Starting phenix.real_space_refine on Thu Mar 21 14:44:12 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6n57_0348/03_2024/6n57_0348_trim_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6n57_0348/03_2024/6n57_0348.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.7 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6n57_0348/03_2024/6n57_0348.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6n57_0348/03_2024/6n57_0348.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6n57_0348/03_2024/6n57_0348_trim_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6n57_0348/03_2024/6n57_0348_trim_updated.pdb" } resolution = 3.7 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= 0.006 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 6 Type Number sf(0) Gaussians Zn 3 6.06 5 Mg 1 5.21 5 S 136 5.16 5 C 18961 2.51 5 N 5327 2.21 5 O 5805 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "H TYR 185": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I TYR 47": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I PHE 57": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I PHE 253": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I ARG 332": "NH1" <-> "NH2" Residue "I PHE 390": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J TYR 46": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J TYR 360": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J ARG 799": "NH1" <-> "NH2" Residue "J PHE 1319": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L TYR 21": "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: 30233 Number of models: 1 Model: "" Number of chains: 11 Chain: "G" Number of atoms: 1766 Number of conformers: 1 Conformer: "" Number of residues, atoms: 228, 1766 Classifications: {'peptide': 228} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 9, 'TRANS': 218} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 5 Unresolved non-hydrogen dihedrals: 3 Planarities with less than four sites: {'GLU:plan': 1} Unresolved non-hydrogen planarities: 4 Chain: "H" Number of atoms: 1678 Number of conformers: 1 Conformer: "" Number of residues, atoms: 219, 1678 Classifications: {'peptide': 219} Incomplete info: {'truncation_to_alanine': 4} Link IDs: {'PCIS': 1, 'PTRANS': 7, 'TRANS': 210} Chain breaks: 1 Unresolved non-hydrogen bonds: 10 Unresolved non-hydrogen angles: 13 Unresolved non-hydrogen dihedrals: 7 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'GLU:plan': 1} Unresolved non-hydrogen planarities: 4 Chain: "I" Number of atoms: 10577 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1341, 10577 Classifications: {'peptide': 1341} Modifications used: {'COO': 1} Link IDs: {'CIS': 1, 'PCIS': 1, 'PTRANS': 55, 'TRANS': 1283} Chain: "J" Number of atoms: 10479 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1347, 10479 Classifications: {'peptide': 1347} Link IDs: {'CIS': 1, 'PTRANS': 55, 'TRANS': 1290} Chain breaks: 2 Chain: "K" Number of atoms: 627 Number of conformers: 1 Conformer: "" Number of residues, atoms: 79, 627 Classifications: {'peptide': 79} Link IDs: {'PTRANS': 2, 'TRANS': 76} Chain: "L" Number of atoms: 4423 Number of conformers: 1 Conformer: "" Number of residues, atoms: 555, 4423 Classifications: {'peptide': 555} Incomplete info: {'truncation_to_alanine': 18} Link IDs: {'CIS': 2, 'PTRANS': 16, 'TRANS': 536} Chain breaks: 2 Unresolved non-hydrogen bonds: 55 Unresolved non-hydrogen angles: 70 Unresolved non-hydrogen dihedrals: 40 Unresolved non-hydrogen chiralities: 5 Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 3, 'ASN:plan1': 1, 'ASP:plan': 5} Unresolved non-hydrogen planarities: 34 Chain: "M" Number of atoms: 571 Number of conformers: 1 Conformer: "" Number of residues, atoms: 72, 571 Classifications: {'peptide': 72} Link IDs: {'PTRANS': 4, 'TRANS': 67} 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 Chain: "M" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {' ZN': 1, '1N7': 1} Classifications: {'undetermined': 2} Link IDs: {None: 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 20313 SG CYS J 814 25.504 89.870 82.477 1.00 34.14 S ATOM 20878 SG CYS J 888 28.493 88.510 84.421 1.00 38.06 S ATOM 20929 SG CYS J 895 27.462 87.320 81.418 1.00 21.90 S ATOM 20950 SG CYS J 898 28.060 90.381 80.150 1.00 24.08 S ATOM 14479 SG CYS J 70 50.502 39.237 119.673 1.00 46.89 S ATOM 14493 SG CYS J 72 52.431 37.499 122.064 1.00 47.01 S ATOM 14601 SG CYS J 85 48.798 37.822 122.466 1.00 68.08 S ATOM 14625 SG CYS J 88 51.793 41.223 122.111 1.00 58.98 S ATOM 29831 SG CYS M 37 76.970 129.893 81.580 1.00 66.53 S ATOM 29851 SG CYS M 40 79.508 131.735 83.020 1.00 64.05 S ATOM 29988 SG CYS M 58 80.825 128.222 80.883 1.00 49.44 S Time building chain proxies: 15.10, per 1000 atoms: 0.50 Number of scatterers: 30233 At special positions: 0 Unit cell: (153.4, 163.8, 193.7, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) Zn 3 29.99 S 136 16.00 Mg 1 11.99 O 5805 8.00 N 5327 7.00 C 18961 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=1, symmetry=0 Number of additional bonds: simple=1, symmetry=0 Coordination: Other bonds: Time building additional restraints: 10.89 Conformation dependent library (CDL) restraints added in 5.1 seconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN J1501 " pdb="ZN ZN J1501 " - pdb=" SG CYS J 888 " pdb="ZN ZN J1501 " - pdb=" SG CYS J 898 " pdb="ZN ZN J1501 " - pdb=" SG CYS J 895 " pdb="ZN ZN J1501 " - pdb=" SG CYS J 814 " pdb=" ZN J1503 " pdb="ZN ZN J1503 " - pdb=" SG CYS J 85 " pdb="ZN ZN J1503 " - pdb=" SG CYS J 88 " pdb="ZN ZN J1503 " - pdb=" SG CYS J 70 " pdb="ZN ZN J1503 " - pdb=" SG CYS J 72 " pdb=" ZN M 101 " pdb="ZN ZN M 101 " - pdb=" SG CYS M 58 " pdb="ZN ZN M 101 " - pdb=" SG CYS M 37 " pdb="ZN ZN M 101 " - pdb=" SG CYS M 40 " Number of angles added : 12 7634 Ramachandran restraints generated. 3817 Oldfield, 0 Emsley, 3817 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 7138 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 123 helices and 31 sheets defined 36.0% alpha, 5.5% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 6.86 Creating SS restraints... Processing helix chain 'G' and resid 35 through 49 Processing helix chain 'G' and resid 78 through 87 removed outlier: 4.286A pdb=" N GLY G 87 " --> pdb=" O LEU G 83 " (cutoff:3.500A) Processing helix chain 'G' and resid 112 through 114 No H-bonds generated for 'chain 'G' and resid 112 through 114' Processing helix chain 'G' and resid 213 through 233 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 230 removed outlier: 4.730A pdb=" N ARG H 218 " --> pdb=" O GLU H 214 " (cutoff:3.500A) removed outlier: 5.831A pdb=" N ALA H 230 " --> pdb=" O GLU H 226 " (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 87 Processing helix chain 'I' and resid 206 through 212 removed outlier: 3.515A pdb=" N ILE I 209 " --> pdb=" O ALA I 206 " (cutoff:3.500A) Processing helix chain 'I' and resid 217 through 223 Processing helix chain 'I' and resid 271 through 278 Processing helix chain 'I' and resid 289 through 292 No H-bonds generated for 'chain 'I' and resid 289 through 292' 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 399 through 408 Processing helix chain 'I' and resid 422 through 437 Processing helix chain 'I' and resid 456 through 480 removed outlier: 3.984A pdb=" N ALA I 474 " --> pdb=" O ARG I 470 " (cutoff:3.500A) Processing helix chain 'I' and resid 495 through 507 Processing helix chain 'I' and resid 520 through 526 Processing helix chain 'I' and resid 545 through 547 No H-bonds generated for 'chain 'I' and resid 545 through 547' Processing helix chain 'I' and resid 647 through 649 No H-bonds generated for 'chain 'I' and resid 647 through 649' 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 688 removed outlier: 4.675A pdb=" N GLN I 688 " --> pdb=" O ASN I 684 " (cutoff:3.500A) Processing helix chain 'I' and resid 704 through 711 Processing helix chain 'I' and resid 820 through 824 Processing helix chain 'I' and resid 899 through 906 Processing helix chain 'I' and resid 943 through 980 removed outlier: 3.844A pdb=" N ILE I 966 " --> pdb=" O GLU I 962 " (cutoff:3.500A) Processing helix chain 'I' and resid 1006 through 1037 Processing helix chain 'I' and resid 1100 through 1102 No H-bonds generated for 'chain 'I' and resid 1100 through 1102' 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 1176 removed outlier: 4.400A pdb=" N ARG I1171 " --> pdb=" O GLU I1167 " (cutoff:3.500A) Processing helix chain 'I' and resid 1192 through 1201 Processing helix chain 'I' and resid 1239 through 1242 No H-bonds generated for 'chain 'I' and resid 1239 through 1242' Processing helix chain 'I' and resid 1272 through 1280 Processing helix chain 'I' and resid 1285 through 1291 Processing helix chain 'I' and resid 1300 through 1309 Processing helix chain 'I' and resid 1322 through 1332 Processing helix chain 'J' and resid 27 through 32 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 96 through 99 Processing helix chain 'J' and resid 115 through 118 No H-bonds generated for 'chain 'J' and resid 115 through 118' Processing helix chain 'J' and resid 125 through 128 No H-bonds generated for 'chain 'J' and resid 125 through 128' Processing helix chain 'J' and resid 132 through 140 Processing helix chain 'J' and resid 162 through 171 removed outlier: 3.562A pdb=" N GLU J 170 " --> pdb=" O LEU J 166 " (cutoff:3.500A) Processing helix chain 'J' and resid 182 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 237 removed outlier: 3.905A pdb=" N MET J 237 " --> pdb=" O PRO J 234 " (cutoff:3.500A) No H-bonds generated for 'chain 'J' and resid 234 through 237' Processing helix chain 'J' and resid 265 through 285 Processing helix chain 'J' and resid 289 through 307 Processing helix chain 'J' and resid 337 through 341 Processing helix chain 'J' and resid 370 through 376 Processing helix chain 'J' and resid 378 through 387 Processing helix chain 'J' and resid 394 through 403 Processing helix chain 'J' and resid 406 through 415 removed outlier: 3.963A pdb=" N ASP J 410 " --> pdb=" O ALA J 406 " (cutoff:3.500A) Processing helix chain 'J' and resid 452 through 457 Processing helix chain 'J' and resid 475 through 482 Processing helix chain 'J' and resid 486 through 488 No H-bonds generated for 'chain 'J' and resid 486 through 488' Processing helix chain 'J' and resid 505 through 513 Processing helix chain 'J' and resid 530 through 539 removed outlier: 3.619A pdb=" N SER J 539 " --> pdb=" O ARG J 535 " (cutoff:3.500A) Processing helix chain 'J' and resid 574 through 580 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 598 through 612 removed outlier: 3.897A pdb=" N LEU J 605 " --> pdb=" O ILE J 601 " (cutoff:3.500A) Processing helix chain 'J' and resid 615 through 634 Processing helix chain 'J' and resid 650 through 668 removed outlier: 3.744A pdb=" N ALA J 662 " --> pdb=" O GLU J 658 " (cutoff:3.500A) 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 786 removed outlier: 3.836A pdb=" N HIS J 777 " --> pdb=" O PHE J 773 " (cutoff:3.500A) removed outlier: 4.429A pdb=" N GLY J 778 " --> pdb=" O ILE J 774 " (cutoff:3.500A) Processing helix chain 'J' and resid 788 through 791 No H-bonds generated for 'chain 'J' and resid 788 through 791' Processing helix chain 'J' and resid 795 through 803 removed outlier: 3.638A pdb=" N VAL J 803 " --> pdb=" O ARG J 799 " (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 929 Proline residue: J 926 - end of helix removed outlier: 4.286A pdb=" N GLN J 929 " --> pdb=" O GLU J 925 " (cutoff:3.500A) Processing helix chain 'J' and resid 1139 through 1146 Processing helix chain 'J' and resid 1217 through 1223 Processing helix chain 'J' and resid 1226 through 1244 removed outlier: 4.196A pdb=" N GLN J1244 " --> pdb=" O VAL J1240 " (cutoff:3.500A) Processing helix chain 'J' and resid 1250 through 1262 removed outlier: 4.301A pdb=" N ARG J1262 " --> pdb=" O ARG J1258 " (cutoff:3.500A) Processing helix chain 'J' and resid 1282 through 1294 Processing helix chain 'J' and resid 1309 through 1312 No H-bonds generated for 'chain 'J' and resid 1309 through 1312' Processing helix chain 'J' and resid 1328 through 1338 Processing helix chain 'J' and resid 1348 through 1353 Processing helix chain 'J' and resid 1361 through 1372 removed outlier: 3.641A pdb=" N ALA J1364 " --> 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 55 Processing helix chain 'K' and resid 61 through 79 removed outlier: 3.603A pdb=" N GLU K 76 " --> pdb=" O GLN K 72 " (cutoff:3.500A) removed outlier: 3.656A pdb=" N ALA K 77 " --> pdb=" O GLN K 73 " (cutoff:3.500A) Processing helix chain 'L' and resid 8 through 19 Processing helix chain 'L' and resid 24 through 30 Processing helix chain 'L' and resid 40 through 50 Processing helix chain 'L' and resid 77 through 89 Processing helix chain 'L' and resid 98 through 105 Processing helix chain 'L' and resid 116 through 136 Processing helix chain 'L' and resid 138 through 153 Processing helix chain 'L' and resid 158 through 161 No H-bonds generated for 'chain 'L' and resid 158 through 161' Processing helix chain 'L' and resid 214 through 232 Processing helix chain 'L' and resid 245 through 256 Processing helix chain 'L' and resid 263 through 295 removed outlier: 4.003A pdb=" N LEU L 290 " --> pdb=" O LEU L 286 " (cutoff:3.500A) removed outlier: 3.912A pdb=" N GLU L 293 " --> pdb=" O LYS L 289 " (cutoff:3.500A) removed outlier: 4.189A pdb=" N GLN L 294 " --> pdb=" O LEU L 290 " (cutoff:3.500A) Processing helix chain 'L' and resid 299 through 306 removed outlier: 4.815A pdb=" N LEU L 305 " --> pdb=" O ASN L 301 " (cutoff:3.500A) Processing helix chain 'L' and resid 314 through 321 removed outlier: 4.266A pdb=" N ALA L 319 " --> pdb=" O TRP L 315 " (cutoff:3.500A) removed outlier: 3.641A pdb=" N ALA L 321 " --> pdb=" O ASN L 317 " (cutoff:3.500A) Processing helix chain 'L' and resid 334 through 351 Processing helix chain 'L' and resid 355 through 394 removed outlier: 4.872A pdb=" N ARG L 385 " --> pdb=" O GLU L 381 " (cutoff:3.500A) removed outlier: 4.859A pdb=" N LEU L 386 " --> pdb=" O ALA L 382 " (cutoff:3.500A) removed outlier: 4.463A pdb=" N LYS L 393 " --> pdb=" O SER L 389 " (cutoff:3.500A) removed outlier: 5.346A pdb=" N TYR L 394 " --> pdb=" O ILE L 390 " (cutoff:3.500A) Processing helix chain 'L' and resid 401 through 418 Processing helix chain 'L' and resid 421 through 423 No H-bonds generated for 'chain 'L' and resid 421 through 423' Processing helix chain 'L' and resid 427 through 445 removed outlier: 3.856A pdb=" N TRP L 433 " --> pdb=" O THR L 429 " (cutoff:3.500A) removed outlier: 3.910A 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 480 through 486 removed outlier: 4.069A pdb=" N GLU L 485 " --> pdb=" O GLU L 481 " (cutoff:3.500A) Processing helix chain 'L' and resid 493 through 500 Processing helix chain 'L' and resid 519 through 522 Processing helix chain 'L' and resid 531 through 549 Processing helix chain 'L' and resid 553 through 561 