Starting phenix.real_space_refine on Thu Mar 21 11:57:26 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7py6_13714/03_2024/7py6_13714.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7py6_13714/03_2024/7py6_13714.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.1 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7py6_13714/03_2024/7py6_13714.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7py6_13714/03_2024/7py6_13714.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7py6_13714/03_2024/7py6_13714.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7py6_13714/03_2024/7py6_13714.pdb" } resolution = 4.1 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= 0.009 sd= 0.065 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: 7 Type Number sf(0) Gaussians Zn 2 6.06 5 P 67 5.49 5 Mg 1 5.21 5 S 113 5.16 5 C 18481 2.51 5 N 5372 2.21 5 O 5923 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A GLU 58": "OE1" <-> "OE2" Residue "A GLU 72": "OE1" <-> "OE2" Residue "A TYR 152": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 229": "OE1" <-> "OE2" Residue "B GLU 181": "OE1" <-> "OE2" Residue "C PHE 224": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 390": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ASP 443": "OD1" <-> "OD2" Residue "C GLU 458": "OE1" <-> "OE2" Residue "C GLU 565": "OE1" <-> "OE2" Residue "C GLU 611": "OE1" <-> "OE2" Residue "C GLU 705": "OE1" <-> "OE2" Residue "C TYR 726": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 813": "OE1" <-> "OE2" Residue "C GLU 949": "OE1" <-> "OE2" Residue "C ASP 1064": "OD1" <-> "OD2" Residue "C GLU 1083": "OE1" <-> "OE2" Residue "C GLU 1272": "OE1" <-> "OE2" Residue "C TYR 1281": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D GLU 37": "OE1" <-> "OE2" Residue "D ASP 67": "OD1" <-> "OD2" Residue "D GLU 106": "OE1" <-> "OE2" Residue "D TYR 269": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 360": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D GLU 404": "OE1" <-> "OE2" Residue "D GLU 475": "OE1" <-> "OE2" Residue "D GLU 556": "OE1" <-> "OE2" Residue "D TYR 609": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D GLU 833": "OE1" <-> "OE2" Residue "D GLU 1281": "OE1" <-> "OE2" Residue "D TYR 1302": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E ASP 36": "OD1" <-> "OD2" Residue "E ASP 44": "OD1" <-> "OD2" Time to flip residues: 0.08s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib" Total number of atoms: 29959 Number of models: 1 Model: "" Number of chains: 11 Chain: "N" Number of atoms: 535 Number of conformers: 1 Conformer: "" Number of residues, atoms: 26, 535 Classifications: {'DNA': 26} Link IDs: {'rna3p': 25} Chain breaks: 1 Chain: "T" Number of atoms: 611 Number of conformers: 1 Conformer: "" Number of residues, atoms: 30, 611 Classifications: {'DNA': 30} Link IDs: {'rna3p': 29} Chain: "R" Number of atoms: 235 Number of conformers: 1 Conformer: "" Number of residues, atoms: 11, 235 Classifications: {'RNA': 11} Modifications used: {'rna2p_pyr': 2, 'rna3p_pur': 5, 'rna3p_pyr': 4} Link IDs: {'rna2p': 2, 'rna3p': 8} Chain: "A" Number of atoms: 1768 Number of conformers: 1 Conformer: "" Number of residues, atoms: 228, 1768 Classifications: {'peptide': 228} Link IDs: {'PTRANS': 9, 'TRANS': 218} Chain: "B" Number of atoms: 1699 Number of conformers: 1 Conformer: "" Number of residues, atoms: 220, 1699 Classifications: {'peptide': 220} Link IDs: {'PCIS': 1, 'PTRANS': 7, 'TRANS': 211} Chain breaks: 1 Chain: "C" Number of atoms: 10577 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1341, 10577 Classifications: {'peptide': 1341} Modifications used: {'COO': 1} Link IDs: {'CIS': 1, 'PCIS': 1, 'PTRANS': 55, 'TRANS': 1283} Chain: "D" Number of atoms: 10388 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1335, 10388 Classifications: {'peptide': 1335} Link IDs: {'PTRANS': 55, 'TRANS': 1279} Chain breaks: 2 Chain: "E" Number of atoms: 709 Number of conformers: 1 Conformer: "" Number of residues, atoms: 90, 709 Classifications: {'peptide': 90} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 2, 'TRANS': 87} Chain: "G" Number of atoms: 987 Number of conformers: 1 Conformer: "" Number of residues, atoms: 123, 987 Classifications: {'peptide': 123} Link IDs: {'PTRANS': 7, 'TRANS': 115} Chain: "F" Number of atoms: 2447 Number of conformers: 1 Conformer: "" Number of residues, atoms: 495, 2447 Classifications: {'peptide': 495} Incomplete info: {'truncation_to_alanine': 409} Link IDs: {'CIS': 1, 'PCIS': 1, 'PTRANS': 13, 'TRANS': 479} Unresolved chain link angles: 14 Unresolved non-hydrogen bonds: 1451 Unresolved non-hydrogen angles: 1853 Unresolved non-hydrogen dihedrals: 1145 Unresolved non-hydrogen chiralities: 145 Planarities with less than four sites: {'GLN:plan1': 19, 'HIS:plan': 4, 'TYR:plan': 6, 'ASN:plan1': 19, 'TRP:plan': 4, 'ASP:plan': 42, 'PHE:plan': 14, 'GLU:plan': 56, 'ARG:plan': 33} Unresolved non-hydrogen planarities: 830 Chain: "D" Number of atoms: 3 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 3 Unusual residues: {' MG': 1, ' ZN': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 15996 SG CYS D 85 86.871 115.163 72.929 1.00135.73 S ATOM 16020 SG CYS D 88 91.015 115.944 71.586 1.00136.03 S ATOM 21708 SG CYS D 814 96.513 46.090 79.493 1.00 91.25 S ATOM 22273 SG CYS D 888 98.157 49.614 77.555 1.00 89.84 S ATOM 22345 SG CYS D 898 99.759 47.049 80.006 1.00 86.97 S Time building chain proxies: 15.31, per 1000 atoms: 0.51 Number of scatterers: 29959 At special positions: 0 Unit cell: (195.11, 153.69, 174.4, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 7 Type Number sf(0) Zn 2 29.99 S 113 16.00 P 67 15.00 Mg 1 11.99 O 5923 8.00 N 5372 7.00 C 18481 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 12.70 Conformation dependent library (CDL) restraints added in 5.5 seconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN D1502 " pdb="ZN ZN D1502 " - pdb=" SG CYS D 88 " pdb="ZN ZN D1502 " - pdb=" SG CYS D 85 " pdb=" ZN D1503 " pdb="ZN ZN D1503 " - pdb=" SG CYS D 898 " pdb="ZN ZN D1503 " - pdb=" SG CYS D 888 " pdb="ZN ZN D1503 " - pdb=" SG CYS D 814 " 7624 Ramachandran restraints generated. 3812 Oldfield, 0 Emsley, 3812 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 7094 Finding SS restraints... Secondary structure from input PDB file: 137 helices and 51 sheets defined 38.3% alpha, 13.4% beta 29 base pairs and 45 stacking pairs defined. Time for finding SS restraints: 10.85 Creating SS restraints... Processing helix chain 'A' and resid 35 through 50 removed outlier: 3.604A pdb=" N ASN A 41 " --> pdb=" O HIS A 37 " (cutoff:3.500A) Processing helix chain 'A' and resid 77 through 87 removed outlier: 4.013A pdb=" N GLY A 87 " --> pdb=" O LEU A 83 " (cutoff:3.500A) Processing helix chain 'A' and resid 113 through 115 No H-bonds generated for 'chain 'A' and resid 113 through 115' Processing helix chain 'A' and resid 156 through 162 removed outlier: 3.550A pdb=" N HIS A 160 " --> pdb=" O THR A 157 " (cutoff:3.500A) removed outlier: 3.611A pdb=" N SER A 161 " --> pdb=" O ARG A 158 " (cutoff:3.500A) removed outlier: 3.637A pdb=" N GLU A 162 " --> pdb=" O ILE A 159 " (cutoff:3.500A) Processing helix chain 'A' and resid 212 through 229 Processing helix chain 'B' and resid 34 through 50 removed outlier: 3.560A pdb=" N THR B 38 " --> pdb=" O GLY B 34 " (cutoff:3.500A) Processing helix chain 'B' and resid 77 through 86 Processing helix chain 'B' and resid 113 through 115 No H-bonds generated for 'chain 'B' and resid 113 through 115' Processing helix chain 'B' and resid 154 through 158 removed outlier: 3.623A pdb=" N THR B 157 " --> pdb=" O PRO B 154 " (cutoff:3.500A) Processing helix chain 'B' and resid 212 through 228 removed outlier: 3.765A pdb=" N ILE B 217 " --> pdb=" O PRO B 213 " (cutoff:3.500A) removed outlier: 3.945A pdb=" N ARG B 218 " --> pdb=" O GLU B 214 " (cutoff:3.500A) Processing helix chain 'C' and resid 5 through 10 removed outlier: 3.515A pdb=" N ARG C 10 " --> pdb=" O GLU C 7 " (cutoff:3.500A) Processing helix chain 'C' and resid 30 through 39 removed outlier: 3.526A pdb=" N PHE C 38 " --> pdb=" O SER C 34 " (cutoff:3.500A) Processing helix chain 'C' and resid 48 through 57 removed outlier: 3.564A pdb=" N VAL C 56 " --> pdb=" O ALA C 52 " (cutoff:3.500A) Processing helix chain 'C' and resid 81 through 89 Processing helix chain 'C' and resid 206 through 213 removed outlier: 3.947A pdb=" N LEU C 210 " --> pdb=" O ALA C 206 " (cutoff:3.500A) Processing helix chain 'C' and resid 216 through 225 Processing helix chain 'C' and resid 242 through 247 Processing helix chain 'C' and resid 270 through 280 removed outlier: 3.938A pdb=" N ASP C 280 " --> pdb=" O GLN C 276 " (cutoff:3.500A) Processing helix chain 'C' and resid 288 through 293 removed outlier: 3.960A pdb=" N ILE C 292 " --> pdb=" O PRO C 288 " (cutoff:3.500A) Processing helix chain 'C' and resid 318 through 328 Processing helix chain 'C' and resid 345 through 354 Processing helix chain 'C' and resid 358 through 371 Processing helix chain 'C' and resid 377 through 389 removed outlier: 3.803A pdb=" N PHE C 389 " --> pdb=" O PHE C 385 " (cutoff:3.500A) Processing helix chain 'C' and resid 398 through 409 removed outlier: 3.524A pdb=" N LEU C 409 " --> pdb=" O PHE C 405 " (cutoff:3.500A) Processing helix chain 'C' and resid 421 through 438 removed outlier: 4.026A pdb=" N VAL C 428 " --> pdb=" O ASP C 424 " (cutoff:3.500A) Processing helix chain 'C' and resid 447 through 449 No H-bonds generated for 'chain 'C' and resid 447 through 449' Processing helix chain 'C' and resid 455 through 480 Processing helix chain 'C' and resid 488 through 493 removed outlier: 4.043A pdb=" N MET C 492 " --> pdb=" O MET C 488 " (cutoff:3.500A) removed outlier: 4.113A pdb=" N ILE C 493 " --> pdb=" O PRO C 489 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 488 through 493' Processing helix chain 'C' and resid 495 through 508 Processing helix chain 'C' and resid 519 through 526 Processing helix chain 'C' and resid 544 through 549 removed outlier: 3.696A pdb=" N ARG C 548 " --> pdb=" O GLY C 544 " (cutoff:3.500A) Processing helix chain 'C' and resid 551 through 555 removed outlier: 3.604A pdb=" N TYR C 555 " --> pdb=" O PRO C 552 " (cutoff:3.500A) Processing helix chain 'C' and resid 565 through 569 removed outlier: 3.854A pdb=" N ASN C 568 " --> pdb=" O GLU C 565 " (cutoff:3.500A) Processing helix chain 'C' and resid 608 through 612 removed outlier: 4.397A pdb=" N GLY C 612 " --> pdb=" O ALA C 608 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 608 through 612' Processing helix chain 'C' and resid 662 through 