Chi-restraints excluded: chain J residue 159 PHE Chi-restraints excluded: chain J residue 161 LEU Chi-restraints excluded: chain J residue 172 ARG Chi-restraints excluded: chain K residue 26 ASP Chi-restraints excluded: chain L residue 46 THR Chi-restraints excluded: chain L residue 66 VAL Chi-restraints excluded: chain L residue 85 THR Chi-restraints excluded: chain L residue 124 ASP Chi-restraints excluded: chain L residue 147 LYS Chi-restraints excluded: chain M residue 40 VAL Chi-restraints excluded: chain M residue 58 VAL Chi-restraints excluded: chain N residue 32 ASP Chi-restraints excluded: chain N residue 87 ASP Chi-restraints excluded: chain O residue 123 VAL Chi-restraints excluded: chain P residue 31 CYS Chi-restraints excluded: chain P residue 33 ILE Chi-restraints excluded: chain P residue 56 VAL Chi-restraints excluded: chain P residue 100 THR Chi-restraints excluded: chain Q residue 20 VAL Chi-restraints excluded: chain Q residue 79 HIS Chi-restraints excluded: chain Q residue 115 TYR Chi-restraints excluded: chain R residue 22 VAL Chi-restraints excluded: chain R residue 32 ILE Chi-restraints excluded: chain S residue 73 LEU Chi-restraints excluded: chain S residue 74 GLN Chi-restraints excluded: chain S residue 85 VAL Chi-restraints excluded: chain S residue 130 THR Chi-restraints excluded: chain T residue 89 ASP Chi-restraints excluded: chain T residue 92 ASP Chi-restraints excluded: chain T residue 126 PHE Chi-restraints excluded: chain U residue 8 ASP Chi-restraints excluded: chain U residue 48 TYR Chi-restraints excluded: chain U residue 134 ILE Chi-restraints excluded: chain V residue 31 SER Chi-restraints excluded: chain V residue 36 CYS Chi-restraints excluded: chain W residue 4 MET Chi-restraints excluded: chain W residue 25 VAL Chi-restraints excluded: chain X residue 72 VAL Chi-restraints excluded: chain X residue 100 VAL Chi-restraints excluded: chain X residue 119 ARG Chi-restraints excluded: chain Y residue 4 THR Chi-restraints excluded: chain Y residue 51 THR Chi-restraints excluded: chain Y residue 117 VAL Chi-restraints excluded: chain a residue 107 VAL Chi-restraints excluded: chain b residue 53 VAL Chi-restraints excluded: chain b residue 63 LEU Chi-restraints excluded: chain d residue 17 VAL Chi-restraints excluded: chain d residue 50 VAL Chi-restraints excluded: chain d residue 55 VAL Chi-restraints excluded: chain d residue 58 LEU Chi-restraints excluded: chain e residue 22 GLN Chi-restraints excluded: chain e residue 46 VAL Chi-restraints excluded: chain g residue 102 VAL Chi-restraints excluded: chain j residue 153 CYS Chi-restraints excluded: chain j residue 174 VAL Chi-restraints excluded: chain j residue 199 THR Chi-restraints excluded: chain j residue 249 CYS Chi-restraints excluded: chain u residue 169 THR Chi-restraints excluded: chain u residue 184 THR Chi-restraints excluded: chain u residue 217 HIS Chi-restraints excluded: chain u residue 362 ASP Chi-restraints excluded: chain u residue 475 TYR Chi-restraints excluded: chain u residue 583 SER Chi-restraints excluded: chain u residue 587 HIS Chi-restraints excluded: chain u residue 597 VAL Chi-restraints excluded: chain u residue 598 VAL Chi-restraints excluded: chain u residue 608 VAL Chi-restraints excluded: chain u residue 729 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 678 random chunks: chunk 404 optimal weight: 6.9990 chunk 260 optimal weight: 40.0000 chunk 390 optimal weight: 0.9990 chunk 196 optimal weight: 5.9990 chunk 128 optimal weight: 1.9990 chunk 126 optimal weight: 5.9990 chunk 415 optimal weight: 4.9990 chunk 445 optimal weight: 8.9990 chunk 323 optimal weight: 30.0000 chunk 60 optimal weight: 2.9990 chunk 513 optimal weight: 7.9990 overall best weight: 3.