Processing helix chain 'L' and resid 573 through 580 Processing helix chain 'L' and resid 585 through 599 Processing helix chain 'L' and resid 605 through 610 Processing helix chain 'M' and resid 6 through 26 Processing helix chain 'M' and resid 46 through 51 Processing helix chain 'M' and resid 59 through 71 removed outlier: 4.187A pdb=" N HIS M 71 " --> pdb=" O ARG M 67 " (cutoff:3.500A) Processing sheet with id= A, first strand: chain 'G' and resid 23 through 27 Processing sheet with id= B, first strand: chain 'G' and resid 102 through 105 Processing sheet with id= C, first strand: chain 'G' and resid 108 through 111 removed outlier: 3.500A pdb=" N GLY G 108 " --> pdb=" O LEU G 133 " (cutoff:3.500A) removed outlier: 3.687A pdb=" N CYS G 131 " --> pdb=" O VAL G 110 " (cutoff:3.500A) Processing sheet with id= D, first strand: chain 'H' and resid 187 through 190 Processing sheet with id= E, first strand: chain 'H' and resid 53 through 61 removed outlier: 3.753A pdb=" N GLY H 53 " --> pdb=" O GLY H 149 " (cutoff:3.500A) removed outlier: 3.805A pdb=" N GLY H 149 " --> pdb=" O GLY H 53 " (cutoff:3.500A) removed outlier: 3.622A pdb=" N ALA H 55 " --> pdb=" O GLN H 147 " (cutoff:3.500A) removed outlier: 6.469A pdb=" N LYS H 145 " --> pdb=" O THR H 57 " (cutoff:3.500A) removed outlier: 4.430A pdb=" N VAL H 59 " --> pdb=" O ARG H 143 " (cutoff:3.500A) removed outlier: 6.604A pdb=" N ARG H 143 " --> pdb=" O VAL H 59 " (cutoff:3.500A) Processing sheet with id= F, first strand: chain 'I' and resid 67 through 69 removed outlier: 3.769A pdb=" N ASP I 116 " --> pdb=" O ILE I 104 " (cutoff:3.500A) Processing sheet with id= G, first strand: chain 'I' and resid 73 through 75 Processing sheet with id= H, first strand: chain 'I' and resid 155 through 157 Processing sheet with id= I, first strand: chain 'I' and resid 184 through 188 Processing sheet with id= J, first strand: chain 'I' and resid 227 through 230 Processing sheet with id= K, first strand: chain 'I' and resid 591 through 593 Processing sheet with id= L, first strand: chain 'I' and resid 633 through 637 Processing sheet with id= M, first strand: chain 'I' and resid 798 through 802 removed outlier: 3.623A pdb=" N GLN I 798 " --> pdb=" O MET I1232 " (cutoff:3.500A) Processing sheet with id= N, first strand: chain 'I' and resid 830 through 833 Processing sheet with id= O, first strand: chain 'I' and resid 887 through 889 Processing sheet with id= P, first strand: chain 'I' and resid 930 through 933 removed outlier: 3.909A pdb=" N ASP I 930 " --> pdb=" O TYR I1053 " (cutoff:3.500A) Processing sheet with id= Q, first strand: chain 'I' and resid 255 through 257 removed outlier: 3.530A pdb=" N VAL I 263 " --> pdb=" O ILE I 255 " (cutoff:3.500A) removed outlier: 7.193A pdb=" N ALA I 257 " --> pdb=" O VAL I 261 " (cutoff:3.500A) removed outlier: 4.490A pdb=" N VAL I 261 " --> pdb=" O ALA I 257 " (cutoff:3.500A) Processing sheet with id= R, first strand: chain 'I' and resid 722 through 727 removed outlier: 6.544A pdb=" N VAL I 733 " --> pdb=" O GLN I 725 " (cutoff:3.500A) Processing sheet with id= S, first strand: chain 'J' and resid 103 through 106 removed outlier: 3.727A pdb=" N GLY J 103 " --> pdb=" O VAL J 244 " (cutoff:3.500A) Processing sheet with id= T, first strand: chain 'J' and resid 252 through 254 removed outlier: 4.169A pdb=" N VAL J 253 " --> pdb=" O ALA J 261 " (cutoff:3.500A) Processing sheet with id= U, first strand: chain 'J' and resid 365 through 369 removed outlier: 5.696A pdb=" N GLU J 438 " --> pdb=" O CYS J 366 " (cutoff:3.500A) removed outlier: 6.810A pdb=" N LEU J 368 " --> pdb=" O GLU J 438 " (cutoff:3.500A) removed outlier: 5.525A pdb=" N VAL J 440 " --> pdb=" O LEU J 368 " (cutoff:3.500A) No H-bonds generated for sheet with id= U Processing sheet with id= V, first strand: chain 'J' and resid 434 through 437 removed outlier: 3.513A pdb=" N GLN J 435 " --> pdb=" O LEU J 423 " (cutoff:3.500A) Processing sheet with id= W, first strand: chain 'J' and resid 553 through 556 removed outlier: 3.891A pdb=" N GLU J 554 " --> pdb=" O LYS J 566 " (cutoff:3.500A) removed outlier: 3.539A pdb=" N LYS J 566 " --> pdb=" O GLU J 554 " (cutoff:3.500A) removed outlier: 3.725A pdb=" N GLU J 556 " --> pdb=" O VAL J 564 " (cutoff:3.500A) Processing sheet with id= X, first strand: chain 'J' and resid 820 through 823 removed outlier: 3.635A pdb=" N MET J 822 " --> pdb=" O VAL J 880 " (cutoff:3.500A) Processing sheet with id= Y, first strand: chain 'J' and resid 957 through 961 removed outlier: 3.573A pdb=" N LYS J 959 " --> pdb=" O LYS J 983 " (cutoff:3.500A) Processing sheet with id= Z, first strand: chain 'J' and resid 965 through 967 removed outlier: 4.379A pdb=" N VAL J 974 " --> pdb=" O VAL J 966 " (cutoff:3.500A) Processing sheet with id= AA, first strand: chain 'J' and resid 1046 through 1049 Processing sheet with id= AB, first strand: chain 'J' and resid 1077 through 1079 Processing sheet with id= AC, first strand: chain 'J' and resid 1162 through 1165 Processing sheet with id= AD, first strand: chain 'J' and resid 1279 through 1281 Processing sheet with id= AE, first strand: chain 'J' and resid 949 through 951 removed outlier: 4.025A pdb=" N ALA J1018 " --> pdb=" O ILE J 950 " (cutoff:3.500A) 972 hydrogen bonds defined for protein. 2820 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 9.38 Time building geometry restraints manager: 11.74 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.34: 10356 1.34 - 1.46: 6246 1.46 - 1.59: 13818 1.59 - 1.72: 14 1.72 - 1.84: 245 Bond restraints: 30679 Sorted by residual: bond pdb=" C19 1N7 I1401 " pdb=" C3 1N7 I1401 " ideal model delta sigma weight residual 1.532 1.841 -0.309 2.00e-02 2.50e+03 2.39e+02 bond pdb=" C19 1N7 J1504 " pdb=" C3 1N7 J1504 " ideal model delta sigma weight residual 1.532 1.827 -0.295 2.00e-02 2.50e+03 2.18e+02 bond pdb=" C19 1N7 L 701 " pdb=" C3 1N7 L 701 " ideal model delta sigma weight residual 1.532 1.825 -0.293 2.00e-02 2.50e+03 2.15e+02 bond pdb=" C19 1N7 M 102 " pdb=" C3 1N7 M 102 " ideal model delta sigma weight residual 1.532 1.815 -0.283 2.00e-02 2.50e+03 2.00e+02 bond pdb=" C3 1N7 I1401 " pdb=" C4 1N7 I1401 " ideal model delta sigma weight residual 1.532 1.738 -0.206 2.00e-02 2.50e+03 1.07e+02 ... (remaining 30674 not shown) Histogram of bond angle deviations from ideal: 90.84 - 100.88: 85 100.88 - 110.91: 11632 110.91 - 120.94: 21186 120.94 - 130.98: 8471 130.98 - 141.01: 73 Bond angle restraints: 41447 Sorted by residual: angle pdb=" N GLU L 58 " pdb=" CA GLU L 58 " pdb=" CB GLU L 58 " ideal model delta sigma weight residual 110.49 141.01 -30.52 1.69e+00 3.50e-01 3.26e+02 angle pdb=" C PHE J 437 " pdb=" N GLU J 438 " pdb=" CA GLU J 438 " ideal model delta sigma weight residual 121.92 104.59 17.33 1.60e+00 3.91e-01 1.17e+02 angle pdb=" N GLU L 58 " pdb=" CA GLU L 58 " pdb=" C GLU L 58 " ideal model delta sigma weight residual 110.80 90.84 19.96 2.13e+00 2.20e-01 8.78e+01 angle pdb=" C GLU H 29 " pdb=" N PRO H 30 " pdb=" CD PRO H 30 " ideal model delta sigma weight residual 120.60 136.83 -16.23 2.20e+00 2.07e-01 5.44e+01 angle pdb=" C PHE I 57 " pdb=" N PRO I 58 " pdb=" CD PRO I 58 " ideal model delta sigma weight residual 120.60 136.16 -15.56 2.20e+00 2.07e-01 5.00e+01 ... (remaining 41442 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 19.50: 18472 19.50 - 39.00: 636 39.00 - 58.50: 47 58.50 - 78.00: 26 78.00 - 97.50: 2 Dihedral angle restraints: 19183 sinusoidal: 8114 harmonic: 11069 Sorted by residual: dihedral pdb=" N GLU L 58 " pdb=" C GLU L 58 " pdb=" CA GLU L 58 " pdb=" CB GLU L 58 " ideal model delta harmonic sigma weight residual 122.80 146.50 -23.70 0 2.50e+00 1.60e-01 8.99e+01 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 180.00 135.88 44.12 0 5.00e+00 4.00e-02 7.79e+01 dihedral pdb=" CA PRO I 897 " pdb=" C PRO I 897 " pdb=" N GLU I 898 " pdb=" CA GLU I 898 " ideal model delta harmonic sigma weight residual -180.00 -139.53 -40.47 0 5.00e+00 4.00e-02 6.55e+01 ... (remaining 19180 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.149: 4683 0.149 - 0.298: 63 0.298 - 0.448: 3 0.448 - 0.597: 1 0.597 - 0.746: 1 Chirality restraints: 4751 Sorted by residual: chirality pdb=" CA GLU L 58 " pdb=" N GLU L 58 " pdb=" C GLU L 58 " pdb=" CB GLU L 58 " both_signs ideal model delta sigma weight residual False 2.51 1.76 0.75 2.00e-01 2.50e+01 1.39e+01 chirality pdb=" CA GLU G 29 " pdb=" N GLU G 29 " pdb=" C GLU G 29 " pdb=" CB GLU G 29 " both_signs ideal model delta sigma weight residual False 2.51 2.05 0.46 2.00e-01 2.50e+01 5.34e+00 chirality pdb=" CB ILE I1079 " pdb=" CA ILE I1079 " pdb=" CG1 ILE I1079 " pdb=" CG2 ILE I1079 " both_signs ideal model delta sigma weight residual False 2.64 2.27 0.38 2.00e-01 2.50e+01 3.56e+00 ... (remaining 4748 not shown) Planarity restraints: 5415 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ASP L 96 " -0.124 5.00e-02 4.00e+02 2.00e-01 6.43e+01 pdb=" N PRO L 97 " 0.347 5.00e-02 4.00e+02 pdb=" CA PRO L 97 " -0.125 5.00e-02 4.00e+02 pdb=" CD PRO L 97 " -0.098 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ALA L 59 " 0.067 5.00e-02 4.00e+02 1.02e-01 1.66e+01 pdb=" N PRO L 60 " -0.176 5.00e-02 4.00e+02 pdb=" CA PRO L 60 " 0.055 5.00e-02 4.00e+02 pdb=" CD PRO L 60 " 0.054 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C GLU J 438 " 0.058 5.00e-02 4.00e+02 8.73e-02 1.22e+01 pdb=" N PRO J 439 " -0.151 5.00e-02 4.00e+02 pdb=" CA PRO J 439 " 0.045 5.00e-02 4.00e+02 pdb=" CD PRO J 439 " 0.048 5.00e-02 4.00e+02 ... (remaining 5412 not shown) Histogram of nonbonded interaction distances: 1.37 - 2.07: 15 2.07 - 2.78: 7389 2.78 - 3.49: 43518 3.49 - 4.19: 68374 4.19 - 4.90: 120685 Nonbonded interactions: 239981 Sorted by model distance: nonbonded pdb=" NH1 ARG J 933 " pdb=" OD2 ASP L 63 " model vdw 1.366 2.520 nonbonded pdb=" O ASP L 63 " pdb=" N LEU L 65 " model vdw 1.570 2.520 nonbonded pdb=" OH TYR L 148 " pdb=" OE2 GLU L 152 " model vdw 1.824 2.440 nonbonded pdb=" O THR I 539 " pdb=" O ALA I 543 " model vdw 1.884 3.040 nonbonded pdb=" OD1 ASP L 96 " pdb=" N PRO L 97 " model vdw 1.956 3.120 ... (remaining 239976 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 8 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 8 through 228 or (resid 229 through 230 and (name N or nam \ e CA or name C or name O or name CB )) or resid 231 through 234)) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.650 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: 4.950 Check model and map are aligned: 0.420 Set scattering table: 0.250 Process input model: 77.170 Find NCS groups from input model: 1.080 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:2.660 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 87.320 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8000 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 : 0.012 0.309 30679 Z= 0.800 Angle : 1.135 30.518 41447 Z= 0.609 Chirality : 0.060 0.746 4751 Planarity : 0.007 0.200 5415 Dihedral : 10.444 97.497 12045 Min Nonbonded Distance : 1.366 Molprobity Statistics. All-atom Clashscore : 39.05 Ramachandran Plot: Outliers : 0.60 % Allowed : 15.43 % Favored : 83.97 % Rotamer: Outliers : 0.37 % Allowed : 3.46 % Favored : 96.17 % Cbeta Deviations : 0.08 % Peptide Plane: Cis-proline : 1.33 % Cis-general : 0.11 % Twisted Proline : 0.67 % Twisted General : 0.22 % 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: -4.55 (0.11), residues: 3817 helix: -2.11 (0.11), residues: 1526 sheet: -3.68 (0.23), residues: 349 loop : -3.76 (0.12), residues: 1942 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.030 0.004 TRP I1276 HIS 0.014 0.003 HIS J 545 PHE 0.036 0.004 PHE J 437 TYR 0.037 0.003 TYR G 177 ARG 0.018 0.001 ARG I1223 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7634 Ramachandran restraints generated. 3817 Oldfield, 0 Emsley, 3817 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7634 Ramachandran restraints generated. 3817 Oldfield, 0 Emsley, 3817 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 813 residues out of total 3287 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 801 time to evaluate : 3.519 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: G 29 GLU cc_start: 0.8311 (OUTLIER) cc_final: 0.8003 (tp30) REVERT: G 200 LYS cc_start: 0.8837 (ttmt) cc_final: 0.8434 (ttmm) REVERT: H 51 MET cc_start: 0.8338 (mmm) cc_final: 0.7877 (mmm) REVERT: H 95 LYS cc_start: 0.8560 (tptm) cc_final: 0.8350 (tppt) REVERT: H 197 ASP cc_start: 0.7505 (p0) cc_final: 0.7204 (p0) REVERT: H 199 ASP cc_start: 0.8146 (m-30) cc_final: 0.7787 (m-30) REVERT: H 200 LYS cc_start: 0.9362 (tttt) cc_final: 0.9126 (tttp) REVERT: H 211 ILE cc_start: 0.8189 (tp) cc_final: 0.7776 (tp) REVERT: I 14 ASP cc_start: 0.7997 (t70) cc_final: 0.7796 (t0) REVERT: I 59 ILE cc_start: 0.7451 (mt) cc_final: 0.7043 (mt) REVERT: I 422 LYS cc_start: 0.7925 (mtmt) cc_final: 0.7696 (mtmm) REVERT: I 545 PHE cc_start: 0.7142 (t80) cc_final: 0.6824 (t80) REVERT: I 684 ASN cc_start: 0.8650 (t0) cc_final: 0.8325 (t0) REVERT: I 699 LEU cc_start: 0.9514 (OUTLIER) cc_final: 0.9256 (tm) REVERT: I 702 THR cc_start: 0.9187 (p) cc_final: 0.8916 (p) REVERT: I 717 VAL cc_start: 0.9486 (t) cc_final: 0.9187 (m) REVERT: I 976 ARG cc_start: 0.6453 (tpt-90) cc_final: 0.6215 (ttt90) REVERT: I 1040 ASP cc_start: 0.8045 (m-30) cc_final: 0.7836 (m-30) REVERT: I 1273 MET cc_start: 0.8379 (mtm) cc_final: 0.8024 (mtp) REVERT: I 1290 MET cc_start: 0.8528 (tpp) cc_final: 0.8221 (tpp) REVERT: J 21 LYS cc_start: 0.8737 (ttpp) cc_final: 0.8521 (tttp) REVERT: J 130 MET cc_start: 0.8355 (ttt) cc_final: 0.7563 (ttp) REVERT: J 157 GLN cc_start: 0.8426 (mm-40) cc_final: 0.7651 (mm-40) REVERT: J 325 LYS cc_start: 0.8869 (tttt) cc_final: 0.8492 (mtmt) REVERT: J 429 LEU cc_start: 0.9171 (mm) cc_final: 0.8872 (mt) REVERT: J 466 MET cc_start: 0.8289 (mtp) cc_final: 0.8081 (mtp) REVERT: J 683 ILE cc_start: 0.9084 (OUTLIER) cc_final: 0.8807 (tt) REVERT: J 725 MET cc_start: 0.8839 (mtm) cc_final: 0.8570 (mtp) REVERT: J 821 MET cc_start: 0.8487 (tpp) cc_final: 0.8170 (tpt) REVERT: J 982 LEU cc_start: 0.8489 (tp) cc_final: 0.8267 (tp) REVERT: J 1286 LYS cc_start: 0.8303 (tmmt) cc_final: 0.8074 (ttpp) REVERT: J 1291 GLU cc_start: 0.8054 (pt0) cc_final: 0.7749 (pp20) REVERT: J 1316 THR cc_start: 0.8985 (m) cc_final: 0.8750 (p) REVERT: K 55 GLU cc_start: 0.8181 (tm-30) cc_final: 0.7763 (tm-30) REVERT: L 21 TYR cc_start: 0.7256 (p90) cc_final: 0.6707 (p90) REVERT: L 46 GLN cc_start: 0.6467 (tp-100) cc_final: 0.6007 (mm110) REVERT: L 117 ILE cc_start: 0.5984 (mp) cc_final: 0.5780 (mp) REVERT: L 273 MET cc_start: 0.5297 (mtt) cc_final: 0.4973 (tpt) REVERT: L 276 MET cc_start: 0.5528 (tpp) cc_final: 0.4941 (mmt) REVERT: L 339 ARG cc_start: 0.5151 (mtp85) cc_final: 0.4227 (mmp-170) REVERT: M 61 CYS cc_start: 0.8008 (m) cc_final: 0.7273 (m) outliers start: 12 outliers final: 3 residues processed: 810 average time/residue: 0.4784 time to fit residues: 583.7408 Evaluate side-chains 434 residues out of total 3287 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 428 time to evaluate : 3.296 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 29 GLU Chi-restraints excluded: chain I residue 412 GLU Chi-restraints excluded: chain I residue 699 LEU Chi-restraints excluded: chain I residue 1094 VAL Chi-restraints excluded: chain J residue 54 ASP Chi-restraints excluded: chain J residue 683 ILE Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 380 random chunks: chunk 320 optimal weight: 0.0770 chunk 288 optimal weight: 0.9980 chunk 159 optimal weight: 0.7980 chunk 98 optimal weight: 0.8980 chunk 194 optimal weight: 0.9990 chunk 153 optimal weight: 0.8980 chunk 297 optimal weight: 0.9990 chunk 115 optimal weight: 0.9990 chunk 181 optimal weight: 0.9990 chunk 221 optimal weight: 0.9990 chunk 345 optimal weight: 8.9990 overall best weight: 0.7338 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: G 23 HIS G 147 GLN ** H 227 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 69 GLN I 133 ASN I 219 GLN I 343 HIS I 510 GLN I 620 ASN I 808 ASN I1017 GLN I1080 ASN I1116 HIS I1209 GLN I1257 GLN J 232 ASN J 341 ASN J 680 ASN J 720 ASN J 910 ASN J1197 ASN J1268 ASN J1295 ASN J1366 HIS K 70 GLN L 40 GLN ** L 227 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 271 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 346 GLN L 383 ASN L 406 GLN L 518 HIS L 568 ASN M 21 ASN M 68 GLN Total number of N/Q/H flips: 32 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7890 moved from start: 0.3125 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.052 30679 Z= 0.207 Angle : 0.700 13.701 41447 Z= 0.354 Chirality : 0.045 0.405 4751 Planarity : 0.005 0.128 5415 Dihedral : 6.223 75.772 4511 Min Nonbonded Distance : 2.091 Molprobity Statistics. All-atom Clashscore : 13.00 Ramachandran Plot: Outliers : 0.31 % Allowed : 7.20 % Favored : 92.48 % Rotamer: Outliers : 2.70 % Allowed : 10.26 % Favored : 87.