Starting phenix.real_space_refine on Fri Mar 22 02:56:45 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6oul_20203/03_2024/6oul_20203_neut_trim_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6oul_20203/03_2024/6oul_20203.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.4 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6oul_20203/03_2024/6oul_20203.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6oul_20203/03_2024/6oul_20203.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6oul_20203/03_2024/6oul_20203_neut_trim_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6oul_20203/03_2024/6oul_20203_neut_trim_updated.pdb" } resolution = 3.4 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.007 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 117 5.49 5 Mg 1 5.21 5 S 130 5.16 5 C 19682 2.51 5 N 5632 2.21 5 O 6363 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "G PHE 231": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I TYR 47": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I PHE 57": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I ARG 268": "NH1" <-> "NH2" Residue "I ARG 332": "NH1" <-> "NH2" Residue "I PHE 514": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I TYR 605": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I PHE 1164": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I TYR 1251": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I TYR 1305": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J TYR 360": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J TYR 1302": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J PHE 1319": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.09s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib" Total number of atoms: 31927 Number of models: 1 Model: "" Number of chains: 12 Chain: "G" Number of atoms: 1785 Number of conformers: 1 Conformer: "" Number of residues, atoms: 231, 1785 Classifications: {'peptide': 231} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'CIS': 2, 'PTRANS': 9, 'TRANS': 219} Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 11 Unresolved non-hydrogen dihedrals: 5 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'GLU:plan': 1} Unresolved non-hydrogen planarities: 4 Chain: "H" Number of atoms: 1681 Number of conformers: 1 Conformer: "" Number of residues, atoms: 219, 1681 Classifications: {'peptide': 219} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PCIS': 1, 'PTRANS': 7, 'TRANS': 210} Chain breaks: 1 Unresolved non-hydrogen bonds: 7 Unresolved non-hydrogen angles: 9 Unresolved non-hydrogen dihedrals: 5 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLU:plan': 1} Unresolved non-hydrogen planarities: 4 Chain: "I" Number of atoms: 10575 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1341, 10575 Classifications: {'peptide': 1341} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'CIS': 1, 'PCIS': 1, 'PTRANS': 55, 'TRANS': 1283} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 3 Unresolved non-hydrogen dihedrals: 1 Unresolved non-hydrogen chiralities: 1 Chain: "J" Number of atoms: 10386 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1337, 10386 Classifications: {'peptide': 1337} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'CIS': 5, 'PTRANS': 55, 'TRANS': 1276} Chain breaks: 2 Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 8 Chain: "K" Number of atoms: 627 Number of conformers: 1 Conformer: "" Number of residues, atoms: 79, 627 Classifications: {'peptide': 79} Link IDs: {'CIS': 1, 'PTRANS': 2, 'TRANS': 75} Chain: "L" Number of atoms: 3821 Number of conformers: 1 Conformer: "" Number of residues, atoms: 471, 3821 Classifications: {'peptide': 471} Incomplete info: {'truncation_to_alanine': 4} Link IDs: {'CIS': 1, 'PTRANS': 14, 'TRANS': 455} Chain breaks: 2 Unresolved non-hydrogen bonds: 16 Unresolved non-hydrogen angles: 20 Unresolved non-hydrogen dihedrals: 12 Planarities with less than four sites: {'GLU:plan': 1, 'ARG:plan': 1, 'ASP:plan': 2} Unresolved non-hydrogen planarities: 15 Chain: "P" Number of atoms: 1253 Number of conformers: 1 Conformer: "" Number of residues, atoms: 61, 1253 Classifications: {'DNA': 61} Link IDs: {'rna3p': 60} Chain breaks: 1 Chain: "Q" Number of atoms: 1143 Number of conformers: 1 Conformer: "" Number of residues, atoms: 56, 1143 Classifications: {'DNA': 56} Link IDs: {'rna3p': 55} Chain breaks: 1 Chain: "R" Number of atoms: 572 Number of conformers: 1 Conformer: "" Number of residues, atoms: 73, 572 Classifications: {'peptide': 73} Link IDs: {'PCIS': 1, 'PTRANS': 3, 'TRANS': 68} Chain: "I" Number of atoms: 27 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 27 Unusual residues: {'1N7': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 16 Unresolved non-hydrogen angles: 24 Unresolved non-hydrogen dihedrals: 13 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'1N7:plan-1': 1} Unresolved non-hydrogen planarities: 3 Chain: "J" Number of atoms: 30 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 30 Unusual residues: {' MG': 1, ' ZN': 2, '1N7': 1} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 16 Unresolved non-hydrogen angles: 24 Unresolved non-hydrogen dihedrals: 13 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'1N7:plan-1': 1} Unresolved non-hydrogen planarities: 3 Chain: "L" Number of atoms: 27 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 27 Unusual residues: {'1N7': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 16 Unresolved non-hydrogen angles: 24 Unresolved non-hydrogen dihedrals: 13 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'1N7:plan-1': 1} Unresolved non-hydrogen planarities: 3 List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 14490 SG CYS J 70 101.624 65.443 73.534 1.00 26.34 S ATOM 14504 SG CYS J 72 99.773 63.370 71.559 1.00 30.73 S ATOM 14612 SG CYS J 85 103.176 63.770 70.385 1.00 24.78 S ATOM 14636 SG CYS J 88 100.008 66.956 70.982 1.00 29.58 S ATOM 20324 SG CYS J 814 132.497 114.536 104.965 1.00 26.70 S ATOM 20889 SG CYS J 888 128.900 114.353 103.856 1.00 24.43 S ATOM 20940 SG CYS J 895 130.617 112.682 107.101 1.00 18.04 S ATOM 20961 SG CYS J 898 130.695 116.116 107.359 1.00 19.69 S Time building chain proxies: 16.18, per 1000 atoms: 0.51 Number of scatterers: 31927 At special positions: 0 Unit cell: (154.7, 189.8, 191.1, 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 130 16.00 P 117 15.00 Mg 1 11.99 O 6363 8.00 N 5632 7.00 C 19682 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: 13.21 Conformation dependent library (CDL) restraints added in 4.5 seconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN J1502 " pdb="ZN ZN J1502 " - pdb=" SG CYS J 70 " pdb="ZN ZN J1502 " - pdb=" SG CYS J 85 " pdb="ZN ZN J1502 " - pdb=" SG CYS J 72 " pdb="ZN ZN J1502 " - pdb=" SG CYS J 88 " pdb=" ZN J1503 " pdb="ZN ZN J1503 " - pdb=" SG CYS J 888 " pdb="ZN ZN J1503 " - pdb=" SG CYS J 895 " pdb="ZN ZN J1503 " - pdb=" SG CYS J 898 " pdb="ZN ZN J1503 " - pdb=" SG CYS J 814 " Number of angles added : 12 7454 Ramachandran restraints generated. 3727 Oldfield, 0 Emsley, 3727 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 6966 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 117 helices and 32 sheets defined 35.2% alpha, 6.6% beta 53 base pairs and 93 stacking pairs defined. Time for finding SS restraints: 14.00 Creating SS restraints... Processing helix chain 'G' and resid 35 through 49 removed outlier: 3.784A pdb=" N ALA G 42 " --> pdb=" O THR G 38 " (cutoff:3.500A) Processing helix chain 'G' and resid 78 through 87 removed outlier: 4.421A pdb=" N GLY G 87 " --> pdb=" O LEU G 83 " (cutoff:3.500A) Processing helix chain 'G' and resid 155 through 158 No H-bonds generated for 'chain 'G' and resid 155 through 158' Processing helix chain 'G' and resid 213 through 228 Processing helix chain 'H' and resid 35 through 49 Processing helix chain 'H' and resid 78 through 86 Processing helix chain 'H' and resid 112 through 114 No H-bonds generated for 'chain 'H' and resid 112 through 114' Processing helix chain 'H' and resid 213 through 228 removed outlier: 4.264A pdb=" N ARG H 218 " --> pdb=" O GLU H 214 " (cutoff:3.500A) removed outlier: 4.054A pdb=" N LEU H 228 " --> pdb=" O LEU H 224 " (cutoff:3.500A) Processing helix chain 'I' and resid 29 through 38 Processing helix chain 'I' and resid 49 through 56 Processing helix chain 'I' and resid 82 through 88 Processing helix chain 'I' and resid 207 through 212 Processing helix chain 'I' and resid 217 through 224 Processing helix chain 'I' and resid 243 through 246 Processing helix chain 'I' and resid 271 through 280 Processing helix chain 'I' and resid 289 through 291 No H-bonds generated for 'chain 'I' and resid 289 through 291' Processing helix chain 'I' and resid 319 through 326 Processing helix chain 'I' and resid 347 through 353 Processing helix chain 'I' and resid 359 through 370 Processing helix chain 'I' and resid 378 through 388 Processing helix chain 'I' and resid 400 through 408 Processing helix chain 'I' and resid 422 through 437 Processing helix chain 'I' and resid 456 through 480 removed outlier: 4.086A pdb=" N ALA I 474 " --> pdb=" O ARG I 470 " (cutoff:3.500A) Processing helix chain 'I' and resid 496 through 507 Processing helix chain 'I' and resid 520 through 526 Processing helix chain 'I' and resid 671 through 673 No H-bonds generated for 'chain 'I' and resid 671 through 673' Processing helix chain 'I' and resid 676 through 685 Processing helix chain 'I' and resid 704 through 710 Processing helix chain 'I' and resid 820 through 824 Processing helix chain 'I' and resid 862 through 864 No H-bonds generated for 'chain 'I' and resid 862 through 864' Processing helix chain 'I' and resid 899 through 905 Processing helix chain 'I' and resid 943 through 980 removed outlier: 3.516A pdb=" N GLY I 970 " --> pdb=" O ILE I 966 " (cutoff:3.500A) Processing helix chain 'I' and resid 1011 through 1037 Processing helix chain 'I' and resid 1100 through 1106 removed outlier: 3.536A pdb=" N VAL I1103 " --> pdb=" O PRO I1100 " (cutoff:3.500A) Proline residue: I1104 - end of helix No H-bonds generated for 'chain 'I' and resid 1100 through 1106' Processing helix chain 'I' and resid 1110 through 1133 Processing helix chain 'I' and resid 1138 through 1150 Processing helix chain 'I' and resid 1166 through 1175 removed outlier: 3.594A pdb=" N MET I1170 " --> pdb=" O ASP I1166 " (cutoff:3.500A) removed outlier: 3.966A pdb=" N ARG I1171 " --> pdb=" O GLU I1167 " (cutoff:3.500A) Processing helix chain 'I' and resid 1186 through 1188 No H-bonds generated for 'chain 'I' and resid 1186 through 1188' Processing helix chain 'I' and resid 1192 through 1201 Processing helix chain 'I' and resid 1239 through 1241 No H-bonds generated for 'chain 'I' and resid 1239 through 1241' Processing helix chain 'I' and resid 1272 through 1280 Processing helix chain 'I' and resid 1284 through 1291 Processing helix chain 'I' and resid 1300 through 1310 Processing helix chain 'I' and resid 1321 through 1331 Processing helix chain 'J' and resid 27 through 33 Processing helix chain 'J' and resid 59 through 62 No H-bonds generated for 'chain 'J' and resid 59 through 62' Processing helix chain 'J' and resid 78 through 80 No H-bonds generated for 'chain 'J' and resid 78 through 80' Processing helix chain 'J' and resid 95 through 99 Processing helix chain 'J' and resid 114 through 118 removed outlier: 4.049A pdb=" N LYS J 118 " --> pdb=" O TRP J 115 " (cutoff:3.500A) Processing helix chain 'J' and resid 123 through 128 Processing helix chain 'J' and resid 132 through 139 Processing helix chain 'J' and resid 162 through 169 Processing helix chain 'J' and resid 181 through 191 Processing helix chain 'J' and resid 194 through 207 Processing helix chain 'J' and resid 211 through 229 Processing helix chain 'J' and resid 234 through 236 No H-bonds generated for 'chain 'J' and resid 234 through 236' Processing helix chain 'J' and resid 265 through 284 Processing helix chain 'J' and resid 289 through 307 Processing helix chain 'J' and resid 327 through 331 Processing helix chain 'J' and resid 370 through 376 Processing helix chain 'J' and resid 378 through 388 Processing helix chain 'J' and resid 394 through 403 Processing helix chain 'J' and resid 406 through 415 removed outlier: 3.952A pdb=" N ASP J 410 " --> pdb=" O ALA J 406 " (cutoff:3.500A) Processing helix chain 'J' and resid 454 through 457 No H-bonds generated for 'chain 'J' and resid 454 through 457' Processing helix chain 'J' and resid 474 through 482 Processing helix chain 'J' and resid 505 through 513 Processing helix chain 'J' and resid 530 through 538 Processing helix chain 'J' and resid 574 through 579 Processing helix chain 'J' and resid 589 through 591 No H-bonds generated for 'chain 'J' and resid 589 through 591' Processing helix chain 'J' and resid 599 through 612 Processing helix chain 'J' and resid 615 through 635 Processing helix chain 'J' and resid 650 through 669 Processing helix chain 'J' and resid 675 through 701 Processing helix chain 'J' and resid 721 through 727 Processing helix chain 'J' and resid 734 through 740 Processing helix chain 'J' and resid 769 through 803 removed outlier: 3.979A pdb=" N HIS J 777 " --> pdb=" O PHE J 773 " (cutoff:3.500A) removed outlier: 4.324A pdb=" N GLY J 778 " --> pdb=" O ILE J 774 " (cutoff:3.500A) removed outlier: 4.447A pdb=" N THR J 790 " --> pdb=" O THR J 786 " (cutoff:3.500A) removed outlier: 4.029A pdb=" N ALA J 791 " --> pdb=" O ALA J 787 " (cutoff:3.500A) removed outlier: 3.567A pdb=" N TYR J 795 " --> pdb=" O ALA J 791 " (cutoff:3.500A) removed outlier: 3.572A pdb=" N ARG J 798 " --> pdb=" O GLY J 794 " (cutoff:3.500A) Processing helix chain 'J' and resid 866 through 874 Processing helix chain 'J' and resid 885 through 887 No H-bonds generated for 'chain 'J' and resid 885 through 887' Processing helix chain 'J' and resid 915 through 927 Proline residue: J 926 - end of helix Processing helix chain 'J' and resid 1139 through 1146 Processing helix chain 'J' and resid 1217 through 1243 removed outlier: 3.571A pdb=" N GLY J1225 " --> pdb=" O LEU J1221 " (cutoff:3.500A) removed outlier: 7.820A pdb=" N VAL J1226 " --> pdb=" O ARG J1222 " (cutoff:3.500A) removed outlier: 9.066A pdb=" N HIS J1227 " --> pdb=" O LEU J1223 " (cutoff:3.500A) removed outlier: 3.688A pdb=" N ALA J1228 " --> pdb=" O ARG J1224 " (cutoff:3.500A) removed outlier: 4.187A pdb=" N VAL J1229 " --> pdb=" O GLY J1225 " (cutoff:3.500A) Processing helix chain 'J' and resid 1250 through 1260 Processing helix chain 'J' and resid 1282 through 1294 Processing helix chain 'J' and resid 1309 through 1314 Processing helix chain 'J' and resid 1320 through 1323 No H-bonds generated for 'chain 'J' and resid 1320 through 1323' Processing helix chain 'J' and resid 1328 through 1338 Processing helix chain 'J' and resid 1348 through 1352 Processing helix chain 'J' and resid 1361 through 1372 removed outlier: 4.389A pdb=" N TYR J1365 " --> pdb=" O THR J1361 " (cutoff:3.500A) Processing helix chain 'K' and resid 7 through 12 Processing helix chain 'K' and resid 18 through 31 Processing helix chain 'K' and resid 46 through 56 Processing helix chain 'K' and resid 61 through 77 removed outlier: 3.547A pdb=" N GLN K 75 " --> pdb=" O GLU K 71 " (cutoff:3.500A) Processing helix chain 'L' and resid 97 through 107 removed outlier: 3.759A pdb=" N GLU L 104 " --> pdb=" O MET L 100 " (cutoff:3.500A) Processing helix chain 'L' and resid 113 through 135 Processing helix chain 'L' and resid 138 through 152 removed outlier: 3.861A pdb=" N LEU L 144 " --> pdb=" O ALA L 140 " (cutoff:3.500A) Processing helix chain 'L' and resid 215 through 233 Processing helix chain 'L' and resid 244 through 257 Processing helix chain 'L' and resid 263 through 289 Processing helix chain 'L' and resid 299 through 306 removed outlier: 4.315A pdb=" N LEU L 305 " --> pdb=" O ASN L 301 " (cutoff:3.500A) Processing helix chain 'L' and resid 317 through 322 Processing helix chain 'L' and resid 331 through 351 removed outlier: 4.051A pdb=" N GLU L 335 " --> pdb=" O HIS L 331 " (cutoff:3.500A) removed outlier: 4.910A pdb=" N GLU L 336 " --> pdb=" O ASP L 332 " (cutoff:3.500A) removed outlier: 3.628A pdb=" N ARG L 339 " --> pdb=" O GLU L 335 " (cutoff:3.500A) Processing helix chain 'L' and resid 356 through 391 removed outlier: 5.372A pdb=" N ARG L 385 " --> pdb=" O GLU L 381 " (cutoff:3.500A) removed outlier: 5.290A pdb=" N LEU L 386 " --> pdb=" O ALA L 382 " (cutoff:3.500A) Processing helix chain 'L' and resid 401 through 418 removed outlier: 3.540A pdb=" N LYS L 418 " --> pdb=" O LYS L 414 " (cutoff:3.500A) Processing helix chain 'L' and resid 427 through 446 removed outlier: 4.549A pdb=" N TRP L 433 " --> pdb=" O THR L 429 " (cutoff:3.500A) removed outlier: 4.100A pdb=" N TRP L 434 " --> pdb=" O TYR L 430 " (cutoff:3.500A) Processing helix chain 'L' and resid 454 through 473 Processing helix chain 'L' and resid 482 through 486 Processing helix chain 'L' and resid 493 through 499 Processing helix chain 'L' and resid 519 through 522 Processing helix chain 'L' and resid 531 through 550 removed outlier: 3.736A pdb=" N GLY L 550 " --> pdb=" O ASP L 546 " (cutoff:3.500A) Processing helix chain 'L' and resid 553 through 562 Processing helix chain 'L' and resid 573 through 580 Processing helix chain 'L' and resid 584 through 599 Processing helix chain 'L' and resid 605 through 610 Processing helix chain 'R' and resid 264 through 273 Processing helix chain 'R' and resid 278 through 281 No H-bonds generated for 'chain 'R' and resid 278 through 281' Processing helix chain 'R' and resid 286 through 290 Processing helix chain 'R' and resid 297 through 309 Processing sheet with id= A, first strand: chain 'G' and resid 25 through 28 removed outlier: 3.870A pdb=" N LEU G 198 " --> pdb=" O ALA G 190 " (cutoff:3.500A) Processing sheet with id= B, first strand: chain 'G' and resid 58 through 61 removed outlier: 3.738A pdb=" N GLU G 58 " --> pdb=" O LYS G 145 " (cutoff:3.500A) Processing sheet with id= C, first strand: chain 'G' and resid 90 through 92 Processing sheet with id= D, first strand: chain 'G' and resid 108 through 111 removed outlier: 3.694A pdb=" N CYS G 131 " --> pdb=" O VAL G 110 " (cutoff:3.500A) Processing sheet with id= E, first strand: chain 'G' and resid 180 through 184 removed outlier: 6.773A pdb=" N GLU G 206 " --> pdb=" O GLU G 181 " (cutoff:3.500A) removed outlier: 4.618A pdb=" N ILE G 183 " --> pdb=" O GLU G 204 " (cutoff:3.500A) removed outlier: 6.919A pdb=" N GLU G 204 " --> pdb=" O ILE G 183 " (cutoff:3.500A) Processing sheet with id= F, first strand: chain 'H' and resid 97 through 101 removed outlier: 3.526A pdb=" N VAL H 98 " --> pdb=" O VAL H 146 " (cutoff:3.500A) removed outlier: 3.646A pdb=" N ARG H 143 " --> pdb=" O GLU H 60 " (cutoff:3.500A) removed outlier: 3.770A pdb=" N GLU H 58 " --> pdb=" O LYS H 145 " (cutoff:3.500A) removed outlier: 6.110A pdb=" N GLN H 147 " --> pdb=" O VAL H 56 " (cutoff:3.500A) removed outlier: 5.798A pdb=" N VAL H 56 " --> pdb=" O GLN H 147 " (cutoff:3.500A) removed outlier: 6.743A pdb=" N GLY H 149 " --> pdb=" O CYS H 54 " (cutoff:3.500A) removed outlier: 4.818A pdb=" N CYS H 54 " --> pdb=" O GLY H 149 " (cutoff:3.500A) Processing sheet with id= G, first strand: chain 'H' and resid 109 through 111 Processing sheet with id= H, first strand: chain 'H' and resid 180 through 183 removed outlier: 6.127A pdb=" N GLU H 206 " --> pdb=" O GLU H 181 " (cutoff:3.500A) Processing sheet with id= I, first strand: chain 'I' and resid 66 through 69 Processing sheet with id= J, first strand: chain 'I' and resid 73 through 75 Processing sheet with id= K, first strand: chain 'I' and resid 93 through 95 Processing sheet with id= L, first strand: chain 'I' and resid 143 through 145 Processing sheet with id= M, first strand: chain 'I' and resid 154 through 158 Processing sheet with id= N, first strand: chain 'I' and resid 185 through 189 removed outlier: 3.670A pdb=" N ASN I 193 " --> pdb=" O ASP I 189 " (cutoff:3.500A) Processing sheet with id= O, first strand: chain 'I' and resid 591 through 593 Processing sheet with id= P, first strand: chain 'I' and resid 633 through 637 Processing sheet with id= Q, first strand: chain 'I' and resid 748 through 751 removed outlier: 3.824A pdb=" N ARG I 731 " --> pdb=" O ASP I 728 " (cutoff:3.500A) removed outlier: 5.411A pdb=" N LYS I 735 " --> pdb=" O VAL I 724 " (cutoff:3.500A) removed outlier: 5.408A pdb=" N VAL I 724 " --> pdb=" O LYS I 735 " (cutoff:3.500A) Processing sheet with id= R, first strand: chain 'I' and resid 798 through 803 removed outlier: 3.776A pdb=" N MET I1230 " --> pdb=" O MET I 800 " (cutoff:3.500A) Processing sheet with id= S, first strand: chain 'I' and resid 830 through 835 Processing sheet with id= T, first strand: chain 'I' and resid 887 through 889 Processing sheet with id= U, first strand: chain 'I' and resid 933 through 935 Processing sheet with id= V, first strand: chain 'I' and resid 1065 through 1067 Processing sheet with id= W, first strand: chain 'I' and resid 816 through 819 removed outlier: 7.318A pdb=" N VAL I 818 " --> pdb=" O SER I1077 " (cutoff:3.500A) removed outlier: 3.915A pdb=" N ILE I1079 " --> pdb=" O VAL I 818 " (cutoff:3.500A) Processing sheet with id= X, first strand: chain 'J' and resid 19 through 21 Processing sheet with id= Y, first strand: chain 'J' and resid 103 through 106 Processing sheet with id= Z, first strand: chain 'J' and resid 350 through 354 removed outlier: 3.676A pdb=" N GLN J 435 " --> pdb=" O LEU J 423 " (cutoff:3.500A) removed outlier: 3.544A pdb=" N CYS J 366 " --> pdb=" O GLU J 438 " (cutoff:3.500A) Processing sheet with id= AA, first strand: chain 'J' and resid 547 through 549 Processing sheet with id= AB, first strand: chain 'J' and resid 820 through 822 Processing sheet with id= AC, first strand: chain 'J' and resid 957 through 961 removed outlier: 4.144A pdb=" N THR J 980 " --> pdb=" O VAL J 997 " (cutoff:3.500A) Processing sheet with id= AD, first strand: chain 'J' and resid 1162 through 1164 Processing sheet with id= AE, first strand: chain 'J' and resid 1173 through 1175 Processing sheet with id= AF, first strand: chain 'J' and resid 1279 through 1281 removed outlier: 6.862A pdb=" N THR J1301 " --> pdb=" O VAL J1267 " (cutoff:3.500A) 957 hydrogen bonds defined for protein. 2778 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 125 hydrogen bonds 250 hydrogen bond angles 0 basepair planarities 53 basepair parallelities 93 stacking parallelities Total time for adding SS restraints: 12.44 Time building geometry restraints manager: 14.13 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.33: 8386 1.33 - 1.46: 8154 1.46 - 1.58: 15628 1.58 - 1.71: 245 1.71 - 1.84: 234 Bond restraints: 32647 Sorted by residual: bond pdb=" C19 1N7 J1504 " pdb=" C3 1N7 J1504 " ideal model delta sigma weight residual 1.532 1.841 -0.309 2.00e-02 2.50e+03 2.38e+02 bond pdb=" C19 1N7 L 701 " pdb=" C3 1N7 L 701 " ideal model delta sigma weight residual 1.532 1.840 -0.308 2.00e-02 2.50e+03 2.38e+02 bond pdb=" C19 1N7 I1401 " pdb=" C3 1N7 I1401 " ideal model delta sigma weight residual 1.532 1.832 -0.300 2.00e-02 2.50e+03 2.25e+02 bond pdb=" C3 1N7 I1401 " pdb=" C4 1N7 I1401 " ideal model delta sigma weight residual 1.532 1.735 -0.203 2.00e-02 2.50e+03 1.03e+02 bond pdb=" C3 1N7 L 701 " pdb=" C4 1N7 L 701 " ideal model delta sigma weight residual 1.532 1.725 -0.193 2.00e-02 2.50e+03 9.32e+01 ... (remaining 32642 not shown) Histogram of bond angle deviations from ideal: 93.19 - 101.43: 153 101.43 - 109.66: 6593 109.66 - 117.90: 18699 117.90 - 126.14: 18495 126.14 - 134.38: 661 Bond angle restraints: 44601 Sorted by residual: angle pdb=" N GLN I 517 " pdb=" CA GLN I 517 " pdb=" C GLN I 517 " ideal model delta sigma weight residual 109.62 119.91 -10.29 1.50e+00 4.44e-01 4.71e+01 angle pdb=" C GLU J 765 " pdb=" N GLY J 766 " pdb=" CA GLY J 766 " ideal model delta sigma weight residual 122.73 116.71 6.02 9.30e-01 1.16e+00 4.20e+01 angle pdb=" C GLY L 512 " pdb=" N ASP L 513 " pdb=" CA ASP L 513 " ideal model delta sigma weight residual 121.70 132.02 -10.32 1.80e+00 3.09e-01 3.29e+01 angle pdb=" C GLY J1171 " pdb=" N LYS J1172 " pdb=" CA LYS J1172 " ideal model delta sigma weight residual 121.70 131.74 -10.04 1.80e+00 3.09e-01 3.11e+01 angle pdb=" N ILE J1210 " pdb=" CA ILE J1210 " pdb=" C ILE J1210 " ideal model delta sigma weight residual 111.77 105.99 5.78 1.04e+00 9.25e-01 3.09e+01 ... (remaining 44596 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 30.19: 19088 30.19 - 60.38: 871 60.38 - 90.57: 33 90.57 - 120.77: 2 120.77 - 150.96: 1 Dihedral angle restraints: 19995 sinusoidal: 9193 harmonic: 10802 Sorted by residual: dihedral pdb=" CA GLU J1168 " pdb=" C GLU J1168 " pdb=" N THR J1169 " pdb=" CA THR J1169 " ideal model delta harmonic sigma weight residual 180.00 120.77 59.23 0 5.00e+00 4.00e-02 1.40e+02 dihedral pdb=" CA THR J 853 " pdb=" C THR J 853 " pdb=" N ALA J 854 " pdb=" CA ALA J 854 " ideal model delta harmonic sigma weight residual 180.00 130.72 49.28 0 5.00e+00 4.00e-02 9.71e+01 dihedral pdb=" CA GLN J1326 " pdb=" C GLN J1326 " pdb=" N GLU J1327 " pdb=" CA GLU J1327 " ideal model delta harmonic sigma weight residual -180.00 -137.51 -42.49 0 5.00e+00 4.00e-02 7.22e+01 ... (remaining 19992 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.077: 4213 0.077 - 0.155: 810 0.155 - 0.232: 78 0.232 - 0.309: 10 0.309 - 0.387: 1 Chirality restraints: 5112 Sorted by residual: chirality pdb=" CA GLN I 517 " pdb=" N GLN I 517 " pdb=" C GLN I 517 " pdb=" CB GLN I 517 " both_signs ideal model delta sigma weight residual False 2.51 2.12 0.39 2.00e-01 2.50e+01 3.74e+00 chirality pdb=" CB ILE J 442 " pdb=" CA ILE J 442 " pdb=" CG1 ILE J 442 " pdb=" CG2 ILE J 442 " both_signs ideal model delta sigma weight residual False 2.64 2.34 0.31 2.00e-01 2.50e+01 2.34e+00 chirality pdb=" CB ILE L 511 " pdb=" CA ILE L 511 " pdb=" CG1 ILE L 511 " pdb=" CG2 ILE L 511 " both_signs ideal model delta sigma weight residual False 2.64 2.38 0.27 2.00e-01 2.50e+01 1.76e+00 ... (remaining 5109 not shown) Planarity restraints: 5398 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA LEU J1138 " 0.025 2.00e-02 2.50e+03 4.87e-02 2.37e+01 pdb=" C LEU J1138 " -0.084 2.00e-02 2.50e+03 pdb=" O LEU J1138 " 0.031 2.00e-02 2.50e+03 pdb=" N PRO J1139 " 0.029 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C LEU J1138 " -0.075 5.00e-02 4.00e+02 1.13e-01 2.05e+01 pdb=" N PRO J1139 " 0.196 5.00e-02 4.00e+02 pdb=" CA PRO J1139 " -0.059 5.00e-02 4.00e+02 pdb=" CD PRO J1139 " -0.062 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C PRO J 246 " -0.064 5.00e-02 4.00e+02 9.65e-02 1.49e+01 pdb=" N PRO J 247 " 0.167 5.00e-02 4.00e+02 pdb=" CA PRO J 247 " -0.051 5.00e-02 4.00e+02 pdb=" CD PRO J 247 " -0.052 5.00e-02 4.00e+02 ... (remaining 5395 not shown) Histogram of nonbonded interaction distances: 2.01 - 2.59: 423 2.59 - 3.17: 29765 3.17 - 3.74: 48330 3.74 - 4.32: 69797 4.32 - 4.90: 112320 Nonbonded interactions: 260635 Sorted by model distance: nonbonded pdb=" OD1 ASN J1268 " pdb=" OG1 THR J1301 " model vdw 2.011 2.440 nonbonded pdb=" OG1 THR I 6 " pdb=" OD1 ASP I 781 " model vdw 2.020 2.440 nonbonded pdb=" O LEU L 598 " pdb=" OG SER L 604 " model vdw 2.047 2.440 nonbonded pdb=" OD2 ASP J 464 " pdb="MG MG J1501 " model vdw 2.054 2.170 nonbonded pdb=" O ILE I 11 " pdb=" OH TYR I1149 " model vdw 2.058 2.440 ... (remaining 260630 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 'G' and (resid 5 through 158 or resid 171 through 233 or (resid 234 and ( \ name N or name CA or name C or name O or name CB )))) selection = (chain 'H' and ((resid 5 through 7 and (name N or name CA or name C or name O or \ name CB )) or resid 8 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 individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.920 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: 0.020 Extract box with map and model: 5.560 Check model and map are aligned: 0.470 Set scattering table: 0.280 Process input model: 93.770 Find NCS groups from input model: 1.130 Set up NCS constraints: 0.120 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: 0.000 Load rotamer database and sin/cos tables:2.830 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 105.100 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7636 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 : 0.015 0.309 32647 Z= 0.972 Angle : 1.196 16.326 44601 Z= 0.658 Chirality : 0.060 0.387 5112 Planarity : 0.007 0.113 5398 Dihedral : 15.135 150.957 13029 Min Nonbonded Distance : 2.011 Molprobity Statistics. All-atom Clashscore : 34.20 Ramachandran Plot: Outliers : 0.27 % Allowed : 12.15 % Favored : 87.58 % Rotamer: Outliers : 0.31 % Allowed : 3.50 % Favored : 96.