Starting phenix.real_space_refine on Wed Feb 21 19:10:53 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6pst_20463/02_2024/6pst_20463_trim_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6pst_20463/02_2024/6pst_20463.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.0 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6pst_20463/02_2024/6pst_20463.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6pst_20463/02_2024/6pst_20463.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6pst_20463/02_2024/6pst_20463_trim_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6pst_20463/02_2024/6pst_20463_trim_updated.pdb" } resolution = 3.0 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: 7 Type Number sf(0) Gaussians Zn 3 6.06 5 P 101 5.49 5 Mg 1 5.21 5 S 137 5.16 5 C 19429 2.51 5 N 5552 2.21 5 O 6229 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "H GLU 229": "OE1" <-> "OE2" Residue "I GLU 316": "OE1" <-> "OE2" Residue "I TYR 1087": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J TYR 46": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J ARG 133": "NH1" <-> "NH2" Residue "J GLU 170": "OE1" <-> "OE2" Residue "J ARG 259": "NH1" <-> "NH2" Residue "J ARG 738": "NH1" <-> "NH2" Residue "J ARG 799": "NH1" <-> "NH2" Residue "J ARG 1372": "NH1" <-> "NH2" Residue "K ARG 69": "NH1" <-> "NH2" Residue "L ARG 422": "NH1" <-> "NH2" Residue "L ARG 476": "NH1" <-> "NH2" Residue "L ARG 608": "NH1" <-> "NH2" Time to flip residues: 0.11s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5238/modules/chem_data/mon_lib" Total number of atoms: 31452 Number of models: 1 Model: "" Number of chains: 13 Chain: "N" Number of atoms: 566 Number of conformers: 1 Conformer: "" Number of residues, atoms: 72, 566 Classifications: {'peptide': 72} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 4, 'TRANS': 67} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 6 Planarities with less than four sites: {'HIS:plan': 1} Unresolved non-hydrogen planarities: 5 Chain: "O" Number of atoms: 1026 Number of conformers: 1 Conformer: "" Number of residues, atoms: 50, 1026 Classifications: {'DNA': 50} Link IDs: {'rna3p': 49} Chain breaks: 1 Chain: "P" Number of atoms: 1045 Number of conformers: 1 Conformer: "" Number of residues, atoms: 51, 1045 Classifications: {'DNA': 51} Link IDs: {'rna3p': 50} Chain: "M" Number of atoms: 572 Number of conformers: 1 Conformer: "" Number of residues, atoms: 73, 572 Classifications: {'peptide': 73} Link IDs: {'PCIS': 1, 'PTRANS': 3, 'TRANS': 68} Chain: "G" Number of atoms: 1769 Number of conformers: 1 Conformer: "" Number of residues, atoms: 232, 1769 Classifications: {'peptide': 232} Incomplete info: {'truncation_to_alanine': 8} Link IDs: {'CIS': 1, 'PTRANS': 9, 'TRANS': 221} Unresolved non-hydrogen bonds: 32 Unresolved non-hydrogen angles: 40 Unresolved non-hydrogen dihedrals: 24 Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 4, 'ARG:plan': 1, 'ASP:plan': 2} Unresolved non-hydrogen planarities: 31 Chain: "H" Number of atoms: 1669 Number of conformers: 1 Conformer: "" Number of residues, atoms: 218, 1669 Classifications: {'peptide': 218} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'CIS': 1, 'PTRANS': 8, 'TRANS': 208} Chain breaks: 1 Unresolved non-hydrogen bonds: 11 Unresolved non-hydrogen angles: 14 Unresolved non-hydrogen dihedrals: 8 Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 11 Chain: "I" Number of atoms: 10512 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1337, 10512 Classifications: {'peptide': 1337} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 7} Link IDs: {'CIS': 1, 'PCIS': 1, 'PTRANS': 55, 'TRANS': 1279} Chain breaks: 2 Unresolved non-hydrogen bonds: 31 Unresolved non-hydrogen angles: 39 Unresolved non-hydrogen dihedrals: 28 Planarities with less than four sites: {'TYR:plan': 1, 'GLU:plan': 2, 'ARG:plan': 1, 'PHE:plan': 1} Unresolved non-hydrogen planarities: 26 Chain: "J" Number of atoms: 9109 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1164, 9109 Classifications: {'peptide': 1164} Link IDs: {'CIS': 2, 'PTRANS': 47, 'TRANS': 1114} Chain breaks: 1 Chain: "K" Number of atoms: 577 Number of conformers: 1 Conformer: "" Number of residues, atoms: 72, 577 Classifications: {'peptide': 72} Link IDs: {'PTRANS': 2, 'TRANS': 69} Chain: "L" Number of atoms: 4495 Number of conformers: 1 Conformer: "" Number of residues, atoms: 558, 4495 Classifications: {'peptide': 558} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'CIS': 5, 'PTRANS': 16, 'TRANS': 536} Chain breaks: 2 Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 9 Unresolved non-hydrogen dihedrals: 7 Planarities with less than four sites: {'GLU:plan': 1} Unresolved non-hydrogen planarities: 4 Chain: "N" 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 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: 57 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 57 Unusual residues: {' MG': 1, ' ZN': 2, '1N7': 2} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 32 Unresolved non-hydrogen angles: 48 Unresolved non-hydrogen dihedrals: 26 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'1N7:plan-1': 2} Unresolved non-hydrogen planarities: 6 List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 276 SG CYS N 37 71.467 155.895 80.709 1.00 65.23 S ATOM 296 SG CYS N 40 74.086 157.690 82.200 1.00 68.45 S ATOM 433 SG CYS N 58 75.810 154.743 80.028 1.00 55.45 S ATOM 455 SG CYS N 61 74.037 154.341 83.014 1.00 58.83 S ATOM 17608 SG CYS J 70 50.517 63.438 118.070 1.00 43.81 S ATOM 17622 SG CYS J 72 52.811 62.337 120.392 1.00 48.86 S ATOM 17730 SG CYS J 85 48.536 62.461 121.062 1.00 51.62 S ATOM 17754 SG CYS J 88 50.816 65.668 120.683 1.00 50.83 S ATOM 23442 SG CYS J 814 20.920 114.756 84.751 1.00 42.80 S ATOM 24007 SG CYS J 888 24.691 113.213 85.642 1.00 32.62 S ATOM 24058 SG CYS J 895 23.079 111.627 82.766 1.00 29.59 S ATOM 24079 SG CYS J 898 23.659 114.993 82.736 1.00 27.55 S Time building chain proxies: 16.62, per 1000 atoms: 0.53 Number of scatterers: 31452 At special positions: 0 Unit cell: (149.5, 183.3, 193.7, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 7 Type Number sf(0) Zn 3 29.99 S 137 16.00 P 101 15.00 Mg 1 11.99 O 6229 8.00 N 5552 7.00 C 19429 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 13.77 Conformation dependent library (CDL) restraints added in 5.5 seconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN J1502 " pdb="ZN ZN J1502 " - pdb=" SG CYS J 70 " pdb="ZN ZN J1502 " - pdb=" SG CYS J 88 " pdb="ZN ZN J1502 " - pdb=" SG CYS J 85 " pdb="ZN ZN J1502 " - pdb=" SG CYS J 72 " pdb=" ZN J1503 " pdb="ZN ZN J1503 " - pdb=" SG CYS J 888 " pdb="ZN ZN J1503 " - pdb=" SG CYS J 895 " pdb="ZN ZN J1503 " - pdb=" SG CYS J 814 " pdb="ZN ZN J1503 " - pdb=" SG CYS J 898 " pdb=" ZN N 101 " pdb="ZN ZN N 101 " - pdb=" SG CYS N 58 " pdb="ZN ZN N 101 " - pdb=" SG CYS N 40 " pdb="ZN ZN N 101 " - pdb=" SG CYS N 37 " pdb="ZN ZN N 101 " - pdb=" SG CYS N 61 " Number of angles added : 18 7396 Ramachandran restraints generated. 3698 Oldfield, 0 Emsley, 3698 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 6938 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 131 helices and 33 sheets defined 38.9% alpha, 10.3% beta 44 base pairs and 84 stacking pairs defined. Time for finding SS restraints: 15.43 Creating SS restraints... Processing helix chain 'N' and resid 6 through 25 Processing helix chain 'N' and resid 46 through 51 Processing helix chain 'N' and resid 59 through 71 Processing helix chain 'M' and resid 264 through 273 Processing helix chain 'M' and resid 278 through 281 No H-bonds generated for 'chain 'M' and resid 278 through 281' Processing helix chain 'M' and resid 286 through 290 Processing helix chain 'M' and resid 297 through 309 Processing helix chain 'G' and resid 35 through 49 Processing helix chain 'G' and resid 78 through 86 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 155 through 158 No H-bonds generated for 'chain 'G' and resid 155 through 158' Processing helix chain 'G' and resid 213 through 232 removed outlier: 3.584A pdb=" N GLN G 227 " --> pdb=" O ILE G 223 " (cutoff:3.500A) Processing helix chain 'H' and resid 35 through 49 removed outlier: 4.006A pdb=" N ALA H 42 " --> pdb=" O THR H 38 " (cutoff:3.500A) Processing helix chain 'H' and resid 80 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 229 removed outlier: 3.570A pdb=" N GLU H 229 " --> pdb=" O ALA H 225 " (cutoff:3.500A) Processing helix chain 'I' and resid 29 through 38 Processing helix chain 'I' and resid 49 through 56 Processing helix chain 'I' and resid 82 through 88 Processing helix chain 'I' and resid 206 through 212 removed outlier: 3.758A pdb=" N LEU I 210 " --> pdb=" O ALA I 206 " (cutoff:3.500A) Processing helix chain 'I' and resid 217 through 224 Processing helix chain 'I' and resid 271 through 279 Processing helix chain 'I' and resid 291 through 293 No H-bonds generated for 'chain 'I' and resid 291 through 293' Processing helix chain 'I' and resid 319 through 328 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 389 removed outlier: 3.877A pdb=" N PHE I 389 " --> pdb=" O PHE I 385 " (cutoff:3.500A) Processing helix chain 'I' and resid 399 through 408 Processing helix chain 'I' and resid 422 through 437 removed outlier: 3.730A pdb=" N VAL I 428 " --> pdb=" O ASP I 424 " (cutoff:3.500A) Processing helix chain 'I' and resid 456 through 480 removed outlier: 3.758A pdb=" N ALA I 474 " --> pdb=" O ARG I 470 " (cutoff:3.500A) Processing helix chain 'I' and resid 496 through 507 removed outlier: 4.281A pdb=" N ALA I 501 " --> pdb=" O PRO I 497 " (cutoff:3.500A) removed outlier: 4.106A pdb=" N VAL I 502 " --> pdb=" O ILE I 498 " (cutoff:3.500A) Processing helix chain 'I' and resid 520 through 527 Processing helix chain 'I' and resid 552 through 554 No H-bonds generated for 'chain 'I' and resid 552 through 554' 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: 3.938A pdb=" N GLN I 688 " --> pdb=" O ASN I 684 " (cutoff:3.500A) Processing helix chain 'I' and resid 705 through 711 Processing helix chain 'I' and resid 738 through 740 No H-bonds generated for 'chain 'I' and resid 738 through 740' 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: 3.557A pdb=" N VAL I 980 " --> pdb=" O ARG I 976 " (cutoff:3.500A) Processing helix chain 'I' and resid 994 through 997 Processing helix chain 'I' and resid 1006 through 1037 Processing helix chain 'I' and resid 1082 through 1084 No H-bonds generated for 'chain 'I' and resid 1082 through 1084' Processing helix chain 'I' and resid 1100 through 1105 Proline residue: I1104 - end of helix Processing helix chain 'I' and resid 1110 through 1133 Processing helix chain 'I' and resid 1138 through 1148 Processing helix chain 'I' and resid 1161 through 1163 No H-bonds generated for 'chain 'I' and resid 1161 through 1163' Processing helix chain 'I' and resid 1166 through 1175 removed outlier: 3.629A pdb=" N MET I1170 " --> pdb=" O ASP I1166 " (cutoff:3.500A) Processing helix chain 'I' and resid 1192 through 1201 Processing helix chain 'I' and resid 1272 through 1280 Processing helix chain 'I' and resid 1284 through 1291 Processing helix chain 'I' and resid 1298 through 1310 removed outlier: 4.088A pdb=" N THR I1302 " --> pdb=" O VAL I1298 " (cutoff:3.500A) removed outlier: 3.760A pdb=" N LYS I1303 " --> pdb=" O ASN I1299 " (cutoff:3.500A) Processing helix chain 'I' and resid 1321 through 1331 Processing helix chain 'J' and resid 27 through 33 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 97 through 99 No H-bonds generated for 'chain 'J' and resid 97 through 99' Processing helix chain 'J' and resid 114 through 118 removed outlier: 4.186A pdb=" N LYS J 118 " --> pdb=" O TRP J 115 " (cutoff:3.500A) Processing helix chain 'J' and resid 123 through 128 Processing helix chain 'J' and resid 132 through 139 Processing helix chain 'J' and resid 162 through 169 Processing helix chain 'J' and resid 182 through 190 Processing helix chain 'J' and resid 194 through 206 Processing helix chain 'J' and resid 211 through 229 removed outlier: 3.967A pdb=" N LEU J 223 " --> pdb=" O LYS J 219 " (cutoff:3.500A) Processing helix chain 'J' and resid 234 through 237 removed outlier: 3.751A 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 247 through 249 No H-bonds generated for 'chain 'J' and resid 247 through 249' Processing helix chain 'J' and resid 264 through 285 Processing helix chain 'J' and resid 289 through 307 Processing helix chain 'J' and resid 327 through 331 Processing helix chain 'J' and resid 337 through 340 No H-bonds generated for 'chain 'J' and resid 337 through 340' 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 407 through 415 Processing helix chain 'J' and resid 431 through 433 No H-bonds generated for 'chain 'J' and resid 431 through 433' Processing helix chain 'J' and resid 451 through 457 removed outlier: 4.623A pdb=" N ALA J 455 " --> pdb=" O LEU J 452 " (cutoff:3.500A) Processing helix chain 'J' and resid 474 through 482 Processing helix chain 'J' and resid 505 through 513 Processing helix chain 'J' and resid 530 through 538 Processing helix chain 'J' and resid 574 through 582 removed outlier: 3.573A pdb=" N MET J 581 " --> pdb=" O ALA J 577 " (cutoff:3.500A) removed outlier: 4.685A pdb=" N ILE J 582 " --> pdb=" O ILE J 578 " (cutoff:3.500A) Processing helix chain 'J' and resid 598 through 612 Processing helix chain 'J' and resid 615 through 635 Processing helix chain 'J' and resid 648 through 669 removed outlier: 4.285A pdb=" N HIS J 651 " --> pdb=" O GLU J 648 " (cutoff:3.500A) removed outlier: 4.087A pdb=" N GLU J 652 " --> pdb=" O LYS J 649 " (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 789 removed outlier: 3.659A pdb=" N THR J 776 " --> pdb=" O TYR J 772 " (cutoff:3.500A) removed outlier: 3.868A pdb=" N HIS J 777 " --> pdb=" O PHE J 773 " (cutoff:3.500A) removed outlier: 4.421A pdb=" N GLY J 778 " --> pdb=" O ILE J 774 " (cutoff:3.500A) Processing helix chain 'J' and resid 795 through 803 removed outlier: 3.797A pdb=" N VAL J 803 " --> pdb=" O ARG J 799 " (cutoff:3.500A) Processing helix chain 'J' and resid 835 through 839 Processing helix chain 'J' and resid 866 through 875 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 896 through 899 No H-bonds generated for 'chain 'J' and resid 896 through 899' Processing helix chain 'J' and resid 915 through 929 Proline residue: J 926 - end of helix removed outlier: 4.051A pdb=" N GLN J 929 " --> pdb=" O GLU J 925 " (cutoff:3.500A) Processing helix chain 'J' and resid 1137 through 1146 removed outlier: 3.610A pdb=" N VAL J1141 " --> pdb=" O GLY J1137 " (cutoff:3.500A) Processing helix chain 'J' and resid 1217 through 1223 Processing helix chain 'J' and resid 1226 through 1244 Processing helix chain 'J' and resid 1250 through 1260 Processing helix chain 'J' and resid 1282 through 1294 removed outlier: 3.800A pdb=" N ILE J1287 " --> pdb=" O SER J1283 " (cutoff:3.500A) 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 1347 through 1353 Processing helix chain 'J' and resid 1361 through 1374 removed outlier: 3.712A pdb=" N ALA J1364 " --> pdb=" O THR J1361 " (cutoff:3.500A) Processing helix chain 'K' and resid 7 through 13 Processing helix chain 'K' and resid 16 through 31 removed outlier: 3.741A pdb=" N VAL K 20 " --> pdb=" O ARG K 16 " (cutoff:3.500A) Processing helix chain 'K' and resid 46 through 55 Processing helix chain 'K' and resid 61 through 73 Processing helix chain 'L' and resid 8 through 19 Processing helix chain 'L' and resid 24 through 30 Processing helix chain 'L' and resid 39 through 50 Processing helix chain 'L' and resid 62 through 67 removed outlier: 3.778A pdb=" N MET L 66 " --> pdb=" O ALA L 62 " (cutoff:3.500A) Processing helix chain 'L' and resid 75 through 87 removed outlier: 3.791A pdb=" N SER L 86 " --> pdb=" O GLN L 82 " (cutoff:3.500A) Processing helix chain 'L' and resid 97 through 106 Processing helix chain 'L' and resid 113 through 135 Processing helix chain 'L' and resid 138 through 152 Processing helix chain 'L' and resid 214 through 232 Processing helix chain 'L' and resid 245 through 257 Processing helix chain 'L' and resid 263 through 292 removed outlier: 3.614A pdb=" N LEU L 290 " --> pdb=" O LEU L 286 " (cutoff:3.500A) Processing helix chain 'L' and resid 299 through 309 removed outlier: 3.858A pdb=" N THR L 307 " --> pdb=" O ILE L 303 " (cutoff:3.500A) removed outlier: 6.270A pdb=" N GLY L 308 " --> pdb=" O THR L 304 " (cutoff:3.500A) removed outlier: 4.322A pdb=" N ASN L 309 " --> pdb=" O LEU L 305 " (cutoff:3.500A) Processing helix chain 'L' and resid 325 through 331 removed outlier: 4.329A pdb=" N HIS L 331 " --> pdb=" O SER L 327 " (cutoff:3.500A) Processing helix chain 'L' and resid 334 through 351 Processing helix chain 'L' and resid 355 through 394 removed outlier: 5.130A pdb=" N ARG L 385 " --> pdb=" O GLU L 381 " (cutoff:3.500A) removed outlier: 5.173A pdb=" N LEU L 386 " --> pdb=" O ALA L 382 " (cutoff:3.500A) removed outlier: 4.404A pdb=" N LYS L 393 " --> pdb=" O SER L 389 " (cutoff:3.500A) removed outlier: 4.457A pdb=" N TYR L 394 " --> pdb=" O ILE L 390 " (cutoff:3.500A) Processing helix chain 'L' and resid 401 through 416 Processing helix chain 'L' and resid 427 through 446 removed outlier: 4.710A pdb=" N TRP L 433 " --> pdb=" O THR L 429 " (cutoff:3.500A) removed outlier: 3.978A pdb=" N TRP L 434 " --> pdb=" O TYR L 430 " (cutoff:3.500A) Processing helix chain 'L' and resid 454 through 474 removed outlier: 4.037A pdb=" N GLN L 472 " --> pdb=" O ARG L 468 " (cutoff:3.500A) Processing helix chain 'L' and resid 480 through 486 Processing helix chain 'L' and resid 493 through 499 Processing helix chain 'L' and resid 519 through 522 Processing helix chain 'L' and resid 531 through 550 removed outlier: 4.257A pdb=" N GLY L 550 " --> pdb=" O ASP L 546 " (cutoff:3.500A) Processing helix chain 'L' and resid 553 through 562 Processing helix chain 'L' and resid 573 through 580 removed outlier: 3.846A pdb=" N GLN L 579 " --> pdb=" O GLU L 575 " (cutoff:3.500A) Processing helix chain 'L' and resid 585 through 598 Processing helix chain 'L' and resid 605 through 610 Processing sheet with id= A, first strand: chain 'G' and resid 183 through 189 removed outlier: 4.206A pdb=" N ASP G 15 " --> pdb=" O THR G 27 " (cutoff:3.500A) Processing sheet with id= B, first strand: chain 'G' and resid 170 through 172 removed outlier: 6.714A pdb=" N LYS G 145 " --> pdb=" O THR G 57 " (cutoff:3.500A) removed outlier: 4.606A pdb=" N VAL G 59 " --> pdb=" O ARG G 143 " (cutoff:3.500A) removed outlier: 6.476A pdb=" N ARG G 143 " --> pdb=" O VAL G 59 " (cutoff:3.500A) Processing sheet with id= C, first strand: chain 'G' and resid 90 through 92 Processing sheet with id= D, first strand: chain 'G' and resid 151 through 153 Processing sheet with id= E, first strand: chain 'G' and resid 108 through 111 Processing sheet with id= F, first strand: chain 'H' and resid 14 through 18 removed outlier: 3.617A pdb=" N ALA H 190 " --> pdb=" O LEU H 198 " (cutoff:3.500A) Processing sheet with id= G, first strand: chain 'H' and resid 90 through 92 Processing sheet with id= H, first strand: chain 'H' and resid 53 through 60 removed outlier: 6.699A pdb=" N LYS H 145 " --> pdb=" O THR H 57 " (cutoff:3.500A) removed outlier: 4.412A pdb=" N VAL H 59 " --> pdb=" O ARG H 143 " (cutoff:3.500A) removed outlier: 6.615A pdb=" N ARG H 143 " --> pdb=" O VAL H 59 " (cutoff:3.500A) removed outlier: 4.227A pdb=" N ASP H 135 " --> pdb=" O GLY H 106 " (cutoff:3.500A) removed outlier: 4.187A pdb=" N GLY H 106 " --> pdb=" O ASP H 135 " (cutoff:3.500A) removed outlier: 8.969A pdb=" N ASN H 137 " --> pdb=" O LYS H 104 " (cutoff:3.500A) removed outlier: 9.684A pdb=" N LYS H 104 " --> pdb=" O ASN H 137 " (cutoff:3.500A) removed outlier: 10.091A pdb=" N SER H 139 " --> pdb=" O LEU H 102 " (cutoff:3.500A) removed outlier: 11.178A pdb=" N LEU H 102 " --> pdb=" O SER H 139 " (cutoff:3.500A) removed