Starting phenix.real_space_refine (version: 1.21rc1) on Sat Oct 14 04:54:29 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8b0j_15785/10_2023/8b0j_15785.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8b0j_15785/10_2023/8b0j_15785.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.99 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8b0j_15785/10_2023/8b0j_15785.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8b0j_15785/10_2023/8b0j_15785.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8b0j_15785/10_2023/8b0j_15785.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8b0j_15785/10_2023/8b0j_15785.pdb" } resolution = 3.99 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.009 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 6 Type Number sf(0) Gaussians P 160 5.49 5 S 17 5.16 5 C 9573 2.51 5 N 2853 2.21 5 O 3599 1.98 5 H 12434 0.53 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A ARG 58": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "A PHE 185": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "B ARG 9": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "B ARG 95": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "B GLU 157": "OE1" <-> "OE2" Residue "D ARG 58": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "D ARG 95": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "C ARG 58": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "L ARG 3": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "L GLU 329": "OE1" <-> "OE2" Residue "L ARG 354": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "L ARG 357": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "L ARG 425": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "L ARG 456": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "N ARG 368": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "N ARG 373": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Time to flip residues: 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5097/modules/chem_data/mon_lib" Total number of atoms: 28636 Number of models: 1 Model: "" Number of chains: 7 Chain: "A" Number of atoms: 3695 Number of conformers: 1 Conformer: "" Number of residues, atoms: 268, 3695 Classifications: {'peptide': 268} Modifications used: {'NH1NOTPRO': 1} Link IDs: {'PTRANS': 14, 'TRANS': 253} Chain breaks: 1 Unresolved non-hydrogen bonds: 246 Unresolved non-hydrogen angles: 304 Unresolved non-hydrogen dihedrals: 205 Unresolved non-hydrogen chiralities: 7 Planarities with less than four sites: {'GLN:plan1': 1, 'HIS:plan': 3, 'TYR:plan': 2, 'ASN:plan1': 2, 'ASP:plan': 10, 'PHE:plan': 2, 'GLU:plan': 11, 'ARG:plan': 10} Unresolved non-hydrogen planarities: 176 Chain: "B" Number of atoms: 3571 Number of conformers: 1 Conformer: "" Number of residues, atoms: 279, 3571 Classifications: {'peptide': 279} Link IDs: {'PTRANS': 15, 'TRANS': 263} Chain breaks: 1 Unresolved non-hydrogen bonds: 333 Unresolved non-hydrogen angles: 410 Unresolved non-hydrogen dihedrals: 272 Unresolved non-hydrogen chiralities: 19 Planarities with less than four sites: {'GLN:plan1': 3, 'HIS:plan': 1, 'TYR:plan': 1, 'ASN:plan1': 6, 'TRP:plan': 1, 'ASP:plan': 10, 'PHE:plan': 2, 'GLU:plan': 10, 'ARG:plan': 15} Unresolved non-hydrogen planarities: 208 Chain: "D" Number of atoms: 3462 Number of conformers: 1 Conformer: "" Number of residues, atoms: 281, 3462 Classifications: {'peptide': 281} Modifications used: {'NH3': 1} Link IDs: {'PTRANS': 15, 'TRANS': 265} Unresolved non-hydrogen bonds: 393 Unresolved non-hydrogen angles: 492 Unresolved non-hydrogen dihedrals: 328 Unresolved non-hydrogen chiralities: 25 Planarities with less than four sites: {'GLN:plan1': 2, 'ASP:plan': 6, 'TYR:plan': 3, 'ASN:plan1': 8, 'TRP:plan': 1, 'HIS:plan': 4, 'PHE:plan': 5, 'GLU:plan': 8, 'ARG:plan': 18} Unresolved non-hydrogen planarities: 252 Chain: "C" Number of atoms: 3239 Number of conformers: 1 Conformer: "" Number of residues, atoms: 266, 3239 Classifications: {'peptide': 266} Modifications used: {'NH3': 1} Link IDs: {'PTRANS': 14, 'TRANS': 251} Chain breaks: 1 Unresolved non-hydrogen bonds: 393 Unresolved non-hydrogen angles: 484 Unresolved non-hydrogen dihedrals: 333 Unresolved non-hydrogen chiralities: 16 Planarities with less than four sites: {'GLN:plan1': 2, 'HIS:plan': 4, 'TYR:plan': 4, 'ASN:plan1': 4, 'TRP:plan': 1, 'ASP:plan': 9, 'PHE:plan': 2, 'GLU:plan': 12, 'ARG:plan': 19} Unresolved non-hydrogen planarities: 259 Chain: "L" Number of atoms: 5605 Number of conformers: 1 Conformer: "" Number of residues, atoms: 481, 5605 Classifications: {'peptide': 481} Link IDs: {'PTRANS': 20, 'TRANS': 460} Chain breaks: 3 Unresolved non-hydrogen bonds: 771 Unresolved non-hydrogen angles: 964 Unresolved non-hydrogen dihedrals: 641 Unresolved non-hydrogen chiralities: 44 Planarities with less than four sites: {'GLN:plan1': 13, 'ASP:plan': 11, 'TYR:plan': 7, 'ASN:plan1': 6, 'TRP:plan': 2, 'HIS:plan': 10, 'PHE:plan': 4, 'GLU:plan': 28, 'ARG:plan': 32} Unresolved non-hydrogen planarities: 516 Chain: "N" Number of atoms: 4220 Number of conformers: 1 Conformer: "" Number of residues, atoms: 356, 4220 Classifications: {'peptide': 356} Modifications used: {'NH3': 1} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 12, 'TRANS': 343} Chain breaks: 7 Unresolved non-hydrogen bonds: 558 Unresolved non-hydrogen angles: 700 Unresolved non-hydrogen dihedrals: 458 Unresolved non-hydrogen chiralities: 34 Planarities with less than four sites: {'GLN:plan1': 10, 'ASP:plan': 11, 'TYR:plan': 5, 'ASN:plan1': 5, 'TRP:plan': 1, 'HIS:plan': 5, 'PHE:plan': 5, 'GLU:plan': 18, 'ARG:plan': 24} Unresolved non-hydrogen planarities: 376 Chain: "K" Number of atoms: 4844 Number of conformers: 1 Conformer: "" Number of residues, atoms: 160, 4844 Classifications: {'RNA': 160} Modifications used: {'3*END': 1, 'rna2p_pur': 22, 'rna2p_pyr': 23, 'rna3p_pur': 49, 'rna3p_pyr': 66} Link IDs: {'rna2p': 45, 'rna3p': 114} Chain breaks: 6 Time building chain proxies: 13.34, per 1000 atoms: 0.47 Number of scatterers: 28636 At special positions: 0 Unit cell: (127.14, 131.052, 180.604, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) S 17 16.00 P 160 15.00 O 3599 8.00 N 2853 7.00 C 9573 6.00 H 12434 1.00 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: 22.61 Conformation dependent library (CDL) restraints added in 2.4 seconds 3786 Ramachandran restraints generated. 1893 Oldfield, 0 Emsley, 1893 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3672 Finding SS restraints... Secondary structure from input PDB file: 80 helices and 17 sheets defined 47.5% alpha, 10.5% beta 4 base pairs and 54 stacking pairs defined. Time for finding SS restraints: 11.18 Creating SS restraints... Processing helix chain 'A' and resid 13 through 25 removed outlier: 3.512A pdb=" N ALA A 17 " --> pdb=" O GLY A 13 " (cutoff:3.500A) Processing helix chain 'A' and resid 33 through 35 No H-bonds generated for 'chain 'A' and resid 33 through 35' Processing helix chain 'A' and resid 36 through 48 removed outlier: 3.542A pdb=" N LEU A 40 " --> pdb=" O LEU A 36 " (cutoff:3.500A) Processing helix chain 'A' and resid 63 through 74 removed outlier: 3.846A pdb=" N PHE A 67 " --> pdb=" O SER A 63 " (cutoff:3.500A) Processing helix chain 'A' and resid 88 through 96 removed outlier: 3.710A pdb=" N ARG A 95 " --> pdb=" O THR A 91 " (cutoff:3.500A) Processing helix chain 'A' and resid 113 through 130 Proline residue: A 125 - end of helix Processing helix chain 'A' and resid 140 through 154 Processing helix chain 'A' and resid 188 through 196 Proline residue: A 193 - end of helix Processing helix chain 'A' and resid 202 through 212 removed outlier: 3.765A pdb=" N HIS A 212 " --> pdb=" O PHE A 208 " (cutoff:3.500A) Processing helix chain 'A' and resid 212 through 235 removed outlier: 3.955A pdb=" N HIS A 216 " --> pdb=" O HIS A 212 " (cutoff:3.500A) Proline residue: A 231 - end of helix Processing helix chain 'A' and resid 252 through 268 removed outlier: 3.616A pdb=" N PHE A 265 " --> pdb=" O LEU A 261 " (cutoff:3.500A) Processing helix chain 'A' and resid 278 through 282 Processing helix chain 'B' and resid 13 through 25 removed outlier: 3.791A pdb=" N ASP B 23 " --> pdb=" O ARG B 19 " (cutoff:3.500A) Processing helix chain 'B' and resid 33 through 35 No H-bonds generated for 'chain 'B' and resid 33 through 35' Processing helix chain 'B' and resid 36 through 48 removed outlier: 3.958A pdb=" N ASP B 46 " --> pdb=" O ARG B 42 " (cutoff:3.500A) removed outlier: 3.539A pdb=" N ARG B 47 " --> pdb=" O THR B 43 " (cutoff:3.500A) Processing helix chain 'B' and resid 63 through 73 removed outlier: 3.663A pdb=" N PHE B 67 " --> pdb=" O SER B 63 " (cutoff:3.500A) Processing helix chain 'B' and resid 88 through 97 Processing helix chain 'B' and resid 104 through 109 removed outlier: 4.054A pdb=" N LYS B 108 " --> pdb=" O PRO B 104 " (cutoff:3.500A) Processing helix chain 'B' and resid 111 through 130 removed outlier: 3.804A pdb=" N ILE B 116 " --> pdb=" O LEU B 112 " (cutoff:3.500A) removed outlier: 3.656A pdb=" N ASP B 121 " --> pdb=" O ASP B 117 " (cutoff:3.500A) Proline residue: B 125 - end of helix Processing helix chain 'B' and resid 140 through 153 removed outlier: 3.764A pdb=" N GLU B 146 " --> pdb=" O HIS B 142 " (cutoff:3.500A) removed outlier: 3.682A pdb=" N ARG B 151 " --> pdb=" O MET B 147 " (cutoff:3.500A) removed outlier: 3.942A pdb=" N LEU B 153 " --> pdb=" O ARG B 149 " (cutoff:3.500A) Processing helix chain 'B' and resid 170 through 172 No H-bonds generated for 'chain 'B' and resid 170 through 172' Processing helix chain 'B' and resid 188 through 192 Processing helix chain 'B' and resid 202 through 212 removed outlier: 3.525A pdb=" N ALA B 206 " --> pdb=" O ASP B 202 " (cutoff:3.500A) Processing helix chain 'B' and resid 212 through 236 removed outlier: 3.973A pdb=" N HIS B 216 " --> pdb=" O HIS B 212 " (cutoff:3.500A) Proline residue: B 231 - end of helix removed outlier: 3.713A pdb=" N ASN B 236 " --> pdb=" O MET B 232 " (cutoff:3.500A) Processing helix chain 'B' and resid 252 through 268 removed outlier: 3.612A pdb=" N TYR B 256 " --> pdb=" O HIS B 252 " (cutoff:3.500A) Processing helix chain 'B' and resid 278 through 280 No H-bonds generated for 'chain 'B' and resid 278 through 280' Processing helix chain 'D' and resid 13 through 25 Processing helix chain 'D' and resid 36 through 48 removed outlier: 3.923A pdb=" N ASP D 46 " --> pdb=" O ARG D 42 " (cutoff:3.500A) removed outlier: 3.868A pdb=" N ARG D 47 " --> pdb=" O THR D 43 " (cutoff:3.500A) Processing helix chain 'D' and resid 64 through 73 removed outlier: 3.829A pdb=" N GLU D 68 " --> pdb=" O PRO D 64 " (cutoff:3.500A) Processing helix chain 'D' and resid 88 through 97 Processing helix chain 'D' and resid 111 through 129 removed outlier: 3.500A pdb=" N SER D 120 " --> pdb=" O ILE D 116 " (cutoff:3.500A) removed outlier: 4.041A pdb=" N ASP D 121 " --> pdb=" O ASP D 117 " (cutoff:3.500A) Proline residue: D 125 - end of helix removed outlier: 3.780A pdb=" N SER D 128 " --> pdb=" O GLU D 124 " (cutoff:3.500A) removed outlier: 4.369A pdb=" N ARG D 129 " --> pdb=" O PRO D 125 " (cutoff:3.500A) Processing helix chain 'D' and resid 142 through 151 removed outlier: 3.655A pdb=" N GLU D 146 " --> pdb=" O HIS D 142 " (cutoff:3.500A) Processing helix chain 'D' and resid 188 through 192 removed outlier: 3.960A pdb=" N TRP D 191 " --> pdb=" O ASN D 188 " (cutoff:3.500A) Processing helix chain 'D' and resid 202 through 211 Processing helix chain 'D' and resid 213 through 228 removed outlier: 3.568A pdb=" N LEU D 228 " --> pdb=" O SER D 224 " (cutoff:3.500A) Processing helix chain 'D' and resid 229 through 235 Processing helix chain 'D' and resid 253 through 269 removed outlier: 3.936A pdb=" N ILE D 257 " --> pdb=" O ARG D 253 " (cutoff:3.500A) Processing helix chain 'D' and resid 276 through 281 removed outlier: 4.114A pdb=" N GLU D 280 " --> pdb=" O HIS D 276 " (cutoff:3.500A) removed outlier: 3.548A pdb=" N LYS D 281 " --> pdb=" O ARG D 277 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 276 through 281' Processing helix chain 'C' and resid 13 through 24 Processing helix chain 'C' and resid 33 through 35 No H-bonds generated for 'chain 'C' and resid 33 through 35' Processing helix chain 'C' and resid 36 through 48 removed outlier: 4.305A pdb=" N ASP C 46 " --> pdb=" O ARG C 42 " (cutoff:3.500A) removed outlier: 4.256A pdb=" N ARG C 47 " --> pdb=" O THR C 43 " (cutoff:3.500A) Processing helix chain 'C' and resid 56 through 60 Processing helix chain 'C' and resid 63 through 74 removed outlier: 3.699A pdb=" N PHE C 67 " --> pdb=" O SER C 63 " (cutoff:3.500A) Processing helix chain 'C' and resid 88 through 95 removed outlier: 3.987A pdb=" N ARG C 95 " --> pdb=" O THR C 91 " (cutoff:3.500A) Processing helix chain 'C' and resid 113 through 129 Proline residue: C 125 - end of helix Processing helix chain 'C' and resid 140 through 152 removed outlier: 3.561A pdb=" N GLU C 146 " --> pdb=" O HIS C 142 " (cutoff:3.500A) removed outlier: 3.596A pdb=" N ARG C 151 " --> pdb=" O MET C 147 " (cutoff:3.500A) Processing helix chain 'C' and resid 188 through 192 Processing helix chain 'C' and resid 202 through 211 Processing helix chain 'C' and resid 212 through 236 removed outlier: 3.687A pdb=" N HIS C 216 " --> pdb=" O HIS C 212 " (cutoff:3.500A) removed outlier: 3.885A pdb=" N TRP C 229 " --> pdb=" O TYR C 225 " (cutoff:3.500A) Proline residue: C 231 - end of helix removed outlier: 3.614A pdb=" N ASN C 236 " --> pdb=" O MET C 232 " (cutoff:3.500A) Processing helix chain 'C' and resid 252 through 267 Processing helix chain 'C' and resid 277 through 281 Processing helix chain 'L' and resid 69 through 73 Processing helix chain 'L' and resid 89 through 94 Processing helix chain 'L' and resid 144 through 158 Processing helix chain 'L' and resid 176 through 199 Processing helix chain 'L' and resid 214 through 220 Processing helix chain 'L' and resid 233 through 235 No H-bonds generated for 'chain 'L' and resid 233 through 235' Processing helix chain 'L' and resid 236 through 245 removed outlier: 4.574A pdb=" N HIS L 243 " --> pdb=" O LEU L 239 " (cutoff:3.500A) removed outlier: 4.414A pdb=" N ALA L 245 " --> pdb=" O ARG L 241 " (cutoff:3.500A) Processing helix chain 'L' and resid 249 through 254 removed outlier: 4.019A pdb=" N PHE L 252 " --> pdb=" O ARG L 249 " (cutoff:3.500A) removed outlier: 3.825A pdb=" N SER L 254 " --> pdb=" O ASP L 251 " (cutoff:3.500A) Processing helix chain 'L' and resid 264 through 269 Processing helix chain 'L' and resid 271 through 278 Processing helix chain 'L' and resid 315 through 338 removed outlier: 3.829A pdb=" N ASP L 328 " --> pdb=" O LEU L 324 " (cutoff:3.500A) removed outlier: 3.794A pdb=" N GLU L 329 " --> pdb=" O GLU L 325 " (cutoff:3.500A) Processing helix chain 'L' and resid 352 through 369 removed outlier: 3.559A pdb=" N ALA L 366 " --> pdb=" O ARG L 362 " (cutoff:3.500A) removed outlier: 3.738A pdb=" N GLN L 369 " --> pdb=" O GLU L 365 " (cutoff:3.500A) Processing helix chain 'L' and resid 415 through 432 Processing helix chain 'L' and resid 444 through 455 removed outlier: 3.544A pdb=" N TYR L 450 " --> pdb=" O PRO L 446 " (cutoff:3.500A) removed outlier: 3.623A pdb=" N LEU L 452 " --> pdb=" O ALA L 448 " (cutoff:3.500A) removed outlier: 4.896A pdb=" N ASN L 453 " --> pdb=" O SER L 449 " (cutoff:3.500A) removed outlier: 4.068A pdb=" N GLU L 454 " --> pdb=" O TYR L 450 " (cutoff:3.500A) Processing helix chain 'L' and resid 455 through 466 removed outlier: 3.732A pdb=" N GLN L 466 " --> pdb=" O ILE L 462 " (cutoff:3.500A) Processing helix chain 'N' and resid 148 through 154 removed outlier: 4.121A pdb=" N GLU N 153 " --> pdb=" O THR N 149 " (cutoff:3.500A) removed outlier: 3.701A pdb=" N ALA N 154 " --> pdb=" O GLU N 150 " (cutoff:3.500A) Processing helix chain 'N' and resid 176 through 190 removed outlier: 3.918A pdb=" N TRP N 182 " --> pdb=" O GLU N 178 " (cutoff:3.500A) removed outlier: 4.249A pdb=" N ASP N 183 " --> pdb=" O ALA N 179 " (cutoff:3.500A) removed outlier: 4.108A pdb=" N PHE N 186 " --> pdb=" O TRP N 182 " (cutoff:3.500A) removed outlier: 3.669A pdb=" N ARG N 187 " --> pdb=" O ASP N 183 " (cutoff:3.500A) Processing helix chain 'N' and resid 214 through 221 removed outlier: 3.628A pdb=" N PHE N 218 " --> pdb=" O ILE N 214 " (cutoff:3.500A) Processing helix chain 'N' and resid 233 through 248 removed outlier: 3.541A pdb=" N ALA N 245 " --> pdb=" O ARG N 241 " (cutoff:3.500A) removed outlier: 3.547A pdb=" N ALA N 246 " --> pdb=" O GLN N 242 " (cutoff:3.500A) Processing helix chain 'N' and resid 251 through 256 removed outlier: 4.290A pdb=" N LYS N 255 " --> pdb=" O PHE N 252 " (cutoff:3.500A) Processing helix chain 'N' and resid 261 through 266 removed outlier: 3.838A pdb=" N LEU N 265 " --> pdb=" O GLY N 261 " (cutoff:3.500A) Processing helix chain 'N' and resid 271 through 278 Processing helix chain 'N' and resid 314 through 338 removed outlier: 3.729A pdb=" N ALA N 331 " --> pdb=" O ALA N 327 " (cutoff:3.500A) removed outlier: 3.861A pdb=" N ARG N 332 " --> pdb=" O ASP N 328 " (cutoff:3.500A) Processing helix chain 'N' and resid 352 through 367 removed outlier: 3.958A pdb=" N VAL N 367 " --> pdb=" O LEU N 363 " (cutoff:3.500A) Processing helix chain 'N' and resid 406 through 410 removed outlier: 4.326A pdb=" N GLY N 409 " --> pdb=" O ARG N 406 " (cutoff:3.500A) Processing helix chain 'N' and resid 415 through 432 removed outlier: 3.817A pdb=" N LEU N 421 " --> pdb=" O GLU N 417 " (cutoff:3.500A) removed outlier: 3.981A pdb=" N LEU N 424 " --> pdb=" O SER N 420 " (cutoff:3.500A) Processing helix chain 'N' and resid 444 through 453 removed outlier: 3.597A pdb=" N TYR N 450 " --> pdb=" O PRO N 446 " (cutoff:3.500A) Processing helix chain 'N' and resid 455 through 466 Processing helix chain 'N' and resid 502 through 510 Processing sheet with id=AA1, first strand: chain 'A' and resid 27 through 29 removed outlier: 5.716A pdb=" N TYR A 27 " --> pdb=" O ALA A 52 " (cutoff:3.500A) removed outlier: 5.117A pdb=" N VAL A 2 " --> pdb=" O ALA A 51 " (cutoff:3.500A) removed outlier: 7.173A pdb=" N VAL A 53 " --> pdb=" O VAL A 2 " (cutoff:3.500A) removed outlier: 6.312A pdb=" N MET A 4 " --> pdb=" O VAL A 53 " (cutoff:3.500A) removed outlier: 3.647A pdb=" N GLN A 81 " --> pdb=" O LEU A 3 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 179 through 182 removed outlier: 5.928A pdb=" N VAL A 163 " --> pdb=" O VAL A 243 " (cutoff:3.500A) removed outlier: 7.356A pdb=" N ILE A 245 " --> pdb=" O VAL A 163 " (cutoff:3.500A) removed outlier: 6.481A pdb=" N GLU A 165 " --> pdb=" O ILE A 245 " (cutoff:3.500A) removed outlier: 7.910A pdb=" N CYS A 247 " --> pdb=" O GLU A 165 " (cutoff:3.500A) removed outlier: 6.520A pdb=" N PHE A 167 " --> pdb=" O CYS A 247 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 28 through 30 removed outlier: 6.374A pdb=" N MET B 4 " --> pdb=" O VAL B 53 " (cutoff:3.500A) removed outlier: 6.072A pdb=" N ILE B 5 " --> pdb=" O LEU B 83 " (cutoff:3.500A) removed outlier: 7.062A pdb=" N LEU B 85 " --> pdb=" O ILE B 5 " (cutoff:3.500A) removed outlier: 6.583A pdb=" N SER B 7 " --> pdb=" O LEU B 85 " (cutoff:3.500A) removed outlier: 6.036A pdb=" N LEU B 82 " --> pdb=" O LEU B 132 " (cutoff:3.500A) removed outlier: 7.459A pdb=" N VAL B 134 " --> pdb=" O LEU B 82 " (cutoff:3.500A) removed outlier: 6.204A pdb=" N PHE B 84 " --> pdb=" O VAL B 134 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 180 through 182 removed outlier: 3.819A pdb=" N GLY B 246 " --> pdb=" O PHE B 181 " (cutoff:3.500A) removed outlier: 4.002A pdb=" N CYS B 247 " --> pdb=" O PHE B 167 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'D' and resid 3 through 6 Processing sheet with id=AA6, first strand: chain 'D' and resid 165 through 168 removed outlier: 5.830A pdb=" N GLU D 165 " --> pdb=" O ILE D 245 " (cutoff:3.500A) removed outlier: 7.263A pdb=" N CYS D 247 " --> pdb=" O GLU D 165 " (cutoff:3.500A) removed outlier: 5.780A pdb=" N PHE D 167 " --> pdb=" O CYS D 247 " (cutoff:3.500A) removed outlier: 6.120A pdb=" N TYR D 179 " --> pdb=" O ALA D 244 " (cutoff:3.500A) removed outlier: 8.123A pdb=" N GLY D 246 " --> pdb=" O TYR D 179 " (cutoff:3.500A) removed outlier: 6.855A pdb=" N PHE D 181 " --> pdb=" O GLY D 246 " (cutoff:3.500A) removed outlier: 4.015A pdb=" N VAL D 180 " --> pdb=" O VAL C 180 " (cutoff:3.500A) removed outlier: 3.889A pdb=" N VAL C 180 " --> pdb=" O VAL D 180 " (cutoff:3.500A) removed outlier: 6.950A pdb=" N TYR C 179 " --> pdb=" O ALA C 244 " (cutoff:3.500A) removed outlier: 8.708A pdb=" N GLY C 246 " --> pdb=" O TYR C 179 " (cutoff:3.500A) removed outlier: 6.905A pdb=" N PHE C 181 " --> pdb=" O GLY C 246 " (cutoff:3.500A) removed outlier: 3.798A pdb=" N LEU C 241 " --> pdb=" O THR C 161 " (cutoff:3.500A) removed outlier: 3.643A pdb=" N CYS C 247 " --> pdb=" O PHE C 167 " (cutoff:3.500A) removed outlier: 7.724A pdb=" N MET C 162 " --> pdb=" O GLN C 273 " (cutoff:3.500A) removed outlier: 8.068A pdb=" N ARG C 275 " --> pdb=" O MET C 162 " (cutoff:3.500A) removed outlier: 6.168A pdb=" N PHE C 164 " --> pdb=" O ARG C 275 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'C' and resid 29 through 30 removed outlier: 7.025A pdb=" N VAL C 29 " --> pdb=" O SER C 54 " (cutoff:3.500A) removed outlier: 3.611A pdb=" N VAL C 53 " --> pdb=" O MET C 4 " (cutoff:3.500A) removed outlier: 6.697A pdb=" N ILE C 5 " --> pdb=" O LEU C 83 " (cutoff:3.500A) removed outlier: 8.552A pdb=" N LEU C 85 " --> pdb=" O ILE C 5 " (cutoff:3.500A) removed outlier: 6.293A pdb=" N LEU C 82 " --> pdb=" O LEU C 132 " (cutoff:3.500A) removed outlier: 7.918A pdb=" N VAL C 134 " --> pdb=" O LEU C 82 " (cutoff:3.500A) removed outlier: 5.936A pdb=" N PHE C 84 " --> pdb=" O VAL C 134 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'L' and resid 23 through 27 removed outlier: 6.380A pdb=" N LEU L 18 " --> pdb=" O TYR L 25 " (cutoff:3.500A) removed outlier: 5.070A pdb=" N LEU L 27 " --> pdb=" O VAL L 16 " (cutoff:3.500A) removed outlier: 7.420A pdb=" N VAL L 16 " --> pdb=" O LEU L 27 " (cutoff:3.500A) removed outlier: 3.710A pdb=" N ILE L 6 " --> pdb=" O LEU L 230 " (cutoff:3.500A) removed outlier: 5.620A pdb=" N ILE L 229 " --> pdb=" O LYS L 257 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'L' and resid 41 through 42 removed outlier: 6.446A pdb=" N ILE L 104 " --> pdb=" O THR L 117 " (cutoff:3.500A) removed outlier: 6.296A pdb=" N THR L 117 " --> pdb=" O ILE L 104 " (cutoff:3.500A) removed outlier: 3.758A pdb=" N ALA L 115 " --> pdb=" O LYS L 106 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'L' and resid 46 through 50 removed outlier: 3.546A pdb=" N ARG L 48 " --> pdb=" O PHE L 57 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'L' and resid 122 through 123 Processing sheet with id=AB3, first strand: chain 'L' and resid 282 through 283 removed outlier: 6.591A pdb=" N THR L 300 " --> pdb=" O VAL L 344 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'L' and resid 412 through 414 Processing sheet with id=AB5, first strand: chain 'L' and resid 441 through 442 Processing sheet with id=AB6, first strand: chain 'N' and resid 26 through 28 Processing sheet with id=AB7, first strand: chain 'N' and resid 282 through 283 removed outlier: 3.558A pdb=" N VAL N 283 " --> pdb=" O ILE N 291 " (cutoff:3.500A) removed outlier: 3.790A pdb=" N ASP N 303 " --> pdb=" O VAL N 292 " (cutoff:3.500A) removed outlier: 3.779A pdb=" N ALA N 301 " --> pdb=" O ASP N 294 " (cutoff:3.500A) removed outlier: 7.062A pdb=" N ILE N 302 " --> pdb=" O CYS N 346 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'N' and resid 474 through 475 608 hydrogen bonds defined for protein. 1716 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 8 hydrogen bonds 16 hydrogen bond angles 0 basepair planarities 4 basepair parallelities 54 stacking parallelities Total time for adding SS restraints: 10.60 Time building geometry restraints manager: 23.60 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.84 - 1.03: 11340 1.03 - 1.23: 1250 1.23 - 1.42: 6921 1.42 - 1.62: 9635 1.62 - 1.82: 64 Bond restraints: 29210 Sorted by residual: bond pdb=" N1 G K 193 " pdb=" H1 G K 193 " ideal model delta sigma weight residual 0.860 1.041 -0.181 2.00e-02 2.50e+03 8.17e+01 bond pdb=" N3 U K 138 " pdb=" H3 U K 138 " ideal model delta sigma weight residual 0.860 1.041 -0.181 2.00e-02 2.50e+03 8.17e+01 bond pdb=" N1 G K 152 " pdb=" H1 G K 152 " ideal model delta sigma weight residual 0.860 1.041 -0.181 2.00e-02 2.50e+03 8.15e+01 bond pdb=" N3 U K 22 " pdb=" H3 U K 22 " ideal model delta sigma weight residual 0.860 1.041 -0.181 2.00e-02 2.50e+03 8.15e+01 bond pdb=" N3 U K 27 " pdb=" H3 U K 27 " ideal model delta sigma weight residual 0.860 1.040 -0.180 2.00e-02 2.50e+03 8.14e+01 ... (remaining 29205 not shown) Histogram of bond angle deviations from ideal: 88.61 - 97.74: 4 97.74 - 106.88: 1771 106.88 - 116.02: 34471 116.02 - 125.16: 14639 125.16 - 134.29: 1305 Bond angle restraints: 52190 Sorted by residual: angle pdb=" O2' C K 177 " pdb=" C2' C K 177 " pdb=" C1' C K 177 " ideal model delta sigma weight residual 111.80 98.43 13.37 1.50e+00 4.44e-01 7.94e+01 angle pdb=" N HIS C 190 " pdb=" CA HIS C 190 " pdb=" C HIS C 190 " ideal model delta sigma weight residual 112.38 101.77 10.61 1.22e+00 6.72e-01 7.56e+01 angle pdb=" O3' G K 185 " pdb=" C3' G K 185 " pdb=" C2' G K 185 " ideal model delta sigma weight residual 113.70 101.74 11.96 1.50e+00 4.44e-01 6.36e+01 angle pdb=" C ASN A 188 " pdb=" CA ASN A 188 " pdb=" CB ASN A 188 " ideal model delta sigma weight residual 109.85 100.87 8.98 1.14e+00 7.69e-01 6.21e+01 angle pdb=" C4' U K 150 " pdb=" C3' U K 150 " pdb=" O3' U K 150 " ideal model delta sigma weight residual 113.00 101.46 11.54 1.50e+00 4.44e-01 5.91e+01 ... (remaining 52185 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 36.00: 11190 36.00 - 72.00: 425 72.00 - 107.99: 156 107.99 - 143.99: 15 143.99 - 179.99: 41 Dihedral angle restraints: 11827 sinusoidal: 5729 harmonic: 6098 Sorted by residual: dihedral pdb=" C5' C K 177 " pdb=" C4' C K 177 " pdb=" C3' C K 177 " pdb=" O3' C K 177 " ideal model delta sinusoidal sigma weight residual 147.00 76.00 71.00 1 8.00e+00 1.56e-02 1.01e+02 dihedral pdb=" C4' A K 42 " pdb=" C3' A K 42 " pdb=" C2' A K 42 " pdb=" C1' A K 42 " ideal model delta sinusoidal sigma weight residual -35.00 30.31 -65.31 1 8.00e+00 1.56e-02 8.73e+01 dihedral pdb=" C5' A K 42 " pdb=" C4' A K 42 " pdb=" C3' A K 42 " pdb=" O3' A K 42 " ideal model delta sinusoidal sigma weight residual 147.00 82.42 64.58 1 8.00e+00 1.56e-02 8.56e+01 ... (remaining 11824 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.108: 2606 0.108 - 0.216: 370 0.216 - 0.324: 60 0.324 - 0.432: 3 0.432 - 0.540: 2 Chirality restraints: 3041 Sorted by residual: chirality pdb=" C3' A K 87 " pdb=" C4' A K 87 " pdb=" O3' A K 87 " pdb=" C2' A K 87 " both_signs ideal model delta sigma weight residual False -2.74 -2.20 -0.54 2.00e-01 2.50e+01 7.29e+00 chirality pdb=" C3' C K 177 " pdb=" C4' C K 177 " pdb=" O3' C K 177 " pdb=" C2' C K 177 " both_signs ideal model delta sigma weight residual False -2.74 -2.27 -0.47 2.00e-01 2.50e+01 5.60e+00 chirality pdb=" C2' C K 77 " pdb=" C3' C K 77 " pdb=" O2' C K 77 " pdb=" C1' C K 77 " both_signs ideal model delta sigma weight residual False -2.52 -2.13 -0.39 2.00e-01 2.50e+01 3.87e+00 ... (remaining 3038 not shown) Planarity restraints: 4457 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB ASN L 323 " -0.016 2.00e-02 2.50e+03 4.41e-01 2.92e+03 pdb=" CG ASN L 323 " -0.003 2.00e-02 2.50e+03 pdb=" OD1 ASN L 323 " 0.017 2.00e-02 2.50e+03 pdb=" ND2 ASN L 323 " 0.000 2.00e-02 2.50e+03 pdb="HD21 ASN L 323 " 0.765 2.00e-02 2.50e+03 pdb="HD22 ASN L 323 " -0.763 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB ASN B 271 " -0.123 2.00e-02 2.50e+03 1.33e-01 2.67e+02 pdb=" CG ASN B 271 " 0.005 2.00e-02 2.50e+03 pdb=" OD1 ASN B 271 " 0.120 2.00e-02 2.50e+03 pdb=" ND2 ASN B 271 " 0.004 2.00e-02 2.50e+03 pdb="HD21 ASN B 271 " -0.200 2.00e-02 2.50e+03 pdb="HD22 ASN B 271 " 0.193 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CG GLN N 478 " -0.117 