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 99 ASN ** C 149 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 105 ASN ** M 32 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 42 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 119 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 79 HIS T 42 HIS ** U 83 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 85 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** U 128 GLN ** V 81 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** V 92 HIS X 97 ASN X 127 ASN Z 47 ASN b 65 GLN ** e 44 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** f 26 ASN ** j 159 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** j 226 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** u 180 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8018 moved from start: 0.2233 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.096 80909 Z= 0.262 Angle : 0.647 13.052 116738 Z= 0.330 Chirality : 0.041 0.344 14312 Planarity : 0.004 0.072 9006 Dihedral : 23.365 179.929 30394 Min Nonbonded Distance : 2.047 Molprobity Statistics. All-atom Clashscore : 12.05 Ramachandran Plot: Outliers : 0.04 % Allowed : 4.70 % Favored : 95.26 % Rotamer: Outliers : 3.06 % Allowed : 23.34 % Favored : 73.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.31 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.04 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.90 (0.12), residues: 5278 helix: 0.31 (0.13), residues: 1597 sheet: -0.72 (0.16), residues: 970 loop : -1.06 (0.12), residues: 2711 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.034 0.001 TRP C 30 HIS 0.014 0.001 HIS u 144 PHE 0.021 0.001 PHE F 79 TYR 0.030 0.001 TYR K 188 ARG 0.018 0.000 ARG G 224 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10556 Ramachandran restraints generated. 5278 Oldfield, 0 Emsley, 5278 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10556 Ramachandran restraints generated. 5278 Oldfield, 0 Emsley, 5278 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 651 residues out of total 4631 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 141 poor density : 510 time to evaluate : 4.695 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: C 103 MET cc_start: 0.7918 (tmm) cc_final: 0.7643 (tmm) REVERT: C 217 MET cc_start: 0.7440 (tpt) cc_final: 0.7162 (tpt) REVERT: J 172 ARG cc_start: 0.9145 (OUTLIER) cc_final: 0.8841 (ptt180) REVERT: L 124 ASP cc_start: 0.7412 (OUTLIER) cc_final: 0.6620 (p0) REVERT: L 147 LYS cc_start: 0.8873 (OUTLIER) cc_final: 0.8571 (mtpp) REVERT: P 128 ARG cc_start: 0.7248 (mmt90) cc_final: 0.6842 (mtt90) REVERT: Q 93 MET cc_start: 0.6131 (mmp) cc_final: 0.5814 (mmp) REVERT: S 101 ASP cc_start: 0.7464 (p0) cc_final: 0.7172 (p0) REVERT: T 126 PHE cc_start: 0.7111 (OUTLIER) cc_final: 0.6780 (t80) REVERT: U 134 ILE cc_start: 0.7614 (OUTLIER) cc_final: 0.7382 (tt) REVERT: V 82 MET cc_start: 0.7662 (OUTLIER) cc_final: 0.7074 (ttp) REVERT: W 4 MET cc_start: 0.8363 (OUTLIER) cc_final: 0.7880 (mpp) REVERT: X 119 ARG cc_start: 0.7540 (OUTLIER) cc_final: 0.7151 (mmt-90) REVERT: Y 74 MET cc_start: 0.7763 (OUTLIER) cc_final: 0.7191 (mpp) REVERT: u 217 HIS cc_start: 0.6965 (OUTLIER) cc_final: 0.5546 (p90) REVERT: u 345 MET cc_start: 0.4587 (pmm) cc_final: 0.4261 (pmm) REVERT: u 597 VAL cc_start: 0.7648 (OUTLIER) cc_final: 0.7440 (p) outliers start: 141 outliers final: 91 residues processed: 604 average time/residue: 1.4963 time to fit residues: 1218.2347 Evaluate side-chains 588 residues out of total 4631 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 102 poor density : 486 time to evaluate : 4.598 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 6 ASP Chi-restraints excluded: chain B residue 79 SER Chi-restraints excluded: chain B residue 82 THR Chi-restraints excluded: chain B residue 198 MET Chi-restraints excluded: chain C residue 106 THR Chi-restraints excluded: chain D residue 160 LEU Chi-restraints excluded: chain D residue 162 ILE Chi-restraints excluded: chain D residue 190 SER Chi-restraints excluded: chain D residue 202 THR Chi-restraints excluded: chain D residue 245 SER Chi-restraints excluded: chain D residue 260 VAL Chi-restraints excluded: chain E residue 19 MET Chi-restraints excluded: chain E residue 42 LEU Chi-restraints excluded: chain E residue 126 VAL Chi-restraints excluded: chain E residue 173 ILE Chi-restraints excluded: chain E residue 233 LYS Chi-restraints excluded: chain E residue 251 GLU Chi-restraints