667 Processing helix chain 'C' and resid 670 through 674 Processing helix chain 'C' and resid 675 through 688 removed outlier: 3.889A pdb=" N GLN C 688 " --> pdb=" O ASN C 684 " (cutoff:3.500A) Processing helix chain 'C' and resid 704 through 712 Processing helix chain 'C' and resid 820 through 825 Processing helix chain 'C' and resid 858 through 863 Processing helix chain 'C' and resid 896 through 904 removed outlier: 3.501A pdb=" N LYS C 900 " --> pdb=" O THR C 896 " (cutoff:3.500A) Processing helix chain 'C' and resid 942 through 981 removed outlier: 3.930A pdb=" N ALA C 981 " --> pdb=" O ALA C 977 " (cutoff:3.500A) Processing helix chain 'C' and resid 993 through 997 removed outlier: 3.687A pdb=" N TRP C 997 " --> pdb=" O ARG C 994 " (cutoff:3.500A) Processing helix chain 'C' and resid 1005 through 1038 removed outlier: 3.517A pdb=" N ASN C1009 " --> pdb=" O GLU C1005 " (cutoff:3.500A) removed outlier: 3.909A pdb=" N GLU C1026 " --> pdb=" O LYS C1022 " (cutoff:3.500A) removed outlier: 3.968A pdb=" N LYS C1027 " --> pdb=" O HIS C1023 " (cutoff:3.500A) Processing helix chain 'C' and resid 1081 through 1085 Processing helix chain 'C' and resid 1099 through 1103 removed outlier: 3.824A pdb=" N GLY C1102 " --> pdb=" O ASN C1099 " (cutoff:3.500A) Processing helix chain 'C' and resid 1109 through 1134 removed outlier: 3.617A pdb=" N LYS C1122 " --> pdb=" O GLY C1118 " (cutoff:3.500A) removed outlier: 3.538A pdb=" N GLY C1125 " --> pdb=" O ALA C1121 " (cutoff:3.500A) removed outlier: 3.886A pdb=" N LYS C1127 " --> pdb=" O GLY C1123 " (cutoff:3.500A) removed outlier: 3.523A pdb=" N LYS C1133 " --> pdb=" O ASN C1129 " (cutoff:3.500A) removed outlier: 4.519A pdb=" N GLN C1134 " --> pdb=" O ALA C1130 " (cutoff:3.500A) Processing helix chain 'C' and resid 1137 through 1151 removed outlier: 4.027A pdb=" N LEU C1141 " --> pdb=" O GLU C1137 " (cutoff:3.500A) removed outlier: 3.606A pdb=" N PHE C1144 " --> pdb=" O LYS C1140 " (cutoff:3.500A) Processing helix chain 'C' and resid 1165 through 1176 Processing helix chain 'C' and resid 1177 through 1179 No H-bonds generated for 'chain 'C' and resid 1177 through 1179' Processing helix chain 'C' and resid 1191 through 1202 removed outlier: 3.789A pdb=" N GLY C1202 " --> pdb=" O LEU C1198 " (cutoff:3.500A) Processing helix chain 'C' and resid 1238 through 1242 Processing helix chain 'C' and resid 1271 through 1281 Processing helix chain 'C' and resid 1283 through 1293 Processing helix chain 'C' and resid 1297 through 1309 removed outlier: 4.245A pdb=" N THR C1302 " --> pdb=" O VAL C1298 " (cutoff:3.500A) removed outlier: 3.812A pdb=" N LYS C1303 " --> pdb=" O ASN C1299 " (cutoff:3.500A) Processing helix chain 'C' and resid 1320 through 1333 removed outlier: 3.508A pdb=" N ASN C1324 " --> pdb=" O PRO C1320 " (cutoff:3.500A) removed outlier: 3.698A pdb=" N ARG C1331 " --> pdb=" O LEU C1327 " (cutoff:3.500A) Processing helix chain 'D' and resid 26 through 34 Processing helix chain 'D' and resid 77 through 81 removed outlier: 3.504A pdb=" N HIS D 80 " --> pdb=" O ARG D 77 " (cutoff:3.500A) Processing helix chain 'D' and resid 94 through 100 removed outlier: 3.678A pdb=" N VAL D 97 " --> pdb=" O GLN D 94 " (cutoff:3.500A) Processing helix chain 'D' and resid 113 through 118 Processing helix chain 'D' and resid 122 through 129 Processing helix chain 'D' and resid 131 through 140 Processing helix chain 'D' and resid 161 through 172 removed outlier: 3.599A pdb=" N ASP D 167 " --> pdb=" O GLU D 163 " (cutoff:3.500A) Processing helix chain 'D' and resid 180 through 191 removed outlier: 4.002A pdb=" N ALA D 184 " --> pdb=" O MET D 180 " (cutoff:3.500A) Processing helix chain 'D' and resid 193 through 208 removed outlier: 4.086A pdb=" N GLU D 197 " --> pdb=" O ASP D 193 " (cutoff:3.500A) removed outlier: 3.515A pdb=" N ASN D 206 " --> pdb=" O ARG D 202 " (cutoff:3.500A) removed outlier: 3.783A pdb=" N GLU D 207 " --> pdb=" O GLU D 203 " (cutoff:3.500A) removed outlier: 3.504A pdb=" N THR D 208 " --> pdb=" O GLU D 204 " (cutoff:3.500A) Processing helix chain 'D' and resid 210 through 230 removed outlier: 3.809A pdb=" N LYS D 215 " --> pdb=" O GLU D 211 " (cutoff:3.500A) removed outlier: 4.600A pdb=" N LYS D 216 " --> pdb=" O THR D 212 " (cutoff:3.500A) Processing helix chain 'D' and resid 233 through 238 Processing helix chain 'D' and resid 246 through 250 Processing helix chain 'D' and resid 263 through 285 removed outlier: 3.596A pdb=" N ASP D 267 " --> pdb=" O SER D 263 " (cutoff:3.500A) removed outlier: 3.659A pdb=" N ASP D 284 " --> pdb=" O LYS D 280 " (cutoff:3.500A) removed outlier: 3.838A pdb=" N LEU D 285 " --> pdb=" O ARG D 281 " (cutoff:3.500A) Processing helix chain 'D' and resid 288 through 308 removed outlier: 3.581A pdb=" N ARG D 293 " --> pdb=" O ASP D 289 " (cutoff:3.500A) removed outlier: 3.975A pdb=" N ASN D 294 " --> pdb=" O ILE D 290 " (cutoff:3.500A) removed outlier: 3.592A pdb=" N GLU D 295 " --> pdb=" O ILE D 291 " (cutoff:3.500A) Processing helix chain 'D' and resid 326 through 332 removed outlier: 3.646A pdb=" N ILE D 331 " --> pdb=" O LEU D 327 " (cutoff:3.500A) Processing helix chain 'D' and resid 336 through 342 Processing helix chain 'D' and resid 370 through 377 Processing helix chain 'D' and resid 377 through 389 Processing helix chain 'D' and resid 393 through 402 Processing helix chain 'D' and resid 405 through 416 removed outlier: 3.676A pdb=" N TRP D 409 " --> pdb=" O GLU D 405 " (cutoff:3.500A) removed outlier: 3.505A pdb=" N ASP D 410 " --> pdb=" O ALA D 406 " (cutoff:3.500A) Processing helix chain 'D' and resid 430 through 432 No H-bonds generated for 'chain 'D' and resid 430 through 432' Processing helix chain 'D' and resid 450 through 455 removed outlier: 3.674A pdb=" N CYS D 454 " --> pdb=" O HIS D 450 " (cutoff:3.500A) removed outlier: 4.148A pdb=" N ALA D 455 " --> pdb=" O PRO D 451 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 450 through 455' Processing helix chain 'D' and resid 473 through 484 Processing helix chain 'D' and resid 505 through 515 Processing helix chain 'D' and resid 529 through 540 removed outlier: 3.663A pdb=" N GLU D 534 " --> pdb=" O PRO D 530 " (cutoff:3.500A) removed outlier: 3.870A pdb=" N ARG D 535 " --> pdb=" O LYS D 531 " (cutoff:3.500A) Processing helix chain 'D' and resid 574 through 580 Processing helix chain 'D' and resid 588 through 592 removed outlier: 3.629A pdb=" N ILE D 591 " --> pdb=" O PRO D 588 " (cutoff:3.500A) Processing helix chain 'D' and resid 597 through 612 removed outlier: 3.520A pdb=" N SER D 602 " --> pdb=" O LYS D 598 " (cutoff:3.500A) Processing helix chain 'D' and resid 614 through 634 Processing helix chain 'D' and resid 640 through 644 removed outlier: 3.908A pdb=" N MET D 644 " --> pdb=" O ILE D 641 " (cutoff:3.500A) Processing helix chain 'D' and resid 649 through 670 removed outlier: 3.610A pdb=" N GLU D 666 " --> pdb=" O ALA D 662 " (cutoff:3.500A) removed outlier: 3.738A pdb=" N GLN D 667 " --> pdb=" O GLU D 663 " (cutoff:3.500A) Processing helix chain 'D' and resid 674 through 703 removed outlier: 3.763A pdb=" N ARG D 678 " --> pdb=" O THR D 674 " (cutoff:3.500A) removed outlier: 3.936A pdb=" N THR D 703 " --> pdb=" O ASP D 699 " (cutoff:3.500A) Processing helix chain 'D' and resid 720 through 728 removed outlier: 3.530A pdb=" N SER D 728 " --> pdb=" O MET D 724 " (cutoff:3.500A) Processing helix chain 'D' and resid 733 through 742 Processing helix chain 'D' and resid 768 through 805 removed outlier: 4.217A pdb=" N HIS D 777 " --> pdb=" O PHE D 773 " (cutoff:3.500A) removed outlier: 4.560A pdb=" N GLY D 778 " --> pdb=" O ILE D 774 " (cutoff:3.500A) removed outlier: 3.757A pdb=" N ALA D 779 " --> pdb=" O SER D 775 " (cutoff:3.500A) removed outlier: 3.939A pdb=" N THR D 790 " --> pdb=" O THR D 786 " (cutoff:3.500A) removed outlier: 4.723A pdb=" N ALA D 791 " --> pdb=" O ALA D 787 " (cutoff:3.500A) removed outlier: 3.588A pdb=" N ASN D 792 " --> pdb=" O LEU D 788 " (cutoff:3.500A) removed outlier: 3.640A pdb=" N GLY D 794 " --> pdb=" O THR D 790 " (cutoff:3.500A) removed outlier: 3.646A pdb=" N ASP D 802 " --> pdb=" O ARG D 798 " (cutoff:3.500A) removed outlier: 3.527A pdb=" N VAL D 803 " --> pdb=" O ARG D 799 " (cutoff:3.500A) Processing helix chain 'D' and resid 835 through 840 removed outlier: 3.547A pdb=" N LEU D 840 " --> pdb=" O ARG D 836 " (cutoff:3.500A) Processing helix chain 'D' and resid 865 through 876 removed outlier: 3.528A pdb=" N ASP D 870 " --> pdb=" O GLU D 866 " (cutoff:3.500A) removed outlier: 4.064A pdb=" N LEU D 871 " --> pdb=" O GLN D 867 " (cutoff:3.500A) removed outlier: 3.672A pdb=" N ASN D 875 " --> pdb=" O LEU D 871 " (cutoff:3.500A) Processing helix chain 'D' and resid 895 through 900 Processing helix chain 'D' and resid 915 through 925 Processing helix chain 'D' and resid 926 through 928 No H-bonds generated for 'chain 'D' and resid 926 through 928' Processing helix chain 'D' and resid 1068 through 1073 removed outlier: 4.021A pdb=" N ASP D1073 " --> pdb=" O ALA D1069 " (cutoff:3.500A) Processing helix chain 'D' and resid 1137 through 1147 removed outlier: 3.529A pdb=" N GLU D1146 " --> pdb=" O ALA D1142 " (cutoff:3.500A) Processing helix chain 'D' and resid 1216 through 1224 Processing helix chain 'D' and resid 1225 through 1243 removed outlier: 3.829A pdb=" N VAL D1229 " --> pdb=" O GLY D1225 " (cutoff:3.500A) removed outlier: 3.610A pdb=" N VAL D1234 " --> pdb=" O THR D1230 " (cutoff:3.500A) Processing helix chain 'D' and resid 1249 through 1259 removed outlier: 3.989A pdb=" N ILE D1253 " --> pdb=" O ASN D1249 " (cutoff:3.500A) removed outlier: 3.887A pdb=" N ILE D1256 " --> pdb=" O HIS D1252 " (cutoff:3.500A) removed outlier: 3.531A pdb=" N VAL D1257 " --> pdb=" O ILE D1253 " (cutoff:3.500A) Processing helix chain 'D' and resid 1282 through 1295 removed outlier: 3.883A pdb=" N GLU D1291 " --> pdb=" O ILE D1287 " (cutoff:3.500A) removed outlier: 3.864A pdb=" N LEU D1292 " --> pdb=" O ALA D1288 " (cutoff:3.500A) removed outlier: 3.759A pdb=" N ASN D1295 " --> pdb=" O GLU D1291 " (cutoff:3.500A) Processing helix chain 'D' and resid 1308 through 1315 Processing helix chain 'D' and resid 1318 through 1324 removed outlier: 4.167A pdb=" N ALA D1322 " --> pdb=" O SER D1318 " (cutoff:3.500A) Processing helix chain 'D' and resid 1327 through 1339 removed outlier: 3.547A pdb=" N VAL D1331 " --> pdb=" O GLU D1327 " (cutoff:3.500A) Processing helix chain 'D' and resid 1347 through 1354 Processing helix chain 'D' and resid 1362 through 1373 Processing helix chain 'E' and resid 6 through 13 Processing helix chain 'E' and resid 17 through 33 removed outlier: 