2.00e-02 2.50e+03 1.31e-01 2.56e+02 pdb=" CD GLN N 478 " 0.002 2.00e-02 2.50e+03 pdb=" OE1 GLN N 478 " 0.117 2.00e-02 2.50e+03 pdb=" NE2 GLN N 478 " -0.004 2.00e-02 2.50e+03 pdb="HE21 GLN N 478 " 0.194 2.00e-02 2.50e+03 pdb="HE22 GLN N 478 " -0.193 2.00e-02 2.50e+03 ... (remaining 4454 not shown) Histogram of nonbonded interaction distances: 1.44 - 2.07: 454 2.07 - 2.70: 40514 2.70 - 3.33: 74414 3.33 - 3.97: 89155 3.97 - 4.60: 132515 Nonbonded interactions: 337052 Sorted by model distance: nonbonded pdb=" O2 U K 179 " pdb=" H2' U K 179 " model vdw 1.437 2.620 nonbonded pdb=" O2 C K 110 " pdb=" H3' C K 110 " model vdw 1.497 2.620 nonbonded pdb=" OP1 G K 51 " pdb=" H21 G K 51 " model vdw 1.497 1.850 nonbonded pdb=" O2 U K 12 " pdb=" H3' U K 12 " model vdw 1.507 2.620 nonbonded pdb="HD12 LEU A 36 " pdb="HD23 LEU D 36 " model vdw 1.549 2.440 ... (remaining 337047 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = (chain 'A' and ((resid 3 through 4 and (name N or name CA or name C or name O or \ name CB or name H or name HA )) or resid 5 or (resid 6 through 7 and (name N or \ name CA or name C or name O or name CB or name H or name HA )) or resid 8 throu \ gh 11 or (resid 12 and (name N or name CA or name C or name O or name CB or name \ H or name HA )) or resid 13 through 15 or (resid 16 and (name N or name CA or n \ ame C or name O or name CB or name H or name HA )) or resid 17 through 18 or (re \ sid 19 and (name N or name CA or name C or name O or name CB or name H or name H \ A )) or resid 20 or (resid 21 through 24 and (name N or name CA or name C or nam \ e O or name CB or name H or name HA )) or resid 25 or (resid 27 through 32 and ( \ name N or name CA or name C or name O or name CB or name H or name HA )) or resi \ d 33 through 35 or (resid 36 through 37 and (name N or name CA or name C or name \ O or name CB or name H or name HA )) or resid 38 or (resid 39 and (name N or na \ me CA or name C or name O or name CB or name H or name HA )) or resid 40 through \ 41 or (resid 42 through 44 and (name N or name CA or name C or name O or name C \ B or name H or name HA )) or resid 45 or (resid 46 through 49 and (name N or nam \ e CA or name C or name O or name CB or name H or name HA )) or resid 50 through \ 55 or (resid 56 and (name N or name CA or name C or name O or name CB or name H \ or name HA )) or resid 57 or (resid 58 through 60 and (name N or name CA or name \ C or name O or name CB or name H or name HA )) or resid 61 through 66 or (resid \ 67 through 68 and (name N or name CA or name C or name O or name CB or name H o \ r name HA )) or resid 69 through 72 or (resid 73 through 74 and (name N or name \ CA or name C or name O or name CB or name H or name HA )) or resid 75 through 80 \ or (resid 81 through 84 and (name N or name CA or name C or name O or name CB o \ r name H or name HA )) or resid 85 through 87 or (resid 88 through 90 and (name \ N or name CA or name C or name O or name CB or name H or name HA )) or resid 91 \ through 95 or (resid 112 through 113 and (name N or name CA or name C or name O \ or name CB or name H or name HA )) or resid 114 through 119 or (resid 120 throug \ h 121 and (name N or name CA or name C or name O or name CB or name H or name HA \ )) or resid 122 through 125 or (resid 126 through 127 and (name N or name CA or \ name C or name O or name CB or name H or name HA )) or resid 128 or (resid 129 \ and (name N or name CA or name C or name O or name CB or name H or name HA )) or \ resid 130 or (resid 131 through 133 and (name N or name CA or name C or name O \ or name CB or name H or name HA )) or resid 134 through 135 or (resid 136 and (n \ ame N or name CA or name C or name O or name CB or name H or name HA )) or resid \ 137 through 140 or (resid 141 through 144 and (name N or name CA or name C or n \ ame O or name CB or name H or name HA )) or resid 145 through 147 or (resid 148 \ through 152 and (name N or name CA or name C or name O or name CB or name H or n \ ame HA )) or resid 153 through 155 or (resid 156 through 160 and (name N or name \ CA or name C or name O or name CB or name H or name HA )) or resid 161 or (resi \ d 162 and (name N or name CA or name C or name O or name CB or name H or name HA \ )) or resid 163 through 165 or (resid 166 and (name N or name CA or name C or n \ ame O or name CB or name H or name HA )) or resid 167 through 169 or (resid 170 \ and (name N or name CA or name C or name O or name CB or name H or name HA )) or \ resid 171 through 178 or (resid 179 through 185 and (name N or name CA or name \ C or name O or name CB or name H or name HA )) or resid 186 through 189 or (resi \ d 190 through 191 and (name N or name CA or name C or name O or name CB or name \ H or name HA )) or resid 192 through 193 or (resid 194 through 196 and (name N o \ r name CA or name C or name O or name CB or name H or name HA )) or resid 197 th \ rough 198 or (resid 199 and (name N or name CA or name C or name O or name CB or \ name H or name HA )) or resid 200 or (resid 201 through 203 and (name N or name \ CA or name C or name O or name CB or name H or name HA )) or resid 204 through \ 207 or (resid 208 and (name N or name CA or name C or name O or name CB or name \ H or name HA )) or resid 209 through 210 or (resid 211 through 214 and (name N o \ r name CA or name C or name O or name CB or name H or name HA )) or resid 215 or \ (resid 216 and (name N or name CA or name C or name O or name CB or name H or n \ ame HA )) or resid 217 or (resid 218 through 223 and (name N or name CA or name \ C or name O or name CB or name H or name HA )) or resid 224 or (resid 225 and (n \ ame N or name CA or name C or name O or name CB or name H or name HA )) or resid \ 226 through 228 or (resid 229 through 230 and (name N or name CA or name C or n \ ame O or name CB or name H or name HA )) or resid 231 or (resid 232 through 243 \ and (name N or name CA or name C or name O or name CB or name H or name HA )) or \ resid 244 or (resid 245 and (name N or name CA or name C or name O or name CB o \ r name H or name HA )) or resid 246 or (resid 247 through 248 and (name N or nam \ e CA or name C or name O or name CB or name H or name HA )) or resid 249 through \ 250 or (resid 251 through 253 and (name N or name CA or name C or name O or nam \ e CB or name H or name HA )) or resid 254 or (resid 255 through 256 and (name N \ or name CA or name C or name O or name CB or name H or name HA )) or resid 257 t \ hrough 258 or (resid 259 through 260 and (name N or name CA or name C or name O \ or name CB or name H or name HA )) or resid 261 through 262 or (resid 263 throug \ h 264 and (name N or name CA or name C or name O or name CB or name H or name HA \ )) or resid 265 through 266 or (resid 267 through 268 and (name N or name CA or \ name C or name O or name CB or name H or name HA )) or resid 269 or (resid 270 \ through 271 and (name N or name CA or name C or name O or name CB or name H or n \ ame HA )) or resid 272 or (resid 273 and (name N or name CA or name C or name O \ or name CB or name H or name HA )) or resid 274 or (resid 275 through 281 and (n \ ame N or name CA or name C or name O or name CB or name H or name HA )))) selection = (chain 'B' and (resid 3 through 6 or (resid 7 and (name N or name CA or name C o \ r name O or name CB or name H or name HA )) or resid 8 or (resid 9 and (name N o \ r name CA or name C or name O or name CB or name H or name HA )) or resid 10 thr \ ough 15 or (resid 16 and (name N or name CA or name C or name O or name CB or na \ me H or name HA )) or resid 17 through 21 or (resid 22 through 24 and (name N or \ name CA or name C or name O or name CB or name H or name HA )) or resid 25 thro \ ugh 27 or (resid 28 through 32 and (name N or name CA or name C or name O or nam \ e CB or name H or name HA )) or resid 33 through 38 or (resid 39 and (name N or \ name CA or name C or name O or name CB or name H or name HA )) or resid 40 throu \ gh 48 or (resid 49 and (name N or name CA or name C or name O or name CB or name \ H or name HA )) or resid 50 through 64 or (resid 65 through 68 and (name N or n \ ame CA or name C or name O or name CB or name H or name HA )) or resid 69 throug \ h 72 or (resid 73 through 74 and (name N or name CA or name C or name O or name \ CB or name H or name HA )) or resid 75 through 83 or (resid 84 and (name N or na \ me CA or name C or name O or name CB or name H or name HA )) or resid 85 through \ 88 or (resid 89 through 90 and (name N or name CA or name C or name O or name C \ B or name H or name HA )) or resid 91 through 94 or (resid 95 and (name N or nam \ e CA or name C or name O or name CB or name H or name HA )) or resid 112 through \ 115 or (resid 116 through 121 and (name N or name CA or name C or name O or nam \ e CB or name H or name HA )) or resid 122 through 123 or (resid 124 and (name N \ or name CA or name C or name O or name CB or name H or name HA )) or resid 125 o \ r (resid 126 through 127 and (name N or name CA or name C or name O or name CB o \ r name H or name HA )) or resid 128 through 130 or (resid 131 through 133 and (n \ ame N or name CA or name C or name O or name CB or name H or name HA )) or resid \ 134 through 135 or (resid 136 and (name N or name CA or name C or name O or nam \ e CB or name H or name HA )) or resid 137 or (resid 138 through 139 and (name N \ or name CA or name C or name O or name CB or name H or name HA )) or resid 140 t \ hrough 141 or (resid 142 through 144 and (name N or name CA or name C or name O \ or name CB or name H or name HA )) or resid 145 through 147 or (resid 148 throug \ h 152 and (name N or name CA or name C or name O or name CB or name H or name HA \ )) or resid 153 through 154 or (resid 155 through 160 and (name N or name CA or \ name C or name O or name CB or name H or name HA )) or resid 161 through 169 or \ (resid 170 and (name N or name CA or name C or name O or name CB or name H or n \ ame HA )) or resid 171 through 177 or (resid 178 through 185 and (name N or name \ CA or name C or name O or name CB or name H or name HA )) or resid 186 through \ 189 or (resid 190 through 191 and (name N or name CA or name C or name O or name \ CB or name H or name HA )) or resid 192 through 194 or (resid 195 through 196 a \ nd (name N or name CA or name C or name O or name CB or name H or name HA )) or \ resid 197 through 198 or (resid 199 and (name N or name CA or name C or name O o \ r name CB or name H or name HA )) or resid 200 or (resid 201 through 203 and (na \ me N or name CA or name C or name O or name CB or name H or name HA )) or resid \ 204 through 207 or (resid 208 and (name N or name CA or name C or name O or name \ CB or name H or name HA )) or resid 209 or (resid 210 through 214 and (name N o \ r name CA or name C or name O or name CB or name H or name HA )) or resid 215 or \ (resid 216 and (name N or name CA or name C or name O or name CB or name H or n \ ame HA )) or resid 217 or (resid 218 through 223 and (name N or name CA or name \ C or name O or name CB or name H or name HA )) or resid 224 or (resid 225 and (n \ ame N or name CA or name C or name O or name CB or name H or name HA )) or resid \ 226 or (resid 227 and (name N or name CA or name C or name O or name CB or name \ H or name HA )) or resid 228 through 229 or (resid 230 and (name N or name CA o \ r name C or name O or name CB or name H or name HA )) or resid 231 through 232 o \ r (resid 233 through 243 and (name N or name CA or name C or name O or name CB o \ r name H or name HA )) or resid 244 or (resid 245 and (name N or name CA or name \ C or name O or name CB or name H or name HA )) or resid 246 through 250 or (res \ id 251 through 253 and (name N or name CA or name C or name O or name CB or name \ H or name HA )) or resid 254 or (resid 255 through 256 and (name N or name CA o \ r name C or name O or name CB or name H or name HA )) or resid 257 through 258 o \ r (resid 259 through 260 and (name N or name CA or name C or name O or name CB o \ r name H or name HA )) or resid 261 through 263 or (resid 264 and (name N or nam \ e CA or name C or name O or name CB or name H or name HA )) or resid 265 through \ 267 or (resid 268 and (name N or name CA or name C or name O or name CB or name \ H or name HA )) or resid 269 through 270 or (resid 271 and (name N or name CA o \ r name C or name O or name CB or name H or name HA )) or resid 272 or (resid 273 \ and (name N or name CA or name C or name O or name CB or name H or name HA )) o \ r resid 274 or (resid 275 through 281 and (name N or name CA or name C or name O \ or name CB or name H or name HA )))) selection = (chain 'C' and ((resid 3 through 4 and (name N or name CA or name C or name O or \ name CB or name H or name HA )) or resid 5 or (resid 6 through 7 and (name N or \ name CA or name C or name O or name CB or name H or name HA )) or resid 8 throu \ gh 20 or (resid 21 through 24 and (name N or name CA or name C or name O or name \ CB or name H or name HA )) or resid 25 or (resid 27 through 32 and (name N or n \ ame CA or name C or name O or name CB or name H or name HA )) or resid 33 throug \ h 35 or (resid 36 through 37 and (name N or name CA or name C or name O or name \ CB or name H or name HA )) or resid 38 or (resid 39 and (name N or name CA or na \ me C or name O or name CB or name H or name HA )) or resid 40 through 42 or (res \ id 43 through 44 and (name N or name CA or name C or name O or name CB or name H \ or name HA )) or resid 45 or (resid 46 through 49 and (name N or name CA or nam \ e C or name O or name CB or name H or name HA )) or resid 50 through 55 or (resi \ d 56 and (name N or name CA or name C or name O or name CB or name H or name HA \ )) or resid 57 or (resid 58 through 60 and (name N or name CA or name C or name \ O or name CB or name H or name HA )) or resid 61 through 65 or (resid 66 through \ 68 and (name N or name CA or name C or name O or name CB or name H or name HA ) \ ) or resid 69 through 70 or (resid 71 and (name N or name CA or name C or name O \ or name CB or name H or name HA )) or resid 72 or (resid 73 through 74 and (nam \ e N or name CA or name C or name O or name CB or name H or name HA )) or resid 7 \ 5 through 77 or (resid 78 and (name N or name CA or name C or name O or name CB \ or name H or name HA )) or resid 79 through 80 or (resid 81 through 84 and (name \ N or name CA or name C or name O or name CB or name H or name HA )) or resid 85 \ or (resid 86 and (name N or name CA or name C or name O or name CB or name H or \ name HA )) or resid 87 or (resid 88 through 90 and (name N or name CA or name C \ or name O or name CB or name H or name HA )) or resid 91 through 112 or (resid \ 113 and (name N or name CA or name C or name O or name CB or name H or name HA ) \ ) or resid 114 through 115 or (resid 116 through 121 and (name N or name CA or n \ ame C or name O or name CB or name H or name HA )) or resid 122 through 126 or ( \ resid 127 and (name N or name CA or name C or name O or name CB or name H or nam \ e HA )) or resid 128 through 130 or (resid 131 through 133 and (name N or name C \ A or name C or name O or name CB or name H or name HA )) or resid 134 or (resid \ 135 through 136 and (name N or name CA or name C or name O or name CB or name H \ or name HA )) or resid 137 through 145 or (resid 146 through 152 and (name N or \ name CA or name C or name O or name CB or name H or name HA )) or resid 153 thro \ ugh 182 or (resid 183 through 185 and (name N or name CA or name C or name O or \ name CB or name H or name HA )) or resid 186 through 187 or (resid 188 and (name \ N or name CA or name C or name O or name CB or name H or name HA )) or resid 18 \ 9 through 193 or (resid 194 through 196 and (name N or name CA or name C or name \ O or name CB or name H or name HA )) or resid 197 through 198 or (resid 199 and \ (name N or name CA or name C or name O or name CB or name H or name HA )) or re \ sid 200 or (resid 201 through 203 and (name N or name CA or name C or name O or \ name CB or name H or name HA )) or resid 204 through 207 or (resid 208 and (name \ N or name CA or name C or name O or name CB or name H or name HA )) or resid 20 \ 9 through 211 or (resid 212 through 214 and (name N or name CA or name C or name \ O or name CB or name H or name HA )) or resid 215 or (resid 216 and (name N or \ name CA or name C or name O or name CB or name H or name HA )) or resid 217 or ( \ resid 218 through 223 and (name N or name CA or name C or name O or name CB or n \ ame H or name HA )) or resid 224 through 226 or (resid 227 and (name N or name C \ A or name C or name O or name CB or name H or name HA )) or resid 228 or (resid \ 229 through 230 and (name N or name CA or name C or name O or name CB or name H \ or name HA )) or resid 231 through 232 or (resid 233 through 243 and (name N or \ name CA or name C or name O or name CB or name H or name HA )) or resid 244 or ( \ resid 245 and (name N or name CA or name C or name O or name CB or name H or nam \ e HA )) or resid 246 through 247 or (resid 248 and (name N or name CA or name C \ or name O or name CB or name H or name HA )) or resid 249 through 255 or (resid \ 256 and (name N or name CA or name C or name O or name CB or name H or name HA ) \ ) or resid 257 through 259 or (resid 260 and (name N or name CA or name C or nam \ e O or name CB or name H or name HA )) or resid 261 through 263 or (resid 264 an \ d (name N or name CA or name C or name O or name CB or name H or name HA )) or r \ esid 265 through 267 or (resid 268 and (name N or name CA or name C or name O or \ name CB or name H or name HA )) or resid 269 through 270 or (resid 271 and (nam \ e N or name CA or name C or name O or name CB or name H or name HA )) or resid 2 \ 72 through 274 or (resid 275 through 281 and (name N or name CA or name C or nam \ e O or name CB or name H or name HA )))) selection = (chain 'D' and ((resid 3 through 4 and (name N or name CA or name C or name O or \ name CB or name H or name HA )) or resid 5 or (resid 6 through 7 and (name N or \ name CA or name C or name O or name CB or name H or name HA )) or resid 8 throu \ gh 11 or (resid 12 and (name N or name CA or name C or name O or name CB or name \ H or name HA )) or resid 13 or (resid 14 and (name N or name CA or name C or na \ me O or name CB or name H or name HA )) or resid 15 or (resid 16 and (name N or \ name CA or name C or name O or name CB or name H or name HA )) or resid 17 throu \ gh 20 or (resid 21 through 24 and (name N or name CA or name C or name O or name \ CB or name H or name HA )) or resid 25 or (resid 27 through 32 and (name N or n \ ame CA or name C or name O or name CB or name H or name HA )) or resid 33 or (re \ sid 34 and (name N or name CA or name C or name O or name CB or name H or name H \ A )) or resid 35 or (resid 36 through 37 and (name N or name CA or name C or nam \ e O or name CB or name H or name HA )) or resid 38 through 41 or (resid 42 throu \ gh 44 and (name N or name CA or name C or name O or name CB or name H or name HA \ )) or resid 45 or (resid 46 through 49 and (name N or name CA or name C or name \ O or name CB or name H or name HA )) or resid 50 through 57 or (resid 58 throug \ h 60 and (name N or name CA or name C or name O or name CB or name H or name HA \ )) or resid 61 or (resid 62 and (name N or name CA or name C or name O or name C \ B or name H or name HA )) or resid 63 through 64 or (resid 65 through 68 and (na \ me N or name CA or name C or name O or name CB or name H or name HA )) or resid \ 69 through 75 or (resid 76 and (name N or name CA or name C or name O or name CB \ or name H or name HA )) or resid 77 through 80 or (resid 81 through 84 and (nam \ e N or name CA or name C or name O or name CB or name H or name HA )) or resid 8 \ 5 through 87 or (resid 88 through 90 and (name N or name CA or name C or name O \ or name CB or name H or name HA )) or resid 91 through 94 or (resid 95 and (name \ N or name CA or name C or name O or name CB or name H or name HA )) or (resid 1 \ 12 through 113 and (name N or name CA or name C or name O or name CB or name H o \ r name HA )) or resid 114 through 115 or (resid 116 through 121 and (name N or n \ ame CA or name C or name O or name CB or name H or name HA )) or resid 122 throu \ gh 123 or (resid 124 and (name N or name CA or name C or name O or name CB or na \ me H or name HA )) or resid 125 or (resid 126 through 127 and (name N or name CA \ or name C or name O or name CB or name H or name HA )) or resid 128 through 134 \ or (resid 135 through 136 and (name N or name CA or name C or name O or name CB \ or name H or name HA )) or resid 137 or (resid 138 through 139 and (name N or n \ ame CA or name C or name O or name CB or name H or name HA )) or resid 140 throu \ gh 147 or (resid 148 through 152 and (name N or name CA or name C or name O or n \ ame CB or name H or name HA )) or resid 153 through 154 or (resid 155 through 16 \ 0 and (name N or name CA or name C or name O or name CB or name H or name HA )) \ or resid 161 through 165 or (resid 166 and (name N or name CA or name C or name \ O or name CB or name H or name HA )) or resid 167 through 169 or (resid 170 and \ (name N or name CA or name C or name O or name CB or name H or name HA )) or res \ id 171 through 178 or (resid 179 through 185 and (name N or name CA or name C or \ name O or name CB or name H or name HA )) or resid 186 through 190 or (resid 19 \ 1 and (name N or name CA or name C or name O or name CB or name H or name HA )) \ or resid 192 through 195 or (resid 196 and (name N or name CA or name C or name \ O or name CB or name H or name HA )) or resid 197 or (resid 198 through 199 and \ (name N or name CA or name C or name O or name CB or name H or name HA )) or res \ id 200 through 201 or (resid 202 through 203 and (name N or name CA or name C or \ name O or name CB or name H or name HA )) or resid 204 through 209 or (resid 21 \ 0 through 214 and (name N or name CA or name C or name O or name CB or name H or \ name HA )) or resid 215 through 221 or (resid 222 through 223 and (name N or na \ me CA or name C or name O or name CB or name H or name HA )) or resid 224 or (re \ sid 225 and (name N or name CA or name C or name O or name CB or name H or name \ HA )) or resid 226 through 241 or (resid 242 through 243 and (name N or name CA \ or name C or name O or name CB or name H or name HA )) or resid 244 through 251 \ or (resid 252 through 253 and (name N or name CA or name C or name O or name CB \ or name H or name HA )) or resid 254 or (resid 255 through 256 and (name N or na \ me CA or name C or name O or name CB or name H or name HA )) or resid 257 throug \ h 258 or (resid 259 through 260 and (name N or name CA or name C or name O or na \ me CB or name H or name HA )) or resid 261 through 262 or (resid 263 through 264 \ and (name N or name CA or name C or name O or name CB or name H or name HA )) o \ r resid 265 through 266 or (resid 267 through 268 and (name N or name CA or name \ C or name O or name CB or name H or name HA )) or resid 269 through 275 or (res \ id 276 through 281 and (name N or name CA or name C or name O or name CB or name \ H or name HA )))) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=0.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 4.360 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: 0.440 Extract box with map and model: 21.380 Check model and map are aligned: 0.410 Set scattering table: 0.250 Process input model: 95.150 Find NCS groups from input model: 1.130 Set up NCS constraints: 0.090 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:3.080 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 126.300 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7051 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 0.081 16776 Z= 0.625 Angle : 1.304 13.370 23691 Z= 0.916 Chirality : 0.078 0.540 3041 Planarity : 0.007 0.053 2530 Dihedral : 19.833 178.023 6067 Min Nonbonded Distance : 1.945 Molprobity Statistics. All-atom Clashscore : 11.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.72 % Favored : 90.28 % Rotamer: Outliers : 0.00 % Allowed : 5.51 % Favored : 94.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.43 (0.18), residues: 1893 helix: -1.24 (0.17), residues: 757 sheet: -2.19 (0.26), residues: 338 loop : -1.50 (0.21), residues: 798 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3786 Ramachandran restraints generated. 1893 Oldfield, 0 Emsley, 1893 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3786 Ramachandran restraints generated. 