outlier: 10.137A pdb=" N SER H 141 " --> pdb=" O LEU H 100 " (cutoff:3.500A) removed outlier: 11.484A pdb=" N LEU H 100 " --> pdb=" O SER H 141 " (cutoff:3.500A) removed outlier: 9.860A pdb=" N ARG H 143 " --> pdb=" O VAL H 98 " (cutoff:3.500A) removed outlier: 10.739A pdb=" N VAL H 98 " --> pdb=" O ARG H 143 " (cutoff:3.500A) Processing sheet with id= I, first strand: chain 'H' and resid 180 through 184 removed outlier: 6.752A pdb=" N GLU H 206 " --> pdb=" O GLU H 181 " (cutoff:3.500A) removed outlier: 4.566A pdb=" N ILE H 183 " --> pdb=" O GLU H 204 " (cutoff:3.500A) removed outlier: 6.840A pdb=" N GLU H 204 " --> pdb=" O ILE H 183 " (cutoff:3.500A) Processing sheet with id= J, first strand: chain 'I' and resid 93 through 95 Processing sheet with id= K, first strand: chain 'I' and resid 143 through 145 Processing sheet with id= L, first strand: chain 'I' and resid 148 through 151 Processing sheet with id= M, first strand: chain 'I' and resid 154 through 159 removed outlier: 5.568A pdb=" N TYR I 172 " --> pdb=" O PHE I 188 " (cutoff:3.500A) removed outlier: 3.804A pdb=" N LEU I 184 " --> pdb=" O ILE I 176 " (cutoff:3.500A) Processing sheet with id= N, first strand: chain 'I' and resid 227 through 230 Processing sheet with id= O, first strand: chain 'I' and resid 238 through 240 Processing sheet with id= P, first strand: chain 'I' and resid 529 through 531 Processing sheet with id= Q, first strand: chain 'I' and resid 603 through 607 Processing sheet with id= R, first strand: chain 'I' and resid 633 through 637 Processing sheet with id= S, first strand: chain 'I' and resid 748 through 752 removed outlier: 6.426A pdb=" N LYS I 735 " --> pdb=" O VAL I 724 " (cutoff:3.500A) removed outlier: 5.645A pdb=" N VAL I 724 " --> pdb=" O LYS I 735 " (cutoff:3.500A) Processing sheet with id= T, first strand: chain 'I' and resid 1226 through 1232 removed outlier: 4.299A pdb=" N THR I1226 " --> pdb=" O PHE I 804 " (cutoff:3.500A) removed outlier: 6.460A pdb=" N ILE I1096 " --> pdb=" O ALA I 803 " (cutoff:3.500A) Processing sheet with id= U, first strand: chain 'I' and resid 66 through 75 removed outlier: 6.782A pdb=" N LYS I 99 " --> pdb=" O VAL I 71 " (cutoff:3.500A) removed outlier: 4.610A pdb=" N TYR I 73 " --> pdb=" O ARG I 97 " (cutoff:3.500A) removed outlier: 6.870A pdb=" N ARG I 97 " --> pdb=" O TYR I 73 " (cutoff:3.500A) removed outlier: 3.875A pdb=" N ASP I 116 " --> pdb=" O ILE I 104 " (cutoff:3.500A) Processing sheet with id= V, first strand: chain 'I' and resid 301 through 303 removed outlier: 5.867A pdb=" N ASP I 303 " --> pdb=" O LEU I 309 " (cutoff:3.500A) removed outlier: 5.764A pdb=" N LEU I 309 " --> pdb=" O ASP I 303 " (cutoff:3.500A) Processing sheet with id= W, first strand: chain 'I' and resid 815 through 819 removed outlier: 5.997A pdb=" N VAL I1075 " --> pdb=" O ILE I 816 " (cutoff:3.500A) removed outlier: 7.426A pdb=" N VAL I 818 " --> pdb=" O VAL I1075 " (cutoff:3.500A) removed outlier: 7.294A pdb=" N SER I1077 " --> pdb=" O VAL I 818 " (cutoff:3.500A) No H-bonds generated for sheet with id= W Processing sheet with id= X, first strand: chain 'I' and resid 830 through 841 removed outlier: 3.889A pdb=" N ASP I 930 " --> pdb=" O TYR I1053 " (cutoff:3.500A) removed outlier: 6.677A pdb=" N ALA I1055 " --> pdb=" O VAL I 928 " (cutoff:3.500A) removed outlier: 5.650A pdb=" N VAL I 928 " --> pdb=" O ALA I1055 " (cutoff:3.500A) Processing sheet with id= Y, first strand: chain 'J' and resid 19 through 21 Processing sheet with id= Z, first strand: chain 'J' and resid 103 through 106 Processing sheet with id= AA, first strand: chain 'J' and resid 252 through 255 removed outlier: 3.611A pdb=" N ARG J 259 " --> pdb=" O LEU J 255 " (cutoff:3.500A) Processing sheet with id= AB, first strand: chain 'J' and resid 446 through 448 removed outlier: 7.507A pdb=" N ILE J 447 " --> pdb=" O ARG J 352 " (cutoff:3.500A) removed outlier: 6.024A pdb=" N VAL J 354 " --> pdb=" O ILE J 447 " (cutoff:3.500A) Processing sheet with id= AC, first strand: chain 'J' and resid 548 through 556 Processing sheet with id= AD, first strand: chain 'J' and resid 703 through 706 Processing sheet with id= AE, first strand: chain 'J' and resid 820 through 823 Processing sheet with id= AF, first strand: chain 'J' and resid 1162 through 1165 Processing sheet with id= AG, first strand: chain 'J' and resid 1279 through 1281 removed outlier: 6.554A pdb=" N THR J1301 " --> pdb=" O VAL J1267 " (cutoff:3.500A) 1095 hydrogen bonds defined for protein. 3129 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 108 hydrogen bonds 216 hydrogen bond angles 0 basepair planarities 44 basepair parallelities 84 stacking parallelities Total time for adding SS restraints: 14.14 Time building geometry restraints manager: 14.48 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 9210 1.33 - 1.45: 6013 1.45 - 1.58: 16446 1.58 - 1.70: 217 1.70 - 1.82: 247 Bond restraints: 32133 Sorted by residual: bond pdb=" C19 1N7 J1505 " pdb=" C3 1N7 J1505 " ideal model delta sigma weight residual 1.532 1.823 -0.291 2.00e-02 2.50e+03 2.12e+02 bond pdb=" C19 1N7 I1401 " pdb=" C3 1N7 I1401 " ideal model delta sigma weight residual 1.532 1.821 -0.289 2.00e-02 2.50e+03 2.08e+02 bond pdb=" C19 1N7 N 102 " pdb=" C3 1N7 N 102 " ideal model delta sigma weight residual 1.532 1.820 -0.288 2.00e-02 2.50e+03 2.08e+02 bond pdb=" C19 1N7 J1504 " pdb=" C3 1N7 J1504 " ideal model delta sigma weight residual 1.532 1.819 -0.287 2.00e-02 2.50e+03 2.06e+02 bond pdb=" C3 1N7 N 102 " pdb=" C4 1N7 N 102 " ideal model delta sigma weight residual 1.532 1.722 -0.190 2.00e-02 2.50e+03 8.99e+01 ... (remaining 32128 not shown) Histogram of bond angle deviations from ideal: 96.82 - 104.27: 817 104.27 - 111.71: 15687 111.71 - 119.16: 11092 119.16 - 126.60: 15688 126.60 - 134.05: 566 Bond angle restraints: 43850 Sorted by residual: angle pdb=" C THR L 569 " pdb=" N ASP L 570 " pdb=" CA ASP L 570 " ideal model delta sigma weight residual 121.70 133.63 -11.93 1.80e+00 3.09e-01 4.39e+01 angle pdb=" C GLU H 7 " pdb=" N PHE H 8 " pdb=" CA PHE H 8 " ideal model delta sigma weight residual 121.90 114.21 7.69 1.26e+00 6.30e-01 3.73e+01 angle pdb=" C ILE J 707 " pdb=" N ASN J 708 " pdb=" CA ASN J 708 " ideal model delta sigma weight residual 121.70 131.66 -9.96 1.80e+00 3.09e-01 3.06e+01 angle pdb=" C GLY I 544 " pdb=" N PHE I 545 " pdb=" CA PHE I 545 " ideal model delta sigma weight residual 121.70 130.49 -8.79 1.80e+00 3.09e-01 2.39e+01 angle pdb=" C ASP J 174 " pdb=" N GLU J 175 " pdb=" CA GLU J 175 " ideal model delta sigma weight residual 121.19 127.70 -6.51 1.59e+00 3.96e-01 1.68e+01 ... (remaining 43845 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.39: 18628 35.39 - 70.78: 1115 70.78 - 106.17: 23 106.17 - 141.56: 1 141.56 - 176.95: 8 Dihedral angle restraints: 19775 sinusoidal: 9026 harmonic: 10749 Sorted by residual: dihedral pdb=" CA ILE J 707 " pdb=" C ILE J 707 " pdb=" N ASN J 708 " pdb=" CA ASN J 708 " ideal model delta harmonic sigma weight residual 0.00 -41.00 41.00 0 5.00e+00 4.00e-02 6.72e+01 dihedral pdb=" CA ASP I 254 " pdb=" C ASP I 254 " pdb=" N ILE I 255 " pdb=" CA ILE I 255 " ideal model delta harmonic sigma weight residual 180.00 146.09 33.91 0 5.00e+00 4.00e-02 4.60e+01 dihedral pdb=" CA GLU J1343 " pdb=" C GLU J1343 " pdb=" N LEU J1344 " pdb=" CA LEU J1344 " ideal model delta harmonic sigma weight residual -180.00 -147.07 -32.93 0 5.00e+00 4.00e-02 4.34e+01 ... (remaining 19772 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.066: 4208 0.066 - 0.133: 759 0.133 - 0.199: 53 0.199 - 0.265: 9 0.265 - 0.332: 2 Chirality restraints: 5031 Sorted by residual: chirality pdb=" C19 1N7 J1505 " pdb=" C18 1N7 J1505 " pdb=" C2 1N7 J1505 " pdb=" C3 1N7 J1505 " both_signs ideal model delta sigma weight residual False -2.53 -2.87 0.33 2.00e-01 2.50e+01 2.75e+00 chirality pdb=" C19 1N7 N 102 " pdb=" C18 1N7 N 102 " pdb=" C2 1N7 N 102 " pdb=" C3 1N7 N 102 " both_signs ideal model delta sigma weight residual False -2.53 -2.84 0.30 2.00e-01 2.50e+01 2.32e+00 chirality pdb=" CB ILE L 505 " pdb=" CA ILE L 505 " pdb=" CG1 ILE L 505 " pdb=" CG2 ILE L 505 " both_signs ideal model delta sigma weight residual False 2.64 2.39 0.25 2.00e-01 2.50e+01 1.58e+00 ... (remaining 5028 not shown) Planarity restraints: 5353 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA LEU H 79 " -0.018 2.00e-02 2.50e+03 3.49e-02 1.22e+01 pdb=" C LEU H 79 " 0.060 2.00e-02 2.50e+03 pdb=" O LEU H 79 " -0.023 2.00e-02 2.50e+03 pdb=" N GLU H 80 " -0.020 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C ARG I1223 " 0.050 5.00e-02 4.00e+02 7.61e-02 9.27e+00 pdb=" N PRO I1224 " -0.132 5.00e-02 4.00e+02 pdb=" CA PRO I1224 " 0.041 5.00e-02 4.00e+02 pdb=" CD PRO I1224 " 0.041 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA GLU I 898 " -0.014 2.00e-02 2.50e+03 2.77e-02 7.68e+00 pdb=" C GLU I 898 " 0.048 2.00e-02 2.50e+03 pdb=" O GLU I 898 " -0.018 2.00e-02 2.50e+03 pdb=" N GLU I 899 " -0.016 2.00e-02 2.50e+03 ... (remaining 5350 not shown) Histogram of nonbonded interaction distances: 1.78 - 2.40: 186 2.40 - 3.03: 20470 3.03 - 3.65: 47809 3.65 - 4.28: 75803 4.28 - 4.90: 122943 Nonbonded interactions: 267211 Sorted by model distance: nonbonded pdb=" CD2 LEU I 237 " pdb=" O PRO I 288 " model vdw 1.777 3.460 nonbonded pdb=" CD1 LEU I 237 " pdb=" CD1 ILE I 292 " model vdw 1.820 3.880 nonbonded pdb=" OD1 ASP J 464 " pdb="MG MG J1501 " model vdw 2.010 2.170 nonbonded pdb=" O ARG L 436 " pdb=" OG1 THR L 440 " model vdw 2.029 2.440 nonbonded pdb=" O ILE J 918 " pdb=" OG SER J 922 " model vdw 2.043 2.440 ... (remaining 267206 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = (chain 'G' and (resid 5 through 61 or (resid 62 and (name N or name CA or name C \ or name O or name CB )) or resid 63 through 158 or resid 171 through 233)) selection = (chain 'H' and (resid 5 through 190 or (resid 191 and (name N or name CA or name \ C or name O or name CB )) or resid 192 through 228 or (resid 229 through 230 an \ d (name N or name CA or name C or name O or name CB )) or resid 231 through 233) \ ) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.720 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.030 Extract box with map and model: 5.530 Check model and map are aligned: 0.410 Set scattering table: 0.240 Process input model: 99.100 Find NCS groups from input model: 1.160 Set up NCS constraints: 0.110 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:12.130 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 119.440 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7913 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 : 0.011 0.291 32133 Z= 0.720 Angle : 0.915 11.928 43850 Z= 0.518 Chirality : 0.050 0.332 5031 Planarity : 0.005 0.076 5353 Dihedral : 19.327 176.954 12837 Min Nonbonded Distance : 1.777 Molprobity Statistics. All-atom Clashscore : 36.23 Ramachandran Plot: Outliers : 0.30 % Allowed : 8.03 % Favored : 91.67 % Rotamer: Outliers : 13.13 % Allowed : 13.38 % Favored : 73.