3.536A pdb=" N LEU E 21 " --> pdb=" O PHE E 17 " (cutoff:3.500A) removed outlier: 4.188A pdb=" N GLY E 33 " --> pdb=" O GLN E 29 " (cutoff:3.500A) Processing helix chain 'E' and resid 45 through 55 removed outlier: 3.560A pdb=" N ILE E 49 " --> pdb=" O LYS E 45 " (cutoff:3.500A) removed outlier: 4.335A pdb=" N LEU E 51 " --> pdb=" O THR E 47 " (cutoff:3.500A) Processing helix chain 'E' and resid 60 through 90 removed outlier: 3.649A pdb=" N ASP E 65 " --> pdb=" O ASN E 61 " (cutoff:3.500A) removed outlier: 4.121A pdb=" N VAL E 66 " --> pdb=" O GLN E 62 " (cutoff:3.500A) Processing helix chain 'G' and resid 18 through 34 Processing helix chain 'G' and resid 76 through 85 Processing helix chain 'G' and resid 104 through 119 Processing helix chain 'F' and resid 4 through 10 removed outlier: 3.623A pdb=" N VAL F 8 " --> pdb=" O GLU F 4 " (cutoff:3.500A) Processing helix chain 'F' and resid 19 through 39 removed outlier: 3.555A pdb=" N LEU F 27 " --> pdb=" O ILE F 23 " (cutoff:3.500A) removed outlier: 3.863A pdb=" N ALA F 30 " --> pdb=" O ALA F 26 " (cutoff:3.500A) Processing helix chain 'F' and resid 80 through 84 Processing helix chain 'F' and resid 106 through 131 Processing helix chain 'F' and resid 132 through 134 No H-bonds generated for 'chain 'F' and resid 132 through 134' Processing helix chain 'F' and resid 155 through 157 No H-bonds generated for 'chain 'F' and resid 155 through 157' Processing helix chain 'F' and resid 202 through 207 removed outlier: 4.538A pdb=" N GLU F 207 " --> pdb=" O GLU F 203 " (cutoff:3.500A) Processing helix chain 'F' and resid 208 through 211 removed outlier: 3.516A pdb=" N ILE F 211 " --> pdb=" O LEU F 208 " (cutoff:3.500A) No H-bonds generated for 'chain 'F' and resid 208 through 211' Processing helix chain 'F' and resid 281 through 286 removed outlier: 3.991A pdb=" N ILE F 285 " --> pdb=" O ALA F 281 " (cutoff:3.500A) removed outlier: 3.835A pdb=" N ASN F 286 " --> pdb=" O GLN F 282 " (cutoff:3.500A) No H-bonds generated for 'chain 'F' and resid 281 through 286' Processing helix chain 'F' and resid 310 through 312 No H-bonds generated for 'chain 'F' and resid 310 through 312' Processing helix chain 'F' and resid 313 through 318 removed outlier: 4.011A pdb=" N ILE F 318 " --> pdb=" O LEU F 314 " (cutoff:3.500A) Processing helix chain 'F' and resid 324 through 330 removed outlier: 3.522A pdb=" N ALA F 328 " --> pdb=" O ASN F 324 " (cutoff:3.500A) removed outlier: 3.769A pdb=" N GLN F 330 " --> pdb=" O ARG F 326 " (cutoff:3.500A) Processing helix chain 'F' and resid 340 through 345 Processing helix chain 'F' and resid 346 through 358 removed outlier: 4.336A pdb=" N ALA F 350 " --> pdb=" O ALA F 346 " (cutoff:3.500A) removed outlier: 4.190A pdb=" N GLU F 351 " --> pdb=" O LYS F 347 " (cutoff:3.500A) removed outlier: 4.319A pdb=" N ALA F 352 " --> pdb=" O HIS F 348 " (cutoff:3.500A) removed outlier: 3.962A pdb=" N HIS F 353 " --> pdb=" O GLN F 349 " (cutoff:3.500A) removed outlier: 4.021A pdb=" N ALA F 355 " --> pdb=" O GLU F 351 " (cutoff:3.500A) removed outlier: 4.022A pdb=" N ILE F 356 " --> pdb=" O ALA F 352 " (cutoff:3.500A) removed outlier: 4.129A pdb=" N THR F 358 " --> pdb=" O ALA F 354 " (cutoff:3.500A) Processing helix chain 'F' and resid 359 through 361 No H-bonds generated for 'chain 'F' and resid 359 through 361' Processing helix chain 'F' and resid 369 through 377 removed outlier: 4.052A pdb=" N LEU F 373 " --> pdb=" O PHE F 369 " (cutoff:3.500A) removed outlier: 4.002A pdb=" N VAL F 374 " --> pdb=" O ALA F 370 " (cutoff:3.500A) Processing helix chain 'F' and resid 388 through 393 Processing helix chain 'F' and resid 399 through 402 Processing helix chain 'F' and resid 403 through 408 Processing helix chain 'F' and resid 417 through 421 removed outlier: 3.879A pdb=" N ALA F 420 " --> pdb=" O ILE F 417 " (cutoff:3.500A) removed outlier: 3.894A pdb=" N GLN F 421 " --> pdb=" O ALA F 418 " (cutoff:3.500A) No H-bonds generated for 'chain 'F' and resid 417 through 421' Processing helix chain 'F' and resid 445 through 450 Processing helix chain 'F' and resid 455 through 459 removed outlier: 3.872A pdb=" N ASP F 458 " --> pdb=" O THR F 455 " (cutoff:3.500A) Processing helix chain 'F' and resid 479 through 491 removed outlier: 3.557A pdb=" N CYS F 489 " --> pdb=" O ALA F 485 " (cutoff:3.500A) removed outlier: 3.873A pdb=" N PHE F 491 " --> pdb=" O ASN F 487 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 13 through 17 removed outlier: 4.499A pdb=" N ASP A 15 " --> pdb=" O THR A 27 " (cutoff:3.500A) removed outlier: 4.134A pdb=" N LEU A 201 " --> pdb=" O LEU A 28 " (cutoff:3.500A) removed outlier: 6.832A pdb=" N LYS A 200 " --> pdb=" O VAL A 187 " (cutoff:3.500A) removed outlier: 4.700A pdb=" N VAL A 187 " --> pdb=" O LYS A 200 " (cutoff:3.500A) removed outlier: 6.782A pdb=" N VAL A 202 " --> pdb=" O TYR A 185 " (cutoff:3.500A) removed outlier: 4.483A pdb=" N TYR A 185 " --> pdb=" O VAL A 202 " (cutoff:3.500A) removed outlier: 6.839A pdb=" N GLU A 204 " --> pdb=" O ILE A 183 " (cutoff:3.500A) removed outlier: 4.608A pdb=" N ILE A 183 " --> pdb=" O GLU A 204 " (cutoff:3.500A) removed outlier: 6.853A pdb=" N GLU A 206 " --> pdb=" O GLU A 181 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 97 through 101 removed outlier: 6.371A pdb=" N ARG A 143 " --> pdb=" O VAL A 59 " (cutoff:3.500A) removed outlier: 4.364A pdb=" N VAL A 59 " --> pdb=" O ARG A 143 " (cutoff:3.500A) removed outlier: 6.969A pdb=" N LYS A 145 " --> pdb=" O THR A 57 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 90 through 92 removed outlier: 3.572A pdb=" N GLU A 122 " --> pdb=" O ARG A 91 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 104 through 105 removed outlier: 3.651A pdb=" N LYS A 104 " --> pdb=" O ILE A 140 " (cutoff:3.500A) removed outlier: 3.613A pdb=" N ILE A 140 " --> pdb=" O LYS A 104 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA4 Processing sheet with id=AA5, first strand: chain 'A' and resid 110 through 111 removed outlier: 6.806A pdb=" N VAL A 110 " --> pdb=" O ILE A 130 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 12 through 18 removed outlier: 5.048A pdb=" N LEU B 13 " --> pdb=" O GLU B 29 " (cutoff:3.500A) removed outlier: 7.065A pdb=" N GLU B 29 " --> pdb=" O LEU B 13 " (cutoff:3.500A) removed outlier: 4.343A pdb=" N ASP B 15 " --> pdb=" O THR B 27 " (cutoff:3.500A) removed outlier: 3.686A pdb=" N THR B 27 " --> pdb=" O ASP B 15 " (cutoff:3.500A) removed outlier: 3.565A pdb=" N ALA B 24 " --> pdb=" O MET B 205 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 12 through 18 removed outlier: 5.048A pdb=" N LEU B 13 " --> pdb=" O GLU B 29 " (cutoff:3.500A) removed outlier: 7.065A pdb=" N GLU B 29 " --> pdb=" O LEU B 13 " (cutoff:3.500A) removed outlier: 4.343A pdb=" N ASP B 15 " --> pdb=" O THR B 27 " (cutoff:3.500A) removed outlier: 3.686A pdb=" N THR B 27 " --> pdb=" O ASP B 15 " (cutoff:3.500A) removed outlier: 3.565A pdb=" N ALA B 24 " --> pdb=" O MET B 205 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 97 through 104 removed outlier: 3.689A pdb=" N ILE B 140 " --> pdb=" O LYS B 104 " (cutoff:3.500A) removed outlier: 8.096A pdb=" N SER B 141 " --> pdb=" O ILE B 61 " (cutoff:3.500A) removed outlier: 4.916A pdb=" N ILE B 61 " --> pdb=" O SER B 141 " (cutoff:3.500A) removed outlier: 6.581A pdb=" N ARG B 143 " --> pdb=" O VAL B 59 " (cutoff:3.500A) removed outlier: 4.474A pdb=" N VAL B 59 " --> pdb=" O ARG B 143 " (cutoff:3.500A) removed outlier: 7.228A pdb=" N LYS B 145 " --> pdb=" O THR B 57 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'B' and resid 90 through 91 removed outlier: 3.557A pdb=" N ARG B 91 " --> pdb=" O GLU B 122 " (cutoff:3.500A) removed outlier: 3.648A pdb=" N GLU B 122 " --> pdb=" O ARG B 91 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA9 Processing sheet with id=AB1, first strand: chain 'B' and resid 108 through 111 removed outlier: 3.961A pdb=" N CYS B 131 " --> pdb=" O VAL B 110 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'C' and resid 13 through 14 removed outlier: 6.448A pdb=" N LYS C 13 " --> pdb=" O ALA C1183 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'C' and resid 59 through 60 removed outlier: 5.978A pdb=" N SER C 66 " --> pdb=" O TYR C 105 " (cutoff:3.500A) removed outlier: 6.719A pdb=" N TYR C 105 " --> pdb=" O SER C 66 " (cutoff:3.500A) removed outlier: 5.226A pdb=" N LEU C 68 " --> pdb=" O VAL C 103 " (cutoff:3.500A) removed outlier: 7.288A pdb=" N VAL C 103 " --> pdb=" O LEU C 68 " (cutoff:3.500A) removed outlier: 5.493A pdb=" N TYR C 70 " --> pdb=" O ARG C 101 " (cutoff:3.500A) removed outlier: 5.474A pdb=" N ARG C 101 " --> pdb=" O TYR C 70 " (cutoff:3.500A) removed outlier: 3.555A pdb=" N SER C 72 " --> pdb=" O LYS C 99 " (cutoff:3.500A) removed outlier: 6.694A pdb=" N ALA C 94 " --> pdb=" O GLY C 125 " (cutoff:3.500A) removed outlier: 6.925A pdb=" N GLY C 125 " --> pdb=" O ALA C 94 " (cutoff:3.500A) removed outlier: 6.870A pdb=" N LEU C 96 " --> pdb=" O TYR C 123 " (cutoff:3.500A) removed outlier: 4.627A pdb=" N TYR C 123 " --> pdb=" O LEU C 96 " (cutoff:3.500A) removed outlier: 6.506A pdb=" N VAL C 98 " --> pdb=" O GLU C 121 " (cutoff:3.500A) removed outlier: 4.760A pdb=" N GLU C 121 " --> pdb=" O VAL C 98 " (cutoff:3.500A) removed outlier: 6.917A pdb=" N LEU C 100 " --> pdb=" O GLU C 119 " (cutoff:3.500A) removed outlier: 4.341A pdb=" N GLU C 119 " --> pdb=" O LEU C 100 " (cutoff:3.500A) removed outlier: 6.530A pdb=" N LEU C 102 " --> pdb=" O ILE C 117 " (cutoff:3.500A) removed outlier: 4.427A pdb=" N ILE C 117 " --> pdb=" O LEU C 102 " (cutoff:3.500A) removed outlier: 6.829A pdb=" N ILE C 104 " --> pdb=" O LYS C 115 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'C' and resid 136 through 137 removed outlier: 3.630A pdb=" N VAL C 144 " --> pdb=" O GLN C 513 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'C' and resid 451 through 454 removed outlier: 3.626A pdb=" N ARG C 452 " --> pdb=" O HIS C 150 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'C' and resid 154 through 158 Processing sheet with id=AB7, first strand: chain 'C' and resid 284 through 286 removed outlier: 5.299A pdb=" N ILE C 229 " --> pdb=" O GLU C 240 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'C' and resid 256 through 257 Processing sheet with id=AB9, first strand: chain 'C' and resid 296 through 297 removed outlier: 3.952A pdb=" N MET C 315 " --> pdb=" O VAL C 297 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'C' and resid 301 through 302 Processing sheet with id=AC2, first strand: chain 'C' and resid 580 through 581 removed outlier: 3.775A pdb=" N LYS C 593 " --> pdb=" O GLU C 602 " (cutoff:3.500A) removed outlier: 6.520A pdb=" N GLU C 602 " --> pdb=" O LYS C 593 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'C' and resid 580 through 581 Processing sheet with id=AC4, first strand: chain 'C' and resid 716 through 717 removed outlier: 7.255A pdb=" N ALA C 716 " --> pdb=" O LEU C 783 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'C' and resid 749 through 752 removed outlier: 6.908A pdb=" N ARG C 731 " --> pdb=" O VAL C 727 " (cutoff:3.500A) removed outlier: 5.116A pdb=" N VAL C 727 " --> pdb=" O ARG C 731 " (cutoff:3.500A) removed outlier: 6.740A pdb=" N VAL C 733 " --> pdb=" O GLN C 725 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'C' and resid 757 through 758 removed outlier: 3.838A pdb=" N THR C 757 " --> pdb=" O ILE C 765 " (cutoff:3.500A) removed outlier: 3.618A pdb=" N ILE C 765 " --> pdb=" O THR C 757 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC6 Processing sheet with id=AC7, first strand: chain 'C' and resid 789 through 790 Processing sheet with id=AC8, first strand: chain 'C' and resid 1076 through 1080 removed outlier: 7.648A pdb=" N ILE C 816 " --> pdb=" O SER C1077 " (cutoff:3.500A) removed outlier: 7.081A pdb=" N ILE C1079 " --> pdb=" O ILE C 816 " (cutoff:3.500A) removed outlier: 7.187A pdb=" N VAL C 818 " --> pdb=" O ILE C1079 " (cutoff:3.500A) removed outlier: 3.567A pdb=" N LEU C 817 " --> pdb=" O VAL C1097 " (cutoff:3.500A) removed outlier: 3.536A pdb=" N VAL C1097 " --> pdb=" O LEU C 817 " (cutoff:3.500A) removed outlier: 8.676A pdb=" N ILE C1096 " --> pdb=" O ASN C 799 " (cutoff:3.500A) removed outlier: 6.470A pdb=" N ARG C 801 " --> pdb=" O ILE C1096 " (cutoff:3.500A) removed outlier: 7.805A pdb=" N LEU C1098 " --> pdb=" O ARG C 801 " (cutoff:3.500A) removed outlier: 6.414A pdb=" N ALA C 803 " --> pdb=" O LEU C1098 " (cutoff:3.500A) removed outlier: 4.837A pdb=" N THR C1226 " --> pdb=" O PHE C 804 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'C' and resid 830 through 838 removed outlier: 6.981A pdb=" N ILE C1049 " --> pdb=" O VAL C 933 " (cutoff:3.500A) removed outlier: 4.830A pdb=" N VAL C 933 " --> pdb=" O ILE C1049 " (cutoff:3.500A) removed outlier: 6.869A pdb=" N LYS C1051 " --> pdb=" O VAL C 931 " (cutoff:3.500A) removed outlier: 4.715A pdb=" N VAL C 931 " --> pdb=" O LYS C1051 " (cutoff:3.500A) removed outlier: 6.975A pdb=" N TYR C1053 " --> pdb=" O ILE C 929 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'C' and resid 1087 through 1088 Processing sheet with id=AD2, first strand: chain 'C' and resid 1244 through 1246 removed outlier: 3.573A pdb=" N HIS C1244 " --> pdb=" O ARG D 352 " (cutoff:3.500A) removed outlier: 3.599A pdb=" N ARG C1246 " --> pdb=" O SER D 350 " (cutoff:3.500A) removed outlier: 3.942A pdb=" N SER D 350 " --> pdb=" O ARG C1246 " (cutoff:3.500A) removed outlier: 3.695A pdb=" N MET D 466 " --> pdb=" O SER D 353 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'C' and resid 1244 through 1246 removed outlier: 3.573A pdb=" N HIS C1244 " --> pdb=" O ARG D 352 " (cutoff:3.500A) removed outlier: 3.599A pdb=" N ARG C1246 " --> pdb=" O SER D 350 " (cutoff:3.500A) removed outlier: 3.942A pdb=" N SER D 350 " --> pdb=" O ARG C1246 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'C' and resid 1335 through 1340 Processing sheet with id=AD5, first strand: chain 'D' and resid 103 through 111 removed outlier: 3.778A pdb=" N GLY D 103 " --> pdb=" O VAL D 244 " (cutoff:3.500A) removed outlier: 6.994A pdb=" N THR D 240 " --> pdb=" O LEU D 107 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'D' and resid 159 through 160 Processing sheet with id=AD7, first strand: chain 'D' and resid 367 through 369 Processing sheet with id=AD8, first strand: chain 'D' and resid 526 through 527 removed outlier: 3.859A pdb=" N GLU D 554 " --> pdb=" O LYS D 566 " (cutoff:3.500A) removed outlier: 3.568A pdb=" N LYS D 566 " --> pdb=" O GLU D 554 " (cutoff:3.500A) removed outlier: 3.522A pdb=" N GLU D 556 " --> pdb=" O VAL D 564 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'D' and resid 820 through 822 removed outlier: 3.845A pdb=" N VAL D 880 " --> pdb=" O MET D 822 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'D' and resid 949 through 951 removed outlier: 6.901A pdb=" N ILE D 950 " --> pdb=" O VAL D1017 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'D' and resid 957 through 961 removed outlier: 3.880A pdb=" N GLU D 981 " --> pdb=" O SER D 961 " (cutoff:3.500A) removed outlier: 4.575A pdb=" N THR D 980 " --> pdb=" O VAL D 997 " (cutoff:3.500A) removed outlier: 4.001A pdb=" N GLU D 993 " --> pdb=" O LEU D 984 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'D' and resid 965 through 967 Processing sheet with id=AE4, first strand: chain 'D' and resid 1024 through 1028 removed outlier: 6.166A pdb=" N MET D1025 " --> pdb=" O ARG D1123 " (cutoff:3.500A) removed outlier: 4.387A pdb=" N ARG D1123 " --> pdb=" O MET D1025 " (cutoff:3.500A) removed outlier: 6.581A pdb=" N VAL D1027 " --> pdb=" O LEU D1121 " (cutoff:3.500A) Processing sheet with id=AE5, first strand: chain 'D' and resid 1034 through 1035 removed outlier: 3.631A pdb=" N VAL D1081 " --> pdb=" O PHE D1034 " (cutoff:3.500A) Processing sheet with id=AE6, first strand: chain 'D' and resid 1046 through 1049 Processing sheet with id=AE7, first strand: chain 'D' and resid 1077 through 1078 Processing sheet with id=AE8, first strand: chain 'D' and resid 1187 through 1190 Processing sheet with id=AE9, first strand: chain 'D' and resid 1279 through 1281 removed outlier: 3.582A pdb=" N VAL D1280 " --> pdb=" O ALA D1264 " (cutoff:3.500A) removed outlier: 6.755A pdb=" N THR D1301 " --> pdb=" O VAL D1267 " (cutoff:3.500A) Processing sheet with id=AF1, first strand: chain 'G' and resid 42 through 43 Processing sheet with id=AF2, first strand: chain 'G' and resid 47 through 48 removed outlier: 3.615A pdb=" N ARG G 62 " --> pdb=" O GLU G 47 " (cutoff:3.500A) Processing sheet with id=AF3, first strand: chain 'F' and resid 47 through 49 Processing sheet with id=AF4, first strand: chain 'F' and resid 141 through 142 removed outlier: 4.165A pdb=" N VAL F 141 " --> pdb=" O ASP F 153 " (cutoff:3.500A) removed outlier: 3.650A pdb=" N ALA F 158 " --> pdb=" O LEU F 154 " (cutoff:3.500A) removed outlier: 8.286A pdb=" N GLU F 159 " --> pdb=" O LEU F 195 " (cutoff:3.500A) removed outlier: 8.436A pdb=" N VAL F 197 " --> pdb=" O GLU F 159 " (cutoff:3.500A) removed outlier: 6.548A pdb=" N VAL F 161 " --> pdb=" O VAL F 197 " (cutoff:3.500A) removed outlier: 3.811A pdb=" N SER F 185 " --> pdb=" O PHE F 196 " (cutoff:3.500A) Processing sheet with id=AF5, first strand: chain 'F' and resid 221 through 222 Processing sheet with id=AF6, first strand: chain 'F' and resid 226 through 228 1094 hydrogen bonds defined for protein. 3030 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 77 hydrogen bonds 150 hydrogen bond angles 0 basepair planarities 29 basepair parallelities 45 stacking parallelities Total time for adding SS restraints: 15.32 Time building geometry restraints manager: 13.70 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 10017 1.34 - 1.46: 4417 1.46 - 1.58: 15745 1.58 - 1.70: 130 1.70 - 1.82: 198 Bond restraints: 30507 Sorted by residual: bond pdb=" N CYS D 85 " pdb=" CA CYS D 85 " ideal model delta sigma weight residual 1.456 1.489 -0.033 1.22e-02 6.72e+03 7.13e+00 bond pdb=" C GLU D 925 " pdb=" N PRO D 926 " ideal model delta sigma weight residual 1.334 1.354 -0.020 8.40e-03 1.42e+04 5.76e+00 bond pdb=" C3' DG T 27 " pdb=" O3' DG T 27 " ideal model delta sigma weight residual 1.422 1.471 -0.049 3.00e-02 1.11e+03 2.68e+00 bond pdb=" C GLU A 29 " pdb=" N PRO A 30 " ideal model delta sigma weight residual 1.334 1.371 -0.037 2.34e-02 1.83e+03 2.55e+00 bond pdb=" C VAL C1103 " pdb=" N PRO C1104 " ideal model delta sigma weight residual 1.334 1.363 -0.029 2.34e-02 1.83e+03 1.52e+00 ... (remaining 30502 not shown) Histogram of bond angle deviations from ideal: 95.60 - 103.29: 373 103.29 - 110.99: 11069 110.99 - 118.68: 13576 118.68 - 126.38: 16139 126.38 - 134.08: 429 Bond angle restraints: 41586 Sorted by residual: angle pdb=" N ILE D 500 " pdb=" CA ILE D 500 " pdb=" C ILE D 500 " ideal model delta sigma weight residual 111.91 107.11 4.80 8.90e-01 1.26e+00 2.91e+01 angle pdb=" C ALA F 11 " pdb=" N VAL F 12 " pdb=" CA VAL F 12 " ideal model delta sigma weight residual 121.70 128.98 -7.28 1.80e+00 3.09e-01 1.63e+01 angle pdb=" C ALA C 910 " pdb=" N SER C 911 " pdb=" CA SER C 911 " ideal model delta sigma weight residual 121.70 128.75 -7.05 1.80e+00 3.09e-01 1.53e+01 angle pdb=" CA GLU C1083 " pdb=" CB GLU C1083 " pdb=" CG GLU C1083 " ideal model delta sigma weight residual 114.10 121.89 -7.79 2.00e+00 2.50e-01 1.52e+01 angle pdb=" N GLU E 79 " pdb=" CA GLU E 79 " pdb=" CB GLU E 79 " ideal model delta sigma weight residual 110.28 115.87 -5.59 1.55e+00 4.16e-01 1.30e+01 ... (remaining 41581 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.05: 18009 35.05 - 70.10: 519 70.10 - 105.14: 35 105.14 - 140.19: 3 140.19 - 175.24: 2 Dihedral angle restraints: 18568 sinusoidal: 7565 harmonic: 11003 Sorted by residual: dihedral pdb=" CA GLU A 29 " pdb=" C GLU A 29 " pdb=" N PRO A 30 " pdb=" CA PRO A 30 " ideal model delta harmonic sigma weight residual -180.00 -134.14 -45.86 0 5.00e+00 4.00e-02 8.41e+01 dihedral pdb=" CA TYR D 140 " pdb=" C TYR D 140 " pdb=" N PHE D 141 " pdb=" CA PHE D 141 " ideal model delta harmonic sigma weight residual 180.00 151.12 28.88 0 5.00e+00 4.00e-02 3.34e+01 dihedral pdb=" CA LEU D 483 " pdb=" C LEU D 483 " pdb=" N MET D 484 " pdb=" CA MET D 484 " ideal model delta harmonic sigma weight residual -180.00 -152.28 -27.72 0 5.00e+00 4.00e-02 3.07e+01 ... (remaining 18565 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.062: 4102 0.062 - 0.123: 676 0.123 - 0.185: 40 0.185 - 0.247: 0 0.247 - 0.309: 2 Chirality restraints: 4820 Sorted by residual: chirality pdb=" CB ILE D 147 " pdb=" CA ILE D 147 " pdb=" CG1 ILE D 147 " pdb=" CG2 ILE D 147 " both_signs ideal model delta sigma weight residual False 2.64 2.34 0.31 2.00e-01 2.50e+01 2.38e+00 chirality pdb=" CB ILE C 30 " pdb=" CA ILE C 30 " pdb=" CG1 ILE C 30 " pdb=" CG2 ILE C 30 " both_signs ideal model delta sigma weight residual False 2.64 2.38 0.27 2.00e-01 2.50e+01 1.81e+00 chirality pdb=" CA PRO C 489 " pdb=" N PRO C 489 " pdb=" C PRO C 489 " pdb=" CB PRO C 489 " both_signs ideal model delta sigma weight residual False 2.72 2.54 0.18 2.00e-01 2.50e+01 8.11e-01 ... (remaining 4817 not shown) Planarity restraints: 5266 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C