Starting phenix.real_space_refine (version: 1.21rc1) on Sat Jul 15 04:09:35 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/4v1a_2787/07_2023/4v1a_2787_neut.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/4v1a_2787/07_2023/4v1a_2787.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.4 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/4v1a_2787/07_2023/4v1a_2787.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/4v1a_2787/07_2023/4v1a_2787.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/4v1a_2787/07_2023/4v1a_2787_neut.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/4v1a_2787/07_2023/4v1a_2787_neut.pdb" } resolution = 3.4 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.004 sd= 0.025 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians Zn 1 6.06 5 S 124 5.16 5 C 20336 2.51 5 N 5766 2.21 5 O 5690 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "b PHE 167": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "c PHE 176": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.08s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5013/modules/chem_data/mon_lib" Total number of atoms: 31917 Number of models: 1 Model: "" Number of chains: 24 Chain: "a" Number of atoms: 3173 Number of conformers: 1 Conformer: "" Number of residues, atoms: 393, 3173 Classifications: {'peptide': 393} Link IDs: {'PTRANS': 35, 'TRANS': 357} Chain: "b" Number of atoms: 2952 Number of conformers: 1 Conformer: "" Number of residues, atoms: 354, 2952 Classifications: {'peptide': 354} Link IDs: {'PTRANS': 32, 'TRANS': 321} Chain: "c" Number of atoms: 2408 Number of conformers: 1 Conformer: "" Number of residues, atoms: 295, 2408 Classifications: {'peptide': 295} Link IDs: {'PTRANS': 15, 'TRANS': 279} Chain: "d" Number of atoms: 832 Number of conformers: 1 Conformer: "" Number of residues, atoms: 99, 832 Classifications: {'peptide': 99} Link IDs: {'PTRANS': 11, 'TRANS': 87} Chain: "e" Number of atoms: 968 Number of conformers: 1 Conformer: "" Number of residues, atoms: 121, 968 Classifications: {'peptide': 121} Link IDs: {'PTRANS': 11, 'TRANS': 109} Chain: "f" Number of atoms: 852 Number of conformers: 1 Conformer: "" Number of residues, atoms: 108, 852 Classifications: {'peptide': 108} Link IDs: {'PTRANS': 10, 'TRANS': 97} Unresolved non-hydrogen bonds: 24 Unresolved non-hydrogen angles: 48 Planarities with less than four sites: {'UNK:plan-1': 24} Unresolved non-hydrogen planarities: 24 Chain: "g" Number of atoms: 1167 Number of conformers: 1 Conformer: "" Number of residues, atoms: 148, 1167 Classifications: {'peptide': 148} Link IDs: {'PTRANS': 10, 'TRANS': 137} Chain: "h" Number of atoms: 2319 Number of conformers: 1 Conformer: "" Number of residues, atoms: 289, 2319 Classifications: {'peptide': 289} Link IDs: {'PTRANS': 18, 'TRANS': 270} Chain: "i" Number of atoms: 1979 Number of conformers: 1 Conformer: "" Number of residues, atoms: 242, 1979 Classifications: {'peptide': 242} Link IDs: {'PTRANS': 20, 'TRANS': 221} Chain: "j" Number of atoms: 1775 Number of conformers: 1 Conformer: "" Number of residues, atoms: 217, 1775 Classifications: {'peptide': 217} Link IDs: {'PTRANS': 9, 'TRANS': 207} Chain breaks: 2 Chain: "k" Number of atoms: 1050 Number of conformers: 1 Conformer: "" Number of residues, atoms: 131, 1050 Classifications: {'peptide': 131} Link IDs: {'PTRANS': 4, 'TRANS': 126} Chain breaks: 2 Chain: "l" Number of atoms: 1097 Number of conformers: 1 Conformer: "" Number of residues, atoms: 133, 1097 Classifications: {'peptide': 133} Link IDs: {'PCIS': 1, 'PTRANS': 15, 'TRANS': 116} Chain: "m" Number of atoms: 893 Number of conformers: 1 Conformer: "" Number of residues, atoms: 109, 893 Classifications: {'peptide': 109} Link IDs: {'PTRANS': 8, 'TRANS': 100} Chain: "n" Number of atoms: 837 Number of conformers: 1 Conformer: "" Number of residues, atoms: 97, 837 Classifications: {'peptide': 97} Link IDs: {'PTRANS': 4, 'TRANS': 92} Chain: "o" Number of atoms: 747 Number of conformers: 1 Conformer: "" Number of residues, atoms: 94, 747 Classifications: {'peptide': 94} Link IDs: {'PTRANS': 6, 'TRANS': 87} Chain: "p" Number of atoms: 742 Number of conformers: 1 Conformer: "" Number of residues, atoms: 97, 742 Classifications: {'peptide': 97} Link IDs: {'PTRANS': 2, 'TRANS': 94} Chain: "q" Number of atoms: 336 Number of conformers: 1 Conformer: "" Number of residues, atoms: 37, 336 Classifications: {'peptide': 37} Link IDs: {'PTRANS': 3, 'TRANS': 33} Chain: "t" Number of atoms: 780 Number of conformers: 1 Conformer: "" Number of residues, atoms: 94, 780 Classifications: {'peptide': 94} Link IDs: {'PTRANS': 5, 'TRANS': 88} Chain: "u" Number of atoms: 1208 Number of conformers: 1 Conformer: "" Number of residues, atoms: 151, 1208 Classifications: {'peptide': 151} Link IDs: {'PTRANS': 5, 'TRANS': 145} Chain breaks: 1 Unresolved non-hydrogen bonds: 10 Unresolved non-hydrogen angles: 20 Planarities with less than four sites: {'UNK:plan-1': 10} Unresolved non-hydrogen planarities: 10 Chain: "v" Number of atoms: 1068 Number of conformers: 1 Conformer: "" Number of residues, atoms: 131, 1068 Classifications: {'peptide': 131} Link IDs: {'PTRANS': 12, 'TRANS': 118} Chain breaks: 1 Unresolved non-hydrogen bonds: 12 Unresolved non-hydrogen angles: 24 Planarities with less than four sites: {'UNK:plan-1': 12} Unresolved non-hydrogen planarities: 12 Chain: "w" Number of atoms: 3126 Number of conformers: 1 Conformer: "" Number of residues, atoms: 387, 3126 Classifications: {'peptide': 387} Link IDs: {'PCIS': 1, 'PTRANS': 25, 'TRANS': 360} Chain: "x" Number of atoms: 1325 Number of conformers: 1 Conformer: "" Number of residues, atoms: 162, 1325 Classifications: {'peptide': 162} Link IDs: {'PTRANS': 18, 'TRANS': 143} Chain: "z" Number of atoms: 282 Number of conformers: 1 Conformer: "" Number of residues, atoms: 47, 282 Classifications: {'peptide': 47} Link IDs: {'TRANS': 46} Chain breaks: 5 Unresolved non-hydrogen bonds: 47 Unresolved non-hydrogen angles: 94 Planarities with less than four sites: {'UNK:plan-1': 47} Unresolved non-hydrogen planarities: 47 Chain: "x" 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 30586 SG CYS x 70 104.313 101.405 191.425 1.00100.37 S ATOM 30607 SG CYS x 73 108.012 102.136 191.452 1.00 79.09 S ATOM 30904 SG CYS x 108 106.515 100.013 188.707 1.00 59.61 S Time building chain proxies: 14.34, per 1000 atoms: 0.45 Number of scatterers: 31917 At special positions: 0 Unit cell: (264.6, 218.4, 229.6, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) Zn 1 29.99 S 124 16.00 O 5690 8.00 N 5766 7.00 C 20336 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: 15.05 Conformation dependent library (CDL) restraints added in 4.7 seconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN x 500 " pdb="ZN ZN x 500 " - pdb=" SG CYS x 70 " pdb="ZN ZN x 500 " - pdb=" SG CYS x 73 " pdb="ZN ZN x 500 " - pdb=" SG CYS x 108 " 7570 Ramachandran restraints generated. 3785 Oldfield, 0 Emsley, 3785 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 7508 Finding SS restraints... Secondary structure from input PDB file: 141 helices and 34 sheets defined 43.2% alpha, 18.2% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.63 Creating SS restraints... Processing helix chain 'a' and resid 47 through 51 Processing helix chain 'a' and resid 60 through 63 Processing helix chain 'a' and resid 92 through 96 Processing helix chain 'a' and resid 115 through 125 Processing helix chain 'a' and resid 133 through 142 Processing helix chain 'a' and resid 149 through 163 removed outlier: 3.607A pdb=" N LEU a 155 " --> pdb=" O ASP a 151 " (cutoff:3.500A) Processing helix chain 'a' and resid 172 through 190 Proline residue: a 178 - end of helix removed outlier: 3.545A pdb=" N SER a 190 " --> pdb=" O GLN a 186 " (cutoff:3.500A) Processing helix chain 'a' and resid 191 through 194 Processing helix chain 'a' and resid 197 through 199 No H-bonds generated for 'chain 'a' and resid 197 through 199' Processing helix chain 'a' and resid 241 through 250 Processing helix chain 'a' and resid 305 through 329 removed outlier: 3.614A pdb=" N ARG a 310 " --> pdb=" O PRO a 306 " (cutoff:3.500A) removed outlier: 3.542A pdb=" N GLN a 324 " --> pdb=" O SER a 320 " (cutoff:3.500A) Processing helix chain 'a' and resid 407 through 419 removed outlier: 4.283A pdb=" N PHE a 411 " --> pdb=" O GLN a 407 " (cutoff:3.500A) Processing helix chain 'b' and resid 44 through 48 Processing helix chain 'b' and resid 53 through 67 removed outlier: 3.711A pdb=" N LYS b 67 " --> pdb=" O GLN b 63 " (cutoff:3.500A) Processing helix chain 'b' and resid 73 through 78 removed outlier: 3.648A pdb=" N HIS b 77 " --> pdb=" O THR b 73 " (cutoff:3.500A) Processing helix chain 'b' and resid 98 through 115 removed outlier: 3.708A pdb=" N GLN b 102 " --> pdb=" O SER b 98 " (cutoff:3.500A) Processing helix chain 'b' and resid 116 through 125 removed outlier: 3.564A pdb=" N GLU b 120 " --> pdb=" O ASN b 116 " (cutoff:3.500A) removed outlier: 3.562A pdb=" N LEU b 125 " --> pdb=" O ARG b 121 " (cutoff:3.500A) Processing helix