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.37 % Cis-general : 0.25 % Twisted Proline : 0.68 % Twisted General : 0.17 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.42 (0.12), residues: 3698 helix: -1.75 (0.11), residues: 1565 sheet: -2.27 (0.23), residues: 394 loop : -2.73 (0.13), residues: 1739 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.003 TRP I 807 HIS 0.010 0.002 HIS I 551 PHE 0.027 0.003 PHE I 586 TYR 0.024 0.003 TYR I1087 ARG 0.009 0.001 ARG I1246 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7396 Ramachandran restraints generated. 3698 Oldfield, 0 Emsley, 3698 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7396 Ramachandran restraints generated. 3698 Oldfield, 0 Emsley, 3698 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 979 residues out of total 3197 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 417 poor density : 562 time to evaluate : 3.447 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: N 70 LYS cc_start: 0.8550 (tttt) cc_final: 0.8287 (tttp) REVERT: N 72 TYR cc_start: 0.7685 (OUTLIER) cc_final: 0.6697 (t80) REVERT: M 294 ASN cc_start: 0.5760 (m-40) cc_final: 0.5223 (p0) REVERT: G 7 GLU cc_start: 0.6830 (OUTLIER) cc_final: 0.6137 (mm-30) REVERT: G 76 GLU cc_start: 0.8327 (OUTLIER) cc_final: 0.7783 (mt-10) REVERT: G 93 GLN cc_start: 0.8312 (tp40) cc_final: 0.8033 (tp-100) REVERT: G 125 LYS cc_start: 0.7992 (tttt) cc_final: 0.7771 (tppp) REVERT: G 231 PHE cc_start: 0.7524 (OUTLIER) cc_final: 0.6809 (t80) REVERT: H 12 ARG cc_start: 0.7650 (OUTLIER) cc_final: 0.6529 (ptp-170) REVERT: I 60 GLN cc_start: 0.7000 (OUTLIER) cc_final: 0.6692 (pt0) REVERT: I 65 ASN cc_start: 0.6339 (OUTLIER) cc_final: 0.5732 (p0) REVERT: I 203 LYS cc_start: 0.8181 (OUTLIER) cc_final: 0.7807 (ttmt) REVERT: I 314 ASN cc_start: 0.8291 (t0) cc_final: 0.7954 (t0) REVERT: I 483 ASP cc_start: 0.4284 (OUTLIER) cc_final: 0.3940 (m-30) REVERT: I 484 LEU cc_start: 0.8036 (OUTLIER) cc_final: 0.7775 (pp) REVERT: I 623 LEU cc_start: 0.8381 (OUTLIER) cc_final: 0.7886 (mt) REVERT: I 631 GLU cc_start: 0.7317 (OUTLIER) cc_final: 0.6802 (pm20) REVERT: I 764 CYS cc_start: 0.8156 (OUTLIER) cc_final: 0.7938 (p) REVERT: I 796 LEU cc_start: 0.9090 (OUTLIER) cc_final: 0.8835 (mp) REVERT: I 1296 ASP cc_start: 0.7890 (OUTLIER) cc_final: 0.7644 (t70) REVERT: J 126 LEU cc_start: 0.9113 (OUTLIER) cc_final: 0.8706 (pp) REVERT: J 169 LEU cc_start: 0.7213 (OUTLIER) cc_final: 0.6958 (tt) REVERT: J 180 MET cc_start: 0.8190 (ptm) cc_final: 0.7909 (ptm) REVERT: J 195 GLU cc_start: 0.7998 (OUTLIER) cc_final: 0.7793 (mp0) REVERT: J 227 PHE cc_start: 0.8915 (OUTLIER) cc_final: 0.7985 (t80) REVERT: J 256 ASP cc_start: 0.6683 (m-30) cc_final: 0.6098 (p0) REVERT: J 304 ASP cc_start: 0.7330 (t70) cc_final: 0.7095 (t0) REVERT: J 545 HIS cc_start: 0.8722 (OUTLIER) cc_final: 0.7963 (p-80) REVERT: J 594 GLN cc_start: 0.9127 (OUTLIER) cc_final: 0.8203 (pp30) REVERT: J 664 ILE cc_start: 0.9241 (OUTLIER) cc_final: 0.9006 (tp) REVERT: J 709 ARG cc_start: 0.7398 (OUTLIER) cc_final: 0.6794 (mtp180) REVERT: J 1222 ARG cc_start: 0.8065 (ttp80) cc_final: 0.7684 (mtm110) REVERT: J 1355 ARG cc_start: 0.8572 (OUTLIER) cc_final: 0.7847 (ptm-80) REVERT: L 56 MET cc_start: 0.7343 (mtm) cc_final: 0.6942 (mtp) REVERT: L 93 ARG cc_start: 0.6655 (OUTLIER) cc_final: 0.6264 (mmm160) REVERT: L 127 ILE cc_start: 0.7960 (OUTLIER) cc_final: 0.7664 (pp) REVERT: L 221 PHE cc_start: 0.3711 (m-80) cc_final: 0.3429 (m-80) REVERT: L 277 MET cc_start: 0.5903 (tpt) cc_final: 0.5572 (tpt) REVERT: L 300 LYS cc_start: 0.5028 (ttpt) cc_final: 0.4608 (tptp) outliers start: 417 outliers final: 229 residues processed: 914 average time/residue: 1.4597 time to fit residues: 1566.8490 Evaluate side-chains 645 residues out of total 3197 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 255 poor density : 390 time to evaluate : 3.363 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain N residue 27 ILE Chi-restraints excluded: chain N residue 59 VAL Chi-restraints excluded: chain N residue 72 TYR Chi-restraints excluded: chain G residue 7 GLU Chi-restraints excluded: chain G residue 26 VAL Chi-restraints excluded: chain G residue 50 SER Chi-restraints excluded: chain G residue 56 VAL Chi-restraints excluded: chain G residue 74 VAL Chi-restraints excluded: chain G residue 76 GLU Chi-restraints excluded: chain G residue 79 LEU Chi-restraints excluded: chain G residue 92 VAL Chi-restraints excluded: chain G residue 99 ILE Chi-restraints excluded: chain G residue 102 LEU Chi-restraints excluded: chain G residue 118 ASP Chi-restraints excluded: chain G residue 129 VAL Chi-restraints excluded: chain G residue 142 MET Chi-restraints excluded: chain G residue 150 ARG Chi-restraints excluded: chain G residue 156 SER Chi-restraints excluded: chain G residue 157 THR Chi-restraints excluded: chain G residue 160 HIS Chi-restraints excluded: chain G residue 171 LEU Chi-restraints excluded: chain G residue 173 VAL Chi-restraints excluded: chain G residue 176 CYS Chi-restraints excluded: chain G residue 178 SER Chi-restraints excluded: chain G residue 186 ASN Chi-restraints excluded: chain G residue 187 VAL Chi-restraints excluded: chain G residue 199 ASP Chi-restraints excluded: chain G residue 203 ILE Chi-restraints excluded: chain G residue 210 THR Chi-restraints excluded: chain G residue 211 ILE Chi-restraints excluded: chain G residue 224 LEU Chi-restraints excluded: chain G residue 231 PHE Chi-restraints excluded: chain H residue 12 ARG Chi-restraints excluded: chain H residue 14 VAL Chi-restraints excluded: chain H residue 19 VAL Chi-restraints excluded: chain H residue 20 SER Chi-restraints excluded: chain H residue 38 THR Chi-restraints excluded: chain H residue 43 LEU Chi-restraints excluded: chain H residue 65 LEU Chi-restraints excluded: chain H residue 70 THR Chi-restraints excluded: chain H residue 79 LEU Chi-restraints excluded: chain H residue 98 VAL Chi-restraints excluded: chain H residue 99 ILE Chi-restraints excluded: chain H residue 124 VAL Chi-restraints excluded: chain H residue 144 ILE Chi-restraints excluded: chain H residue 156 SER Chi-restraints excluded: chain H residue 173 VAL Chi-restraints excluded: chain H residue 176 CYS Chi-restraints excluded: chain H residue 188 GLU Chi-restraints excluded: chain H residue 198 LEU Chi-restraints excluded: chain H residue 202 VAL Chi-restraints excluded: chain H residue 218 ARG Chi-restraints excluded: chain I residue 7 GLU Chi-restraints excluded: chain I residue 30 ILE Chi-restraints excluded: chain I residue 56 VAL Chi-restraints excluded: chain I residue 60 GLN Chi-restraints excluded: chain I residue 65 ASN Chi-restraints excluded: chain I residue 79 VAL Chi-restraints excluded: chain I residue 82 VAL Chi-restraints excluded: chain I residue 104 ILE Chi-restraints excluded: chain I residue 117 ILE Chi-restraints excluded: chain I residue 129 LEU Chi-restraints excluded: chain I residue 138 ILE Chi-restraints excluded: chain I residue 155 VAL Chi-restraints excluded: chain I residue 203 LYS Chi-restraints excluded: chain I residue 204 LEU Chi-restraints excluded: chain I residue 208 ILE Chi-restraints excluded: chain I residue 216 THR Chi-restraints excluded: chain I residue 228 VAL Chi-restraints excluded: chain I residue 263 VAL Chi-restraints excluded: chain I residue 270 THR Chi-restraints excluded: chain I residue 335 THR Chi-restraints excluded: chain I residue 350 THR Chi-restraints excluded: chain I residue 398 SER Chi-restraints excluded: chain I residue 450 ASN Chi-restraints excluded: chain I residue 456 VAL Chi-restraints excluded: chain I residue 468 LEU Chi-restraints excluded: chain I residue 469 VAL Chi-restraints excluded: chain I residue 471 VAL Chi-restraints excluded: chain I residue 472 GLU Chi-restraints excluded: chain I residue 483 ASP Chi-restraints excluded: chain I residue 484 LEU Chi-restraints excluded: chain I residue 513 GLN Chi-restraints excluded: chain I residue 522 SER Chi-restraints excluded: chain I residue 524 ILE Chi-restraints excluded: chain I residue 573 ASN Chi-restraints excluded: chain I residue 589 THR Chi-restraints excluded: chain I residue 592 ARG Chi-restraints excluded: chain I residue 596 ASP Chi-restraints excluded: chain I residue 609 ILE Chi-restraints excluded: chain I residue 615 VAL Chi-restraints excluded: chain I residue 618 GLN Chi-restraints excluded: chain I residue 623 LEU Chi-restraints excluded: chain I residue 630 VAL Chi-restraints excluded: chain I residue 631 GLU Chi-restraints excluded: chain I residue 639 LYS Chi-restraints excluded: chain I residue 655 VAL Chi-restraints excluded: chain I residue 656 SER Chi-restraints excluded: chain I residue 663 VAL Chi-restraints excluded: chain I residue 672 GLU Chi-restraints excluded: chain I residue 690 VAL Chi-restraints excluded: chain I residue 734 ILE Chi-restraints excluded: chain I residue 748 ILE Chi-restraints excluded: chain I residue 