excluded: chain F residue 26 THR Chi-restraints excluded: chain F residue 91 VAL Chi-restraints excluded: chain F residue 139 SER Chi-restraints excluded: chain G residue 89 THR Chi-restraints excluded: chain G residue 126 ASP Chi-restraints excluded: chain G residue 181 THR Chi-restraints excluded: chain G residue 225 GLN Chi-restraints excluded: chain H residue 105 THR Chi-restraints excluded: chain H residue 133 LEU Chi-restraints excluded: chain I residue 130 THR Chi-restraints excluded: chain I residue 138 ASN Chi-restraints excluded: chain J residue 100 LEU Chi-restraints excluded: chain J residue 112 THR Chi-restraints excluded: chain J residue 161 LEU Chi-restraints excluded: chain J residue 172 ARG Chi-restraints excluded: chain K residue 26 ASP Chi-restraints excluded: chain L residue 46 THR Chi-restraints excluded: chain L residue 66 VAL Chi-restraints excluded: chain L residue 85 THR Chi-restraints excluded: chain L residue 124 ASP Chi-restraints excluded: chain L residue 147 LYS Chi-restraints excluded: chain M residue 26 ASP Chi-restraints excluded: chain M residue 40 VAL Chi-restraints excluded: chain M residue 58 VAL Chi-restraints excluded: chain N residue 32 ASP Chi-restraints excluded: chain N residue 87 ASP Chi-restraints excluded: chain O residue 123 VAL Chi-restraints excluded: chain P residue 31 CYS Chi-restraints excluded: chain P residue 33 ILE Chi-restraints excluded: chain P residue 56 VAL Chi-restraints excluded: chain P residue 100 THR Chi-restraints excluded: chain Q residue 20 VAL Chi-restraints excluded: chain Q residue 79 HIS Chi-restraints excluded: chain Q residue 115 TYR Chi-restraints excluded: chain R residue 22 VAL Chi-restraints excluded: chain R residue 32 ILE Chi-restraints excluded: chain S residue 73 LEU Chi-restraints excluded: chain S residue 74 GLN Chi-restraints excluded: chain S residue 85 VAL Chi-restraints excluded: chain T residue 89 ASP Chi-restraints excluded: chain T residue 92 ASP Chi-restraints excluded: chain T residue 126 PHE Chi-restraints excluded: chain U residue 8 ASP Chi-restraints excluded: chain U residue 48 TYR Chi-restraints excluded: chain U residue 134 ILE Chi-restraints excluded: chain V residue 31 SER Chi-restraints excluded: chain V residue 36 CYS Chi-restraints excluded: chain V residue 82 MET Chi-restraints excluded: chain W residue 4 MET Chi-restraints excluded: chain W residue 25 VAL Chi-restraints excluded: chain W residue 30 CYS Chi-restraints excluded: chain X residue 72 VAL Chi-restraints excluded: chain X residue 100 VAL Chi-restraints excluded: chain X residue 119 ARG Chi-restraints excluded: chain Y residue 4 THR Chi-restraints excluded: chain Y residue 51 THR Chi-restraints excluded: chain Y residue 74 MET Chi-restraints excluded: chain Y residue 117 VAL Chi-restraints excluded: chain a residue 107 VAL Chi-restraints excluded: chain b residue 53 VAL Chi-restraints excluded: chain b residue 63 LEU Chi-restraints excluded: chain d residue 17 VAL Chi-restraints excluded: chain d residue 50 VAL Chi-restraints excluded: chain d residue 55 VAL Chi-restraints excluded: chain e residue 22 GLN Chi-restraints excluded: chain e residue 46 VAL Chi-restraints excluded: chain g residue 102 VAL Chi-restraints excluded: chain g residue 146 LEU Chi-restraints excluded: chain j residue 52 TYR Chi-restraints excluded: chain j residue 144 ASP Chi-restraints excluded: chain j residue 153 CYS Chi-restraints excluded: chain j residue 174 VAL Chi-restraints excluded: chain j residue 199 THR Chi-restraints excluded: chain j residue 249 CYS Chi-restraints excluded: chain u residue 169 THR Chi-restraints excluded: chain u residue 184 THR Chi-restraints excluded: chain u residue 217 HIS Chi-restraints excluded: chain u residue 362 ASP Chi-restraints excluded: chain u residue 475 TYR Chi-restraints excluded: chain u residue 583 SER Chi-restraints excluded: chain u residue 587 HIS Chi-restraints excluded: chain u residue 597 VAL Chi-restraints excluded: chain u residue 598 VAL Chi-restraints excluded: chain u residue 608 VAL Chi-restraints excluded: chain u residue 729 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 678 random chunks: chunk 594 optimal weight: 20.0000 chunk 626 optimal weight: 9.9990 chunk 571 optimal weight: 10.0000 chunk 608 optimal weight: 8.9990 chunk 625 optimal weight: 8.9990 chunk 366 optimal weight: 3.9990 chunk 265 optimal weight: 30.0000 chunk 478 optimal weight: 30.0000 chunk 186 optimal weight: 7.9990 chunk 550 optimal weight: 10.0000 chunk 575 optimal weight: 10.0000 overall best weight: 7.