chain 'b' and resid 131 through 142 Processing helix chain 'b' and resid 143 through 155 removed outlier: 3.756A pdb=" N GLN b 149 " --> pdb=" O PRO b 145 " (cutoff:3.500A) removed outlier: 3.575A pdb=" N ARG b 150 " --> pdb=" O TYR b 146 " (cutoff:3.500A) Processing helix chain 'b' and resid 196 through 200 removed outlier: 4.076A pdb=" N GLN b 200 " --> pdb=" O GLU b 197 " (cutoff:3.500A) Processing helix chain 'b' and resid 299 through 308 Processing helix chain 'b' and resid 326 through 334 removed outlier: 3.579A pdb=" N HIS b 332 " --> pdb=" O THR b 328 " (cutoff:3.500A) Processing helix chain 'b' and resid 362 through 369 removed outlier: 3.607A pdb=" N TYR b 369 " --> pdb=" O LEU b 366 " (cutoff:3.500A) Processing helix chain 'c' and resid 33 through 54 removed outlier: 3.537A pdb=" N ILE c 38 " --> pdb=" O PRO c 34 " (cutoff:3.500A) Processing helix chain 'c' and resid 84 through 90 Processing helix chain 'c' and resid 93 through 100 removed outlier: 3.547A pdb=" N CYS c 97 " --> pdb=" O SER c 93 " (cutoff:3.500A) Processing helix chain 'c' and resid 132 through 153 removed outlier: 3.573A pdb=" N MET c 147 " --> pdb=" O CYS c 143 " (cutoff:3.500A) removed outlier: 3.744A pdb=" N CYS c 149 " --> pdb=" O MET c 145 " (cutoff:3.500A) removed outlier: 3.759A pdb=" N ARG c 153 " --> pdb=" O CYS c 149 " (cutoff:3.500A) Processing helix chain 'c' and resid 184 through 187 Processing helix chain 'c' and resid 192 through 209 removed outlier: 3.745A pdb=" N LYS c 209 " --> pdb=" O ALA c 205 " (cutoff:3.500A) Processing helix chain 'c' and resid 220 through 228 removed outlier: 3.961A pdb=" N GLU c 225 " --> pdb=" O LYS c 221 " (cutoff:3.500A) removed outlier: 4.045A pdb=" N ILE c 226 " --> pdb=" O VAL c 222 " (cutoff:3.500A) removed outlier: 3.655A pdb=" N PHE c 227 " --> pdb=" O ALA c 223 " (cutoff:3.500A) Processing helix chain 'c' and resid 230 through 244 removed outlier: 3.769A pdb=" N ASN c 244 " --> pdb=" O LYS c 240 " (cutoff:3.500A) Processing helix chain 'c' and resid 305 through 316 removed outlier: 3.757A pdb=" N ASN c 310 " --> pdb=" O PHE c 306 " (cutoff:3.500A) Processing helix chain 'd' and resid 91 through 95 Processing helix chain 'd' and resid 95 through 100 removed outlier: 4.000A pdb=" N GLU d 98 " --> pdb=" O LEU d 95 " (cutoff:3.500A) removed outlier: 4.247A pdb=" N ARG d 99 " --> pdb=" O ASN d 96 " (cutoff:3.500A) removed outlier: 3.607A pdb=" N GLN d 100 " --> pdb=" O LYS d 97 " (cutoff:3.500A) No H-bonds generated for 'chain 'd' and resid 95 through 100' Processing helix chain 'd' and resid 107 through 154 removed outlier: 3.528A pdb=" N GLU d 130 " --> pdb=" O GLN d 126 " (cutoff:3.500A) Processing helix chain 'd' and resid 155 through 161 Processing helix chain 'd' and resid 165 through 169 removed outlier: 3.700A pdb=" N LEU d 168 " --> pdb=" O ASP d 165 " (cutoff:3.500A) Processing helix chain 'e' and resid 52 through 55 Processing helix chain 'e' and resid 85 through 93 removed outlier: 3.629A pdb=" N THR e 93 " --> pdb=" O LEU e 89 " (cutoff:3.500A) Processing helix chain 'e' and resid 93 through 104 removed outlier: 4.173A pdb=" N ALA e 97 " --> pdb=" O THR e 93 " (cutoff:3.500A) Processing helix chain 'e' and resid 112 through 116 Processing helix chain 'f' and resid 68 through 72 Processing helix chain 'f' and resid 88 through 95 Processing helix chain 'f' and resid 104 through 116 Processing helix chain 'f' and resid 127 through 133 removed outlier: 3.770A pdb=" N ARG f 133 " --> pdb=" O TYR f 129 " (cutoff:3.500A) Processing helix chain 'g' and resid 13 through 17 removed outlier: 3.952A pdb=" N HIS g 16 " --> pdb=" O SER g 13 " (cutoff:3.500A) Processing helix chain 'g' and resid 37 through 39 No H-bonds generated for 'chain 'g' and resid 37 through 39' Processing helix chain 'g' and resid 40 through 49 Processing helix chain 'g' and resid 49 through 58 removed outlier: 4.584A pdb=" N ASP g 53 " --> pdb=" O ARG g 49 " (cutoff:3.500A) Processing helix chain 'g' and resid 93 through 106 removed outlier: 3.956A pdb=" N ASP g 106 " --> pdb=" O GLN g 102 " (cutoff:3.500A) Processing helix chain 'g' and resid 139 through 143 removed outlier: 3.706A pdb=" N GLY g 142 " --> pdb=" O THR g 139 " (cutoff:3.500A) Processing helix chain 'h' and resid 34 through 53 removed outlier: 3.686A pdb=" N LYS h 43 " --> pdb=" O TYR h 39 " (cutoff:3.500A) removed outlier: 3.715A pdb=" N GLU h 44 " --> pdb=" O ARG h 40 " (cutoff:3.500A) Processing helix chain 'h' and resid 67 through 79 removed outlier: 3.506A pdb=" N GLY h 76 " --> pdb=" O ILE h 72 " (cutoff:3.500A) removed outlier: 3.567A pdb=" N LEU h 79 " --> pdb=" O PHE h 75 " (cutoff:3.500A) Processing helix chain 'h' and resid 84 through 92 Processing helix chain 'h' and resid 94 through 108 Processing helix chain 'h' and resid 112 through 118 Processing helix chain 'h' and resid 122 through 145 Processing helix chain 'h' and resid 149 through 161 Processing helix chain 'h' and resid 162 through 173 Processing helix chain 'h' and resid 174 through 179 removed outlier: 3.527A pdb=" N LEU h 178 " --> pdb=" O ALA h 174 " (cutoff:3.500A) Processing helix chain 'h' and resid 187 through 206 removed outlier: 3.535A pdb=" N GLN h 193 " --> pdb=" O PRO h 189 " (cutoff:3.500A) removed outlier: 3.500A pdb=" N VAL h 198 " --> pdb=" O THR h 194 " (cutoff:3.500A) Processing helix chain 'h' and resid 207 through 219 removed outlier: 3.625A pdb=" N LEU h 213 " --> pdb=" O GLU h 209 " (cutoff:3.500A) Processing helix chain 'h' and resid 220 through 224 Processing helix chain 'h' and resid 227 through 233 removed outlier: 3.650A pdb=" N MET h 231 " --> pdb=" O GLU h 227 " (cutoff:3.500A) removed outlier: 3.512A pdb=" N THR h 233 " --> pdb=" O PHE h 229 " (cutoff:3.500A) Processing helix chain 'h' and resid 236 through 248 Processing helix chain 'h' and resid 288 through 306 Processing helix chain 'i' and resid 93 through 98 Processing helix chain 'i' and resid 100 through 115 removed outlier: 3.989A pdb=" N ALA i 106 " --> pdb=" O LYS i 102 " (cutoff:3.500A) removed outlier: 3.642A pdb=" N ASN i 115 " --> pdb=" O ARG i 111 " (cutoff:3.500A) Processing helix chain 'i' and resid 115 through 129 Processing helix chain 'i' and resid 136 through 155 removed outlier: 3.554A pdb=" N LYS i 140 " --> pdb=" O ASP i 136 " (cutoff:3.500A) removed outlier: 3.788A pdb=" N PHE i 145 " --> pdb=" O ALA i 141 " (cutoff:3.500A) removed outlier: 3.621A pdb=" N ILE i 146 " --> pdb=" O LYS i 142 " (cutoff:3.500A) removed outlier: 3.661A pdb=" N LEU i 150 " --> pdb=" O ILE i 146 " (cutoff:3.500A) Processing helix chain 'i' and resid 156 through 164 removed outlier: 3.665A pdb=" N LEU i 160 " --> pdb=" O ASP i 156 " (cutoff:3.500A) removed outlier: 3.723A pdb=" N THR i 162 " --> pdb=" O ASP i 158 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N VAL i 164 " --> pdb=" O LEU i 160 " (cutoff:3.500A) Processing helix chain 'i' and resid 167 through 177 removed outlier: 4.563A pdb=" N ASP i 171 " --> pdb=" O ASN i 167 " (cutoff:3.500A) removed outlier: 3.810A pdb=" N MET i 172 " --> pdb=" O CYS i 168 " (cutoff:3.500A) removed outlier: 3.812A pdb=" N ILE i 176 " --> pdb=" O MET i 172 " (cutoff:3.500A) Processing helix chain 'j' and resid 64 through 81 Processing helix chain 'j' and resid 85 through 104 removed outlier: 3.943A pdb=" N GLU j 94 " --> pdb=" O ARG j 90 " (cutoff:3.500A) removed outlier: 3.699A pdb=" N ALA j 99 " --> pdb=" O ALA j 95 " (cutoff:3.500A) removed outlier: 3.562A pdb=" N LYS j 100 " --> pdb=" O GLN j 96 " (cutoff:3.500A) Processing helix chain 'j' and resid 116 through 130 Processing helix chain 'j' and resid 183 through 197 removed outlier: 3.553A pdb=" N SER j 196 " --> pdb=" O LEU j 192 " (cutoff:3.500A) removed outlier: 3.677A pdb=" N GLU j 197 " --> pdb=" O ALA j 193 " (cutoff:3.500A) Processing helix chain 'j' and resid 256 through 264 removed outlier: 3.579A pdb=" N ASP j 262 " --> pdb=" O GLU j 258 " (cutoff:3.500A) removed outlier: 3.618A pdb=" N LEU j 264 " --> pdb=" O LEU j 260 " (cutoff:3.500A) Processing helix chain 'j' and resid 266 through 271 Processing helix chain 'k' and resid 99 through 117 Processing helix chain 'k' and resid 163 through 177 removed outlier: 3.795A pdb=" N GLU k 172 " --> pdb=" O GLU k 168 " (cutoff:3.500A) removed outlier: 3.584A pdb=" N ILE k 173 " --> pdb=" O ILE k 169 " (cutoff:3.500A) Processing helix chain 'l' and resid 42 through 44 No H-bonds generated for 'chain 'l' and resid 42 through 44' Processing helix chain 'l' and resid 45 through 50 removed outlier: 3.611A pdb=" N ARG l 50 " --> pdb=" O HIS l 46 " (cutoff:3.500A) Processing helix chain 'l' and resid 116 through 133 removed outlier: 3.609A pdb=" N LEU l 120 " --> pdb=" O ASP l 116 " (cutoff:3.500A) Proline residue: l 130 - end of helix Processing helix chain 'l' and resid 153 through 164 Processing helix chain 'm' and resid 66 through 80 Processing helix chain 'm' and resid 94 through 109 Processing helix chain 'm' and resid 115 through 120 Processing helix chain 'm' and resid 123 through 132 removed outlier: 4.071A