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.04 % Cis-general : 0.22 % Twisted Proline : 0.68 % Twisted General : 0.28 % 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: -4.17 (0.11), residues: 3727 helix: -2.10 (0.11), residues: 1430 sheet: -3.45 (0.23), residues: 366 loop : -3.21 (0.12), residues: 1931 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.039 0.005 TRP J 33 HIS 0.015 0.003 HIS I 832 PHE 0.051 0.005 PHE I1187 TYR 0.050 0.005 TYR J 144 ARG 0.019 0.002 ARG I 143 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7454 Ramachandran restraints generated. 3727 Oldfield, 0 Emsley, 3727 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7454 Ramachandran restraints generated. 3727 Oldfield, 0 Emsley, 3727 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 655 residues out of total 3214 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 645 time to evaluate : 3.382 Fit side-chains revert: symmetry clash REVERT: G 130 ILE cc_start: 0.8931 (OUTLIER) cc_final: 0.8663 (mt) REVERT: G 157 THR cc_start: 0.8584 (m) cc_final: 0.8175 (p) REVERT: I 158 ASP cc_start: 0.7803 (t70) cc_final: 0.7581 (t0) REVERT: I 337 PHE cc_start: 0.7891 (t80) cc_final: 0.7678 (t80) REVERT: I 369 MET cc_start: 0.8395 (tmm) cc_final: 0.8182 (ttp) REVERT: I 516 ASP cc_start: 0.8368 (t0) cc_final: 0.8098 (t70) REVERT: I 582 ASN cc_start: 0.8340 (t0) cc_final: 0.8115 (t0) REVERT: I 684 ASN cc_start: 0.9014 (OUTLIER) cc_final: 0.8696 (m-40) REVERT: I 1232 MET cc_start: 0.8452 (mtp) cc_final: 0.8186 (mtp) REVERT: J 129 ASP cc_start: 0.7748 (t70) cc_final: 0.7500 (t0) REVERT: J 137 ARG cc_start: 0.8161 (mtp180) cc_final: 0.7861 (mtm-85) REVERT: J 821 MET cc_start: 0.7322 (mmm) cc_final: 0.7077 (mmm) REVERT: L 430 TYR cc_start: 0.8730 (t80) cc_final: 0.8473 (t80) REVERT: L 507 MET cc_start: 0.8487 (ttp) cc_final: 0.8149 (ttm) outliers start: 10 outliers final: 4 residues processed: 654 average time/residue: 0.4966 time to fit residues: 492.4691 Evaluate side-chains 395 residues out of total 3214 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 389 time to evaluate : 3.757 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 56 VAL Chi-restraints excluded: chain G residue 130 ILE Chi-restraints excluded: chain H residue 183 ILE Chi-restraints excluded: chain I residue 91 THR Chi-restraints excluded: chain I residue 684 ASN Chi-restraints excluded: chain I residue 802 VAL Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 383 random chunks: chunk 323 optimal weight: 6.9990 chunk 290 optimal weight: 8.9990 chunk 161 optimal weight: 0.8980 chunk 99 optimal weight: 0.9980 chunk 195 optimal weight: 0.7980 chunk 155 optimal weight: 2.9990 chunk 300 optimal weight: 3.9990 chunk 116 optimal weight: 0.7980 chunk 182 optimal weight: 0.4980 chunk 223 optimal weight: 1.9990 chunk 347 optimal weight: 0.8980 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: G 23 HIS ** G 160 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 84 ASN H 103 ASN H 208 ASN I 69 GLN I 165 HIS ** I 193 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 273 HIS I 330 HIS ** I 519 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 580 GLN ** I 618 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 760 ASN I 808 ASN I 856 ASN I 955 GLN ** I1080 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I1116 HIS ** I1236 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I1237 HIS ** I1268 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 45 ASN J 80 HIS ** J 294 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 365 GLN ** J 488 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 720 ASN J 817 HIS J1010 GLN J1108 GLN J1197 ASN J1366 HIS J1367 GLN K 31 GLN ** L 309 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 331 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 362 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 518 HIS L 600 HIS ** R 283 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 28 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7507 moved from start: 0.2427 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 32647 Z= 0.222 Angle : 0.695 15.510 44601 Z= 0.357 Chirality : 0.044 0.223 5112 Planarity : 0.005 0.105 5398 Dihedral : 17.798 145.976 5638 Min Nonbonded Distance : 2.084 Molprobity Statistics. All-atom Clashscore : 13.93 Ramachandran Plot: Outliers : 0.08 % Allowed : 6.68 % Favored : 93.24 % Rotamer: Outliers : 2.47 % Allowed : 8.81 % Favored : 88.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.04 % Cis-general : 0.25 % Twisted Proline : 0.68 % Twisted General : 0.17 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.64 (0.13), residues: 3727 helix: -0.56 (0.13), residues: 1461 sheet: -3.03 (0.23), residues: 361 loop : -2.50 (0.13), residues: 1905 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP I 997 HIS 0.007 0.001 HIS G 160 PHE 0.017 0.002 PHE I 828 TYR 0.028 0.002 TYR L 137 ARG 0.007 0.001 ARG I 678 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7454 Ramachandran restraints generated. 3727 Oldfield, 0 Emsley, 3727 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7454 Ramachandran restraints generated. 3727 Oldfield, 0 Emsley, 3727 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 566 residues out of total 3214 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 79 poor density : 487 time to evaluate : 3.016 Fit side-chains revert: symmetry clash REVERT: G 120 ASP cc_start: 0.6846 (p0) cc_final: 0.6563 (p0) REVERT: G 123 ILE cc_start: 0.8735 (mm) cc_final: 0.8480 (mm) REVERT: I 158 ASP cc_start: 0.7853 (t70) cc_final: 0.7567 (t0) REVERT: I 299 LYS cc_start: 0.6077 (mtmt) cc_final: 0.5679 (pttt) REVERT: I 337 PHE cc_start: 0.7854 (t80) cc_final: 0.7639 (t80) REVERT: I 508 SER cc_start: 0.8708 (t) cc_final: 0.8408 (p) REVERT: I 516 ASP cc_start: 0.8046 (t0) cc_final: 0.7576 (t70) REVERT: I 545 PHE cc_start: 0.7057 (t80) cc_final: 0.6719 (t80) REVERT: I 705 GLU cc_start: 0.7783 (OUTLIER) cc_final: 0.7373 (mt-10) REVERT: I 788 SER cc_start: 0.8933 (m) cc_final: 0.8731 (m) REVERT: I 1135 GLN cc_start: 0.7217 (pm20) cc_final: 0.6997 (pm20) REVERT: J 96 LYS cc_start: 0.8703 (ptpt) cc_final: 0.8333 (pttm) REVERT: J 129 ASP cc_start: 0.7482 (t70) cc_final: 0.7219 (t0) REVERT: J 137 ARG cc_start: 0.8184 (mtp180) cc_final: 0.7978 (mtm110) REVERT: J 753 SER cc_start: 0.8854 (OUTLIER) cc_final: 0.8433 (p) REVERT: J 788 LEU cc_start: 0.8312 (tt) cc_final: 0.7925 (tt) REVERT: J 821 MET cc_start: 0.7326 (mmm) cc_final: 0.7107 (mmt) REVERT: J 1220 ILE cc_start: 0.8888 (mm) cc_final: 0.8533 (mt) REVERT: J 1284 ARG cc_start: 0.7532 (mtm-85) cc_final: 0.7178 (mtp85) REVERT: J 1345 ARG cc_start: 0.8560 (ttp80) cc_final: 0.8309 (ttp80) REVERT: K 74 GLU cc_start: 0.6640 (mt-10) cc_final: 0.6109 (tt0) REVERT: L 137 TYR cc_start: 0.2162 (t80) cc_final: 0.1823 (t80) REVERT: L 221 PHE cc_start: 0.2626 (m-80) cc_final: 0.1793 (m-80) outliers start: 79 outliers final: 39 residues processed: 543 average time/residue: 0.4321 time to fit residues: 373.9036 Evaluate side-chains 411 residues out of total 3214 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 41 poor density : 370 time to evaluate : 3.370 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 56 VAL Chi-restraints excluded: chain G residue 136 GLU Chi-restraints excluded: chain G residue 211 ILE Chi-restraints excluded: chain G residue 217 ILE Chi-restraints excluded: chain H residue 183 ILE Chi-restraints excluded: chain I residue 20 GLN Chi-restraints excluded: chain I residue 455 SER Chi-restraints excluded: chain I residue 471 VAL Chi-restraints excluded: chain I residue 521 LEU Chi-restraints excluded: chain I residue 550 VAL Chi-restraints excluded: chain I residue 576 SER Chi-restraints excluded: chain I residue 633 LEU Chi-restraints excluded: chain I residue 699 LEU Chi-restraints excluded: chain I residue 705 GLU Chi-restraints excluded: chain I residue 731 ARG Chi-restraints excluded: chain I residue 796 LEU Chi-restraints excluded: chain I residue 823 VAL Chi-restraints excluded: chain I residue 851 THR Chi-restraints excluded: chain I residue 1056 VAL Chi-restraints excluded: chain I residue 1082 ILE Chi-restraints excluded: chain I residue 1248 THR Chi-restraints excluded: chain J residue 32 SER Chi-restraints excluded: chain J residue 43 THR Chi-restraints excluded: chain J residue 120 LEU Chi-restraints excluded: chain J residue 126 LEU Chi-restraints excluded: chain J residue 217 LEU Chi-restraints excluded: chain J residue 228 VAL Chi-restraints excluded: chain J residue 416 ILE Chi-restraints excluded: chain J residue 506 VAL Chi-restraints excluded: chain J residue 532 GLU Chi-restraints excluded: chain J residue 548 VAL Chi-restraints excluded: chain J residue 567 THR Chi-restraints excluded: chain J residue 682 VAL Chi-restraints excluded: chain J residue 707 ILE Chi-restraints excluded: chain J residue 708 ASN Chi-restraints excluded: chain J residue 753 SER Chi-restraints excluded: chain J residue 1173 ARG Chi-restraints excluded: chain K residue 58 LEU Chi-restraints excluded: chain K residue 59 ILE Chi-restraints excluded: chain L residue 395 THR Chi-restraints excluded: chain L residue 529 GLU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 383 random chunks: chunk 193 optimal weight: 10.0000 chunk 107 optimal weight: 10.0000 chunk 289 optimal weight: 4.9990 chunk 236 optimal weight: 0.9980 chunk 95 optimal weight: 0.0270 chunk 348 optimal weight: 8.9990 chunk 376 optimal weight: 7.9990 chunk 310 optimal weight: 1.9990 chunk 345 optimal weight: 8.9990 chunk 118 optimal weight: 4.9990 chunk 279 optimal weight: 10.0000 overall best weight: 2.6044 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: G 132 HIS ** G 160 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 66 HIS H 103 ASN I 193 ASN I 618 GLN I 832 HIS ** I1236 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I1268 GLN ** I1312 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 294 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 341 ASN J 365 GLN ** J 488 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J1326 GLN ** L 309 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 331 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 446 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 283 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7606 moved from start: 0.2694 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.062 32647 Z= 0.383 Angle : 0.715 14.717 44601 Z= 0.367 Chirality : 0.045 0.343 5112 Planarity : 0.005 0.099 5398 Dihedral : 17.604 143.524 5632 Min Nonbonded Distance : 2.041 Molprobity Statistics. All-atom Clashscore : 13.64 Ramachandran Plot: Outliers : 0.08 % Allowed : 8.24 % Favored : 91.68 % Rotamer: Outliers : 3.75 % Allowed : 11.46 % Favored : 84.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.04 % Cis-general : 0.25 % Twisted Proline : 0.68 % Twisted General : 0.14 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.15 (0.13), residues: 3727 helix: -0.11 (0.13), residues: 1465 sheet: -2.70 (0.24), residues: 365 loop : -2.27 (0.13), residues: 1897 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP I 997 HIS 0.007 0.002 HIS G 160 PHE 0.019 0.002 PHE I1187 TYR 0.018 0.002 TYR I1229 ARG 0.007 0.001 ARG I 678 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7454 Ramachandran restraints generated. 3727 Oldfield, 0 Emsley, 3727 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7454 Ramachandran restraints generated. 