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 99 ASN H 112 ASN H 126 HIS ** M 32 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 42 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 119 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 79 HIS S 26 ASN S 93 GLN T 42 HIS ** U 83 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 85 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 126 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** U 128 GLN ** V 81 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** V 92 HIS X 127 ASN ** Z 47 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** e 44 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** f 26 ASN ** j 159 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** j 222 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** u 312 ASN Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8086 moved from start: 0.2209 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.009 0.152 80909 Z= 0.540 Angle : 0.798 14.237 116738 Z= 0.402 Chirality : 0.049 0.419 14312 Planarity : 0.006 0.075 9006 Dihedral : 23.473 179.773 30394 Min Nonbonded Distance : 2.055 Molprobity Statistics. All-atom Clashscore : 13.81 Ramachandran Plot: Outliers : 0.09 % Allowed : 5.67 % Favored : 94.24 % Rotamer: Outliers : 3.02 % Allowed : 23.80 % Favored : 73.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.31 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.08 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.14 (0.11), residues: 5278 helix: 0.08 (0.13), residues: 1604 sheet: -0.89 (0.16), residues: 998 loop : -1.17 (0.12), residues: 2676 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.037 0.002 TRP C 30 HIS 0.020 0.001 HIS Q 79 PHE 0.034 0.002 PHE J 147 TYR 0.031 0.002 TYR K 188 ARG 0.013 0.001 ARG d 31 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10556 Ramachandran restraints generated. 5278 Oldfield, 0 Emsley, 5278 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10556 Ramachandran restraints generated. 5278 Oldfield, 0 Emsley, 5278 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 642 residues out of total 4631 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 139 poor density : 503 time to evaluate : 4.620 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: C 103 MET cc_start: 0.8014 (tmm) cc_final: 0.7740 (tmm) REVERT: C 217 MET cc_start: 0.7508 (tpt) cc_final: 0.7179 (tpt) REVERT: E 230 LYS cc_start: 0.9014 (OUTLIER) cc_final: 0.8606 (ttpp) REVERT: L 124 ASP cc_start: 0.7673 (OUTLIER) cc_final: 0.7010 (p0) REVERT: L 147 LYS cc_start: 0.8928 (OUTLIER) cc_final: 0.8699 (mtpp) REVERT: P 128 ARG cc_start: 0.7273 (mmt90) cc_final: 0.7044 (mtt90) REVERT: R 68 ILE cc_start: 0.8029 (OUTLIER) cc_final: 0.7649 (pp) REVERT: T 126 PHE cc_start: 0.7140 (OUTLIER) cc_final: 0.6797 (t80) REVERT: U 134 ILE cc_start: 0.7725 (OUTLIER) cc_final: 0.7474 (tt) REVERT: V 82 MET cc_start: 0.7685 (OUTLIER) cc_final: 0.7025 (ttp) REVERT: W 4 MET cc_start: 0.8572 (OUTLIER) cc_final: 0.8108 (mpp) REVERT: X 119 ARG cc_start: 0.7632 (OUTLIER) cc_final: 0.7268 (mmt-90) REVERT: Y 74 MET cc_start: 0.7801 (OUTLIER) cc_final: 0.7188 (mpp) REVERT: g 97 LYS cc_start: 0.2030 (pttt) cc_final: 0.1772 (pttt) REVERT: u 217 HIS cc_start: 0.7253 (OUTLIER) cc_final: 0.5689 (p90) REVERT: u 345 MET cc_start: 0.4618 (pmm) cc_final: 0.4310 (pmm) outliers start: 139 outliers final: 95 residues processed: 601 average time/residue: 1.5533 time to fit residues: 1271.2772 Evaluate side-chains 595 residues out of total 4631 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 106 poor density : 489 time to evaluate : 4.605 