pdb=" N VAL m 127 " --> pdb=" O ARG m 123 " (cutoff:3.500A) Processing helix chain 'm' and resid 139 through 146 Processing helix chain 'n' and resid 48 through 53 Processing helix chain 'n' and resid 59 through 64 Processing helix chain 'n' and resid 69 through 74 Processing helix chain 'n' and resid 86 through 98 Processing helix chain 'n' and resid 99 through 102 Processing helix chain 'n' and resid 103 through 124 Processing helix chain 'o' and resid 24 through 32 Processing helix chain 'o' and resid 41 through 46 removed outlier: 3.513A pdb=" N GLU o 45 " --> pdb=" O GLY o 41 " (cutoff:3.500A) removed outlier: 3.755A pdb=" N LEU o 46 " --> pdb=" O PRO o 42 " (cutoff:3.500A) No H-bonds generated for 'chain 'o' and resid 41 through 46' Processing helix chain 'o' and resid 60 through 109 removed outlier: 3.686A pdb=" N GLU o 103 " --> pdb=" O LEU o 99 " (cutoff:3.500A) removed outlier: 3.854A pdb=" N GLN o 106 " --> pdb=" O GLU o 102 " (cutoff:3.500A) Processing helix chain 'p' and resid 2 through 7 Processing helix chain 'p' and resid 8 through 11 removed outlier: 5.733A pdb=" N ARG p 11 " --> pdb=" O LEU p 8 " (cutoff:3.500A) No H-bonds generated for 'chain 'p' and resid 8 through 11' Processing helix chain 'p' and resid 27 through 38 Processing helix chain 'p' and resid 39 through 46 removed outlier: 3.947A pdb=" N ASN p 46 " --> pdb=" O VAL p 42 " (cutoff:3.500A) Processing helix chain 'p' and resid 82 through 95 removed outlier: 3.549A pdb=" N LEU p 87 " --> pdb=" O ALA p 83 " (cutoff:3.500A) Processing helix chain 'q' and resid 117 through 132 removed outlier: 3.696A pdb=" N LEU q 121 " --> pdb=" O TYR q 117 " (cutoff:3.500A) removed outlier: 3.549A pdb=" N HIS q 129 " --> pdb=" O ASN q 125 " (cutoff:3.500A) Processing helix chain 't' and resid 28 through 50 Processing helix chain 't' and resid 64 through 80 removed outlier: 3.750A pdb=" N PHE t 71 " --> pdb=" O ARG t 67 " (cutoff:3.500A) removed outlier: 3.828A pdb=" N GLN t 78 " --> pdb=" O LEU t 74 " (cutoff:3.500A) Processing helix chain 't' and resid 87 through 94 removed outlier: 4.107A pdb=" N GLN t 91 " --> pdb=" O ARG t 87 " (cutoff:3.500A) Processing helix chain 't' and resid 95 through 99 removed outlier: 3.501A pdb=" N THR t 98 " --> pdb=" O LEU t 95 " (cutoff:3.500A) Processing helix chain 'u' and resid 44 through 49 Processing helix chain 'u' and resid 54 through 58 removed outlier: 3.673A pdb=" N ALA u 58 " --> pdb=" O SER u 55 " (cutoff:3.500A) Processing helix chain 'u' and resid 72 through 76 Processing helix chain 'u' and resid 111 through 118 Processing helix chain 'u' and resid 141 through 162 removed outlier: 3.743A pdb=" N ASN u 145 " --> pdb=" O TYR u 141 " (cutoff:3.500A) Processing helix chain 'u' and resid 170 through 189 removed outlier: 3.768A pdb=" N LEU u 174 " --> pdb=" O UNK u 170 " (cutoff:3.500A) removed outlier: 5.493A pdb=" N ARG u 176 " --> pdb=" O UNK u 172 " (cutoff:3.500A) removed outlier: 4.848A pdb=" N SER u 177 " --> pdb=" O UNK u 173 " (cutoff:3.500A) removed outlier: 3.668A pdb=" N LEU u 187 " --> pdb=" O ASN u 183 " (cutoff:3.500A) Processing helix chain 'v' and resid 48 through 52 Processing helix chain 'v' and resid 53 through 64 removed outlier: 3.630A pdb=" N ALA v 57 " --> pdb=" O SER v 53 " (cutoff:3.500A) removed outlier: 3.555A pdb=" N ALA v 58 " --> pdb=" O PRO v 54 " (cutoff:3.500A) Processing helix chain 'v' and resid 71 through 76 removed outlier: 3.599A pdb=" N TRP v 76 " --> pdb=" O GLY v 73 " (cutoff:3.500A) Processing helix chain 'v' and resid 78 through 93 Processing helix chain 'v' and resid 95 through 154 removed outlier: 3.650A pdb=" N VAL v 105 " --> pdb=" O GLU v 101 " (cutoff:3.500A) removed outlier: 3.756A pdb=" N GLN v 106 " --> pdb=" O SER v 102 " (cutoff:3.500A) Proline residue: v 129 - end of helix removed outlier: 3.569A pdb=" N UNK v 144 " --> pdb=" O GLN v 140 " (cutoff:3.500A) Processing helix chain 'w' and resid 55 through 72 Processing helix chain 'w' and resid 75 through 85 removed outlier: 3.582A pdb=" N LYS w 79 " --> pdb=" O SER w 75 " (cutoff:3.500A) Processing helix chain 'w' and resid 101 through 111 removed outlier: 4.143A pdb=" N TRP w 105 " --> pdb=" O ASN w 101 " (cutoff:3.500A) Processing helix chain 'w' and resid 132 through 149 removed outlier: 3.684A pdb=" N LEU w 136 " --> pdb=" O ASP w 132 " (cutoff:3.500A) removed outlier: 3.590A pdb=" N CYS w 143 " --> pdb=" O ALA w 139 " (cutoff:3.500A) Processing helix chain 'w' and resid 162 through 184 removed outlier: 3.655A pdb=" N SER w 168 " --> pdb=" O GLU w 164 " (cutoff:3.500A) Proline residue: w 169 - end of helix removed outlier: 3.885A pdb=" N GLY w 180 " --> pdb=" O ALA w 176 " (cutoff:3.500A) removed outlier: 3.597A pdb=" N LEU w 181 " --> pdb=" O SER w 177 " (cutoff:3.500A) Processing helix chain 'w' and resid 186 through 191 removed outlier: 3.622A pdb=" N ALA w 191 " --> pdb=" O VAL w 188 " (cutoff:3.500A) Processing helix chain 'w' and resid 261 through 265 Processing helix chain 'w' and resid 297 through 300 Processing helix chain 'w' and resid 301 through 308 Processing helix chain 'w' and resid 312 through 337 removed outlier: 3.788A pdb=" N PHE w 318 " --> pdb=" O ILE w 314 " (cutoff:3.500A) removed outlier: 3.773A pdb=" N PHE w 327 " --> pdb=" O ILE w 323 " (cutoff:3.500A) removed outlier: 3.729A pdb=" N GLN w 333 " --> pdb=" O TRP w 329 " (cutoff:3.500A) Processing helix chain 'w' and resid 340 through 344 removed outlier: 3.749A pdb=" N ASP w 344 " --> pdb=" O SER w 341 " (cutoff:3.500A) Processing helix chain 'w' and resid 374 through 381 removed outlier: 4.521A pdb=" N ASN w 380 " --> pdb=" O GLN w 376 " (cutoff:3.500A) removed outlier: 3.654A pdb=" N ASN w 381 " --> pdb=" O ALA w 377 " (cutoff:3.500A) Processing helix chain 'w' and resid 408 through 420 removed outlier: 3.960A pdb=" N LEU w 412 " --> pdb=" O ASN w 408 " (cutoff:3.500A) Processing helix chain 'x' and resid 70 through 75 removed outlier: 3.855A pdb=" N TRP x 75 " --> pdb=" O PRO x 71 " (cutoff:3.500A) Processing helix chain 'x' and resid 85 through 90 removed outlier: 3.513A pdb=" N LEU x 89 " --> pdb=" O ASP x 85 " (cutoff:3.500A) Processing helix chain 'x' and resid 101 through 106 Processing helix chain 'x' and resid 108 through 125 Processing helix chain 'x' and resid 128 through 132 removed outlier: 3.941A pdb=" N ARG x 132 " --> pdb=" O PRO x 129 " (cutoff:3.500A) Processing helix chain 'x' and resid 135 through 139 removed outlier: 3.672A pdb=" N PHE x 139 " --> pdb=" O PRO x 136 " (cutoff:3.500A) Processing helix chain 'x' and resid 178 through 182 Processing helix chain 'z' and resid 9 through 35 Processing helix chain 'z' and resid 201 through 210 Processing sheet with id= AA, first strand: chain 'a' and resid 208 through 215 removed outlier: 4.982A pdb=" N LEU a 219 " --> pdb=" O ALA a 103 " (cutoff:3.500A) removed outlier: 10.217A pdb=" N GLN a 102 " --> pdb=" O VAL a 270 " (cutoff:3.500A) removed outlier: 6.482A pdb=" N VAL a 270 " --> pdb=" O GLN a 102 " (cutoff:3.500A) Processing sheet with id= AB, first strand: chain 'a' and resid 126 through 129 removed outlier: 6.498A pdb=" N ASN a 372 " --> pdb=" O ASN a 360 " (cutoff:3.500A) removed outlier: 6.411A pdb=" N ASN a 360 " --> pdb=" O ASN a 372 " (cutoff:3.500A) removed outlier: 5.079A pdb=" N ALA a 374 " --> pdb=" O GLN a 358 " (cutoff:3.500A) removed outlier: 7.098A pdb=" N GLN a 358 " --> pdb=" O ALA a 374 " (cutoff:3.500A) removed outlier: 5.555A pdb=" N VAL a 376 " --> pdb=" O VAL a 356 " (cutoff:3.500A) removed outlier: 7.590A pdb=" N VAL a 356 " --> pdb=" O VAL a 376 " (cutoff:3.500A) removed outlier: 4.956A pdb=" N SER a 378 " --> pdb=" O PHE a 354 " (cutoff:3.500A) removed outlier: 6.867A pdb=" N PHE a 354 " --> pdb=" O SER a 378 " (cutoff:3.500A) removed outlier: 10.052A pdb=" N PHE a 352 " --> pdb=" O SER a 344 " (cutoff:3.500A) removed outlier: 11.444A pdb=" N SER a 344 " --> pdb=" O PHE a 352 " (cutoff:3.500A) removed outlier: 10.836A pdb=" N PHE a 354 " --> pdb=" O VAL a 342 " (cutoff:3.500A) removed outlier: 11.807A pdb=" N VAL a 342 " --> pdb=" O PHE a 354 " (cutoff:3.500A) removed outlier: 10.099A pdb=" N VAL a 356 " --> pdb=" O VAL a 340 " (cutoff:3.500A) removed outlier: 10.822A pdb=" N VAL a 340 " --> pdb=" O VAL a 356 " (cutoff:3.500A) removed outlier: 10.410A pdb=" N GLN a 358 " --> pdb=" O GLN a 338 " (cutoff:3.500A) removed outlier: 11.380A pdb=" N GLN a 338 " --> pdb=" O GLN a 358 " (cutoff:3.500A) removed outlier: 7.011A pdb=" N ASN a 360 " --> pdb=" O LEU a 336 " (cutoff:3.500A) removed outlier: 12.069A pdb=" N CYS a 287 " --> pdb=" O PRO a 339 " (cutoff:3.500A) removed outlier: 9.215A pdb=" N VAL a 341 " --> pdb=" O CYS a 287 " (cutoff:3.500A) removed outlier: 6.014A pdb=" N HIS a 289 " --> pdb=" O VAL a 341 " (cutoff:3.500A) removed outlier: 5.710A pdb=" N ALA a 232 " --> pdb=" O PRO a 288 " (cutoff:3.500A) Processing sheet with id= AC, first strand: chain 'a' and resid 385 through 387 removed outlier: 3.847A pdb=" N HIS a 385 " --> pdb=" O ILE a 404 " (cutoff:3.500A) Processing sheet with id= AD, first