1893 Oldfield, 0 Emsley, 1893 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue MET 1 is missing expected H atoms. Skipping. Residue MET 4 is missing expected H atoms. Skipping. Residue LYS 14 is missing expected H atoms. Skipping. Residue MET 24 is missing expected H atoms. Skipping. Residue TYR 27 is missing expected H atoms. Skipping. Residue VAL 29 is missing expected H atoms. Skipping. Residue VAL 34 is missing expected H atoms. Skipping. Residue MET 60 is missing expected H atoms. Skipping. Residue ILE 66 is missing expected H atoms. Skipping. Residue MET 71 is missing expected H atoms. Skipping. Residue LEU 82 is missing expected H atoms. Skipping. Residue LEU 83 is missing expected H atoms. Skipping. Residue TYR 96 is missing expected H atoms. Skipping. Residue ILE 116 is missing expected H atoms. Skipping. Residue LYS 118 is missing expected H atoms. Skipping. Residue MET 139 is missing expected H atoms. Skipping. Residue MET 147 is missing expected H atoms. Skipping. Residue LYS 155 is missing expected H atoms. Skipping. Residue MET 198 is missing expected H atoms. Skipping. Residue ILE 219 is missing expected H atoms. Skipping. Residue TYR 264 is missing expected H atoms. Skipping. Residue LEU 3 is missing expected H atoms. Skipping. Residue MET 4 is missing expected H atoms. Skipping. Residue VAL 6 is missing expected H atoms. Skipping. Residue SER 12 is missing expected H atoms. Skipping. Residue LYS 14 is missing expected H atoms. Skipping. Residue LEU 21 is missing expected H atoms. Skipping. Residue MET 24 is missing expected H atoms. Skipping. Residue TYR 27 is missing expected H atoms. Skipping. Residue VAL 34 is missing expected H atoms. Skipping. Residue LEU 36 is missing expected H atoms. Skipping. Residue LEU 37 is missing expected H atoms. Skipping. Residue THR 43 is missing expected H atoms. Skipping. Residue LEU 44 is missing expected H atoms. Skipping. Residue MET 60 is missing expected H atoms. Skipping. Residue MET 71 is missing expected H atoms. Skipping. Residue LEU 82 is missing expected H atoms. Skipping. Residue LEU 83 is missing expected H atoms. Skipping. Residue THR 99 is missing expected H atoms. Skipping. Residue LEU 102 is missing expected H atoms. Skipping. Residue LEU 105 is missing expected H atoms. Skipping. Residue LYS 108 is missing expected H atoms. Skipping. Residue LEU 110 is missing expected H atoms. Skipping. Residue LEU 112 is missing expected H atoms. Skipping. Residue LYS 118 is missing expected H atoms. Skipping. Residue SER 120 is missing expected H atoms. Skipping. Residue MET 139 is missing expected H atoms. Skipping. Residue VAL 141 is missing expected H atoms. Skipping. Residue MET 147 is missing expected H atoms. Skipping. Residue LEU 152 is missing expected H atoms. Skipping. Residue MET 162 is missing expected H atoms. Skipping. Residue SER 166 is missing expected H atoms. Skipping. Residue LYS 194 is missing expected H atoms. Skipping. Residue MET 198 is missing expected H atoms. Skipping. Residue LYS 203 is missing expected H atoms. Skipping. Residue THR 213 is missing expected H atoms. Skipping. Residue MET 232 is missing expected H atoms. Skipping. Residue THR 248 is missing expected H atoms. Skipping. Residue SER 267 is missing expected H atoms. Skipping. Residue LYS 270 is missing expected H atoms. Skipping. Residue VAL 2 is missing expected H atoms. Skipping. Residue MET 4 is missing expected H atoms. Skipping. Residue SER 7 is missing expected H atoms. Skipping. Residue LYS 14 is missing expected H atoms. Skipping. Residue MET 24 is missing expected H atoms. Skipping. Residue LEU 32 is missing expected H atoms. Skipping. Residue THR 43 is missing expected H atoms. Skipping. Residue ILE 49 is missing expected H atoms. Skipping. Residue MET 71 is missing expected H atoms. Skipping. Residue LEU 74 is missing expected H atoms. Skipping. Residue THR 99 is missing expected H atoms. Skipping. Residue SER 111 is missing expected H atoms. Skipping. Residue SER 120 is missing expected H atoms. Skipping. Residue LEU 132 is missing expected H atoms. Skipping. Residue ILE 133 is missing expected H atoms. Skipping. Residue THR 136 is missing expected H atoms. Skipping. Residue MET 139 is missing expected H atoms. Skipping. Residue VAL 141 is missing expected H atoms. Skipping. Residue LEU 144 is missing expected H atoms. Skipping. Residue MET 147 is missing expected H atoms. Skipping. Residue THR 150 is missing expected H atoms. Skipping. Residue LEU 160 is missing expected H atoms. Skipping. Residue MET 162 is missing expected H atoms. Skipping. Residue LYS 170 is missing expected H atoms. Skipping. Residue VAL 183 is missing expected H atoms. Skipping. Residue LYS 194 is missing expected H atoms. Skipping. Residue LEU 195 is missing expected H atoms. Skipping. Residue THR 199 is missing expected H atoms. Skipping. Residue LEU 201 is missing expected H atoms. Skipping. Residue LYS 203 is missing expected H atoms. Skipping. Residue ILE 219 is missing expected H atoms. Skipping. Residue TYR 220 is missing expected H atoms. Skipping. Residue LEU 230 is missing expected H atoms. Skipping. Residue MET 232 is missing expected H atoms. Skipping. Residue LEU 233 is missing expected H atoms. Skipping. Residue THR 235 is missing expected H atoms. Skipping. Residue SER 239 is missing expected H atoms. Skipping. Residue TYR 240 is missing expected H atoms. Skipping. Residue LEU 241 is missing expected H atoms. Skipping. Residue ILE 245 is missing expected H atoms. Skipping. Residue THR 248 is missing expected H atoms. Skipping. Residue LYS 251 is missing expected H atoms. Skipping. Residue TYR 256 is missing expected H atoms. Skipping. Residue LYS 270 is missing expected H atoms. Skipping. Residue THR 278 is missing expected H atoms. Skipping. Residue MET 1 is missing expected H atoms. Skipping. Residue MET 4 is missing expected H atoms. Skipping. Residue SER 12 is missing expected H atoms. Skipping. Residue LYS 14 is missing expected H atoms. Skipping. Residue VAL 16 is missing expected H atoms. Skipping. Residue MET 24 is missing expected H atoms. Skipping. Residue TYR 27 is missing expected H atoms. Skipping. Residue VAL 34 is missing expected H atoms. Skipping. Residue LEU 44 is missing expected H atoms. Skipping. Residue MET 60 is missing expected H atoms. Skipping. Residue LEU 112 is missing expected H atoms. Skipping. Residue LYS 118 is missing expected H atoms. Skipping. Residue LEU 126 is missing expected H atoms. Skipping. Residue MET 139 is missing expected H atoms. Skipping. Residue VAL 141 is missing expected H atoms. Skipping. Residue LEU 144 is missing expected H atoms. Skipping. Residue MET 147 is missing expected H atoms. Skipping. Residue LEU 148 is missing expected H atoms. Skipping. Residue LYS 155 is missing expected H atoms. Skipping. Residue LEU 160 is missing expected H atoms. Skipping. Residue MET 162 is missing expected H atoms. Skipping. Residue SER 166 is missing expected H atoms. Skipping. Residue LYS 170 is missing expected H atoms. Skipping. Residue TYR 179 is missing expected H atoms. Skipping. Residue VAL 180 is missing expected H atoms. Skipping. Residue MET 198 is missing expected H atoms. Skipping. Residue LYS 203 is missing expected H atoms. Skipping. Residue THR 222 is missing expected H atoms. Skipping. Residue TYR 225 is missing expected H atoms. Skipping. Residue MET 232 is missing expected H atoms. Skipping. Residue TYR 240 is missing expected H atoms. Skipping. Residue LEU 241 is missing expected H atoms. Skipping. Residue THR 242 is missing expected H atoms. Skipping. Residue VAL 243 is missing expected H atoms. Skipping. Residue LYS 251 is missing expected H atoms. Skipping. Residue VAL 255 is missing expected H atoms. Skipping. Residue SER 267 is missing expected H atoms. Skipping. Residue LYS 270 is missing expected H atoms. Skipping. Residue LEU 279 is missing expected H atoms. Skipping. Residue LYS 281 is missing expected H atoms. Skipping. Residue LYS 2 is missing expected H atoms. Skipping. Residue MET 4 is missing expected H atoms. Skipping. Residue LEU 14 is missing expected H atoms. Skipping. Residue VAL 19 is missing expected H atoms. Skipping. Residue LEU 24 is missing expected H atoms. Skipping. Residue TYR 25 is missing expected H atoms. Skipping. Residue LEU 27 is missing expected H atoms. Skipping. Residue ILE 29 is missing expected H atoms. Skipping. Residue LYS 38 is missing expected H atoms. Skipping. Residue ILE 41 is missing expected H atoms. Skipping. Residue TYR 42 is missing expected H atoms. Skipping. Residue LYS 43 is missing expected H atoms. Skipping. Residue LYS 45 is missing expected H atoms. Skipping. Residue LEU 70 is missing expected H atoms. Skipping. Residue TYR 77 is missing expected H atoms. Skipping. Residue TYR 82 is missing expected H atoms. Skipping. Residue ILE 90 is missing expected H atoms. Skipping. Residue LYS 91 is missing expected H atoms. Skipping. Residue LEU 94 is missing expected H atoms. Skipping. Residue ILE 104 is missing expected H atoms. Skipping. Residue LYS 112 is missing expected H atoms. Skipping. Residue VAL 128 is missing expected H atoms. Skipping. Residue MET 130 is missing expected H atoms. Skipping. Residue ILE 143 is missing expected H atoms. Skipping. Residue LYS 152 is missing expected H atoms. Skipping. Residue LEU 158 is missing expected H atoms. Skipping. Residue LEU 160 is missing expected H atoms. Skipping. Residue MET 164 is missing expected H atoms. Skipping. Residue LEU 166 is missing expected H atoms. Skipping. Residue LYS 175 is missing expected H atoms. Skipping. Residue LYS 189 is missing expected H atoms. Skipping. Residue ILE 194 is missing expected H atoms. Skipping. Residue LYS 195 is missing expected H atoms. Skipping. Residue ILE 214 is missing expected H atoms. Skipping. Residue VAL 215 is missing expected H atoms. Skipping. Residue TYR 221 is missing expected H atoms. Skipping. Residue ILE 229 is missing expected H atoms. Skipping. Residue LEU 230 is missing expected H atoms. Skipping. Residue LYS 255 is missing expected H atoms. Skipping. Residue LYS 257 is missing expected H atoms. Skipping. Residue LEU 258 is missing expected H atoms. Skipping. Residue TYR 259 is missing expected H atoms. Skipping. Residue LEU 265 is missing expected H atoms. Skipping. Residue LEU 285 is missing expected H atoms. Skipping. Residue SER 290 is missing expected H atoms. Skipping. Residue ILE 291 is missing expected H atoms. Skipping. Residue THR 296 is missing expected H atoms. Skipping. Residue THR 310 is missing expected H atoms. Skipping. Residue LEU 324 is missing expected H atoms. Skipping. Residue LEU 336 is missing expected H atoms. Skipping. Residue LEU 339 is missing expected H atoms. Skipping. Residue MET 350 is missing expected H atoms. Skipping. Residue LEU 363 is missing expected H atoms. Skipping. Residue VAL 367 is missing expected H atoms. Skipping. Residue ILE 376 is missing expected H atoms. Skipping. Residue LEU 384 is missing expected H atoms. Skipping. Residue MET 387 is missing expected H atoms. Skipping. Residue VAL 403 is missing expected H atoms. Skipping. Residue THR 410 is missing expected H atoms. Skipping. Residue VAL 413 is missing expected H atoms. Skipping. Residue SER 420 is missing expected H atoms. Skipping. Residue ILE 423 is missing expected H atoms. Skipping. Residue LEU 426 is missing expected H atoms. Skipping. Residue ILE 427 is missing expected H atoms. Skipping. Residue LYS 433 is missing expected H atoms. Skipping. Residue VAL 439 is missing expected H atoms. Skipping. Residue ILE 447 is missing expected H atoms. Skipping. Residue LYS 455 is missing expected H atoms. Skipping. Residue THR 481 is missing expected H atoms. Skipping. Residue TYR 484 is missing expected H atoms. Skipping. Residue VAL 486 is missing expected H atoms. Skipping. Residue LEU 487 is missing expected H atoms. Skipping. Residue MET 501 is missing expected H atoms. Skipping. Residue LEU 5 is missing expected H atoms. Skipping. Residue LEU 24 is missing expected H atoms. Skipping. Residue TYR 25 is missing expected H atoms. Skipping. Residue LEU 27 is missing expected H atoms. Skipping. Residue LYS 37 is missing expected H atoms. Skipping. Residue LYS 38 is missing expected H atoms. Skipping. Residue ILE 41 is missing expected H atoms. Skipping. Residue TYR 42 is missing expected H atoms. Skipping. Residue LYS 43 is missing expected H atoms. Skipping. Residue VAL 58 is missing expected H atoms. Skipping. Residue LYS 175 is missing expected H atoms. Skipping. Residue LYS 189 is missing expected H atoms. Skipping. Residue ILE 214 is missing expected H atoms. Skipping. Residue VAL 215 is missing expected H atoms. Skipping. Residue TYR 221 is missing expected H atoms. Skipping. Residue LEU 230 is missing expected H atoms. Skipping. Residue LYS 235 is missing expected H atoms. Skipping. Residue LEU 258 is missing expected H atoms. Skipping. Residue ILE 263 is missing expected H atoms. Skipping. Residue TYR 269 is missing expected H atoms. Skipping. Residue ILE 291 is missing expected H atoms. Skipping. Residue ILE 293 is missing expected H atoms. Skipping. Residue SER 295 is missing expected H atoms. Skipping. Residue THR 296 is missing expected H atoms. Skipping. Residue LEU 299 is missing expected H atoms. Skipping. Residue ILE 302 is missing expected H atoms. Skipping. Residue THR 310 is missing expected H atoms. Skipping. Residue ILE 330 is missing expected H atoms. Skipping. Residue LEU 334 is missing expected H atoms. Skipping. Residue LEU 339 is missing expected H atoms. Skipping. Residue ILE 343 is missing expected H atoms. Skipping. Residue ILE 345 is missing expected H atoms. Skipping. Residue ILE 348 is missing expected H atoms. Skipping. Residue MET 350 is missing expected H atoms. Skipping. Residue VAL 353 is missing expected H atoms. Skipping. Residue SER 380 is missing expected H atoms. Skipping. Residue MET 387 is missing expected H atoms. Skipping. Residue THR 412 is missing expected H atoms. Skipping. Residue VAL 413 is missing expected H atoms. Skipping. Residue SER 418 is missing expected H atoms. Skipping. Residue LEU 421 is missing expected H atoms. Skipping. Residue LYS 433 is missing expected H atoms. Skipping. Residue VAL 439 is missing expected H atoms. Skipping. Residue ILE 442 is missing expected H atoms. Skipping. Residue VAL 445 is missing expected H atoms. Skipping. Residue TYR 450 is missing expected H atoms. Skipping. Residue LEU 451 is missing expected H atoms. Skipping. Residue LYS 455 is missing expected H atoms. Skipping. Residue ILE 462 is missing expected H atoms. Skipping. Residue ILE 473 is missing expected H atoms. Skipping. Residue VAL 474 is missing expected H atoms. Skipping. Residue MET 479 is missing expected H atoms. Skipping. Residue MET 501 is missing expected H atoms. Skipping. Residue LEU 502 is missing expected H atoms. Skipping. Evaluate side-chains 512 residues out of total 1691 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 512 time to evaluate : 1.928 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash 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: 0 outliers final: 0 residues processed: 512 average time/residue: 0.6195 time to fit residues: 451.6409 Evaluate side-chains 379 residues out of total 1691 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 379 time to evaluate : 2.097 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 2.4455 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 206 random chunks: chunk 173 optimal weight: 5.9990 chunk 156 optimal weight: 20.0000 chunk 86 optimal weight: 5.9990 chunk 53 optimal weight: 0.9990 chunk 105 optimal weight: 1.9990 chunk 83 optimal weight: 1.9990 chunk 161 optimal weight: 1.9990 chunk 62 optimal weight: 0.6980 chunk 98 optimal weight: 3.9990 chunk 120 optimal weight: 2.9990 chunk 187 optimal weight: 4.9990 overall best weight: 1.5388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 81 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 260 GLN ** N 321 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7097 moved from start: 0.3096 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 16776 Z= 0.204 Angle : 0.671 6.297 23691 Z= 0.360 Chirality : 0.042 0.301 3041 Planarity : 0.005 0.046 2530 Dihedral : 20.902 179.805 3905 Min Nonbonded Distance : 1.929 Molprobity Statistics. All-atom Clashscore : 11.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.86 % Favored : 95.14 % Rotamer: Outliers : 2.80 % Allowed : 20.39 % Favored : 76.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.67 (0.19), residues: 1893 helix: -0.46 (0.17), residues: 796 sheet: -1.84 (0.27), residues: 340 loop : -1.26 (0.22), residues: 757 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3786 Ramachandran restraints generated. 1893 Oldfield, 0 Emsley, 1893 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3786 Ramachandran restraints generated. 1893 Oldfield, 0 Emsley, 1893 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue MET 1 is missing expected H atoms. Skipping. Residue MET 4 is missing expected H atoms. Skipping. Residue LYS 14 is missing expected H atoms. Skipping. Residue MET 24 is missing expected H atoms. Skipping. Residue TYR 27 is missing expected H atoms. Skipping. Residue VAL 29 is missing expected H atoms. Skipping. Residue VAL 34 is missing expected H atoms. Skipping. Residue MET 60 is missing expected H atoms. Skipping. Residue ILE 66 is missing expected H atoms. Skipping. Residue MET 71 is missing expected H atoms. Skipping. Residue LEU 82 is missing expected H atoms. Skipping. Residue LEU 83 is missing expected H atoms. Skipping. Residue TYR 96 is missing expected H atoms. Skipping. Residue ILE 116 is missing expected H atoms. Skipping. Residue LYS 118 is missing expected H atoms. Skipping. Residue MET 139 is missing expected H atoms. Skipping. Residue MET 147 is missing expected H atoms. Skipping. Residue LYS 155 is missing expected H atoms. Skipping. Residue MET 198 is missing expected H atoms. Skipping. Residue ILE 219 is missing expected H atoms. Skipping. Residue TYR 264 is missing expected H atoms. Skipping. Residue LEU 3 is missing expected H atoms. Skipping. Residue MET 4 is missing expected H atoms. Skipping. Residue VAL 6 is missing expected H atoms. Skipping. Residue SER 12 is missing expected H atoms. Skipping. Residue LYS 14 is missing expected H atoms. Skipping. Residue LEU 21 is missing expected H atoms. Skipping. Residue MET 24 is missing expected H atoms. Skipping. Residue TYR 27 is missing expected H atoms. Skipping. Residue VAL 34 is missing expected H atoms. Skipping. Residue LEU 36 is missing expected H atoms. Skipping. Residue LEU 37 is missing expected H atoms. Skipping. Residue THR 43 is missing expected H atoms. Skipping. Residue LEU 44 is missing expected H atoms. Skipping. Residue MET 60 is missing expected H atoms. Skipping. Residue MET 71 is missing expected H atoms. Skipping. Residue LEU 82 is missing expected H atoms. Skipping. Residue LEU 83 is missing expected H atoms. Skipping. Residue THR 99 is missing expected H atoms. Skipping. Residue LEU 102 is missing expected H atoms. Skipping. Residue LEU 105 is missing expected H atoms. Skipping. Residue LYS 108 is missing expected H atoms. Skipping. Residue LEU 110 is missing expected H atoms. Skipping. Residue LEU 112 is missing expected H atoms. Skipping. Residue LYS 118 is missing expected H atoms. Skipping. Residue SER 120 is missing expected H atoms. Skipping. Residue MET 139 is missing expected H atoms. Skipping. Residue VAL 141 is missing expected H atoms. Skipping. Residue MET 147 is missing expected H atoms. Skipping. Residue LEU 152 is missing expected H atoms. Skipping. Residue MET 162 is missing expected H atoms. Skipping. Residue SER 166 is missing expected H atoms. Skipping. Residue LYS 194 is missing expected H atoms. Skipping. Residue MET 198 is missing expected H atoms. Skipping. Residue LYS 203 is missing expected H atoms. Skipping. Residue THR 213 is missing expected H atoms. Skipping. Residue MET 232 is missing expected H atoms. Skipping. Residue THR 248 is missing expected H atoms. Skipping. Residue SER 267 is missing expected H atoms. Skipping. Residue LYS 270 is missing expected H atoms. Skipping. Residue VAL 2 is missing expected H atoms. Skipping. Residue MET 4 is missing expected H atoms. Skipping. Residue SER 7 is missing expected H atoms. Skipping. Residue LYS 14 is missing expected H atoms. Skipping. Residue MET 24 is missing expected H atoms. Skipping. Residue LEU 32 is missing expected H atoms. Skipping. Residue THR 43 is missing expected H atoms. Skipping. Residue ILE 49 is missing expected H atoms. Skipping. Residue MET 71 is missing expected H atoms. Skipping. Residue LEU 74 is missing expected H atoms. Skipping. Residue THR 99 is missing expected H atoms. Skipping. Residue SER 111 is missing expected H atoms. Skipping. Residue SER 120 is missing expected H atoms. Skipping. Residue LEU 132 is missing expected H atoms. Skipping. Residue ILE 133 is missing expected H atoms. Skipping. Residue THR 136 is missing expected H atoms. Skipping. Residue MET 139 is missing expected H atoms. Skipping. Residue VAL 141 is missing expected H atoms. Skipping. Residue LEU 144 is missing expected H atoms. Skipping. Residue MET 147 is missing expected H atoms. Skipping. Residue THR 150 is missing expected H atoms. Skipping. Residue LEU 160 is missing expected H atoms. Skipping. Residue MET 162 is missing expected H atoms. Skipping. Residue LYS 170 is missing expected H atoms. Skipping. Residue VAL 183 is missing expected H atoms. Skipping. Residue LYS 194 is missing expected H atoms. Skipping. Residue LEU 195 is missing expected H atoms. Skipping. Residue THR 199 is missing expected H atoms. Skipping. Residue LEU 201 is missing expected H atoms. Skipping. Residue LYS 203 is missing expected H atoms. Skipping. Residue ILE 219 is missing expected H atoms. Skipping. Residue TYR 220 is missing expected H atoms. Skipping. Residue LEU 230 is missing expected H atoms. Skipping. Residue MET 232 is missing expected H atoms. Skipping. Residue LEU 233 is missing expected H atoms. Skipping. Residue THR 235 is missing expected H atoms. Skipping. Residue SER 239 is missing expected H atoms. Skipping. Residue TYR 240 is missing expected H atoms. Skipping. Residue LEU 241 is missing expected H atoms. Skipping. Residue ILE 245 is missing expected H atoms. Skipping. Residue THR 248 is missing expected H atoms. Skipping. Residue LYS 251 is missing expected H atoms. Skipping. Residue TYR 256 is missing expected H atoms. Skipping. Residue LYS 270 is missing expected H atoms. Skipping. Residue THR 278 is missing expected H atoms. Skipping. Residue MET 1 is missing expected H atoms. Skipping. Residue MET 4 is missing expected H atoms. Skipping. Residue SER 12 is missing expected H atoms. Skipping. Residue LYS 14 is missing expected H atoms. Skipping. Residue VAL 16 is missing expected H atoms. Skipping. Residue MET 24 is missing expected H atoms. Skipping. Residue TYR 27 is missing expected H atoms. Skipping. Residue VAL 34 is missing expected H atoms. Skipping. Residue LEU 44 is missing expected H atoms. Skipping. Residue MET 60 is missing expected H atoms. Skipping. Residue LEU 112 is missing expected H atoms. Skipping. Residue LYS 118 is missing expected H atoms. Skipping. Residue LEU 126 is missing expected H atoms. Skipping. Residue MET 139 is missing expected H atoms. Skipping. Residue VAL 141 is missing expected H atoms. Skipping. Residue LEU 144 is missing expected H atoms. Skipping. Residue MET 147 is missing expected H atoms. Skipping. Residue LEU 148 is missing expected H atoms. Skipping. Residue LYS 155 is missing expected H atoms. Skipping. Residue LEU 160 is missing expected H atoms. Skipping. Residue MET 162 is missing expected H atoms. Skipping. Residue SER 166 is missing expected H atoms. Skipping. Residue LYS 170 is missing expected H atoms. Skipping. Residue TYR 179 is missing expected H atoms. Skipping. Residue VAL 180 is missing expected H atoms. Skipping. Residue MET 198 is missing expected H atoms. Skipping. Residue LYS 203 is missing expected H atoms. Skipping. Residue THR 222 is missing expected H atoms. Skipping. Residue TYR 225 is missing expected H atoms. Skipping. Residue MET 232 is missing expected H atoms. Skipping. Residue TYR 240 is missing expected H atoms. Skipping. Residue LEU 241 is missing expected H atoms. Skipping. Residue THR 242 is missing expected H atoms. Skipping. Residue VAL 243 is missing expected H atoms. Skipping. Residue LYS 251 is missing expected H atoms. Skipping. Residue VAL 255 is missing expected H atoms. Skipping. Residue SER 267 is missing expected H atoms. Skipping. Residue LYS 270 is missing expected H atoms. Skipping. Residue LEU 279 is missing expected H atoms. Skipping. Residue LYS 281 is missing expected H atoms. Skipping. Residue LYS 2 is missing expected H atoms. Skipping. Residue MET 4 is missing expected H atoms. Skipping. Residue LEU 14 is missing expected H atoms. Skipping. Residue VAL 19 is missing expected H atoms. Skipping. Residue LEU 24 is missing expected H atoms. Skipping. Residue TYR 25 is missing expected H atoms. Skipping. Residue LEU 27 is missing expected H atoms. Skipping. Residue ILE 29 is missing expected H atoms. Skipping. Residue LYS 38 is missing expected H atoms. Skipping. Residue ILE 41 is missing expected H atoms. Skipping. Residue TYR 42 is missing expected H atoms. Skipping. Residue LYS 43 is missing expected H atoms. Skipping. Residue LYS 45 is missing expected H atoms. Skipping. Residue LEU 70 is missing expected H atoms. Skipping. Residue TYR 77 is missing expected H atoms. Skipping. Residue TYR 82 is missing expected H atoms. Skipping. Residue ILE 90 is missing expected H atoms. Skipping. Residue LYS 91 is missing expected H atoms. Skipping. Residue LEU 94 is missing expected H atoms. Skipping. Residue ILE 104 is missing expected H atoms. Skipping. Residue LYS 112 is missing expected H atoms. Skipping. Residue VAL 128 is missing expected H atoms. Skipping. Residue MET 130 is missing expected H atoms. Skipping. Residue ILE 143 is missing expected H atoms. Skipping. Residue LYS 152 is missing expected H atoms. Skipping. Residue LEU 158 is missing expected H atoms. Skipping. Residue LEU 160 is missing expected H atoms. Skipping. Residue MET 164 is missing expected H atoms. Skipping. Residue LEU 166 is missing expected H atoms. Skipping. Residue LYS 175 is missing expected H atoms. Skipping. Residue LYS 189 is missing expected H atoms. Skipping. Residue ILE 194 is missing expected H atoms. Skipping. Residue LYS 195 is missing expected H atoms. Skipping. Residue ILE 214 is missing expected H atoms. Skipping. Residue VAL 215 is missing expected H atoms. Skipping. Residue TYR 221 is missing expected H atoms. Skipping. Residue ILE 229 is missing expected H atoms. Skipping. Residue LEU 230 is missing expected H atoms. Skipping. Residue LYS 255 is missing expected H atoms. Skipping. Residue LYS 257 is missing expected H atoms. Skipping. Residue LEU 258 is missing expected H atoms. Skipping. Residue TYR 259 is missing expected H atoms. Skipping. Residue LEU 265 is missing expected H atoms. Skipping. Residue LEU 285 is missing expected H atoms. Skipping. Residue SER 290 is missing expected H atoms. Skipping. Residue ILE 291 is missing expected H atoms. Skipping. Residue THR 296 is missing expected H atoms. Skipping. Residue THR 310 is missing expected H atoms. Skipping. Residue LEU 324 is missing expected H atoms. Skipping. Residue LEU 336 is missing expected H atoms. Skipping. Residue LEU 339 is missing expected H atoms. Skipping. Residue MET 350 is missing expected H atoms. Skipping. Residue LEU 363 is missing expected H atoms. Skipping. Residue VAL 367 is missing expected H atoms. Skipping. Residue ILE 376 is missing expected H atoms. Skipping. Residue LEU 384 is missing expected H atoms. Skipping. Residue MET 387 is missing expected H atoms. Skipping. Residue VAL 403 is missing expected H atoms. Skipping. Residue THR 410 is missing expected H atoms. Skipping. Residue VAL 413 is missing expected H atoms. Skipping. Residue SER 420 is missing expected H atoms. Skipping. Residue ILE 423 is missing expected H atoms. Skipping. Residue LEU 426 is missing expected H atoms. Skipping. Residue ILE 427 is missing expected H atoms. Skipping. Residue LYS 433 is missing expected H atoms. Skipping. Residue VAL 439 is missing expected H atoms. Skipping. Residue ILE 447 is missing expected H atoms. Skipping. Residue LYS 455 is missing expected H atoms. Skipping. Residue THR 481 is missing expected H atoms. Skipping. Residue TYR 484 is missing expected H atoms. Skipping. Residue VAL 486 is missing expected H atoms. Skipping. Residue LEU 487 is missing expected H atoms. Skipping. Residue MET 501 is missing expected H atoms. Skipping. Residue LEU 5 is missing expected H atoms. Skipping. Residue LEU 24 is missing expected H atoms. Skipping. Residue TYR 25 is missing expected H atoms. Skipping. Residue LEU 27 is missing expected H atoms. Skipping. Residue LYS 37 is missing expected H atoms. Skipping. Residue LYS 38 is missing expected H atoms. Skipping. Residue ILE 41 is missing expected H atoms. Skipping. Residue TYR 42 is missing expected H atoms. Skipping. Residue LYS 43 is missing expected H atoms. Skipping. Residue VAL 58 is missing expected H atoms. Skipping. Residue LYS 175 is missing expected H atoms. Skipping. Residue LYS 189 is missing expected H atoms. Skipping. Residue ILE 214 is missing expected H atoms. Skipping. Residue VAL 215 is missing expected H atoms. Skipping. Residue TYR 221 is missing expected H atoms. Skipping. Residue LEU 230 is missing expected H atoms. Skipping. Residue LYS 235 is missing expected H atoms. Skipping. Residue LEU 258 is missing expected H atoms. Skipping. Residue ILE 263 is missing expected H atoms. Skipping. Residue TYR 269 is missing expected H atoms. Skipping. Residue ILE 291 is missing expected H atoms. Skipping. Residue ILE 293 is missing expected H atoms. Skipping. Residue SER 295 is missing expected H atoms. Skipping. Residue THR 296 is missing expected H atoms. Skipping. Residue LEU 299 is missing expected H atoms. Skipping. Residue ILE 302 is missing expected H atoms. Skipping. Residue THR 310 is missing expected H atoms. Skipping. Residue ILE 330 is missing expected H atoms. Skipping. Residue LEU 334 is missing expected H atoms. Skipping. Residue LEU 339 is missing expected H atoms. Skipping. Residue ILE 343 is missing expected H atoms. Skipping. Residue ILE 345 is missing expected H atoms. Skipping. Residue ILE 348 is missing expected H atoms. Skipping. Residue MET 350 is missing expected H atoms. Skipping. Residue VAL 353 is missing expected H atoms. Skipping. Residue SER 380 is missing expected H atoms. Skipping. Residue MET 387 is missing expected H atoms. Skipping. Residue THR 412 is missing expected H atoms. Skipping. Residue VAL 413 is missing expected H atoms. Skipping. Residue SER 418 is missing expected H atoms. Skipping. Residue LEU 421 is missing expected H atoms. Skipping. Residue LYS 433 is missing expected H atoms. Skipping. Residue VAL 439 is missing expected H atoms. Skipping. Residue ILE 442 is missing expected H atoms. Skipping. Residue VAL 445 is missing expected H atoms. Skipping. Residue TYR 450 is missing expected H atoms. Skipping. Residue LEU 451 is missing expected H atoms. Skipping. Residue LYS 455 is missing expected H atoms. Skipping. Residue ILE 462 is missing expected H atoms. Skipping. Residue ILE 473 is missing expected H atoms. Skipping. Residue VAL 474 is missing expected H atoms. Skipping. Residue MET 479 is missing expected H atoms. Skipping. Residue MET 501 is missing expected H atoms. Skipping. Residue LEU 502 is missing expected H atoms. Skipping. Evaluate side-chains 440 residues out of total 1691 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 411 time to evaluate : 2.271 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 29 outliers final: 27 residues processed: 421 average time/residue: 0.5938 time to fit residues: 361.0001 Evaluate side-chains 391 residues out of total 1691 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 364 time to evaluate : 2.092 Switching outliers to nearest non-outliers revert: symmetry clash outliers start: 27 outliers final: 1 residues processed: 27 average time/residue: 0.3265 time to fit residues: 18.2555 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 206 random chunks: chunk 103 optimal weight: 0.7980 chunk 58 optimal weight: 4.9990 chunk 155 optimal weight: 8.9990 chunk 127 optimal weight: 4.9990 chunk 51 optimal weight: 2.9990 chunk 187 optimal weight: 5.9990 chunk 202 optimal weight: 20.0000 chunk 166 optimal weight: 6.9990 chunk 185 optimal weight: 2.9990 chunk 63 optimal weight: 4.9990 chunk 150 optimal weight: 10.0000 overall best weight: 3.3588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 69 GLN ** C 81 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 268 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7265 moved from start: 0.4195 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.064 16776 Z= 0.293 Angle : 0.653 6.457 23691 Z= 0.353 Chirality : 0.041 0.309 3041 Planarity : 0.005 0.092 2530 Dihedral : 20.950 178.293 3905 Min Nonbonded Distance : 1.931 Molprobity Statistics. All-atom Clashscore : 16.