GLU A 29 " -0.061 5.00e-02 4.00e+02 9.37e-02 1.40e+01 pdb=" N PRO A 30 " 0.162 5.00e-02 4.00e+02 pdb=" CA PRO A 30 " -0.050 5.00e-02 4.00e+02 pdb=" CD PRO A 30 " -0.051 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C GLY D 358 " 0.055 5.00e-02 4.00e+02 8.45e-02 1.14e+01 pdb=" N PRO D 359 " -0.146 5.00e-02 4.00e+02 pdb=" CA PRO D 359 " 0.045 5.00e-02 4.00e+02 pdb=" CD PRO D 359 " 0.046 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C LYS D 233 " -0.038 5.00e-02 4.00e+02 5.79e-02 5.37e+00 pdb=" N PRO D 234 " 0.100 5.00e-02 4.00e+02 pdb=" CA PRO D 234 " -0.030 5.00e-02 4.00e+02 pdb=" CD PRO D 234 " -0.032 5.00e-02 4.00e+02 ... (remaining 5263 not shown) Histogram of nonbonded interaction distances: 2.11 - 2.66: 551 2.66 - 3.22: 28889 3.22 - 3.78: 46697 3.78 - 4.34: 59418 4.34 - 4.90: 93623 Nonbonded interactions: 229178 Sorted by model distance: nonbonded pdb=" O3' G R 14 " pdb="MG MG D1501 " model vdw 2.105 2.170 nonbonded pdb=" OD1 ASP D 460 " pdb="MG MG D1501 " model vdw 2.135 2.170 nonbonded pdb=" OG SER C 421 " pdb=" OD1 ASP C 423 " model vdw 2.141 2.440 nonbonded pdb=" OG1 THR D1038 " pdb=" O ALA D1077 " model vdw 2.157 2.440 nonbonded pdb=" O2 DC N 35 " pdb=" N2 DG T 5 " model vdw 2.176 2.496 ... (remaining 229173 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 7 through 158 or resid 170 through 234)) selection = (chain 'B' and resid 7 through 234) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as 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: 0.980 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: 0.030 Extract box with map and model: 6.230 Check model and map are aligned: 0.460 Set scattering table: 0.290 Process input model: 93.440 Find NCS groups from input model: 1.200 Set up NCS constraints: 0.170 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.020 Load rotamer database and sin/cos tables:3.210 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 106.030 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8231 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 : 0.003 0.049 30507 Z= 0.172 Angle : 0.651 9.938 41586 Z= 0.344 Chirality : 0.044 0.309 4820 Planarity : 0.005 0.094 5266 Dihedral : 15.825 175.241 11474 Min Nonbonded Distance : 2.105 Molprobity Statistics. All-atom Clashscore : 10.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.49 % Favored : 95.51 % Rotamer: Outliers : 0.04 % Allowed : 0.18 % Favored : 99.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.99 % Cis-general : 0.05 % Twisted Proline : 0.66 % 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: -1.20 (0.13), residues: 3812 helix: 0.09 (0.15), residues: 1220 sheet: -0.56 (0.27), residues: 375 loop : -1.37 (0.13), residues: 2217 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.002 TRP D 236 HIS 0.016 0.001 HIS C 165 PHE 0.020 0.001 PHE D1100 TYR 0.024 0.001 TYR G 68 ARG 0.006 0.001 ARG C 272 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7624 Ramachandran restraints generated. 3812 Oldfield, 0 Emsley, 3812 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7624 Ramachandran restraints generated. 3812 Oldfield, 0 Emsley, 3812 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 304 residues out of total 3251 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 303 time to evaluate : 3.984 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 177 TYR cc_start: 0.6554 (m-80) cc_final: 0.5972 (m-10) REVERT: A 194 GLN cc_start: 0.8874 (pm20) cc_final: 0.8585 (pm20) REVERT: C 195 PHE cc_start: 0.7940 (m-80) cc_final: 0.6865 (m-80) REVERT: C 239 MET cc_start: 0.7870 (tpt) cc_final: 0.7515 (tpp) REVERT: C 684 ASN cc_start: 0.8222 (t0) cc_final: 0.7935 (t0) REVERT: C 951 MET cc_start: 0.9203 (tmm) cc_final: 0.8472 (tmm) REVERT: C 1131 MET cc_start: 0.8773 (ppp) cc_final: 0.7645 (ppp) REVERT: C 1243 MET cc_start: 0.8410 (tmm) cc_final: 0.8191 (tmm) REVERT: C 1315 MET cc_start: 0.8516 (ptm) cc_final: 0.8309 (ptt) REVERT: D 192 MET cc_start: 0.8436 (ttp) cc_final: 0.7893 (tmm) REVERT: D 581 MET cc_start: 0.8119 (mtp) cc_final: 0.7822 (mtt) REVERT: D 747 MET cc_start: 0.8155 (tpp) cc_final: 0.7672 (mmt) REVERT: D 1260 MET cc_start: 0.8324 (mtp) cc_final: 0.8116 (mtp) REVERT: E 10 VAL cc_start: 0.8985 (t) cc_final: 0.8755 (p) REVERT: E 60 ASN cc_start: 0.8459 (p0) cc_final: 0.7955 (p0) REVERT: G 9 TRP cc_start: 0.7715 (m100) cc_final: 0.7442 (m100) REVERT: G 35 MET cc_start: 0.9091 (mpp) cc_final: 0.8744 (mpp) outliers start: 1 outliers final: 0 residues processed: 304 average time/residue: 0.3885 time to fit residues: 194.1214 Evaluate side-chains 211 residues out of total 3251 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 211 time to evaluate : 3.533 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 387 random chunks: chunk 326 optimal weight: 20.0000 chunk 293 optimal weight: 0.1980 chunk 162 optimal weight: 7.9990 chunk 100 optimal weight: 0.2980 chunk 197 optimal weight: 5.9990 chunk 156 optimal weight: 0.9990 chunk 303 optimal weight: 0.7980 chunk 117 optimal weight: 6.9990 chunk 184 optimal weight: 10.0000 chunk 225 optimal weight: 1.9990 chunk 351 optimal weight: 50.0000 overall best weight: 0.8584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 41 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 761 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C1111 GLN ** D 435 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 488 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 62 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 73 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 75 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 113 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8231 moved from start: 0.0955 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.050 30507 Z= 0.148 Angle : 0.534 10.812 41586 Z= 0.281 Chirality : 0.042 0.184 4820 Planarity : 0.004 0.088 5266 Dihedral : 13.583 176.618 4930 Min Nonbonded Distance : 2.025 Molprobity Statistics. All-atom Clashscore : 10.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.43 % Favored : 95.57 % Rotamer: Outliers : 0.04 % Allowed : 5.45 % Favored : 94.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.99 % Cis-general : 0.05 % Twisted Proline : 0.66 % 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: -0.88 (0.14), residues: 3812 helix: 0.60 (0.15), residues: 1251 sheet: -0.62 (0.25), residues: 427 loop : -1.32 (0.13), residues: 2134 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP D 115 HIS 0.004 0.001 HIS C1116 PHE 0.017 0.001 PHE D 141 TYR 0.014 0.001 TYR C1229 ARG 0.006 0.000 ARG D1231 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7624 Ramachandran restraints generated. 3812 Oldfield, 0 Emsley, 3812 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7624 Ramachandran restraints generated. 3812 Oldfield, 0 Emsley, 3812 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 278 residues out of total 3251 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 277 time to evaluate : 3.382 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: A 68 TYR cc_start: 0.8842 (m-10) cc_final: 0.8581 (m-10) REVERT: A 137 ASN cc_start: 0.8615 (p0) cc_final: 0.8340 (p0) REVERT: A 177 TYR cc_start: 0.6781 (m-80) cc_final: 0.6189 (m-10) REVERT: C 760 ASN cc_start: 0.7924 (m110) cc_final: 0.7671 (m-40) REVERT: C 951 MET cc_start: 0.9227 (tmm) cc_final: 0.8471 (tmm) REVERT: C 1066 MET cc_start: 0.9073 (ppp) cc_final: 0.8842 (ppp) REVERT: C 1131 MET cc_start: 0.8703 (ppp) cc_final: 0.7880 (ppp) REVERT: C 1170 MET cc_start: 0.8732 (tpp) cc_final: 0.8524 (tpt) REVERT: C 1243 MET cc_start: 0.8695 (tmm) cc_final: 0.8222 (tmm) REVERT: D 130 MET cc_start: 0.7804 (mpp) cc_final: 0.7583 (mpp) REVERT: D 192 MET cc_start: 0.8358 (ttp) cc_final: 0.7956 (tmm) REVERT: D 466 MET cc_start: 0.9072 (pmm) cc_final: 0.8760 (ppp) REVERT: D 581 MET cc_start: 0.8087 (mtp) cc_final: 0.7829 (mtt) REVERT: D 1254 GLU cc_start: 0.8124 (tm-30) cc_final: 0.7867 (tm-30) REVERT: E 10 VAL cc_start: 0.8929 (t) cc_final: 0.8694 (p) REVERT: G 9 TRP cc_start: 0.7735 (m100) cc_final: 0.7110 (m100) REVERT: G 41 GLU cc_start: 0.8659 (pp20) cc_final: 0.7761 (pp20) REVERT: G 43 MET cc_start: 0.7484 (tmm) cc_final: 0.5651 (ptp) outliers start: 1 outliers final: 1 residues processed: 278 average time/residue: 0.3588 time to fit residues: 169.7006 Evaluate side-chains 215 residues out of total 3251 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 214 time to evaluate : 3.464 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 387 random chunks: chunk 195 optimal weight: 0.8980 chunk 109 optimal weight: 9.9990 chunk 292 optimal weight: 6.9990 chunk 239 optimal weight: 8.9990 chunk 96 optimal weight: 5.9990 chunk 352 optimal weight: 50.0000 chunk 380 optimal weight: 0.3980 chunk 313 optimal weight: 5.9990 chunk 349 optimal weight: 10.0000 chunk 120 optimal weight: 10.0000 chunk 282 optimal weight: 30.0000 overall best weight: 4.0586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 128 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 41 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 93 GLN ** C 46 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 69 GLN ** C 120 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 387 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 684 ASN ** C 761 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1136 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 232 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 424 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 435 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 488 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 771 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D1279 GLN ** E 62 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 73 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 75 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 13 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 113 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8348 moved from start: 0.1598 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.054 30507 Z= 0.317 Angle : 0.607 8.350 41586 Z= 0.321 Chirality : 0.043 0.199 4820 Planarity : 0.004 0.089 5266 Dihedral : 13.716 174.404 4930 Min Nonbonded Distance : 1.955 Molprobity Statistics. All-atom Clashscore : 14.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.64 % Favored : 94.36 % Rotamer: Outliers : 0.04 % Allowed : 5.17 % Favored : 94.