strand: chain 'a' and resid 391 through 393 removed outlier: 6.764A pdb=" N VAL a 391 " --> pdb=" O VAL a 398 " (cutoff:3.500A) Processing sheet with id= BA, first strand: chain 'b' and resid 88 through 89 Processing sheet with id= BB, first strand: chain 'b' and resid 203 through 205 removed outlier: 4.546A pdb=" N VAL b 175 " --> pdb=" O VAL b 187 " (cutoff:3.500A) removed outlier: 4.240A pdb=" N LYS u 190 " --> pdb=" O LEU b 184 " (cutoff:3.500A) Processing sheet with id= BC, first strand: chain 'b' and resid 191 through 192 removed outlier: 4.087A pdb=" N ASN b 191 " --> pdb=" O PHE b 318 " (cutoff:3.500A) removed outlier: 6.001A pdb=" N LYS b 274 " --> pdb=" O PRO b 313 " (cutoff:3.500A) removed outlier: 3.765A pdb=" N GLY b 315 " --> pdb=" O LEU b 272 " (cutoff:3.500A) removed outlier: 6.725A pdb=" N TRP b 214 " --> pdb=" O THR b 238 " (cutoff:3.500A) removed outlier: 5.064A pdb=" N THR b 238 " --> pdb=" O TRP b 214 " (cutoff:3.500A) removed outlier: 7.106A pdb=" N LEU b 216 " --> pdb=" O LEU b 236 " (cutoff:3.500A) removed outlier: 4.866A pdb=" N LEU b 236 " --> pdb=" O LEU b 216 " (cutoff:3.500A) removed outlier: 6.853A pdb=" N LEU b 218 " --> pdb=" O HIS b 234 " (cutoff:3.500A) removed outlier: 6.467A pdb=" N LEU b 236 " --> pdb=" O THR b 251 " (cutoff:3.500A) Processing sheet with id= CA, first strand: chain 'c' and resid 108 through 111 removed outlier: 3.902A pdb=" N LEU c 102 " --> pdb=" O LEU c 125 " (cutoff:3.500A) removed outlier: 4.330A pdb=" N THR c 74 " --> pdb=" O HIS c 66 " (cutoff:3.500A) Processing sheet with id= CB, first strand: chain 'c' and resid 161 through 163 removed outlier: 4.724A pdb=" N LEU c 182 " --> pdb=" O LEU c 289 " (cutoff:3.500A) removed outlier: 7.135A pdb=" N LEU c 289 " --> pdb=" O LEU c 182 " (cutoff:3.500A) removed outlier: 6.694A pdb=" N VAL c 290 " --> pdb=" O HIS c 281 " (cutoff:3.500A) removed outlier: 6.807A pdb=" N HIS c 281 " --> pdb=" O VAL c 290 " (cutoff:3.500A) removed outlier: 6.921A pdb=" N ARG c 292 " --> pdb=" O ALA c 279 " (cutoff:3.500A) removed outlier: 6.760A pdb=" N ALA c 279 " --> pdb=" O ARG c 292 " (cutoff:3.500A) removed outlier: 7.197A pdb=" N GLN c 294 " --> pdb=" O VAL c 277 " (cutoff:3.500A) removed outlier: 5.208A pdb=" N VAL c 277 " --> pdb=" O GLN c 294 " (cutoff:3.500A) removed outlier: 6.698A pdb=" N LEU c 296 " --> pdb=" O TYR c 275 " (cutoff:3.500A) removed outlier: 4.491A pdb=" N TYR c 275 " --> pdb=" O LEU c 296 " (cutoff:3.500A) removed outlier: 6.423A pdb=" N LEU c 298 " --> pdb=" O PHE c 273 " (cutoff:3.500A) Processing sheet with id= CC, first strand: chain 'c' and resid 214 through 219 Processing sheet with id= DA, first strand: chain 'd' and resid 172 through 174 removed outlier: 7.614A pdb=" N THR k 152 " --> pdb=" O PRO k 128 " (cutoff:3.500A) removed outlier: 7.299A pdb=" N GLU k 154 " --> pdb=" O ALA k 126 " (cutoff:3.500A) removed outlier: 5.002A pdb=" N ALA k 126 " --> pdb=" O GLU k 154 " (cutoff:3.500A) removed outlier: 6.478A pdb=" N VAL k 156 " --> pdb=" O SER k 124 " (cutoff:3.500A) removed outlier: 4.317A pdb=" N SER k 124 " --> pdb=" O VAL k 156 " (cutoff:3.500A) removed outlier: 6.713A pdb=" N GLN k 158 " --> pdb=" O GLU k 122 " (cutoff:3.500A) Processing sheet with id= EA, first strand: chain 'e' and resid 40 through 42 Processing sheet with id= FA, first strand: chain 'f' and resid 48 through 51 Processing sheet with id= FB, first strand: chain 'f' and resid 73 through 74 removed outlier: 5.744A pdb=" N SER h 255 " --> pdb=" O TYR h 275 " (cutoff:3.500A) removed outlier: 6.751A pdb=" N TYR h 275 " --> pdb=" O SER h 255 " (cutoff:3.500A) removed outlier: 5.312A pdb=" N LEU h 257 " --> pdb=" O GLY h 273 " (cutoff:3.500A) removed outlier: 6.424A pdb=" N GLY h 273 " --> pdb=" O LEU h 257 " (cutoff:3.500A) removed outlier: 3.746A pdb=" N ARG h 259 " --> pdb=" O PHE h 271 " (cutoff:3.500A) removed outlier: 6.183A pdb=" N TYR h 270 " --> pdb=" O PRO h 285 " (cutoff:3.500A) removed outlier: 6.400A pdb=" N VAL h 272 " --> pdb=" O GLU h 283 " (cutoff:3.500A) removed outlier: 4.354A pdb=" N GLU h 283 " --> pdb=" O VAL h 272 " (cutoff:3.500A) removed outlier: 6.765A pdb=" N LEU h 274 " --> pdb=" O ILE h 281 " (cutoff:3.500A) Processing sheet with id= GA, first strand: chain 'g' and resid 84 through 88 removed outlier: 6.868A pdb=" N ARG g 74 " --> pdb=" O PHE g 31 " (cutoff:3.500A) removed outlier: 4.577A pdb=" N PHE g 31 " --> pdb=" O ARG g 74 " (cutoff:3.500A) removed outlier: 6.436A pdb=" N VAL g 76 " --> pdb=" O LEU g 29 " (cutoff:3.500A) removed outlier: 4.523A pdb=" N LEU g 29 " --> pdb=" O VAL g 76 " (cutoff:3.500A) removed outlier: 6.782A pdb=" N GLU g 78 " --> pdb=" O GLN g 27 " (cutoff:3.500A) Processing sheet with id= IA, first strand: chain 'i' and resid 180 through 187 removed outlier: 30.827A pdb=" N THR i 180 " --> pdb=" O THR i 213 " (cutoff:3.500A) removed outlier: 26.782A pdb=" N ARG i 215 " --> pdb=" O THR i 180 " (cutoff:3.500A) removed outlier: 23.216A pdb=" N ARG i 182 " --> pdb=" O ARG i 215 " (cutoff:3.500A) removed outlier: 18.368A pdb=" N HIS i 217 " --> pdb=" O ARG i 182 " (cutoff:3.500A) removed outlier: 13.111A pdb=" N SER i 184 " --> pdb=" O HIS i 217 " (cutoff:3.500A) removed outlier: 6.530A pdb=" N ARG i 219 " --> pdb=" O SER i 184 " (cutoff:3.500A) removed outlier: 9.030A pdb=" N THR i 221 " --> pdb=" O VAL i 186 " (cutoff:3.500A) Processing sheet with id= IB, first strand: chain 'i' and resid 193 through 201 removed outlier: 5.719A pdb=" N VAL i 194 " --> pdb=" O ARG i 215 " (cutoff:3.500A) removed outlier: 6.572A pdb=" N ARG i 215 " --> pdb=" O VAL i 194 " (cutoff:3.500A) removed outlier: 3.904A pdb=" N GLN i 196 " --> pdb=" O THR i 213 " (cutoff:3.500A) Processing sheet with id= IC, first strand: chain 'i' and resid 259 through 265 removed outlier: 6.718A pdb=" N TRP i 259 " --> pdb=" O HIS i 251 " (cutoff:3.500A) removed outlier: 8.147A pdb=" N HIS i 251 " --> pdb=" O TRP i 259 " (cutoff:3.500A) removed outlier: 5.340A pdb=" N MET i 261 " --> pdb=" O GLU i 249 " (cutoff:3.500A) removed outlier: 5.627A pdb=" N GLU i 249 " --> pdb=" O MET i 261 " (cutoff:3.500A) removed outlier: 6.147A pdb=" N TYR i 209 " --> pdb=" O CYS i 199 " (cutoff:3.500A) removed outlier: 4.302A pdb=" N CYS i 199 " --> pdb=" O TYR i 209 " (cutoff:3.500A) removed outlier: 6.526A pdb=" N GLN i 211 " --> pdb=" O VAL i 197 " (cutoff:3.500A) removed outlier: 4.241A pdb=" N VAL i 197 " --> pdb=" O GLN i 211 " (cutoff:3.500A) removed outlier: 6.721A pdb=" N THR i 213 " --> pdb=" O VAL i 195 " (cutoff:3.500A) Processing sheet with id= ID, first strand: chain 'i' and resid 259 through 265 removed outlier: 6.718A pdb=" N TRP i 259 " --> pdb=" O HIS i 251 " (cutoff:3.500A) removed outlier: 8.147A pdb=" N HIS i 251 " --> pdb=" O TRP i 259 " (cutoff:3.500A) removed outlier: 5.340A pdb=" N MET i 261 " --> pdb=" O GLU i 249 " (cutoff:3.500A) removed outlier: 5.627A pdb=" N GLU i 249 " --> pdb=" O MET i 261 " (cutoff:3.500A) removed outlier: 6.623A pdb=" N THR i 180 " --> pdb=" O ALA i 223 " (cutoff:3.500A) removed outlier: 7.484A pdb=" N ARG i 182 " --> pdb=" O TYR i 225 " (cutoff:3.500A) Processing sheet with id= JA, first strand: chain 'j' and resid 175 through 177 removed outlier: 6.547A pdb=" N GLY j 211 " --> pdb=" O VAL j 231 " (cutoff:3.500A) removed outlier: 8.100A pdb=" N TYR j 213 " --> pdb=" O PHE j 233 " (cutoff:3.500A) removed outlier: 14.530A pdb=" N LYS j 235 " --> pdb=" O TYR j 213 " (cutoff:3.500A) removed outlier: 21.069A pdb=" N PHE j 215 " --> pdb=" O LYS j 235 " (cutoff:3.500A) removed outlier: 26.338A pdb=" N LEU j 237 " --> pdb=" O PHE j 215 " (cutoff:3.500A) Processing sheet with id= JB, first strand: chain 'j' and resid 175 through 177 removed outlier: 4.965A pdb=" N LEU j 238 " --> pdb=" O LYS j 203 " (cutoff:3.500A) removed outlier: 6.106A pdb=" N LYS j 203 " --> pdb=" O LEU j 238 " (cutoff:3.500A) removed outlier: 3.526A pdb=" N THR j 240 " --> pdb=" O GLU j 201 " (cutoff:3.500A) Processing sheet with id= JC, first strand: chain 'j' and resid 211 through 215 removed outlier: 6.779A pdb=" N ALA j 229 " --> pdb=" O TYR j 213 " (cutoff:3.500A) removed outlier: 7.018A pdb=" N VAL j 231 " --> pdb=" O PHE j 215 " (cutoff:3.500A) Processing sheet with id= JD, first strand: chain 'j' and resid 168 through 172 removed outlier: 4.577A pdb=" N HIS j 251 " --> pdb=" O ARG j 162 " (cutoff:3.500A) Processing sheet with id= KA, first strand: chain 'k' and resid 80 through 81 Processing sheet with id= KB, first strand: chain 'k' and resid 145 through 149 removed outlier: 3.622A pdb=" N ALA k 148 " --> pdb=" O VAL k 134 " (cutoff:3.500A) removed outlier: 3.555A pdb=" N VAL k 134 " --> pdb=" O ALA k 148 " (cutoff:3.500A) Processing sheet with id= LA, first strand: chain 'l' and resid 84 through 86 Processing sheet with id= LB, first strand: chain 'l' and resid 96 through 101 Processing sheet with id= PA, first strand: chain 'p' and resid 50 through 55 removed outlier: 3.659A pdb=" N SER p 50 " --> pdb=" O LYS p 14 " (cutoff:3.500A) removed outlier: 3.569A pdb=" N GLN p 15 " --> pdb=" O LEU p 67 " (cutoff:3.500A) removed outlier: 4.432A pdb=" N GLY x 51 " --> pdb=" O ARG p 77 " (cutoff:3.500A) Processing sheet with id= UA, first strand: chain 'u' and resid 77 through 83 removed outlier: 3.565A pdb=" N ASN u 95 " --> pdb=" O SER u 83 " (cutoff:3.500A) removed outlier: 3.669A pdb=" N PHE u 102 " --> pdb=" O LEU u 132 " (cutoff:3.500A) Processing sheet with id= WA, first strand: chain 'w' and resid 200 through 210 removed outlier: 5.200A pdb=" N HIS w 201 " --> pdb=" O ASP w 229 " (cutoff:3.500A) removed outlier: 6.946A pdb=" N ASP w 229 " --> pdb=" O HIS w 201 " (cutoff:3.500A) removed outlier: 5.663A pdb=" N PHE w 203 " --> pdb=" O ILE w 227 " (cutoff:3.500A) removed outlier: 7.440A pdb=" N ILE w 227 " --> pdb=" O PHE w 203 " (cutoff:3.500A) removed outlier: 5.635A pdb=" N LEU w 205 " --> pdb=" O TYR w 225 " (cutoff:3.500A) removed outlier: 6.533A pdb=" N TYR w 225 " --> pdb=" O LEU w 205 " (cutoff:3.500A) removed outlier: 5.257A pdb=" N GLY w 207 " --> pdb=" O LEU w 223 " (cutoff:3.500A) removed outlier: 3.631A pdb=" N LEU w 223 " --> pdb=" O GLY w 207 " (cutoff:3.500A) Processing sheet with id= WB, first strand: chain 'w' and resid 112 through 116 Processing sheet with id= WC, first strand: chain 'w' and resid 112 through 116 removed outlier: 9.531A pdb=" N VAL w 350 " --> pdb=" O TYR w 288 " (cutoff:3.500A) removed outlier: 5.881A pdb=" N HIS w 290 " --> pdb=" O VAL w 350 " (cutoff:3.500A) removed outlier: 4.958A pdb=" N GLY w 289 " --> pdb=" O ILE w 237 " (cutoff:3.500A) removed outlier: 5.656A pdb=" N ILE w 237 " --> pdb=" O GLY w 289 " (cutoff:3.500A) removed outlier: 3.843A pdb=" N THR w 291 " --> pdb=" O ILE w 235 " (cutoff:3.500A) removed outlier: 3.519A pdb=" N ASN w 233 " --> pdb=" O PHE w 293 " (cutoff:3.500A) Processing sheet with id= WD, first strand: chain 'w' and resid 393 through 394 Processing sheet with id= WE, first strand: chain 'w' and resid 396 through 400 removed outlier: 6.907A pdb=" N TYR w 396 " --> pdb=" O PHE w 407 " (cutoff:3.500A) removed outlier: 6.541A pdb=" N PHE w 407 " --> pdb=" O TYR w 396 " (cutoff:3.500A) removed outlier: 7.353A pdb=" N THR w 398 " --> pdb=" O LYS w 405 " (cutoff:3.500A) removed outlier: 3.757A pdb=" N LYS w 405 " --> pdb=" O THR w 398 " (cutoff:3.500A) 1352 hydrogen bonds defined for protein. 3780 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 10.50 Time building geometry restraints manager: 15.99 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.34: 10185 1.34 - 1.47: 7285 1.47 - 1.60: 15026 1.60 - 1.73: 31 1.73 - 1.86: 187 Bond restraints: 32714 Sorted by residual: bond pdb=" CA UNK z 34 " pdb=" C UNK z 34 " ideal model delta sigma weight residual 1.525 1.627 -0.102 2.10e-02 2.27e+03 2.34e+01 bond pdb=" CA UNK z 30 " pdb=" C UNK z 30 " ideal model delta sigma weight residual 1.525 1.626 -0.101 2.10e-02 2.27e+03 2.33e+01 bond pdb=" CA UNK v 153 " pdb=" C UNK v 153 " ideal model delta sigma weight residual 1.525 1.626 -0.101 2.10e-02 2.27e+03 2.30e+01 bond pdb=" CA UNK z 20 " pdb=" C UNK z 20 " ideal model delta sigma weight residual 1.525 1.622 -0.097 2.10e-02 2.27e+03 2.13e+01 bond pdb=" CA UNK v 149 " pdb=" C UNK v 149 " ideal model delta sigma weight residual 1.525 1.620 -0.095 2.10e-02 2.27e+03 2.04e+01 ... (remaining 32709 not shown) Histogram of bond angle deviations from ideal: 98.53 - 105.89: 1076 105.89 - 113.25: 17131 113.25 - 120.61: 13790 120.61 - 127.97: 11942 127.97 - 135.33: 325 Bond angle restraints: 44264 Sorted by residual: angle pdb=" C GLY h 284 " pdb=" N PRO h 285 " pdb=" CA PRO h 285 " ideal model delta sigma weight residual 120.31 130.89 -10.58 9.80e-01 1.04e+00 1.17e+02 angle pdb=" C GLY e 26 " pdb=" N PRO e 27 " pdb=" CA PRO e 27 " ideal model delta sigma weight residual 120.21 129.69 -9.48 9.60e-01 1.09e+00 9.75e+01 angle pdb=" C ALA j 208 " pdb=" N PRO j 209 " pdb=" CA PRO j 209 " ideal model delta sigma weight residual 119.99 130.01 -10.02 1.08e+00 8.57e-01 8.61e+01 angle pdb=" C ARG t 25 " pdb=" N PRO t 26 " pdb=" CA PRO t 26 " ideal model delta sigma weight residual 120.14 129.76 -9.62 1.06e+00 8.90e-01 8.23e+01 angle pdb=" C CYS p 21 " pdb=" N PRO p 22 " pdb=" CA PRO p 22 " ideal model delta sigma weight residual 119.47 129.48 -10.01 1.16e+00 7.43e-01 7.44e+01 ... (remaining 44259 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 16.71: 17950 16.71 - 33.42: 1580 33.42 - 50.12: 374 50.12 - 66.83: 108 66.83 - 83.54: 8 Dihedral angle restraints: 20020 sinusoidal: 8487 harmonic: 11533 Sorted by residual: dihedral pdb=" CA ASP w 357 " pdb=" C ASP w 357 " pdb=" N GLY w 358 " pdb=" CA GLY w 358 " ideal model delta harmonic sigma weight residual -180.00 -140.73 -39.27 0 5.00e+00 4.00e-02 6.17e+01 dihedral pdb=" CA GLU b 210 " pdb=" C GLU b 210 " pdb=" N GLY b 211 " pdb=" CA GLY b 211 " ideal model delta harmonic sigma weight residual 180.00 141.19 38.81 0 5.00e+00 4.00e-02 6.03e+01 dihedral pdb=" CA ASN n 65 " pdb=" C ASN n 65 " pdb=" N PHE n 66 " pdb=" CA PHE n 66 " ideal model delta harmonic sigma weight residual -180.00 -141.60 -38.40 0 5.00e+00 4.00e-02 5.90e+01 ... (remaining 20017 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.072: 4037 0.072 - 0.144: 614 0.144 - 0.216: 59 0.216 - 0.288: 3 0.288 - 0.360: 2 Chirality restraints: 4715 Sorted by residual: chirality pdb=" CA PHE b 78 " pdb=" N PHE b 78 " pdb=" C PHE b 78 " pdb=" CB PHE b 78 " both_signs ideal model delta sigma weight residual False 2.51 2.15 0.36 2.00e-01 2.50e+01 3.24e+00 chirality pdb=" CA ASN x 164 " pdb=" N ASN x 164 " pdb=" C ASN x 164 " pdb=" CB ASN x 164 " both_signs ideal model delta sigma weight residual False 2.51 2.19 0.32 2.00e-01 2.50e+01 2.62e+00 chirality pdb=" CA ILE g 113 " pdb=" N ILE g 113 " pdb=" C ILE g 113 " pdb=" CB ILE g 113 " both_signs ideal model delta sigma weight residual False 2.43 2.67 -0.24 2.00e-01 2.50e+01 1.43e+00 ... (remaining 4712 not shown) Planarity restraints: 5776 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C PRO d 180 " -0.077 5.00e-02 4.00e+02 1.19e-01 2.26e+01 pdb=" N PRO d 181 " 0.206 5.00e-02 4.00e+02 pdb=" CA PRO d 181 " -0.071 5.00e-02 4.00e+02 pdb=" CD PRO d 181 " -0.057 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C PHE b 357 " -0.045 5.00e-02 4.00e+02 6.86e-02 7.54e+00 pdb=" N PRO b 358 " 0.119 5.00e-02 4.00e+02 pdb=" CA PRO b 358 " -0.035 5.00e-02 4.00e+02 pdb=" CD PRO b 358 " -0.039 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C LYS h 63 " 0.042 5.00e-02 4.00e+02 6.30e-02 6.35e+00 pdb=" N PRO h 64 " -0.109 5.00e-02 4.00e+02 pdb=" CA PRO h 64 " 0.034 5.00e-02 4.00e+02 pdb=" CD PRO h 64 " 0.034 5.00e-02 4.00e+02 ... (remaining 5773 not shown) Histogram of nonbonded interaction distances: 2.07 - 2.63: 277 2.63 - 3.20: 27095 3.20 - 3.77: 45109 3.77 - 4.33: 61616 4.33 - 4.90: 97302 Nonbonded interactions: 231399 Sorted by model distance: nonbonded pdb=" NH1 ARG a 173 " pdb=" O ASP a 348 " model vdw 2.067 2.520 nonbonded pdb=" NH1 ARG a 162 " pdb=" OH TYR a 383 " model vdw 2.115 2.520 nonbonded pdb=" N ASP o 48 " pdb=" OD1 ASP o 48 " model vdw 2.121 2.520 nonbonded pdb=" OG SER g 34 " pdb=" O CYS g 70 " model vdw 2.129 2.440 nonbonded pdb=" O GLU a 244 " pdb=" OG1 THR a 248 " model vdw 2.131 2.440 ... (remaining 231394 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: 3.170 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.000 Extract box with map and model: 4.070 Check model and map are aligned: 0.450 Set scattering table: 0.260 Process input model: 81.660 Find NCS groups from input model: 1.080 Set up NCS constraints: 0.100 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.680 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 93.480 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7758 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 : 0.009 0.102 32714 Z= 0.553 Angle : 1.285 15.947 44264 Z= 0.869 Chirality : 0.051 0.360 4715 Planarity : 0.005 0.119 5776 Dihedral : 13.807 83.541 12512 Min Nonbonded Distance : 2.067 Molprobity Statistics. All-atom Clashscore : 12.17 Ramachandran Plot: Outliers : 0.13 % Allowed : 4.57 % Favored : 95.30 % Rotamer Outliers : 6.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.71 % Cis-general : 0.00 % Twisted Proline : 0.36 % 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: -2.62 (0.11), residues: 3785 helix: -2.58 (0.10), residues: 1348 sheet: -0.20 (0.20), residues: 514 loop : -1.45 (0.12), residues: 1923 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7570 Ramachandran restraints generated. 3785 Oldfield, 0 Emsley, 3785 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7570 Ramachandran restraints generated. 