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.33 % Cis-general : 0.11 % Twisted Proline : 0.00 % Twisted General : 0.08 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.99 (0.12), residues: 3817 helix: -0.45 (0.13), residues: 1504 sheet: -3.28 (0.24), residues: 350 loop : -3.09 (0.12), residues: 1963 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.001 TRP I 807 HIS 0.012 0.001 HIS I 273 PHE 0.021 0.002 PHE I 38 TYR 0.024 0.002 TYR I 262 ARG 0.009 0.001 ARG J 322 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7634 Ramachandran restraints generated. 3817 Oldfield, 0 Emsley, 3817 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7634 Ramachandran restraints generated. 3817 Oldfield, 0 Emsley, 3817 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 705 residues out of total 3287 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 88 poor density : 617 time to evaluate : 3.566 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: G 83 LEU cc_start: 0.8913 (OUTLIER) cc_final: 0.8508 (tt) REVERT: G 185 TYR cc_start: 0.8814 (p90) cc_final: 0.8352 (p90) REVERT: G 200 LYS cc_start: 0.8439 (ttmt) cc_final: 0.8209 (ttmm) REVERT: G 207 THR cc_start: 0.8565 (m) cc_final: 0.8090 (p) REVERT: H 84 ASN cc_start: 0.8984 (m110) cc_final: 0.8533 (m110) REVERT: H 199 ASP cc_start: 0.8027 (m-30) cc_final: 0.7699 (m-30) REVERT: H 211 ILE cc_start: 0.8116 (tp) cc_final: 0.7833 (tp) REVERT: I 272 ARG cc_start: 0.6941 (tmt170) cc_final: 0.6737 (ttt-90) REVERT: I 422 LYS cc_start: 0.7874 (mtmt) cc_final: 0.7565 (mtpp) REVERT: I 470 ARG cc_start: 0.7328 (ppp80) cc_final: 0.6903 (tpm170) REVERT: I 699 LEU cc_start: 0.9394 (OUTLIER) cc_final: 0.9186 (tp) REVERT: I 717 VAL cc_start: 0.9331 (t) cc_final: 0.8981 (m) REVERT: I 817 LEU cc_start: 0.8792 (OUTLIER) cc_final: 0.8316 (tt) REVERT: I 1240 ASP cc_start: 0.7983 (p0) cc_final: 0.7497 (p0) REVERT: I 1290 MET cc_start: 0.8309 (tpp) cc_final: 0.7910 (tpp) REVERT: I 1296 ASP cc_start: 0.8353 (t0) cc_final: 0.8098 (t70) REVERT: J 130 MET cc_start: 0.8504 (ttt) cc_final: 0.7823 (ttp) REVERT: J 169 LEU cc_start: 0.7141 (OUTLIER) cc_final: 0.6910 (tt) REVERT: J 180 MET cc_start: 0.7253 (ptm) cc_final: 0.6604 (ptm) REVERT: J 237 MET cc_start: 0.8164 (mtm) cc_final: 0.7887 (mtp) REVERT: J 326 SER cc_start: 0.8997 (OUTLIER) cc_final: 0.8583 (t) REVERT: J 429 LEU cc_start: 0.9039 (mm) cc_final: 0.8658 (mt) REVERT: J 466 MET cc_start: 0.8136 (mtp) cc_final: 0.7768 (mtp) REVERT: J 472 LEU cc_start: 0.8741 (mt) cc_final: 0.8429 (mt) REVERT: J 489 ASN cc_start: 0.8754 (m-40) cc_final: 0.8493 (m110) REVERT: J 849 LEU cc_start: 0.7476 (OUTLIER) cc_final: 0.7195 (mt) REVERT: J 1371 ARG cc_start: 0.7230 (OUTLIER) cc_final: 0.6920 (ttm-80) REVERT: L 21 TYR cc_start: 0.7145 (p90) cc_final: 0.6759 (p90) REVERT: L 24 TYR cc_start: 0.6633 (m-80) cc_final: 0.5152 (t80) REVERT: L 46 GLN cc_start: 0.6160 (tp-100) cc_final: 0.5696 (mm-40) REVERT: L 121 LYS cc_start: 0.7793 (tppt) cc_final: 0.7106 (tptt) REVERT: L 273 MET cc_start: 0.5481 (mtt) cc_final: 0.5113 (tpp) REVERT: L 288 MET cc_start: 0.0384 (ttt) cc_final: 0.0039 (ptt) REVERT: L 339 ARG cc_start: 0.4787 (mtp85) cc_final: 0.4054 (mmp-170) REVERT: M 49 ARG cc_start: 0.8446 (ttp-110) cc_final: 0.7797 (ttp-110) REVERT: M 61 CYS cc_start: 0.7708 (m) cc_final: 0.7393 (m) outliers start: 88 outliers final: 33 residues processed: 672 average time/residue: 0.4464 time to fit residues: 467.9655 Evaluate side-chains 451 residues out of total 3287 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 40 poor density : 411 time to evaluate : 3.244 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 61 ILE Chi-restraints excluded: chain G residue 83 LEU Chi-restraints excluded: chain G residue 137 ASN Chi-restraints excluded: chain H residue 28 LEU Chi-restraints excluded: chain H residue 65 LEU Chi-restraints excluded: chain H residue 183 ILE Chi-restraints excluded: chain H residue 212 ASP Chi-restraints excluded: chain I residue 82 VAL Chi-restraints excluded: chain I residue 412 GLU Chi-restraints excluded: chain I residue 699 LEU Chi-restraints excluded: chain I residue 817 LEU Chi-restraints excluded: chain I residue 896 THR Chi-restraints excluded: chain I residue 924 VAL Chi-restraints excluded: chain I residue 925 SER Chi-restraints excluded: chain I residue 1094 VAL Chi-restraints excluded: chain I residue 1289 GLU Chi-restraints excluded: chain J residue 46 TYR Chi-restraints excluded: chain J residue 92 VAL Chi-restraints excluded: chain J residue 169 LEU Chi-restraints excluded: chain J residue 201 LEU Chi-restraints excluded: chain J residue 326 SER Chi-restraints excluded: chain J residue 363 LEU Chi-restraints excluded: chain J residue 428 THR Chi-restraints excluded: chain J residue 506 VAL Chi-restraints excluded: chain J residue 674 THR Chi-restraints excluded: chain J residue 754 ILE Chi-restraints excluded: chain J residue 849 LEU Chi-restraints excluded: chain J residue 853 THR Chi-restraints excluded: chain J residue 935 PHE Chi-restraints excluded: chain J residue 1159 ILE Chi-restraints excluded: chain J residue 1239 ASP Chi-restraints excluded: chain J residue 1281 GLU Chi-restraints excluded: chain J residue 1371 ARG Chi-restraints excluded: chain K residue 39 VAL Chi-restraints excluded: chain K residue 60 ASN Chi-restraints excluded: chain L residue 55 VAL Chi-restraints excluded: chain L residue 379 MET Chi-restraints excluded: chain L residue 395 THR Chi-restraints excluded: chain L residue 552 THR Chi-restraints excluded: chain L residue 570 ASP Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 380 random chunks: chunk 191 optimal weight: 10.0000 chunk 107 optimal weight: 5.9990 chunk 287 optimal weight: 8.9990 chunk 234 optimal weight: 0.8980 chunk 95 optimal weight: 0.9980 chunk 345 optimal weight: 7.9990 chunk 373 optimal weight: 5.9990 chunk 307 optimal weight: 3.9990 chunk 342 optimal weight: 7.9990 chunk 117 optimal weight: 9.9990 chunk 277 optimal weight: 6.9990 overall best weight: 3.5786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: G 23 HIS G 132 HIS H 128 HIS H 132 HIS I 31 GLN I 613 ASN I 620 ASN ** I 659 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I1072 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I1111 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I1268 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I1314 GLN J 979 ASN J1350 ASN L 129 GLN ** L 227 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 271 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 437 GLN Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8059 moved from start: 0.3434 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.067 30679 Z= 0.466 Angle : 0.781 15.039 41447 Z= 0.394 Chirality : 0.049 0.316 4751 Planarity : 0.006 0.100 5415 Dihedral : 6.264 53.912 4504 Min Nonbonded Distance : 2.079 Molprobity Statistics. All-atom Clashscore : 15.29 Ramachandran Plot: Outliers : 0.26 % Allowed : 10.48 % Favored : 89.26 % Rotamer: Outliers : 4.47 % Allowed : 13.30 % Favored : 82.23 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.33 % Cis-general : 0.11 % Twisted Proline : 0.00 % Twisted General : 0.11 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.68 (0.13), residues: 3817 helix: -0.21 (0.13), residues: 1502 sheet: -2.95 (0.27), residues: 310 loop : -2.95 (0.12), residues: 2005 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.002 TRP I 807 HIS 0.010 0.002 HIS I 273 PHE 0.020 0.002 PHE J1319 TYR 0.020 0.002 TYR G 177 ARG 0.009 0.001 ARG G 148 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7634 Ramachandran restraints generated. 3817 Oldfield, 0 Emsley, 3817 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7634 Ramachandran restraints generated. 3817 Oldfield, 0 Emsley, 3817 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 580 residues out of total 3287 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 146 poor density : 434 time to evaluate : 3.452 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: G 68 TYR cc_start: 0.9221 (m-80) cc_final: 0.8897 (m-10) REVERT: G 185 TYR cc_start: 0.8920 (p90) cc_final: 0.8711 (p90) REVERT: G 200 LYS cc_start: 0.8774 (ttmt) cc_final: 0.8506 (ttmm) REVERT: G 207 THR cc_start: 0.8679 (m) cc_final: 0.8235 (p) REVERT: I 272 ARG cc_start: 0.7131 (tmt170) cc_final: 0.6723 (ttt-90) REVERT: I 349 GLU cc_start: 0.7360 (OUTLIER) cc_final: 0.7096 (mt-10) REVERT: I 379 GLU cc_start: 0.6390 (mm-30) cc_final: 0.6179 (tp30) REVERT: I 422 LYS cc_start: 0.8098 (mtmt) cc_final: 0.7721 (mtpp) REVERT: I 429 MET cc_start: 0.8006 (mtt) cc_final: 0.7717 (mtm) REVERT: I 470 ARG cc_start: 0.7608 (ppp80) cc_final: 0.7042 (tpm170) REVERT: I 600 THR cc_start: 0.8875 (m) cc_final: 0.8673 (t) REVERT: I 717 VAL cc_start: 0.9355 (t) cc_final: 0.9026 (m) REVERT: I 842 ASP cc_start: 0.8421 (OUTLIER) cc_final: 0.8212 (m-30) REVERT: I 1253 LEU cc_start: 0.9406 (OUTLIER) cc_final: 0.9161 (tm) REVERT: I 1290 MET cc_start: 0.8553 (tpp) cc_final: 0.8005 (tpp) REVERT: I 1296 ASP cc_start: 0.8244 (OUTLIER) cc_final: 0.7945 (t70) REVERT: I 1330 ILE cc_start: 0.8910 (mt) cc_final: 0.8704 (mp) REVERT: J 130 MET cc_start: 0.8407 (ttt) cc_final: 0.8205 (ttt) REVERT: J 169 LEU cc_start: 0.7229 (OUTLIER) cc_final: 0.6849 (tt) REVERT: J 180 MET cc_start: 0.7465 (ptm) cc_final: 0.6900 (ptm) REVERT: J 325 LYS cc_start: 0.8875 (mptt) cc_final: 0.8637 (mtmt) REVERT: J 414 GLU cc_start: 0.7978 (tm-30) cc_final: 0.7778 (tm-30) REVERT: J 466 MET cc_start: 0.8249 (mtp) cc_final: 0.8005 (mtp) REVERT: J 472 LEU cc_start: 0.8732 (mt) cc_final: 0.8457 (mt) REVERT: J 849 LEU cc_start: 0.7605 (OUTLIER) cc_final: 0.7357 (mt) REVERT: J 1330 ARG cc_start: 0.8283 (tmm-80) cc_final: 0.7894 (ttp80) REVERT: J 1371 ARG cc_start: 0.7423 (OUTLIER) cc_final: 0.7134 (ttm-80) REVERT: K 3 ARG cc_start: 0.8713 (OUTLIER) cc_final: 0.8028 (ttm170) REVERT: L 21 TYR cc_start: 0.6872 (p90) cc_final: 0.6452 (p90) REVERT: L 46 GLN cc_start: 0.6332 (tp-100) cc_final: 0.6024 (mm110) REVERT: L 105 MET cc_start: 0.7410 (ppp) cc_final: 0.7142 (ppp) REVERT: L 121 LYS cc_start: 0.7907 (tppt) cc_final: 0.7162 (tptt) REVERT: L 288 MET cc_start: 0.0815 (ttt) cc_final: -0.0026 (ptt) REVERT: L 339 ARG cc_start: 0.5258 (mtp85) cc_final: 0.4054 (mmp-170) REVERT: M 61 CYS cc_start: 0.7604 (m) cc_final: 0.6997 (m) REVERT: M 68 GLN cc_start: 0.7805 (mt0) cc_final: 0.7599 (mt0) outliers start: 146 outliers final: 94 residues processed: 540 average time/residue: 0.4101 time to fit residues: 354.7540 Evaluate side-chains 477 residues out of total 3287 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 102 poor density : 375 time to evaluate : 3.577 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 23 HIS Chi-restraints excluded: chain G residue 50 SER Chi-restraints excluded: chain G residue 56 VAL Chi-restraints excluded: chain G residue 64 VAL Chi-restraints excluded: chain G residue 70 THR Chi-restraints excluded: chain G residue 77 ASP Chi-restraints excluded: chain G residue 83 LEU Chi-restraints excluded: chain G residue 95 LYS Chi-restraints excluded: chain G residue 124 VAL Chi-restraints excluded: chain G residue 137 ASN Chi-restraints excluded: chain G residue 176 CYS Chi-restraints excluded: chain H residue 28 LEU Chi-restraints excluded: chain H residue 212 ASP Chi-restraints excluded: chain H residue 223 ILE Chi-restraints excluded: chain I residue 66 SER Chi-restraints excluded: chain I residue 82 VAL Chi-restraints excluded: chain I residue 91 THR Chi-restraints excluded: chain I residue 131 THR Chi-restraints excluded: chain I residue 289 VAL Chi-restraints excluded: chain I residue 336 LEU Chi-restraints excluded: chain I residue 349 GLU Chi-restraints excluded: chain I residue 387 ASN Chi-restraints excluded: chain I residue 412 GLU Chi-restraints excluded: chain I residue 428 VAL Chi-restraints excluded: chain I residue 445 ILE Chi-restraints excluded: chain I residue 446 ASP Chi-restraints excluded: chain I residue 475 VAL Chi-restraints excluded: chain I residue 493 ILE Chi-restraints excluded: chain I residue 563 THR Chi-restraints excluded: chain I residue 623 LEU Chi-restraints excluded: chain I residue 639 LYS Chi-restraints excluded: chain I residue 642 SER Chi-restraints excluded: chain I residue 660 VAL Chi-restraints excluded: chain I residue 699 LEU Chi-restraints excluded: chain I residue 702 THR Chi-restraints excluded: chain I residue 754 THR Chi-restraints excluded: chain I residue 772 SER Chi-restraints excluded: chain I residue 802 VAL Chi-restraints excluded: chain I residue 842 ASP Chi-restraints excluded: chain I residue 845 LEU Chi-restraints excluded: chain I residue 895 LEU Chi-restraints excluded: chain I residue 896 THR Chi-restraints excluded: chain I residue 924 VAL Chi-restraints excluded: chain I residue 968 GLU Chi-restraints excluded: chain I residue 1094 VAL Chi-restraints excluded: chain I residue 1253 LEU Chi-restraints excluded: chain I residue 1254 VAL Chi-restraints excluded: chain I residue 1289 