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.99 % Cis-general : 0.05 % Twisted Proline : 0.66 % 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: -0.91 (0.14), residues: 3812 helix: 0.63 (0.15), residues: 1261 sheet: -0.67 (0.25), residues: 434 loop : -1.38 (0.13), residues: 2117 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.002 TRP D 236 HIS 0.006 0.001 HIS D 545 PHE 0.023 0.002 PHE D 141 TYR 0.022 0.002 TYR C 726 ARG 0.006 0.001 ARG C 678 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7624 Ramachandran restraints generated. 3812 Oldfield, 0 Emsley, 3812 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7624 Ramachandran restraints generated. 3812 Oldfield, 0 Emsley, 3812 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 245 residues out of total 3251 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 244 time to evaluate : 3.329 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 68 TYR cc_start: 0.8894 (m-10) cc_final: 0.8672 (m-10) REVERT: A 177 TYR cc_start: 0.7441 (m-80) cc_final: 0.7032 (m-80) REVERT: B 29 GLU cc_start: 0.8263 (tm-30) cc_final: 0.7914 (tm-30) REVERT: C 515 MET cc_start: 0.9012 (tmm) cc_final: 0.8604 (tmm) REVERT: C 1243 MET cc_start: 0.8932 (tmm) cc_final: 0.8390 (tmm) REVERT: C 1273 MET cc_start: 0.8715 (mmm) cc_final: 0.8457 (mpp) REVERT: D 130 MET cc_start: 0.8052 (mpp) cc_final: 0.7838 (mpp) REVERT: D 192 MET cc_start: 0.8478 (ttp) cc_final: 0.7987 (tmm) REVERT: D 610 ARG cc_start: 0.8664 (mmt-90) cc_final: 0.8030 (tpp80) REVERT: D 644 MET cc_start: 0.8977 (mpp) cc_final: 0.8732 (mpp) REVERT: D 697 MET cc_start: 0.8731 (tmm) cc_final: 0.8479 (tmm) REVERT: E 10 VAL cc_start: 0.9007 (t) cc_final: 0.8738 (p) REVERT: G 41 GLU cc_start: 0.8702 (pp20) cc_final: 0.7916 (pp20) REVERT: G 43 MET cc_start: 0.7391 (tmm) cc_final: 0.5899 (ptp) REVERT: G 73 MET cc_start: 0.8634 (tpp) cc_final: 0.7359 (tpp) outliers start: 1 outliers final: 0 residues processed: 245 average time/residue: 0.3747 time to fit residues: 155.2720 Evaluate side-chains 195 residues out of total 3251 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 195 time to evaluate : 3.236 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 387 random chunks: chunk 347 optimal weight: 20.0000 chunk 264 optimal weight: 5.9990 chunk 182 optimal weight: 0.9980 chunk 38 optimal weight: 10.0000 chunk 168 optimal weight: 3.9990 chunk 236 optimal weight: 0.5980 chunk 353 optimal weight: 7.9990 chunk 374 optimal weight: 50.0000 chunk 184 optimal weight: 7.9990 chunk 334 optimal weight: 2.9990 chunk 100 optimal weight: 1.9990 overall best weight: 2.1186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 128 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 41 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 227 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 46 GLN C 69 GLN ** C 120 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 387 ASN C 604 HIS ** C 799 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 232 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 435 GLN ** D 465 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 488 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 771 GLN ** E 62 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 73 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 75 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 13 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8305 moved from start: 0.1729 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 30507 Z= 0.206 Angle : 0.544 7.898 41586 Z= 0.288 Chirality : 0.042 0.219 4820 Planarity : 0.004 0.087 5266 Dihedral : 13.687 175.869 4930 Min Nonbonded Distance : 1.997 Molprobity Statistics. All-atom Clashscore : 12.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.88 % Favored : 95.12 % Rotamer: Outliers : 0.11 % Allowed : 4.54 % Favored : 95.36 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.99 % Cis-general : 0.05 % Twisted Proline : 0.66 % 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: -0.85 (0.14), residues: 3812 helix: 0.62 (0.15), residues: 1278 sheet: -0.61 (0.25), residues: 436 loop : -1.33 (0.13), residues: 2098 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP D 236 HIS 0.005 0.001 HIS D 364 PHE 0.016 0.001 PHE C 53 TYR 0.016 0.001 TYR C1229 ARG 0.006 0.000 ARG D 275 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7624 Ramachandran restraints generated. 3812 Oldfield, 0 Emsley, 3812 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7624 Ramachandran restraints generated. 3812 Oldfield, 0 Emsley, 3812 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 259 residues out of total 3251 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 256 time to evaluate : 3.230 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 68 TYR cc_start: 0.8905 (m-10) cc_final: 0.8652 (m-10) REVERT: A 137 ASN cc_start: 0.8735 (p0) cc_final: 0.8313 (p0) REVERT: A 177 TYR cc_start: 0.7539 (m-80) cc_final: 0.7042 (m-80) REVERT: B 29 GLU cc_start: 0.8281 (tm-30) cc_final: 0.8016 (tm-30) REVERT: B 186 ASN cc_start: 0.8342 (t0) cc_final: 0.8105 (t0) REVERT: C 515 MET cc_start: 0.9106 (tmm) cc_final: 0.8737 (tmm) REVERT: C 1119 MET cc_start: 0.9214 (tpp) cc_final: 0.8533 (tpp) REVERT: C 1243 MET cc_start: 0.8906 (tmm) cc_final: 0.8520 (tmm) REVERT: C 1290 MET cc_start: 0.8512 (tpp) cc_final: 0.7710 (tpp) REVERT: D 192 MET cc_start: 0.8456 (ttp) cc_final: 0.7995 (tmm) REVERT: D 610 ARG cc_start: 0.8633 (mmt-90) cc_final: 0.8062 (tpp80) REVERT: D 644 MET cc_start: 0.8956 (mpp) cc_final: 0.8746 (mpp) REVERT: D 1189 MET cc_start: 0.7242 (tpt) cc_final: 0.6982 (tpt) REVERT: D 1349 GLU cc_start: 0.7930 (pm20) cc_final: 0.7639 (pm20) REVERT: E 10 VAL cc_start: 0.8992 (t) cc_final: 0.8734 (p) REVERT: G 9 TRP cc_start: 0.7831 (m100) cc_final: 0.7472 (m100) REVERT: G 41 GLU cc_start: 0.8620 (pp20) cc_final: 0.8221 (pp20) REVERT: G 73 MET cc_start: 0.8595 (tpp) cc_final: 0.7392 (tpp) outliers start: 3 outliers final: 0 residues processed: 259 average time/residue: 0.3694 time to fit residues: 161.4347 Evaluate side-chains 205 residues out of total 3251 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 205 time to evaluate : 2.959 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 387 random chunks: chunk 311 optimal weight: 6.9990 chunk 212 optimal weight: 0.9980 chunk 5 optimal weight: 10.0000 chunk 278 optimal weight: 20.0000 chunk 154 optimal weight: 0.8980 chunk 319 optimal weight: 1.9990 chunk 258 optimal weight: 5.9990 chunk 0 optimal weight: 20.0000 chunk 191 optimal weight: 6.9990 chunk 335 optimal weight: 20.0000 chunk 94 optimal weight: 7.9990 overall best weight: 3.3786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 128 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 41 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 93 GLN C 69 GLN ** C 120 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 387 ASN C 798 GLN C1244 HIS ** D 232 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 488 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 771 GLN ** E 62 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 73 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 75 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8351 moved from start: 0.2086 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 30507 Z= 0.284 Angle : 0.587 7.629 41586 Z= 0.310 Chirality : 0.043 0.187 4820 Planarity : 0.004 0.100 5266 Dihedral : 13.744 175.215 4930 Min Nonbonded Distance : 1.952 Molprobity Statistics. All-atom Clashscore : 14.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.90 % Favored : 94.10 % Rotamer: Outliers : 0.00 % Allowed : 4.29 % Favored : 95.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.99 % Cis-general : 0.05 % Twisted Proline : 0.66 % 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: -0.89 (0.14), residues: 3812 helix: 0.62 (0.15), residues: 1276 sheet: -0.70 (0.25), residues: 438 loop : -1.35 (0.13), residues: 2098 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP D 236 HIS 0.006 0.001 HIS D 545 PHE 0.017 0.001 PHE D1100 TYR 0.019 0.001 TYR C 726 ARG 0.009 0.000 ARG A 45 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7624 Ramachandran restraints generated. 3812 Oldfield, 0 Emsley, 3812 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7624 Ramachandran restraints generated. 3812 Oldfield, 0 Emsley, 3812 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 245 residues out of total 3251 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 245 time to evaluate : 3.633 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 68 TYR cc_start: 0.8880 (m-10) cc_final: 0.8629 (m-10) REVERT: A 137 ASN cc_start: 0.8903 (p0) cc_final: 0.8472 (p0) REVERT: A 177 TYR cc_start: 0.7681 (m-80) cc_final: 0.6924 (m-80) REVERT: B 29 GLU cc_start: 0.8270 (tm-30) cc_final: 0.8014 (tm-30) REVERT: C 130 MET cc_start: 0.8840 (tpt) cc_final: 0.8611 (tpt) REVERT: C 237 LEU cc_start: 0.7998 (mp) cc_final: 0.7788 (tt) REVERT: C 515 MET cc_start: 0.9205 (tmm) cc_final: 0.8738 (tmm) REVERT: C 1243 MET cc_start: 0.8971 (tmm) cc_final: 0.8586 (tmm) REVERT: C 1315 MET cc_start: 0.8206 (ptm) cc_final: 0.7981 (ptt) REVERT: D 192 MET cc_start: 0.8404 (ttp) cc_final: 0.7986 (tmm) REVERT: D 304 ASP cc_start: 0.7957 (m-30) cc_final: 0.7395 (t0) REVERT: D 581 MET cc_start: 0.8035 (mtp) cc_final: 0.7831 (mtt) REVERT: D 1260 MET cc_start: 0.8408 (mtp) cc_final: 0.8190 (mtp) REVERT: D 1349 GLU cc_start: 0.7952 (pm20) cc_final: 0.7388 (pm20) REVERT: G 9 TRP cc_start: 0.7970 (m100) cc_final: 0.7359 (m100) REVERT: G 41 GLU cc_start: 0.8622 (pp20) cc_final: 0.7924 (pp20) REVERT: G 43 MET cc_start: 0.7477 (tmm) cc_final: 0.5973 (ptp) REVERT: G 73 MET cc_start: 0.8489 (tpp) cc_final: 0.7294 (tpp) outliers start: 0 outliers final: 0 residues processed: 245 average time/residue: 0.3564 time to fit residues: 148.7124 Evaluate side-chains 203 residues out of total 3251 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 203 time to evaluate : 3.303 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 387 random chunks: chunk 125 optimal weight: 6.9990 chunk 336 optimal weight: 20.0000 chunk 73 optimal weight: 10.0000 chunk 219 optimal weight: 3.9990 chunk 92 optimal weight: 0.8980 chunk 374 optimal weight: 50.0000 chunk 310 optimal weight: 6.9990 chunk 173 optimal weight: 5.9990 chunk 31 optimal weight: 0.7980 chunk 123 optimal weight: 5.9990 chunk 196 optimal weight: 4.9990 overall best weight: 3.3386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 128 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 41 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 69 GLN ** C 120 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 238 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 387 ASN ** D 232 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 424 ASN ** D 488 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 771 GLN ** D 921 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D1244 GLN ** E 62 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 73 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 75 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 13 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8357 moved from start: 0.2277 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 30507 Z= 0.279 Angle : 0.590 8.644 41586 Z= 0.311 Chirality : 0.043 0.174 4820 Planarity : 0.004 0.101 5266 Dihedral : 13.757 175.851 4930 Min Nonbonded Distance : 1.943 Molprobity Statistics. All-atom Clashscore : 14.