3727 Oldfield, 0 Emsley, 3727 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 489 residues out of total 3214 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 120 poor density : 369 time to evaluate : 3.689 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: G 50 SER cc_start: 0.9194 (OUTLIER) cc_final: 0.8816 (p) REVERT: G 120 ASP cc_start: 0.6986 (p0) cc_final: 0.6597 (p0) REVERT: H 15 ASP cc_start: 0.5644 (m-30) cc_final: 0.5268 (m-30) REVERT: I 81 ASP cc_start: 0.7936 (OUTLIER) cc_final: 0.7521 (p0) REVERT: I 337 PHE cc_start: 0.7883 (t80) cc_final: 0.7641 (t80) REVERT: I 369 MET cc_start: 0.8492 (tmm) cc_final: 0.8245 (ttp) REVERT: I 387 ASN cc_start: 0.8100 (m-40) cc_final: 0.7494 (m110) REVERT: I 445 ILE cc_start: 0.7438 (OUTLIER) cc_final: 0.7234 (mm) REVERT: I 516 ASP cc_start: 0.8220 (t0) cc_final: 0.7719 (t70) REVERT: I 705 GLU cc_start: 0.7874 (OUTLIER) cc_final: 0.7246 (mt-10) REVERT: I 788 SER cc_start: 0.8884 (m) cc_final: 0.8673 (m) REVERT: I 1172 LEU cc_start: 0.8956 (OUTLIER) cc_final: 0.8595 (tp) REVERT: I 1327 LEU cc_start: 0.8937 (OUTLIER) cc_final: 0.8122 (mp) REVERT: J 58 CYS cc_start: 0.7517 (t) cc_final: 0.7283 (t) REVERT: J 96 LYS cc_start: 0.8657 (ptpt) cc_final: 0.8395 (pttp) REVERT: J 129 ASP cc_start: 0.7527 (t70) cc_final: 0.7222 (t0) REVERT: J 132 LEU cc_start: 0.8514 (OUTLIER) cc_final: 0.8159 (tp) REVERT: J 368 LEU cc_start: 0.8916 (OUTLIER) cc_final: 0.8677 (tt) REVERT: J 429 LEU cc_start: 0.9069 (OUTLIER) cc_final: 0.8852 (mt) REVERT: J 431 ARG cc_start: 0.8904 (OUTLIER) cc_final: 0.8683 (ptt180) REVERT: J 460 ASP cc_start: 0.8042 (m-30) cc_final: 0.7696 (m-30) REVERT: J 698 MET cc_start: 0.8872 (tpt) cc_final: 0.8459 (tpt) REVERT: J 753 SER cc_start: 0.8888 (OUTLIER) cc_final: 0.8462 (p) REVERT: J 754 ILE cc_start: 0.8453 (OUTLIER) cc_final: 0.8147 (mt) REVERT: J 1115 ILE cc_start: 0.5086 (OUTLIER) cc_final: 0.4209 (pt) REVERT: L 102 MET cc_start: 0.7904 (mmm) cc_final: 0.7429 (mmm) REVERT: L 221 PHE cc_start: 0.2577 (m-80) cc_final: 0.1950 (m-80) REVERT: L 430 TYR cc_start: 0.8604 (t80) cc_final: 0.8279 (t80) outliers start: 120 outliers final: 79 residues processed: 460 average time/residue: 0.4415 time to fit residues: 325.4987 Evaluate side-chains 419 residues out of total 3214 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 92 poor density : 327 time to evaluate : 3.391 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 49 SER Chi-restraints excluded: chain G residue 50 SER Chi-restraints excluded: chain G residue 56 VAL Chi-restraints excluded: chain G residue 67 GLU Chi-restraints excluded: chain G residue 136 GLU Chi-restraints excluded: chain G residue 210 THR Chi-restraints excluded: chain G residue 211 ILE Chi-restraints excluded: chain H residue 6 THR Chi-restraints excluded: chain H residue 13 LEU Chi-restraints excluded: chain H residue 17 GLU Chi-restraints excluded: chain H residue 98 VAL Chi-restraints excluded: chain H residue 103 ASN Chi-restraints excluded: chain H residue 115 ILE Chi-restraints excluded: chain H residue 183 ILE Chi-restraints excluded: chain I residue 20 GLN Chi-restraints excluded: chain I residue 36 GLN Chi-restraints excluded: chain I residue 47 TYR Chi-restraints excluded: chain I residue 81 ASP Chi-restraints excluded: chain I residue 82 VAL Chi-restraints excluded: chain I residue 169 LYS Chi-restraints excluded: chain I residue 397 LEU Chi-restraints excluded: chain I residue 414 ILE Chi-restraints excluded: chain I residue 445 ILE Chi-restraints excluded: chain I residue 471 VAL Chi-restraints excluded: chain I residue 508 SER Chi-restraints excluded: chain I residue 521 LEU Chi-restraints excluded: chain I residue 550 VAL Chi-restraints excluded: chain I residue 576 SER Chi-restraints excluded: chain I residue 630 VAL Chi-restraints excluded: chain I residue 633 LEU Chi-restraints excluded: chain I residue 690 VAL Chi-restraints excluded: chain I residue 699 LEU Chi-restraints excluded: chain I residue 705 GLU Chi-restraints excluded: chain I residue 730 SER Chi-restraints excluded: chain I residue 750 ILE Chi-restraints excluded: chain I residue 796 LEU Chi-restraints excluded: chain I residue 802 VAL Chi-restraints excluded: chain I residue 817 LEU Chi-restraints excluded: chain I residue 823 VAL Chi-restraints excluded: chain I residue 829 THR Chi-restraints excluded: chain I residue 853 ASP Chi-restraints excluded: chain I residue 898 GLU Chi-restraints excluded: chain I residue 960 LEU Chi-restraints excluded: chain I residue 1056 VAL Chi-restraints excluded: chain I residue 1082 ILE Chi-restraints excluded: chain I residue 1172 LEU Chi-restraints excluded: chain I residue 1225 VAL Chi-restraints excluded: chain I residue 1248 THR Chi-restraints excluded: chain I residue 1254 VAL Chi-restraints excluded: chain I residue 1327 LEU Chi-restraints excluded: chain J residue 32 SER Chi-restraints excluded: chain J residue 43 THR Chi-restraints excluded: chain J residue 46 TYR Chi-restraints excluded: chain J residue 48 THR Chi-restraints excluded: chain J residue 120 LEU Chi-restraints excluded: chain J residue 126 LEU Chi-restraints excluded: chain J residue 132 LEU Chi-restraints excluded: chain J residue 217 LEU Chi-restraints excluded: chain J residue 228 VAL Chi-restraints excluded: chain J residue 255 LEU Chi-restraints excluded: chain J residue 320 ASN Chi-restraints excluded: chain J residue 368 LEU Chi-restraints excluded: chain J residue 392 THR Chi-restraints excluded: chain J residue 416 ILE Chi-restraints excluded: chain J residue 429 LEU Chi-restraints excluded: chain J residue 431 ARG Chi-restraints excluded: chain J residue 506 VAL Chi-restraints excluded: chain J residue 510 LEU Chi-restraints excluded: chain J residue 532 GLU Chi-restraints excluded: chain J residue 548 VAL Chi-restraints excluded: chain J residue 567 THR Chi-restraints excluded: chain J residue 638 SER Chi-restraints excluded: chain J residue 682 VAL Chi-restraints excluded: chain J residue 693 VAL Chi-restraints excluded: chain J residue 707 ILE Chi-restraints excluded: chain J residue 708 ASN Chi-restraints excluded: chain J residue 717 VAL Chi-restraints excluded: chain J residue 753 SER Chi-restraints excluded: chain J residue 754 ILE Chi-restraints excluded: chain J residue 805 GLN Chi-restraints excluded: chain J residue 909 ILE Chi-restraints excluded: chain J residue 1115 ILE Chi-restraints excluded: chain J residue 1221 LEU Chi-restraints excluded: chain K residue 4 VAL Chi-restraints excluded: chain K residue 32 VAL Chi-restraints excluded: chain L residue 270 VAL Chi-restraints excluded: chain L residue 273 MET Chi-restraints excluded: chain L residue 395 THR Chi-restraints excluded: chain L residue 457 ILE Chi-restraints excluded: chain L residue 527 THR Chi-restraints excluded: chain L residue 529 GLU Chi-restraints excluded: chain L residue 530 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 383 random chunks: chunk 344 optimal weight: 2.9990 chunk 261 optimal weight: 0.0770 chunk 180 optimal weight: 0.8980 chunk 38 optimal weight: 6.9990 chunk 166 optimal weight: 0.9990 chunk 233 optimal weight: 3.9990 chunk 349 optimal weight: 3.9990 chunk 370 optimal weight: 10.0000 chunk 182 optimal weight: 0.9980 chunk 331 optimal weight: 7.9990 chunk 99 optimal weight: 1.9990 overall best weight: 0.9942 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 208 ASN I 193 ASN ** I 519 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I1236 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 294 ASN ** J 488 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 43 ASN ** L 309 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 331 HIS L 446 GLN ** R 283 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7534 moved from start: 0.3164 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 32647 Z= 0.205 Angle : 0.615 14.100 44601 Z= 0.317 Chirality : 0.042 0.323 5112 Planarity : 0.004 0.093 5398 Dihedral : 17.311 140.249 5632 Min Nonbonded Distance : 2.049 Molprobity Statistics. All-atom Clashscore : 11.77 Ramachandran Plot: Outliers : 0.08 % Allowed : 6.25 % Favored : 93.67 % Rotamer: Outliers : 3.31 % Allowed : 12.71 % Favored : 83.98 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.04 % Cis-general : 0.25 % Twisted Proline : 0.68 % Twisted General : 0.14 % 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: -1.57 (0.13), residues: 3727 helix: 0.43 (0.14), residues: 1467 sheet: -2.33 (0.25), residues: 361 loop : -2.01 (0.14), residues: 1899 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP I 807 HIS 0.007 0.001 HIS G 160 PHE 0.014 0.001 PHE I1025 TYR 0.018 0.001 TYR G 177 ARG 0.014 0.000 ARG J 60 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7454 Ramachandran restraints generated. 3727 Oldfield, 0 Emsley, 3727 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7454 Ramachandran restraints generated. 3727 Oldfield, 0 Emsley, 3727 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 477 residues out of total 3214 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 106 poor density : 371 time to evaluate : 3.462 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: G 120 ASP cc_start: 0.6935 (p0) cc_final: 0.6536 (p0) REVERT: H 15 ASP cc_start: 0.5927 (m-30) cc_final: 0.5587 (m-30) REVERT: I 337 PHE cc_start: 0.7910 (t80) cc_final: 0.7649 (t80) REVERT: I 369 MET cc_start: 0.8468 (tmm) cc_final: 0.8226 (ttp) REVERT: I 516 ASP cc_start: 0.7987 (t0) cc_final: 0.7393 (t70) REVERT: I 705 GLU cc_start: 0.7678 (OUTLIER) cc_final: 0.7244 (mt-10) REVERT: I 1029 LEU cc_start: 0.8033 (tt) cc_final: 0.7802 (tp) REVERT: I 1057 LYS cc_start: 0.8802 (ttmt) cc_final: 0.8478 (ttmm) REVERT: I 1172 LEU cc_start: 0.8861 (OUTLIER) cc_final: 0.8558 (tp) REVERT: J 96 LYS cc_start: 0.8589 (ptpt) cc_final: 0.8339 (pttp) REVERT: J 129 ASP cc_start: 0.7450 (t70) cc_final: 0.7174 (t0) REVERT: J 132 LEU cc_start: 0.8520 (OUTLIER) cc_final: 0.8130 (tp) REVERT: J 227 PHE cc_start: 0.8659 (OUTLIER) cc_final: 0.7857 (t80) REVERT: J 465 GLN cc_start: 0.9082 (mt0) cc_final: 0.8868 (mt0) REVERT: J 698 MET cc_start: 0.8826 (tpt) cc_final: 0.8387 (tpt) REVERT: J 701 LEU cc_start: 0.8840 (OUTLIER) cc_final: 0.8555 (tp) REVERT: J 738 ARG cc_start: 0.7034 (ttm170) cc_final: 0.6615 (ttp80) REVERT: J 753 SER cc_start: 0.8753 (OUTLIER) cc_final: 0.8540 (p) REVERT: J 1115 ILE cc_start: 0.4984 (OUTLIER) cc_final: 0.4125 (pt) REVERT: L 221 PHE cc_start: 0.2667 (m-80) cc_final: 0.2288 (m-80) outliers start: 106 outliers final: 65 residues processed: 449 average time/residue: 0.4363 time to fit residues: 316.0130 Evaluate side-chains 405 residues out of total 3214 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 72 poor density : 333 time to evaluate : 3.519 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 49 SER Chi-restraints excluded: chain G residue 56 VAL Chi-restraints excluded: chain G residue 136 GLU Chi-restraints excluded: chain H residue 6 THR Chi-restraints excluded: chain H residue 13 LEU Chi-restraints excluded: chain H residue 98 VAL Chi-restraints excluded: chain H residue 115 ILE Chi-restraints excluded: chain H residue 183 ILE Chi-restraints excluded: chain I residue 81 ASP Chi-restraints excluded: chain I residue 82 VAL Chi-restraints excluded: chain I residue 113 THR Chi-restraints excluded: chain I residue 122 VAL Chi-restraints excluded: chain I residue 158 ASP Chi-restraints excluded: chain I residue 397 LEU Chi-restraints excluded: chain I residue 414 ILE Chi-restraints excluded: chain I residue 471 VAL Chi-restraints excluded: chain I residue 508 SER Chi-restraints excluded: chain I residue 521 LEU Chi-restraints excluded: chain I residue 550 VAL Chi-restraints excluded: chain I residue 576 SER Chi-restraints excluded: chain I residue 630 VAL Chi-restraints excluded: chain I residue 633 LEU Chi-restraints excluded: chain I residue 690 VAL Chi-restraints excluded: chain I residue 699 LEU Chi-restraints excluded: chain I residue 705 GLU Chi-restraints excluded: chain I residue 730 SER Chi-restraints excluded: chain I residue 731 ARG Chi-restraints excluded: chain I residue 750 ILE Chi-restraints excluded: chain I residue 765 ILE Chi-restraints excluded: chain I residue 796 LEU Chi-restraints excluded: chain I residue 817 LEU Chi-restraints excluded: chain I residue 823 VAL Chi-restraints excluded: chain I residue 851 THR Chi-restraints excluded: chain I residue 960 LEU Chi-restraints excluded: chain I residue 1056 VAL Chi-restraints excluded: chain I residue 1082 ILE Chi-restraints excluded: chain I residue 1172 LEU Chi-restraints excluded: chain I residue 1227 VAL Chi-restraints excluded: chain I residue 1248 THR Chi-restraints excluded: chain I residue 1254 VAL Chi-restraints excluded: chain I residue 1292 THR Chi-restraints excluded: chain I residue 1293 VAL Chi-restraints excluded: chain I residue 1298 VAL Chi-restraints excluded: chain J residue 32 SER Chi-restraints excluded: chain J residue 43 THR Chi-restraints excluded: chain J residue 46 TYR Chi-restraints excluded: chain J residue 120 LEU Chi-restraints excluded: chain J residue 126 LEU Chi-restraints excluded: chain J residue 132 LEU Chi-restraints excluded: chain J residue 217 LEU Chi-restraints excluded: chain J residue 227 PHE Chi-restraints excluded: chain J residue 357 VAL Chi-restraints excluded: chain J residue 392 THR Chi-restraints excluded: chain J residue 416 ILE Chi-restraints excluded: chain J residue 506 VAL Chi-restraints excluded: chain J residue 510 LEU Chi-restraints excluded: chain J residue 567 THR Chi-restraints excluded: chain J residue 664 ILE Chi-restraints excluded: chain J residue 693 VAL Chi-restraints excluded: chain J residue 701 LEU Chi-restraints excluded: chain J residue 707 ILE Chi-restraints excluded: chain J residue 743 MET Chi-restraints excluded: chain J residue 753 SER Chi-restraints excluded: chain J residue 805 GLN Chi-restraints excluded: chain J residue 849 LEU Chi-restraints excluded: chain J residue 909 ILE Chi-restraints excluded: chain J residue 1115 ILE Chi-restraints excluded: chain J residue 1221 LEU Chi-restraints excluded: chain J residue 1316 THR Chi-restraints excluded: chain L residue 395 THR Chi-restraints excluded: chain L residue 529 GLU Chi-restraints excluded: chain L residue 530 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 383 random chunks: chunk 308 optimal weight: 3.9990 chunk 210 optimal weight: 0.0770 chunk 5 optimal weight: 6.9990 chunk 275 optimal weight: 20.0000 chunk 152 optimal weight: 2.9990 chunk 315 optimal weight: 4.9990 chunk 255 optimal weight: 0.9980 chunk 0 optimal weight: 4.9990 chunk 189 optimal weight: 4.9990 chunk 332 optimal weight: 8.9990 chunk 93 optimal weight: 4.9990 overall best weight: 2.6144 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** G 147 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 103 ASN H 208 ASN I 193 ASN I 580 GLN ** I1236 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I1244 HIS ** J 488 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 43 ASN ** L 309 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 283 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7613 moved from start: 0.3182 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.063 32647 Z= 0.370 Angle : 0.676 15.933 44601 Z= 0.346 Chirality : 0.044 0.287 5112 Planarity : 0.005 0.096 5398 Dihedral : 17.320 137.727 5632 Min Nonbonded Distance : 2.067 Molprobity Statistics. All-atom Clashscore : 12.12 Ramachandran Plot: Outliers : 0.08 % Allowed : 7.59 % Favored : 92.33 % Rotamer: Outliers : 4.22 % Allowed : 13.09 % Favored : 82.