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.34 % Favored : 92.66 % Rotamer: Outliers : 2.71 % Allowed : 22.32 % Favored : 74.98 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.52 (0.19), residues: 1893 helix: -0.27 (0.18), residues: 809 sheet: -1.73 (0.27), residues: 351 loop : -1.28 (0.22), residues: 733 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3786 Ramachandran restraints generated. 1893 Oldfield, 0 Emsley, 1893 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3786 Ramachandran restraints generated. 1893 Oldfield, 0 Emsley, 1893 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue MET 1 is missing expected H atoms. Skipping. Residue MET 4 is missing expected H atoms. Skipping. Residue LYS 14 is missing expected H atoms. Skipping. Residue MET 24 is missing expected H atoms. Skipping. Residue TYR 27 is missing expected H atoms. Skipping. Residue VAL 29 is missing expected H atoms. Skipping. Residue VAL 34 is missing expected H atoms. Skipping. Residue MET 60 is missing expected H atoms. Skipping. Residue ILE 66 is missing expected H atoms. Skipping. Residue MET 71 is missing expected H atoms. Skipping. Residue LEU 82 is missing expected H atoms. Skipping. Residue LEU 83 is missing expected H atoms. Skipping. Residue TYR 96 is missing expected H atoms. Skipping. Residue ILE 116 is missing expected H atoms. Skipping. Residue LYS 118 is missing expected H atoms. Skipping. Residue MET 139 is missing expected H atoms. Skipping. Residue MET 147 is missing expected H atoms. Skipping. Residue LYS 155 is missing expected H atoms. Skipping. Residue MET 198 is missing expected H atoms. Skipping. Residue ILE 219 is missing expected H atoms. Skipping. Residue TYR 264 is missing expected H atoms. Skipping. Residue LEU 3 is missing expected H atoms. Skipping. Residue MET 4 is missing expected H atoms. Skipping. Residue VAL 6 is missing expected H atoms. Skipping. Residue SER 12 is missing expected H atoms. Skipping. Residue LYS 14 is missing expected H atoms. Skipping. Residue LEU 21 is missing expected H atoms. Skipping. Residue MET 24 is missing expected H atoms. Skipping. Residue TYR 27 is missing expected H atoms. Skipping. Residue VAL 34 is missing expected H atoms. Skipping. Residue LEU 36 is missing expected H atoms. Skipping. Residue LEU 37 is missing expected H atoms. Skipping. Residue THR 43 is missing expected H atoms. Skipping. Residue LEU 44 is missing expected H atoms. Skipping. Residue MET 60 is missing expected H atoms. Skipping. Residue MET 71 is missing expected H atoms. Skipping. Residue LEU 82 is missing expected H atoms. Skipping. Residue LEU 83 is missing expected H atoms. Skipping. Residue THR 99 is missing expected H atoms. Skipping. Residue LEU 102 is missing expected H atoms. Skipping. Residue LEU 105 is missing expected H atoms. Skipping. Residue LYS 108 is missing expected H atoms. Skipping. Residue LEU 110 is missing expected H atoms. Skipping. Residue LEU 112 is missing expected H atoms. Skipping. Residue LYS 118 is missing expected H atoms. Skipping. Residue SER 120 is missing expected H atoms. Skipping. Residue MET 139 is missing expected H atoms. Skipping. Residue VAL 141 is missing expected H atoms. Skipping. Residue MET 147 is missing expected H atoms. Skipping. Residue LEU 152 is missing expected H atoms. Skipping. Residue MET 162 is missing expected H atoms. Skipping. Residue SER 166 is missing expected H atoms. Skipping. Residue LYS 194 is missing expected H atoms. Skipping. Residue MET 198 is missing expected H atoms. Skipping. Residue LYS 203 is missing expected H atoms. Skipping. Residue THR 213 is missing expected H atoms. Skipping. Residue MET 232 is missing expected H atoms. Skipping. Residue THR 248 is missing expected H atoms. Skipping. Residue SER 267 is missing expected H atoms. Skipping. Residue LYS 270 is missing expected H atoms. Skipping. Residue VAL 2 is missing expected H atoms. Skipping. Residue MET 4 is missing expected H atoms. Skipping. Residue SER 7 is missing expected H atoms. Skipping. Residue LYS 14 is missing expected H atoms. Skipping. Residue MET 24 is missing expected H atoms. Skipping. Residue LEU 32 is missing expected H atoms. Skipping. Residue THR 43 is missing expected H atoms. Skipping. Residue ILE 49 is missing expected H atoms. Skipping. Residue MET 71 is missing expected H atoms. Skipping. Residue LEU 74 is missing expected H atoms. Skipping. Residue THR 99 is missing expected H atoms. Skipping. Residue SER 111 is missing expected H atoms. Skipping. Residue SER 120 is missing expected H atoms. Skipping. Residue LEU 132 is missing expected H atoms. Skipping. Residue ILE 133 is missing expected H atoms. Skipping. Residue THR 136 is missing expected H atoms. Skipping. Residue MET 139 is missing expected H atoms. Skipping. Residue VAL 141 is missing expected H atoms. Skipping. Residue LEU 144 is missing expected H atoms. Skipping. Residue MET 147 is missing expected H atoms. Skipping. Residue THR 150 is missing expected H atoms. Skipping. Residue LEU 160 is missing expected H atoms. Skipping. Residue MET 162 is missing expected H atoms. Skipping. Residue LYS 170 is missing expected H atoms. Skipping. Residue VAL 183 is missing expected H atoms. Skipping. Residue LYS 194 is missing expected H atoms. Skipping. Residue LEU 195 is missing expected H atoms. Skipping. Residue THR 199 is missing expected H atoms. Skipping. Residue LEU 201 is missing expected H atoms. Skipping. Residue LYS 203 is missing expected H atoms. Skipping. Residue ILE 219 is missing expected H atoms. Skipping. Residue TYR 220 is missing expected H atoms. Skipping. Residue LEU 230 is missing expected H atoms. Skipping. Residue MET 232 is missing expected H atoms. Skipping. Residue LEU 233 is missing expected H atoms. Skipping. Residue THR 235 is missing expected H atoms. Skipping. Residue SER 239 is missing expected H atoms. Skipping. Residue TYR 240 is missing expected H atoms. Skipping. Residue LEU 241 is missing expected H atoms. Skipping. Residue ILE 245 is missing expected H atoms. Skipping. Residue THR 248 is missing expected H atoms. Skipping. Residue LYS 251 is missing expected H atoms. Skipping. Residue TYR 256 is missing expected H atoms. Skipping. Residue LYS 270 is missing expected H atoms. Skipping. Residue THR 278 is missing expected H atoms. Skipping. Residue MET 1 is missing expected H atoms. Skipping. Residue MET 4 is missing expected H atoms. Skipping. Residue SER 12 is missing expected H atoms. Skipping. Residue LYS 14 is missing expected H atoms. Skipping. Residue VAL 16 is missing expected H atoms. Skipping. Residue MET 24 is missing expected H atoms. Skipping. Residue TYR 27 is missing expected H atoms. Skipping. Residue VAL 34 is missing expected H atoms. Skipping. Residue LEU 44 is missing expected H atoms. Skipping. Residue MET 60 is missing expected H atoms. Skipping. Residue LEU 112 is missing expected H atoms. Skipping. Residue LYS 118 is missing expected H atoms. Skipping. Residue LEU 126 is missing expected H atoms. Skipping. Residue MET 139 is missing expected H atoms. Skipping. Residue VAL 141 is missing expected H atoms. Skipping. Residue LEU 144 is missing expected H atoms. Skipping. Residue MET 147 is missing expected H atoms. Skipping. Residue LEU 148 is missing expected H atoms. Skipping. Residue LYS 155 is missing expected H atoms. Skipping. Residue LEU 160 is missing expected H atoms. Skipping. Residue MET 162 is missing expected H atoms. Skipping. Residue SER 166 is missing expected H atoms. Skipping. Residue LYS 170 is missing expected H atoms. Skipping. Residue TYR 179 is missing expected H atoms. Skipping. Residue VAL 180 is missing expected H atoms. Skipping. Residue MET 198 is missing expected H atoms. Skipping. Residue LYS 203 is missing expected H atoms. Skipping. Residue THR 222 is missing expected H atoms. Skipping. Residue TYR 225 is missing expected H atoms. Skipping. Residue MET 232 is missing expected H atoms. Skipping. Residue TYR 240 is missing expected H atoms. Skipping. Residue LEU 241 is missing expected H atoms. Skipping. Residue THR 242 is missing expected H atoms. Skipping. Residue VAL 243 is missing expected H atoms. Skipping. Residue LYS 251 is missing expected H atoms. Skipping. Residue VAL 255 is missing expected H atoms. Skipping. Residue SER 267 is missing expected H atoms. Skipping. Residue LYS 270 is missing expected H atoms. Skipping. Residue LEU 279 is missing expected H atoms. Skipping. Residue LYS 281 is missing expected H atoms. Skipping. Residue LYS 2 is missing expected H atoms. Skipping. Residue MET 4 is missing expected H atoms. Skipping. Residue LEU 14 is missing expected H atoms. Skipping. Residue VAL 19 is missing expected H atoms. Skipping. Residue LEU 24 is missing expected H atoms. Skipping. Residue TYR 25 is missing expected H atoms. Skipping. Residue LEU 27 is missing expected H atoms. Skipping. Residue ILE 29 is missing expected H atoms. Skipping. Residue LYS 38 is missing expected H atoms. Skipping. Residue ILE 41 is missing expected H atoms. Skipping. Residue TYR 42 is missing expected H atoms. Skipping. Residue LYS 43 is missing expected H atoms. Skipping. Residue LYS 45 is missing expected H atoms. Skipping. Residue LEU 70 is missing expected H atoms. Skipping. Residue TYR 77 is missing expected H atoms. Skipping. Residue TYR 82 is missing expected H atoms. Skipping. Residue ILE 90 is missing expected H atoms. Skipping. Residue LYS 91 is missing expected H atoms. Skipping. Residue LEU 94 is missing expected H atoms. Skipping. Residue ILE 104 is missing expected H atoms. Skipping. Residue LYS 112 is missing expected H atoms. Skipping. Residue VAL 128 is missing expected H atoms. Skipping. Residue MET 130 is missing expected H atoms. Skipping. Residue ILE 143 is missing expected H atoms. Skipping. Residue LYS 152 is missing expected H atoms. Skipping. Residue LEU 158 is missing expected H atoms. Skipping. Residue LEU 160 is missing expected H atoms. Skipping. Residue MET 164 is missing expected H atoms. Skipping. Residue LEU 166 is missing expected H atoms. Skipping. Residue LYS 175 is missing expected H atoms. Skipping. Residue LYS 189 is missing expected H atoms. Skipping. Residue ILE 194 is missing expected H atoms. Skipping. Residue LYS 195 is missing expected H atoms. Skipping. Residue ILE 214 is missing expected H atoms. Skipping. Residue VAL 215 is missing expected H atoms. Skipping. Residue TYR 221 is missing expected H atoms. Skipping. Residue ILE 229 is missing expected H atoms. Skipping. Residue LEU 230 is missing expected H atoms. Skipping. Residue LYS 255 is missing expected H atoms. Skipping. Residue LYS 257 is missing expected H atoms. Skipping. Residue LEU 258 is missing expected H atoms. Skipping. Residue TYR 259 is missing expected H atoms. Skipping. Residue LEU 265 is missing expected H atoms. Skipping. Residue LEU 285 is missing expected H atoms. Skipping. Residue SER 290 is missing expected H atoms. Skipping. Residue ILE 291 is missing expected H atoms. Skipping. Residue THR 296 is missing expected H atoms. Skipping. Residue THR 310 is missing expected H atoms. Skipping. Residue LEU 324 is missing expected H atoms. Skipping. Residue LEU 336 is missing expected H atoms. Skipping. Residue LEU 339 is missing expected H atoms. Skipping. Residue MET 350 is missing expected H atoms. Skipping. Residue LEU 363 is missing expected H atoms. Skipping. Residue VAL 367 is missing expected H atoms. Skipping. Residue ILE 376 is missing expected H atoms. Skipping. Residue LEU 384 is missing expected H atoms. Skipping. Residue MET 387 is missing expected H atoms. Skipping. Residue VAL 403 is missing expected H atoms. Skipping. Residue THR 410 is missing expected H atoms. Skipping. Residue VAL 413 is missing expected H atoms. Skipping. Residue SER 420 is missing expected H atoms. Skipping. Residue ILE 423 is missing expected H atoms. Skipping. Residue LEU 426 is missing expected H atoms. Skipping. Residue ILE 427 is missing expected H atoms. Skipping. Residue LYS 433 is missing expected H atoms. Skipping. Residue VAL 439 is missing expected H atoms. Skipping. Residue ILE 447 is missing expected H atoms. Skipping. Residue LYS 455 is missing expected H atoms. Skipping. Residue THR 481 is missing expected H atoms. Skipping. Residue TYR 484 is missing expected H atoms. Skipping. Residue VAL 486 is missing expected H atoms. Skipping. Residue LEU 487 is missing expected H atoms. Skipping. Residue MET 501 is missing expected H atoms. Skipping. Residue LEU 5 is missing expected H atoms. Skipping. Residue LEU 24 is missing expected H atoms. Skipping. Residue TYR 25 is missing expected H atoms. Skipping. Residue LEU 27 is missing expected H atoms. Skipping. Residue LYS 37 is missing expected H atoms. Skipping. Residue LYS 38 is missing expected H atoms. Skipping. Residue ILE 41 is missing expected H atoms. Skipping. Residue TYR 42 is missing expected H atoms. Skipping. Residue LYS 43 is missing expected H atoms. Skipping. Residue VAL 58 is missing expected H atoms. Skipping. Residue LYS 175 is missing expected H atoms. Skipping. Residue LYS 189 is missing expected H atoms. Skipping. Residue ILE 214 is missing expected H atoms. Skipping. Residue VAL 215 is missing expected H atoms. Skipping. Residue TYR 221 is missing expected H atoms. Skipping. Residue LEU 230 is missing expected H atoms. Skipping. Residue LYS 235 is missing expected H atoms. Skipping. Residue LEU 258 is missing expected H atoms. Skipping. Residue ILE 263 is missing expected H atoms. Skipping. Residue TYR 269 is missing expected H atoms. Skipping. Residue ILE 291 is missing expected H atoms. Skipping. Residue ILE 293 is missing expected H atoms. Skipping. Residue SER 295 is missing expected H atoms. Skipping. Residue THR 296 is missing expected H atoms. Skipping. Residue LEU 299 is missing expected H atoms. Skipping. Residue ILE 302 is missing expected H atoms. Skipping. Residue THR 310 is missing expected H atoms. Skipping. Residue ILE 330 is missing expected H atoms. Skipping. Residue LEU 334 is missing expected H atoms. Skipping. Residue LEU 339 is missing expected H atoms. Skipping. Residue ILE 343 is missing expected H atoms. Skipping. Residue ILE 345 is missing expected H atoms. Skipping. Residue ILE 348 is missing expected H atoms. Skipping. Residue MET 350 is missing expected H atoms. Skipping. Residue VAL 353 is missing expected H atoms. Skipping. Residue SER 380 is missing expected H atoms. Skipping. Residue MET 387 is missing expected H atoms. Skipping. Residue THR 412 is missing expected H atoms. Skipping. Residue VAL 413 is missing expected H atoms. Skipping. Residue SER 418 is missing expected H atoms. Skipping. Residue LEU 421 is missing expected H atoms. Skipping. Residue LYS 433 is missing expected H atoms. Skipping. Residue VAL 439 is missing expected H atoms. Skipping. Residue ILE 442 is missing expected H atoms. Skipping. Residue VAL 445 is missing expected H atoms. Skipping. Residue TYR 450 is missing expected H atoms. Skipping. Residue LEU 451 is missing expected H atoms. Skipping. Residue LYS 455 is missing expected H atoms. Skipping. Residue ILE 462 is missing expected H atoms. Skipping. Residue ILE 473 is missing expected H atoms. Skipping. Residue VAL 474 is missing expected H atoms. Skipping. Residue MET 479 is missing expected H atoms. Skipping. Residue MET 501 is missing expected H atoms. Skipping. Residue LEU 502 is missing expected H atoms. Skipping. Evaluate side-chains 403 residues out of total 1691 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 375 time to evaluate : 1.877 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 28 outliers final: 22 residues processed: 389 average time/residue: 0.5967 time to fit residues: 331.9798 Evaluate side-chains 376 residues out of total 1691 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 354 time to evaluate : 2.158 Switching outliers to nearest non-outliers outliers start: 22 outliers final: 0 residues processed: 22 average time/residue: 0.2962 time to fit residues: 14.8771 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 206 random chunks: chunk 185 optimal weight: 10.0000 chunk 140 optimal weight: 7.9990 chunk 97 optimal weight: 8.9990 chunk 20 optimal weight: 1.9990 chunk 89 optimal weight: 20.0000 chunk 125 optimal weight: 4.9990 chunk 188 optimal weight: 5.9990 chunk 199 optimal weight: 6.9990 chunk 98 optimal weight: 4.9990 chunk 178 optimal weight: 7.9990 chunk 53 optimal weight: 5.9990 overall best weight: 4.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 90 ASN ** A 237 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 69 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 81 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 11 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 270 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** N 270 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7385 moved from start: 0.5239 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.061 16776 Z= 0.365 Angle : 0.717 8.770 23691 Z= 0.384 Chirality : 0.042 0.249 3041 Planarity : 0.006 0.079 2530 Dihedral : 21.028 179.925 3905 Min Nonbonded Distance : 1.877 Molprobity Statistics. All-atom Clashscore : 23.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.82 % Favored : 91.18 % Rotamer: Outliers : 4.83 % Allowed : 22.90 % Favored : 72.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.95 (0.18), residues: 1893 helix: -0.68 (0.17), residues: 796 sheet: -1.87 (0.28), residues: 324 loop : -1.51 (0.22), residues: 773 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3786 Ramachandran restraints generated. 1893 Oldfield, 0 Emsley, 1893 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3786 Ramachandran restraints generated. 1893 Oldfield, 0 Emsley, 1893 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue MET 1 is missing expected H atoms. Skipping. Residue MET 4 is missing expected H atoms. Skipping. Residue LYS 14 is missing expected H atoms. Skipping. Residue MET 24 is missing expected H atoms. Skipping. Residue TYR 27 is missing expected H atoms. Skipping. Residue VAL 29 is missing expected H atoms. Skipping. Residue VAL 34 is missing expected H atoms. Skipping. Residue MET 60 is missing expected H atoms. Skipping. Residue ILE 66 is missing expected H atoms. Skipping. Residue MET 71 is missing expected H atoms. Skipping. Residue LEU 82 is missing expected H atoms. Skipping. Residue LEU 83 is missing expected H atoms. Skipping. Residue TYR 96 is missing expected H atoms. Skipping. Residue ILE 116 is missing expected H atoms. Skipping. Residue LYS 118 is missing expected H atoms. Skipping. Residue MET 139 is missing expected H atoms. Skipping. Residue MET 147 is missing expected H atoms. Skipping. Residue LYS 155 is missing expected H atoms. Skipping. Residue MET 198 is missing expected H atoms. Skipping. Residue ILE 219 is missing expected H atoms. Skipping. Residue TYR 264 is missing expected H atoms. Skipping. Residue LEU 3 is missing expected H atoms. Skipping. Residue MET 4 is missing expected H atoms. Skipping. Residue VAL 6 is missing expected H atoms. Skipping. Residue SER 12 is missing expected H atoms. Skipping. Residue LYS 14 is missing expected H atoms. Skipping. Residue LEU 21 is missing expected H atoms. Skipping. Residue MET 24 is missing expected H atoms. Skipping. Residue TYR 27 is missing expected H atoms. Skipping. Residue VAL 34 is missing expected H atoms. Skipping. Residue LEU 36 is missing expected H atoms. Skipping. Residue LEU 37 is missing expected H atoms. Skipping. Residue THR 43 is missing expected H atoms. Skipping. Residue LEU 44 is missing expected H atoms. Skipping. Residue MET 60 is missing expected H atoms. Skipping. Residue MET 71 is missing expected H atoms. Skipping. Residue LEU 82 is missing expected H atoms. Skipping. Residue LEU 83 is missing expected H atoms. Skipping. Residue THR 99 is missing expected H atoms. Skipping. Residue LEU 102 is missing expected H atoms. Skipping. Residue LEU 105 is missing expected H atoms. Skipping. Residue LYS 108 is missing expected H atoms. Skipping. Residue LEU 110 is missing expected H atoms. Skipping. Residue LEU 112 is missing expected H atoms. Skipping. Residue LYS 118 is missing expected H atoms. Skipping. Residue SER 120 is missing expected H atoms. Skipping. Residue MET 139 is missing expected H atoms. Skipping. Residue VAL 141 is missing expected H atoms. Skipping. Residue MET 147 is missing expected H atoms. Skipping. Residue LEU 152 is missing expected H atoms. Skipping. Residue MET 162 is missing expected H atoms. Skipping. Residue SER 166 is missing expected H atoms. Skipping. Residue LYS 194 is missing expected H atoms. Skipping. Residue MET 198 is missing expected H atoms. Skipping. Residue LYS 203 is missing expected H atoms. Skipping. Residue THR 213 is missing expected H atoms. Skipping. Residue MET 232 is missing expected H atoms. Skipping. Residue THR 248 is missing expected H atoms. Skipping. Residue SER 267 is missing expected H atoms. Skipping. Residue LYS 270 is missing expected H atoms. Skipping. Residue VAL 2 is missing expected H atoms. Skipping. Residue MET 4 is missing expected H atoms. Skipping. Residue SER 7 is missing expected H atoms. Skipping. Residue LYS 14 is missing expected H atoms. Skipping. Residue MET 24 is missing expected H atoms. Skipping. Residue LEU 32 is missing expected H atoms. Skipping. Residue THR 43 is missing expected H atoms. Skipping. Residue ILE 49 is missing expected H atoms. Skipping. Residue MET 71 is missing expected H atoms. Skipping. Residue LEU 74 is missing expected H atoms. Skipping. Residue THR 99 is missing expected H atoms. Skipping. Residue SER 111 is missing expected H atoms. Skipping. Residue SER 120 is missing expected H atoms. Skipping. Residue LEU 132 is missing expected H atoms. Skipping. Residue ILE 133 is missing expected H atoms. Skipping. Residue THR 136 is missing expected H atoms. Skipping. Residue MET 139 is missing expected H atoms. Skipping. Residue VAL 141 is missing expected H atoms. Skipping. Residue LEU 144 is missing expected H atoms. Skipping. Residue MET 147 is missing expected H atoms. Skipping. Residue THR 150 is missing expected H atoms. Skipping. Residue LEU 160 is missing expected H atoms. Skipping. Residue MET 162 is missing expected H atoms. Skipping. Residue LYS 170 is missing expected H atoms. Skipping. Residue VAL 183 is missing expected H atoms. Skipping. Residue LYS 194 is missing expected H atoms. Skipping. Residue LEU 195 is missing expected H atoms. Skipping. Residue THR 199 is missing expected H atoms. Skipping. Residue LEU 201 is missing expected H atoms. Skipping. Residue LYS 203 is missing expected H atoms. Skipping. Residue ILE 219 is missing expected H atoms. Skipping. Residue TYR 220 is missing expected H atoms. Skipping. Residue LEU 230 is missing expected H atoms. Skipping. Residue MET 232 is missing expected H atoms. Skipping. Residue LEU 233 is missing expected H atoms. Skipping. Residue THR 235 is missing expected H atoms. Skipping. Residue SER 239 is missing expected H atoms. Skipping. Residue TYR 240 is missing expected H atoms. Skipping. Residue LEU 241 is missing expected H atoms. Skipping. Residue ILE 245 is missing expected H atoms. Skipping. Residue THR 248 is missing expected H atoms. Skipping. Residue LYS 251 is missing expected H atoms. Skipping. Residue TYR 256 is missing expected H atoms. Skipping. Residue LYS 270 is missing expected H atoms. Skipping. Residue THR 278 is missing expected H atoms. Skipping. Residue MET 1 is missing expected H atoms. Skipping. Residue MET 4 is missing expected H atoms. Skipping. Residue SER 12 is missing expected H atoms. Skipping. Residue LYS 14 is missing expected H atoms. Skipping. Residue VAL 16 is missing expected H atoms. Skipping. Residue MET 24 is missing expected H atoms. Skipping. Residue TYR 27 is missing expected H atoms. Skipping. Residue VAL 34 is missing expected H atoms. Skipping. Residue LEU 44 is missing expected H atoms. Skipping. Residue MET 60 is missing expected H atoms. Skipping. Residue LEU 112 is missing expected H atoms. Skipping. Residue LYS 118 is missing expected H atoms. Skipping. Residue LEU 126 is missing expected H atoms. Skipping. Residue MET 139 is missing expected H atoms. Skipping. Residue VAL 141 is missing expected H atoms. Skipping. Residue LEU 144 is missing expected H atoms. Skipping. Residue MET 147 is missing expected H atoms. Skipping. Residue LEU 148 is missing expected H atoms. Skipping. Residue LYS 155 is missing expected H atoms. Skipping. Residue LEU 160 is missing expected H atoms. Skipping. Residue MET 162 is missing expected H atoms. Skipping. Residue SER 166 is missing expected H atoms. Skipping. Residue LYS 170 is missing expected H atoms. Skipping. Residue TYR 179 is missing expected H atoms. Skipping. Residue VAL 180 is missing expected H atoms. Skipping. Residue MET 198 is missing expected H atoms. Skipping. Residue LYS 203 is missing expected H atoms. Skipping. Residue THR 222 is missing expected H atoms. Skipping. Residue TYR 225 is missing expected H atoms. Skipping. Residue MET 232 is missing expected H atoms. Skipping. Residue TYR 240 is missing expected H atoms. Skipping. Residue LEU 241 is missing expected H atoms. Skipping. Residue THR 242 is missing expected H atoms. Skipping. Residue VAL 243 is missing expected H atoms. Skipping. Residue LYS 251 is missing expected H atoms. Skipping. Residue VAL 255 is missing expected H atoms. Skipping. Residue SER 267 is missing expected H atoms. Skipping. Residue LYS 270 is missing expected H atoms. Skipping. Residue LEU 279 is missing expected H atoms. Skipping. Residue LYS 281 is missing expected H atoms. Skipping. Residue LYS 2 is missing expected H atoms. Skipping. Residue MET 4 is missing expected H atoms. Skipping. Residue LEU 14 is missing expected H atoms. Skipping. Residue VAL 19 is missing expected H atoms. Skipping. Residue LEU 24 is missing expected H atoms. Skipping. Residue TYR 25 is missing expected H atoms. Skipping. Residue LEU 27 is missing expected H atoms. Skipping. Residue ILE 29 is missing expected H atoms. Skipping. Residue LYS 