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 6 ASP Chi-restraints excluded: chain B residue 79 SER Chi-restraints excluded: chain B residue 82 THR Chi-restraints excluded: chain C residue 106 THR Chi-restraints excluded: chain D residue 63 VAL Chi-restraints excluded: chain D residue 160 LEU Chi-restraints excluded: chain D residue 162 ILE Chi-restraints excluded: chain D residue 190 SER Chi-restraints excluded: chain D residue 202 THR Chi-restraints excluded: chain D residue 215 MET Chi-restraints excluded: chain D residue 240 THR Chi-restraints excluded: chain D residue 245 SER Chi-restraints excluded: chain D residue 260 VAL Chi-restraints excluded: chain E residue 19 MET Chi-restraints excluded: chain E residue 42 LEU Chi-restraints excluded: chain E residue 126 VAL Chi-restraints excluded: chain E residue 173 ILE Chi-restraints excluded: chain E residue 230 LYS Chi-restraints excluded: chain E residue 233 LYS Chi-restraints excluded: chain E residue 251 GLU Chi-restraints excluded: chain F residue 26 THR Chi-restraints excluded: chain F residue 91 VAL Chi-restraints excluded: chain F residue 139 SER Chi-restraints excluded: chain G residue 89 THR Chi-restraints excluded: chain G residue 126 ASP Chi-restraints excluded: chain G residue 127 THR Chi-restraints excluded: chain G residue 157 VAL Chi-restraints excluded: chain G residue 181 THR Chi-restraints excluded: chain G residue 225 GLN Chi-restraints excluded: chain H residue 105 THR Chi-restraints excluded: chain H residue 133 LEU Chi-restraints excluded: chain I residue 130 THR Chi-restraints excluded: chain I residue 138 ASN Chi-restraints excluded: chain J residue 100 LEU Chi-restraints excluded: chain J residue 112 THR Chi-restraints excluded: chain J residue 161 LEU Chi-restraints excluded: chain K residue 26 ASP Chi-restraints excluded: chain K residue 79 HIS Chi-restraints excluded: chain L residue 46 THR Chi-restraints excluded: chain L residue 66 VAL Chi-restraints excluded: chain L residue 85 THR Chi-restraints excluded: chain L residue 124 ASP Chi-restraints excluded: chain L residue 147 LYS Chi-restraints excluded: chain M residue 40 VAL Chi-restraints excluded: chain M residue 58 VAL Chi-restraints excluded: chain N residue 32 ASP Chi-restraints excluded: chain N residue 87 ASP Chi-restraints excluded: chain O residue 123 VAL Chi-restraints excluded: chain P residue 31 CYS Chi-restraints excluded: chain P residue 33 ILE Chi-restraints excluded: chain P residue 56 VAL Chi-restraints excluded: chain P residue 100 THR Chi-restraints excluded: chain Q residue 20 VAL Chi-restraints excluded: chain R residue 22 VAL Chi-restraints excluded: chain R residue 68 ILE Chi-restraints excluded: chain R residue 127 CYS Chi-restraints excluded: chain S residue 57 LEU Chi-restraints excluded: chain S residue 73 LEU Chi-restraints excluded: chain S residue 74 GLN Chi-restraints excluded: chain S residue 85 VAL Chi-restraints excluded: chain T residue 89 ASP Chi-restraints excluded: chain T residue 92 ASP Chi-restraints excluded: chain T residue 126 PHE Chi-restraints excluded: chain U residue 8 ASP Chi-restraints excluded: chain U residue 48 TYR Chi-restraints excluded: chain U residue 134 ILE Chi-restraints excluded: chain V residue 31 SER Chi-restraints excluded: chain V residue 36 CYS Chi-restraints excluded: chain V residue 82 MET Chi-restraints excluded: chain W residue 4 MET Chi-restraints excluded: chain W residue 25 VAL Chi-restraints excluded: chain W residue 30 CYS Chi-restraints excluded: chain X residue 72 VAL Chi-restraints excluded: chain X residue 100 VAL Chi-restraints excluded: chain X residue 119 ARG Chi-restraints excluded: chain Y residue 4 THR Chi-restraints excluded: chain Y residue 51 THR Chi-restraints excluded: chain Y residue 74 MET Chi-restraints excluded: chain Y residue 117 VAL Chi-restraints excluded: chain Z residue 82 ASN Chi-restraints excluded: chain a residue 107 VAL Chi-restraints excluded: chain b residue 53 VAL Chi-restraints excluded: chain b residue 57 VAL Chi-restraints excluded: chain b residue 63 LEU Chi-restraints excluded: chain d residue 17 VAL Chi-restraints