764 CYS Chi-restraints excluded: chain I residue 796 LEU Chi-restraints excluded: chain I residue 799 ASN Chi-restraints excluded: chain I residue 802 VAL Chi-restraints excluded: chain I residue 817 LEU Chi-restraints excluded: chain I residue 823 VAL Chi-restraints excluded: chain I residue 833 ILE Chi-restraints excluded: chain I residue 839 VAL Chi-restraints excluded: chain I residue 845 LEU Chi-restraints excluded: chain I residue 848 GLU Chi-restraints excluded: chain I residue 882 ILE Chi-restraints excluded: chain I residue 895 LEU Chi-restraints excluded: chain I residue 909 LYS Chi-restraints excluded: chain I residue 912 ASP Chi-restraints excluded: chain I residue 924 VAL Chi-restraints excluded: chain I residue 933 VAL Chi-restraints excluded: chain I residue 937 ASP Chi-restraints excluded: chain I residue 953 LEU Chi-restraints excluded: chain I residue 957 LYS Chi-restraints excluded: chain I residue 963 GLU Chi-restraints excluded: chain I residue 968 GLU Chi-restraints excluded: chain I residue 984 VAL Chi-restraints excluded: chain I residue 1037 THR Chi-restraints excluded: chain I residue 1046 VAL Chi-restraints excluded: chain I residue 1060 ILE Chi-restraints excluded: chain I residue 1072 ASN Chi-restraints excluded: chain I residue 1082 ILE Chi-restraints excluded: chain I residue 1085 MET Chi-restraints excluded: chain I residue 1092 THR Chi-restraints excluded: chain I residue 1109 ILE Chi-restraints excluded: chain I residue 1117 LEU Chi-restraints excluded: chain I residue 1133 LYS Chi-restraints excluded: chain I residue 1163 THR Chi-restraints excluded: chain I residue 1164 PHE Chi-restraints excluded: chain I residue 1172 LEU Chi-restraints excluded: chain I residue 1182 ILE Chi-restraints excluded: chain I residue 1206 THR Chi-restraints excluded: chain I residue 1222 GLU Chi-restraints excluded: chain I residue 1225 VAL Chi-restraints excluded: chain I residue 1290 MET Chi-restraints excluded: chain I residue 1293 VAL Chi-restraints excluded: chain I residue 1296 ASP Chi-restraints excluded: chain I residue 1302 THR Chi-restraints excluded: chain I residue 1309 VAL Chi-restraints excluded: chain I residue 1325 VAL Chi-restraints excluded: chain I residue 1336 ASN Chi-restraints excluded: chain J residue 22 ILE Chi-restraints excluded: chain J residue 46 TYR Chi-restraints excluded: chain J residue 70 CYS Chi-restraints excluded: chain J residue 92 VAL Chi-restraints excluded: chain J residue 93 THR Chi-restraints excluded: chain J residue 94 GLN Chi-restraints excluded: chain J residue 96 LYS Chi-restraints excluded: chain J residue 105 ILE Chi-restraints excluded: chain J residue 120 LEU Chi-restraints excluded: chain J residue 126 LEU Chi-restraints excluded: chain J residue 151 MET Chi-restraints excluded: chain J residue 159 ILE Chi-restraints excluded: chain J residue 169 LEU Chi-restraints excluded: chain J residue 170 GLU Chi-restraints excluded: chain J residue 195 GLU Chi-restraints excluded: chain J residue 212 THR Chi-restraints excluded: chain J residue 218 THR Chi-restraints excluded: chain J residue 227 PHE Chi-restraints excluded: chain J residue 237 MET Chi-restraints excluded: chain J residue 279 LEU Chi-restraints excluded: chain J residue 357 VAL Chi-restraints excluded: chain J residue 393 THR Chi-restraints excluded: chain J residue 401 VAL Chi-restraints excluded: chain J residue 408 VAL Chi-restraints excluded: chain J residue 412 LEU Chi-restraints excluded: chain J residue 416 ILE Chi-restraints excluded: chain J residue 429 LEU Chi-restraints excluded: chain J residue 430 HIS Chi-restraints excluded: chain J residue 464 ASP Chi-restraints excluded: chain J residue 468 VAL Chi-restraints excluded: chain J residue 489 ASN Chi-restraints excluded: chain J residue 507 VAL Chi-restraints excluded: chain J residue 527 LEU Chi-restraints excluded: chain J residue 536 LEU Chi-restraints excluded: chain J residue 545 HIS Chi-restraints excluded: chain J residue 554 GLU Chi-restraints excluded: chain J residue 560 ASN Chi-restraints excluded: chain J residue 567 THR Chi-restraints excluded: chain J residue 568 SER Chi-restraints excluded: chain J residue 571 ASP Chi-restraints excluded: chain J residue 594 GLN Chi-restraints excluded: chain J residue 596 LEU Chi-restraints excluded: chain J residue 614 LEU Chi-restraints excluded: chain J residue 624 ILE Chi-restraints excluded: chain J residue 635 SER Chi-restraints excluded: chain J residue 664 ILE Chi-restraints excluded: chain J residue 697 MET Chi-restraints excluded: chain J residue 705 THR Chi-restraints excluded: chain J residue 707 ILE Chi-restraints excluded: chain J residue 709 ARG Chi-restraints excluded: chain J residue 710 ASP Chi-restraints excluded: chain J residue 740 LEU Chi-restraints excluded: chain J residue 774 ILE Chi-restraints excluded: chain J residue 783 LEU Chi-restraints excluded: chain J residue 788 LEU Chi-restraints excluded: chain J residue 792 ASN Chi-restraints excluded: chain J residue 801 VAL Chi-restraints excluded: chain J residue 803 VAL Chi-restraints excluded: chain J residue 810 THR Chi-restraints excluded: chain J residue 820 ILE Chi-restraints excluded: chain J residue 835 LEU Chi-restraints excluded: chain J residue 869 CYS Chi-restraints excluded: chain J residue 885 VAL Chi-restraints excluded: chain J residue 901 ARG Chi-restraints excluded: chain J residue 908 ILE Chi-restraints excluded: chain J residue 922 SER Chi-restraints excluded: chain J residue 934 THR Chi-restraints excluded: chain J residue 1155 ILE Chi-restraints excluded: chain J residue 1244 GLN Chi-restraints excluded: chain J residue 1248 ILE Chi-restraints excluded: chain J residue 1253 ILE Chi-restraints excluded: chain J residue 1255 VAL Chi-restraints excluded: chain J residue 1261 LEU Chi-restraints excluded: chain J residue 1285 VAL Chi-restraints excluded: chain J residue 1286 LYS Chi-restraints excluded: chain J residue 1292 LEU Chi-restraints excluded: chain J residue 1318 SER Chi-restraints excluded: chain J residue 1355 ARG Chi-restraints excluded: chain K residue 10 VAL Chi-restraints excluded: chain K residue 13 ILE Chi-restraints excluded: chain K residue 39 VAL Chi-restraints excluded: chain K residue 59 ILE Chi-restraints excluded: chain L residue 13 VAL Chi-restraints excluded: chain L residue 34 ASP Chi-restraints excluded: chain L residue 49 ASN Chi-restraints excluded: chain L residue 55 VAL Chi-restraints excluded: chain L residue 93 ARG Chi-restraints excluded: chain L residue 95 THR Chi-restraints excluded: chain L residue 98 VAL Chi-restraints excluded: chain L residue 108 VAL Chi-restraints excluded: chain L residue 127 ILE Chi-restraints excluded: chain L residue 134 VAL Chi-restraints excluded: chain L residue 387 VAL Chi-restraints excluded: chain L residue 440 THR Chi-restraints excluded: chain L residue 449 THR Chi-restraints excluded: chain L residue 471 LEU Chi-restraints excluded: chain L residue 473 GLU Chi-restraints excluded: chain L residue 505 ILE Chi-restraints excluded: chain L residue 506 SER Chi-restraints excluded: chain L residue 526 THR Chi-restraints excluded: chain L residue 544 THR Chi-restraints excluded: chain L residue 552 THR Chi-restraints excluded: chain L residue 573 LEU Chi-restraints excluded: chain L residue 587 ILE Chi-restraints excluded: chain L residue 604 SER Chi-restraints excluded: chain L residue 611 LEU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 379 random chunks: chunk 320 optimal weight: 7.9990 chunk 287 optimal weight: 4.9990 chunk 159 optimal weight: 0.8980 chunk 98 optimal weight: 20.0000 chunk 193 optimal weight: 1.9990 chunk 153 optimal weight: 6.9990 chunk 297 optimal weight: 0.9990 chunk 114 optimal weight: 0.7980 chunk 180 optimal weight: 1.9990 chunk 221 optimal weight: 0.5980 chunk 344 optimal weight: 10.0000 overall best weight: 1.0584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: N 21 ASN N 28 ASN N 65 GLN N 68 GLN ** M 268 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** M 320 ASN H 84 ASN H 93 GLN H 227 GLN ** I 314 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 343 HIS ** I 450 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 526 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** I 554 HIS I 620 ASN I 628 HIS I 761 GLN I 811 ASN I 922 ASN I 965 GLN I1116 HIS I1237 HIS J 364 HIS ** J 365 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 450 HIS J 488 ASN J 665 GLN J 680 ASN ** J 875 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J1227 HIS J1244 GLN J1268 ASN ** J1279 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J1350 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J1366 HIS L 30 HIS L 227 GLN L 246 GLN ** L 362 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 446 GLN L 464 ASN L 589 GLN Total number of N/Q/H flips: 33 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7841 moved from start: 0.2335 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.062 32133 Z= 0.211 Angle : 0.658 13.276 43850 Z= 0.342 Chirality : 0.043 0.369 5031 Planarity : 0.005 0.058 5353 Dihedral : 19.018 179.486 5948 Min Nonbonded Distance : 2.054 Molprobity Statistics. All-atom Clashscore : 14.59 Ramachandran Plot: Outliers : 0.16 % Allowed : 5.35 % Favored : 94.48 % Rotamer: Outliers : 9.16 % Allowed : 20.78 % Favored : 70.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.37 % Cis-general : 0.25 % Twisted Proline : 0.00 % Twisted General : 0.06 % 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: -1.93 (0.13), residues: 3698 helix: -0.24 (0.12), residues: 1552 sheet: -1.63 (0.25), residues: 369 loop : -2.16 (0.14), residues: 1777 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP I 807 HIS 0.005 0.001 HIS J1252 PHE 0.015 0.001 PHE L 306 TYR 0.018 0.002 TYR N 35 ARG 0.008 0.001 ARG I 272 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7396 Ramachandran restraints generated. 