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.75 % Favored : 94.25 % Rotamer: Outliers : 0.07 % Allowed : 2.74 % Favored : 97.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.99 % Cis-general : 0.05 % Twisted Proline : 0.66 % 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: -0.90 (0.14), residues: 3812 helix: 0.62 (0.15), residues: 1285 sheet: -0.69 (0.25), residues: 427 loop : -1.38 (0.13), residues: 2100 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP D 236 HIS 0.005 0.001 HIS C1070 PHE 0.021 0.001 PHE G 39 TYR 0.018 0.001 TYR C 726 ARG 0.008 0.000 ARG D 275 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7624 Ramachandran restraints generated. 3812 Oldfield, 0 Emsley, 3812 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7624 Ramachandran restraints generated. 3812 Oldfield, 0 Emsley, 3812 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 240 residues out of total 3251 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 238 time to evaluate : 3.302 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 68 TYR cc_start: 0.8969 (m-10) cc_final: 0.8768 (m-10) REVERT: A 137 ASN cc_start: 0.8933 (p0) cc_final: 0.8496 (p0) REVERT: A 177 TYR cc_start: 0.7799 (m-80) cc_final: 0.6963 (m-80) REVERT: B 29 GLU cc_start: 0.8262 (tm-30) cc_final: 0.7983 (tm-30) REVERT: C 515 MET cc_start: 0.9232 (tmm) cc_final: 0.8791 (tmm) REVERT: C 1119 MET cc_start: 0.9190 (tpp) cc_final: 0.8548 (tpp) REVERT: C 1243 MET cc_start: 0.8902 (tmm) cc_final: 0.8634 (tmm) REVERT: D 192 MET cc_start: 0.8433 (ttp) cc_final: 0.7971 (tmm) REVERT: D 666 GLU cc_start: 0.8917 (mp0) cc_final: 0.8625 (mp0) REVERT: D 932 MET cc_start: 0.6287 (mmm) cc_final: 0.6060 (mmm) REVERT: D 1189 MET cc_start: 0.7142 (tpt) cc_final: 0.6888 (tpt) REVERT: D 1260 MET cc_start: 0.8379 (mtp) cc_final: 0.8160 (mtp) REVERT: D 1349 GLU cc_start: 0.8078 (pm20) cc_final: 0.7404 (pm20) REVERT: G 9 TRP cc_start: 0.7953 (m100) cc_final: 0.7429 (m100) REVERT: G 41 GLU cc_start: 0.8554 (pp20) cc_final: 0.7850 (pp20) REVERT: G 43 MET cc_start: 0.7331 (tmm) cc_final: 0.5813 (ptt) REVERT: G 73 MET cc_start: 0.8468 (tpp) cc_final: 0.7902 (tpt) outliers start: 2 outliers final: 0 residues processed: 240 average time/residue: 0.3627 time to fit residues: 149.8175 Evaluate side-chains 199 residues out of total 3251 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 199 time to evaluate : 3.517 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 387 random chunks: chunk 361 optimal weight: 20.0000 chunk 42 optimal weight: 5.9990 chunk 213 optimal weight: 0.8980 chunk 273 optimal weight: 2.9990 chunk 211 optimal weight: 5.9990 chunk 315 optimal weight: 3.9990 chunk 209 optimal weight: 0.8980 chunk 373 optimal weight: 4.9990 chunk 233 optimal weight: 0.7980 chunk 227 optimal weight: 4.9990 chunk 172 optimal weight: 1.9990 overall best weight: 1.5184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 128 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 41 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 69 GLN ** C 120 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 387 ASN ** D 232 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 488 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1259 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 62 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 73 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 75 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 13 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8302 moved from start: 0.2261 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 30507 Z= 0.174 Angle : 0.542 8.653 41586 Z= 0.284 Chirality : 0.042 0.258 4820 Planarity : 0.004 0.099 5266 Dihedral : 13.670 176.879 4930 Min Nonbonded Distance : 1.976 Molprobity Statistics. All-atom Clashscore : 12.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.91 % Favored : 95.09 % Rotamer: Outliers : 0.00 % Allowed : 1.97 % Favored : 98.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.99 % Cis-general : 0.05 % Twisted Proline : 0.66 % 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: -0.80 (0.14), residues: 3812 helix: 0.73 (0.15), residues: 1290 sheet: -0.62 (0.25), residues: 426 loop : -1.34 (0.13), residues: 2096 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP D 236 HIS 0.004 0.001 HIS D 364 PHE 0.026 0.001 PHE C1270 TYR 0.014 0.001 TYR D 512 ARG 0.005 0.000 ARG D 388 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7624 Ramachandran restraints generated. 3812 Oldfield, 0 Emsley, 3812 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7624 Ramachandran restraints generated. 3812 Oldfield, 0 Emsley, 3812 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 250 residues out of total 3251 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 250 time to evaluate : 3.603 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 137 ASN cc_start: 0.8939 (p0) cc_final: 0.8444 (p0) REVERT: A 177 TYR cc_start: 0.7633 (m-80) cc_final: 0.6847 (m-80) REVERT: B 186 ASN cc_start: 0.8677 (t0) cc_final: 0.8314 (t0) REVERT: C 515 MET cc_start: 0.9205 (tmm) cc_final: 0.8748 (tmm) REVERT: C 1119 MET cc_start: 0.9121 (tpp) cc_final: 0.8376 (tpp) REVERT: C 1243 MET cc_start: 0.8901 (tmm) cc_final: 0.8564 (tmm) REVERT: C 1290 MET cc_start: 0.8324 (tpp) cc_final: 0.7477 (tpp) REVERT: D 129 ASP cc_start: 0.8124 (t0) cc_final: 0.7741 (t0) REVERT: D 192 MET cc_start: 0.8483 (ttp) cc_final: 0.7997 (tmm) REVERT: D 651 HIS cc_start: 0.8187 (t-90) cc_final: 0.7971 (t-90) REVERT: D 666 GLU cc_start: 0.8810 (mp0) cc_final: 0.8458 (mp0) REVERT: D 932 MET cc_start: 0.6379 (mmm) cc_final: 0.6164 (mpp) REVERT: D 1254 GLU cc_start: 0.8112 (tm-30) cc_final: 0.7723 (tm-30) REVERT: D 1260 MET cc_start: 0.8399 (mtp) cc_final: 0.8160 (mtp) REVERT: D 1349 GLU cc_start: 0.7989 (pm20) cc_final: 0.7294 (pm20) REVERT: G 35 MET cc_start: 0.9118 (mpp) cc_final: 0.8867 (mpp) REVERT: G 41 GLU cc_start: 0.8536 (pp20) cc_final: 0.8004 (pp20) REVERT: G 73 MET cc_start: 0.8414 (tpp) cc_final: 0.8117 (mmm) outliers start: 0 outliers final: 0 residues processed: 250 average time/residue: 0.3634 time to fit residues: 155.6559 Evaluate side-chains 200 residues out of total 3251 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 200 time to evaluate : 3.398 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 387 random chunks: chunk 230 optimal weight: 0.9980 chunk 148 optimal weight: 20.0000 chunk 222 optimal weight: 0.0010 chunk 112 optimal weight: 8.9990 chunk 73 optimal weight: 0.7980 chunk 72 optimal weight: 0.9980 chunk 237 optimal weight: 0.9990 chunk 254 optimal weight: 3.9990 chunk 184 optimal weight: 3.9990 chunk 34 optimal weight: 7.9990 chunk 293 optimal weight: 40.0000 overall best weight: 0.7588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 128 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 93 GLN ** B 227 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 69 GLN ** C 120 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 387 ASN D 164 GLN ** D 488 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 489 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1259 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 62 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 73 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 75 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 13 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8262 moved from start: 0.2309 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.041 30507 Z= 0.144 Angle : 0.540 13.123 41586 Z= 0.278 Chirality : 0.042 0.216 4820 Planarity : 0.004 0.097 5266 Dihedral : 13.583 176.985 4930 Min Nonbonded Distance : 2.002 Molprobity Statistics. All-atom Clashscore : 11.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.51 % Favored : 95.49 % Rotamer: Outliers : 0.00 % Allowed : 1.27 % Favored : 98.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.99 % Cis-general : 0.05 % Twisted Proline : 0.66 % 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: -0.71 (0.14), residues: 3812 helix: 0.81 (0.15), residues: 1289 sheet: -0.69 (0.25), residues: 440 loop : -1.27 (0.14), residues: 2083 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP G 9 HIS 0.003 0.001 HIS D 364 PHE 0.018 0.001 PHE D1100 TYR 0.012 0.001 TYR D 512 ARG 0.008 0.000 ARG A 45 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7624 Ramachandran restraints generated. 3812 Oldfield, 0 Emsley, 3812 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7624 Ramachandran restraints generated. 