excluded: chain d residue 50 VAL Chi-restraints excluded: chain d residue 55 VAL Chi-restraints excluded: chain e residue 22 GLN Chi-restraints excluded: chain e residue 46 VAL Chi-restraints excluded: chain g residue 102 VAL Chi-restraints excluded: chain g residue 146 LEU Chi-restraints excluded: chain j residue 52 TYR Chi-restraints excluded: chain j residue 97 THR Chi-restraints excluded: chain j residue 174 VAL Chi-restraints excluded: chain j residue 249 CYS Chi-restraints excluded: chain i residue 166 SER Chi-restraints excluded: chain u residue 169 THR Chi-restraints excluded: chain u residue 184 THR Chi-restraints excluded: chain u residue 217 HIS Chi-restraints excluded: chain u residue 362 ASP Chi-restraints excluded: chain u residue 475 TYR Chi-restraints excluded: chain u residue 583 SER Chi-restraints excluded: chain u residue 587 HIS Chi-restraints excluded: chain u residue 597 VAL Chi-restraints excluded: chain u residue 608 VAL Chi-restraints excluded: chain u residue 729 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 678 random chunks: chunk 606 optimal weight: 40.0000 chunk 399 optimal weight: 3.9990 chunk 643 optimal weight: 5.9990 chunk 393 optimal weight: 9.9990 chunk 305 optimal weight: 5.9990 chunk 447 optimal weight: 6.9990 chunk 675 optimal weight: 40.0000 chunk 621 optimal weight: 5.9990 chunk 537 optimal weight: 50.0000 chunk 55 optimal weight: 3.9990 chunk 415 optimal weight: 2.9990 overall best weight: 4.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 99 ASN ** C 149 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 105 ASN H 112 ASN ** M 32 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 42 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 119 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** R 80 GLN S 93 GLN T 42 HIS U 83 GLN ** U 128 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 81 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** V 92 HIS X 97 ASN X 127 ASN ** Z 47 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** e 44 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** f 26 ASN ** j 159 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** u 180 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8048 moved from start: 0.2266 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.100 80909 Z= 0.334 Angle : 0.707 16.286 116738 Z= 0.359 Chirality : 0.043 0.403 14312 Planarity : 0.005 0.072 9006 Dihedral : 23.442 179.960 30394 Min Nonbonded Distance : 2.058 Molprobity Statistics. All-atom Clashscore : 13.06 Ramachandran Plot: Outliers : 0.06 % Allowed : 4.83 % Favored : 95.11 % Rotamer: Outliers : 2.67 % Allowed : 24.10 % Favored : 73.23 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.31 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.06 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.04 (0.11), residues: 5278 helix: 0.17 (0.13), residues: 1591 sheet: -0.83 (0.16), residues: 988 loop : -1.12 (0.12), residues: 2699 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.050 0.002 TRP C 30 HIS 0.012 0.001 HIS u 144 PHE 0.023 0.002 PHE F 79 TYR 0.031 0.002 TYR K 188 ARG 0.015 0.001 ARG d 31 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10556 Ramachandran restraints generated. 5278 Oldfield, 0 Emsley, 5278 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10556 Ramachandran restraints generated. 5278 Oldfield, 0 Emsley, 5278 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 621 residues out of total 4631 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 123 poor density : 498 time to evaluate : 4.755 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: L 124 ASP cc_start: 0.7478 (OUTLIER) cc_final: 0.6865 (p0) REVERT: L 147 LYS cc_start: 0.8891 (OUTLIER) cc_final: 0.8605 (mtpp) REVERT: R 68 ILE cc_start: 0.8055 (OUTLIER) cc_final: 0.7671 (pp) REVERT: T 126 PHE cc_start: 0.7165 (OUTLIER) cc_final: 0.6803 (t80) REVERT: U 83 GLN cc_start: 0.7598 (tt0) cc_final: 0.7346 (tt0) REVERT: V 82 MET cc_start: 0.7679 (OUTLIER) cc_final: 0.7004 (ttp) REVERT: W 4 MET cc_start: 0.8485 (OUTLIER) cc_final: 0.7986 (mpp) REVERT: X 119 ARG