3698 Oldfield, 0 Emsley, 3698 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7396 Ramachandran restraints generated. 3698 Oldfield, 0 Emsley, 3698 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 744 residues out of total 3197 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 291 poor density : 453 time to evaluate : 3.434 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: N 18 THR cc_start: 0.8940 (t) cc_final: 0.8517 (p) REVERT: N 70 LYS cc_start: 0.8335 (tttt) cc_final: 0.8089 (tmmm) REVERT: N 72 TYR cc_start: 0.7638 (OUTLIER) cc_final: 0.7077 (t80) REVERT: G 147 GLN cc_start: 0.8305 (pt0) cc_final: 0.8047 (pt0) REVERT: G 160 HIS cc_start: 0.6918 (OUTLIER) cc_final: 0.6656 (p90) REVERT: G 231 PHE cc_start: 0.7412 (OUTLIER) cc_final: 0.6720 (t80) REVERT: H 79 LEU cc_start: 0.7862 (OUTLIER) cc_final: 0.7632 (tt) REVERT: H 199 ASP cc_start: 0.7936 (t70) cc_final: 0.7665 (t70) REVERT: I 7 GLU cc_start: 0.6978 (OUTLIER) cc_final: 0.6772 (mm-30) REVERT: I 65 ASN cc_start: 0.6983 (OUTLIER) cc_final: 0.6539 (p0) REVERT: I 161 LYS cc_start: 0.8735 (OUTLIER) cc_final: 0.8424 (ptpt) REVERT: I 309 LEU cc_start: 0.7839 (tp) cc_final: 0.7621 (tp) REVERT: I 319 LEU cc_start: 0.7902 (mp) cc_final: 0.7654 (mp) REVERT: I 820 GLU cc_start: 0.7742 (tt0) cc_final: 0.7492 (tt0) REVERT: I 922 ASN cc_start: 0.6905 (t0) cc_final: 0.6695 (t0) REVERT: I 953 LEU cc_start: 0.8735 (OUTLIER) cc_final: 0.8494 (mt) REVERT: I 1133 LYS cc_start: 0.8148 (OUTLIER) cc_final: 0.7914 (ptmt) REVERT: I 1211 ARG cc_start: 0.7811 (ptt180) cc_final: 0.7590 (ptt90) REVERT: I 1254 VAL cc_start: 0.7743 (OUTLIER) cc_final: 0.7518 (m) REVERT: J 97 VAL cc_start: 0.8613 (OUTLIER) cc_final: 0.8207 (m) REVERT: J 170 GLU cc_start: 0.6270 (OUTLIER) cc_final: 0.5328 (mp0) REVERT: J 227 PHE cc_start: 0.8836 (OUTLIER) cc_final: 0.7615 (t80) REVERT: J 245 LEU cc_start: 0.8986 (tp) cc_final: 0.8743 (tp) REVERT: J 322 ARG cc_start: 0.7488 (ptm160) cc_final: 0.7194 (ptm160) REVERT: J 399 LYS cc_start: 0.8391 (OUTLIER) cc_final: 0.7817 (mptt) REVERT: J 500 ILE cc_start: 0.8288 (OUTLIER) cc_final: 0.7861 (mp) REVERT: J 545 HIS cc_start: 0.8493 (OUTLIER) cc_final: 0.7529 (p-80) REVERT: J 594 GLN cc_start: 0.8904 (OUTLIER) cc_final: 0.7727 (pp30) REVERT: J 821 MET cc_start: 0.7186 (tpt) cc_final: 0.6920 (tpt) REVERT: J 1148 ARG cc_start: 0.7212 (mtt180) cc_final: 0.6786 (mtt180) REVERT: J 1149 ARG cc_start: 0.7104 (tpp-160) cc_final: 0.6787 (tpp-160) REVERT: J 1253 ILE cc_start: 0.8523 (OUTLIER) cc_final: 0.8208 (mm) REVERT: J 1326 GLN cc_start: 0.8471 (mt0) cc_final: 0.8143 (mt0) REVERT: J 1373 ARG cc_start: 0.7189 (ttp-110) cc_final: 0.6865 (ttp-110) REVERT: L 45 ILE cc_start: 0.8477 (OUTLIER) cc_final: 0.8236 (tt) REVERT: L 221 PHE cc_start: 0.3076 (m-80) cc_final: 0.2788 (m-80) REVERT: L 341 LEU cc_start: 0.1482 (OUTLIER) cc_final: 0.1174 (tm) REVERT: L 386 LEU cc_start: 0.9049 (OUTLIER) cc_final: 0.8679 (tp) REVERT: L 511 ILE cc_start: 0.7286 (OUTLIER) cc_final: 0.7076 (tp) REVERT: L 554 ARG cc_start: 0.7315 (mtp85) cc_final: 0.6898 (ttt180) outliers start: 291 outliers final: 119 residues processed: 682 average time/residue: 1.4258 time to fit residues: 1160.5624 Evaluate side-chains 522 residues out of total 3197 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 141 poor density : 381 time to evaluate : 3.667 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain N residue 27 ILE Chi-restraints excluded: chain N residue 59 VAL Chi-restraints excluded: chain N residue 60 GLU Chi-restraints excluded: chain N residue 72 TYR Chi-restraints excluded: chain M residue 300 LEU Chi-restraints excluded: chain G residue 26 VAL Chi-restraints excluded: chain G residue 50 SER Chi-restraints excluded: chain G residue 56 VAL Chi-restraints excluded: chain G residue 74 VAL Chi-restraints excluded: chain G residue 90 VAL Chi-restraints excluded: chain G residue 118 ASP Chi-restraints excluded: chain G residue 150 ARG Chi-restraints excluded: chain G residue 160 HIS Chi-restraints excluded: chain G residue 171 LEU Chi-restraints excluded: chain G residue 173 VAL Chi-restraints excluded: chain G residue 199 ASP Chi-restraints excluded: chain G residue 231 PHE Chi-restraints excluded: chain H residue 19 VAL Chi-restraints excluded: chain H residue 27 THR Chi-restraints excluded: chain H residue 38 THR Chi-restraints excluded: chain H residue 43 LEU Chi-restraints excluded: chain H residue 70 THR Chi-restraints excluded: chain H residue 72 GLU Chi-restraints excluded: chain H residue 79 LEU Chi-restraints excluded: chain H residue 98 VAL Chi-restraints excluded: chain H residue 124 VAL Chi-restraints excluded: chain H residue 174 ASP Chi-restraints excluded: chain H residue 188 GLU Chi-restraints excluded: chain H residue 198 LEU Chi-restraints excluded: chain I residue 7 GLU Chi-restraints excluded: chain I residue 56 VAL Chi-restraints excluded: chain I residue 60 GLN Chi-restraints excluded: chain I residue 65 ASN Chi-restraints excluded: chain I residue 79 VAL Chi-restraints excluded: chain I residue 117 ILE Chi-restraints excluded: chain I residue 161 LYS Chi-restraints excluded: chain I residue 208 ILE Chi-restraints excluded: chain I residue 216 THR Chi-restraints excluded: chain I residue 263 VAL Chi-restraints excluded: chain I residue 456 VAL Chi-restraints excluded: chain I residue 468 LEU Chi-restraints excluded: chain I residue 496 LYS Chi-restraints excluded: chain I residue 589 THR Chi-restraints excluded: chain I residue 639 LYS Chi-restraints excluded: chain I residue 648 ASP Chi-restraints excluded: chain I residue 655 VAL Chi-restraints excluded: chain I residue 663 VAL Chi-restraints excluded: chain I residue 690 VAL Chi-restraints excluded: chain I residue 748 ILE Chi-restraints excluded: chain I residue 796 LEU Chi-restraints excluded: chain I residue 799 ASN Chi-restraints excluded: chain I residue 802 VAL Chi-restraints excluded: chain I residue 817 LEU Chi-restraints excluded: chain I residue 823 VAL Chi-restraints excluded: chain I residue 845 LEU Chi-restraints excluded: chain I residue 878 THR Chi-restraints excluded: chain I residue 893 THR Chi-restraints excluded: chain I residue 912 ASP Chi-restraints excluded: chain I residue 924 VAL Chi-restraints excluded: chain I residue 937 ASP Chi-restraints excluded: chain I residue 953 LEU Chi-restraints excluded: chain I residue 980 VAL Chi-restraints excluded: chain I residue 984 VAL Chi-restraints excluded: chain I residue 1046 VAL Chi-restraints excluded: chain I residue 1060 ILE Chi-restraints excluded: chain I residue 1082 ILE Chi-restraints excluded: chain I residue 1092 THR Chi-restraints excluded: chain I residue 1109 ILE Chi-restraints excluded: chain I residue 1117 LEU Chi-restraints excluded: chain I residue 1133 LYS Chi-restraints excluded: chain I residue 1163 THR Chi-restraints excluded: chain I residue 1206 THR Chi-restraints excluded: chain I residue 1225 VAL Chi-restraints excluded: chain I residue 1250 SER Chi-restraints excluded: chain I residue 1254 VAL Chi-restraints excluded: chain I residue 1290 MET Chi-restraints excluded: chain I residue 1293 VAL Chi-restraints excluded: chain I residue 1298 VAL Chi-restraints excluded: chain J residue 46 TYR Chi-restraints excluded: chain J residue 78 LEU Chi-restraints excluded: chain J residue 92 VAL Chi-restraints excluded: chain J residue 96 LYS Chi-restraints excluded: chain J residue 97 VAL Chi-restraints excluded: chain J residue 159 ILE Chi-restraints excluded: chain J residue 170 GLU Chi-restraints excluded: chain J residue 212 THR Chi-restraints excluded: chain J residue 218 THR Chi-restraints excluded: chain J residue 227 PHE Chi-restraints excluded: chain J residue 279 LEU Chi-restraints excluded: chain J residue 357 VAL Chi-restraints excluded: chain J residue 399 LYS Chi-restraints excluded: chain J residue 428 THR Chi-restraints excluded: chain J residue 468 VAL Chi-restraints excluded: chain J residue 489 ASN Chi-restraints excluded: chain J residue 500 ILE Chi-restraints excluded: chain J residue 507 VAL Chi-restraints excluded: chain J residue 536 LEU Chi-restraints excluded: chain J residue 545 HIS Chi-restraints excluded: chain J residue 560 ASN Chi-restraints excluded: chain J residue 567 THR Chi-restraints excluded: chain J residue 594 GLN Chi-restraints excluded: chain J residue 614 LEU Chi-restraints excluded: chain J residue 705 THR Chi-restraints excluded: chain J residue 710 ASP Chi-restraints excluded: chain J residue 740 LEU Chi-restraints excluded: chain J residue 775 SER Chi-restraints excluded: chain J residue 783 LEU Chi-restraints excluded: chain J residue 786 THR Chi-restraints excluded: chain J residue 788 LEU Chi-restraints excluded: chain J residue 792 ASN Chi-restraints excluded: chain J residue 803 VAL Chi-restraints excluded: chain J residue 835 LEU Chi-restraints excluded: chain J residue 839 VAL Chi-restraints excluded: chain J residue 847 ASP Chi-restraints excluded: chain J residue 869 CYS Chi-restraints excluded: chain J residue 1248 ILE Chi-restraints excluded: chain J residue 1253 ILE Chi-restraints excluded: chain J residue 1255 VAL Chi-restraints excluded: chain J residue 1267 VAL Chi-restraints excluded: chain J residue 1286 LYS Chi-restraints excluded: chain K residue 13 ILE Chi-restraints excluded: chain K residue 39 VAL Chi-restraints excluded: chain L residue 45 ILE Chi-restraints excluded: chain L residue 49 ASN Chi-restraints excluded: chain L residue 95 THR Chi-restraints excluded: chain L residue 98 VAL Chi-restraints excluded: chain L residue 134 VAL Chi-restraints excluded: chain L residue 341 LEU Chi-restraints excluded: chain L residue 355 ILE Chi-restraints excluded: chain L residue 386 LEU Chi-restraints excluded: chain L residue 387 VAL Chi-restraints excluded: chain L residue 440 THR Chi-restraints excluded: chain L residue 449 THR Chi-restraints excluded: chain L residue 499 LYS Chi-restraints excluded: chain L residue 505 ILE Chi-restraints excluded: chain L residue 511 ILE Chi-restraints excluded: chain L residue 526 THR Chi-restraints excluded: chain L residue 552 THR Chi-restraints excluded: chain L residue 559 LEU Chi-restraints excluded: chain L residue 581 ASP Chi-restraints excluded: chain L residue 604 SER Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 379 random chunks: chunk 191 optimal weight: 1.9990 chunk 106 optimal weight: 6.9990 chunk 286 optimal weight: 4.9990 chunk 234 optimal weight: 0.9990 chunk 94 optimal weight: 5.9990 chunk 344 optimal weight: 20.0000 chunk 372 optimal weight: 2.9990 chunk 307 optimal weight: 10.0000 chunk 341 optimal weight: 8.9990 chunk 117 optimal weight: 4.9990 chunk 276 optimal weight: 1.9990 overall best weight: 2.