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.04 % Cis-general : 0.25 % Twisted Proline : 0.68 % Twisted General : 0.14 % 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: -1.51 (0.14), residues: 3727 helix: 0.38 (0.14), residues: 1472 sheet: -2.17 (0.26), residues: 364 loop : -1.93 (0.14), residues: 1891 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP L 315 HIS 0.007 0.001 HIS J 430 PHE 0.016 0.002 PHE J 620 TYR 0.018 0.002 TYR G 177 ARG 0.008 0.000 ARG J1173 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7454 Ramachandran restraints generated. 3727 Oldfield, 0 Emsley, 3727 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7454 Ramachandran restraints generated. 3727 Oldfield, 0 Emsley, 3727 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 488 residues out of total 3214 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 135 poor density : 353 time to evaluate : 3.395 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: G 120 ASP cc_start: 0.7021 (p0) cc_final: 0.6643 (p0) REVERT: H 15 ASP cc_start: 0.5506 (m-30) cc_final: 0.5275 (m-30) REVERT: I 337 PHE cc_start: 0.7906 (t80) cc_final: 0.7627 (t80) REVERT: I 369 MET cc_start: 0.8454 (tmm) cc_final: 0.8241 (ttp) REVERT: I 516 ASP cc_start: 0.8300 (t0) cc_final: 0.7795 (t70) REVERT: I 705 GLU cc_start: 0.7800 (OUTLIER) cc_final: 0.7325 (mt-10) REVERT: I 1172 LEU cc_start: 0.8909 (OUTLIER) cc_final: 0.8568 (tp) REVERT: J 96 LYS cc_start: 0.8674 (ptpt) cc_final: 0.8432 (pttp) REVERT: J 129 ASP cc_start: 0.7495 (t70) cc_final: 0.7229 (t0) REVERT: J 132 LEU cc_start: 0.8509 (OUTLIER) cc_final: 0.8129 (tp) REVERT: J 180 MET cc_start: 0.7696 (ttm) cc_final: 0.7379 (ttm) REVERT: J 227 PHE cc_start: 0.8824 (OUTLIER) cc_final: 0.8105 (t80) REVERT: J 429 LEU cc_start: 0.9073 (OUTLIER) cc_final: 0.8858 (mt) REVERT: J 460 ASP cc_start: 0.7933 (m-30) cc_final: 0.7573 (m-30) REVERT: J 698 MET cc_start: 0.8893 (tpt) cc_final: 0.8511 (tpt) REVERT: J 701 LEU cc_start: 0.8906 (OUTLIER) cc_final: 0.8644 (tp) REVERT: J 753 SER cc_start: 0.8769 (OUTLIER) cc_final: 0.8562 (p) REVERT: J 1115 ILE cc_start: 0.4972 (OUTLIER) cc_final: 0.4103 (pt) REVERT: J 1194 ARG cc_start: 0.8123 (mtm110) cc_final: 0.7790 (mtp85) REVERT: J 1215 GLU cc_start: 0.7163 (OUTLIER) cc_final: 0.6909 (tp30) REVERT: L 102 MET cc_start: 0.7824 (mmm) cc_final: 0.7487 (mmm) REVERT: L 221 PHE cc_start: 0.2697 (m-80) cc_final: 0.2403 (m-80) REVERT: L 430 TYR cc_start: 0.8592 (t80) cc_final: 0.8130 (t80) REVERT: L 600 HIS cc_start: 0.7603 (t-90) cc_final: 0.7036 (t-90) outliers start: 135 outliers final: 99 residues processed: 459 average time/residue: 0.4184 time to fit residues: 309.3032 Evaluate side-chains 438 residues out of total 3214 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 108 poor density : 330 time to evaluate : 3.121 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 49 SER Chi-restraints excluded: chain G residue 56 VAL Chi-restraints excluded: chain G residue 67 GLU Chi-restraints excluded: chain G residue 136 GLU Chi-restraints excluded: chain G residue 210 THR Chi-restraints excluded: chain G residue 211 ILE Chi-restraints excluded: chain H residue 6 THR Chi-restraints excluded: chain H residue 13 LEU Chi-restraints excluded: chain H residue 17 GLU Chi-restraints excluded: chain H residue 46 ILE Chi-restraints excluded: chain H residue 98 VAL Chi-restraints excluded: chain H residue 115 ILE Chi-restraints excluded: chain H residue 183 ILE Chi-restraints excluded: chain I residue 20 GLN Chi-restraints excluded: chain I residue 21 VAL Chi-restraints excluded: chain I residue 30 ILE Chi-restraints excluded: chain I residue 36 GLN Chi-restraints excluded: chain I residue 81 ASP Chi-restraints excluded: chain I residue 82 VAL Chi-restraints excluded: chain I residue 113 THR Chi-restraints excluded: chain I residue 122 VAL Chi-restraints excluded: chain I residue 152 SER Chi-restraints excluded: chain I residue 158 ASP Chi-restraints excluded: chain I residue 161 LYS Chi-restraints excluded: chain I residue 397 LEU Chi-restraints excluded: chain I residue 414 ILE Chi-restraints excluded: chain I residue 444 ASP Chi-restraints excluded: chain I residue 471 VAL Chi-restraints excluded: chain I residue 508 SER Chi-restraints excluded: chain I residue 521 LEU Chi-restraints excluded: chain I residue 550 VAL Chi-restraints excluded: chain I residue 576 SER Chi-restraints excluded: chain I residue 589 THR Chi-restraints excluded: chain I residue 630 VAL Chi-restraints excluded: chain I residue 633 LEU Chi-restraints excluded: chain I residue 690 VAL Chi-restraints excluded: chain I residue 699 LEU Chi-restraints excluded: chain I residue 705 GLU Chi-restraints excluded: chain I residue 730 SER Chi-restraints excluded: chain I residue 750 ILE Chi-restraints excluded: chain I residue 765 ILE Chi-restraints excluded: chain I residue 796 LEU Chi-restraints excluded: chain I residue 802 VAL Chi-restraints excluded: chain I residue 817 LEU Chi-restraints excluded: chain I residue 823 VAL Chi-restraints excluded: chain I residue 829 THR Chi-restraints excluded: chain I residue 851 THR Chi-restraints excluded: chain I residue 960 LEU Chi-restraints excluded: chain I residue 1010 GLN Chi-restraints excluded: chain I residue 1056 VAL Chi-restraints excluded: chain I residue 1082 ILE Chi-restraints excluded: chain I residue 1172 LEU Chi-restraints excluded: chain I residue 1225 VAL Chi-restraints excluded: chain I residue 1227 VAL Chi-restraints excluded: chain I residue 1248 THR Chi-restraints excluded: chain I residue 1254 VAL Chi-restraints excluded: chain I residue 1292 THR Chi-restraints excluded: chain I residue 1293 VAL Chi-restraints excluded: chain I residue 1298 VAL Chi-restraints excluded: chain J residue 32 SER Chi-restraints excluded: chain J residue 42 GLU Chi-restraints excluded: chain J residue 43 THR Chi-restraints excluded: chain J residue 46 TYR Chi-restraints excluded: chain J residue 80 HIS Chi-restraints excluded: chain J residue 120 LEU Chi-restraints excluded: chain J residue 126 LEU Chi-restraints excluded: chain J residue 132 LEU Chi-restraints excluded: chain J residue 217 LEU Chi-restraints excluded: chain J residue 227 PHE Chi-restraints excluded: chain J residue 228 VAL Chi-restraints excluded: chain J residue 255 LEU Chi-restraints excluded: chain J residue 320 ASN Chi-restraints excluded: chain J residue 357 VAL Chi-restraints excluded: chain J residue 392 THR Chi-restraints excluded: chain J residue 429 LEU Chi-restraints excluded: chain J residue 506 VAL Chi-restraints excluded: chain J residue 510 LEU Chi-restraints excluded: chain J residue 518 VAL Chi-restraints excluded: chain J residue 548 VAL Chi-restraints excluded: chain J residue 567 THR Chi-restraints excluded: chain J residue 638 SER Chi-restraints excluded: chain J residue 648 GLU Chi-restraints excluded: chain J residue 693 VAL Chi-restraints excluded: chain J residue 701 LEU Chi-restraints excluded: chain J residue 706 VAL Chi-restraints excluded: chain J residue 707 ILE Chi-restraints excluded: chain J residue 708 ASN Chi-restraints excluded: chain J residue 717 VAL Chi-restraints excluded: chain J residue 743 MET Chi-restraints excluded: chain J residue 753 SER Chi-restraints excluded: chain J residue 788 LEU Chi-restraints excluded: chain J residue 805 GLN Chi-restraints excluded: chain J residue 849 LEU Chi-restraints excluded: chain J residue 901 ARG Chi-restraints excluded: chain J residue 909 ILE Chi-restraints excluded: chain J residue 1115 ILE Chi-restraints excluded: chain J residue 1215 GLU Chi-restraints excluded: chain J residue 1221 LEU Chi-restraints excluded: chain J residue 1273 ASP Chi-restraints excluded: chain J residue 1316 THR Chi-restraints excluded: chain K residue 4 VAL Chi-restraints excluded: chain K residue 59 ILE Chi-restraints excluded: chain L residue 98 VAL Chi-restraints excluded: chain L residue 395 THR Chi-restraints excluded: chain L residue 457 ILE Chi-restraints excluded: chain L residue 527 THR Chi-restraints excluded: chain L residue 529 GLU Chi-restraints excluded: chain L residue 530 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 383 random chunks: chunk 124 optimal weight: 0.9990 chunk 333 optimal weight: 20.0000 chunk 73 optimal weight: 10.0000 chunk 217 optimal weight: 2.9990 chunk 91 optimal weight: 10.0000 chunk 370 optimal weight: 10.0000 chunk 307 optimal weight: 2.9990 chunk 171 optimal weight: 0.5980 chunk 30 optimal weight: 4.9990 chunk 122 optimal weight: 2.9990 chunk 194 optimal weight: 7.9990 overall best weight: 2.1188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: G 23 HIS I 193 ASN ** I 519 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 832 HIS ** I1236 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 488 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J1227 HIS K 43 ASN ** L 309 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 283 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7599 moved from start: 0.3395 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.046 32647 Z= 0.310 Angle : 0.641 14.784 44601 Z= 0.329 Chirality : 0.043 0.260 5112 Planarity : 0.004 0.099 5398 Dihedral : 17.196 136.313 5632 Min Nonbonded Distance : 2.058 Molprobity Statistics. All-atom Clashscore : 11.68 Ramachandran Plot: Outliers : 0.08 % Allowed : 7.11 % Favored : 92.81 % Rotamer: Outliers : 3.94 % Allowed : 14.46 % Favored : 81.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.04 % Cis-general : 0.25 % Twisted Proline : 0.68 % Twisted General : 0.14 % 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: -1.35 (0.14), residues: 3727 helix: 0.47 (0.14), residues: 1484 sheet: -2.02 (0.26), residues: 364 loop : -1.83 (0.14), residues: 1879 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP I 997 HIS 0.006 0.001 HIS G 160 PHE 0.017 0.002 PHE J1037 TYR 0.018 0.002 TYR G 177 ARG 0.006 0.000 ARG J1231 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7454 Ramachandran restraints generated. 3727 Oldfield, 0 Emsley, 3727 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7454 Ramachandran restraints generated. 3727 Oldfield, 0 Emsley, 3727 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 479 residues out of total 3214 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 126 poor density : 353 time to evaluate : 3.354 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: G 33 ARG cc_start: 0.8256 (tpp80) cc_final: 0.8028 (tpp80) REVERT: G 120 ASP cc_start: 0.6968 (p0) cc_final: 0.6592 (p0) REVERT: H 15 ASP cc_start: 0.5928 (m-30) cc_final: 0.5646 (m-30) REVERT: I 130 MET cc_start: 0.9020 (ttm) cc_final: 0.8757 (ttt) REVERT: I 169 LYS cc_start: 0.8417 (OUTLIER) cc_final: 0.8176 (mtpp) REVERT: I 337 PHE cc_start: 0.7836 (t80) cc_final: 0.7591 (t80) REVERT: I 346 TYR cc_start: 0.7426 (m-80) cc_final: 0.7146 (m-80) REVERT: I 369 MET cc_start: 0.8444 (tmm) cc_final: 0.8195 (ttp) REVERT: I 387 ASN cc_start: 0.8124 (m-40) cc_final: 0.7486 (m110) REVERT: I 516 ASP cc_start: 0.8135 (t0) cc_final: 0.7583 (t70) REVERT: I 705 GLU cc_start: 0.7754 (OUTLIER) cc_final: 0.7278 (mt-10) REVERT: I 1029 LEU cc_start: 0.8059 (tt) cc_final: 0.7805 (tp) REVERT: I 1172 LEU cc_start: 0.8907 (OUTLIER) cc_final: 0.8579 (tp) REVERT: J 96 LYS cc_start: 0.8671 (ptpt) cc_final: 0.8417 (pttp) REVERT: J 129 ASP cc_start: 0.7469 (t70) cc_final: 0.7177 (t0) REVERT: J 132 LEU cc_start: 0.8501 (OUTLIER) cc_final: 0.8117 (tp) REVERT: J 227 PHE cc_start: 0.8791 (OUTLIER) cc_final: 0.8106 (t80) REVERT: J 317 THR cc_start: 0.8229 (m) cc_final: 0.7783 (p) REVERT: J 460 ASP cc_start: 0.7900 (m-30) cc_final: 0.7554 (m-30) REVERT: J 698 MET cc_start: 0.8921 (tpt) cc_final: 0.8512 (tpt) REVERT: J 701 LEU cc_start: 0.8884 (OUTLIER) cc_final: 0.8605 (tp) REVERT: J 738 ARG cc_start: 0.7315 (ttm170) cc_final: 0.6887 (ttp80) REVERT: J 1115 ILE cc_start: 0.4960 (OUTLIER) cc_final: 0.4103 (pt) REVERT: J 1215 GLU cc_start: 0.7159 (OUTLIER) cc_final: 0.6902 (tp30) REVERT: L 102 MET cc_start: 0.7733 (mmm) cc_final: 0.7445 (mmm) REVERT: L 221 PHE cc_start: 0.2632 (m-80) cc_final: 0.2356 (m-80) REVERT: L 430 TYR cc_start: 0.8539 (t80) cc_final: 0.8070 (t80) REVERT: L 600 HIS cc_start: 0.7697 (t-90) cc_final: 0.7089 (t-90) outliers start: 126 outliers final: 96 residues processed: 449 average time/residue: 0.4256 time to fit residues: 309.1179 Evaluate side-chains 435 residues out of total 3214 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 104 poor density : 331 time to evaluate : 3.454 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 49 SER Chi-restraints excluded: chain G residue 56 VAL Chi-restraints excluded: chain G residue 67 GLU Chi-restraints excluded: chain G residue 111 THR Chi-restraints excluded: chain G residue 136 GLU Chi-restraints excluded: chain G residue 210 THR Chi-restraints excluded: chain G residue 211 ILE Chi-restraints excluded: chain G residue 217 ILE Chi-restraints excluded: chain H residue 6 THR Chi-restraints excluded: chain H residue 13 LEU Chi-restraints excluded: chain H residue 17 GLU Chi-restraints excluded: chain H residue 98 VAL Chi-restraints excluded: chain H residue 104 LYS Chi-restraints excluded: chain H residue 115 ILE Chi-restraints excluded: chain H residue 183 ILE Chi-restraints excluded: chain I residue 20 GLN Chi-restraints excluded: chain I residue 21 VAL Chi-restraints excluded: chain I residue 30 ILE Chi-restraints excluded: chain I residue 81 ASP Chi-restraints excluded: chain I residue 82 VAL Chi-restraints excluded: chain I residue 113 THR Chi-restraints excluded: chain I residue 122 VAL Chi-restraints excluded: chain I residue 132 ASP Chi-restraints excluded: chain I residue 158 ASP Chi-restraints excluded: chain I residue 161 LYS Chi-restraints excluded: chain I residue 169 LYS Chi-restraints excluded: chain I residue 397 LEU Chi-restraints excluded: chain I residue 414 ILE Chi-restraints excluded: chain I residue 444 ASP Chi-restraints excluded: chain I residue 471 VAL Chi-restraints excluded: chain I residue 508 SER Chi-restraints excluded: chain I residue 521 LEU Chi-restraints excluded: chain I residue 550 VAL Chi-restraints excluded: chain I residue 576 SER Chi-restraints excluded: chain I residue 589 THR Chi-restraints excluded: chain I residue 630 VAL Chi-restraints excluded: chain I residue 633 LEU Chi-restraints excluded: chain I residue 690 VAL Chi-restraints excluded: chain I residue 699 LEU Chi-restraints excluded: chain I residue 705 GLU Chi-restraints excluded: chain I residue 730 SER Chi-restraints excluded: chain I residue 750 ILE Chi-restraints excluded: chain I residue 765 ILE Chi-restraints excluded: chain I residue 788 SER Chi-restraints excluded: chain I residue 796 LEU Chi-restraints excluded: chain I residue 802 VAL Chi-restraints excluded: chain I residue 817 LEU Chi-restraints excluded: chain I residue 823 VAL Chi-restraints excluded: chain I residue 829 THR Chi-restraints excluded: chain I residue 851 THR Chi-restraints excluded: chain I residue 960 LEU Chi-restraints excluded: chain I residue 1010 GLN Chi-restraints excluded: chain I residue 1056 VAL Chi-restraints excluded: chain I residue 1082 ILE Chi-restraints excluded: chain I residue 1098 LEU Chi-restraints excluded: chain I residue 1172 LEU Chi-restraints excluded: chain I residue 1248 THR Chi-restraints excluded: chain I residue 1254 VAL Chi-restraints excluded: chain I residue 1292 THR Chi-restraints excluded: chain I residue 1293 VAL Chi-restraints excluded: chain I residue 1298 VAL Chi-restraints excluded: chain J residue 32 SER Chi-restraints excluded: chain J residue 43 THR Chi-restraints excluded: chain J residue 46 TYR Chi-restraints excluded: chain J residue 48 THR Chi-restraints excluded: chain J residue 120 LEU Chi-restraints excluded: chain J residue 126 LEU Chi-restraints excluded: chain J residue 132 LEU Chi-restraints excluded: chain J residue 217 LEU Chi-restraints excluded: chain J residue 227 PHE Chi-restraints excluded: chain J residue 320 ASN Chi-restraints excluded: chain J residue 357 VAL Chi-restraints excluded: chain J residue 392 THR Chi-restraints excluded: chain J residue 401 VAL Chi-restraints excluded: chain J residue 506 VAL Chi-restraints excluded: chain J residue 510 LEU Chi-restraints excluded: chain J residue 518 VAL Chi-restraints excluded: chain J residue 548 VAL Chi-restraints excluded: chain J residue 567 THR Chi-restraints excluded: chain J residue 638 SER Chi-restraints excluded: chain J residue 693 VAL Chi-restraints excluded: chain J residue 701 LEU Chi-restraints excluded: chain J residue 707 ILE Chi-restraints excluded: chain J residue 708 ASN Chi-restraints excluded: chain J residue 717 VAL Chi-restraints excluded: chain J residue 743 MET Chi-restraints excluded: chain J residue 805 GLN Chi-restraints excluded: chain J residue 839 VAL Chi-restraints excluded: chain J residue 849 LEU Chi-restraints excluded: chain J residue 901 ARG Chi-restraints excluded: chain J residue 909 ILE Chi-restraints excluded: chain J residue 1115 ILE Chi-restraints excluded: chain J residue 1215 GLU Chi-restraints excluded: chain J residue 1221 LEU Chi-restraints excluded: chain J residue 1273 ASP Chi-restraints excluded: chain J residue 1316 THR Chi-restraints excluded: chain K residue 4 VAL Chi-restraints excluded: chain K residue 59 ILE Chi-restraints excluded: chain L residue 98 VAL Chi-restraints excluded: chain L residue 105 MET Chi-restraints excluded: chain L residue 395 THR Chi-restraints excluded: chain L residue 527 THR Chi-restraints excluded: chain L residue 529 GLU Chi-restraints excluded: chain L residue 530 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 383 random chunks: chunk 357 optimal weight: 0.9980 chunk 41 optimal weight: 4.9990 chunk 211 optimal weight: 0.7980 chunk 270 optimal weight: 9.9990 chunk 209 optimal weight: 4.9990 chunk 311 optimal weight: 0.7980 chunk 206 optimal weight: 0.7980 chunk 369 optimal weight: 10.0000 chunk 231 optimal weight: 0.8980 chunk 225 optimal weight: 0.9980 chunk 170 optimal weight: 0.6980 overall best weight: 0.7980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 208 ASN I 193 ASN ** I 519 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 832 HIS ** I1236 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 450 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 488 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J1227 HIS K 43 ASN ** L 309 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 383 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7528 moved from start: 0.3746 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 32647 Z= 0.180 Angle : 0.577 14.602 44601 Z= 0.297 Chirality : 0.040 0.160 5112 Planarity : 0.004 0.094 5398 Dihedral : 16.955 133.948 5632 Min Nonbonded Distance : 2.058 Molprobity Statistics. All-atom Clashscore : 11.08 Ramachandran Plot: Outliers : 0.08 % Allowed : 6.31 % Favored : 93.61 % Rotamer: Outliers : 3.15 % Allowed : 15.49 % Favored : 81.36 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.04 % Cis-general : 0.25 % Twisted Proline : 0.68 % Twisted General : 0.14 % 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: -0.99 (0.14), residues: 3727 helix: 0.81 (0.14), residues: 1486 sheet: -1.78 (0.27), residues: 362 loop : -1.66 (0.14), residues: 1879 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP I 807 HIS 0.005 0.001 HIS G 160 PHE 0.014 0.001 PHE I1025 TYR 0.016 0.001 TYR G 177 ARG 0.009 0.000 ARG J1173 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7454 Ramachandran restraints generated. 3727 Oldfield, 0 Emsley, 3727 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7454 Ramachandran restraints generated. 3727 Oldfield, 0 Emsley, 3727 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 468 residues out of total 3214 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 101 poor density : 367 time to evaluate : 3.352 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: G 120 ASP cc_start: 0.7067 (p0) cc_final: 0.6696 (p0) REVERT: H 15 ASP cc_start: 0.5515 (m-30) cc_final: 0.5302 (m-30) REVERT: I 337 PHE cc_start: 0.7825 (t80) cc_final: 0.7588 (t80) REVERT: I 346 TYR cc_start: 0.7445 (m-80) cc_final: 0.7242 (m-80) REVERT: I 369 MET cc_start: 0.8383 (tmm) cc_final: 0.8103 (ttp) REVERT: I 516 ASP cc_start: 0.7945 (t0) cc_final: 0.7369 (t70) REVERT: I 1033 ARG cc_start: 0.7004 (ttm110) cc_final: 0.6785 (ttm170) REVERT: I 1057 LYS cc_start: 0.8684 (ttmt) cc_final: 0.8111 (ttmm) REVERT: I 1172 LEU cc_start: 0.8860 (OUTLIER) cc_final: 0.8562 (tp) REVERT: J 96 LYS cc_start: 0.8617 (ptpt) cc_final: 0.8397 (pttp) REVERT: J 129 ASP cc_start: 0.7442 (t70) cc_final: 0.7140 (t0) REVERT: J 132 LEU cc_start: 0.8515 (OUTLIER) cc_final: 0.8108 (tp) REVERT: J 227 PHE cc_start: 0.8648 (OUTLIER) cc_final: 0.7877 (t80) REVERT: J 317 THR cc_start: 0.8095 (m) cc_final: 0.7632 (p) REVERT: J 698 MET cc_start: 0.8812 (tpt) cc_final: 0.8515 (tpt) REVERT: J 701 LEU cc_start: 0.8817 (OUTLIER) cc_final: 0.8545 (tp) REVERT: J 738 ARG cc_start: 0.7114 (ttm170) cc_final: 0.6646 (ttp80) REVERT: J 788 LEU cc_start: 0.8254 (tt) cc_final: 0.7937 (tt) REVERT: J 1115 ILE cc_start: 0.4715 (OUTLIER) cc_final: 0.3936 (pt) REVERT: J 1215 GLU cc_start: 0.7145 (OUTLIER) cc_final: 0.6921 (tp30) REVERT: L 221 PHE cc_start: 0.2363 (m-80) cc_final: 0.2093 (m-80) REVERT: L 385 ARG cc_start: 0.8314 (mtt-85) cc_final: 0.8050 (mtp180) REVERT: L 600 HIS cc_start: 0.7519 (t-90) cc_final: 0.7037 (t-90) outliers start: 101 outliers final: 72 residues processed: 439 average time/residue: 0.4339 time to fit residues: 306.4281 Evaluate side-chains 421 residues out of total 3214 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 78 poor density : 343 time to evaluate : 2.856 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 23 HIS Chi-restraints excluded: chain G residue 49 SER Chi-restraints excluded: chain G residue 56 VAL Chi-restraints excluded: chain G residue 136 GLU Chi-restraints excluded: chain G residue 211 ILE Chi-restraints excluded: chain H residue 6 THR Chi-restraints excluded: chain H residue 13 LEU Chi-restraints excluded: chain H residue 98 VAL Chi-restraints excluded: chain H residue 103 ASN Chi-restraints excluded: chain H residue 104 LYS Chi-restraints excluded: chain H residue 183 ILE Chi-restraints excluded: chain I residue 81 ASP Chi-restraints excluded: chain I residue 82 VAL Chi-restraints excluded: chain I residue 122 VAL Chi-restraints excluded: chain I residue 158 ASP Chi-restraints excluded: chain I residue 161 LYS Chi-restraints excluded: chain I residue 397 LEU Chi-restraints excluded: chain I residue 414 ILE Chi-restraints excluded: chain I residue 444 ASP Chi-restraints excluded: chain I residue 455 SER Chi-restraints excluded: chain I residue 471 VAL Chi-restraints excluded: chain I residue 481 LEU Chi-restraints excluded: chain I residue 508 SER Chi-restraints excluded: chain I residue 521 LEU Chi-restraints excluded: chain I residue 550 VAL Chi-restraints excluded: chain I residue 576 SER Chi-restraints excluded: chain I residue 589 THR Chi-restraints excluded: chain I residue 630 VAL Chi-restraints excluded: chain I residue 633 LEU Chi-restraints excluded: chain I residue 699 LEU Chi-restraints excluded: chain I residue 730 SER Chi-restraints excluded: chain I residue 765 ILE Chi-restraints excluded: chain I residue 788 SER Chi-restraints excluded: chain I residue 796 LEU Chi-restraints excluded: chain I residue 802 VAL Chi-restraints excluded: chain I residue 817 LEU Chi-restraints excluded: chain I residue 823 VAL Chi-restraints excluded: chain I residue 1056 VAL Chi-restraints excluded: chain I residue 1082 ILE Chi-restraints excluded: chain I residue 1172 LEU Chi-restraints excluded: chain I residue 1248 THR Chi-restraints excluded: chain I residue 1254 VAL Chi-restraints excluded: chain I residue 1293 VAL Chi-restraints excluded: chain I residue 1298 VAL Chi-restraints excluded: chain J residue 32 SER Chi-restraints excluded: chain J residue 46 TYR Chi-restraints excluded: chain J residue 48 THR Chi-restraints excluded: chain J residue 120 LEU Chi-restraints excluded: chain J residue 132 LEU Chi-restraints excluded: chain J residue 159 ILE Chi-restraints excluded: chain J residue 217 LEU Chi-restraints excluded: chain J residue 227 PHE Chi-restraints excluded: chain J residue 320 ASN Chi-restraints excluded: chain J residue 357 VAL Chi-restraints excluded: chain J residue 368 LEU Chi-restraints excluded: chain J residue 392 THR Chi-restraints excluded: chain J residue 506 VAL Chi-restraints excluded: chain J residue 510 LEU Chi-restraints excluded: chain J residue 518 VAL Chi-restraints excluded: chain J residue 638 SER Chi-restraints excluded: chain J residue 693 VAL Chi-restraints excluded: chain J residue 701 LEU Chi-restraints excluded: chain J residue 707 ILE Chi-restraints excluded: chain J residue 839 VAL Chi-restraints excluded: chain J residue 849 LEU Chi-restraints excluded: chain J residue 901 ARG Chi-restraints excluded: chain J residue 1115 ILE Chi-restraints excluded: chain J residue 1215 GLU Chi-restraints excluded: chain J residue 1221 LEU Chi-restraints excluded: chain J residue 1316 THR Chi-restraints excluded: chain J residue 1324 SER Chi-restraints excluded: chain K residue 4 VAL Chi-restraints excluded: chain L residue 98 VAL Chi-restraints excluded: chain L residue 105 MET Chi-restraints excluded: chain L residue 225 ARG Chi-restraints excluded: chain L residue 395 THR Chi-restraints excluded: chain L residue 457 ILE Chi-restraints excluded: chain L residue 529 GLU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 383 random chunks: chunk 228 optimal weight: 0.9990 chunk 147 optimal weight: 9.9990 chunk 220 optimal weight: 0.3980 chunk 111 optimal weight: 4.9990 chunk 72 optimal weight: 8.9990 chunk 71 optimal weight: 6.9990 chunk 234 optimal weight: 0.9990 chunk 251 optimal weight: 2.9990 chunk 182 optimal weight: 0.5980 chunk 34 optimal weight: 1.9990 chunk 290 optimal weight: 5.9990 overall best weight: 0.9986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: I 193 ASN I 517 GLN ** I 519 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 465 GLN ** J 488 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J1227 HIS K 43 ASN ** L 309 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7533 moved from start: 0.3874 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 32647 Z= 0.193 Angle : 0.586 14.175 44601 Z= 0.300 Chirality : 0.041 0.166 5112 Planarity : 0.004 0.092 5398 Dihedral : 16.874 132.096 5632 Min Nonbonded Distance : 2.063 Molprobity Statistics. All-atom Clashscore : 10.84 Ramachandran Plot: Outliers : 0.08 % Allowed : 6.39 % Favored : 93.53 % Rotamer: Outliers : 3.40 % Allowed : 15.68 % Favored : 80.