cc_start: 0.7581 (OUTLIER) cc_final: 0.7197 (mmt-90) REVERT: u 217 HIS cc_start: 0.7089 (OUTLIER) cc_final: 0.5624 (p90) REVERT: u 345 MET cc_start: 0.4606 (pmm) cc_final: 0.4319 (pmm) outliers start: 123 outliers final: 98 residues processed: 587 average time/residue: 1.4983 time to fit residues: 1183.9234 Evaluate side-chains 596 residues out of total 4631 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 106 poor density : 490 time to evaluate : 4.574 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 6 ASP Chi-restraints excluded: chain B residue 79 SER Chi-restraints excluded: chain B residue 82 THR Chi-restraints excluded: chain C residue 106 THR Chi-restraints excluded: chain D residue 160 LEU Chi-restraints excluded: chain D residue 162 ILE Chi-restraints excluded: chain D residue 190 SER Chi-restraints excluded: chain D residue 202 THR Chi-restraints excluded: chain D residue 245 SER Chi-restraints excluded: chain D residue 260 VAL Chi-restraints excluded: chain E residue 19 MET Chi-restraints excluded: chain E residue 26 VAL Chi-restraints excluded: chain E residue 42 LEU Chi-restraints excluded: chain E residue 126 VAL Chi-restraints excluded: chain E residue 173 ILE Chi-restraints excluded: chain E residue 251 GLU Chi-restraints excluded: chain F residue 26 THR Chi-restraints excluded: chain F residue 91 VAL Chi-restraints excluded: chain F residue 139 SER Chi-restraints excluded: chain G residue 89 THR Chi-restraints excluded: chain G residue 126 ASP Chi-restraints excluded: chain G residue 127 THR Chi-restraints excluded: chain G residue 157 VAL Chi-restraints excluded: chain G residue 181 THR Chi-restraints excluded: chain H residue 92 VAL Chi-restraints excluded: chain H residue 105 THR Chi-restraints excluded: chain H residue 112 ASN Chi-restraints excluded: chain H residue 133 LEU Chi-restraints excluded: chain I residue 130 THR Chi-restraints excluded: chain I residue 138 ASN Chi-restraints excluded: chain J residue 100 LEU Chi-restraints excluded: chain J residue 112 THR Chi-restraints excluded: chain J residue 161 LEU Chi-restraints excluded: chain K residue 26 ASP Chi-restraints excluded: chain K residue 79 HIS Chi-restraints excluded: chain L residue 46 THR Chi-restraints excluded: chain L residue 66 VAL Chi-restraints excluded: chain L residue 85 THR Chi-restraints excluded: chain L residue 124 ASP Chi-restraints excluded: chain L residue 147 LYS Chi-restraints excluded: chain M residue 26 ASP Chi-restraints excluded: chain M residue 35 LEU Chi-restraints excluded: chain M residue 58 VAL Chi-restraints excluded: chain N residue 32 ASP Chi-restraints excluded: chain N residue 87 ASP Chi-restraints excluded: chain O residue 123 VAL Chi-restraints excluded: chain P residue 31 CYS Chi-restraints excluded: chain P residue 33 ILE Chi-restraints excluded: chain P residue 100 THR Chi-restraints excluded: chain Q residue 20 VAL Chi-restraints excluded: chain Q residue 79 HIS Chi-restraints excluded: chain R residue 22 VAL Chi-restraints excluded: chain R residue 68 ILE Chi-restraints excluded: chain R residue 127 CYS Chi-restraints excluded: chain S residue 57 LEU Chi-restraints excluded: chain S residue 73 LEU Chi-restraints excluded: chain S residue 74 GLN Chi-restraints excluded: chain S residue 85 VAL Chi-restraints excluded: chain T residue 89 ASP Chi-restraints excluded: chain T residue 92 ASP Chi-restraints excluded: chain T residue 126 PHE Chi-restraints excluded: chain U residue 8 ASP Chi-restraints excluded: chain U residue 35 ASP Chi-restraints excluded: chain U residue 48 TYR Chi-restraints excluded: chain V residue 31 SER Chi-restraints excluded: chain V residue 36 CYS Chi-restraints excluded: chain V residue 82 MET Chi-restraints excluded: chain V residue 97 ILE Chi-restraints excluded: chain W residue 4 MET Chi-restraints excluded: chain W residue 25 VAL Chi-restraints excluded: chain W residue 30 CYS Chi-restraints excluded: chain X residue 72 VAL Chi-restraints excluded: chain X residue 100 VAL Chi-restraints excluded: chain X residue 119 ARG Chi-restraints excluded: chain Y residue 4 THR Chi-restraints