3812 Oldfield, 0 Emsley, 3812 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 262 residues out of total 3251 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 262 time to evaluate : 3.571 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: A 137 ASN cc_start: 0.8895 (p0) cc_final: 0.8396 (p0) REVERT: A 177 TYR cc_start: 0.7666 (m-80) cc_final: 0.6858 (m-80) REVERT: B 186 ASN cc_start: 0.8676 (t0) cc_final: 0.8340 (t0) REVERT: C 31 GLN cc_start: 0.8481 (mm110) cc_final: 0.8163 (tp40) REVERT: C 515 MET cc_start: 0.9189 (tmm) cc_final: 0.8708 (tmm) REVERT: C 951 MET cc_start: 0.9289 (tmm) cc_final: 0.8471 (tmm) REVERT: C 1066 MET cc_start: 0.9048 (ppp) cc_final: 0.8842 (ppp) REVERT: C 1119 MET cc_start: 0.9077 (tpp) cc_final: 0.8343 (tpp) REVERT: C 1243 MET cc_start: 0.8919 (tmm) cc_final: 0.8575 (tmm) REVERT: D 129 ASP cc_start: 0.8016 (t0) cc_final: 0.7630 (t70) REVERT: D 192 MET cc_start: 0.8511 (ttp) cc_final: 0.7967 (tmm) REVERT: D 651 HIS cc_start: 0.8137 (t-90) cc_final: 0.7923 (t-90) REVERT: D 666 GLU cc_start: 0.8840 (mp0) cc_final: 0.8467 (mp0) REVERT: D 1189 MET cc_start: 0.7349 (tpt) cc_final: 0.7098 (tpt) REVERT: D 1254 GLU cc_start: 0.8107 (tm-30) cc_final: 0.7722 (tm-30) REVERT: D 1349 GLU cc_start: 0.7893 (pm20) cc_final: 0.7269 (pm20) REVERT: G 9 TRP cc_start: 0.7776 (m100) cc_final: 0.6892 (m100) REVERT: G 35 MET cc_start: 0.9127 (mpp) cc_final: 0.8846 (mpp) REVERT: G 41 GLU cc_start: 0.8623 (pp20) cc_final: 0.7987 (pp20) REVERT: G 43 MET cc_start: 0.7416 (tmm) cc_final: 0.6064 (ptm) outliers start: 0 outliers final: 0 residues processed: 262 average time/residue: 0.3734 time to fit residues: 165.9954 Evaluate side-chains 207 residues out of total 3251 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 207 time to evaluate : 3.344 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 387 random chunks: chunk 339 optimal weight: 0.0010 chunk 357 optimal weight: 50.0000 chunk 326 optimal weight: 20.0000 chunk 347 optimal weight: 8.9990 chunk 209 optimal weight: 0.2980 chunk 151 optimal weight: 6.9990 chunk 272 optimal weight: 4.9990 chunk 106 optimal weight: 0.3980 chunk 314 optimal weight: 0.8980 chunk 328 optimal weight: 7.9990 chunk 346 optimal weight: 8.9990 overall best weight: 1.3188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 128 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 69 GLN ** C 120 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 387 ASN C 799 ASN D 164 GLN ** D 294 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 488 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 62 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 73 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 75 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 13 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8275 moved from start: 0.2405 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 30507 Z= 0.162 Angle : 0.537 8.626 41586 Z= 0.278 Chirality : 0.042 0.216 4820 Planarity : 0.004 0.095 5266 Dihedral : 13.571 176.602 4930 Min Nonbonded Distance : 1.986 Molprobity Statistics. All-atom Clashscore : 12.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.62 % Favored : 95.38 % Rotamer: Outliers : 0.04 % Allowed : 0.67 % Favored : 99.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.99 % Cis-general : 0.05 % Twisted Proline : 0.66 % 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: -0.67 (0.14), residues: 3812 helix: 0.87 (0.15), residues: 1284 sheet: -0.63 (0.25), residues: 446 loop : -1.27 (0.14), residues: 2082 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP D 236 HIS 0.003 0.001 HIS C 628 PHE 0.021 0.001 PHE D1100 TYR 0.013 0.001 TYR D 512 ARG 0.007 0.000 ARG D 933 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7624 Ramachandran restraints generated. 3812 Oldfield, 0 Emsley, 3812 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7624 Ramachandran restraints generated. 3812 Oldfield, 0 Emsley, 3812 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 253 residues out of total 3251 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 252 time to evaluate : 3.244 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 68 TYR cc_start: 0.8872 (m-10) cc_final: 0.8552 (m-10) REVERT: A 137 ASN cc_start: 0.8893 (p0) cc_final: 0.8395 (p0) REVERT: A 177 TYR cc_start: 0.7654 (m-80) cc_final: 0.6765 (m-80) REVERT: B 186 ASN cc_start: 0.8719 (t0) cc_final: 0.8370 (t0) REVERT: C 515 MET cc_start: 0.9193 (tmm) cc_final: 0.8669 (tmm) REVERT: C 951 MET cc_start: 0.9285 (tmm) cc_final: 0.8483 (tmm) REVERT: C 1066 MET cc_start: 0.9061 (ppp) cc_final: 0.8823 (ppp) REVERT: C 1085 MET cc_start: 0.9139 (tpp) cc_final: 0.8816 (mmm) REVERT: C 1119 MET cc_start: 0.9086 (tpp) cc_final: 0.8323 (tpp) REVERT: C 1243 MET cc_start: 0.8889 (tmm) cc_final: 0.8565 (tmm) REVERT: D 129 ASP cc_start: 0.7922 (t0) cc_final: 0.7630 (t70) REVERT: D 192 MET cc_start: 0.8554 (ttp) cc_final: 0.7987 (tmm) REVERT: D 651 HIS cc_start: 0.8150 (t-90) cc_final: 0.7950 (t70) REVERT: D 1189 MET cc_start: 0.7370 (tpt) cc_final: 0.7102 (tpt) REVERT: D 1254 GLU cc_start: 0.8156 (tm-30) cc_final: 0.7939 (tm-30) REVERT: D 1349 GLU cc_start: 0.7933 (pm20) cc_final: 0.7302 (pm20) REVERT: G 41 GLU cc_start: 0.8584 (pp20) cc_final: 0.7965 (pp20) REVERT: G 43 MET cc_start: 0.7363 (tmm) cc_final: 0.6029 (ptp) outliers start: 1 outliers final: 0 residues processed: 253 average time/residue: 0.3537 time to fit residues: 154.7422 Evaluate side-chains 199 residues out of total 3251 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 199 time to evaluate : 3.383 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 387 random chunks: chunk 228 optimal weight: 9.9990 chunk 367 optimal weight: 9.9990 chunk 224 optimal weight: 2.9990 chunk 174 optimal weight: 5.9990 chunk 255 optimal weight: 8.9990 chunk 385 optimal weight: 0.0170 chunk 354 optimal weight: 50.0000 chunk 307 optimal weight: 1.9990 chunk 31 optimal weight: 0.9980 chunk 237 optimal weight: 4.9990 chunk 188 optimal weight: 0.7980 overall best weight: 1.3622 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 128 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 93 GLN C 69 GLN C 120 GLN C 387 ASN D 164 GLN ** D 488 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1259 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 62 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 73 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 75 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 13 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8273 moved from start: 0.2487 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 30507 Z= 0.164 Angle : 0.542 8.691 41586 Z= 0.281 Chirality : 0.042 0.212 4820 Planarity : 0.004 0.096 5266 Dihedral : 13.573 176.697 4930 Min Nonbonded Distance : 1.990 Molprobity Statistics. All-atom Clashscore : 12.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.59 % Favored : 95.41 % Rotamer: Outliers : 0.04 % Allowed : 0.35 % Favored : 99.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.99 % Cis-general : 0.05 % Twisted Proline : 0.66 % 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: -0.63 (0.14), residues: 3812 helix: 0.91 (0.15), residues: 1285 sheet: -0.52 (0.26), residues: 417 loop : -1.28 (0.13), residues: 2110 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP D 236 HIS 0.003 0.001 HIS D 364 PHE 0.019 0.001 PHE D1100 TYR 0.014 0.001 TYR D 140 ARG 0.006 0.000 ARG C 378 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7624 Ramachandran restraints generated. 3812 Oldfield, 0 Emsley, 3812 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7624 Ramachandran restraints generated. 3812 Oldfield, 0 Emsley, 3812 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 246 residues out of total 3251 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 245 time to evaluate : 3.436 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 68 TYR cc_start: 0.8879 (m-10) cc_final: 0.8554 (m-10) REVERT: A 137 ASN cc_start: 0.8880 (p0) cc_final: 0.8384 (p0) REVERT: A 177 TYR cc_start: 0.7748 (m-80) cc_final: 0.6761 (m-80) REVERT: B 186 ASN cc_start: 0.8724 (t0) cc_final: 0.8367 (t0) REVERT: C 515 MET cc_start: 0.9230 (tmm) cc_final: 0.8711 (tmm) REVERT: C 951 MET cc_start: 0.9297 (tmm) cc_final: 0.8502 (tmm) REVERT: C 1085 MET cc_start: 0.9144 (tpp) cc_final: 0.8821 (mmm) REVERT: C 1243 MET cc_start: 0.8900 (tmm) cc_final: 0.8595 (tmm) REVERT: D 129 ASP cc_start: 0.7951 (t0) cc_final: 0.7646 (t70) REVERT: D 192 MET cc_start: 0.8602 (ttp) cc_final: 0.8009 (tmm) REVERT: D 1189 MET cc_start: 0.7346 (tpt) cc_final: 0.7058 (tpt) REVERT: D 1254 GLU cc_start: 0.8096 (tm-30) cc_final: 0.7850 (tm-30) REVERT: D 1349 GLU cc_start: 0.7934 (pm20) cc_final: 0.7317 (pm20) REVERT: G 9 TRP cc_start: 0.7760 (m100) cc_final: 0.7080 (m100) REVERT: G 41 GLU cc_start: 0.8610 (pp20) cc_final: 0.7915 (pp20) REVERT: G 43 MET cc_start: 0.7233 (tmm) cc_final: 0.5894 (ptp) outliers start: 1 outliers final: 0 residues processed: 246 average time/residue: 0.3904 time to fit residues: 165.3053 Evaluate side-chains 199 residues out of total 3251 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 199 time to evaluate : 3.548 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 387 random chunks: chunk 243 optimal weight: 0.8980 chunk 327 optimal weight: 20.0000 chunk 94 optimal weight: 10.0000 chunk 283 optimal weight: 6.9990 chunk 45 optimal weight: 6.9990 chunk 85 optimal weight: 10.0000 chunk 307 optimal weight: 4.9990 chunk 128 optimal weight: 6.9990 chunk 315 optimal weight: 0.8980 chunk 38 optimal weight: 0.0070 chunk 56 optimal weight: 5.9990 overall best weight: 2.5602 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 128 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 41 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 46 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 69 GLN C 387 ASN D 164 GLN ** D 232 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 341 ASN ** D 488 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 771 GLN ** E 62 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 73 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 75 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 13 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3589 r_free = 0.3589 target = 0.084568 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.2995 r_free = 0.2995 target = 0.058218 restraints weight = 113291.826| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 60)----------------| | r_work = 0.3037 r_free = 0.3037 target = 0.059828 restraints weight = 63708.926| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3065 r_free = 0.3065 target = 0.060926 restraints weight = 42733.413| |-----------------------------------------------------------------------------| r_work (final): 0.3010 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8313 moved from start: 0.2596 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 30507 Z= 0.234 Angle : 0.576 8.533 41586 Z= 0.299 Chirality : 0.043 0.218 4820 Planarity : 0.004 0.096 5266 Dihedral : 13.620 176.128 4930 Min Nonbonded Distance : 1.959 Molprobity Statistics. All-atom Clashscore : 13.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.38 % Favored : 94.62 % Rotamer: Outliers : 0.00 % Allowed : 0.46 % Favored : 99.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.99 % Cis-general : 0.05 % Twisted Proline : 0.66 % 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: -0.68 (0.14), residues: 3812 helix: 0.88 (0.15), residues: 1285 sheet: -0.58 (0.26), residues: 409 loop : -1.29 (0.13), residues: 2118 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP C 807 HIS 0.005 0.001 HIS D 545 PHE 0.017 0.001 PHE D1100 TYR 0.018 0.001 TYR D 609 ARG 0.006 0.000 ARG D 388 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5061.59 seconds wall clock time: 93 minutes 10.69 seconds (5590.69 seconds total)