38 is missing expected H atoms. Skipping. Residue ILE 41 is missing expected H atoms. Skipping. Residue TYR 42 is missing expected H atoms. Skipping. Residue LYS 43 is missing expected H atoms. Skipping. Residue LYS 45 is missing expected H atoms. Skipping. Residue LEU 70 is missing expected H atoms. Skipping. Residue TYR 77 is missing expected H atoms. Skipping. Residue TYR 82 is missing expected H atoms. Skipping. Residue ILE 90 is missing expected H atoms. Skipping. Residue LYS 91 is missing expected H atoms. Skipping. Residue LEU 94 is missing expected H atoms. Skipping. Residue ILE 104 is missing expected H atoms. Skipping. Residue LYS 112 is missing expected H atoms. Skipping. Residue VAL 128 is missing expected H atoms. Skipping. Residue MET 130 is missing expected H atoms. Skipping. Residue ILE 143 is missing expected H atoms. Skipping. Residue LYS 152 is missing expected H atoms. Skipping. Residue LEU 158 is missing expected H atoms. Skipping. Residue LEU 160 is missing expected H atoms. Skipping. Residue MET 164 is missing expected H atoms. Skipping. Residue LEU 166 is missing expected H atoms. Skipping. Residue LYS 175 is missing expected H atoms. Skipping. Residue LYS 189 is missing expected H atoms. Skipping. Residue ILE 194 is missing expected H atoms. Skipping. Residue LYS 195 is missing expected H atoms. Skipping. Residue ILE 214 is missing expected H atoms. Skipping. Residue VAL 215 is missing expected H atoms. Skipping. Residue TYR 221 is missing expected H atoms. Skipping. Residue ILE 229 is missing expected H atoms. Skipping. Residue LEU 230 is missing expected H atoms. Skipping. Residue LYS 255 is missing expected H atoms. Skipping. Residue LYS 257 is missing expected H atoms. Skipping. Residue LEU 258 is missing expected H atoms. Skipping. Residue TYR 259 is missing expected H atoms. Skipping. Residue LEU 265 is missing expected H atoms. Skipping. Residue LEU 285 is missing expected H atoms. Skipping. Residue SER 290 is missing expected H atoms. Skipping. Residue ILE 291 is missing expected H atoms. Skipping. Residue THR 296 is missing expected H atoms. Skipping. Residue THR 310 is missing expected H atoms. Skipping. Residue LEU 324 is missing expected H atoms. Skipping. Residue LEU 336 is missing expected H atoms. Skipping. Residue LEU 339 is missing expected H atoms. Skipping. Residue MET 350 is missing expected H atoms. Skipping. Residue LEU 363 is missing expected H atoms. Skipping. Residue VAL 367 is missing expected H atoms. Skipping. Residue ILE 376 is missing expected H atoms. Skipping. Residue LEU 384 is missing expected H atoms. Skipping. Residue MET 387 is missing expected H atoms. Skipping. Residue VAL 403 is missing expected H atoms. Skipping. Residue THR 410 is missing expected H atoms. Skipping. Residue VAL 413 is missing expected H atoms. Skipping. Residue SER 420 is missing expected H atoms. Skipping. Residue ILE 423 is missing expected H atoms. Skipping. Residue LEU 426 is missing expected H atoms. Skipping. Residue ILE 427 is missing expected H atoms. Skipping. Residue LYS 433 is missing expected H atoms. Skipping. Residue VAL 439 is missing expected H atoms. Skipping. Residue ILE 447 is missing expected H atoms. Skipping. Residue LYS 455 is missing expected H atoms. Skipping. Residue THR 481 is missing expected H atoms. Skipping. Residue TYR 484 is missing expected H atoms. Skipping. Residue VAL 486 is missing expected H atoms. Skipping. Residue LEU 487 is missing expected H atoms. Skipping. Residue MET 501 is missing expected H atoms. Skipping. Residue LEU 5 is missing expected H atoms. Skipping. Residue LEU 24 is missing expected H atoms. Skipping. Residue TYR 25 is missing expected H atoms. Skipping. Residue LEU 27 is missing expected H atoms. Skipping. Residue LYS 37 is missing expected H atoms. Skipping. Residue LYS 38 is missing expected H atoms. Skipping. Residue ILE 41 is missing expected H atoms. Skipping. Residue TYR 42 is missing expected H atoms. Skipping. Residue LYS 43 is missing expected H atoms. Skipping. Residue VAL 58 is missing expected H atoms. Skipping. Residue LYS 175 is missing expected H atoms. Skipping. Residue LYS 189 is missing expected H atoms. Skipping. Residue ILE 214 is missing expected H atoms. Skipping. Residue VAL 215 is missing expected H atoms. Skipping. Residue TYR 221 is missing expected H atoms. Skipping. Residue LEU 230 is missing expected H atoms. Skipping. Residue LYS 235 is missing expected H atoms. Skipping. Residue LEU 258 is missing expected H atoms. Skipping. Residue ILE 263 is missing expected H atoms. Skipping. Residue TYR 269 is missing expected H atoms. Skipping. Residue ILE 291 is missing expected H atoms. Skipping. Residue ILE 293 is missing expected H atoms. Skipping. Residue SER 295 is missing expected H atoms. Skipping. Residue THR 296 is missing expected H atoms. Skipping. Residue LEU 299 is missing expected H atoms. Skipping. Residue ILE 302 is missing expected H atoms. Skipping. Residue THR 310 is missing expected H atoms. Skipping. Residue ILE 330 is missing expected H atoms. Skipping. Residue LEU 334 is missing expected H atoms. Skipping. Residue LEU 339 is missing expected H atoms. Skipping. Residue ILE 343 is missing expected H atoms. Skipping. Residue ILE 345 is missing expected H atoms. Skipping. Residue ILE 348 is missing expected H atoms. Skipping. Residue MET 350 is missing expected H atoms. Skipping. Residue VAL 353 is missing expected H atoms. Skipping. Residue SER 380 is missing expected H atoms. Skipping. Residue MET 387 is missing expected H atoms. Skipping. Residue THR 412 is missing expected H atoms. Skipping. Residue VAL 413 is missing expected H atoms. Skipping. Residue SER 418 is missing expected H atoms. Skipping. Residue LEU 421 is missing expected H atoms. Skipping. Residue LYS 433 is missing expected H atoms. Skipping. Residue VAL 439 is missing expected H atoms. Skipping. Residue ILE 442 is missing expected H atoms. Skipping. Residue VAL 445 is missing expected H atoms. Skipping. Residue TYR 450 is missing expected H atoms. Skipping. Residue LEU 451 is missing expected H atoms. Skipping. Residue LYS 455 is missing expected H atoms. Skipping. Residue ILE 462 is missing expected H atoms. Skipping. Residue ILE 473 is missing expected H atoms. Skipping. Residue VAL 474 is missing expected H atoms. Skipping. Residue MET 479 is missing expected H atoms. Skipping. Residue MET 501 is missing expected H atoms. Skipping. Residue LEU 502 is missing expected H atoms. Skipping. Evaluate side-chains 394 residues out of total 1691 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 50 poor density : 344 time to evaluate : 2.068 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 50 outliers final: 38 residues processed: 361 average time/residue: 0.5728 time to fit residues: 297.8588 Evaluate side-chains 363 residues out of total 1691 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 38 poor density : 325 time to evaluate : 2.104 Switching outliers to nearest non-outliers revert: symmetry clash outliers start: 38 outliers final: 1 residues processed: 38 average time/residue: 0.3112 time to fit residues: 23.9035 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 206 random chunks: chunk 165 optimal weight: 10.0000 chunk 113 optimal weight: 7.9990 chunk 2 optimal weight: 5.9990 chunk 148 optimal weight: 7.9990 chunk 82 optimal weight: 9.9990 chunk 169 optimal weight: 0.7980 chunk 137 optimal weight: 3.9990 chunk 0 optimal weight: 10.0000 chunk 101 optimal weight: 2.9990 chunk 178 optimal weight: 8.9990 chunk 50 optimal weight: 0.9990 overall best weight: 2.9588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 171 HIS ** C 69 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 81 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7349 moved from start: 0.5504 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 16776 Z= 0.237 Angle : 0.599 6.486 23691 Z= 0.316 Chirality : 0.040 0.255 3041 Planarity : 0.005 0.068 2530 Dihedral : 20.731 179.747 3905 Min Nonbonded Distance : 1.939 Molprobity Statistics. All-atom Clashscore : 17.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.92 % Favored : 93.08 % Rotamer: Outliers : 1.35 % Allowed : 25.60 % Favored : 73.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.41 (0.19), residues: 1893 helix: -0.10 (0.18), residues: 796 sheet: -1.90 (0.28), residues: 321 loop : -1.23 (0.22), residues: 776 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3786 Ramachandran restraints generated. 1893 Oldfield, 0 Emsley, 1893 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3786 Ramachandran restraints generated. 1893 Oldfield, 0 Emsley, 1893 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue MET 1 is missing expected H atoms. Skipping. Residue MET 4 is missing expected H atoms. Skipping. Residue LYS 14 is missing expected H atoms. Skipping. Residue MET 24 is missing expected H atoms. Skipping. Residue TYR 27 is missing expected H atoms. Skipping. Residue VAL 29 is missing expected H atoms. Skipping. Residue VAL 34 is missing expected H atoms. Skipping. Residue MET 60 is missing expected H atoms. Skipping. Residue ILE 66 is missing expected H atoms. Skipping. Residue MET 71 is missing expected H atoms. Skipping. Residue LEU 82 is missing expected H atoms. Skipping. Residue LEU 83 is missing expected H atoms. Skipping. Residue TYR 96 is missing expected H atoms. Skipping. Residue ILE 116 is missing expected H atoms. Skipping. Residue LYS 118 is missing expected H atoms. Skipping. Residue MET 139 is missing expected H atoms. Skipping. Residue MET 147 is missing expected H atoms. Skipping. Residue LYS 155 is missing expected H atoms. Skipping. Residue MET 198 is missing expected H atoms. Skipping. Residue ILE 219 is missing expected H atoms. Skipping. Residue TYR 264 is missing expected H atoms. Skipping. Residue LEU 3 is missing expected H atoms. Skipping. Residue MET 4 is missing expected H atoms. Skipping. Residue VAL 6 is missing expected H atoms. Skipping. Residue SER 12 is missing expected H atoms. Skipping. Residue LYS 14 is missing expected H atoms. Skipping. Residue LEU 21 is missing expected H atoms. Skipping. Residue MET 24 is missing expected H atoms. Skipping. Residue TYR 27 is missing expected H atoms. Skipping. Residue VAL 34 is missing expected H atoms. Skipping. Residue LEU 36 is missing expected H atoms. Skipping. Residue LEU 37 is missing expected H atoms. Skipping. Residue THR 43 is missing expected H atoms. Skipping. Residue LEU 44 is missing expected H atoms. Skipping. Residue MET 60 is missing expected H atoms. Skipping. Residue MET 71 is missing expected H atoms. Skipping. Residue LEU 82 is missing expected H atoms. Skipping. Residue LEU 83 is missing expected H atoms. Skipping. Residue THR 99 is missing expected H atoms. Skipping. Residue LEU 102 is missing expected H atoms. Skipping. Residue LEU 105 is missing expected H atoms. Skipping. Residue LYS 108 is missing expected H atoms. Skipping. Residue LEU 110 is missing expected H atoms. Skipping. Residue LEU 112 is missing expected H atoms. Skipping. Residue LYS 118 is missing expected H atoms. Skipping. Residue SER 120 is missing expected H atoms. Skipping. Residue MET 139 is missing expected H atoms. Skipping. Residue VAL 141 is missing expected H atoms. Skipping. Residue MET 147 is missing expected H atoms. Skipping. Residue LEU 152 is missing expected H atoms. Skipping. Residue MET 162 is missing expected H atoms. Skipping. Residue SER 166 is missing expected H atoms. Skipping. Residue LYS 194 is missing expected H atoms. Skipping. Residue MET 198 is missing expected H atoms. Skipping. Residue LYS 203 is missing expected H atoms. Skipping. Residue THR 213 is missing expected H atoms. Skipping. Residue MET 232 is missing expected H atoms. Skipping. Residue THR 248 is missing expected H atoms. Skipping. Residue SER 267 is missing expected H atoms. Skipping. Residue LYS 270 is missing expected H atoms. Skipping. Residue VAL 2 is missing expected H atoms. Skipping. Residue MET 4 is missing expected H atoms. Skipping. Residue SER 7 is missing expected H atoms. Skipping. Residue LYS 14 is missing expected H atoms. Skipping. Residue MET 24 is missing expected H atoms. Skipping. Residue LEU 32 is missing expected H atoms. Skipping. Residue THR 43 is missing expected H atoms. Skipping. Residue ILE 49 is missing expected H atoms. Skipping. Residue MET 71 is missing expected H atoms. Skipping. Residue LEU 74 is missing expected H atoms. Skipping. Residue THR 99 is missing expected H atoms. Skipping. Residue SER 111 is missing expected H atoms. Skipping. Residue SER 120 is missing expected H atoms. Skipping. Residue LEU 132 is missing expected H atoms. Skipping. Residue ILE 133 is missing expected H atoms. Skipping. Residue THR 136 is missing expected H atoms. Skipping. Residue MET 139 is missing expected H atoms. Skipping. Residue VAL 141 is missing expected H atoms. Skipping. Residue LEU 144 is missing expected H atoms. Skipping. Residue MET 147 is missing expected H atoms. Skipping. Residue THR 150 is missing expected H atoms. Skipping. Residue LEU 160 is missing expected H atoms. Skipping. Residue MET 162 is missing expected H atoms. Skipping. Residue LYS 170 is missing expected H atoms. Skipping. Residue VAL 183 is missing expected H atoms. Skipping. Residue LYS 194 is missing expected H atoms. Skipping. Residue LEU 195 is missing expected H atoms. Skipping. Residue THR 199 is missing expected H atoms. Skipping. Residue LEU 201 is missing expected H atoms. Skipping. Residue LYS 203 is missing expected H atoms. Skipping. Residue ILE 219 is missing expected H atoms. Skipping. Residue TYR 220 is missing expected H atoms. Skipping. Residue LEU 230 is missing expected H atoms. Skipping. Residue MET 232 is missing expected H atoms. Skipping. Residue LEU 233 is missing expected H atoms. Skipping. Residue THR 235 is missing expected H atoms. Skipping. Residue SER 239 is missing expected H atoms. Skipping. Residue TYR 240 is missing expected H atoms. Skipping. Residue LEU 241 is missing expected H atoms. Skipping. Residue ILE 245 is missing expected H atoms. Skipping. Residue THR 248 is missing expected H atoms. Skipping. Residue LYS 251 is missing expected H atoms. Skipping. Residue TYR 256 is missing expected H atoms. Skipping. Residue LYS 270 is missing expected H atoms. Skipping. Residue THR 278 is missing expected H atoms. Skipping. Residue MET 1 is missing expected H atoms. Skipping. Residue MET 4 is missing expected H atoms. Skipping. Residue SER 12 is missing expected H atoms. Skipping. Residue LYS 14 is missing expected H atoms. Skipping. Residue VAL 16 is missing expected H atoms. Skipping. Residue MET 24 is missing expected H atoms. Skipping. Residue TYR 27 is missing expected H atoms. Skipping. Residue VAL 34 is missing expected H atoms. Skipping. Residue LEU 44 is missing expected H atoms. Skipping. Residue MET 60 is missing expected H atoms. Skipping. Residue LEU 112 is missing expected H atoms. Skipping. Residue LYS 118 is missing expected H atoms. Skipping. Residue LEU 126 is missing expected H atoms. Skipping. Residue MET 139 is missing expected H atoms. Skipping. Residue VAL 141 is missing expected H atoms. Skipping. Residue LEU 144 is missing expected H atoms. Skipping. Residue MET 147 is missing expected H atoms. Skipping. Residue LEU 148 is missing expected H atoms. Skipping. Residue LYS 155 is missing expected H atoms. Skipping. Residue LEU 160 is missing expected H atoms. Skipping. Residue MET 162 is missing expected H atoms. Skipping. Residue SER 166 is missing expected H atoms. Skipping. Residue LYS 170 is missing expected H atoms. Skipping. Residue TYR 179 is missing expected H atoms. Skipping. Residue VAL 180 is missing expected H atoms. Skipping. Residue MET 198 is missing expected H atoms. Skipping. Residue LYS 203 is missing expected H atoms. Skipping. Residue THR 222 is missing expected H atoms. Skipping. Residue TYR 225 is missing expected H atoms. Skipping. Residue MET 232 is missing expected H atoms. Skipping. Residue TYR 240 is missing expected H atoms. Skipping. Residue LEU 241 is missing expected H atoms. Skipping. Residue THR 242 is missing expected H atoms. Skipping. Residue VAL 243 is missing expected H atoms. Skipping. Residue LYS 251 is missing expected H atoms. Skipping. Residue VAL 255 is missing expected H atoms. Skipping. Residue SER 267 is missing expected H atoms. Skipping. Residue LYS 270 is missing expected H atoms. Skipping. Residue LEU 279 is missing expected H atoms. Skipping. Residue LYS 281 is missing expected H atoms. Skipping. Residue LYS 2 is missing expected H atoms. Skipping. Residue MET 4 is missing expected H atoms. Skipping. Residue LEU 14 is missing expected H atoms. Skipping. Residue VAL 19 is missing expected H atoms. Skipping. Residue LEU 24 is missing expected H atoms. Skipping. Residue TYR 25 is missing expected H atoms. Skipping. Residue LEU 27 is missing expected H atoms. Skipping. Residue ILE 29 is missing expected H atoms. Skipping. Residue LYS 38 is missing expected H atoms. Skipping. Residue ILE 41 is missing expected H atoms. Skipping. Residue TYR 42 is missing expected H atoms. Skipping. Residue LYS 43 is missing expected H atoms. Skipping. Residue LYS 45 is missing expected H atoms. Skipping. Residue LEU 70 is missing expected H atoms. Skipping. Residue TYR 77 is missing expected H atoms. Skipping. Residue TYR 82 is missing expected H atoms. Skipping. Residue ILE 90 is missing expected H atoms. Skipping. Residue LYS 91 is missing expected H atoms. Skipping. Residue LEU 94 is missing expected H atoms. Skipping. Residue ILE 104 is missing expected H atoms. Skipping. Residue LYS 112 is missing expected H atoms. Skipping. Residue VAL 128 is missing expected H atoms. Skipping. Residue MET 130 is missing expected H atoms. Skipping. Residue ILE 143 is missing expected H atoms. Skipping. Residue LYS 152 is missing expected H atoms. Skipping. Residue LEU 158 is missing expected H atoms. Skipping. Residue LEU 160 is missing expected H atoms. Skipping. Residue MET 164 is missing expected H atoms. Skipping. Residue LEU 166 is missing expected H atoms. Skipping. Residue LYS 175 is missing expected H atoms. Skipping. Residue LYS 189 is missing expected H atoms. Skipping. Residue ILE 194 is missing expected H atoms. Skipping. Residue LYS 195 is missing expected H atoms. Skipping. Residue ILE 214 is missing expected H atoms. Skipping. Residue VAL 215 is missing expected H atoms. Skipping. Residue TYR 221 is missing expected H atoms. Skipping. Residue ILE 229 is missing expected H atoms. Skipping. Residue LEU 230 is missing expected H atoms. Skipping. Residue LYS 255 is missing expected H atoms. Skipping. Residue LYS 257 is missing expected H atoms. Skipping. Residue LEU 258 is missing expected H atoms. Skipping. Residue TYR 259 is missing expected H atoms. Skipping. Residue LEU 265 is missing expected H atoms. Skipping. Residue LEU 285 is missing expected H atoms. Skipping. Residue SER 290 is missing expected H atoms. Skipping. Residue ILE 291 is missing expected H atoms. Skipping. Residue THR 296 is missing expected H atoms. Skipping. Residue THR 310 is missing expected H atoms. Skipping. Residue LEU 324 is missing expected H atoms. Skipping. Residue LEU 336 is missing expected H atoms. Skipping. Residue LEU 339 is missing expected H atoms. Skipping. Residue MET 350 is missing expected H atoms. Skipping. Residue LEU 363 is missing expected H atoms. Skipping. Residue VAL 367 is missing expected H atoms. Skipping. Residue ILE 376 is missing expected H atoms. Skipping. Residue LEU 384 is missing expected H atoms. Skipping. Residue MET 387 is missing expected H atoms. Skipping. Residue VAL 403 is missing expected H atoms. Skipping. Residue THR 410 is missing expected H atoms. Skipping. Residue VAL 413 is missing expected H atoms. Skipping. Residue SER 420 is missing expected H atoms. Skipping. Residue ILE 423 is missing expected H atoms. Skipping. Residue LEU 426 is missing expected H atoms. Skipping. Residue ILE 427 is missing expected H atoms. Skipping. Residue LYS 433 is missing expected H atoms. Skipping. Residue VAL 439 is missing expected H atoms. Skipping. Residue ILE 447 is missing expected H atoms. Skipping. Residue LYS 455 is missing expected H atoms. Skipping. Residue THR 481 is missing expected H atoms. Skipping. Residue TYR 484 is missing expected H atoms. Skipping. Residue VAL 486 is missing expected H atoms. Skipping. Residue LEU 487 is missing expected H atoms. Skipping. Residue MET 501 is missing expected H atoms. Skipping. Residue LEU 5 is missing expected H atoms. Skipping. Residue LEU 24 is missing expected H atoms. Skipping. Residue TYR 25 is missing expected H atoms. Skipping. Residue LEU 27 is missing expected H atoms. Skipping. Residue LYS 37 is missing expected H atoms. Skipping. Residue LYS 38 is missing expected H atoms. Skipping. Residue ILE 41 is missing expected H atoms. Skipping. Residue TYR 42 is missing expected H atoms. Skipping. Residue LYS 43 is missing expected H atoms. Skipping. Residue VAL 58 is missing expected H atoms. Skipping. Residue LYS 175 is missing expected H atoms. Skipping. Residue LYS 189 is missing expected H atoms. Skipping. Residue ILE 214 is missing expected H atoms. Skipping. Residue VAL 215 is missing expected H atoms. Skipping. Residue TYR 221 is missing expected H atoms. Skipping. Residue LEU 230 is missing expected H atoms. Skipping. Residue LYS 235 is missing expected H atoms. Skipping. Residue LEU 258 is missing expected H atoms. Skipping. Residue ILE 263 is missing expected H atoms. Skipping. Residue TYR 269 is missing expected H atoms. Skipping. Residue ILE 291 is missing expected H atoms. Skipping. Residue ILE 293 is missing expected H atoms. Skipping. Residue SER 295 is missing expected H atoms. Skipping. Residue THR 296 is missing expected H atoms. Skipping. Residue LEU 299 is missing expected H atoms. Skipping. Residue ILE 302 is missing expected H atoms. Skipping. Residue THR 310 is missing expected H atoms. Skipping. Residue ILE 330 is missing expected H atoms. Skipping. Residue LEU 334 is missing expected H atoms. Skipping. Residue LEU 339 is missing expected H atoms. Skipping. Residue ILE 343 is missing expected H atoms. Skipping. Residue ILE 345 is missing expected H atoms. Skipping. Residue ILE 348 is missing expected H atoms. Skipping. Residue MET 350 is missing expected H atoms. Skipping. Residue VAL 353 is missing expected H atoms. Skipping. Residue SER 380 is missing expected H atoms. Skipping. Residue MET 387 is missing expected H atoms. Skipping. Residue THR 412 is missing expected H atoms. Skipping. Residue VAL 413 is missing expected H atoms. Skipping. Residue SER 418 is missing expected H atoms. Skipping. Residue LEU 421 is missing expected H atoms. Skipping. Residue LYS 433 is missing expected H atoms. Skipping. Residue VAL 439 is missing expected H atoms. Skipping. Residue ILE 442 is missing expected H atoms. Skipping. Residue VAL 445 is missing expected H atoms. Skipping. Residue TYR 450 is missing expected H atoms. Skipping. Residue LEU 451 is missing expected H atoms. Skipping. Residue LYS 455 is missing expected H atoms. Skipping. Residue ILE 462 is missing expected H atoms. Skipping. Residue ILE 473 is missing expected H atoms. Skipping. Residue VAL 474 is missing expected H atoms. Skipping. Residue MET 479 is missing expected H atoms. Skipping. Residue MET 501 is missing expected H atoms. Skipping. Residue LEU 502 is missing expected H atoms. Skipping. Evaluate side-chains 354 residues out of total 1691 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 340 time to evaluate : 2.161 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 14 outliers final: 12 residues processed: 344 average time/residue: 0.5684 time to fit residues: 282.0422 Evaluate side-chains 336 residues out of total 1691 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 324 time to evaluate : 1.905 Switching outliers to nearest non-outliers revert: symmetry clash outliers start: 12 outliers final: 1 residues processed: 12 average time/residue: 0.2752 time to fit residues: 8.4133 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 206 random chunks: chunk 66 optimal weight: 6.9990 chunk 179 optimal weight: 8.9990 chunk 39 optimal weight: 6.9990 chunk 116 optimal weight: 0.0980 chunk 49 optimal weight: 1.9990 chunk 199 optimal weight: 6.9990 chunk 165 optimal weight: 6.9990 chunk 92 optimal weight: 9.9990 chunk 16 optimal weight: 0.6980 chunk 65 optimal weight: 0.6980 chunk 104 optimal weight: 9.9990 overall best weight: 2.0984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 237 ASN ** C 69 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 81 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 268 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7329 moved from start: 0.5786 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.054 16776 Z= 0.198 Angle : 0.575 7.461 23691 Z= 0.299 Chirality : 0.039 0.235 3041 Planarity : 0.004 0.057 2530 Dihedral : 20.442 176.994 3905 Min Nonbonded Distance : 1.935 Molprobity Statistics. All-atom Clashscore : 14.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.23 % Favored : 93.77 % Rotamer: Outliers : 0.97 % Allowed : 28.02 % Favored : 71.01 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.95 (0.20), residues: 1893 helix: 0.41 (0.19), residues: 793 sheet: -1.76 (0.29), residues: 319 loop : -1.09 (0.22), residues: 781 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3786 Ramachandran restraints generated. 1893 Oldfield, 0 Emsley, 1893 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3786 Ramachandran restraints generated. 