excluded: chain Y residue 51 THR Chi-restraints excluded: chain Y residue 117 VAL Chi-restraints excluded: chain Y residue 120 THR Chi-restraints excluded: chain a residue 68 ILE Chi-restraints excluded: chain a residue 107 VAL Chi-restraints excluded: chain b residue 53 VAL Chi-restraints excluded: chain b residue 57 VAL Chi-restraints excluded: chain b residue 63 LEU Chi-restraints excluded: chain d residue 17 VAL Chi-restraints excluded: chain d residue 50 VAL Chi-restraints excluded: chain d residue 55 VAL Chi-restraints excluded: chain e residue 22 GLN Chi-restraints excluded: chain e residue 46 VAL Chi-restraints excluded: chain g residue 102 VAL Chi-restraints excluded: chain g residue 146 LEU Chi-restraints excluded: chain j residue 52 TYR Chi-restraints excluded: chain j residue 174 VAL Chi-restraints excluded: chain j residue 249 CYS Chi-restraints excluded: chain i residue 166 SER Chi-restraints excluded: chain u residue 169 THR Chi-restraints excluded: chain u residue 184 THR Chi-restraints excluded: chain u residue 186 THR Chi-restraints excluded: chain u residue 217 HIS Chi-restraints excluded: chain u residue 362 ASP Chi-restraints excluded: chain u residue 475 TYR Chi-restraints excluded: chain u residue 583 SER Chi-restraints excluded: chain u residue 587 HIS Chi-restraints excluded: chain u residue 597 VAL Chi-restraints excluded: chain u residue 598 VAL Chi-restraints excluded: chain u residue 608 VAL Chi-restraints excluded: chain u residue 729 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 678 random chunks: chunk 329 optimal weight: 9.9990 chunk 427 optimal weight: 10.0000 chunk 572 optimal weight: 7.9990 chunk 164 optimal weight: 8.9990 chunk 495 optimal weight: 5.9990 chunk 79 optimal weight: 7.9990 chunk 149 optimal weight: 5.9990 chunk 538 optimal weight: 50.0000 chunk 225 optimal weight: 20.0000 chunk 553 optimal weight: 6.9990 chunk 68 optimal weight: 0.9980 overall best weight: 5.5988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 99 ASN G 105 ASN ** M 32 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 42 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 119 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** R 80 GLN S 93 GLN T 42 HIS ** V 81 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** V 92 HIS X 97 ASN X 127 ASN ** Z 47 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** e 44 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** f 26 ASN ** j 159 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** j 222 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** u 180 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3893 r_free = 0.3893 target = 0.093780 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3383 r_free = 0.3383 target = 0.069328 restraints weight = 218884.698| |-----------------------------------------------------------------------------| r_work (start): 0.3297 rms_B_bonded: 2.97 r_work: 0.2640 rms_B_bonded: 3.85 restraints_weight: 0.5000 r_work (final): 0.2640 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8804 moved from start: 0.2297 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.117 80909 Z= 0.395 Angle : 0.735 17.025 116738 Z= 0.372 Chirality : 0.045 0.438 14312 Planarity : 0.005 0.073 9006 Dihedral : 23.430 179.827 30394 Min Nonbonded Distance : 2.050 Molprobity Statistics. All-atom Clashscore : 13.34 Ramachandran Plot: Outliers : 0.06 % Allowed : 5.44 % Favored : 94.51 % Rotamer: Outliers : 2.65 % Allowed : 24.29 % Favored : 73.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.31 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.08 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.09 (0.11), residues: 5278 helix: 0.11 (0.13), residues: 1588 sheet: -0.85 (0.16), residues: 989 loop : -1.13 (0.12), residues: 2701 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.074 0.002 TRP U 52 HIS 0.012 0.001 HIS u 144 PHE 0.036 0.002 PHE U 21 TYR 0.032 0.002 TYR K 188 ARG 0.015 0.001 ARG d 31 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 20361.60 seconds wall clock time: 357 minutes 50.73 seconds (21470.73 seconds total)