GLU Chi-restraints excluded: chain I residue 1296 ASP Chi-restraints excluded: chain I residue 1327 LEU Chi-restraints excluded: chain J residue 46 TYR Chi-restraints excluded: chain J residue 48 THR Chi-restraints excluded: chain J residue 92 VAL Chi-restraints excluded: chain J residue 132 LEU Chi-restraints excluded: chain J residue 169 LEU Chi-restraints excluded: chain J residue 174 ASP Chi-restraints excluded: chain J residue 201 LEU Chi-restraints excluded: chain J residue 253 VAL Chi-restraints excluded: chain J residue 290 ILE Chi-restraints excluded: chain J residue 319 SER Chi-restraints excluded: chain J residue 320 ASN Chi-restraints excluded: chain J residue 326 SER Chi-restraints excluded: chain J residue 342 LEU Chi-restraints excluded: chain J residue 350 SER Chi-restraints excluded: chain J residue 363 LEU Chi-restraints excluded: chain J residue 428 THR Chi-restraints excluded: chain J residue 506 VAL Chi-restraints excluded: chain J residue 514 THR Chi-restraints excluded: chain J residue 532 GLU Chi-restraints excluded: chain J residue 573 THR Chi-restraints excluded: chain J residue 642 ASP Chi-restraints excluded: chain J residue 674 THR Chi-restraints excluded: chain J residue 708 ASN Chi-restraints excluded: chain J residue 770 LEU Chi-restraints excluded: chain J residue 806 ASP Chi-restraints excluded: chain J residue 823 THR Chi-restraints excluded: chain J residue 849 LEU Chi-restraints excluded: chain J residue 853 THR Chi-restraints excluded: chain J residue 869 CYS Chi-restraints excluded: chain J residue 884 SER Chi-restraints excluded: chain J residue 918 ILE Chi-restraints excluded: chain J residue 922 SER Chi-restraints excluded: chain J residue 934 THR Chi-restraints excluded: chain J residue 935 PHE Chi-restraints excluded: chain J residue 1120 THR Chi-restraints excluded: chain J residue 1159 ILE Chi-restraints excluded: chain J residue 1239 ASP Chi-restraints excluded: chain J residue 1272 SER Chi-restraints excluded: chain J residue 1329 THR Chi-restraints excluded: chain J residue 1344 LEU Chi-restraints excluded: chain J residue 1371 ARG Chi-restraints excluded: chain K residue 3 ARG Chi-restraints excluded: chain K residue 39 VAL Chi-restraints excluded: chain K residue 60 ASN Chi-restraints excluded: chain L residue 55 VAL Chi-restraints excluded: chain L residue 395 THR Chi-restraints excluded: chain L residue 429 THR Chi-restraints excluded: chain L residue 450 ILE Chi-restraints excluded: chain L residue 570 ASP Chi-restraints excluded: chain L residue 582 VAL Chi-restraints excluded: chain M residue 2 SER Chi-restraints excluded: chain M residue 16 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 380 random chunks: chunk 341 optimal weight: 7.9990 chunk 259 optimal weight: 4.9990 chunk 179 optimal weight: 2.9990 chunk 38 optimal weight: 3.9990 chunk 164 optimal weight: 3.9990 chunk 232 optimal weight: 5.9990 chunk 346 optimal weight: 7.9990 chunk 367 optimal weight: 0.9980 chunk 181 optimal weight: 0.6980 chunk 328 optimal weight: 2.9990 chunk 98 optimal weight: 0.8980 overall best weight: 1.7184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: G 93 GLN I 613 ASN ** I 659 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I1268 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 294 ASN ** L 227 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 406 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7993 moved from start: 0.3915 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.058 30679 Z= 0.262 Angle : 0.656 13.807 41447 Z= 0.331 Chirality : 0.045 0.293 4751 Planarity : 0.005 0.071 5415 Dihedral : 5.763 58.562 4504 Min Nonbonded Distance : 2.135 Molprobity Statistics. All-atom Clashscore : 13.02 Ramachandran Plot: Outliers : 0.24 % Allowed : 8.33 % Favored : 91.43 % Rotamer: Outliers : 4.23 % Allowed : 15.81 % Favored : 79.96 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.33 % Cis-general : 0.11 % Twisted Proline : 0.00 % Twisted General : 0.08 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.23 (0.13), residues: 3817 helix: 0.19 (0.13), residues: 1518 sheet: -2.64 (0.27), residues: 323 loop : -2.74 (0.13), residues: 1976 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.001 TRP I 807 HIS 0.019 0.001 HIS I 551 PHE 0.017 0.002 PHE J1319 TYR 0.013 0.001 TYR G 177 ARG 0.005 0.000 ARG G 148 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7634 Ramachandran restraints generated. 3817 Oldfield, 0 Emsley, 3817 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7634 Ramachandran restraints generated. 3817 Oldfield, 0 Emsley, 3817 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 569 residues out of total 3287 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 138 poor density : 431 time to evaluate : 3.518 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: G 68 TYR cc_start: 0.9153 (m-80) cc_final: 0.8848 (m-80) REVERT: G 185 TYR cc_start: 0.8920 (p90) cc_final: 0.8371 (p90) REVERT: G 200 LYS cc_start: 0.8729 (ttmt) cc_final: 0.8394 (ttmm) REVERT: G 207 THR cc_start: 0.8648 (m) cc_final: 0.8239 (p) REVERT: H 95 LYS cc_start: 0.8431 (tppt) cc_final: 0.7925 (mmtm) REVERT: I 349 GLU cc_start: 0.7375 (OUTLIER) cc_final: 0.7118 (mt-10) REVERT: I 470 ARG cc_start: 0.7536 (OUTLIER) cc_final: 0.7085 (tpm170) REVERT: I 515 MET cc_start: 0.8152 (ttp) cc_final: 0.7938 (ttp) REVERT: I 684 ASN cc_start: 0.8738 (m-40) cc_final: 0.8474 (m-40) REVERT: I 699 LEU cc_start: 0.9557 (OUTLIER) cc_final: 0.9344 (tp) REVERT: I 717 VAL cc_start: 0.9292 (t) cc_final: 0.8945 (m) REVERT: I 842 ASP cc_start: 0.8389 (OUTLIER) cc_final: 0.8143 (m-30) REVERT: I 1172 LEU cc_start: 0.9110 (OUTLIER) cc_final: 0.8865 (tt) REVERT: I 1240 ASP cc_start: 0.7708 (p0) cc_final: 0.7347 (p0) REVERT: I 1253 LEU cc_start: 0.9356 (OUTLIER) cc_final: 0.9087 (tm) REVERT: I 1290 MET cc_start: 0.8355 (tpp) cc_final: 0.7799 (tpp) REVERT: I 1330 ILE cc_start: 0.8852 (mt) cc_final: 0.8642 (mp) REVERT: J 130 MET cc_start: 0.8382 (ttt) cc_final: 0.8161 (ttt) REVERT: J 180 MET cc_start: 0.7227 (ptm) cc_final: 0.6965 (ptm) REVERT: J 325 LYS cc_start: 0.8841 (mptt) cc_final: 0.8563 (mtmt) REVERT: J 398 LYS cc_start: 0.8483 (OUTLIER) cc_final: 0.8143 (ttmt) REVERT: J 466 MET cc_start: 0.8087 (mtp) cc_final: 0.7763 (mtp) REVERT: J 472 LEU cc_start: 0.8686 (mt) cc_final: 0.8340 (mt) REVERT: J 707 ILE cc_start: 0.8148 (OUTLIER) cc_final: 0.7769 (tt) REVERT: J 849 LEU cc_start: 0.7931 (OUTLIER) cc_final: 0.7626 (mt) REVERT: J 935 PHE cc_start: 0.8143 (OUTLIER) cc_final: 0.7637 (t80) REVERT: J 1190 ILE cc_start: 0.7834 (mt) cc_final: 0.7614 (mp) REVERT: J 1330 ARG cc_start: 0.8093 (tmm-80) cc_final: 0.7746 (ttp80) REVERT: K 3 ARG cc_start: 0.8683 (OUTLIER) cc_final: 0.7841 (ttm170) REVERT: L 21 TYR cc_start: 0.6839 (p90) cc_final: 0.6469 (p90) REVERT: L 46 GLN cc_start: 0.6434 (tp-100) cc_final: 0.6155 (mm110) REVERT: L 121 LYS cc_start: 0.7825 (tppt) cc_final: 0.6993 (tptt) REVERT: L 268 TYR cc_start: 0.5497 (t80) cc_final: 0.5276 (t80) REVERT: L 339 ARG cc_start: 0.5020 (mtp85) cc_final: 0.3795 (mmp-170) REVERT: L 605 GLU cc_start: 0.6757 (mm-30) cc_final: 0.5255 (tm-30) REVERT: M 46 GLU cc_start: 0.7751 (tp30) cc_final: 0.7544 (tp30) REVERT: M 61 CYS cc_start: 0.7667 (m) cc_final: 0.7113 (m) REVERT: M 68 GLN cc_start: 0.7871 (mt0) cc_final: 0.7582 (mt0) outliers start: 138 outliers final: 74 residues processed: 530 average time/residue: 0.4076 time to fit residues: 345.5375 Evaluate side-chains 469 residues out of total 3287 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 85 poor density : 384 time to evaluate : 2.616 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 23 HIS Chi-restraints excluded: chain G residue 50 SER Chi-restraints excluded: chain G residue 61 ILE Chi-restraints excluded: chain G residue 64 VAL Chi-restraints excluded: chain G residue 70 THR Chi-restraints excluded: chain G residue 83 LEU Chi-restraints excluded: chain G residue 134 THR Chi-restraints excluded: chain G residue 176 CYS Chi-restraints excluded: chain H residue 28 LEU Chi-restraints excluded: chain H residue 118 ASP Chi-restraints excluded: chain H residue 205 MET Chi-restraints excluded: chain I residue 82 VAL Chi-restraints excluded: chain I residue 131 THR Chi-restraints excluded: chain I residue 289 VAL Chi-restraints excluded: chain I residue 336 LEU Chi-restraints excluded: chain I residue 349 GLU Chi-restraints excluded: chain I residue 387 ASN Chi-restraints excluded: chain I residue 412 GLU Chi-restraints excluded: chain I residue 435 ILE Chi-restraints excluded: chain I residue 470 ARG Chi-restraints excluded: chain I residue 493 ILE Chi-restraints excluded: chain I residue 563 THR Chi-restraints excluded: chain I residue 623 LEU Chi-restraints excluded: chain I residue 633 LEU Chi-restraints excluded: chain I residue 639 LYS Chi-restraints excluded: chain I residue 642 SER Chi-restraints excluded: chain I residue 699 LEU Chi-restraints excluded: chain I residue 842 ASP Chi-restraints excluded: chain I residue 845 LEU Chi-restraints excluded: chain I residue 896 THR Chi-restraints excluded: chain I residue 924 VAL Chi-restraints excluded: chain I residue 968 GLU Chi-restraints excluded: chain I residue 1094 VAL Chi-restraints excluded: chain I residue 1172 LEU Chi-restraints excluded: chain I residue 1253 LEU Chi-restraints excluded: chain J residue 46 TYR Chi-restraints excluded: chain J residue 48 THR Chi-restraints excluded: chain J residue 92 VAL Chi-restraints excluded: chain J residue 132 LEU Chi-restraints excluded: chain J residue 174 ASP Chi-restraints excluded: chain J residue 201 LEU Chi-restraints excluded: chain J residue 253 VAL Chi-restraints excluded: chain J residue 306 LEU Chi-restraints excluded: chain J residue 319 SER Chi-restraints excluded: chain J residue 326 SER Chi-restraints excluded: chain J residue 350 SER Chi-restraints excluded: chain J residue 363 LEU Chi-restraints excluded: chain J residue 398 LYS Chi-restraints excluded: chain J residue 428 THR Chi-restraints excluded: chain J residue 506 VAL Chi-restraints excluded: chain J residue 514 THR Chi-restraints excluded: chain J residue 573 THR Chi-restraints excluded: chain J residue 624 ILE Chi-restraints excluded: chain J residue 638 SER Chi-restraints excluded: chain J residue 642 ASP Chi-restraints excluded: chain J residue 661 VAL Chi-restraints excluded: chain J residue 707 ILE Chi-restraints excluded: chain J residue 708 ASN Chi-restraints excluded: chain J residue 806 ASP Chi-restraints excluded: chain J residue 823 THR Chi-restraints excluded: chain J residue 849 LEU Chi-restraints excluded: chain J residue 853 THR Chi-restraints excluded: chain J residue 884 SER Chi-restraints excluded: chain J residue 922 SER Chi-restraints excluded: chain J residue 934 THR Chi-restraints excluded: chain J residue 935 PHE Chi-restraints excluded: chain J residue 1081 VAL Chi-restraints excluded: chain J residue 1120 THR Chi-restraints excluded: chain J residue 1159 ILE Chi-restraints excluded: chain J residue 1239 ASP Chi-restraints excluded: chain J residue 1248 ILE Chi-restraints excluded: chain J residue 1275 LEU Chi-restraints excluded: chain J residue 1329 THR Chi-restraints excluded: chain J residue 1344 LEU Chi-restraints excluded: chain K residue 3 ARG Chi-restraints excluded: chain K residue 39 VAL Chi-restraints excluded: chain K residue 60 ASN Chi-restraints excluded: chain L residue 55 VAL Chi-restraints excluded: chain L residue 266 PHE Chi-restraints excluded: chain L residue 395 THR Chi-restraints excluded: chain L residue 429 THR Chi-restraints excluded: chain L residue 570 ASP Chi-restraints excluded: chain L residue 582 VAL Chi-restraints excluded: chain M residue 2 SER Chi-restraints excluded: chain M residue 16 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 380 random chunks: chunk 305 optimal weight: 0.5980 chunk 208 optimal weight: 2.9990 chunk 5 optimal weight: 6.9990 chunk 273 optimal weight: 5.9990 chunk 151 optimal weight: 0.9980 chunk 313 optimal weight: 6.9990 chunk 253 optimal weight: 0.9980 chunk 0 optimal weight: 6.9990 chunk 187 optimal weight: 4.9990 chunk 329 optimal weight: 5.9990 chunk 92 optimal weight: 6.9990 overall best weight: 2.1184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: G 93 GLN I 69 GLN I 613 ASN I1268 GLN I1288 GLN J 294 ASN ** L 227 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 406 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8015 moved from start: 0.4109 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.054 30679 Z= 0.300 Angle : 0.658 13.151 41447 Z= 0.331 Chirality : 0.045 0.234 4751 Planarity : 0.005 0.063 5415 Dihedral : 5.653 59.260 4504 Min Nonbonded Distance : 2.142 Molprobity Statistics. All-atom Clashscore : 12.87 Ramachandran Plot: Outliers : 0.24 % Allowed : 9.14 % Favored : 90.62 % Rotamer: Outliers : 4.75 % Allowed : 16.36 % Favored : 78.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.33 % Cis-general : 0.11 % Twisted Proline : 0.00 % Twisted General : 0.08 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.99 (0.13), residues: 3817 helix: 0.36 (0.13), residues: 1524 sheet: -2.45 (0.29), residues: 302 loop : -2.60 (0.13), residues: 1991 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP I 807 HIS 0.013 0.001 HIS I 551 PHE 0.017 0.002 PHE G 231 TYR 0.015 0.001 TYR G 177 ARG 0.005 0.000 ARG I 247 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7634 Ramachandran restraints generated. 3817 Oldfield, 0 Emsley, 3817 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7634 Ramachandran restraints generated. 