1893 Oldfield, 0 Emsley, 1893 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue MET 1 is missing expected H atoms. Skipping. Residue MET 4 is missing expected H atoms. Skipping. Residue LYS 14 is missing expected H atoms. Skipping. Residue MET 24 is missing expected H atoms. Skipping. Residue TYR 27 is missing expected H atoms. Skipping. Residue VAL 29 is missing expected H atoms. Skipping. Residue VAL 34 is missing expected H atoms. Skipping. Residue MET 60 is missing expected H atoms. Skipping. Residue ILE 66 is missing expected H atoms. Skipping. Residue MET 71 is missing expected H atoms. Skipping. Residue LEU 82 is missing expected H atoms. Skipping. Residue LEU 83 is missing expected H atoms. Skipping. Residue TYR 96 is missing expected H atoms. Skipping. Residue ILE 116 is missing expected H atoms. Skipping. Residue LYS 118 is missing expected H atoms. Skipping. Residue MET 139 is missing expected H atoms. Skipping. Residue MET 147 is missing expected H atoms. Skipping. Residue LYS 155 is missing expected H atoms. Skipping. Residue MET 198 is missing expected H atoms. Skipping. Residue ILE 219 is missing expected H atoms. Skipping. Residue TYR 264 is missing expected H atoms. Skipping. Residue LEU 3 is missing expected H atoms. Skipping. Residue MET 4 is missing expected H atoms. Skipping. Residue VAL 6 is missing expected H atoms. Skipping. Residue SER 12 is missing expected H atoms. Skipping. Residue LYS 14 is missing expected H atoms. Skipping. Residue LEU 21 is missing expected H atoms. Skipping. Residue MET 24 is missing expected H atoms. Skipping. Residue TYR 27 is missing expected H atoms. Skipping. Residue VAL 34 is missing expected H atoms. Skipping. Residue LEU 36 is missing expected H atoms. Skipping. Residue LEU 37 is missing expected H atoms. Skipping. Residue THR 43 is missing expected H atoms. Skipping. Residue LEU 44 is missing expected H atoms. Skipping. Residue MET 60 is missing expected H atoms. Skipping. Residue MET 71 is missing expected H atoms. Skipping. Residue LEU 82 is missing expected H atoms. Skipping. Residue LEU 83 is missing expected H atoms. Skipping. Residue THR 99 is missing expected H atoms. Skipping. Residue LEU 102 is missing expected H atoms. Skipping. Residue LEU 105 is missing expected H atoms. Skipping. Residue LYS 108 is missing expected H atoms. Skipping. Residue LEU 110 is missing expected H atoms. Skipping. Residue LEU 112 is missing expected H atoms. Skipping. Residue LYS 118 is missing expected H atoms. Skipping. Residue SER 120 is missing expected H atoms. Skipping. Residue MET 139 is missing expected H atoms. Skipping. Residue VAL 141 is missing expected H atoms. Skipping. Residue MET 147 is missing expected H atoms. Skipping. Residue LEU 152 is missing expected H atoms. Skipping. Residue MET 162 is missing expected H atoms. Skipping. Residue SER 166 is missing expected H atoms. Skipping. Residue LYS 194 is missing expected H atoms. Skipping. Residue MET 198 is missing expected H atoms. Skipping. Residue LYS 203 is missing expected H atoms. Skipping. Residue THR 213 is missing expected H atoms. Skipping. Residue MET 232 is missing expected H atoms. Skipping. Residue THR 248 is missing expected H atoms. Skipping. Residue SER 267 is missing expected H atoms. Skipping. Residue LYS 270 is missing expected H atoms. Skipping. Residue VAL 2 is missing expected H atoms. Skipping. Residue MET 4 is missing expected H atoms. Skipping. Residue SER 7 is missing expected H atoms. Skipping. Residue LYS 14 is missing expected H atoms. Skipping. Residue MET 24 is missing expected H atoms. Skipping. Residue LEU 32 is missing expected H atoms. Skipping. Residue THR 43 is missing expected H atoms. Skipping. Residue ILE 49 is missing expected H atoms. Skipping. Residue MET 71 is missing expected H atoms. Skipping. Residue LEU 74 is missing expected H atoms. Skipping. Residue THR 99 is missing expected H atoms. Skipping. Residue SER 111 is missing expected H atoms. Skipping. Residue SER 120 is missing expected H atoms. Skipping. Residue LEU 132 is missing expected H atoms. Skipping. Residue ILE 133 is missing expected H atoms. Skipping. Residue THR 136 is missing expected H atoms. Skipping. Residue MET 139 is missing expected H atoms. Skipping. Residue VAL 141 is missing expected H atoms. Skipping. Residue LEU 144 is missing expected H atoms. Skipping. Residue MET 147 is missing expected H atoms. Skipping. Residue THR 150 is missing expected H atoms. Skipping. Residue LEU 160 is missing expected H atoms. Skipping. Residue MET 162 is missing expected H atoms. Skipping. Residue LYS 170 is missing expected H atoms. Skipping. Residue VAL 183 is missing expected H atoms. Skipping. Residue LYS 194 is missing expected H atoms. Skipping. Residue LEU 195 is missing expected H atoms. Skipping. Residue THR 199 is missing expected H atoms. Skipping. Residue LEU 201 is missing expected H atoms. Skipping. Residue LYS 203 is missing expected H atoms. Skipping. Residue ILE 219 is missing expected H atoms. Skipping. Residue TYR 220 is missing expected H atoms. Skipping. Residue LEU 230 is missing expected H atoms. Skipping. Residue MET 232 is missing expected H atoms. Skipping. Residue LEU 233 is missing expected H atoms. Skipping. Residue THR 235 is missing expected H atoms. Skipping. Residue SER 239 is missing expected H atoms. Skipping. Residue TYR 240 is missing expected H atoms. Skipping. Residue LEU 241 is missing expected H atoms. Skipping. Residue ILE 245 is missing expected H atoms. Skipping. Residue THR 248 is missing expected H atoms. Skipping. Residue LYS 251 is missing expected H atoms. Skipping. Residue TYR 256 is missing expected H atoms. Skipping. Residue LYS 270 is missing expected H atoms. Skipping. Residue THR 278 is missing expected H atoms. Skipping. Residue MET 1 is missing expected H atoms. Skipping. Residue MET 4 is missing expected H atoms. Skipping. Residue SER 12 is missing expected H atoms. Skipping. Residue LYS 14 is missing expected H atoms. Skipping. Residue VAL 16 is missing expected H atoms. Skipping. Residue MET 24 is missing expected H atoms. Skipping. Residue TYR 27 is missing expected H atoms. Skipping. Residue VAL 34 is missing expected H atoms. Skipping. Residue LEU 44 is missing expected H atoms. Skipping. Residue MET 60 is missing expected H atoms. Skipping. Residue LEU 112 is missing expected H atoms. Skipping. Residue LYS 118 is missing expected H atoms. Skipping. Residue LEU 126 is missing expected H atoms. Skipping. Residue MET 139 is missing expected H atoms. Skipping. Residue VAL 141 is missing expected H atoms. Skipping. Residue LEU 144 is missing expected H atoms. Skipping. Residue MET 147 is missing expected H atoms. Skipping. Residue LEU 148 is missing expected H atoms. Skipping. Residue LYS 155 is missing expected H atoms. Skipping. Residue LEU 160 is missing expected H atoms. Skipping. Residue MET 162 is missing expected H atoms. Skipping. Residue SER 166 is missing expected H atoms. Skipping. Residue LYS 170 is missing expected H atoms. Skipping. Residue TYR 179 is missing expected H atoms. Skipping. Residue VAL 180 is missing expected H atoms. Skipping. Residue MET 198 is missing expected H atoms. Skipping. Residue LYS 203 is missing expected H atoms. Skipping. Residue THR 222 is missing expected H atoms. Skipping. Residue TYR 225 is missing expected H atoms. Skipping. Residue MET 232 is missing expected H atoms. Skipping. Residue TYR 240 is missing expected H atoms. Skipping. Residue LEU 241 is missing expected H atoms. Skipping. Residue THR 242 is missing expected H atoms. Skipping. Residue VAL 243 is missing expected H atoms. Skipping. Residue LYS 251 is missing expected H atoms. Skipping. Residue VAL 255 is missing expected H atoms. Skipping. Residue SER 267 is missing expected H atoms. Skipping. Residue LYS 270 is missing expected H atoms. Skipping. Residue LEU 279 is missing expected H atoms. Skipping. Residue LYS 281 is missing expected H atoms. Skipping. Residue LYS 2 is missing expected H atoms. Skipping. Residue MET 4 is missing expected H atoms. Skipping. Residue LEU 14 is missing expected H atoms. Skipping. Residue VAL 19 is missing expected H atoms. Skipping. Residue LEU 24 is missing expected H atoms. Skipping. Residue TYR 25 is missing expected H atoms. Skipping. Residue LEU 27 is missing expected H atoms. Skipping. Residue ILE 29 is missing expected H atoms. Skipping. Residue LYS 38 is missing expected H atoms. Skipping. Residue ILE 41 is missing expected H atoms. Skipping. Residue TYR 42 is missing expected H atoms. Skipping. Residue LYS 43 is missing expected H atoms. Skipping. Residue LYS 45 is missing expected H atoms. Skipping. Residue LEU 70 is missing expected H atoms. Skipping. Residue TYR 77 is missing expected H atoms. Skipping. Residue TYR 82 is missing expected H atoms. Skipping. Residue ILE 90 is missing expected H atoms. Skipping. Residue LYS 91 is missing expected H atoms. Skipping. Residue LEU 94 is missing expected H atoms. Skipping. Residue ILE 104 is missing expected H atoms. Skipping. Residue LYS 112 is missing expected H atoms. Skipping. Residue VAL 128 is missing expected H atoms. Skipping. Residue MET 130 is missing expected H atoms. Skipping. Residue ILE 143 is missing expected H atoms. Skipping. Residue LYS 152 is missing expected H atoms. Skipping. Residue LEU 158 is missing expected H atoms. Skipping. Residue LEU 160 is missing expected H atoms. Skipping. Residue MET 164 is missing expected H atoms. Skipping. Residue LEU 166 is missing expected H atoms. Skipping. Residue LYS 175 is missing expected H atoms. Skipping. Residue LYS 189 is missing expected H atoms. Skipping. Residue ILE 194 is missing expected H atoms. Skipping. Residue LYS 195 is missing expected H atoms. Skipping. Residue ILE 214 is missing expected H atoms. Skipping. Residue VAL 215 is missing expected H atoms. Skipping. Residue TYR 221 is missing expected H atoms. Skipping. Residue ILE 229 is missing expected H atoms. Skipping. Residue LEU 230 is missing expected H atoms. Skipping. Residue LYS 255 is missing expected H atoms. Skipping. Residue LYS 257 is missing expected H atoms. Skipping. Residue LEU 258 is missing expected H atoms. Skipping. Residue TYR 259 is missing expected H atoms. Skipping. Residue LEU 265 is missing expected H atoms. Skipping. Residue LEU 285 is missing expected H atoms. Skipping. Residue SER 290 is missing expected H atoms. Skipping. Residue ILE 291 is missing expected H atoms. Skipping. Residue THR 296 is missing expected H atoms. Skipping. Residue THR 310 is missing expected H atoms. Skipping. Residue LEU 324 is missing expected H atoms. Skipping. Residue LEU 336 is missing expected H atoms. Skipping. Residue LEU 339 is missing expected H atoms. Skipping. Residue MET 350 is missing expected H atoms. Skipping. Residue LEU 363 is missing expected H atoms. Skipping. Residue VAL 367 is missing expected H atoms. Skipping. Residue ILE 376 is missing expected H atoms. Skipping. Residue LEU 384 is missing expected H atoms. Skipping. Residue MET 387 is missing expected H atoms. Skipping. Residue VAL 403 is missing expected H atoms. Skipping. Residue THR 410 is missing expected H atoms. Skipping. Residue VAL 413 is missing expected H atoms. Skipping. Residue SER 420 is missing expected H atoms. Skipping. Residue ILE 423 is missing expected H atoms. Skipping. Residue LEU 426 is missing expected H atoms. Skipping. Residue ILE 427 is missing expected H atoms. Skipping. Residue LYS 433 is missing expected H atoms. Skipping. Residue VAL 439 is missing expected H atoms. Skipping. Residue ILE 447 is missing expected H atoms. Skipping. Residue LYS 455 is missing expected H atoms. Skipping. Residue THR 481 is missing expected H atoms. Skipping. Residue TYR 484 is missing expected H atoms. Skipping. Residue VAL 486 is missing expected H atoms. Skipping. Residue LEU 487 is missing expected H atoms. Skipping. Residue MET 501 is missing expected H atoms. Skipping. Residue LEU 5 is missing expected H atoms. Skipping. Residue LEU 24 is missing expected H atoms. Skipping. Residue TYR 25 is missing expected H atoms. Skipping. Residue LEU 27 is missing expected H atoms. Skipping. Residue LYS 37 is missing expected H atoms. Skipping. Residue LYS 38 is missing expected H atoms. Skipping. Residue ILE 41 is missing expected H atoms. Skipping. Residue TYR 42 is missing expected H atoms. Skipping. Residue LYS 43 is missing expected H atoms. Skipping. Residue VAL 58 is missing expected H atoms. Skipping. Residue LYS 175 is missing expected H atoms. Skipping. Residue LYS 189 is missing expected H atoms. Skipping. Residue ILE 214 is missing expected H atoms. Skipping. Residue VAL 215 is missing expected H atoms. Skipping. Residue TYR 221 is missing expected H atoms. Skipping. Residue LEU 230 is missing expected H atoms. Skipping. Residue LYS 235 is missing expected H atoms. Skipping. Residue LEU 258 is missing expected H atoms. Skipping. Residue ILE 263 is missing expected H atoms. Skipping. Residue TYR 269 is missing expected H atoms. Skipping. Residue ILE 291 is missing expected H atoms. Skipping. Residue ILE 293 is missing expected H atoms. Skipping. Residue SER 295 is missing expected H atoms. Skipping. Residue THR 296 is missing expected H atoms. Skipping. Residue LEU 299 is missing expected H atoms. Skipping. Residue ILE 302 is missing expected H atoms. Skipping. Residue THR 310 is missing expected H atoms. Skipping. Residue ILE 330 is missing expected H atoms. Skipping. Residue LEU 334 is missing expected H atoms. Skipping. Residue LEU 339 is missing expected H atoms. Skipping. Residue ILE 343 is missing expected H atoms. Skipping. Residue ILE 345 is missing expected H atoms. Skipping. Residue ILE 348 is missing expected H atoms. Skipping. Residue MET 350 is missing expected H atoms. Skipping. Residue VAL 353 is missing expected H atoms. Skipping. Residue SER 380 is missing expected H atoms. Skipping. Residue MET 387 is missing expected H atoms. Skipping. Residue THR 412 is missing expected H atoms. Skipping. Residue VAL 413 is missing expected H atoms. Skipping. Residue SER 418 is missing expected H atoms. Skipping. Residue LEU 421 is missing expected H atoms. Skipping. Residue LYS 433 is missing expected H atoms. Skipping. Residue VAL 439 is missing expected H atoms. Skipping. Residue ILE 442 is missing expected H atoms. Skipping. Residue VAL 445 is missing expected H atoms. Skipping. Residue TYR 450 is missing expected H atoms. Skipping. Residue LEU 451 is missing expected H atoms. Skipping. Residue LYS 455 is missing expected H atoms. Skipping. Residue ILE 462 is missing expected H atoms. Skipping. Residue ILE 473 is missing expected H atoms. Skipping. Residue VAL 474 is missing expected H atoms. Skipping. Residue MET 479 is missing expected H atoms. Skipping. Residue MET 501 is missing expected H atoms. Skipping. Residue LEU 502 is missing expected H atoms. Skipping. Evaluate side-chains 348 residues out of total 1691 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 338 time to evaluate : 2.388 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 10 outliers final: 8 residues processed: 338 average time/residue: 0.5804 time to fit residues: 287.4276 Evaluate side-chains 338 residues out of total 1691 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 330 time to evaluate : 2.016 Switching outliers to nearest non-outliers revert: symmetry clash revert: symmetry clash outliers start: 8 outliers final: 2 residues processed: 8 average time/residue: 0.2904 time to fit residues: 6.8641 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 206 random chunks: chunk 192 optimal weight: 20.0000 chunk 22 optimal weight: 4.9990 chunk 113 optimal weight: 4.9990 chunk 145 optimal weight: 10.0000 chunk 112 optimal weight: 0.9980 chunk 167 optimal weight: 0.0980 chunk 111 optimal weight: 6.9990 chunk 198 optimal weight: 8.9990 chunk 124 optimal weight: 8.9990 chunk 121 optimal weight: 6.9990 chunk 91 optimal weight: 5.9990 overall best weight: 3.4186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 69 GLN A 90 ASN ** C 69 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 81 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7382 moved from start: 0.6109 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 16776 Z= 0.270 Angle : 0.609 7.870 23691 Z= 0.323 Chirality : 0.039 0.236 3041 Planarity : 0.005 0.057 2530 Dihedral : 20.468 178.128 3905 Min Nonbonded Distance : 1.907 Molprobity Statistics. All-atom Clashscore : 20.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.29 % Favored : 91.71 % Rotamer: Outliers : 2.80 % Allowed : 27.54 % Favored : 69.66 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.11 (0.19), residues: 1893 helix: 0.17 (0.19), residues: 791 sheet: -1.78 (0.28), residues: 321 loop : -1.07 (0.22), residues: 781 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3786 Ramachandran restraints generated. 1893 Oldfield, 0 Emsley, 1893 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3786 Ramachandran restraints generated. 1893 Oldfield, 0 Emsley, 1893 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue MET 1 is missing expected H atoms. Skipping. Residue MET 4 is missing expected H atoms. Skipping. Residue LYS 14 is missing expected H atoms. Skipping. Residue MET 24 is missing expected H atoms. Skipping. Residue TYR 27 is missing expected H atoms. Skipping. Residue VAL 29 is missing expected H atoms. Skipping. Residue VAL 34 is missing expected H atoms. Skipping. Residue MET 60 is missing expected H atoms. Skipping. Residue ILE 66 is missing expected H atoms. Skipping. Residue MET 71 is missing expected H atoms. Skipping. Residue LEU 82 is missing expected H atoms. Skipping. Residue LEU 83 is missing expected H atoms. Skipping. Residue TYR 96 is missing expected H atoms. Skipping. Residue ILE 116 is missing expected H atoms. Skipping. Residue LYS 118 is missing expected H atoms. Skipping. Residue MET 139 is missing expected H atoms. Skipping. Residue MET 147 is missing expected H atoms. Skipping. Residue LYS 155 is missing expected H atoms. Skipping. Residue MET 198 is missing expected H atoms. Skipping. Residue ILE 219 is missing expected H atoms. Skipping. Residue TYR 264 is missing expected H atoms. Skipping. Residue LEU 3 is missing expected H atoms. Skipping. Residue MET 4 is missing expected H atoms. Skipping. Residue VAL 6 is missing expected H atoms. Skipping. Residue SER 12 is missing expected H atoms. Skipping. Residue LYS 14 is missing expected H atoms. Skipping. Residue LEU 21 is missing expected H atoms. Skipping. Residue MET 24 is missing expected H atoms. Skipping. Residue TYR 27 is missing expected H atoms. Skipping. Residue VAL 34 is missing expected H atoms. Skipping. Residue LEU 36 is missing expected H atoms. Skipping. Residue LEU 37 is missing expected H atoms. Skipping. Residue THR 43 is missing expected H atoms. Skipping. Residue LEU 44 is missing expected H atoms. Skipping. Residue MET 60 is missing expected H atoms. Skipping. Residue MET 71 is missing expected H atoms. Skipping. Residue LEU 82 is missing expected H atoms. Skipping. Residue LEU 83 is missing expected H atoms. Skipping. Residue THR 99 is missing expected H atoms. Skipping. Residue LEU 102 is missing expected H atoms. Skipping. Residue LEU 105 is missing expected H atoms. Skipping. Residue LYS 108 is missing expected H atoms. Skipping. Residue LEU 110 is missing expected H atoms. Skipping. Residue LEU 112 is missing expected H atoms. Skipping. Residue LYS 118 is missing expected H atoms. Skipping. Residue SER 120 is missing expected H atoms. Skipping. Residue MET 139 is missing expected H atoms. Skipping. Residue VAL 141 is missing expected H atoms. Skipping. Residue MET 147 is missing expected H atoms. Skipping. Residue LEU 152 is missing expected H atoms. Skipping. Residue MET 162 is missing expected H atoms. Skipping. Residue SER 166 is missing expected H atoms. Skipping. Residue LYS 194 is missing expected H atoms. Skipping. Residue MET 198 is missing expected H atoms. Skipping. Residue LYS 203 is missing expected H atoms. Skipping. Residue THR 213 is missing expected H atoms. Skipping. Residue MET 232 is missing expected H atoms. Skipping. Residue THR 248 is missing expected H atoms. Skipping. Residue SER 267 is missing expected H atoms. Skipping. Residue LYS 270 is missing expected H atoms. Skipping. Residue VAL 2 is missing expected H atoms. Skipping. Residue MET 4 is missing expected H atoms. Skipping. Residue SER 7 is missing expected H atoms. Skipping. Residue LYS 14 is missing expected H atoms. Skipping. Residue MET 24 is missing expected H atoms. Skipping. Residue LEU 32 is missing expected H atoms. Skipping. Residue THR 43 is missing expected H atoms. Skipping. Residue ILE 49 is missing expected H atoms. Skipping. Residue MET 71 is missing expected H atoms. Skipping. Residue LEU 74 is missing expected H atoms. Skipping. Residue THR 99 is missing expected H atoms. Skipping. Residue SER 111 is missing expected H atoms. Skipping. Residue SER 120 is missing expected H atoms. Skipping. Residue LEU 132 is missing expected H atoms. Skipping. Residue ILE 133 is missing expected H atoms. Skipping. Residue THR 136 is missing expected H atoms. Skipping. Residue MET 139 is missing expected H atoms. Skipping. Residue VAL 141 is missing expected H atoms. Skipping. Residue LEU 144 is missing expected H atoms. Skipping. Residue MET 147 is missing expected H atoms. Skipping. Residue THR 150 is missing expected H atoms. Skipping. Residue LEU 160 is missing expected H atoms. Skipping. Residue MET 162 is missing expected H atoms. Skipping. Residue LYS 170 is missing expected H atoms. Skipping. Residue VAL 183 is missing expected H atoms. Skipping. Residue LYS 194 is missing expected H atoms. Skipping. Residue LEU 195 is missing expected H atoms. Skipping. Residue THR 199 is missing expected H atoms. Skipping. Residue LEU 201 is missing expected H atoms. Skipping. Residue LYS 203 is missing expected H atoms. Skipping. Residue ILE 219 is missing expected H atoms. Skipping. Residue TYR 220 is missing expected H atoms. Skipping. Residue LEU 230 is missing expected H atoms. Skipping. Residue MET 232 is missing expected H atoms. Skipping. Residue LEU 233 is missing expected H atoms. Skipping. Residue THR 235 is missing expected H atoms. Skipping. Residue SER 239 is missing expected H atoms. Skipping. Residue TYR 240 is missing expected H atoms. Skipping. Residue LEU 241 is missing expected H atoms. Skipping. Residue ILE 245 is missing expected H atoms. Skipping. Residue THR 248 is missing expected H atoms. Skipping. Residue LYS 251 is missing expected H atoms. Skipping. Residue TYR 256 is missing expected H atoms. Skipping. Residue LYS 270 is missing expected H atoms. Skipping. Residue THR 278 is missing expected H atoms. Skipping. Residue MET 1 is missing expected H atoms. Skipping. Residue MET 4 is missing expected H atoms. Skipping. Residue SER 12 is missing expected H atoms. Skipping. Residue LYS 14 is missing expected H atoms. Skipping. Residue VAL 16 is missing expected H atoms. Skipping. Residue MET 24 is missing expected H atoms. Skipping. Residue TYR 27 is missing expected H atoms. Skipping. Residue VAL 34 is missing expected H atoms. Skipping. Residue LEU 44 is missing expected H atoms. Skipping. Residue MET 60 is missing expected H atoms. Skipping. Residue LEU 112 is missing expected H atoms. Skipping. Residue LYS 118 is missing expected H atoms. Skipping. Residue LEU 126 is missing expected H atoms. Skipping. Residue MET 139 is missing expected H atoms. Skipping. Residue VAL 141 is missing expected H atoms. Skipping. Residue LEU 144 is missing expected H atoms. Skipping. Residue MET 147 is missing expected H atoms. Skipping. Residue LEU 148 is missing expected H atoms. Skipping. Residue LYS 155 is missing expected H atoms. Skipping. Residue LEU 160 is missing expected H atoms. Skipping. Residue MET 162 is missing expected H atoms. Skipping. Residue SER 166 is missing expected H atoms. Skipping. Residue LYS 170 is missing expected H atoms. Skipping. Residue TYR 179 is missing expected H atoms. Skipping. Residue VAL 180 is missing expected H atoms. Skipping. Residue MET 198 is missing expected H atoms. Skipping. Residue LYS 203 is missing expected H atoms. Skipping. Residue THR 222 is missing expected H atoms. Skipping. Residue TYR 225 is missing expected H atoms. Skipping. Residue MET 232 is missing expected H atoms. Skipping. Residue TYR 240 is missing expected H atoms. Skipping. Residue LEU 241 is missing expected H atoms. Skipping. Residue THR 242 is missing expected H atoms. Skipping. Residue VAL 243 is missing expected H atoms. Skipping. Residue LYS 251 is missing expected H atoms. Skipping. Residue VAL 255 is missing expected H atoms. Skipping. Residue SER 267 is missing expected H atoms. Skipping. Residue LYS 270 is missing expected H atoms. Skipping. Residue LEU 279 is missing expected H atoms. Skipping. Residue LYS 281 is missing expected H atoms. Skipping. Residue LYS 2 is missing expected H atoms. Skipping. Residue MET 4 is missing expected H atoms. Skipping. Residue LEU 14 is missing expected H atoms. Skipping. Residue VAL 19 is missing expected H atoms. Skipping. Residue LEU 24 is missing expected H atoms. Skipping. Residue TYR 25 is missing expected H atoms. Skipping. Residue LEU 27 is missing expected H atoms. Skipping. Residue ILE 29 is missing expected H atoms. Skipping. Residue LYS 38 is missing expected H atoms. Skipping. Residue ILE 41 is missing expected H atoms. Skipping. Residue TYR 42 is missing expected H atoms. Skipping. Residue LYS 43 is missing expected H atoms. Skipping. Residue LYS 45 is missing expected H atoms. Skipping. Residue LEU 70 is missing expected H atoms. Skipping. Residue TYR 77 is missing expected H atoms. Skipping. Residue TYR 82 is missing expected H atoms. Skipping. Residue ILE 90 is missing expected H atoms. Skipping. Residue LYS 91 is missing expected H atoms. Skipping. Residue LEU 94 is missing expected H atoms. Skipping. Residue ILE 104 is missing expected H atoms. Skipping. Residue LYS 112 is missing expected H atoms. Skipping. Residue VAL 128 is missing expected H atoms. Skipping. Residue MET 130 is missing expected H atoms. Skipping. Residue ILE 143 is missing expected H atoms. Skipping. Residue LYS 152 is missing expected H atoms. Skipping. Residue LEU 158 is missing expected H atoms. Skipping. Residue LEU 160 is missing expected H atoms. Skipping. Residue MET 164 is missing expected H atoms. Skipping. Residue LEU 166 is missing expected H atoms. Skipping. Residue LYS 175 is missing expected H atoms. Skipping. Residue LYS 189 is missing expected H atoms. Skipping. Residue ILE 194 is missing expected H atoms. Skipping. Residue LYS 195 is missing expected H atoms. Skipping. Residue ILE 214 is missing expected H atoms. Skipping. Residue VAL 215 is missing expected H atoms. Skipping. Residue TYR 221 is missing expected H atoms. Skipping. Residue ILE 229 is missing expected H atoms. Skipping. Residue LEU 230 is missing expected H atoms. Skipping. Residue LYS 255 is missing expected H atoms. Skipping. Residue LYS 257 is missing expected H atoms. Skipping. Residue LEU 258 is missing expected H atoms. Skipping. Residue TYR 259 is missing expected H atoms. Skipping. Residue LEU 265 is missing expected H atoms. Skipping. Residue LEU 285 is missing expected H atoms. Skipping. Residue SER 290 is missing expected H atoms. Skipping. Residue ILE 291 is missing expected H atoms. Skipping. Residue THR 296 is missing expected H atoms. Skipping. Residue THR 310 is missing expected H atoms. Skipping. Residue LEU 324 is missing expected H atoms. Skipping. Residue LEU 336 is missing expected H atoms. Skipping. Residue LEU 339 is missing expected H atoms. Skipping. Residue MET 350 is missing expected H atoms. Skipping. Residue LEU 363 is missing expected H atoms. Skipping. Residue VAL 367 is missing expected H atoms. Skipping. Residue ILE 376 is missing expected H atoms. Skipping. Residue LEU 384 is missing expected H atoms. Skipping. Residue MET 387 is missing expected H atoms. Skipping. Residue VAL 403 is missing expected H atoms. Skipping. Residue THR 410 is missing expected H atoms. Skipping. Residue VAL 413 is missing expected H atoms. Skipping. Residue SER 420 is missing expected H atoms. Skipping. Residue ILE 423 is missing expected H atoms. Skipping. Residue LEU 426 is missing expected H atoms. Skipping. Residue ILE 427 is missing expected H atoms. Skipping. Residue LYS 433 is missing expected H atoms. Skipping. Residue VAL 439 is missing expected H atoms. Skipping. Residue ILE 447 is missing expected H atoms. Skipping. Residue LYS 455 is missing expected H atoms. Skipping. Residue THR 481 is missing expected H atoms. Skipping. Residue TYR 484 is missing expected H atoms. Skipping. Residue VAL 486 is missing expected H atoms. Skipping. Residue LEU 487 is missing expected H atoms. Skipping. Residue MET 501 is missing expected H atoms. Skipping. Residue LEU 5 is missing expected H atoms. Skipping. Residue LEU 24 is missing expected H atoms. Skipping. Residue TYR 25 is missing expected H atoms. Skipping. Residue LEU 27 is missing expected H atoms. Skipping. Residue LYS 37 is missing expected H atoms. Skipping. Residue LYS 38 is missing expected H atoms. Skipping. Residue ILE 41 is missing expected H atoms. Skipping. Residue TYR 42 is missing expected H atoms. Skipping. Residue LYS 43 is missing expected H atoms. Skipping. Residue VAL 58 is missing expected H atoms. Skipping. Residue LYS 175 is missing expected H atoms. Skipping. Residue LYS 189 is missing expected H atoms. Skipping. Residue ILE 214 is missing expected H atoms. Skipping. Residue VAL 215 is missing expected H atoms. Skipping. Residue TYR 221 is missing expected H atoms. Skipping. Residue LEU 230 is missing expected H atoms. Skipping. Residue LYS 235 is missing expected H atoms. Skipping. Residue LEU 258 is missing expected H atoms. Skipping. Residue ILE 263 is missing expected H atoms. Skipping. Residue TYR 269 is missing expected H atoms. Skipping. Residue ILE 291 is missing expected H atoms. Skipping. Residue ILE 293 is missing expected H atoms. Skipping. Residue SER 295 is missing expected H atoms. Skipping. Residue THR 296 is missing expected H atoms. Skipping. Residue LEU 299 is missing expected H atoms. Skipping. Residue ILE 302 is missing expected H atoms. Skipping. Residue THR 310 is missing expected H atoms. Skipping. Residue ILE 330 is missing expected H atoms. Skipping. Residue LEU 334 is missing expected H atoms. Skipping. Residue LEU 339 is missing expected H atoms. Skipping. Residue ILE 343 is missing expected H atoms. Skipping. Residue ILE 345 is missing expected H atoms. Skipping. Residue ILE 348 is missing expected H atoms. Skipping. Residue MET 350 is missing expected H atoms. Skipping. Residue VAL 353 is missing expected H atoms. Skipping. Residue SER 380 is missing expected H atoms. Skipping. Residue MET 387 is missing expected H atoms. Skipping. Residue THR 412 is missing expected H atoms. Skipping. Residue VAL 413 is missing expected H atoms. Skipping. Residue SER 418 is missing expected H atoms. Skipping. Residue LEU 421 is missing expected H atoms. Skipping. Residue LYS 433 is missing expected H atoms. Skipping. Residue VAL 439 is missing expected H atoms. Skipping. Residue ILE 442 is missing expected H atoms. Skipping. Residue VAL 445 is missing expected H atoms. Skipping. Residue TYR 450 is missing expected H atoms. Skipping. Residue LEU 451 is missing expected H atoms. Skipping. Residue LYS 455 is missing expected H atoms. Skipping. Residue ILE 462 is missing expected H atoms. Skipping. Residue ILE 473 is missing expected H atoms. Skipping. Residue VAL 474 is missing expected H atoms. Skipping. Residue MET 479 is missing expected H atoms. Skipping. Residue MET 501 is missing expected H atoms. Skipping. Residue LEU 502 is missing expected H atoms. Skipping. Evaluate side-chains 356 residues out of total 1691 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 327 time to evaluate : 2.287 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 29 outliers final: 20 residues processed: 338 average time/residue: 0.5652 time to fit residues: 276.6035 Evaluate side-chains 338 residues out of total 1691 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 318 time to evaluate : 2.171 Switching outliers to nearest non-outliers revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 20 outliers final: 3 residues processed: 20 average time/residue: 0.3448 time to fit residues: 14.3813 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 206 random chunks: chunk 122 optimal weight: 4.9990 chunk 79 optimal weight: 2.9990 chunk 118 optimal weight: 4.9990 chunk 59 optimal weight: 5.9990 chunk 39 optimal weight: 0.9990 chunk 38 optimal weight: 6.9990 chunk 126 optimal weight: 0.9990 chunk 135 optimal weight: 10.0000 chunk 98 optimal weight: 0.0470 chunk 18 optimal weight: 3.9990 chunk 156 optimal weight: 30.0000 overall best weight: 1.8086 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 221 GLN ** C 69 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 81 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7325 moved from start: 0.6285 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 16776 Z= 0.173 Angle : 0.562 8.007 23691 Z= 0.289 Chirality : 0.039 0.212 3041 Planarity : 0.004 0.055 2530 Dihedral : 20.185 176.174 3905 Min Nonbonded Distance : 1.952 Molprobity Statistics. All-atom Clashscore : 15.