3785 Oldfield, 0 Emsley, 3785 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1305 residues out of total 3397 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 205 poor density : 1100 time to evaluate : 4.032 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 outliers start: 205 outliers final: 49 residues processed: 1252 average time/residue: 0.5164 time to fit residues: 948.7627 Evaluate side-chains 570 residues out of total 3397 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 49 poor density : 521 time to evaluate : 3.435 Switching outliers to nearest non-outliers outliers start: 49 outliers final: 0 residues processed: 49 average time/residue: 0.2877 time to fit residues: 30.1902 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 372 random chunks: chunk 314 optimal weight: 8.9990 chunk 281 optimal weight: 6.9990 chunk 156 optimal weight: 10.0000 chunk 96 optimal weight: 5.9990 chunk 190 optimal weight: 30.0000 chunk 150 optimal weight: 6.9990 chunk 291 optimal weight: 7.9990 chunk 112 optimal weight: 10.0000 chunk 177 optimal weight: 6.9990 chunk 217 optimal weight: 10.0000 chunk 337 optimal weight: 1.9990 overall best weight: 5.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: a 108 HIS a 150 GLN a 156 ASN a 207 ASN a 223 HIS ** a 274 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** a 289 HIS a 360 ASN a 420 HIS b 63 GLN b 116 ASN b 163 HIS b 220 ASN b 224 HIS ** b 249 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** b 266 HIS ** b 275 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** b 308 GLN c 274 GLN c 305 HIS ** d 100 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** d 158 HIS e 50 GLN ** e 88 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** f 44 ASN f 121 HIS g 107 GLN g 131 HIS h 118 ASN h 204 GLN i 107 GLN j 87 HIS ** j 179 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** j 198 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** k 108 GLN k 116 HIS k 136 GLN l 93 ASN l 141 ASN ** m 119 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** n 69 HIS n 124 HIS p 19 GLN p 57 HIS p 72 HIS p 93 HIS q 129 HIS t 34 ASN t 45 ASN t 85 HIS ** u 103 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** u 145 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** v 79 GLN w 101 ASN w 148 HIS w 173 GLN ** w 228 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** w 321 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** w 385 ASN w 391 GLN ** w 421 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** x 65 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** x 164 ASN x 184 ASN Total number of N/Q/H flips: 50 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7748 moved from start: 0.4312 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.056 32714 Z= 0.345 Angle : 0.758 12.284 44264 Z= 0.391 Chirality : 0.046 0.263 4715 Planarity : 0.007 0.115 5776 Dihedral : 6.270 49.361 4439 Min Nonbonded Distance : 2.050 Molprobity Statistics. All-atom Clashscore : 12.38 Ramachandran Plot: Outliers : 0.13 % Allowed : 2.96 % Favored : 96.91 % Rotamer Outliers : 5.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.71 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.78 (0.12), residues: 3785 helix: -0.28 (0.13), residues: 1370 sheet: 0.19 (0.21), residues: 509 loop : -0.81 (0.13), residues: 1906 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7570 Ramachandran restraints generated. 3785 Oldfield, 0 Emsley, 3785 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7570 Ramachandran restraints generated. 3785 Oldfield, 0 Emsley, 3785 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 774 residues out of total 3397 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 172 poor density : 602 time to evaluate : 4.056 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 172 outliers final: 105 residues processed: 721 average time/residue: 0.4677 time to fit residues: 518.3523 Evaluate side-chains 591 residues out of total 3397 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 105 poor density : 486 time to evaluate : 3.689 Switching outliers to nearest non-outliers outliers start: 105 outliers final: 0 residues processed: 105 average time/residue: 0.2954 time to fit residues: 61.6413 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 372 random chunks: chunk 187 optimal weight: 40.0000 chunk 104 optimal weight: 6.9990 chunk 281 optimal weight: 0.0570 chunk 230 optimal weight: 5.9990 chunk 93 optimal weight: 9.9990 chunk 338 optimal weight: 8.9990 chunk 365 optimal weight: 3.9990 chunk 301 optimal weight: 0.1980 chunk 335 optimal weight: 8.9990 chunk 115 optimal weight: 9.9990 chunk 271 optimal weight: 5.9990 overall best weight: 3.2504 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: a 94 HIS a 195 HIS ** a 274 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** b 249 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** b 275 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** e 88 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** f 71 HIS g 107 GLN g 135 ASN h 69 HIS h 172 ASN i 107 GLN i 207 ASN ** j 179 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** k 116 HIS l 73 GLN ** u 103 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** v 79 GLN w 173 GLN ** w 228 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** w 271 GLN ** w 321 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** w 421 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** x 65 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7728 moved from start: 0.4926 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.043 32714 Z= 0.224 Angle : 0.639 11.928 44264 Z= 0.330 Chirality : 0.043 0.243 4715 Planarity : 0.005 0.057 5776 Dihedral : 5.718 52.651 4439 Min Nonbonded Distance : 2.143 Molprobity Statistics. All-atom Clashscore : 10.99 Ramachandran Plot: Outliers : 0.08 % Allowed : 3.51 % Favored : 96.41 % Rotamer Outliers : 2.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.71 % 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: -0.07 (0.13), residues: 3785 helix: 0.58 (0.14), residues: 1378 sheet: 0.45 (0.21), residues: 544 loop : -0.61 (0.14), residues: 1863 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7570 Ramachandran restraints generated. 3785 Oldfield, 0 Emsley, 3785 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7570 Ramachandran restraints generated. 3785 Oldfield, 0 Emsley, 3785 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 615 residues out of total 3397 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 69 poor density : 546 time to evaluate : 4.079 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 69 outliers final: 25 residues processed: 594 average time/residue: 0.4845 time to fit residues: 442.6956 Evaluate side-chains 486 residues out of total 3397 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 461 time to evaluate : 3.652 Switching outliers to nearest non-outliers outliers start: 25 outliers final: 0 residues processed: 25 average time/residue: 0.2975 time to fit residues: 18.6972 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 372 random chunks: chunk 334 optimal weight: 2.9990 chunk 254 optimal weight: 9.9990 chunk 175 optimal weight: 7.9990 chunk 37 optimal weight: 6.9990 chunk 161 optimal weight: 5.9990 chunk 227 optimal weight: 7.9990 chunk 339 optimal weight: 5.9990 chunk 359 optimal weight: 7.9990 chunk 177 optimal weight: 8.9990 chunk 321 optimal weight: 10.0000 chunk 96 optimal weight: 20.0000 overall best weight: 5.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: a 65 HIS ** a 274 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** b 163 HIS ** b 249 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** b 275 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** e 88 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** g 107 GLN i 107 GLN i 207 ASN j 67 GLN ** j 179 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** j 198 ASN j 252 HIS k 177 ASN ** o 82 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** q 129 HIS ** u 103 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** w 71 HIS w 228 ASN w 233 ASN ** w 321 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** w 421 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7796 moved from start: 0.5637 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.060 32714 Z= 0.336 Angle : 0.690 12.763 44264 Z= 0.353 Chirality : 0.044 0.187 4715 Planarity : 0.006 0.058 5776 Dihedral : 5.764 46.935 4439 Min Nonbonded Distance : 2.073 Molprobity Statistics. All-atom Clashscore : 11.91 Ramachandran Plot: Outliers : 0.13 % Allowed : 4.07 % Favored : 95.80 % Rotamer Outliers : 3.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.71 % 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: -0.08 (0.13), residues: 3785 helix: 0.68 (0.14), residues: 1409 sheet: 0.29 (0.22), residues: 537 loop : -0.67 (0.14), residues: 1839 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7570 Ramachandran restraints generated. 3785 Oldfield, 0 Emsley, 3785 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7570 Ramachandran restraints generated. 