3817 Oldfield, 0 Emsley, 3817 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 556 residues out of total 3287 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 155 poor density : 401 time to evaluate : 3.664 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: G 68 TYR cc_start: 0.9199 (m-80) cc_final: 0.8907 (m-80) REVERT: G 185 TYR cc_start: 0.8930 (p90) cc_final: 0.8351 (p90) REVERT: G 200 LYS cc_start: 0.8754 (ttmt) cc_final: 0.8459 (ttmm) REVERT: G 207 THR cc_start: 0.8603 (m) cc_final: 0.8179 (p) REVERT: G 231 PHE cc_start: 0.8123 (OUTLIER) cc_final: 0.7082 (t80) REVERT: H 28 LEU cc_start: 0.8833 (OUTLIER) cc_final: 0.8154 (mt) REVERT: H 95 LYS cc_start: 0.8448 (tppt) cc_final: 0.7944 (mmtm) REVERT: I 66 SER cc_start: 0.8367 (OUTLIER) cc_final: 0.7838 (p) REVERT: I 239 MET cc_start: 0.6889 (OUTLIER) cc_final: 0.5736 (tpp) REVERT: I 349 GLU cc_start: 0.7421 (OUTLIER) cc_final: 0.7110 (mt-10) REVERT: I 470 ARG cc_start: 0.7503 (OUTLIER) cc_final: 0.7079 (tpm170) REVERT: I 681 MET cc_start: 0.7741 (mtm) cc_final: 0.7499 (mtp) REVERT: I 717 VAL cc_start: 0.9253 (t) cc_final: 0.8941 (m) REVERT: I 1172 LEU cc_start: 0.9148 (OUTLIER) cc_final: 0.8915 (tt) REVERT: I 1240 ASP cc_start: 0.7574 (p0) cc_final: 0.7315 (p0) REVERT: I 1253 LEU cc_start: 0.9335 (OUTLIER) cc_final: 0.9015 (tm) REVERT: I 1290 MET cc_start: 0.8483 (tpp) cc_final: 0.7936 (tpp) REVERT: J 130 MET cc_start: 0.8370 (ttt) cc_final: 0.8060 (ttt) REVERT: J 169 LEU cc_start: 0.7168 (OUTLIER) cc_final: 0.6918 (mm) REVERT: J 180 MET cc_start: 0.7250 (ptm) cc_final: 0.6982 (ptm) REVERT: J 325 LYS cc_start: 0.8796 (mptt) cc_final: 0.8565 (mtmt) REVERT: J 398 LYS cc_start: 0.8494 (OUTLIER) cc_final: 0.8155 (ttmt) REVERT: J 466 MET cc_start: 0.8115 (mtp) cc_final: 0.7912 (mtp) REVERT: J 478 LEU cc_start: 0.8868 (OUTLIER) cc_final: 0.8648 (mt) REVERT: J 849 LEU cc_start: 0.7615 (OUTLIER) cc_final: 0.7374 (mt) REVERT: J 932 MET cc_start: 0.8918 (tmm) cc_final: 0.8679 (tmm) REVERT: J 1330 ARG cc_start: 0.8120 (tmm-80) cc_final: 0.7779 (ttp80) REVERT: K 3 ARG cc_start: 0.8625 (OUTLIER) cc_final: 0.7802 (ttm170) REVERT: K 55 GLU cc_start: 0.8473 (tm-30) cc_final: 0.7943 (tm-30) REVERT: L 21 TYR cc_start: 0.6915 (p90) cc_final: 0.6532 (p90) REVERT: L 46 GLN cc_start: 0.6340 (tp-100) cc_final: 0.6136 (mm110) REVERT: L 105 MET cc_start: 0.7519 (ppp) cc_final: 0.6717 (ppp) REVERT: L 121 LYS cc_start: 0.7895 (tppt) cc_final: 0.7088 (tptt) REVERT: L 268 TYR cc_start: 0.5624 (t80) cc_final: 0.5265 (t80) REVERT: L 297 MET cc_start: 0.3851 (ptp) cc_final: 0.3494 (ptp) REVERT: L 339 ARG cc_start: 0.5022 (mtp85) cc_final: 0.3736 (mmp-170) REVERT: M 46 GLU cc_start: 0.7763 (tp30) cc_final: 0.7281 (mp0) REVERT: M 61 CYS cc_start: 0.7656 (m) cc_final: 0.7167 (m) outliers start: 155 outliers final: 103 residues processed: 514 average time/residue: 0.4205 time to fit residues: 347.9727 Evaluate side-chains 481 residues out of total 3287 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 116 poor density : 365 time to evaluate : 3.498 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 23 HIS Chi-restraints excluded: chain G residue 61 ILE Chi-restraints excluded: chain G residue 64 VAL Chi-restraints excluded: chain G residue 70 THR Chi-restraints excluded: chain G residue 77 ASP Chi-restraints excluded: chain G residue 83 LEU Chi-restraints excluded: chain G residue 134 THR Chi-restraints excluded: chain G residue 176 CYS Chi-restraints excluded: chain G residue 202 VAL Chi-restraints excluded: chain G residue 231 PHE Chi-restraints excluded: chain G residue 234 LEU Chi-restraints excluded: chain H residue 28 LEU Chi-restraints excluded: chain H residue 118 ASP Chi-restraints excluded: chain H residue 174 ASP Chi-restraints excluded: chain H residue 205 MET Chi-restraints excluded: chain I residue 66 SER Chi-restraints excluded: chain I residue 82 VAL Chi-restraints excluded: chain I residue 131 THR Chi-restraints excluded: chain I residue 239 MET Chi-restraints excluded: chain I residue 289 VAL Chi-restraints excluded: chain I residue 321 LEU Chi-restraints excluded: chain I residue 336 LEU Chi-restraints excluded: chain I residue 349 GLU Chi-restraints excluded: chain I residue 387 ASN Chi-restraints excluded: chain I residue 412 GLU Chi-restraints excluded: chain I residue 435 ILE Chi-restraints excluded: chain I residue 445 ILE Chi-restraints excluded: chain I residue 446 ASP Chi-restraints excluded: chain I residue 470 ARG Chi-restraints excluded: chain I residue 493 ILE Chi-restraints excluded: chain I residue 549 ASP Chi-restraints excluded: chain I residue 563 THR Chi-restraints excluded: chain I residue 623 LEU Chi-restraints excluded: chain I residue 633 LEU Chi-restraints excluded: chain I residue 639 LYS Chi-restraints excluded: chain I residue 642 SER Chi-restraints excluded: chain I residue 702 THR Chi-restraints excluded: chain I residue 754 THR Chi-restraints excluded: chain I residue 802 VAL Chi-restraints excluded: chain I residue 817 LEU Chi-restraints excluded: chain I residue 845 LEU Chi-restraints excluded: chain I residue 896 THR Chi-restraints excluded: chain I residue 920 VAL Chi-restraints excluded: chain I residue 924 VAL Chi-restraints excluded: chain I residue 953 LEU Chi-restraints excluded: chain I residue 968 GLU Chi-restraints excluded: chain I residue 1094 VAL Chi-restraints excluded: chain I residue 1172 LEU Chi-restraints excluded: chain I residue 1253 LEU Chi-restraints excluded: chain I residue 1289 GLU Chi-restraints excluded: chain I residue 1298 VAL 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 92 VAL Chi-restraints excluded: chain J residue 132 LEU Chi-restraints excluded: chain J residue 169 LEU Chi-restraints excluded: chain J residue 174 ASP Chi-restraints excluded: chain J residue 177 ASP Chi-restraints excluded: chain J residue 218 THR Chi-restraints excluded: chain J residue 253 VAL Chi-restraints excluded: chain J residue 291 ILE Chi-restraints excluded: chain J residue 319 SER Chi-restraints excluded: chain J residue 326 SER Chi-restraints excluded: chain J residue 342 LEU Chi-restraints excluded: chain J residue 350 SER Chi-restraints excluded: chain J residue 363 LEU Chi-restraints excluded: chain J residue 398 LYS Chi-restraints excluded: chain J residue 428 THR Chi-restraints excluded: chain J residue 434 ILE Chi-restraints excluded: chain J residue 478 LEU Chi-restraints excluded: chain J residue 506 VAL Chi-restraints excluded: chain J residue 514 THR Chi-restraints excluded: chain J residue 573 THR Chi-restraints excluded: chain J residue 578 ILE Chi-restraints excluded: chain J residue 601 ILE Chi-restraints excluded: chain J residue 624 ILE Chi-restraints excluded: chain J residue 638 SER Chi-restraints excluded: chain J residue 642 ASP Chi-restraints excluded: chain J residue 661 VAL Chi-restraints excluded: chain J residue 674 THR Chi-restraints excluded: chain J residue 708 ASN Chi-restraints excluded: chain J residue 770 LEU Chi-restraints excluded: chain J residue 806 ASP Chi-restraints excluded: chain J residue 823 THR Chi-restraints excluded: chain J residue 849 LEU Chi-restraints excluded: chain J residue 853 THR Chi-restraints excluded: chain J residue 869 CYS Chi-restraints excluded: chain J residue 884 SER Chi-restraints excluded: chain J residue 918 ILE Chi-restraints excluded: chain J residue 922 SER Chi-restraints excluded: chain J residue 934 THR Chi-restraints excluded: chain J residue 935 PHE Chi-restraints excluded: chain J residue 1081 VAL Chi-restraints excluded: chain J residue 1120 THR Chi-restraints excluded: chain J residue 1159 ILE Chi-restraints excluded: chain J residue 1239 ASP Chi-restraints excluded: chain J residue 1248 ILE Chi-restraints excluded: chain J residue 1272 SER Chi-restraints excluded: chain J residue 1329 THR Chi-restraints excluded: chain J residue 1332 LEU Chi-restraints excluded: chain J residue 1344 LEU Chi-restraints excluded: chain J residue 1357 ILE Chi-restraints excluded: chain J residue 1371 ARG Chi-restraints excluded: chain K residue 3 ARG Chi-restraints excluded: chain K residue 39 VAL Chi-restraints excluded: chain K residue 60 ASN Chi-restraints excluded: chain L residue 55 VAL Chi-restraints excluded: chain L residue 266 PHE Chi-restraints excluded: chain L residue 341 LEU Chi-restraints excluded: chain L residue 395 THR Chi-restraints excluded: chain L residue 429 THR Chi-restraints excluded: chain L residue 570 ASP Chi-restraints excluded: chain L residue 582 VAL Chi-restraints excluded: chain M residue 2 SER Chi-restraints excluded: chain M residue 16 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 380 random chunks: chunk 123 optimal weight: 1.9990 chunk 330 optimal weight: 10.0000 chunk 72 optimal weight: 0.2980 chunk 215 optimal weight: 0.7980 chunk 90 optimal weight: 9.9990 chunk 367 optimal weight: 10.0000 chunk 305 optimal weight: 7.9990 chunk 170 optimal weight: 3.9990 chunk 30 optimal weight: 3.9990 chunk 121 optimal weight: 0.0060 chunk 193 optimal weight: 3.9990 overall best weight: 1.4200 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: G 93 GLN I 613 ASN J 196 GLN J 294 ASN ** L 227 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 406 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7978 moved from start: 0.4400 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 30679 Z= 0.222 Angle : 0.609 11.514 41447 Z= 0.306 Chirality : 0.043 0.230 4751 Planarity : 0.004 0.064 5415 Dihedral : 5.250 49.417 4502 Min Nonbonded Distance : 2.113 Molprobity Statistics. All-atom Clashscore : 11.85 Ramachandran Plot: Outliers : 0.18 % Allowed : 7.86 % Favored : 91.96 % Rotamer: Outliers : 4.44 % Allowed : 16.97 % Favored : 78.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.33 % Cis-general : 0.11 % Twisted Proline : 0.00 % Twisted General : 0.08 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.72 (0.13), residues: 3817 helix: 0.59 (0.14), residues: 1524 sheet: -2.17 (0.29), residues: 305 loop : -2.48 (0.13), residues: 1988 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP I 807 HIS 0.010 0.001 HIS I 273 PHE 0.015 0.001 PHE G 231 TYR 0.012 0.001 TYR M 64 ARG 0.005 0.000 ARG M 49 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7634 Ramachandran restraints generated. 3817 Oldfield, 0 Emsley, 3817 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7634 Ramachandran restraints generated. 3817 Oldfield, 0 Emsley, 3817 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 543 residues out of total 3287 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 145 poor density : 398 time to evaluate : 3.275 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: G 68 TYR cc_start: 0.9126 (m-80) cc_final: 0.8808 (m-80) REVERT: G 102 LEU cc_start: 0.9221 (OUTLIER) cc_final: 0.8984 (tt) REVERT: G 185 TYR cc_start: 0.8865 (p90) cc_final: 0.8422 (p90) REVERT: G 200 LYS cc_start: 0.8689 (ttmt) cc_final: 0.8403 (ttmm) REVERT: G 231 PHE cc_start: 0.8060 (OUTLIER) cc_final: 0.7027 (t80) REVERT: H 28 LEU cc_start: 0.8795 (OUTLIER) cc_final: 0.8153 (mt) REVERT: H 95 LYS cc_start: 0.8269 (tppt) cc_final: 0.7772 (mmtm) REVERT: H 201 LEU cc_start: 0.9060 (OUTLIER) cc_final: 0.8853 (tp) REVERT: I 66 SER cc_start: 0.8297 (OUTLIER) cc_final: 0.7766 (p) REVERT: I 239 MET cc_start: 0.6947 (OUTLIER) cc_final: 0.5746 (tpp) REVERT: I 316 GLU cc_start: 0.7627 (pt0) cc_final: 0.7290 (pp20) REVERT: I 470 ARG cc_start: 0.7469 (OUTLIER) cc_final: 0.7110 (tpm170) REVERT: I 684 ASN cc_start: 0.8692 (m-40) cc_final: 0.8389 (m-40) REVERT: I 717 VAL cc_start: 0.9213 (t) cc_final: 0.8868 (m) REVERT: I 1240 ASP cc_start: 0.7612 (p0) cc_final: 0.7356 (p0) REVERT: I 1253 LEU cc_start: 0.9368 (OUTLIER) cc_final: 0.8942 (tm) REVERT: I 1268 GLN cc_start: 0.8545 (mm-40) cc_final: 0.8169 (mm-40) REVERT: I 1290 MET cc_start: 0.8450 (tpp) cc_final: 0.7914 (tpp) REVERT: J 97 VAL cc_start: 0.9623 (OUTLIER) cc_final: 0.9337 (p) REVERT: J 137 ARG cc_start: 0.7999 (OUTLIER) cc_final: 0.7306 (mtt90) REVERT: J 169 LEU cc_start: 0.7373 (OUTLIER) cc_final: 0.7127 (mm) REVERT: J 180 MET cc_start: 0.7086 (ptm) cc_final: 0.6840 (ptm) REVERT: J 398 LYS cc_start: 0.8449 (OUTLIER) cc_final: 0.8116 (ttmt) REVERT: J 466 MET cc_start: 0.8090 (mtp) cc_final: 0.7853 (mtp) REVERT: J 472 LEU cc_start: 0.8680 (mt) cc_final: 0.8414 (mt) REVERT: J 478 LEU cc_start: 0.8821 (OUTLIER) cc_final: 0.8620 (mt) REVERT: J 707 ILE cc_start: 0.8153 (OUTLIER) cc_final: 0.7833 (tt) REVERT: J 849 LEU cc_start: 0.7289 (OUTLIER) cc_final: 0.7043 (mt) REVERT: J 1330 ARG cc_start: 0.8046 (tmm-80) cc_final: 0.7711 (ttp80) REVERT: K 3 ARG cc_start: 0.8539 (OUTLIER) cc_final: 0.7669 (ttm170) REVERT: K 55 GLU cc_start: 0.8457 (tm-30) cc_final: 0.7925 (tm-30) REVERT: L 21 TYR cc_start: 0.7169 (p90) cc_final: 0.6820 (p90) REVERT: L 46 GLN cc_start: 0.6195 (tp-100) cc_final: 0.5955 (mm110) REVERT: L 105 MET cc_start: 0.7507 (ppp) cc_final: 0.7036 (ppp) REVERT: L 121 LYS cc_start: 0.7853 (tppt) cc_final: 0.7078 (tptt) REVERT: L 268 TYR cc_start: 0.5458 (t80) cc_final: 0.5165 (t80) REVERT: L 297 MET cc_start: 0.3973 (ptp) cc_final: 0.3452 (ptp) REVERT: L 339 ARG cc_start: 0.5159 (mtp85) cc_final: 0.3812 (mmp-170) REVERT: L 508 GLU cc_start: 0.7643 (tm-30) cc_final: 0.7247 (tm-30) REVERT: L 511 ILE cc_start: 0.8434 (tp) cc_final: 0.8204 (tt) REVERT: M 46 GLU cc_start: 0.7575 (tp30) cc_final: 0.7133 (mp0) REVERT: M 61 CYS cc_start: 0.7628 (m) cc_final: 0.7152 (m) outliers start: 145 outliers final: 102 residues processed: 502 average time/residue: 0.4112 time to fit residues: 331.4928 Evaluate side-chains 491 residues out of total 3287 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 118 poor density : 373 time to evaluate : 3.419 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 50 SER Chi-restraints excluded: chain G residue 61 ILE Chi-restraints excluded: chain G residue 64 VAL Chi-restraints excluded: chain G residue 70 THR Chi-restraints excluded: chain G residue 75 GLN Chi-restraints excluded: chain G residue 77 ASP Chi-restraints excluded: chain G residue 83 LEU Chi-restraints excluded: chain G residue 102 LEU Chi-restraints excluded: chain G residue 134 THR Chi-restraints excluded: chain G residue 231 PHE Chi-restraints excluded: chain G residue 234 LEU Chi-restraints excluded: chain H residue 28 LEU Chi-restraints excluded: chain H residue 118 ASP Chi-restraints excluded: chain H residue 174 ASP Chi-restraints excluded: chain H residue 201 LEU Chi-restraints excluded: chain I residue 66 SER Chi-restraints excluded: chain I residue 82 VAL Chi-restraints excluded: chain I residue 84 GLU Chi-restraints excluded: chain I residue 131 THR Chi-restraints excluded: chain I residue 239 MET Chi-restraints excluded: chain I residue 241 LEU Chi-restraints excluded: chain I residue 321 LEU Chi-restraints excluded: chain I residue 412 GLU Chi-restraints excluded: chain I residue 435 ILE Chi-restraints excluded: chain I residue 445 ILE Chi-restraints excluded: chain I residue 470 ARG Chi-restraints excluded: chain I residue 493 ILE Chi-restraints excluded: chain I residue 524 ILE Chi-restraints excluded: chain I residue 549 ASP Chi-restraints excluded: chain I residue 563 THR Chi-restraints excluded: chain I residue 623 LEU Chi-restraints excluded: chain I residue 633 LEU Chi-restraints excluded: chain I residue 639 LYS Chi-restraints excluded: chain I residue 642 SER Chi-restraints excluded: chain I residue 690 VAL Chi-restraints excluded: chain I residue 800 MET Chi-restraints excluded: chain I residue 802 VAL Chi-restraints excluded: chain I residue 817 LEU Chi-restraints excluded: chain I residue 845 LEU Chi-restraints excluded: chain I residue 920 VAL Chi-restraints excluded: chain I residue 924 VAL Chi-restraints excluded: chain I residue 953 LEU Chi-restraints excluded: chain I residue 968 GLU Chi-restraints excluded: chain I residue 984 VAL Chi-restraints excluded: chain I residue 1094 VAL Chi-restraints excluded: chain I residue 1225 VAL Chi-restraints excluded: chain I residue 1253 LEU Chi-restraints excluded: chain I residue 1254 VAL Chi-restraints excluded: chain I residue 1289 GLU Chi-restraints excluded: chain I residue 1298 VAL 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 92 VAL Chi-restraints excluded: chain J residue 97 VAL Chi-restraints