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.60 % Favored : 94.40 % Rotamer: Outliers : 1.06 % Allowed : 28.12 % Favored : 70.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.59 (0.20), residues: 1893 helix: 0.68 (0.19), residues: 796 sheet: -1.62 (0.29), residues: 318 loop : -0.85 (0.23), residues: 779 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3786 Ramachandran restraints generated. 1893 Oldfield, 0 Emsley, 1893 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3786 Ramachandran restraints generated. 1893 Oldfield, 0 Emsley, 1893 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue MET 1 is missing expected H atoms. Skipping. Residue MET 4 is missing expected H atoms. Skipping. Residue LYS 14 is missing expected H atoms. Skipping. Residue MET 24 is missing expected H atoms. Skipping. Residue TYR 27 is missing expected H atoms. Skipping. Residue VAL 29 is missing expected H atoms. Skipping. Residue VAL 34 is missing expected H atoms. Skipping. Residue MET 60 is missing expected H atoms. Skipping. Residue ILE 66 is missing expected H atoms. Skipping. Residue MET 71 is missing expected H atoms. Skipping. Residue LEU 82 is missing expected H atoms. Skipping. Residue LEU 83 is missing expected H atoms. Skipping. Residue TYR 96 is missing expected H atoms. Skipping. Residue ILE 116 is missing expected H atoms. Skipping. Residue LYS 118 is missing expected H atoms. Skipping. Residue MET 139 is missing expected H atoms. Skipping. Residue MET 147 is missing expected H atoms. Skipping. Residue LYS 155 is missing expected H atoms. Skipping. Residue MET 198 is missing expected H atoms. Skipping. Residue ILE 219 is missing expected H atoms. Skipping. Residue TYR 264 is missing expected H atoms. Skipping. Residue LEU 3 is missing expected H atoms. Skipping. Residue MET 4 is missing expected H atoms. Skipping. Residue VAL 6 is missing expected H atoms. Skipping. Residue SER 12 is missing expected H atoms. Skipping. Residue LYS 14 is missing expected H atoms. Skipping. Residue LEU 21 is missing expected H atoms. Skipping. Residue MET 24 is missing expected H atoms. Skipping. Residue TYR 27 is missing expected H atoms. Skipping. Residue VAL 34 is missing expected H atoms. Skipping. Residue LEU 36 is missing expected H atoms. Skipping. Residue LEU 37 is missing expected H atoms. Skipping. Residue THR 43 is missing expected H atoms. Skipping. Residue LEU 44 is missing expected H atoms. Skipping. Residue MET 60 is missing expected H atoms. Skipping. Residue MET 71 is missing expected H atoms. Skipping. Residue LEU 82 is missing expected H atoms. Skipping. Residue LEU 83 is missing expected H atoms. Skipping. Residue THR 99 is missing expected H atoms. Skipping. Residue LEU 102 is missing expected H atoms. Skipping. Residue LEU 105 is missing expected H atoms. Skipping. Residue LYS 108 is missing expected H atoms. Skipping. Residue LEU 110 is missing expected H atoms. Skipping. Residue LEU 112 is missing expected H atoms. Skipping. Residue LYS 118 is missing expected H atoms. Skipping. Residue SER 120 is missing expected H atoms. Skipping. Residue MET 139 is missing expected H atoms. Skipping. Residue VAL 141 is missing expected H atoms. Skipping. Residue MET 147 is missing expected H atoms. Skipping. Residue LEU 152 is missing expected H atoms. Skipping. Residue MET 162 is missing expected H atoms. Skipping. Residue SER 166 is missing expected H atoms. Skipping. Residue LYS 194 is missing expected H atoms. Skipping. Residue MET 198 is missing expected H atoms. Skipping. Residue LYS 203 is missing expected H atoms. Skipping. Residue THR 213 is missing expected H atoms. Skipping. Residue MET 232 is missing expected H atoms. Skipping. Residue THR 248 is missing expected H atoms. Skipping. Residue SER 267 is missing expected H atoms. Skipping. Residue LYS 270 is missing expected H atoms. Skipping. Residue VAL 2 is missing expected H atoms. Skipping. Residue MET 4 is missing expected H atoms. Skipping. Residue SER 7 is missing expected H atoms. Skipping. Residue LYS 14 is missing expected H atoms. Skipping. Residue MET 24 is missing expected H atoms. Skipping. Residue LEU 32 is missing expected H atoms. Skipping. Residue THR 43 is missing expected H atoms. Skipping. Residue ILE 49 is missing expected H atoms. Skipping. Residue MET 71 is missing expected H atoms. Skipping. Residue LEU 74 is missing expected H atoms. Skipping. Residue THR 99 is missing expected H atoms. Skipping. Residue SER 111 is missing expected H atoms. Skipping. Residue SER 120 is missing expected H atoms. Skipping. Residue LEU 132 is missing expected H atoms. Skipping. Residue ILE 133 is missing expected H atoms. Skipping. Residue THR 136 is missing expected H atoms. Skipping. Residue MET 139 is missing expected H atoms. Skipping. Residue VAL 141 is missing expected H atoms. Skipping. Residue LEU 144 is missing expected H atoms. Skipping. Residue MET 147 is missing expected H atoms. Skipping. Residue THR 150 is missing expected H atoms. Skipping. Residue LEU 160 is missing expected H atoms. Skipping. Residue MET 162 is missing expected H atoms. Skipping. Residue LYS 170 is missing expected H atoms. Skipping. Residue VAL 183 is missing expected H atoms. Skipping. Residue LYS 194 is missing expected H atoms. Skipping. Residue LEU 195 is missing expected H atoms. Skipping. Residue THR 199 is missing expected H atoms. Skipping. Residue LEU 201 is missing expected H atoms. Skipping. Residue LYS 203 is missing expected H atoms. Skipping. Residue ILE 219 is missing expected H atoms. Skipping. Residue TYR 220 is missing expected H atoms. Skipping. Residue LEU 230 is missing expected H atoms. Skipping. Residue MET 232 is missing expected H atoms. Skipping. Residue LEU 233 is missing expected H atoms. Skipping. Residue THR 235 is missing expected H atoms. Skipping. Residue SER 239 is missing expected H atoms. Skipping. Residue TYR 240 is missing expected H atoms. Skipping. Residue LEU 241 is missing expected H atoms. Skipping. Residue ILE 245 is missing expected H atoms. Skipping. Residue THR 248 is missing expected H atoms. Skipping. Residue LYS 251 is missing expected H atoms. Skipping. Residue TYR 256 is missing expected H atoms. Skipping. Residue LYS 270 is missing expected H atoms. Skipping. Residue THR 278 is missing expected H atoms. Skipping. Residue MET 1 is missing expected H atoms. Skipping. Residue MET 4 is missing expected H atoms. Skipping. Residue SER 12 is missing expected H atoms. Skipping. Residue LYS 14 is missing expected H atoms. Skipping. Residue VAL 16 is missing expected H atoms. Skipping. Residue MET 24 is missing expected H atoms. Skipping. Residue TYR 27 is missing expected H atoms. Skipping. Residue VAL 34 is missing expected H atoms. Skipping. Residue LEU 44 is missing expected H atoms. Skipping. Residue MET 60 is missing expected H atoms. Skipping. Residue LEU 112 is missing expected H atoms. Skipping. Residue LYS 118 is missing expected H atoms. Skipping. Residue LEU 126 is missing expected H atoms. Skipping. Residue MET 139 is missing expected H atoms. Skipping. Residue VAL 141 is missing expected H atoms. Skipping. Residue LEU 144 is missing expected H atoms. Skipping. Residue MET 147 is missing expected H atoms. Skipping. Residue LEU 148 is missing expected H atoms. Skipping. Residue LYS 155 is missing expected H atoms. Skipping. Residue LEU 160 is missing expected H atoms. Skipping. Residue MET 162 is missing expected H atoms. Skipping. Residue SER 166 is missing expected H atoms. Skipping. Residue LYS 170 is missing expected H atoms. Skipping. Residue TYR 179 is missing expected H atoms. Skipping. Residue VAL 180 is missing expected H atoms. Skipping. Residue MET 198 is missing expected H atoms. Skipping. Residue LYS 203 is missing expected H atoms. Skipping. Residue THR 222 is missing expected H atoms. Skipping. Residue TYR 225 is missing expected H atoms. Skipping. Residue MET 232 is missing expected H atoms. Skipping. Residue TYR 240 is missing expected H atoms. Skipping. Residue LEU 241 is missing expected H atoms. Skipping. Residue THR 242 is missing expected H atoms. Skipping. Residue VAL 243 is missing expected H atoms. Skipping. Residue LYS 251 is missing expected H atoms. Skipping. Residue VAL 255 is missing expected H atoms. Skipping. Residue SER 267 is missing expected H atoms. Skipping. Residue LYS 270 is missing expected H atoms. Skipping. Residue LEU 279 is missing expected H atoms. Skipping. Residue LYS 281 is missing expected H atoms. Skipping. Residue LYS 2 is missing expected H atoms. Skipping. Residue MET 4 is missing expected H atoms. Skipping. Residue LEU 14 is missing expected H atoms. Skipping. Residue VAL 19 is missing expected H atoms. Skipping. Residue LEU 24 is missing expected H atoms. Skipping. Residue TYR 25 is missing expected H atoms. Skipping. Residue LEU 27 is missing expected H atoms. Skipping. Residue ILE 29 is missing expected H atoms. Skipping. Residue LYS 38 is missing expected H atoms. Skipping. Residue ILE 41 is missing expected H atoms. Skipping. Residue TYR 42 is missing expected H atoms. Skipping. Residue LYS 43 is missing expected H atoms. Skipping. Residue LYS 45 is missing expected H atoms. Skipping. Residue LEU 70 is missing expected H atoms. Skipping. Residue TYR 77 is missing expected H atoms. Skipping. Residue TYR 82 is missing expected H atoms. Skipping. Residue ILE 90 is missing expected H atoms. Skipping. Residue LYS 91 is missing expected H atoms. Skipping. Residue LEU 94 is missing expected H atoms. Skipping. Residue ILE 104 is missing expected H atoms. Skipping. Residue LYS 112 is missing expected H atoms. Skipping. Residue VAL 128 is missing expected H atoms. Skipping. Residue MET 130 is missing expected H atoms. Skipping. Residue ILE 143 is missing expected H atoms. Skipping. Residue LYS 152 is missing expected H atoms. Skipping. Residue LEU 158 is missing expected H atoms. Skipping. Residue LEU 160 is missing expected H atoms. Skipping. Residue MET 164 is missing expected H atoms. Skipping. Residue LEU 166 is missing expected H atoms. Skipping. Residue LYS 175 is missing expected H atoms. Skipping. Residue LYS 189 is missing expected H atoms. Skipping. Residue ILE 194 is missing expected H atoms. Skipping. Residue LYS 195 is missing expected H atoms. Skipping. Residue ILE 214 is missing expected H atoms. Skipping. Residue VAL 215 is missing expected H atoms. Skipping. Residue TYR 221 is missing expected H atoms. Skipping. Residue ILE 229 is missing expected H atoms. Skipping. Residue LEU 230 is missing expected H atoms. Skipping. Residue LYS 255 is missing expected H atoms. Skipping. Residue LYS 257 is missing expected H atoms. Skipping. Residue LEU 258 is missing expected H atoms. Skipping. Residue TYR 259 is missing expected H atoms. Skipping. Residue LEU 265 is missing expected H atoms. Skipping. Residue LEU 285 is missing expected H atoms. Skipping. Residue SER 290 is missing expected H atoms. Skipping. Residue ILE 291 is missing expected H atoms. Skipping. Residue THR 296 is missing expected H atoms. Skipping. Residue THR 310 is missing expected H atoms. Skipping. Residue LEU 324 is missing expected H atoms. Skipping. Residue LEU 336 is missing expected H atoms. Skipping. Residue LEU 339 is missing expected H atoms. Skipping. Residue MET 350 is missing expected H atoms. Skipping. Residue LEU 363 is missing expected H atoms. Skipping. Residue VAL 367 is missing expected H atoms. Skipping. Residue ILE 376 is missing expected H atoms. Skipping. Residue LEU 384 is missing expected H atoms. Skipping. Residue MET 387 is missing expected H atoms. Skipping. Residue VAL 403 is missing expected H atoms. Skipping. Residue THR 410 is missing expected H atoms. Skipping. Residue VAL 413 is missing expected H atoms. Skipping. Residue SER 420 is missing expected H atoms. Skipping. Residue ILE 423 is missing expected H atoms. Skipping. Residue LEU 426 is missing expected H atoms. Skipping. Residue ILE 427 is missing expected H atoms. Skipping. Residue LYS 433 is missing expected H atoms. Skipping. Residue VAL 439 is missing expected H atoms. Skipping. Residue ILE 447 is missing expected H atoms. Skipping. Residue LYS 455 is missing expected H atoms. Skipping. Residue THR 481 is missing expected H atoms. Skipping. Residue TYR 484 is missing expected H atoms. Skipping. Residue VAL 486 is missing expected H atoms. Skipping. Residue LEU 487 is missing expected H atoms. Skipping. Residue MET 501 is missing expected H atoms. Skipping. Residue LEU 5 is missing expected H atoms. Skipping. Residue LEU 24 is missing expected H atoms. Skipping. Residue TYR 25 is missing expected H atoms. Skipping. Residue LEU 27 is missing expected H atoms. Skipping. Residue LYS 37 is missing expected H atoms. Skipping. Residue LYS 38 is missing expected H atoms. Skipping. Residue ILE 41 is missing expected H atoms. Skipping. Residue TYR 42 is missing expected H atoms. Skipping. Residue LYS 43 is missing expected H atoms. Skipping. Residue VAL 58 is missing expected H atoms. Skipping. Residue LYS 175 is missing expected H atoms. Skipping. Residue LYS 189 is missing expected H atoms. Skipping. Residue ILE 214 is missing expected H atoms. Skipping. Residue VAL 215 is missing expected H atoms. Skipping. Residue TYR 221 is missing expected H atoms. Skipping. Residue LEU 230 is missing expected H atoms. Skipping. Residue LYS 235 is missing expected H atoms. Skipping. Residue LEU 258 is missing expected H atoms. Skipping. Residue ILE 263 is missing expected H atoms. Skipping. Residue TYR 269 is missing expected H atoms. Skipping. Residue ILE 291 is missing expected H atoms. Skipping. Residue ILE 293 is missing expected H atoms. Skipping. Residue SER 295 is missing expected H atoms. Skipping. Residue THR 296 is missing expected H atoms. Skipping. Residue LEU 299 is missing expected H atoms. Skipping. Residue ILE 302 is missing expected H atoms. Skipping. Residue THR 310 is missing expected H atoms. Skipping. Residue ILE 330 is missing expected H atoms. Skipping. Residue LEU 334 is missing expected H atoms. Skipping. Residue LEU 339 is missing expected H atoms. Skipping. Residue ILE 343 is missing expected H atoms. Skipping. Residue ILE 345 is missing expected H atoms. Skipping. Residue ILE 348 is missing expected H atoms. Skipping. Residue MET 350 is missing expected H atoms. Skipping. Residue VAL 353 is missing expected H atoms. Skipping. Residue SER 380 is missing expected H atoms. Skipping. Residue MET 387 is missing expected H atoms. Skipping. Residue THR 412 is missing expected H atoms. Skipping. Residue VAL 413 is missing expected H atoms. Skipping. Residue SER 418 is missing expected H atoms. Skipping. Residue LEU 421 is missing expected H atoms. Skipping. Residue LYS 433 is missing expected H atoms. Skipping. Residue VAL 439 is missing expected H atoms. Skipping. Residue ILE 442 is missing expected H atoms. Skipping. Residue VAL 445 is missing expected H atoms. Skipping. Residue TYR 450 is missing expected H atoms. Skipping. Residue LEU 451 is missing expected H atoms. Skipping. Residue LYS 455 is missing expected H atoms. Skipping. Residue ILE 462 is missing expected H atoms. Skipping. Residue ILE 473 is missing expected H atoms. Skipping. Residue VAL 474 is missing expected H atoms. Skipping. Residue MET 479 is missing expected H atoms. Skipping. Residue MET 501 is missing expected H atoms. Skipping. Residue LEU 502 is missing expected H atoms. Skipping. Evaluate side-chains 348 residues out of total 1691 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 337 time to evaluate : 2.056 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 revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash 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: 11 outliers final: 9 residues processed: 340 average time/residue: 0.5581 time to fit residues: 278.1187 Evaluate side-chains 333 residues out of total 1691 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 324 time to evaluate : 2.113 Switching outliers to nearest non-outliers revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 9 outliers final: 3 residues processed: 9 average time/residue: 0.4083 time to fit residues: 8.5607 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 206 random chunks: chunk 180 optimal weight: 10.0000 chunk 190 optimal weight: 9.9990 chunk 173 optimal weight: 0.6980 chunk 185 optimal weight: 0.8980 chunk 111 optimal weight: 8.9990 chunk 80 optimal weight: 5.9990 chunk 145 optimal weight: 20.0000 chunk 56 optimal weight: 0.1980 chunk 167 optimal weight: 0.1980 chunk 174 optimal weight: 1.9990 chunk 184 optimal weight: 5.9990 overall best weight: 0.7982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 69 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 69 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 81 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7274 moved from start: 0.6451 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.031 16776 Z= 0.146 Angle : 0.546 8.247 23691 Z= 0.278 Chirality : 0.039 0.192 3041 Planarity : 0.004 0.049 2530 Dihedral : 19.862 176.854 3905 Min Nonbonded Distance : 1.965 Molprobity Statistics. All-atom Clashscore : 13.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.07 % Favored : 94.93 % Rotamer: Outliers : 0.29 % Allowed : 30.05 % Favored : 69.66 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.10 (0.20), residues: 1893 helix: 1.09 (0.19), residues: 797 sheet: -1.37 (0.29), residues: 333 loop : -0.55 (0.24), residues: 763 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3786 Ramachandran restraints generated. 1893 Oldfield, 0 Emsley, 1893 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3786 Ramachandran restraints generated. 1893 Oldfield, 0 Emsley, 1893 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue MET 1 is missing expected H atoms. Skipping. Residue MET 4 is missing expected H atoms. Skipping. Residue LYS 14 is missing expected H atoms. Skipping. Residue MET 24 is missing expected H atoms. Skipping. Residue TYR 27 is missing expected H atoms. Skipping. Residue VAL 29 is missing expected H atoms. Skipping. Residue VAL 34 is missing expected H atoms. Skipping. Residue MET 60 is missing expected H atoms. Skipping. Residue ILE 66 is missing expected H atoms. Skipping. Residue MET 71 is missing expected H atoms. Skipping. Residue LEU 82 is missing expected H atoms. Skipping. Residue LEU 83 is missing expected H atoms. Skipping. Residue TYR 96 is missing expected H atoms. Skipping. Residue ILE 116 is missing expected H atoms. Skipping. Residue LYS 118 is missing expected H atoms. Skipping. Residue MET 139 is missing expected H atoms. Skipping. Residue MET 147 is missing expected H atoms. Skipping. Residue LYS 155 is missing expected H atoms. Skipping. Residue MET 198 is missing expected H atoms. Skipping. Residue ILE 219 is missing expected H atoms. Skipping. Residue TYR 264 is missing expected H atoms. Skipping. Residue LEU 3 is missing expected H atoms. Skipping. Residue MET 4 is missing expected H atoms. Skipping. Residue VAL 6 is missing expected H atoms. Skipping. Residue SER 12 is missing expected H atoms. Skipping. Residue LYS 14 is missing expected H atoms. Skipping. Residue LEU 21 is missing expected H atoms. Skipping. Residue MET 24 is missing expected H atoms. Skipping. Residue TYR 27 is missing expected H atoms. Skipping. Residue VAL 34 is missing expected H atoms. Skipping. Residue LEU 36 is missing expected H atoms. Skipping. Residue LEU 37 is missing expected H atoms. Skipping. Residue THR 43 is missing expected H atoms. Skipping. Residue LEU 44 is missing expected H atoms. Skipping. Residue MET 60 is missing expected H atoms. Skipping. Residue MET 71 is missing expected H atoms. Skipping. Residue LEU 82 is missing expected H atoms. Skipping. Residue LEU 83 is missing expected H atoms. Skipping. Residue THR 99 is missing expected H atoms. Skipping. Residue LEU 102 is missing expected H atoms. Skipping. Residue LEU 105 is missing expected H atoms. Skipping. Residue LYS 108 is missing expected H atoms. Skipping. Residue LEU 110 is missing expected H atoms. Skipping. Residue LEU 112 is missing expected H atoms. Skipping. Residue LYS 118 is missing expected H atoms. Skipping. Residue SER 120 is missing expected H atoms. Skipping. Residue MET 139 is missing expected H atoms. Skipping. Residue VAL 141 is missing expected H atoms. Skipping. Residue MET 147 is missing expected H atoms. Skipping. Residue LEU 152 is missing expected H atoms. Skipping. Residue MET 162 is missing expected H atoms. Skipping. Residue SER 166 is missing expected H atoms. Skipping. Residue LYS 194 is missing expected H atoms. Skipping. Residue MET 198 is missing expected H atoms. Skipping. Residue LYS 203 is missing expected H atoms. Skipping. Residue THR 213 is missing expected H atoms. Skipping. Residue MET 232 is missing expected H atoms. Skipping. Residue THR 248 is missing expected H atoms. Skipping. Residue SER 267 is missing expected H atoms. Skipping. Residue LYS 270 is missing expected H atoms. Skipping. Residue VAL 2 is missing expected H atoms. Skipping. Residue MET 4 is missing expected H atoms. Skipping. Residue SER 7 is missing expected H atoms. Skipping. Residue LYS 14 is missing expected H atoms. Skipping. Residue MET 24 is missing expected H atoms. Skipping. Residue LEU 32 is missing expected H atoms. Skipping. Residue THR 43 is missing expected H atoms. Skipping. Residue ILE 49 is missing expected H atoms. Skipping. Residue MET 71 is missing expected H atoms. Skipping. Residue LEU 74 is missing expected H atoms. Skipping. Residue THR 99 is missing expected H atoms. Skipping. Residue SER 111 is missing expected H atoms. Skipping. Residue SER 120 is missing expected H atoms. Skipping. Residue LEU 132 is missing expected H atoms. Skipping. Residue ILE 133 is missing expected H atoms. Skipping. Residue THR 136 is missing expected H atoms. Skipping. Residue MET 139 is missing expected H atoms. Skipping. Residue VAL 141 is missing expected H atoms. Skipping. Residue LEU 144 is missing expected H atoms. Skipping. Residue MET 147 is missing expected H atoms. Skipping. Residue THR 150 is missing expected H atoms. Skipping. Residue LEU 160 is missing expected H atoms. Skipping. Residue MET 162 is missing expected H atoms. Skipping. Residue LYS 170 is missing expected H atoms. Skipping. Residue VAL 183 is missing expected H atoms. Skipping. Residue LYS 194 is missing expected H atoms. Skipping. Residue LEU 195 is missing expected H atoms. Skipping. Residue THR 199 is missing expected H atoms. Skipping. Residue LEU 201 is missing expected H atoms. Skipping. Residue LYS 203 is missing expected H atoms. Skipping. Residue ILE 219 is missing expected H atoms. Skipping. Residue TYR 220 is missing expected H atoms. Skipping. Residue LEU 230 is missing expected H atoms. Skipping. Residue MET 232 is missing expected H atoms. Skipping. Residue LEU 233 is missing expected H atoms. Skipping. Residue THR 235 is missing expected H atoms. Skipping. Residue SER 239 is missing expected H atoms. Skipping. Residue TYR 240 is missing expected H atoms. Skipping. Residue LEU 241 is missing expected H atoms. Skipping. Residue ILE 245 is missing expected H atoms. Skipping. Residue THR 248 is missing expected H atoms. Skipping. Residue LYS 251 is missing expected H atoms. Skipping. Residue TYR 256 is missing expected H atoms. Skipping. Residue LYS 270 is missing expected H atoms. Skipping. Residue THR 278 is missing expected H atoms. Skipping. Residue MET 1 is missing expected H atoms. Skipping. Residue MET 4 is missing expected H atoms. Skipping. Residue SER 12 is missing expected H atoms. Skipping. Residue LYS 14 is missing expected H atoms. Skipping. Residue VAL 16 is missing expected H atoms. Skipping. Residue MET 24 is missing expected H atoms. Skipping. Residue TYR 27 is missing expected H atoms. Skipping. Residue VAL 34 is missing expected H atoms. Skipping. Residue LEU 44 is missing expected H atoms. Skipping. Residue MET 60 is missing expected H atoms. Skipping. Residue LEU 112 is missing expected H atoms. Skipping. Residue LYS 118 is missing expected H atoms. Skipping. Residue LEU 126 is missing expected H atoms. Skipping. Residue MET 139 is missing expected H atoms. Skipping. Residue VAL 141 is missing expected H atoms. Skipping. Residue LEU 144 is missing expected H atoms. Skipping. Residue MET 147 is missing expected H atoms. Skipping. Residue LEU 148 is missing expected H atoms. Skipping. Residue LYS 155 is missing expected H atoms. Skipping. Residue LEU 160 is missing expected H atoms. Skipping. Residue MET 162 is missing expected H atoms. Skipping. Residue SER 166 is missing expected H atoms. Skipping. Residue LYS 170 is missing expected H atoms. Skipping. Residue TYR 179 is missing expected H atoms. Skipping. Residue VAL 180 is missing expected H