3785 Oldfield, 0 Emsley, 3785 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 629 residues out of total 3397 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 118 poor density : 511 time to evaluate : 4.079 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 118 outliers final: 78 residues processed: 586 average time/residue: 0.4779 time to fit residues: 428.9315 Evaluate side-chains 523 residues out of total 3397 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 78 poor density : 445 time to evaluate : 3.665 Switching outliers to nearest non-outliers outliers start: 78 outliers final: 0 residues processed: 78 average time/residue: 0.2885 time to fit residues: 46.2007 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 372 random chunks: chunk 299 optimal weight: 20.0000 chunk 204 optimal weight: 30.0000 chunk 5 optimal weight: 3.9990 chunk 267 optimal weight: 9.9990 chunk 148 optimal weight: 5.9990 chunk 306 optimal weight: 7.9990 chunk 248 optimal weight: 9.9990 chunk 0 optimal weight: 10.0000 chunk 183 optimal weight: 20.0000 chunk 322 optimal weight: 0.0870 chunk 90 optimal weight: 8.9990 overall best weight: 5.4166 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** a 274 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** b 249 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** b 275 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** e 88 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** g 107 GLN i 107 GLN ** j 179 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** k 116 HIS w 71 HIS ** w 321 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** w 421 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** x 131 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7794 moved from start: 0.5970 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.057 32714 Z= 0.296 Angle : 0.652 11.612 44264 Z= 0.335 Chirality : 0.043 0.185 4715 Planarity : 0.005 0.065 5776 Dihedral : 5.592 49.464 4439 Min Nonbonded Distance : 2.132 Molprobity Statistics. All-atom Clashscore : 11.52 Ramachandran Plot: Outliers : 0.11 % Allowed : 3.88 % Favored : 96.01 % Rotamer Outliers : 1.77 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.71 % 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: 0.04 (0.13), residues: 3785 helix: 0.80 (0.14), residues: 1415 sheet: 0.23 (0.22), residues: 550 loop : -0.59 (0.14), residues: 1820 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7570 Ramachandran restraints generated. 3785 Oldfield, 0 Emsley, 3785 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7570 Ramachandran restraints generated. 3785 Oldfield, 0 Emsley, 3785 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 548 residues out of total 3397 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 60 poor density : 488 time to evaluate : 4.018 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 60 outliers final: 34 residues processed: 533 average time/residue: 0.4709 time to fit residues: 386.3734 Evaluate side-chains 483 residues out of total 3397 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 34 poor density : 449 time to evaluate : 3.632 Switching outliers to nearest non-outliers outliers start: 34 outliers final: 0 residues processed: 34 average time/residue: 0.3030 time to fit residues: 23.9646 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 372 random chunks: chunk 120 optimal weight: 9.9990 chunk 323 optimal weight: 6.9990 chunk 71 optimal weight: 10.0000 chunk 211 optimal weight: 8.9990 chunk 88 optimal weight: 4.9990 chunk 359 optimal weight: 0.9990 chunk 298 optimal weight: 50.0000 chunk 166 optimal weight: 0.5980 chunk 29 optimal weight: 9.9990 chunk 119 optimal weight: 9.9990 chunk 188 optimal weight: 0.1980 overall best weight: 2.7586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** a 274 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** b 163 HIS ** b 249 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** b 307 HIS ** e 88 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** g 107 GLN i 107 GLN i 157 HIS ** i 220 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** j 179 GLN l 156 GLN ** w 321 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** w 421 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** x 170 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7757 moved from start: 0.6210 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.051 32714 Z= 0.199 Angle : 0.603 11.408 44264 Z= 0.309 Chirality : 0.041 0.263 4715 Planarity : 0.005 0.064 5776 Dihedral : 5.338 50.208 4439 Min Nonbonded Distance : 2.143 Molprobity Statistics. All-atom Clashscore : 10.22 Ramachandran Plot: Outliers : 0.08 % Allowed : 3.70 % Favored : 96.22 % Rotamer Outliers : 1.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.71 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.11 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.33 (0.14), residues: 3785 helix: 1.12 (0.14), residues: 1398 sheet: 0.32 (0.22), residues: 557 loop : -0.46 (0.14), residues: 1830 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7570 Ramachandran restraints generated. 3785 Oldfield, 0 Emsley, 3785 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7570 Ramachandran restraints generated. 3785 Oldfield, 0 Emsley, 3785 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 549 residues out of total 3397 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 54 poor density : 495 time to evaluate : 4.022 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 54 outliers final: 26 residues processed: 529 average time/residue: 0.4797 time to fit residues: 389.9738 Evaluate side-chains 491 residues out of total 3397 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 465 time to evaluate : 3.543 Switching outliers to nearest non-outliers outliers start: 26 outliers final: 0 residues processed: 26 average time/residue: 0.2975 time to fit residues: 19.5682 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 372 random chunks: chunk 347 optimal weight: 10.0000 chunk 40 optimal weight: 6.9990 chunk 205 optimal weight: 30.0000 chunk 262 optimal weight: 9.9990 chunk 203 optimal weight: 6.9990 chunk 302 optimal weight: 20.0000 chunk 200 optimal weight: 30.0000 chunk 358 optimal weight: 5.9990 chunk 224 optimal weight: 7.9990 chunk 218 optimal weight: 40.0000 chunk 165 optimal weight: 10.0000 overall best weight: 7.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** a 274 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** b 249 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** b 275 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** c 274 GLN e 88 GLN e 111 HIS g 107 GLN i 107 GLN ** i 220 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** j 198 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** k 66 GLN k 116 HIS ** w 321 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** w 421 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7822 moved from start: 0.6514 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.006 0.081 32714 Z= 0.386 Angle : 0.700 10.880 44264 Z= 0.359 Chirality : 0.045 0.232 4715 Planarity : 0.006 0.067 5776 Dihedral : 5.667 47.595 4439 Min Nonbonded Distance : 2.077 Molprobity Statistics. All-atom Clashscore : 11.90 Ramachandran Plot: Outliers : 0.11 % Allowed : 4.86 % Favored : 95.03 % Rotamer Outliers : 1.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.71 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.11 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.08 (0.13), residues: 3785 helix: 0.87 (0.14), residues: 1411 sheet: 0.27 (0.22), residues: 536 loop : -0.61 (0.14), residues: 1838 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7570 Ramachandran restraints generated. 3785 Oldfield, 0 Emsley, 3785 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7570 Ramachandran restraints generated. 3785 Oldfield, 0 Emsley, 3785 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 532 residues out of total 3397 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 54 poor density : 478 time to evaluate : 3.699 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 54 outliers final: 35 residues processed: 519 average time/residue: 0.5008 time to fit residues: 397.1191 Evaluate side-chains 485 residues out of total 3397 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 35 poor density : 450 time to evaluate : 3.617 Switching outliers to nearest non-outliers outliers start: 35 outliers final: 0 residues processed: 35 average time/residue: 0.2720 time to fit residues: 23.2215 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 372 random chunks: chunk 221 optimal weight: 5.9990 chunk 143 optimal weight: 10.0000 chunk 214 optimal weight: 6.9990 chunk 108 optimal weight: 30.0000 chunk 70 optimal weight: 5.9990 chunk 69 optimal weight: 2.9990 chunk 227 optimal weight: 2.9990 chunk 244 optimal weight: 0.6980 chunk 177 optimal weight: 7.9990 chunk 33 optimal weight: 20.0000 chunk 281 optimal weight: 0.6980 overall best weight: 2.6786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: a 274 ASN b 163 HIS ** b 249 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** g 107 GLN i 107 GLN ** i 220 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** j 198 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** m 132 ASN m 148 ASN ** w 321 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** w 421 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7771 moved from start: 0.6642 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.042 32714 Z= 0.197 Angle : 0.611 11.406 44264 Z= 0.314 Chirality : 0.041 0.226 4715 Planarity : 0.005 0.069 5776 Dihedral : 5.357 51.053 4439 Min Nonbonded Distance : 2.079 Molprobity Statistics. All-atom Clashscore : 10.85 Ramachandran Plot: Outliers : 0.08 % Allowed : 3.88 % Favored : 96.04 % Rotamer Outliers : 0.