excluded: chain J residue 137 ARG Chi-restraints excluded: chain J residue 169 LEU Chi-restraints excluded: chain J residue 174 ASP Chi-restraints excluded: chain J residue 177 ASP Chi-restraints excluded: chain J residue 218 THR Chi-restraints excluded: chain J residue 253 VAL Chi-restraints excluded: chain J residue 290 ILE Chi-restraints excluded: chain J residue 291 ILE Chi-restraints excluded: chain J residue 320 ASN Chi-restraints excluded: chain J residue 326 SER Chi-restraints excluded: chain J residue 342 LEU Chi-restraints excluded: chain J residue 350 SER Chi-restraints excluded: chain J residue 363 LEU Chi-restraints excluded: chain J residue 398 LYS Chi-restraints excluded: chain J residue 428 THR Chi-restraints excluded: chain J residue 434 ILE Chi-restraints excluded: chain J residue 442 ILE Chi-restraints excluded: chain J residue 478 LEU Chi-restraints excluded: chain J residue 506 VAL Chi-restraints excluded: chain J residue 514 THR Chi-restraints excluded: chain J residue 526 VAL Chi-restraints excluded: chain J residue 573 THR Chi-restraints excluded: chain J residue 601 ILE Chi-restraints excluded: chain J residue 638 SER Chi-restraints excluded: chain J residue 642 ASP Chi-restraints excluded: chain J residue 661 VAL Chi-restraints excluded: chain J residue 674 THR Chi-restraints excluded: chain J residue 707 ILE Chi-restraints excluded: chain J residue 708 ASN Chi-restraints excluded: chain J residue 806 ASP Chi-restraints excluded: chain J residue 823 THR Chi-restraints excluded: chain J residue 849 LEU Chi-restraints excluded: chain J residue 853 THR Chi-restraints excluded: chain J residue 884 SER Chi-restraints excluded: chain J residue 894 VAL Chi-restraints excluded: chain J residue 922 SER Chi-restraints excluded: chain J residue 934 THR Chi-restraints excluded: chain J residue 935 PHE Chi-restraints excluded: chain J residue 1081 VAL Chi-restraints excluded: chain J residue 1159 ILE Chi-restraints excluded: chain J residue 1175 LEU Chi-restraints excluded: chain J residue 1239 ASP Chi-restraints excluded: chain J residue 1248 ILE Chi-restraints excluded: chain J residue 1272 SER Chi-restraints excluded: chain J residue 1275 LEU Chi-restraints excluded: chain J residue 1329 THR Chi-restraints excluded: chain J residue 1332 LEU Chi-restraints excluded: chain J residue 1344 LEU Chi-restraints excluded: chain J residue 1357 ILE Chi-restraints excluded: chain J residue 1371 ARG Chi-restraints excluded: chain K residue 3 ARG Chi-restraints excluded: chain K residue 39 VAL Chi-restraints excluded: chain K residue 60 ASN Chi-restraints excluded: chain L residue 55 VAL Chi-restraints excluded: chain L residue 266 PHE Chi-restraints excluded: chain L residue 395 THR Chi-restraints excluded: chain L residue 429 THR Chi-restraints excluded: chain L residue 570 ASP Chi-restraints excluded: chain L residue 582 VAL Chi-restraints excluded: chain M residue 2 SER Chi-restraints excluded: chain M residue 12 THR Chi-restraints excluded: chain M residue 38 GLU Chi-restraints excluded: chain M residue 60 GLU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 380 random chunks: chunk 354 optimal weight: 4.9990 chunk 41 optimal weight: 6.9990 chunk 209 optimal weight: 6.9990 chunk 268 optimal weight: 0.9990 chunk 208 optimal weight: 0.8980 chunk 309 optimal weight: 0.7980 chunk 205 optimal weight: 4.9990 chunk 366 optimal weight: 9.9990 chunk 229 optimal weight: 6.9990 chunk 223 optimal weight: 0.8980 chunk 169 optimal weight: 6.9990 overall best weight: 1.7184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: I 613 ASN I1017 GLN ** I1257 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 294 ASN ** L 227 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 406 GLN L 568 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7995 moved from start: 0.4496 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.047 30679 Z= 0.252 Angle : 0.620 11.688 41447 Z= 0.310 Chirality : 0.044 0.233 4751 Planarity : 0.004 0.063 5415 Dihedral : 5.204 49.649 4502 Min Nonbonded Distance : 2.117 Molprobity Statistics. All-atom Clashscore : 11.96 Ramachandran Plot: Outliers : 0.21 % Allowed : 8.59 % Favored : 91.20 % Rotamer: Outliers : 4.72 % Allowed : 17.46 % Favored : 77.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.33 % Cis-general : 0.11 % Twisted Proline : 0.00 % Twisted General : 0.08 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.58 (0.13), residues: 3817 helix: 0.66 (0.14), residues: 1523 sheet: -1.93 (0.30), residues: 295 loop : -2.39 (0.13), residues: 1999 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP I 807 HIS 0.008 0.001 HIS I 273 PHE 0.016 0.001 PHE G 231 TYR 0.024 0.001 TYR I1229 ARG 0.009 0.000 ARG I 201 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7634 Ramachandran restraints generated. 3817 Oldfield, 0 Emsley, 3817 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7634 Ramachandran restraints generated. 3817 Oldfield, 0 Emsley, 3817 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 542 residues out of total 3287 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 154 poor density : 388 time to evaluate : 3.465 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: G 68 TYR cc_start: 0.9181 (m-80) cc_final: 0.8891 (m-80) REVERT: G 102 LEU cc_start: 0.9221 (OUTLIER) cc_final: 0.8988 (tt) REVERT: G 185 TYR cc_start: 0.8844 (p90) cc_final: 0.8350 (p90) REVERT: G 200 LYS cc_start: 0.8714 (ttmt) cc_final: 0.8396 (ttmm) REVERT: G 231 PHE cc_start: 0.8016 (OUTLIER) cc_final: 0.7051 (t80) REVERT: H 28 LEU cc_start: 0.8807 (OUTLIER) cc_final: 0.8156 (mt) REVERT: H 201 LEU cc_start: 0.9065 (OUTLIER) cc_final: 0.8842 (tp) REVERT: I 239 MET cc_start: 0.6944 (OUTLIER) cc_final: 0.5727 (tpp) REVERT: I 316 GLU cc_start: 0.7648 (pt0) cc_final: 0.7275 (pp20) REVERT: I 349 GLU cc_start: 0.7443 (OUTLIER) cc_final: 0.7148 (mt-10) REVERT: I 470 ARG cc_start: 0.7465 (OUTLIER) cc_final: 0.7104 (tpm170) REVERT: I 717 VAL cc_start: 0.9200 (t) cc_final: 0.8883 (m) REVERT: I 1240 ASP cc_start: 0.7612 (p0) cc_final: 0.7365 (p0) REVERT: I 1253 LEU cc_start: 0.9374 (OUTLIER) cc_final: 0.8950 (tm) REVERT: I 1268 GLN cc_start: 0.8623 (mm-40) cc_final: 0.8301 (mm-40) REVERT: I 1290 MET cc_start: 0.8500 (tpp) cc_final: 0.7934 (tpp) REVERT: J 97 VAL cc_start: 0.9617 (OUTLIER) cc_final: 0.9328 (p) REVERT: J 130 MET cc_start: 0.8121 (ttt) cc_final: 0.7736 (ttt) REVERT: J 137 ARG cc_start: 0.8165 (OUTLIER) cc_final: 0.7475 (mtt90) REVERT: J 169 LEU cc_start: 0.7455 (OUTLIER) cc_final: 0.7221 (mm) REVERT: J 398 LYS cc_start: 0.8468 (OUTLIER) cc_final: 0.8130 (ttmt) REVERT: J 466 MET cc_start: 0.8079 (mtp) cc_final: 0.7852 (mtp) REVERT: J 478 LEU cc_start: 0.8846 (OUTLIER) cc_final: 0.8641 (mt) REVERT: J 513 MET cc_start: 0.8552 (ttp) cc_final: 0.8282 (ttm) REVERT: J 707 ILE cc_start: 0.8102 (OUTLIER) cc_final: 0.7783 (tt) REVERT: J 823 THR cc_start: 0.8168 (OUTLIER) cc_final: 0.7874 (m) REVERT: J 849 LEU cc_start: 0.7212 (OUTLIER) cc_final: 0.6979 (mt) REVERT: K 3 ARG cc_start: 0.8547 (OUTLIER) cc_final: 0.7741 (ttm170) REVERT: K 55 GLU cc_start: 0.8513 (tm-30) cc_final: 0.7979 (tm-30) REVERT: L 21 TYR cc_start: 0.7045 (p90) cc_final: 0.6801 (p90) REVERT: L 105 MET cc_start: 0.7553 (ppp) cc_final: 0.7007 (ppp) REVERT: L 121 LYS cc_start: 0.7849 (tppt) cc_final: 0.7055 (tptt) REVERT: L 268 TYR cc_start: 0.5631 (t80) cc_final: 0.5311 (t80) REVERT: L 277 MET cc_start: 0.5452 (mmp) cc_final: 0.5096 (mmm) REVERT: L 297 MET cc_start: 0.3590 (ptp) cc_final: 0.3153 (ptp) REVERT: L 339 ARG cc_start: 0.5313 (mtp85) cc_final: 0.3880 (mmp-170) REVERT: L 508 GLU cc_start: 0.7650 (tm-30) cc_final: 0.7267 (tm-30) REVERT: M 46 GLU cc_start: 0.7563 (tp30) cc_final: 0.7079 (mp0) REVERT: M 61 CYS cc_start: 0.7635 (m) cc_final: 0.7136 (m) outliers start: 154 outliers final: 110 residues processed: 501 average time/residue: 0.4233 time to fit residues: 343.5305 Evaluate side-chains 493 residues out of total 3287 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 127 poor density : 366 time to evaluate : 3.602 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 61 ILE Chi-restraints excluded: chain G residue 64 VAL Chi-restraints excluded: chain G residue 70 THR Chi-restraints excluded: chain G residue 75 GLN Chi-restraints excluded: chain G residue 77 ASP Chi-restraints excluded: chain G residue 83 LEU Chi-restraints excluded: chain G residue 102 LEU Chi-restraints excluded: chain G residue 134 THR Chi-restraints excluded: chain G residue 176 CYS Chi-restraints excluded: chain G residue 202 VAL Chi-restraints excluded: chain G residue 231 PHE Chi-restraints excluded: chain G residue 234 LEU Chi-restraints excluded: chain H residue 28 LEU Chi-restraints excluded: chain H residue 118 ASP Chi-restraints excluded: chain H residue 174 ASP Chi-restraints excluded: chain H residue 201 LEU Chi-restraints excluded: chain I residue 66 SER Chi-restraints excluded: chain I residue 82 VAL Chi-restraints excluded: chain I residue 84 GLU Chi-restraints excluded: chain I residue 131 THR Chi-restraints excluded: chain I residue 239 MET Chi-restraints excluded: chain I residue 241 LEU Chi-restraints excluded: chain I residue 321 LEU Chi-restraints excluded: chain I residue 336 LEU Chi-restraints excluded: chain I residue 349 GLU Chi-restraints excluded: chain I residue 412 GLU Chi-restraints excluded: chain I residue 435 ILE Chi-restraints excluded: chain I residue 445 ILE Chi-restraints excluded: chain I residue 470 ARG Chi-restraints excluded: chain I residue 493 ILE Chi-restraints excluded: chain I residue 524 ILE Chi-restraints excluded: chain I residue 549 ASP Chi-restraints excluded: chain I residue 563 THR Chi-restraints excluded: chain I residue 623 LEU Chi-restraints excluded: chain I residue 633 LEU Chi-restraints excluded: chain I residue 639 LYS Chi-restraints excluded: chain I residue 690 VAL Chi-restraints excluded: chain I residue 754 THR Chi-restraints excluded: chain I residue 800 MET Chi-restraints excluded: chain I residue 802 VAL Chi-restraints excluded: chain I residue 817 LEU Chi-restraints excluded: chain I residue 845 LEU Chi-restraints excluded: chain I residue 920 VAL Chi-restraints excluded: chain I residue 924 VAL Chi-restraints excluded: chain I residue 953 LEU Chi-restraints excluded: chain I residue 968 GLU Chi-restraints excluded: chain I residue 984 VAL Chi-restraints excluded: chain I residue 1094 VAL Chi-restraints excluded: chain I residue 1225 VAL Chi-restraints excluded: chain I residue 1244 HIS Chi-restraints excluded: chain I residue 1253 LEU Chi-restraints excluded: chain I residue 1254 VAL Chi-restraints excluded: chain I residue 1289 GLU Chi-restraints excluded: chain I residue 1298 VAL Chi-restraints excluded: chain J residue 26 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 92 VAL Chi-restraints excluded: chain J residue 97 VAL Chi-restraints excluded: chain J residue 137 ARG Chi-restraints excluded: chain J residue 169 LEU Chi-restraints excluded: chain J residue 174 ASP Chi-restraints excluded: chain J residue 177 ASP Chi-restraints excluded: chain J residue 194 LEU Chi-restraints excluded: chain J residue 218 THR Chi-restraints excluded: chain J residue 253 VAL Chi-restraints excluded: chain J residue 291 ILE Chi-restraints excluded: chain J residue 320 ASN Chi-restraints excluded: chain J residue 326 SER Chi-restraints excluded: chain J residue 342 LEU Chi-restraints excluded: chain J residue 350 SER Chi-restraints excluded: chain J residue 363 LEU Chi-restraints excluded: chain J residue 398 LYS Chi-restraints excluded: chain J residue 428 THR Chi-restraints excluded: chain J residue 434 ILE Chi-restraints excluded: chain J residue 442 ILE Chi-restraints excluded: chain J residue 478 LEU Chi-restraints excluded: chain J residue 506 VAL Chi-restraints excluded: chain J residue 514 THR Chi-restraints excluded: chain J residue 526 VAL Chi-restraints excluded: chain J residue 573 THR Chi-restraints excluded: chain J residue 601 ILE Chi-restraints excluded: chain J residue 618 VAL Chi-restraints excluded: chain J residue 624 ILE Chi-restraints excluded: chain J residue 638 SER Chi-restraints excluded: chain J residue 642 ASP Chi-restraints excluded: chain J residue 661 VAL Chi-restraints excluded: chain J residue 674 THR Chi-restraints excluded: chain J residue 707 ILE Chi-restraints excluded: chain J residue 708 ASN Chi-restraints excluded: chain J residue 806 ASP Chi-restraints excluded: chain J residue 823 THR Chi-restraints excluded: chain J residue 849 LEU Chi-restraints excluded: chain J residue 853 THR Chi-restraints excluded: chain J residue 884 SER Chi-restraints excluded: chain J residue 894 VAL Chi-restraints excluded: chain J residue 922 SER Chi-restraints excluded: chain J residue 934 THR Chi-restraints excluded: chain J residue 935 PHE Chi-restraints excluded: chain J residue 1081 VAL Chi-restraints excluded: chain J residue 1159 ILE Chi-restraints excluded: chain J residue 1175 LEU Chi-restraints excluded: chain J residue 1239 ASP Chi-restraints excluded: chain J residue 1248 ILE Chi-restraints excluded: chain J residue 1272 SER Chi-restraints excluded: chain J residue 1275 LEU Chi-restraints excluded: chain J residue 1329 THR Chi-restraints excluded: chain J residue 1332 LEU Chi-restraints excluded: chain J residue 1344 LEU Chi-restraints excluded: chain J residue 1357 ILE Chi-restraints excluded: chain J residue 1371 ARG Chi-restraints excluded: chain K residue 3 ARG Chi-restraints excluded: chain K residue 4 VAL Chi-restraints excluded: chain K residue 39 VAL Chi-restraints excluded: chain K residue 60 ASN Chi-restraints excluded: chain L residue 55 VAL Chi-restraints excluded: chain L residue 266 PHE Chi-restraints excluded: chain L residue 341 LEU Chi-restraints excluded: chain L residue 395 THR Chi-restraints excluded: chain L residue 429 THR Chi-restraints excluded: chain L residue 570 ASP Chi-restraints excluded: chain L residue 582 VAL Chi-restraints excluded: chain M residue 2 SER Chi-restraints excluded: chain M residue 12 THR Chi-restraints excluded: chain M residue 38 GLU Chi-restraints excluded: chain M residue 60 GLU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 380 random chunks: chunk 226 optimal weight: 4.9990 chunk 146 optimal weight: 0.0270 chunk 218 optimal weight: 0.2980 chunk 110 optimal weight: 6.9990 chunk 71 optimal weight: 6.9990 chunk 70 optimal weight: 4.9990 chunk 232 optimal weight: 4.9990 chunk 249 optimal weight: 0.6980 chunk 181 optimal weight: 0.6980 chunk 34 optimal weight: 0.0000 chunk 287 optimal weight: 9.9990 overall best weight: 0.3442 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: I 573 ASN I 613 ASN ** I1080 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I1116 HIS I1257 GLN J 294 ASN J 907 HIS ** L 227 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 406 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7889 moved from start: 0.4935 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.038 30679 Z= 0.145 Angle : 0.572 11.104 41447 Z= 0.286 Chirality : 0.042 0.288 4751 Planarity : 0.004 0.062 5415 Dihedral : 4.789 48.591 4502 Min Nonbonded Distance : 2.120 Molprobity Statistics. All-atom Clashscore : 11.16 Ramachandran Plot: Outliers : 0.21 % Allowed : 6.65 % Favored : 93.14 % Rotamer: Outliers : 3.03 % Allowed : 19.39 % Favored : 77.