atoms. Skipping. Residue MET 198 is missing expected H atoms. Skipping. Residue LYS 203 is missing expected H atoms. Skipping. Residue THR 222 is missing expected H atoms. Skipping. Residue TYR 225 is missing expected H atoms. Skipping. Residue MET 232 is missing expected H atoms. Skipping. Residue TYR 240 is missing expected H atoms. Skipping. Residue LEU 241 is missing expected H atoms. Skipping. Residue THR 242 is missing expected H atoms. Skipping. Residue VAL 243 is missing expected H atoms. Skipping. Residue LYS 251 is missing expected H atoms. Skipping. Residue VAL 255 is missing expected H atoms. Skipping. Residue SER 267 is missing expected H atoms. Skipping. Residue LYS 270 is missing expected H atoms. Skipping. Residue LEU 279 is missing expected H atoms. Skipping. Residue LYS 281 is missing expected H atoms. Skipping. Residue LYS 2 is missing expected H atoms. Skipping. Residue MET 4 is missing expected H atoms. Skipping. Residue LEU 14 is missing expected H atoms. Skipping. Residue VAL 19 is missing expected H atoms. Skipping. Residue LEU 24 is missing expected H atoms. Skipping. Residue TYR 25 is missing expected H atoms. Skipping. Residue LEU 27 is missing expected H atoms. Skipping. Residue ILE 29 is missing expected H atoms. Skipping. Residue LYS 38 is missing expected H atoms. Skipping. Residue ILE 41 is missing expected H atoms. Skipping. Residue TYR 42 is missing expected H atoms. Skipping. Residue LYS 43 is missing expected H atoms. Skipping. Residue LYS 45 is missing expected H atoms. Skipping. Residue LEU 70 is missing expected H atoms. Skipping. Residue TYR 77 is missing expected H atoms. Skipping. Residue TYR 82 is missing expected H atoms. Skipping. Residue ILE 90 is missing expected H atoms. Skipping. Residue LYS 91 is missing expected H atoms. Skipping. Residue LEU 94 is missing expected H atoms. Skipping. Residue ILE 104 is missing expected H atoms. Skipping. Residue LYS 112 is missing expected H atoms. Skipping. Residue VAL 128 is missing expected H atoms. Skipping. Residue MET 130 is missing expected H atoms. Skipping. Residue ILE 143 is missing expected H atoms. Skipping. Residue LYS 152 is missing expected H atoms. Skipping. Residue LEU 158 is missing expected H atoms. Skipping. Residue LEU 160 is missing expected H atoms. Skipping. Residue MET 164 is missing expected H atoms. Skipping. Residue LEU 166 is missing expected H atoms. Skipping. Residue LYS 175 is missing expected H atoms. Skipping. Residue LYS 189 is missing expected H atoms. Skipping. Residue ILE 194 is missing expected H atoms. Skipping. Residue LYS 195 is missing expected H atoms. Skipping. Residue ILE 214 is missing expected H atoms. Skipping. Residue VAL 215 is missing expected H atoms. Skipping. Residue TYR 221 is missing expected H atoms. Skipping. Residue ILE 229 is missing expected H atoms. Skipping. Residue LEU 230 is missing expected H atoms. Skipping. Residue LYS 255 is missing expected H atoms. Skipping. Residue LYS 257 is missing expected H atoms. Skipping. Residue LEU 258 is missing expected H atoms. Skipping. Residue TYR 259 is missing expected H atoms. Skipping. Residue LEU 265 is missing expected H atoms. Skipping. Residue LEU 285 is missing expected H atoms. Skipping. Residue SER 290 is missing expected H atoms. Skipping. Residue ILE 291 is missing expected H atoms. Skipping. Residue THR 296 is missing expected H atoms. Skipping. Residue THR 310 is missing expected H atoms. Skipping. Residue LEU 324 is missing expected H atoms. Skipping. Residue LEU 336 is missing expected H atoms. Skipping. Residue LEU 339 is missing expected H atoms. Skipping. Residue MET 350 is missing expected H atoms. Skipping. Residue LEU 363 is missing expected H atoms. Skipping. Residue VAL 367 is missing expected H atoms. Skipping. Residue ILE 376 is missing expected H atoms. Skipping. Residue LEU 384 is missing expected H atoms. Skipping. Residue MET 387 is missing expected H atoms. Skipping. Residue VAL 403 is missing expected H atoms. Skipping. Residue THR 410 is missing expected H atoms. Skipping. Residue VAL 413 is missing expected H atoms. Skipping. Residue SER 420 is missing expected H atoms. Skipping. Residue ILE 423 is missing expected H atoms. Skipping. Residue LEU 426 is missing expected H atoms. Skipping. Residue ILE 427 is missing expected H atoms. Skipping. Residue LYS 433 is missing expected H atoms. Skipping. Residue VAL 439 is missing expected H atoms. Skipping. Residue ILE 447 is missing expected H atoms. Skipping. Residue LYS 455 is missing expected H atoms. Skipping. Residue THR 481 is missing expected H atoms. Skipping. Residue TYR 484 is missing expected H atoms. Skipping. Residue VAL 486 is missing expected H atoms. Skipping. Residue LEU 487 is missing expected H atoms. Skipping. Residue MET 501 is missing expected H atoms. Skipping. Residue LEU 5 is missing expected H atoms. Skipping. Residue LEU 24 is missing expected H atoms. Skipping. Residue TYR 25 is missing expected H atoms. Skipping. Residue LEU 27 is missing expected H atoms. Skipping. Residue LYS 37 is missing expected H atoms. Skipping. Residue LYS 38 is missing expected H atoms. Skipping. Residue ILE 41 is missing expected H atoms. Skipping. Residue TYR 42 is missing expected H atoms. Skipping. Residue LYS 43 is missing expected H atoms. Skipping. Residue VAL 58 is missing expected H atoms. Skipping. Residue LYS 175 is missing expected H atoms. Skipping. Residue LYS 189 is missing expected H atoms. Skipping. Residue ILE 214 is missing expected H atoms. Skipping. Residue VAL 215 is missing expected H atoms. Skipping. Residue TYR 221 is missing expected H atoms. Skipping. Residue LEU 230 is missing expected H atoms. Skipping. Residue LYS 235 is missing expected H atoms. Skipping. Residue LEU 258 is missing expected H atoms. Skipping. Residue ILE 263 is missing expected H atoms. Skipping. Residue TYR 269 is missing expected H atoms. Skipping. Residue ILE 291 is missing expected H atoms. Skipping. Residue ILE 293 is missing expected H atoms. Skipping. Residue SER 295 is missing expected H atoms. Skipping. Residue THR 296 is missing expected H atoms. Skipping. Residue LEU 299 is missing expected H atoms. Skipping. Residue ILE 302 is missing expected H atoms. Skipping. Residue THR 310 is missing expected H atoms. Skipping. Residue ILE 330 is missing expected H atoms. Skipping. Residue LEU 334 is missing expected H atoms. Skipping. Residue LEU 339 is missing expected H atoms. Skipping. Residue ILE 343 is missing expected H atoms. Skipping. Residue ILE 345 is missing expected H atoms. Skipping. Residue ILE 348 is missing expected H atoms. Skipping. Residue MET 350 is missing expected H atoms. Skipping. Residue VAL 353 is missing expected H atoms. Skipping. Residue SER 380 is missing expected H atoms. Skipping. Residue MET 387 is missing expected H atoms. Skipping. Residue THR 412 is missing expected H atoms. Skipping. Residue VAL 413 is missing expected H atoms. Skipping. Residue SER 418 is missing expected H atoms. Skipping. Residue LEU 421 is missing expected H atoms. Skipping. Residue LYS 433 is missing expected H atoms. Skipping. Residue VAL 439 is missing expected H atoms. Skipping. Residue ILE 442 is missing expected H atoms. Skipping. Residue VAL 445 is missing expected H atoms. Skipping. Residue TYR 450 is missing expected H atoms. Skipping. Residue LEU 451 is missing expected H atoms. Skipping. Residue LYS 455 is missing expected H atoms. Skipping. Residue ILE 462 is missing expected H atoms. Skipping. Residue ILE 473 is missing expected H atoms. Skipping. Residue VAL 474 is missing expected H atoms. Skipping. Residue MET 479 is missing expected H atoms. Skipping. Residue MET 501 is missing expected H atoms. Skipping. Residue LEU 502 is missing expected H atoms. Skipping. Evaluate side-chains 350 residues out of total 1691 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 347 time to evaluate : 2.176 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 3 outliers final: 3 residues processed: 348 average time/residue: 0.5551 time to fit residues: 284.6104 Evaluate side-chains 339 residues out of total 1691 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 336 time to evaluate : 2.083 Switching outliers to nearest non-outliers revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 3 outliers final: 3 residues processed: 3 average time/residue: 0.3382 time to fit residues: 4.2517 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 206 random chunks: chunk 121 optimal weight: 6.9990 chunk 195 optimal weight: 10.0000 chunk 119 optimal weight: 6.9990 chunk 92 optimal weight: 0.1980 chunk 136 optimal weight: 5.9990 chunk 205 optimal weight: 10.0000 chunk 188 optimal weight: 4.9990 chunk 163 optimal weight: 20.0000 chunk 16 optimal weight: 2.9990 chunk 126 optimal weight: 1.9990 chunk 100 optimal weight: 0.7980 overall best weight: 2.1986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 69 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 69 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 81 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 243 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7321 moved from start: 0.6625 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 16776 Z= 0.199 Angle : 0.565 7.574 23691 Z= 0.293 Chirality : 0.038 0.191 3041 Planarity : 0.004 0.068 2530 Dihedral : 19.919 175.523 3905 Min Nonbonded Distance : 1.936 Molprobity Statistics. All-atom Clashscore : 16.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.76 % Favored : 94.24 % Rotamer: Outliers : 0.97 % Allowed : 30.53 % Favored : 68.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.16 (0.20), residues: 1893 helix: 0.98 (0.19), residues: 799 sheet: -1.38 (0.29), residues: 318 loop : -0.56 (0.23), residues: 776 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3786 Ramachandran restraints generated. 1893 Oldfield, 0 Emsley, 1893 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3786 Ramachandran restraints generated. 1893 Oldfield, 0 Emsley, 1893 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue MET 1 is missing expected H atoms. Skipping. Residue MET 4 is missing expected H atoms. Skipping. Residue LYS 14 is missing expected H atoms. Skipping. Residue MET 24 is missing expected H atoms. Skipping. Residue TYR 27 is missing expected H atoms. Skipping. Residue VAL 29 is missing expected H atoms. Skipping. Residue VAL 34 is missing expected H atoms. Skipping. Residue MET 60 is missing expected H atoms. Skipping. Residue ILE 66 is missing expected H atoms. Skipping. Residue MET 71 is missing expected H atoms. Skipping. Residue LEU 82 is missing expected H atoms. Skipping. Residue LEU 83 is missing expected H atoms. Skipping. Residue TYR 96 is missing expected H atoms. Skipping. Residue ILE 116 is missing expected H atoms. Skipping. Residue LYS 118 is missing expected H atoms. Skipping. Residue MET 139 is missing expected H atoms. Skipping. Residue MET 147 is missing expected H atoms. Skipping. Residue LYS 155 is missing expected H atoms. Skipping. Residue MET 198 is missing expected H atoms. Skipping. Residue ILE 219 is missing expected H atoms. Skipping. Residue TYR 264 is missing expected H atoms. Skipping. Residue LEU 3 is missing expected H atoms. Skipping. Residue MET 4 is missing expected H atoms. Skipping. Residue VAL 6 is missing expected H atoms. Skipping. Residue SER 12 is missing expected H atoms. Skipping. Residue LYS 14 is missing expected H atoms. Skipping. Residue LEU 21 is missing expected H atoms. Skipping. Residue MET 24 is missing expected H atoms. Skipping. Residue TYR 27 is missing expected H atoms. Skipping. Residue VAL 34 is missing expected H atoms. Skipping. Residue LEU 36 is missing expected H atoms. Skipping. Residue LEU 37 is missing expected H atoms. Skipping. Residue THR 43 is missing expected H atoms. Skipping. Residue LEU 44 is missing expected H atoms. Skipping. Residue MET 60 is missing expected H atoms. Skipping. Residue MET 71 is missing expected H atoms. Skipping. Residue LEU 82 is missing expected H atoms. Skipping. Residue LEU 83 is missing expected H atoms. Skipping. Residue THR 99 is missing expected H atoms. Skipping. Residue LEU 102 is missing expected H atoms. Skipping. Residue LEU 105 is missing expected H atoms. Skipping. Residue LYS 108 is missing expected H atoms. Skipping. Residue LEU 110 is missing expected H atoms. Skipping. Residue LEU 112 is missing expected H atoms. Skipping. Residue LYS 118 is missing expected H atoms. Skipping. Residue SER 120 is missing expected H atoms. Skipping. Residue MET 139 is missing expected H atoms. Skipping. Residue VAL 141 is missing expected H atoms. Skipping. Residue MET 147 is missing expected H atoms. Skipping. Residue LEU 152 is missing expected H atoms. Skipping. Residue MET 162 is missing expected H atoms. Skipping. Residue SER 166 is missing expected H atoms. Skipping. Residue LYS 194 is missing expected H atoms. Skipping. Residue MET 198 is missing expected H atoms. Skipping. Residue LYS 203 is missing expected H atoms. Skipping. Residue THR 213 is missing expected H atoms. Skipping. Residue MET 232 is missing expected H atoms. Skipping. Residue THR 248 is missing expected H atoms. Skipping. Residue SER 267 is missing expected H atoms. Skipping. Residue LYS 270 is missing expected H atoms. Skipping. Residue VAL 2 is missing expected H atoms. Skipping. Residue MET 4 is missing expected H atoms. Skipping. Residue SER 7 is missing expected H atoms. Skipping. Residue LYS 14 is missing expected H atoms. Skipping. Residue MET 24 is missing expected H atoms. Skipping. Residue LEU 32 is missing expected H atoms. Skipping. Residue THR 43 is missing expected H atoms. Skipping. Residue ILE 49 is missing expected H atoms. Skipping. Residue MET 71 is missing expected H atoms. Skipping. Residue LEU 74 is missing expected H atoms. Skipping. Residue THR 99 is missing expected H atoms. Skipping. Residue SER 111 is missing expected H atoms. Skipping. Residue SER 120 is missing expected H atoms. Skipping. Residue LEU 132 is missing expected H atoms. Skipping. Residue ILE 133 is missing expected H atoms. Skipping. Residue THR 136 is missing expected H atoms. Skipping. Residue MET 139 is missing expected H atoms. Skipping. Residue VAL 141 is missing expected H atoms. Skipping. Residue LEU 144 is missing expected H atoms. Skipping. Residue MET 147 is missing expected H atoms. Skipping. Residue THR 150 is missing expected H atoms. Skipping. Residue LEU 160 is missing expected H atoms. Skipping. Residue MET 162 is missing expected H atoms. Skipping. Residue LYS 170 is missing expected H atoms. Skipping. Residue VAL 183 is missing expected H atoms. Skipping. Residue LYS 194 is missing expected H atoms. Skipping. Residue LEU 195 is missing expected H atoms. Skipping. Residue THR 199 is missing expected H atoms. Skipping. Residue LEU 201 is missing expected H atoms. Skipping. Residue LYS 203 is missing expected H atoms. Skipping. Residue ILE 219 is missing expected H atoms. Skipping. Residue TYR 220 is missing expected H atoms. Skipping. Residue LEU 230 is missing expected H atoms. Skipping. Residue MET 232 is missing expected H atoms. Skipping. Residue LEU 233 is missing expected H atoms. Skipping. Residue THR 235 is missing expected H atoms. Skipping. Residue SER 239 is missing expected H atoms. Skipping. Residue TYR 240 is missing expected H atoms. Skipping. Residue LEU 241 is missing expected H atoms. Skipping. Residue ILE 245 is missing expected H atoms. Skipping. Residue THR 248 is missing expected H atoms. Skipping. Residue LYS 251 is missing expected H atoms. Skipping. Residue TYR 256 is missing expected H atoms. Skipping. Residue LYS 270 is missing expected H atoms. Skipping. Residue THR 278 is missing expected H atoms. Skipping. Residue MET 1 is missing expected H atoms. Skipping. Residue MET 4 is missing expected H atoms. Skipping. Residue SER 12 is missing expected H atoms. Skipping. Residue LYS 14 is missing expected H atoms. Skipping. Residue VAL 16 is missing expected H atoms. Skipping. Residue MET 24 is missing expected H atoms. Skipping. Residue TYR 27 is missing expected H atoms. Skipping. Residue VAL 34 is missing expected H atoms. Skipping. Residue LEU 44 is missing expected H atoms. Skipping. Residue MET 60 is missing expected H atoms. Skipping. Residue LEU 112 is missing expected H atoms. Skipping. Residue LYS 118 is missing expected H atoms. Skipping. Residue LEU 126 is missing expected H atoms. Skipping. Residue MET 139 is missing expected H atoms. Skipping. Residue VAL 141 is missing expected H atoms. Skipping. Residue LEU 144 is missing expected H atoms. Skipping. Residue MET 147 is missing expected H atoms. Skipping. Residue LEU 148 is missing expected H atoms. Skipping. Residue LYS 155 is missing expected H atoms. Skipping. Residue LEU 160 is missing expected H atoms. Skipping. Residue MET 162 is missing expected H atoms. Skipping. Residue SER 166 is missing expected H atoms. Skipping. Residue LYS 170 is missing expected H atoms. Skipping. Residue TYR 179 is missing expected H atoms. Skipping. Residue VAL 180 is missing expected H atoms. Skipping. Residue MET 198 is missing expected H atoms. Skipping. Residue LYS 203 is missing expected H atoms. Skipping. Residue THR 222 is missing expected H atoms. Skipping. Residue TYR 225 is missing expected H atoms. Skipping. Residue MET 232 is missing expected H atoms. Skipping. Residue TYR 240 is missing expected H atoms. Skipping. Residue LEU 241 is missing expected H atoms. Skipping. Residue THR 242 is missing expected H atoms. Skipping. Residue VAL 243 is missing expected H atoms. Skipping. Residue LYS 251 is missing expected H atoms. Skipping. Residue VAL 255 is missing expected H atoms. Skipping. Residue SER 267 is missing expected H atoms. Skipping. Residue LYS 270 is missing expected H atoms. Skipping. Residue LEU 279 is missing expected H atoms. Skipping. Residue LYS 281 is missing expected H atoms. Skipping. Residue LYS 2 is missing expected H atoms. Skipping. Residue MET 4 is missing expected H atoms. Skipping. Residue LEU 14 is missing expected H atoms. Skipping. Residue VAL 19 is missing expected H atoms. Skipping. Residue LEU 24 is missing expected H atoms. Skipping. Residue TYR 25 is missing expected H atoms. Skipping. Residue LEU 27 is missing expected H atoms. Skipping. Residue ILE 29 is missing expected H atoms. Skipping. Residue LYS 38 is missing expected H atoms. Skipping. Residue ILE 41 is missing expected H atoms. Skipping. Residue TYR 42 is missing expected H atoms. Skipping. Residue LYS 43 is missing expected H atoms. Skipping. Residue LYS 45 is missing expected H atoms. Skipping. Residue LEU 70 is missing expected H atoms. Skipping. Residue TYR 77 is missing expected H atoms. Skipping. Residue TYR 82 is missing expected H atoms. Skipping. Residue ILE 90 is missing expected H atoms. Skipping. Residue LYS 91 is missing expected H atoms. Skipping. Residue LEU 94 is missing expected H atoms. Skipping. Residue ILE 104 is missing expected H atoms. Skipping. Residue LYS 112 is missing expected H atoms. Skipping. Residue VAL 128 is missing expected H atoms. Skipping. Residue MET 130 is missing expected H atoms. Skipping. Residue ILE 143 is missing expected H atoms. Skipping. Residue LYS 152 is missing expected H atoms. Skipping. Residue LEU 158 is missing expected H atoms. Skipping. Residue LEU 160 is missing expected H atoms. Skipping. Residue MET 164 is missing expected H atoms. Skipping. Residue LEU 166 is missing expected H atoms. Skipping. Residue LYS 175 is missing expected H atoms. Skipping. Residue LYS 189 is missing expected H atoms. Skipping. Residue ILE 194 is missing expected H atoms. Skipping. Residue LYS 195 is missing expected H atoms. Skipping. Residue ILE 214 is missing expected H atoms. Skipping. Residue VAL 215 is missing expected H atoms. Skipping. Residue TYR 221 is missing expected H atoms. Skipping. Residue ILE 229 is missing expected H atoms. Skipping. Residue LEU 230 is missing expected H atoms. Skipping. Residue LYS 255 is missing expected H atoms. Skipping. Residue LYS 257 is missing expected H atoms. Skipping. Residue LEU 258 is missing expected H atoms. Skipping. Residue TYR 259 is missing expected H atoms. Skipping. Residue LEU 265 is missing expected H atoms. Skipping. Residue LEU 285 is missing expected H atoms. Skipping. Residue SER 290 is missing expected H atoms. Skipping. Residue ILE 291 is missing expected H atoms. Skipping. Residue THR 296 is missing expected H atoms. Skipping. Residue THR 310 is missing expected H atoms. Skipping. Residue LEU 324 is missing expected H atoms. Skipping. Residue LEU 336 is missing expected H atoms. Skipping. Residue LEU 339 is missing expected H atoms. Skipping. Residue MET 350 is missing expected H atoms. Skipping. Residue LEU 363 is missing expected H atoms. Skipping. Residue VAL 367 is missing expected H atoms. Skipping. Residue ILE 376 is missing expected H atoms. Skipping. Residue LEU 384 is missing expected H atoms. Skipping. Residue MET 387 is missing expected H atoms. Skipping. Residue VAL 403 is missing expected H atoms. Skipping. Residue THR 410 is missing expected H atoms. Skipping. Residue VAL 413 is missing expected H atoms. Skipping. Residue SER 420 is missing expected H atoms. Skipping. Residue ILE 423 is missing expected H atoms. Skipping. Residue LEU 426 is missing expected H atoms. Skipping. Residue ILE 427 is missing expected H atoms. Skipping. Residue LYS 433 is missing expected H atoms. Skipping. Residue VAL 439 is missing expected H atoms. Skipping. Residue ILE 447 is missing expected H atoms. Skipping. Residue LYS 455 is missing expected H atoms. Skipping. Residue THR 481 is missing expected H atoms. Skipping. Residue TYR 484 is missing expected H atoms. Skipping. Residue VAL 486 is missing expected H atoms. Skipping. Residue LEU 487 is missing expected H atoms. Skipping. Residue MET 501 is missing expected H atoms. Skipping. Residue LEU 5 is missing expected H atoms. Skipping. Residue LEU 24 is missing expected H atoms. Skipping. Residue TYR 25 is missing expected H atoms. Skipping. Residue LEU 27 is missing expected H atoms. Skipping. Residue LYS 37 is missing expected H atoms. Skipping. Residue LYS 38 is missing expected H atoms. Skipping. Residue ILE 41 is missing expected H atoms. Skipping. Residue TYR 42 is missing expected H atoms. Skipping. Residue LYS 43 is missing expected H atoms. Skipping. Residue VAL 58 is missing expected H atoms. Skipping. Residue LYS 175 is missing expected H atoms. Skipping. Residue LYS 189 is missing expected H atoms. Skipping. Residue ILE 214 is missing expected H atoms. Skipping. Residue VAL 215 is missing expected H atoms. Skipping. Residue TYR 221 is missing expected H atoms. Skipping. Residue LEU 230 is missing expected H atoms. Skipping. Residue LYS 235 is missing expected H atoms. Skipping. Residue LEU 258 is missing expected H atoms. Skipping. Residue ILE 263 is missing expected H atoms. Skipping. Residue TYR 269 is missing expected H atoms. Skipping. Residue ILE 291 is missing expected H atoms. Skipping. Residue ILE 293 is missing expected H atoms. Skipping. Residue SER 295 is missing expected H atoms. Skipping. Residue THR 296 is missing expected H atoms. Skipping. Residue LEU 299 is missing expected H atoms. Skipping. Residue ILE 302 is missing expected H atoms. Skipping. Residue THR 310 is missing expected H atoms. Skipping. Residue ILE 330 is missing expected H atoms. Skipping. Residue LEU 334 is missing expected H atoms. Skipping. Residue LEU 339 is missing expected H atoms. Skipping. Residue ILE 343 is missing expected H atoms. Skipping. Residue ILE 345 is missing expected H atoms. Skipping. Residue ILE 348 is missing expected H atoms. Skipping. Residue MET 350 is missing expected H atoms. Skipping. Residue VAL 353 is missing expected H atoms. Skipping. Residue SER 380 is missing expected H atoms. Skipping. Residue MET 387 is missing expected H atoms. Skipping. Residue THR 412 is missing expected H atoms. Skipping. Residue VAL 413 is missing expected H atoms. Skipping. Residue SER 418 is missing expected H atoms. Skipping. Residue LEU 421 is missing expected H atoms. Skipping. Residue LYS 433 is missing expected H atoms. Skipping. Residue VAL 439 is missing expected H atoms. Skipping. Residue ILE 442 is missing expected H atoms. Skipping. Residue VAL 445 is missing expected H atoms. Skipping. Residue TYR 450 is missing expected H atoms. Skipping. Residue LEU 451 is missing expected H atoms. Skipping. Residue LYS 455 is missing expected H atoms. Skipping. Residue ILE 462 is missing expected H atoms. Skipping. Residue ILE 473 is missing expected H atoms. Skipping. Residue VAL 474 is missing expected H atoms. Skipping. Residue MET 479 is missing expected H atoms. Skipping. Residue MET 501 is missing expected H atoms. Skipping. Residue LEU 502 is missing expected H atoms. Skipping. Evaluate side-chains 341 residues out of total 1691 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 331 time to evaluate : 2.044 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 10 outliers final: 9 residues processed: 334 average time/residue: 0.5422 time to fit residues: 268.1691 Evaluate side-chains 337 residues out of total 1691 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 328 time to evaluate : 2.042 Switching outliers to nearest non-outliers revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 9 outliers final: 3 residues processed: 9 average time/residue: 0.2896 time to fit residues: 7.2527 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 206 random chunks: chunk 129 optimal weight: 0.0370 chunk 174 optimal weight: 3.9990 chunk 50 optimal weight: 2.9990 chunk 150 optimal weight: 1.9990 chunk 24 optimal weight: 0.9980 chunk 45 optimal weight: 0.8980 chunk 163 optimal weight: 20.0000 chunk 68 optimal weight: 0.5980 chunk 168 optimal weight: 6.9990 chunk 20 optimal weight: 0.9990 chunk 30 optimal weight: 0.5980 overall best weight: 0.6258 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 69 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 81 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4059 r_free = 0.4059 target = 0.125795 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3454 r_free = 0.3454 target = 0.092214 restraints weight = 168024.119| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 45)----------------| | r_work = 0.3508 r_free = 0.3508 target = 0.095578 restraints weight = 73324.966| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 41)----------------| | r_work = 0.3543 r_free = 0.3543 target = 0.097640 restraints weight = 44485.061| |-----------------------------------------------------------------------------| r_work (final): 0.3498 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3498 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3498 r_free = 0.3498 target_work(ls_wunit_k1) = 0.094 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 3 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3497 r_free = 0.3497 target_work(ls_wunit_k1) = 0.094 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 4 | |-----------------------------------------------------------------------------| r_final: 0.3497 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7659 moved from start: 0.6743 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.037 16776 Z= 0.149 Angle : 0.551 7.835 23691 Z= 0.278 Chirality : 0.038 0.173 3041 Planarity : 0.004 0.053 2530 Dihedral : 19.706 177.513 3905 Min Nonbonded Distance : 1.972 Molprobity Statistics. All-atom Clashscore : 14.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.54 % Favored : 95.46 % Rotamer: Outliers : 0.58 % Allowed : 30.63 % Favored : 68.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.21 (0.20), residues: 1893 helix: 1.29 (0.19), residues: 799 sheet: -1.25 (0.29), residues: 332 loop : -0.31 (0.24), residues: 762 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 7932.44 seconds wall clock time: 141 minutes 3.79 seconds (8463.79 seconds total)