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.04 % Cis-general : 0.25 % Twisted Proline : 0.68 % Twisted General : 0.08 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.79 (0.14), residues: 3727 helix: 0.94 (0.14), residues: 1487 sheet: -1.64 (0.27), residues: 358 loop : -1.54 (0.14), residues: 1882 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP I 807 HIS 0.005 0.001 HIS G 160 PHE 0.018 0.001 PHE I1025 TYR 0.023 0.001 TYR H 185 ARG 0.007 0.000 ARG J1231 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7454 Ramachandran restraints generated. 3727 Oldfield, 0 Emsley, 3727 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7454 Ramachandran restraints generated. 3727 Oldfield, 0 Emsley, 3727 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 462 residues out of total 3214 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 109 poor density : 353 time to evaluate : 3.520 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: G 120 ASP cc_start: 0.7103 (p0) cc_final: 0.6662 (p0) REVERT: I 130 MET cc_start: 0.8997 (ttm) cc_final: 0.8720 (ttm) REVERT: I 346 TYR cc_start: 0.7443 (m-80) cc_final: 0.7214 (m-80) REVERT: I 369 MET cc_start: 0.8421 (tmm) cc_final: 0.8144 (ttp) REVERT: I 516 ASP cc_start: 0.7972 (t0) cc_final: 0.7376 (t70) REVERT: I 783 LEU cc_start: 0.8168 (OUTLIER) cc_final: 0.7852 (mt) REVERT: I 1057 LYS cc_start: 0.8746 (ttmt) cc_final: 0.8106 (ttmm) REVERT: I 1292 THR cc_start: 0.9080 (OUTLIER) cc_final: 0.8769 (p) REVERT: J 96 LYS cc_start: 0.8613 (ptpt) cc_final: 0.8363 (pttp) REVERT: J 129 ASP cc_start: 0.7424 (t70) cc_final: 0.7127 (t0) REVERT: J 132 LEU cc_start: 0.8561 (OUTLIER) cc_final: 0.8157 (tp) REVERT: J 227 PHE cc_start: 0.8628 (OUTLIER) cc_final: 0.7879 (t80) REVERT: J 317 THR cc_start: 0.8132 (m) cc_final: 0.7699 (p) REVERT: J 414 GLU cc_start: 0.7155 (tp30) cc_final: 0.6834 (tp30) REVERT: J 698 MET cc_start: 0.8820 (tpt) cc_final: 0.8509 (tpt) REVERT: J 701 LEU cc_start: 0.8826 (OUTLIER) cc_final: 0.8570 (tp) REVERT: J 738 ARG cc_start: 0.7142 (ttm170) cc_final: 0.6656 (ttp80) REVERT: J 1115 ILE cc_start: 0.4712 (OUTLIER) cc_final: 0.3960 (pt) REVERT: J 1194 ARG cc_start: 0.8046 (mtp85) cc_final: 0.7782 (mtp85) REVERT: J 1215 GLU cc_start: 0.7142 (OUTLIER) cc_final: 0.6931 (tp30) REVERT: L 221 PHE cc_start: 0.2158 (m-80) cc_final: 0.1885 (m-80) REVERT: L 600 HIS cc_start: 0.7503 (t-90) cc_final: 0.7019 (t-90) outliers start: 109 outliers final: 88 residues processed: 433 average time/residue: 0.4500 time to fit residues: 316.3084 Evaluate side-chains 426 residues out of total 3214 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 95 poor density : 331 time to evaluate : 3.485 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 23 HIS Chi-restraints excluded: chain G residue 49 SER Chi-restraints excluded: chain G residue 56 VAL Chi-restraints excluded: chain G residue 111 THR Chi-restraints excluded: chain G residue 136 GLU Chi-restraints excluded: chain G residue 210 THR Chi-restraints excluded: chain G residue 211 ILE Chi-restraints excluded: chain H residue 6 THR Chi-restraints excluded: chain H residue 13 LEU Chi-restraints excluded: chain H residue 98 VAL Chi-restraints excluded: chain H residue 103 ASN Chi-restraints excluded: chain H residue 104 LYS Chi-restraints excluded: chain H residue 115 ILE Chi-restraints excluded: chain H residue 146 VAL Chi-restraints excluded: chain H residue 176 CYS Chi-restraints excluded: chain H residue 183 ILE Chi-restraints excluded: chain I residue 21 VAL Chi-restraints excluded: chain I residue 81 ASP Chi-restraints excluded: chain I residue 82 VAL Chi-restraints excluded: chain I residue 122 VAL Chi-restraints excluded: chain I residue 132 ASP Chi-restraints excluded: chain I residue 158 ASP Chi-restraints excluded: chain I residue 161 LYS Chi-restraints excluded: chain I residue 397 LEU Chi-restraints excluded: chain I residue 414 ILE Chi-restraints excluded: chain I residue 444 ASP Chi-restraints excluded: chain I residue 471 VAL Chi-restraints excluded: chain I residue 481 LEU Chi-restraints excluded: chain I residue 504 GLU Chi-restraints excluded: chain I residue 508 SER Chi-restraints excluded: chain I residue 521 LEU Chi-restraints excluded: chain I residue 550 VAL Chi-restraints excluded: chain I residue 576 SER Chi-restraints excluded: chain I residue 589 THR Chi-restraints excluded: chain I residue 630 VAL Chi-restraints excluded: chain I residue 633 LEU Chi-restraints excluded: chain I residue 699 LEU Chi-restraints excluded: chain I residue 730 SER Chi-restraints excluded: chain I residue 765 ILE Chi-restraints excluded: chain I residue 783 LEU Chi-restraints excluded: chain I residue 788 SER Chi-restraints excluded: chain I residue 796 LEU Chi-restraints excluded: chain I residue 802 VAL Chi-restraints excluded: chain I residue 817 LEU Chi-restraints excluded: chain I residue 823 VAL Chi-restraints excluded: chain I residue 829 THR Chi-restraints excluded: chain I residue 1056 VAL Chi-restraints excluded: chain I residue 1082 ILE Chi-restraints excluded: chain I residue 1225 VAL Chi-restraints excluded: chain I residue 1248 THR Chi-restraints excluded: chain I residue 1254 VAL Chi-restraints excluded: chain I residue 1292 THR Chi-restraints excluded: chain I residue 1293 VAL Chi-restraints excluded: chain I residue 1298 VAL Chi-restraints excluded: chain J residue 32 SER Chi-restraints excluded: chain J residue 46 TYR Chi-restraints excluded: chain J residue 120 LEU Chi-restraints excluded: chain J residue 126 LEU Chi-restraints excluded: chain J residue 132 LEU Chi-restraints excluded: chain J residue 217 LEU Chi-restraints excluded: chain J residue 227 PHE Chi-restraints excluded: chain J residue 320 ASN Chi-restraints excluded: chain J residue 357 VAL Chi-restraints excluded: chain J residue 368 LEU Chi-restraints excluded: chain J residue 392 THR Chi-restraints excluded: chain J residue 506 VAL Chi-restraints excluded: chain J residue 510 LEU Chi-restraints excluded: chain J residue 518 VAL Chi-restraints excluded: chain J residue 548 VAL Chi-restraints excluded: chain J residue 618 VAL Chi-restraints excluded: chain J residue 693 VAL Chi-restraints excluded: chain J residue 701 LEU Chi-restraints excluded: chain J residue 707 ILE Chi-restraints excluded: chain J residue 708 ASN Chi-restraints excluded: chain J residue 717 VAL Chi-restraints excluded: chain J residue 805 GLN Chi-restraints excluded: chain J residue 832 LYS Chi-restraints excluded: chain J residue 839 VAL Chi-restraints excluded: chain J residue 849 LEU Chi-restraints excluded: chain J residue 1115 ILE Chi-restraints excluded: chain J residue 1215 GLU Chi-restraints excluded: chain J residue 1221 LEU Chi-restraints excluded: chain J residue 1273 ASP Chi-restraints excluded: chain J residue 1316 THR Chi-restraints excluded: chain J residue 1324 SER Chi-restraints excluded: chain K residue 4 VAL Chi-restraints excluded: chain K residue 59 ILE Chi-restraints excluded: chain L residue 98 VAL Chi-restraints excluded: chain L residue 105 MET Chi-restraints excluded: chain L residue 225 ARG Chi-restraints excluded: chain L residue 395 THR Chi-restraints excluded: chain L residue 457 ILE Chi-restraints excluded: chain L residue 529 GLU Chi-restraints excluded: chain L residue 552 THR Chi-restraints excluded: chain L residue 609 SER Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 383 random chunks: chunk 335 optimal weight: 4.9990 chunk 353 optimal weight: 0.8980 chunk 322 optimal weight: 8.9990 chunk 344 optimal weight: 2.9990 chunk 207 optimal weight: 5.9990 chunk 149 optimal weight: 1.9990 chunk 270 optimal weight: 5.9990 chunk 105 optimal weight: 2.9990 chunk 310 optimal weight: 1.9990 chunk 325 optimal weight: 20.0000 chunk 342 optimal weight: 0.6980 overall best weight: 1.7186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: I 193 ASN I 517 GLN ** I 519 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 832 HIS ** I1236 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 488 ASN J1227 HIS K 43 ASN ** L 309 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7571 moved from start: 0.3852 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.061 32647 Z= 0.267 Angle : 0.615 14.038 44601 Z= 0.315 Chirality : 0.042 0.165 5112 Planarity : 0.004 0.094 5398 Dihedral : 16.872 130.513 5632 Min Nonbonded Distance : 2.104 Molprobity Statistics. All-atom Clashscore : 11.11 Ramachandran Plot: Outliers : 0.08 % Allowed : 6.87 % Favored : 93.05 % Rotamer: Outliers : 3.53 % Allowed : 15.71 % Favored : 80.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.04 % Cis-general : 0.25 % Twisted Proline : 0.68 % Twisted General : 0.11 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.82 (0.14), residues: 3727 helix: 0.89 (0.14), residues: 1483 sheet: -1.60 (0.28), residues: 359 loop : -1.53 (0.14), residues: 1885 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP I 997 HIS 0.006 0.001 HIS G 23 PHE 0.020 0.002 PHE I 337 TYR 0.022 0.002 TYR H 185 ARG 0.008 0.000 ARG J1231 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7454 Ramachandran restraints generated. 3727 Oldfield, 0 Emsley, 3727 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7454 Ramachandran restraints generated. 3727 Oldfield, 0 Emsley, 3727 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 458 residues out of total 3214 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 113 poor density : 345 time to evaluate : 3.136 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: G 120 ASP cc_start: 0.7032 (p0) cc_final: 0.6645 (p0) REVERT: I 130 MET cc_start: 0.9049 (ttm) cc_final: 0.8786 (ttt) REVERT: I 169 LYS cc_start: 0.8347 (OUTLIER) cc_final: 0.8060 (mtpp) REVERT: I 346 TYR cc_start: 0.7474 (m-80) cc_final: 0.7215 (m-80) REVERT: I 369 MET cc_start: 0.8444 (tmm) cc_final: 0.8194 (ttp) REVERT: I 516 ASP cc_start: 0.8102 (t0) cc_final: 0.7504 (t70) REVERT: I 705 GLU cc_start: 0.7726 (OUTLIER) cc_final: 0.7278 (mt-10) REVERT: I 728 ASP cc_start: 0.7696 (t0) cc_final: 0.7439 (t0) REVERT: I 783 LEU cc_start: 0.8214 (OUTLIER) cc_final: 0.7912 (mt) REVERT: I 1057 LYS cc_start: 0.8793 (ttmt) cc_final: 0.8467 (ttmm) REVERT: I 1172 LEU cc_start: 0.8905 (OUTLIER) cc_final: 0.8568 (tp) REVERT: J 26 SER cc_start: 0.8761 (OUTLIER) cc_final: 0.8470 (p) REVERT: J 56 LEU cc_start: 0.8797 (OUTLIER) cc_final: 0.8584 (mt) REVERT: J 96 LYS cc_start: 0.8649 (ptpt) cc_final: 0.8397 (pttp) REVERT: J 129 ASP cc_start: 0.7409 (t70) cc_final: 0.7121 (t0) REVERT: J 132 LEU cc_start: 0.8539 (OUTLIER) cc_final: 0.8135 (tp) REVERT: J 227 PHE cc_start: 0.8791 (OUTLIER) cc_final: 0.8040 (t80) REVERT: J 316 ILE cc_start: 0.8241 (pt) cc_final: 0.8024 (mt) REVERT: J 317 THR cc_start: 0.8099 (m) cc_final: 0.7675 (p) REVERT: J 698 MET cc_start: 0.8886 (tpt) cc_final: 0.8533 (tpt) REVERT: J 701 LEU cc_start: 0.8832 (OUTLIER) cc_final: 0.8581 (tp) REVERT: J 738 ARG cc_start: 0.7350 (ttm170) cc_final: 0.6873 (ttp80) REVERT: J 1040 MET cc_start: -0.0548 (ptt) cc_final: -0.1188 (ptt) REVERT: J 1115 ILE cc_start: 0.4745 (OUTLIER) cc_final: 0.3978 (pt) REVERT: J 1215 GLU cc_start: 0.7083 (OUTLIER) cc_final: 0.6831 (tp30) REVERT: L 221 PHE cc_start: 0.2286 (m-80) cc_final: 0.2068 (m-80) REVERT: L 600 HIS cc_start: 0.7372 (t-90) cc_final: 0.6888 (t-90) outliers start: 113 outliers final: 90 residues processed: 428 average time/residue: 0.4286 time to fit residues: 296.7805 Evaluate side-chains 433 residues out of total 3214 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 101 poor density : 332 time to evaluate : 3.026 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 23 HIS Chi-restraints excluded: chain G residue 49 SER Chi-restraints excluded: chain G residue 56 VAL Chi-restraints excluded: chain G residue 67 GLU Chi-restraints excluded: chain G residue 111 THR Chi-restraints excluded: chain G residue 136 GLU Chi-restraints excluded: chain G residue 210 THR Chi-restraints excluded: chain G residue 211 ILE Chi-restraints excluded: chain H residue 6 THR Chi-restraints excluded: chain H residue 13 LEU Chi-restraints excluded: chain H residue 46 ILE Chi-restraints excluded: chain H residue 115 ILE Chi-restraints excluded: chain H residue 176 CYS Chi-restraints excluded: chain H residue 183 ILE Chi-restraints excluded: chain I residue 21 VAL Chi-restraints excluded: chain I residue 30 ILE Chi-restraints excluded: chain I residue 81 ASP Chi-restraints excluded: chain I residue 82 VAL Chi-restraints excluded: chain I residue 122 VAL Chi-restraints excluded: chain I residue 132 ASP Chi-restraints excluded: chain I residue 158 ASP Chi-restraints excluded: chain I residue 161 LYS Chi-restraints excluded: chain I residue 169 LYS Chi-restraints excluded: chain I residue 397 LEU Chi-restraints excluded: chain I residue 414 ILE Chi-restraints excluded: chain I residue 444 ASP Chi-restraints excluded: chain I residue 455 SER Chi-restraints excluded: chain I residue 471 VAL Chi-restraints excluded: chain I residue 481 LEU Chi-restraints excluded: chain I residue 504 GLU Chi-restraints excluded: chain I residue 508 SER Chi-restraints excluded: chain I residue 521 LEU Chi-restraints excluded: chain I residue 550 VAL Chi-restraints excluded: chain I residue 576 SER Chi-restraints excluded: chain I residue 589 THR Chi-restraints excluded: chain I residue 630 VAL Chi-restraints excluded: chain I residue 633 LEU Chi-restraints excluded: chain I residue 655 VAL Chi-restraints excluded: chain I residue 699 LEU Chi-restraints excluded: chain I residue 705 GLU Chi-restraints excluded: chain I residue 730 SER Chi-restraints excluded: chain I residue 765 ILE Chi-restraints excluded: chain I residue 783 LEU Chi-restraints excluded: chain I residue 788 SER Chi-restraints excluded: chain I residue 796 LEU Chi-restraints excluded: chain I residue 802 VAL Chi-restraints excluded: chain I residue 817 LEU Chi-restraints excluded: chain I residue 823 VAL Chi-restraints excluded: chain I residue 1056 VAL Chi-restraints excluded: chain I residue 1082 ILE Chi-restraints excluded: chain I residue 1098 LEU Chi-restraints excluded: chain I residue 1172 LEU Chi-restraints excluded: chain I residue 1225 VAL Chi-restraints excluded: chain I residue 1248 THR Chi-restraints excluded: chain I residue 1254 VAL Chi-restraints excluded: chain I residue 1292 THR Chi-restraints excluded: chain I residue 1293 VAL Chi-restraints excluded: chain I residue 1298 VAL Chi-restraints excluded: chain J residue 26 SER Chi-restraints excluded: chain J residue 32 SER Chi-restraints excluded: chain J residue 46 TYR Chi-restraints excluded: chain J residue 56 LEU Chi-restraints excluded: chain J residue 120 LEU Chi-restraints excluded: chain J residue 126 LEU Chi-restraints excluded: chain J residue 132 LEU Chi-restraints excluded: chain J residue 217 LEU Chi-restraints excluded: chain J residue 227 PHE Chi-restraints excluded: chain J residue 320 ASN Chi-restraints excluded: chain J residue 357 VAL Chi-restraints excluded: chain J residue 368 LEU Chi-restraints excluded: chain J residue 392 THR Chi-restraints excluded: chain J residue 401 VAL Chi-restraints excluded: chain J residue 506 VAL Chi-restraints excluded: chain J residue 510 LEU Chi-restraints excluded: chain J residue 518 VAL Chi-restraints excluded: chain J residue 548 VAL Chi-restraints excluded: chain J residue 618 VAL Chi-restraints excluded: chain J residue 638 SER Chi-restraints excluded: chain J residue 693 VAL Chi-restraints excluded: chain J residue 701 LEU Chi-restraints excluded: chain J residue 707 ILE Chi-restraints excluded: chain J residue 708 ASN Chi-restraints excluded: chain J residue 717 VAL Chi-restraints excluded: chain J residue 805 GLN Chi-restraints excluded: chain J residue 839 VAL Chi-restraints excluded: chain J residue 849 LEU Chi-restraints excluded: chain J residue 958 ILE Chi-restraints excluded: chain J residue 1115 ILE Chi-restraints excluded: chain J residue 1215 GLU Chi-restraints excluded: chain J residue 1221 LEU Chi-restraints excluded: chain J residue 1273 ASP Chi-restraints excluded: chain J residue 1316 THR Chi-restraints excluded: chain J residue 1324 SER Chi-restraints excluded: chain K residue 4 VAL Chi-restraints excluded: chain K residue 59 ILE Chi-restraints excluded: chain L residue 98 VAL Chi-restraints excluded: chain L residue 395 THR Chi-restraints excluded: chain L residue 457 ILE Chi-restraints excluded: chain L residue 529 GLU Chi-restraints excluded: chain L residue 552 THR Chi-restraints excluded: chain L residue 609 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 383 random chunks: chunk 225 optimal weight: 0.3980 chunk 363 optimal weight: 2.9990 chunk 222 optimal weight: 2.9990 chunk 172 optimal weight: 0.5980 chunk 252 optimal weight: 0.9990 chunk 381 optimal weight: 10.0000 chunk 351 optimal weight: 8.9990 chunk 303 optimal weight: 0.8980 chunk 31 optimal weight: 5.9990 chunk 234 optimal weight: 0.5980 chunk 186 optimal weight: 4.9990 overall best weight: 0.6982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 103 ASN I 193 ASN I 517 GLN ** I 519 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 832 HIS I 955 GLN J 450 HIS J1227 HIS K 43 ASN ** L 309 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7510 moved from start: 0.4102 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 32647 Z= 0.164 Angle : 0.571 14.070 44601 Z= 0.293 Chirality : 0.040 0.164 5112 Planarity : 0.004 0.091 5398 Dihedral : 16.692 128.876 5632 Min Nonbonded Distance : 2.075 Molprobity Statistics. All-atom Clashscore : 10.89 Ramachandran Plot: Outliers : 0.08 % Allowed : 5.74 % Favored : 94.18 % Rotamer: Outliers : 3.00 % Allowed : 16.46 % Favored : 80.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.04 % Cis-general : 0.25 % Twisted Proline : 0.68 % Twisted General : 0.11 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.63 (0.14), residues: 3727 helix: 1.08 (0.14), residues: 1487 sheet: -1.47 (0.28), residues: 356 loop : -1.46 (0.14), residues: 1884 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP I 807 HIS 0.005 0.001 HIS J 80 PHE 0.017 0.001 PHE I 337 TYR 0.023 0.001 TYR H 185 ARG 0.008 0.000 ARG J1231 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7454 Ramachandran restraints generated. 3727 Oldfield, 0 Emsley, 3727 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7454 Ramachandran restraints generated. 3727 Oldfield, 0 Emsley, 3727 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 445 residues out of total 3214 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 96 poor density : 349 time to evaluate : 3.686 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: G 120 ASP cc_start: 0.7115 (p0) cc_final: 0.6771 (p0) REVERT: I 130 MET cc_start: 0.9004 (ttm) cc_final: 0.8738 (ttt) REVERT: I 346 TYR cc_start: 0.7469 (m-80) cc_final: 0.7228 (m-80) REVERT: I 369 MET cc_start: 0.8412 (tmm) cc_final: 0.8131 (ttp) REVERT: I 516 ASP cc_start: 0.7833 (t0) cc_final: 0.7121 (t0) REVERT: I 783 LEU cc_start: 0.8115 (OUTLIER) cc_final: 0.7784 (mt) REVERT: I 1057 LYS cc_start: 0.8632 (ttmt) cc_final: 0.8076 (ttmm) REVERT: I 1172 LEU cc_start: 0.8879 (OUTLIER) cc_final: 0.8594 (tp) REVERT: J 26 SER cc_start: 0.8720 (OUTLIER) cc_final: 0.8409 (p) REVERT: J 96 LYS cc_start: 0.8605 (ptpt) cc_final: 0.8372 (pttp) REVERT: J 129 ASP cc_start: 0.7380 (t70) cc_final: 0.7083 (t0) REVERT: J 132 LEU cc_start: 0.8510 (OUTLIER) cc_final: 0.8080 (tp) REVERT: J 227 PHE cc_start: 0.8610 (OUTLIER) cc_final: 0.7840 (t80) REVERT: J 316 ILE cc_start: 0.8159 (pt) cc_final: 0.7958 (mt) REVERT: J 317 THR cc_start: 0.7938 (m) cc_final: 0.7512 (p) REVERT: J 701 LEU cc_start: 0.8733 (OUTLIER) cc_final: 0.8516 (tp) REVERT: J 738 ARG cc_start: 0.7319 (ttm170) cc_final: 0.6893 (ttp80) REVERT: J 1040 MET cc_start: -0.0875 (ptt) cc_final: -0.1496 (ptt) REVERT: J 1115 ILE cc_start: 0.4640 (OUTLIER) cc_final: 0.3927 (pt) REVERT: J 1215 GLU cc_start: 0.7128 (OUTLIER) cc_final: 0.6922 (tp30) REVERT: L 600 HIS cc_start: 0.7127 (t-90) cc_final: 0.6701 (t-90) outliers start: 96 outliers final: 80 residues processed: 420 average time/residue: 0.4154 time to fit residues: 284.1469 Evaluate side-chains 418 residues out of total 3214 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 88 poor density : 330 time to evaluate : 3.374 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 23 HIS Chi-restraints excluded: chain G residue 56 VAL Chi-restraints excluded: chain G residue 67 GLU Chi-restraints excluded: chain G residue 111 THR Chi-restraints excluded: chain G residue 136 GLU Chi-restraints excluded: chain G residue 211 ILE Chi-restraints excluded: chain H residue 6 THR Chi-restraints excluded: chain H residue 13 LEU Chi-restraints excluded: chain H residue 46 ILE Chi-restraints excluded: chain H residue 103 ASN Chi-restraints excluded: chain H residue 146 VAL Chi-restraints excluded: chain H residue 183 ILE Chi-restraints excluded: chain I residue 21 VAL Chi-restraints excluded: chain I residue 30 ILE Chi-restraints excluded: chain I residue 81 ASP Chi-restraints excluded: chain I residue 82 VAL Chi-restraints excluded: chain I residue 122 VAL Chi-restraints excluded: chain I residue 132 ASP Chi-restraints excluded: chain I residue 158 ASP Chi-restraints excluded: chain I residue 161 LYS Chi-restraints excluded: chain I residue 397 LEU Chi-restraints excluded: chain I residue 414 ILE Chi-restraints excluded: chain I residue 444 ASP Chi-restraints excluded: chain I residue 455 SER Chi-restraints excluded: chain I residue 471 VAL Chi-restraints excluded: chain I residue 481 LEU Chi-restraints excluded: chain I residue 504 GLU Chi-restraints excluded: chain I residue 508 SER Chi-restraints excluded: chain I residue 521 LEU Chi-restraints excluded: chain I residue 550 VAL Chi-restraints excluded: chain I residue 576 SER Chi-restraints excluded: chain I residue 630 VAL Chi-restraints excluded: chain I residue 633 LEU Chi-restraints excluded: chain I residue 699 LEU Chi-restraints excluded: chain I residue 730 SER Chi-restraints excluded: chain I residue 765 ILE Chi-restraints excluded: chain I residue 783 LEU Chi-restraints excluded: chain I residue 788 SER Chi-restraints excluded: chain I residue 796 LEU Chi-restraints excluded: chain I residue 802 VAL Chi-restraints excluded: chain I residue 817 LEU Chi-restraints excluded: chain I residue 823 VAL Chi-restraints excluded: chain I residue 1056 VAL Chi-restraints excluded: chain I residue 1082 ILE Chi-restraints excluded: chain I residue 1098 LEU Chi-restraints excluded: chain I residue 1172 LEU Chi-restraints excluded: chain I residue 1248 THR Chi-restraints excluded: chain I residue 1254 VAL Chi-restraints excluded: chain I residue 1293 VAL Chi-restraints excluded: chain I residue 1298 VAL Chi-restraints excluded: chain J residue 26 SER Chi-restraints excluded: chain J residue 46 TYR Chi-restraints excluded: chain J residue 114 ILE Chi-restraints excluded: chain J residue 120 LEU Chi-restraints excluded: chain J residue 126 LEU Chi-restraints excluded: chain J residue 132 LEU Chi-restraints excluded: chain J residue 217 LEU Chi-restraints excluded: chain J residue 227 PHE Chi-restraints excluded: chain J residue 320 ASN Chi-restraints excluded: chain J residue 368 LEU Chi-restraints excluded: chain J residue 392 THR Chi-restraints excluded: chain J residue 506 VAL Chi-restraints excluded: chain J residue 510 LEU Chi-restraints excluded: chain J residue 518 VAL Chi-restraints excluded: chain J residue 548 VAL Chi-restraints excluded: chain J residue 618 VAL Chi-restraints excluded: chain J residue 693 VAL Chi-restraints excluded: chain J residue 701 LEU Chi-restraints excluded: chain J residue 707 ILE Chi-restraints excluded: chain J residue 717 VAL Chi-restraints excluded: chain J residue 805 GLN Chi-restraints excluded: chain J residue 839 VAL Chi-restraints excluded: chain J residue 849 LEU Chi-restraints excluded: chain J residue 1115 ILE Chi-restraints excluded: chain J residue 1215 GLU Chi-restraints excluded: chain J residue 1221 LEU Chi-restraints excluded: chain J residue 1273 ASP Chi-restraints excluded: chain J residue 1316 THR Chi-restraints excluded: chain J residue 1324 SER Chi-restraints excluded: chain K residue 4 VAL Chi-restraints excluded: chain K residue 59 ILE Chi-restraints excluded: chain L residue 98 VAL Chi-restraints excluded: chain L residue 365 MET Chi-restraints excluded: chain L residue 395 THR Chi-restraints excluded: chain L residue 457 ILE Chi-restraints excluded: chain L residue 529 GLU Chi-restraints excluded: chain L residue 552 THR Chi-restraints excluded: chain L residue 609 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 383 random chunks: chunk 241 optimal weight: 3.9990 chunk 323 optimal weight: 20.0000 chunk 93 optimal weight: 1.9990 chunk 280 optimal weight: 10.0000 chunk 44 optimal weight: 0.0870 chunk 84 optimal weight: 4.9990 chunk 304 optimal weight: 4.9990 chunk 127 optimal weight: 3.9990 chunk 312 optimal weight: 6.9990 chunk 38 optimal weight: 5.9990 chunk 56 optimal weight: 1.9990 overall best weight: 2.4166 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 103 ASN I 193 ASN I 517 GLN ** I 519 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 832 HIS J 450 HIS J1227 HIS K 43 ASN ** L 309 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4046 r_free = 0.4046 target = 0.183891 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3556 r_free = 0.3556 target = 0.138798 restraints weight = 37903.501| |-----------------------------------------------------------------------------| r_work (start): 0.3502 rms_B_bonded: 3.21 r_work: 0.2998 rms_B_bonded: 3.85 restraints_weight: 0.5000 r_work (final): 0.2998 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8031 moved from start: 0.4112 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.126 32647 Z= 0.231 Angle : 0.684 59.199 44601 Z= 0.379 Chirality : 0.044 1.007 5112 Planarity : 0.004 0.091 5398 Dihedral : 16.697 128.878 5632 Min Nonbonded Distance : 1.858 Molprobity Statistics. All-atom Clashscore : 11.35 Ramachandran Plot: Outliers : 0.11 % Allowed : 5.88 % Favored : 94.02 % Rotamer: Outliers : 3.06 % Allowed : 16.46 % Favored : 80.48 % Cbeta Deviations : 0.03 % Peptide Plane: Cis-proline : 2.04 % Cis-general : 0.25 % Twisted Proline : 0.68 % Twisted General : 0.11 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.64 (0.14), residues: 3727 helix: 1.06 (0.14), residues: 1488 sheet: -1.46 (0.28), residues: 356 loop : -1.46 (0.14), residues: 1883 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP I 807 HIS 0.005 0.001 HIS G 23 PHE 0.014 0.001 PHE I 337 TYR 0.021 0.001 TYR H 185 ARG 0.030 0.000 ARG J 709 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 7124.45 seconds wall clock time: 128 minutes 44.11 seconds (7724.11 seconds total)