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: N 28 ASN N 68 GLN ** M 268 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 147 GLN ** I 450 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 526 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** I 618 GLN I 760 ASN I 811 ASN I 932 GLN ** J 320 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 875 ASN ** J1350 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 129 GLN ** L 362 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7899 moved from start: 0.2654 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.067 32133 Z= 0.332 Angle : 0.680 13.268 43850 Z= 0.353 Chirality : 0.044 0.316 5031 Planarity : 0.005 0.066 5353 Dihedral : 18.391 179.503 5667 Min Nonbonded Distance : 2.099 Molprobity Statistics. All-atom Clashscore : 14.76 Ramachandran Plot: Outliers : 0.16 % Allowed : 6.17 % Favored : 93.67 % Rotamer: Outliers : 8.41 % Allowed : 22.95 % Favored : 68.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.37 % Cis-general : 0.28 % Twisted Proline : 0.00 % Twisted General : 0.06 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.57 (0.13), residues: 3698 helix: 0.03 (0.13), residues: 1571 sheet: -1.38 (0.25), residues: 376 loop : -1.98 (0.14), residues: 1751 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP I 807 HIS 0.005 0.001 HIS J 545 PHE 0.017 0.002 PHE J 461 TYR 0.019 0.002 TYR G 177 ARG 0.008 0.001 ARG I 272 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7396 Ramachandran restraints generated. 3698 Oldfield, 0 Emsley, 3698 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7396 Ramachandran restraints generated. 3698 Oldfield, 0 Emsley, 3698 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 676 residues out of total 3197 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 267 poor density : 409 time to evaluate : 3.810 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: N 18 THR cc_start: 0.8842 (t) cc_final: 0.8460 (p) REVERT: N 70 LYS cc_start: 0.8472 (tttt) cc_final: 0.8252 (tmmm) REVERT: G 231 PHE cc_start: 0.7435 (OUTLIER) cc_final: 0.6746 (t80) REVERT: H 199 ASP cc_start: 0.7849 (t70) cc_final: 0.7545 (t70) REVERT: I 7 GLU cc_start: 0.7049 (OUTLIER) cc_final: 0.6809 (mm-30) REVERT: I 161 LYS cc_start: 0.8761 (OUTLIER) cc_final: 0.8472 (ptpt) REVERT: I 631 GLU cc_start: 0.7367 (OUTLIER) cc_final: 0.6720 (pm20) REVERT: I 639 LYS cc_start: 0.8033 (OUTLIER) cc_final: 0.7763 (mppt) REVERT: I 779 ARG cc_start: 0.7640 (OUTLIER) cc_final: 0.6819 (ttm-80) REVERT: I 953 LEU cc_start: 0.8782 (OUTLIER) cc_final: 0.8526 (mt) REVERT: I 955 GLN cc_start: 0.8712 (tp40) cc_final: 0.8483 (tp-100) REVERT: I 1296 ASP cc_start: 0.7537 (OUTLIER) cc_final: 0.7324 (t0) REVERT: J 97 VAL cc_start: 0.8711 (OUTLIER) cc_final: 0.8222 (m) REVERT: J 227 PHE cc_start: 0.8928 (OUTLIER) cc_final: 0.7616 (t80) REVERT: J 399 LYS cc_start: 0.8491 (OUTLIER) cc_final: 0.7897 (mptt) REVERT: J 500 ILE cc_start: 0.8315 (OUTLIER) cc_final: 0.7858 (mp) REVERT: J 545 HIS cc_start: 0.8647 (OUTLIER) cc_final: 0.7111 (p-80) REVERT: J 594 GLN cc_start: 0.8950 (OUTLIER) cc_final: 0.7792 (pp30) REVERT: J 821 MET cc_start: 0.7221 (tpt) cc_final: 0.6939 (tpt) REVERT: J 1149 ARG cc_start: 0.7264 (tpp-160) cc_final: 0.6815 (mmm160) REVERT: J 1189 MET cc_start: 0.5792 (mmp) cc_final: 0.5322 (mmm) REVERT: J 1253 ILE cc_start: 0.8565 (OUTLIER) cc_final: 0.8173 (mm) REVERT: L 40 GLN cc_start: 0.6654 (OUTLIER) cc_final: 0.6379 (mt0) REVERT: L 45 ILE cc_start: 0.8590 (OUTLIER) cc_final: 0.8322 (tt) REVERT: L 341 LEU cc_start: 0.1481 (OUTLIER) cc_final: 0.1153 (tm) REVERT: L 386 LEU cc_start: 0.9136 (OUTLIER) cc_final: 0.8750 (tp) REVERT: L 554 ARG cc_start: 0.7389 (mtp85) cc_final: 0.6904 (ttt180) outliers start: 267 outliers final: 153 residues processed: 613 average time/residue: 1.3518 time to fit residues: 988.1380 Evaluate side-chains 534 residues out of total 3197 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 172 poor density : 362 time to evaluate : 3.564 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain N residue 27 ILE Chi-restraints excluded: chain N residue 60 GLU Chi-restraints excluded: chain N residue 72 TYR Chi-restraints excluded: chain M residue 285 THR Chi-restraints excluded: chain M residue 300 LEU Chi-restraints excluded: chain G residue 26 VAL Chi-restraints excluded: chain G residue 50 SER Chi-restraints excluded: chain G residue 56 VAL Chi-restraints excluded: chain G residue 74 VAL Chi-restraints excluded: chain G residue 90 VAL Chi-restraints excluded: chain G residue 118 ASP Chi-restraints excluded: chain G residue 127 GLN Chi-restraints excluded: chain G residue 160 HIS Chi-restraints excluded: chain G residue 168 ILE Chi-restraints excluded: chain G residue 171 LEU Chi-restraints excluded: chain G residue 173 VAL Chi-restraints excluded: chain G residue 199 ASP Chi-restraints excluded: chain G residue 231 PHE Chi-restraints excluded: chain H residue 19 VAL Chi-restraints excluded: chain H residue 27 THR Chi-restraints excluded: chain H residue 38 THR Chi-restraints excluded: chain H residue 43 LEU Chi-restraints excluded: chain H residue 70 THR Chi-restraints excluded: chain H residue 72 GLU Chi-restraints excluded: chain H residue 98 VAL Chi-restraints excluded: chain H residue 99 ILE Chi-restraints excluded: chain H residue 116 THR Chi-restraints excluded: chain H residue 124 VAL Chi-restraints excluded: chain H residue 140 ILE Chi-restraints excluded: chain H residue 144 ILE Chi-restraints excluded: chain H residue 156 SER Chi-restraints excluded: chain H residue 174 ASP Chi-restraints excluded: chain H residue 178 SER Chi-restraints excluded: chain H residue 188 GLU Chi-restraints excluded: chain H residue 198 LEU Chi-restraints excluded: chain H residue 202 VAL Chi-restraints excluded: chain H residue 231 PHE Chi-restraints excluded: chain I residue 2 VAL Chi-restraints excluded: chain I residue 7 GLU Chi-restraints excluded: chain I residue 56 VAL Chi-restraints excluded: chain I residue 79 VAL Chi-restraints excluded: chain I residue 104 ILE Chi-restraints excluded: chain I residue 117 ILE Chi-restraints excluded: chain I residue 132 ASP Chi-restraints excluded: chain I residue 161 LYS Chi-restraints excluded: chain I residue 263 VAL Chi-restraints excluded: chain I residue 333 ILE Chi-restraints excluded: chain I residue 414 ILE Chi-restraints excluded: chain I residue 415 GLU Chi-restraints excluded: chain I residue 445 ILE Chi-restraints excluded: chain I residue 446 ASP Chi-restraints excluded: chain I residue 456 VAL Chi-restraints excluded: chain I residue 471 VAL Chi-restraints excluded: chain I residue 508 SER Chi-restraints excluded: chain I residue 550 VAL Chi-restraints excluded: chain I residue 558 VAL Chi-restraints excluded: chain I residue 589 THR Chi-restraints excluded: chain I residue 609 ILE Chi-restraints excluded: chain I residue 631 GLU Chi-restraints excluded: chain I residue 639 LYS Chi-restraints excluded: chain I residue 648 ASP Chi-restraints excluded: chain I residue 653 MET Chi-restraints excluded: chain I residue 655 VAL Chi-restraints excluded: chain I residue 663 VAL Chi-restraints excluded: chain I residue 690 VAL Chi-restraints excluded: chain I residue 704 MET Chi-restraints excluded: chain I residue 740 GLU Chi-restraints excluded: chain I residue 748 ILE Chi-restraints excluded: chain I residue 779 ARG Chi-restraints excluded: chain I residue 796 LEU Chi-restraints excluded: chain I residue 799 ASN Chi-restraints excluded: chain I residue 802 VAL Chi-restraints excluded: chain I residue 817 LEU Chi-restraints excluded: chain I residue 823 VAL Chi-restraints excluded: chain I residue 835 GLU Chi-restraints excluded: chain I residue 845 LEU Chi-restraints excluded: chain I residue 878 THR Chi-restraints excluded: chain I residue 893 THR Chi-restraints excluded: chain I residue 912 ASP Chi-restraints excluded: chain I residue 924 VAL Chi-restraints excluded: chain I residue 937 ASP Chi-restraints excluded: chain I residue 953 LEU Chi-restraints excluded: chain I residue 980 VAL Chi-restraints excluded: chain I residue 984 VAL Chi-restraints excluded: chain I residue 1037 THR Chi-restraints excluded: chain I residue 1046 VAL Chi-restraints excluded: chain I residue 1060 ILE Chi-restraints excluded: chain I residue 1082 ILE Chi-restraints excluded: chain I residue 1092 THR Chi-restraints excluded: chain I residue 1109 ILE Chi-restraints excluded: chain I residue 1117 LEU Chi-restraints excluded: chain I residue 1159 VAL Chi-restraints excluded: chain I residue 1206 THR Chi-restraints excluded: chain I residue 1225 VAL Chi-restraints excluded: chain I residue 1250 SER Chi-restraints excluded: chain I residue 1290 MET Chi-restraints excluded: chain I residue 1296 ASP Chi-restraints excluded: chain I residue 1298 VAL Chi-restraints excluded: chain J residue 46 TYR Chi-restraints excluded: chain J residue 92 VAL Chi-restraints excluded: chain J residue 97 VAL Chi-restraints excluded: chain J residue 153 ASN Chi-restraints excluded: chain J residue 159 ILE Chi-restraints excluded: chain J residue 170 GLU Chi-restraints excluded: chain J residue 212 THR Chi-restraints excluded: chain J residue 218 THR Chi-restraints excluded: chain J residue 