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.33 % Cis-general : 0.11 % Twisted Proline : 0.00 % Twisted General : 0.08 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.27 (0.14), residues: 3817 helix: 0.93 (0.14), residues: 1515 sheet: -1.52 (0.29), residues: 324 loop : -2.26 (0.13), residues: 1978 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP I 807 HIS 0.008 0.001 HIS I 551 PHE 0.015 0.001 PHE G 231 TYR 0.025 0.001 TYR I1229 ARG 0.008 0.000 ARG M 49 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7634 Ramachandran restraints generated. 3817 Oldfield, 0 Emsley, 3817 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7634 Ramachandran restraints generated. 3817 Oldfield, 0 Emsley, 3817 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 534 residues out of total 3287 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 99 poor density : 435 time to evaluate : 3.591 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: G 68 TYR cc_start: 0.9104 (m-80) cc_final: 0.8707 (m-80) REVERT: G 102 LEU cc_start: 0.9229 (OUTLIER) cc_final: 0.8967 (tt) REVERT: G 185 TYR cc_start: 0.8831 (p90) cc_final: 0.8369 (p90) REVERT: G 200 LYS cc_start: 0.8499 (ttmt) cc_final: 0.8195 (ttmm) REVERT: G 231 PHE cc_start: 0.7953 (OUTLIER) cc_final: 0.6979 (t80) REVERT: H 28 LEU cc_start: 0.8735 (OUTLIER) cc_final: 0.8208 (mt) REVERT: H 84 ASN cc_start: 0.8933 (m110) cc_final: 0.8572 (m110) REVERT: H 201 LEU cc_start: 0.9009 (OUTLIER) cc_final: 0.8773 (tp) REVERT: I 230 PHE cc_start: 0.8249 (m-80) cc_final: 0.7966 (m-10) REVERT: I 239 MET cc_start: 0.6936 (OUTLIER) cc_final: 0.5788 (tpp) REVERT: I 316 GLU cc_start: 0.7529 (pt0) cc_final: 0.7313 (pp20) REVERT: I 470 ARG cc_start: 0.7291 (OUTLIER) cc_final: 0.6975 (tpm170) REVERT: I 684 ASN cc_start: 0.8513 (m-40) cc_final: 0.7913 (m-40) REVERT: I 717 VAL cc_start: 0.9103 (t) cc_final: 0.8743 (m) REVERT: I 1240 ASP cc_start: 0.7500 (p0) cc_final: 0.7052 (p0) REVERT: I 1253 LEU cc_start: 0.9422 (OUTLIER) cc_final: 0.9049 (tm) REVERT: I 1268 GLN cc_start: 0.8302 (mm-40) cc_final: 0.7948 (mm-40) REVERT: I 1290 MET cc_start: 0.8319 (tpp) cc_final: 0.7792 (tpp) REVERT: J 97 VAL cc_start: 0.9629 (OUTLIER) cc_final: 0.9360 (p) REVERT: J 137 ARG cc_start: 0.7928 (OUTLIER) cc_final: 0.7298 (mtt90) REVERT: J 169 LEU cc_start: 0.7552 (mm) cc_final: 0.7285 (mm) REVERT: J 291 ILE cc_start: 0.8608 (OUTLIER) cc_final: 0.8331 (tp) REVERT: J 398 LYS cc_start: 0.8368 (OUTLIER) cc_final: 0.8142 (ttmt) REVERT: J 466 MET cc_start: 0.8057 (mtp) cc_final: 0.7788 (mtp) REVERT: J 472 LEU cc_start: 0.8705 (mt) cc_final: 0.8494 (mt) REVERT: J 513 MET cc_start: 0.8547 (ttp) cc_final: 0.8187 (ttm) REVERT: J 707 ILE cc_start: 0.7903 (OUTLIER) cc_final: 0.7625 (tt) REVERT: J 849 LEU cc_start: 0.6839 (OUTLIER) cc_final: 0.6584 (mt) REVERT: J 918 ILE cc_start: 0.8743 (pt) cc_final: 0.8055 (mt) REVERT: J 1239 ASP cc_start: 0.8211 (OUTLIER) cc_final: 0.7662 (t0) REVERT: K 3 ARG cc_start: 0.8420 (OUTLIER) cc_final: 0.7576 (ttm170) REVERT: K 52 ARG cc_start: 0.8466 (mtp180) cc_final: 0.8223 (mtp180) REVERT: K 55 GLU cc_start: 0.8392 (tm-30) cc_final: 0.7843 (tm-30) REVERT: L 46 GLN cc_start: 0.5641 (mm110) cc_final: 0.5439 (mm110) REVERT: L 105 MET cc_start: 0.7243 (ppp) cc_final: 0.6775 (ppp) REVERT: L 121 LYS cc_start: 0.7781 (tppt) cc_final: 0.6938 (tptt) REVERT: L 268 TYR cc_start: 0.5463 (t80) cc_final: 0.4857 (t80) REVERT: L 276 MET cc_start: 0.4145 (mmm) cc_final: 0.3513 (ttm) REVERT: L 288 MET cc_start: 0.1468 (mmm) cc_final: 0.1258 (tpt) REVERT: L 297 MET cc_start: 0.3336 (ptp) cc_final: 0.3014 (ptp) REVERT: L 339 ARG cc_start: 0.5207 (mtp85) cc_final: 0.3867 (mmp-170) REVERT: L 508 GLU cc_start: 0.7711 (tm-30) cc_final: 0.7273 (tm-30) REVERT: M 46 GLU cc_start: 0.7600 (tp30) cc_final: 0.7137 (mp0) REVERT: M 61 CYS cc_start: 0.7608 (m) cc_final: 0.7124 (m) outliers start: 99 outliers final: 61 residues processed: 502 average time/residue: 0.4172 time to fit residues: 335.2716 Evaluate side-chains 463 residues out of total 3287 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 76 poor density : 387 time to evaluate : 3.450 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 61 ILE Chi-restraints excluded: chain G residue 64 VAL Chi-restraints excluded: chain G residue 83 LEU Chi-restraints excluded: chain G residue 102 LEU Chi-restraints excluded: chain G residue 134 THR Chi-restraints excluded: chain G residue 231 PHE Chi-restraints excluded: chain H residue 28 LEU Chi-restraints excluded: chain H residue 201 LEU Chi-restraints excluded: chain I residue 82 VAL Chi-restraints excluded: chain I residue 84 GLU Chi-restraints excluded: chain I residue 131 THR Chi-restraints excluded: chain I residue 239 MET Chi-restraints excluded: chain I residue 241 LEU Chi-restraints excluded: chain I residue 412 GLU Chi-restraints excluded: chain I residue 445 ILE Chi-restraints excluded: chain I residue 470 ARG Chi-restraints excluded: chain I residue 493 ILE Chi-restraints excluded: chain I residue 633 LEU Chi-restraints excluded: chain I residue 639 LYS Chi-restraints excluded: chain I residue 642 SER Chi-restraints excluded: chain I residue 690 VAL Chi-restraints excluded: chain I residue 817 LEU Chi-restraints excluded: chain I residue 845 LEU Chi-restraints excluded: chain I residue 862 LEU Chi-restraints excluded: chain I residue 896 THR Chi-restraints excluded: chain I residue 953 LEU Chi-restraints excluded: chain I residue 968 GLU Chi-restraints excluded: chain I residue 984 VAL Chi-restraints excluded: chain I residue 1094 VAL Chi-restraints excluded: chain I residue 1225 VAL Chi-restraints excluded: chain I residue 1253 LEU Chi-restraints excluded: chain I residue 1254 VAL Chi-restraints excluded: chain I residue 1298 VAL Chi-restraints excluded: chain J residue 46 TYR Chi-restraints excluded: chain J residue 48 THR Chi-restraints excluded: chain J residue 56 LEU Chi-restraints excluded: chain J residue 92 VAL Chi-restraints excluded: chain J residue 97 VAL Chi-restraints excluded: chain J residue 137 ARG Chi-restraints excluded: chain J residue 174 ASP Chi-restraints excluded: chain J residue 218 THR Chi-restraints excluded: chain J residue 253 VAL Chi-restraints excluded: chain J residue 291 ILE Chi-restraints excluded: chain J residue 350 SER Chi-restraints excluded: chain J residue 363 LEU Chi-restraints excluded: chain J residue 398 LYS Chi-restraints excluded: chain J residue 428 THR Chi-restraints excluded: chain J residue 442 ILE Chi-restraints excluded: chain J residue 506 VAL Chi-restraints excluded: chain J residue 514 THR Chi-restraints excluded: chain J residue 526 VAL Chi-restraints excluded: chain J residue 573 THR Chi-restraints excluded: chain J residue 601 ILE Chi-restraints excluded: chain J residue 674 THR Chi-restraints excluded: chain J residue 707 ILE Chi-restraints excluded: chain J residue 849 LEU Chi-restraints excluded: chain J residue 853 THR Chi-restraints excluded: chain J residue 922 SER Chi-restraints excluded: chain J residue 935 PHE Chi-restraints excluded: chain J residue 1081 VAL Chi-restraints excluded: chain J residue 1159 ILE Chi-restraints excluded: chain J residue 1239 ASP Chi-restraints excluded: chain J residue 1248 ILE Chi-restraints excluded: chain J residue 1272 SER Chi-restraints excluded: chain J residue 1275 LEU Chi-restraints excluded: chain J residue 1332 LEU Chi-restraints excluded: chain J residue 1344 LEU Chi-restraints excluded: chain K residue 3 ARG Chi-restraints excluded: chain K residue 4 VAL Chi-restraints excluded: chain K residue 39 VAL Chi-restraints excluded: chain K residue 60 ASN Chi-restraints excluded: chain L residue 55 VAL Chi-restraints excluded: chain L residue 395 THR Chi-restraints excluded: chain L residue 570 ASP Chi-restraints excluded: chain L residue 582 VAL Chi-restraints excluded: chain M residue 60 GLU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 380 random chunks: chunk 333 optimal weight: 20.0000 chunk 350 optimal weight: 9.9990 chunk 320 optimal weight: 10.0000 chunk 341 optimal weight: 10.0000 chunk 205 optimal weight: 5.9990 chunk 148 optimal weight: 0.9980 chunk 268 optimal weight: 0.0980 chunk 104 optimal weight: 7.9990 chunk 308 optimal weight: 4.9990 chunk 322 optimal weight: 1.9990 chunk 340 optimal weight: 9.9990 overall best weight: 2.8186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** I 437 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 580 GLN I1116 HIS J 294 ASN J 907 HIS ** L 227 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 406 GLN M 25 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8030 moved from start: 0.4678 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.064 30679 Z= 0.372 Angle : 0.688 13.881 41447 Z= 0.343 Chirality : 0.046 0.366 4751 Planarity : 0.005 0.061 5415 Dihedral : 5.256 48.893 4502 Min Nonbonded Distance : 2.103 Molprobity Statistics. All-atom Clashscore : 13.61 Ramachandran Plot: Outliers : 0.21 % Allowed : 9.20 % Favored : 90.59 % Rotamer: Outliers : 3.52 % Allowed : 19.70 % Favored : 76.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.33 % Cis-general : 0.11 % Twisted Proline : 0.00 % Twisted General : 0.08 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.36 (0.14), residues: 3817 helix: 0.77 (0.13), residues: 1509 sheet: -1.69 (0.30), residues: 311 loop : -2.19 (0.13), residues: 1997 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP J 236 HIS 0.019 0.001 HIS I 551 PHE 0.017 0.002 PHE J 437 TYR 0.054 0.002 TYR I1229 ARG 0.008 0.001 ARG I 201 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7634 Ramachandran restraints generated. 3817 Oldfield, 0 Emsley, 3817 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7634 Ramachandran restraints generated. 3817 Oldfield, 0 Emsley, 3817 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 483 residues out of total 3287 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 115 poor density : 368 time to evaluate : 3.666 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: G 68 TYR cc_start: 0.9275 (m-80) cc_final: 0.8979 (m-80) REVERT: G 102 LEU cc_start: 0.9309 (OUTLIER) cc_final: 0.9024 (tt) REVERT: G 185 TYR cc_start: 0.8902 (p90) cc_final: 0.8422 (p90) REVERT: G 200 LYS cc_start: 0.8707 (ttmt) cc_final: 0.8416 (ttmm) REVERT: G 231 PHE cc_start: 0.8111 (OUTLIER) cc_final: 0.7099 (t80) REVERT: H 28 LEU cc_start: 0.8830 (OUTLIER) cc_final: 0.8166 (mt) REVERT: H 199 ASP cc_start: 0.7942 (m-30) cc_final: 0.7565 (m-30) REVERT: H 201 LEU cc_start: 0.9118 (OUTLIER) cc_final: 0.8878 (tp) REVERT: I 239 MET cc_start: 0.7110 (OUTLIER) cc_final: 0.5839 (tpp) REVERT: I 316 GLU cc_start: 0.7678 (pt0) cc_final: 0.7330 (pp20) REVERT: I 349 GLU cc_start: 0.7323 (OUTLIER) cc_final: 0.7101 (mt-10) REVERT: I 470 ARG cc_start: 0.7513 (OUTLIER) cc_final: 0.7099 (tpm170) REVERT: I 717 VAL cc_start: 0.9213 (t) cc_final: 0.8928 (m) REVERT: I 1240 ASP cc_start: 0.7621 (p0) cc_final: 0.7329 (p0) REVERT: I 1253 LEU cc_start: 0.9388 (OUTLIER) cc_final: 0.8993 (tm) REVERT: I 1290 MET cc_start: 0.8568 (tpp) cc_final: 0.7989 (tpp) REVERT: J 97 VAL cc_start: 0.9651 (OUTLIER) cc_final: 0.9360 (p) REVERT: J 137 ARG cc_start: 0.8177 (OUTLIER) cc_final: 0.7453 (mtt90) REVERT: J 169 LEU cc_start: 0.7400 (OUTLIER) cc_final: 0.7194 (mm) REVERT: J 180 MET cc_start: 0.7259 (ptm) cc_final: 0.6673 (ptm) REVERT: J 697 MET cc_start: 0.8875 (ttp) cc_final: 0.8381 (tmm) REVERT: J 707 ILE cc_start: 0.8158 (OUTLIER) cc_final: 0.7788 (tt) REVERT: J 736 GLN cc_start: 0.8065 (mt0) cc_final: 0.7814 (mt0) REVERT: J 849 LEU cc_start: 0.6911 (OUTLIER) cc_final: 0.6649 (mt) REVERT: J 935 PHE cc_start: 0.7983 (OUTLIER) cc_final: 0.7406 (t80) REVERT: J 1248 ILE cc_start: 0.8291 (OUTLIER) cc_final: 0.8087 (mt) REVERT: K 55 GLU cc_start: 0.8453 (tm-30) cc_final: 0.7911 (tm-30) REVERT: L 46 GLN cc_start: 0.5680 (mm110) cc_final: 0.5477 (mm110) REVERT: L 102 MET cc_start: 0.6534 (mmm) cc_final: 0.6249 (mmm) REVERT: L 105 MET cc_start: 0.7536 (ppp) cc_final: 0.6743 (ppp) REVERT: L 121 LYS cc_start: 0.7874 (tppt) cc_final: 0.7047 (tptt) REVERT: L 268 TYR cc_start: 0.5347 (t80) cc_final: 0.4854 (t80) REVERT: L 288 MET cc_start: 0.1486 (mmm) cc_final: 0.1271 (tpt) REVERT: L 297 MET cc_start: 0.3526 (ptp) cc_final: 0.3132 (ptp) REVERT: L 339 ARG cc_start: 0.5415 (mtp85) cc_final: 0.3899 (mmp-170) REVERT: L 508 GLU cc_start: 0.7782 (tm-30) cc_final: 0.7353 (tm-30) REVERT: M 46 GLU cc_start: 0.7558 (tp30) cc_final: 0.6999 (mp0) REVERT: M 61 CYS cc_start: 0.7562 (m) cc_final: 0.7049 (m) outliers start: 115 outliers final: 85 residues processed: 453 average time/residue: 0.4116 time to fit residues: 298.9527 Evaluate side-chains 458 residues out of total 3287 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 100 poor density : 358 time to evaluate : 3.265 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 61 ILE Chi-restraints excluded: chain G residue 64 VAL Chi-restraints excluded: chain G residue 83 LEU Chi-restraints excluded: chain G residue 102 LEU Chi-restraints excluded: chain G residue 134 THR Chi-restraints excluded: chain G residue 202 VAL Chi-restraints excluded: chain G residue 231 PHE Chi-restraints excluded: chain H residue 28 LEU Chi-restraints excluded: chain H residue 118 ASP Chi-restraints excluded: chain H residue 201 LEU Chi-restraints excluded: chain I residue 66 SER Chi-restraints excluded: chain I residue 82 VAL Chi-restraints excluded: chain I residue 131 THR Chi-restraints excluded: chain I residue 239 MET Chi-restraints excluded: chain I residue 241 LEU Chi-restraints excluded: chain I residue 349 GLU Chi-restraints excluded: chain I residue 387 ASN Chi-restraints excluded: chain I residue 412 GLU Chi-restraints excluded: chain I residue 435 ILE Chi-restraints excluded: chain I residue 445 ILE Chi-restraints excluded: chain I residue 470 ARG Chi-restraints excluded: chain I residue 493 ILE Chi-restraints excluded: chain I residue 633 LEU Chi-restraints excluded: chain I residue 639 LYS Chi-restraints excluded: chain I residue 642 SER Chi-restraints excluded: chain I residue 690 VAL Chi-restraints excluded: chain I residue 802 VAL Chi-restraints excluded: chain I residue 817 LEU Chi-restraints excluded: chain I residue 845 LEU Chi-restraints excluded: chain I residue 896 THR Chi-restraints excluded: chain I residue 953 LEU Chi-restraints excluded: chain I residue 968 GLU Chi-restraints excluded: chain I residue 984 VAL Chi-restraints excluded: chain I residue 1094 VAL Chi-restraints excluded: chain I residue 1225 VAL Chi-restraints excluded: chain