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.71 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.11 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.32 (0.14), residues: 3785 helix: 1.15 (0.14), residues: 1392 sheet: 0.33 (0.22), residues: 545 loop : -0.50 (0.14), residues: 1848 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7570 Ramachandran restraints generated. 3785 Oldfield, 0 Emsley, 3785 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7570 Ramachandran restraints generated. 3785 Oldfield, 0 Emsley, 3785 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 518 residues out of total 3397 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 494 time to evaluate : 3.836 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 24 outliers final: 13 residues processed: 506 average time/residue: 0.4972 time to fit residues: 387.0185 Evaluate side-chains 466 residues out of total 3397 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 453 time to evaluate : 3.810 Switching outliers to nearest non-outliers outliers start: 13 outliers final: 0 residues processed: 13 average time/residue: 0.3101 time to fit residues: 12.5715 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 372 random chunks: chunk 326 optimal weight: 9.9990 chunk 343 optimal weight: 7.9990 chunk 313 optimal weight: 100.0000 chunk 334 optimal weight: 0.0010 chunk 201 optimal weight: 9.9990 chunk 145 optimal weight: 0.0670 chunk 262 optimal weight: 3.9990 chunk 102 optimal weight: 6.9990 chunk 301 optimal weight: 5.9990 chunk 316 optimal weight: 3.9990 chunk 332 optimal weight: 5.9990 overall best weight: 2.8130 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: a 338 GLN ** b 249 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** e 88 GLN g 107 GLN i 107 GLN ** i 220 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** j 198 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** k 116 HIS ** w 421 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7767 moved from start: 0.6760 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.044 32714 Z= 0.203 Angle : 0.612 11.174 44264 Z= 0.312 Chirality : 0.041 0.219 4715 Planarity : 0.005 0.067 5776 Dihedral : 5.233 49.775 4439 Min Nonbonded Distance : 2.083 Molprobity Statistics. All-atom Clashscore : 10.63 Ramachandran Plot: Outliers : 0.11 % Allowed : 4.41 % Favored : 95.48 % Rotamer Outliers : 0.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.71 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.11 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.38 (0.14), residues: 3785 helix: 1.22 (0.14), residues: 1396 sheet: 0.34 (0.22), residues: 546 loop : -0.48 (0.15), residues: 1843 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7570 Ramachandran restraints generated. 3785 Oldfield, 0 Emsley, 3785 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7570 Ramachandran restraints generated. 3785 Oldfield, 0 Emsley, 3785 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 499 residues out of total 3397 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 479 time to evaluate : 3.708 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 20 outliers final: 12 residues processed: 489 average time/residue: 0.4884 time to fit residues: 366.9605 Evaluate side-chains 466 residues out of total 3397 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 454 time to evaluate : 3.758 Switching outliers to nearest non-outliers outliers start: 12 outliers final: 0 residues processed: 12 average time/residue: 0.3274 time to fit residues: 12.0416 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 372 random chunks: chunk 219 optimal weight: 0.6980 chunk 353 optimal weight: 7.9990 chunk 215 optimal weight: 20.0000 chunk 167 optimal weight: 0.6980 chunk 245 optimal weight: 0.7980 chunk 370 optimal weight: 40.0000 chunk 341 optimal weight: 5.9990 chunk 295 optimal weight: 6.9990 chunk 30 optimal weight: 0.9980 chunk 227 optimal weight: 0.0980 chunk 180 optimal weight: 8.9990 overall best weight: 0.6580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: b 163 HIS ** b 249 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** d 143 GLN g 107 GLN ** h 128 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** h 168 HIS ** h 204 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** h 310 ASN i 107 GLN ** i 220 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** j 150 HIS j 168 GLN ** j 198 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** u 151 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** v 60 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7708 moved from start: 0.6879 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.043 32714 Z= 0.159 Angle : 0.599 11.354 44264 Z= 0.307 Chirality : 0.041 0.215 4715 Planarity : 0.005 0.065 5776 Dihedral : 5.060 58.787 4439 Min Nonbonded Distance : 2.123 Molprobity Statistics. All-atom Clashscore : 9.80 Ramachandran Plot: Outliers : 0.11 % Allowed : 3.38 % Favored : 96.51 % Rotamer Outliers : 0.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.71 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.11 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.56 (0.14), residues: 3785 helix: 1.34 (0.14), residues: 1395 sheet: 0.62 (0.22), residues: 538 loop : -0.41 (0.14), residues: 1852 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7570 Ramachandran restraints generated. 3785 Oldfield, 0 Emsley, 3785 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7570 Ramachandran restraints generated. 3785 Oldfield, 0 Emsley, 3785 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 511 residues out of total 3397 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 503 time to evaluate : 3.874 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 8 outliers final: 5 residues processed: 506 average time/residue: 0.5163 time to fit residues: 404.5401 Evaluate side-chains 459 residues out of total 3397 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 454 time to evaluate : 3.515 Switching outliers to nearest non-outliers outliers start: 5 outliers final: 0 residues processed: 5 average time/residue: 0.2748 time to fit residues: 8.0010 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 372 random chunks: chunk 234 optimal weight: 6.9990 chunk 314 optimal weight: 0.9980 chunk 90 optimal weight: 20.0000 chunk 272 optimal weight: 40.0000 chunk 43 optimal weight: 10.0000 chunk 82 optimal weight: 9.9990 chunk 295 optimal weight: 6.9990 chunk 123 optimal weight: 5.9990 chunk 303 optimal weight: 2.9990 chunk 37 optimal weight: 4.9990 chunk 54 optimal weight: 0.9990 overall best weight: 3.1988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** b 249 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** b 275 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** g 107 GLN ** h 128 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** h 204 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** i 107 GLN j 54 GLN ** j 198 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** k 116 HIS k 158 GLN ** v 60 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** w 234 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** w 421 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4034 r_free = 0.4034 target = 0.142686 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3746 r_free = 0.3746 target = 0.122997 restraints weight = 85435.349| |-----------------------------------------------------------------------------| r_work (start): 0.3770 rms_B_bonded: 4.35 r_work: 0.3524 rms_B_bonded: 4.50 restraints_weight: 0.5000 r_work (final): 0.3524 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7785 moved from start: 0.6954 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.044 32714 Z= 0.210 Angle : 0.616 11.220 44264 Z= 0.313 Chirality : 0.042 0.214 4715 Planarity : 0.005 0.065 5776 Dihedral : 5.038 53.288 4439 Min Nonbonded Distance : 2.082 Molprobity Statistics. All-atom Clashscore : 10.94 Ramachandran Plot: Outliers : 0.11 % Allowed : 4.33 % Favored : 95.56 % Rotamer Outliers : 0.18 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.71 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.11 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.59 (0.14), residues: 3785 helix: 1.41 (0.14), residues: 1388 sheet: 0.51 (0.22), residues: 554 loop : -0.39 (0.15), residues: 1843 =============================================================================== Job complete usr+sys time: 8332.10 seconds wall clock time: 150 minutes 51.75 seconds (9051.75 seconds total)