I residue 1244 HIS Chi-restraints excluded: chain I residue 1253 LEU Chi-restraints excluded: chain I residue 1254 VAL Chi-restraints excluded: chain I residue 1298 VAL Chi-restraints excluded: chain J residue 46 TYR Chi-restraints excluded: chain J residue 48 THR Chi-restraints excluded: chain J residue 92 VAL Chi-restraints excluded: chain J residue 97 VAL Chi-restraints excluded: chain J residue 137 ARG Chi-restraints excluded: chain J residue 169 LEU Chi-restraints excluded: chain J residue 174 ASP Chi-restraints excluded: chain J residue 177 ASP Chi-restraints excluded: chain J residue 218 THR Chi-restraints excluded: chain J residue 253 VAL Chi-restraints excluded: chain J residue 332 LYS Chi-restraints excluded: chain J residue 342 LEU Chi-restraints excluded: chain J residue 350 SER Chi-restraints excluded: chain J residue 363 LEU Chi-restraints excluded: chain J residue 428 THR Chi-restraints excluded: chain J residue 434 ILE Chi-restraints excluded: chain J residue 442 ILE Chi-restraints excluded: chain J residue 495 ASN Chi-restraints excluded: chain J residue 506 VAL Chi-restraints excluded: chain J residue 514 THR Chi-restraints excluded: chain J residue 573 THR Chi-restraints excluded: chain J residue 601 ILE Chi-restraints excluded: chain J residue 618 VAL Chi-restraints excluded: chain J residue 624 ILE Chi-restraints excluded: chain J residue 661 VAL Chi-restraints excluded: chain J residue 674 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 770 LEU Chi-restraints excluded: chain J residue 806 ASP Chi-restraints excluded: chain J residue 823 THR Chi-restraints excluded: chain J residue 849 LEU Chi-restraints excluded: chain J residue 853 THR Chi-restraints excluded: chain J residue 869 CYS Chi-restraints excluded: chain J residue 922 SER Chi-restraints excluded: chain J residue 935 PHE Chi-restraints excluded: chain J residue 1081 VAL Chi-restraints excluded: chain J residue 1159 ILE Chi-restraints excluded: chain J residue 1175 LEU Chi-restraints excluded: chain J residue 1239 ASP Chi-restraints excluded: chain J residue 1248 ILE Chi-restraints excluded: chain J residue 1260 MET Chi-restraints excluded: chain J residue 1272 SER Chi-restraints excluded: chain J residue 1275 LEU Chi-restraints excluded: chain J residue 1332 LEU Chi-restraints excluded: chain J residue 1344 LEU Chi-restraints excluded: chain J residue 1357 ILE Chi-restraints excluded: chain J residue 1371 ARG Chi-restraints excluded: chain K residue 4 VAL Chi-restraints excluded: chain K residue 39 VAL Chi-restraints excluded: chain K residue 60 ASN Chi-restraints excluded: chain L residue 55 VAL Chi-restraints excluded: chain L residue 256 PHE Chi-restraints excluded: chain L residue 395 THR Chi-restraints excluded: chain L residue 429 THR Chi-restraints excluded: chain L residue 570 ASP Chi-restraints excluded: chain L residue 582 VAL Chi-restraints excluded: chain M residue 12 THR Chi-restraints excluded: chain M residue 16 THR Chi-restraints excluded: chain M residue 60 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 380 random chunks: chunk 224 optimal weight: 0.2980 chunk 360 optimal weight: 4.9990 chunk 220 optimal weight: 2.9990 chunk 171 optimal weight: 0.6980 chunk 250 optimal weight: 0.8980 chunk 378 optimal weight: 5.9990 chunk 348 optimal weight: 4.9990 chunk 301 optimal weight: 9.9990 chunk 31 optimal weight: 20.0000 chunk 232 optimal weight: 4.9990 chunk 184 optimal weight: 4.9990 overall best weight: 1.9784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** H 227 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 613 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I1080 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 294 ASN ** L 227 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 406 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8000 moved from start: 0.4782 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.053 30679 Z= 0.281 Angle : 0.641 12.975 41447 Z= 0.320 Chirality : 0.044 0.315 4751 Planarity : 0.004 0.063 5415 Dihedral : 5.186 48.534 4502 Min Nonbonded Distance : 2.098 Molprobity Statistics. All-atom Clashscore : 12.80 Ramachandran Plot: Outliers : 0.21 % Allowed : 8.36 % Favored : 91.43 % Rotamer: Outliers : 3.09 % Allowed : 20.34 % Favored : 76.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.33 % Cis-general : 0.11 % Twisted Proline : 0.00 % Twisted General : 0.08 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.33 (0.14), residues: 3817 helix: 0.74 (0.13), residues: 1519 sheet: -1.48 (0.31), residues: 299 loop : -2.18 (0.13), residues: 1999 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP J 236 HIS 0.016 0.001 HIS I 551 PHE 0.015 0.001 PHE G 231 TYR 0.048 0.002 TYR I1229 ARG 0.008 0.000 ARG M 49 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7634 Ramachandran restraints generated. 3817 Oldfield, 0 Emsley, 3817 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7634 Ramachandran restraints generated. 3817 Oldfield, 0 Emsley, 3817 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 472 residues out of total 3287 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 101 poor density : 371 time to evaluate : 3.575 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: G 68 TYR cc_start: 0.9230 (m-80) cc_final: 0.8897 (m-80) REVERT: G 102 LEU cc_start: 0.9268 (OUTLIER) cc_final: 0.9016 (tt) REVERT: G 185 TYR cc_start: 0.8925 (p90) cc_final: 0.8448 (p90) REVERT: G 200 LYS cc_start: 0.8651 (ttmt) cc_final: 0.8374 (ttmm) REVERT: G 207 THR cc_start: 0.8612 (m) cc_final: 0.8123 (p) REVERT: G 231 PHE cc_start: 0.8059 (OUTLIER) cc_final: 0.7082 (t80) REVERT: H 28 LEU cc_start: 0.8804 (OUTLIER) cc_final: 0.8161 (mt) REVERT: H 199 ASP cc_start: 0.7853 (m-30) cc_final: 0.7630 (m-30) REVERT: I 239 MET cc_start: 0.7077 (OUTLIER) cc_final: 0.5824 (tpp) REVERT: I 316 GLU cc_start: 0.7663 (pt0) cc_final: 0.7332 (pp20) REVERT: I 349 GLU cc_start: 0.7265 (OUTLIER) cc_final: 0.7031 (mt-10) REVERT: I 429 MET cc_start: 0.7611 (mtt) cc_final: 0.7308 (mtt) REVERT: I 470 ARG cc_start: 0.7489 (OUTLIER) cc_final: 0.7110 (tpm170) REVERT: I 613 ASN cc_start: 0.7933 (t0) cc_final: 0.7702 (t0) REVERT: I 717 VAL cc_start: 0.9186 (t) cc_final: 0.8879 (m) REVERT: I 1107 MET cc_start: 0.8053 (mpp) cc_final: 0.7577 (mtp) REVERT: I 1240 ASP cc_start: 0.7641 (p0) cc_final: 0.7306 (p0) REVERT: I 1253 LEU cc_start: 0.9380 (OUTLIER) cc_final: 0.8974 (tm) REVERT: I 1290 MET cc_start: 0.8532 (tpp) cc_final: 0.7899 (tpp) REVERT: I 1304 MET cc_start: 0.9176 (tpp) cc_final: 0.8431 (tpp) REVERT: J 97 VAL cc_start: 0.9629 (OUTLIER) cc_final: 0.9330 (p) REVERT: J 137 ARG cc_start: 0.8140 (OUTLIER) cc_final: 0.7448 (mtt90) REVERT: J 169 LEU cc_start: 0.7551 (OUTLIER) cc_final: 0.7284 (mm) REVERT: J 180 MET cc_start: 0.7213 (ptm) cc_final: 0.6592 (ptm) REVERT: J 697 MET cc_start: 0.8760 (ttp) cc_final: 0.8242 (tmm) REVERT: J 707 ILE cc_start: 0.8177 (OUTLIER) cc_final: 0.7804 (tt) REVERT: J 849 LEU cc_start: 0.6884 (OUTLIER) cc_final: 0.6616 (mt) REVERT: J 935 PHE cc_start: 0.7958 (OUTLIER) cc_final: 0.7473 (t80) REVERT: J 1025 MET cc_start: 0.6689 (tmm) cc_final: 0.6378 (tmm) REVERT: K 16 ARG cc_start: 0.7489 (ttt180) cc_final: 0.7007 (ttm170) REVERT: K 55 GLU cc_start: 0.8489 (tm-30) cc_final: 0.7951 (tm-30) REVERT: L 105 MET cc_start: 0.7475 (ppp) cc_final: 0.6972 (ppp) REVERT: L 121 LYS cc_start: 0.7840 (tppt) cc_final: 0.6977 (tptt) REVERT: L 268 TYR cc_start: 0.5779 (t80) cc_final: 0.5027 (t80) REVERT: L 288 MET cc_start: 0.1464 (mmm) cc_final: 0.1252 (tpt) REVERT: L 297 MET cc_start: 0.3476 (ptp) cc_final: 0.3104 (ptp) REVERT: L 339 ARG cc_start: 0.5432 (mtp85) cc_final: 0.3890 (mmp-170) REVERT: L 508 GLU cc_start: 0.7769 (tm-30) cc_final: 0.7296 (tm-30) REVERT: M 46 GLU cc_start: 0.7453 (tp30) cc_final: 0.6952 (mp0) REVERT: M 61 CYS cc_start: 0.7549 (m) cc_final: 0.7044 (m) outliers start: 101 outliers final: 82 residues processed: 447 average time/residue: 0.4186 time to fit residues: 298.9390 Evaluate side-chains 459 residues out of total 3287 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 95 poor density : 364 time to evaluate : 3.563 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 61 ILE Chi-restraints excluded: chain G residue 64 VAL Chi-restraints excluded: chain G residue 83 LEU Chi-restraints excluded: chain G residue 102 LEU Chi-restraints excluded: chain G residue 134 THR Chi-restraints excluded: chain G residue 176 CYS Chi-restraints excluded: chain G residue 202 VAL Chi-restraints excluded: chain G residue 231 PHE Chi-restraints excluded: chain H residue 28 LEU Chi-restraints excluded: chain I residue 82 VAL Chi-restraints excluded: chain I residue 131 THR Chi-restraints excluded: chain I residue 239 MET Chi-restraints excluded: chain I residue 241 LEU Chi-restraints excluded: chain I residue 349 GLU Chi-restraints excluded: chain I residue 412 GLU Chi-restraints excluded: chain I residue 435 ILE Chi-restraints excluded: chain I residue 445 ILE Chi-restraints excluded: chain I residue 470 ARG Chi-restraints excluded: chain I residue 493 ILE Chi-restraints excluded: chain I residue 633 LEU Chi-restraints excluded: chain I residue 639 LYS Chi-restraints excluded: chain I residue 642 SER Chi-restraints excluded: chain I residue 690 VAL Chi-restraints excluded: chain I residue 800 MET Chi-restraints excluded: chain I residue 817 LEU Chi-restraints excluded: chain I residue 845 LEU Chi-restraints excluded: chain I residue 896 THR Chi-restraints excluded: chain I residue 953 LEU Chi-restraints excluded: chain I residue 968 GLU Chi-restraints excluded: chain I residue 984 VAL Chi-restraints excluded: chain I residue 1094 VAL Chi-restraints excluded: chain I residue 1225 VAL Chi-restraints excluded: chain I residue 1244 HIS Chi-restraints excluded: chain I residue 1253 LEU Chi-restraints excluded: chain I residue 1254 VAL Chi-restraints excluded: chain I residue 1298 VAL 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 56 LEU Chi-restraints excluded: chain J residue 92 VAL Chi-restraints excluded: chain J residue 97 VAL Chi-restraints excluded: chain J residue 137 ARG Chi-restraints excluded: chain J residue 169 LEU Chi-restraints excluded: chain J residue 174 ASP Chi-restraints excluded: chain J residue 177 ASP Chi-restraints excluded: chain J residue 218 THR Chi-restraints excluded: chain J residue 253 VAL Chi-restraints excluded: chain J residue 332 LYS Chi-restraints excluded: chain J residue 350 SER Chi-restraints excluded: chain J residue 363 LEU Chi-restraints excluded: chain J residue 428 THR Chi-restraints excluded: chain J residue 434 ILE Chi-restraints excluded: chain J residue 442 ILE Chi-restraints excluded: chain J residue 495 ASN Chi-restraints excluded: chain J residue 506 VAL Chi-restraints excluded: chain J residue 514 THR Chi-restraints excluded: chain J residue 545 HIS Chi-restraints excluded: chain J residue 573 THR Chi-restraints excluded: chain J residue 592 VAL Chi-restraints excluded: chain J residue 601 ILE Chi-restraints excluded: chain J residue 618 VAL Chi-restraints excluded: chain J residue 624 ILE Chi-restraints excluded: chain J residue 661 VAL Chi-restraints excluded: chain J residue 674 THR Chi-restraints excluded: chain J residue 707 ILE Chi-restraints excluded: chain J residue 708 ASN Chi-restraints excluded: chain J residue 770 LEU Chi-restraints excluded: chain J residue 806 ASP Chi-restraints excluded: chain J residue 823 THR Chi-restraints excluded: chain J residue 849 LEU Chi-restraints excluded: chain J residue 853 THR Chi-restraints excluded: chain J residue 922 SER Chi-restraints excluded: chain J residue 935 PHE Chi-restraints excluded: chain J residue 1081 VAL Chi-restraints excluded: chain J residue 1159 ILE Chi-restraints excluded: chain J residue 1175 LEU Chi-restraints excluded: chain J residue 1239 ASP Chi-restraints excluded: chain J residue 1260 MET Chi-restraints excluded: chain J residue 1272 SER Chi-restraints excluded: chain J residue 1275 LEU Chi-restraints excluded: chain J residue 1332 LEU Chi-restraints excluded: chain J residue 1344 LEU Chi-restraints excluded: chain J residue 1357 ILE Chi-restraints excluded: chain J residue 1371 ARG Chi-restraints excluded: chain K residue 4 VAL Chi-restraints excluded: chain K residue 39 VAL Chi-restraints excluded: chain K residue 60 ASN Chi-restraints excluded: chain L residue 55 VAL Chi-restraints excluded: chain L residue 395 THR Chi-restraints excluded: chain L residue 429 THR Chi-restraints excluded: chain L residue 570 ASP Chi-restraints excluded: chain L residue 582 VAL Chi-restraints excluded: chain M residue 12 THR Chi-restraints excluded: chain M residue 60 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 380 random chunks: chunk 239 optimal weight: 2.9990 chunk 321 optimal weight: 10.0000 chunk 92 optimal weight: 2.9990 chunk 277 optimal weight: 20.0000 chunk 44 optimal weight: 2.9990 chunk 83 optimal weight: 4.9990 chunk 301 optimal weight: 0.7980 chunk 126 optimal weight: 1.9990 chunk 310 optimal weight: 0.5980 chunk 38 optimal weight: 0.6980 chunk 55 optimal weight: 0.7980 overall best weight: 0.9782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 227 GLN I 613 ASN ** I1080 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J1023 HIS ** L 227 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3703 r_free = 0.3703 target = 0.145852 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3318 r_free = 0.3318 target = 0.114915 restraints weight = 45122.895| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3287 r_free = 0.3287 target = 0.112901 restraints weight = 69612.440| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3304 r_free = 0.3304 target = 0.114278 restraints weight = 64065.425| |-----------------------------------------------------------------------------| r_work (final): 0.3301 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7847 moved from start: 0.5039 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 30679 Z= 0.189 Angle : 0.594 12.902 41447 Z= 0.296 Chirality : 0.042 0.274 4751 Planarity : 0.004 0.061 5415 Dihedral : 4.888 48.061 4502 Min Nonbonded Distance : 2.139 Molprobity Statistics. All-atom Clashscore : 11.81 Ramachandran Plot: Outliers : 0.21 % Allowed : 7.70 % Favored : 92.09 % Rotamer: Outliers : 3.06 % Allowed : 20.59 % Favored : 76.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.33 % Cis-general : 0.11 % Twisted Proline : 0.00 % Twisted General : 0.08 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.13 (0.14), residues: 3817 helix: 0.91 (0.14), residues: 1528 sheet: -1.11 (0.32), residues: 297 loop : -2.13 (0.13), residues: 1992 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP I 807 HIS 0.022 0.001 HIS J1023 PHE 0.015 0.001 PHE J 461 TYR 0.042 0.001 TYR I1229 ARG 0.009 0.000 ARG M 49 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 6890.77 seconds wall clock time: 126 minutes 16.27 seconds (7576.27 seconds total)