227 PHE Chi-restraints excluded: chain J residue 237 MET Chi-restraints excluded: chain J residue 279 LEU Chi-restraints excluded: chain J residue 357 VAL Chi-restraints excluded: chain J residue 399 LYS Chi-restraints excluded: chain J residue 401 VAL Chi-restraints excluded: chain J residue 428 THR Chi-restraints excluded: chain J residue 429 LEU Chi-restraints excluded: chain J residue 468 VAL Chi-restraints excluded: chain J residue 489 ASN Chi-restraints excluded: chain J residue 500 ILE Chi-restraints excluded: chain J residue 507 VAL Chi-restraints excluded: chain J residue 536 LEU Chi-restraints excluded: chain J residue 545 HIS Chi-restraints excluded: chain J residue 560 ASN Chi-restraints excluded: chain J residue 567 THR Chi-restraints excluded: chain J residue 571 ASP Chi-restraints excluded: chain J residue 594 GLN Chi-restraints excluded: chain J residue 614 LEU Chi-restraints excluded: chain J residue 644 MET Chi-restraints excluded: chain J residue 705 THR Chi-restraints excluded: chain J residue 709 ARG Chi-restraints excluded: chain J residue 710 ASP Chi-restraints excluded: chain J residue 740 LEU Chi-restraints excluded: chain J residue 783 LEU Chi-restraints excluded: chain J residue 786 THR Chi-restraints excluded: chain J residue 788 LEU Chi-restraints excluded: chain J residue 792 ASN Chi-restraints excluded: chain J residue 803 VAL Chi-restraints excluded: chain J residue 835 LEU Chi-restraints excluded: chain J residue 839 VAL Chi-restraints excluded: chain J residue 847 ASP Chi-restraints excluded: chain J residue 869 CYS Chi-restraints excluded: chain J residue 1177 ILE Chi-restraints excluded: chain J residue 1209 VAL Chi-restraints excluded: chain J residue 1248 ILE Chi-restraints excluded: chain J residue 1253 ILE Chi-restraints excluded: chain J residue 1255 VAL Chi-restraints excluded: chain J residue 1267 VAL Chi-restraints excluded: chain J residue 1286 LYS Chi-restraints excluded: chain J residue 1295 ASN Chi-restraints excluded: chain K residue 39 VAL Chi-restraints excluded: chain K residue 66 VAL Chi-restraints excluded: chain L residue 40 GLN Chi-restraints excluded: chain L residue 45 ILE Chi-restraints excluded: chain L residue 49 ASN Chi-restraints excluded: chain L residue 95 THR Chi-restraints excluded: chain L residue 98 VAL Chi-restraints excluded: chain L residue 108 VAL Chi-restraints excluded: chain L residue 341 LEU Chi-restraints excluded: chain L residue 344 LEU Chi-restraints excluded: chain L residue 355 ILE Chi-restraints excluded: chain L residue 386 LEU Chi-restraints excluded: chain L residue 387 VAL Chi-restraints excluded: chain L residue 399 LEU Chi-restraints excluded: chain L residue 440 THR Chi-restraints excluded: chain L residue 449 THR Chi-restraints excluded: chain L residue 454 VAL Chi-restraints excluded: chain L residue 468 ARG Chi-restraints excluded: chain L residue 473 GLU Chi-restraints excluded: chain L residue 485 GLU Chi-restraints excluded: chain L residue 505 ILE Chi-restraints excluded: chain L residue 552 THR Chi-restraints excluded: chain L residue 559 LEU Chi-restraints excluded: chain L residue 568 ASN Chi-restraints excluded: chain L residue 604 SER Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 379 random chunks: chunk 340 optimal weight: 9.9990 chunk 259 optimal weight: 0.6980 chunk 178 optimal weight: 2.9990 chunk 38 optimal weight: 4.9990 chunk 164 optimal weight: 1.9990 chunk 231 optimal weight: 0.7980 chunk 346 optimal weight: 10.0000 chunk 366 optimal weight: 2.9990 chunk 180 optimal weight: 1.9990 chunk 327 optimal weight: 3.9990 chunk 98 optimal weight: 7.9990 overall best weight: 1.6986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: N 28 ASN ** M 268 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 526 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** I 618 GLN I 811 ASN J 365 GLN J1279 GLN ** J1350 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 129 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 309 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 362 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 600 HIS Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7867 moved from start: 0.3034 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.051 32133 Z= 0.242 Angle : 0.628 11.522 43850 Z= 0.326 Chirality : 0.042 0.291 5031 Planarity : 0.004 0.061 5353 Dihedral : 18.067 179.484 5636 Min Nonbonded Distance : 2.080 Molprobity Statistics. All-atom Clashscore : 13.49 Ramachandran Plot: Outliers : 0.14 % Allowed : 5.71 % Favored : 94.16 % Rotamer: Outliers : 7.68 % Allowed : 24.24 % Favored : 68.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.37 % Cis-general : 0.28 % Twisted Proline : 0.00 % Twisted General : 0.06 % 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: -1.16 (0.13), residues: 3698 helix: 0.42 (0.13), residues: 1557 sheet: -1.14 (0.26), residues: 369 loop : -1.79 (0.14), residues: 1772 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP I 807 HIS 0.004 0.001 HIS H 66 PHE 0.016 0.001 PHE L 259 TYR 0.015 0.001 TYR G 177 ARG 0.010 0.001 ARG I 272 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7396 Ramachandran restraints generated. 3698 Oldfield, 0 Emsley, 3698 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7396 Ramachandran restraints generated. 3698 Oldfield, 0 Emsley, 3698 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 641 residues out of total 3197 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 244 poor density : 397 time to evaluate : 3.655 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: N 18 THR cc_start: 0.8791 (t) cc_final: 0.8475 (p) REVERT: N 70 LYS cc_start: 0.8405 (tttt) cc_final: 0.8084 (pttp) REVERT: H 12 ARG cc_start: 0.7384 (OUTLIER) cc_final: 0.6925 (ptp-170) REVERT: H 116 THR cc_start: 0.7521 (OUTLIER) cc_final: 0.7123 (m) REVERT: H 188 GLU cc_start: 0.7483 (OUTLIER) cc_final: 0.7273 (mt-10) REVERT: H 191 ARG cc_start: 0.7267 (ptt-90) cc_final: 0.6997 (ptt-90) REVERT: I 7 GLU cc_start: 0.6986 (OUTLIER) cc_final: 0.6757 (mm-30) REVERT: I 319 LEU cc_start: 0.8023 (mp) cc_final: 0.7708 (mp) REVERT: I 337 PHE cc_start: 0.7911 (t80) cc_final: 0.7552 (t80) REVERT: I 639 LYS cc_start: 0.8072 (OUTLIER) cc_final: 0.7818 (mppt) REVERT: I 779 ARG cc_start: 0.7582 (OUTLIER) cc_final: 0.6761 (ttm-80) REVERT: I 953 LEU cc_start: 0.8731 (OUTLIER) cc_final: 0.8484 (mt) REVERT: I 955 GLN cc_start: 0.8580 (tp40) cc_final: 0.8375 (tp-100) REVERT: J 81 ARG cc_start: 0.7424 (OUTLIER) cc_final: 0.6822 (ttm170) REVERT: J 97 VAL cc_start: 0.8675 (p) cc_final: 0.8225 (m) REVERT: J 170 GLU cc_start: 0.7036 (OUTLIER) cc_final: 0.6789 (mm-30) REVERT: J 194 LEU cc_start: 0.8057 (mm) cc_final: 0.7719 (mt) REVERT: J 227 PHE cc_start: 0.8848 (OUTLIER) cc_final: 0.7478 (t80) REVERT: J 365 GLN cc_start: 0.9027 (OUTLIER) cc_final: 0.8715 (pt0) REVERT: J 399 LYS cc_start: 0.8412 (OUTLIER) cc_final: 0.7848 (mptt) REVERT: J 594 GLN cc_start: 0.8971 (OUTLIER) cc_final: 0.7812 (pp30) REVERT: J 821 MET cc_start: 0.7183 (tpt) cc_final: 0.6938 (tpt) REVERT: J 1149 ARG cc_start: 0.7262 (tpp-160) cc_final: 0.6861 (mmm160) REVERT: J 1189 MET cc_start: 0.5729 (mmp) cc_final: 0.5297 (mmm) REVERT: J 1253 ILE cc_start: 0.8499 (mm) cc_final: 0.8188 (mm) REVERT: J 1373 ARG cc_start: 0.7197 (OUTLIER) cc_final: 0.6582 (ttp-110) REVERT: L 45 ILE cc_start: 0.8559 (OUTLIER) cc_final: 0.8296 (tt) REVERT: L 49 ASN cc_start: 0.6146 (OUTLIER) cc_final: 0.5915 (t0) REVERT: L 288 MET cc_start: 0.4203 (mpp) cc_final: 0.3748 (mmt) REVERT: L 341 LEU cc_start: 0.1095 (OUTLIER) cc_final: 0.0786 (tm) REVERT: L 386 LEU cc_start: 0.9084 (OUTLIER) cc_final: 0.8685 (tp) REVERT: L 554 ARG cc_start: 0.7362 (mtp85) cc_final: 0.6823 (ttt180) outliers start: 244 outliers final: 138 residues processed: 586 average time/residue: 1.3383 time to fit residues: 938.6223 Evaluate side-chains 516 residues out of total 3197 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 156 poor density : 360 time to evaluate : 3.358 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain N residue 27 ILE Chi-restraints excluded: chain N residue 59 VAL Chi-restraints excluded: chain N residue 60 GLU Chi-restraints excluded: chain N residue 72 TYR Chi-restraints excluded: chain M residue 300 LEU Chi-restraints excluded: chain G residue 26 VAL Chi-restraints excluded: chain G residue 56 VAL Chi-restraints excluded: chain G residue 74 VAL Chi-restraints excluded: chain G residue 90 VAL Chi-restraints excluded: chain G residue 118 ASP Chi-restraints excluded: chain G residue 160 HIS Chi-restraints excluded: chain G residue 168 ILE Chi-restraints excluded: chain G residue 171 LEU Chi-restraints excluded: chain G residue 173 VAL Chi-restraints excluded: chain G residue 199 ASP Chi-restraints excluded: chain H residue 12 ARG Chi-restraints excluded: chain H residue 18 GLN Chi-restraints excluded: chain H residue 19 VAL Chi-restraints excluded: chain H residue 38 THR Chi-restraints excluded: chain H residue 43 LEU Chi-restraints excluded: chain H residue 72 GLU Chi-restraints excluded: chain H residue 98 VAL Chi-restraints excluded: chain H residue 99 ILE Chi-restraints excluded: chain H residue 116 THR Chi-restraints excluded: chain H residue 120 ASP Chi-restraints excluded: chain H residue 124 VAL Chi-restraints excluded: chain H residue 144 ILE Chi-restraints excluded: chain H residue 156 SER Chi-restraints excluded: chain H residue 174 ASP Chi-restraints excluded: chain H residue 178 SER Chi-restraints excluded: chain H residue 188 GLU Chi-restraints excluded: chain H residue 198 LEU Chi-restraints excluded: chain H residue 202 VAL Chi-restraints excluded: chain H residue 207 THR Chi-restraints excluded: chain H residue 231 PHE Chi-restraints excluded: chain I residue 7 GLU Chi-restraints excluded: chain I residue 56 VAL Chi-restraints excluded: chain I residue 79 VAL Chi-restraints excluded: chain I residue 104 ILE Chi-restraints excluded: chain I residue 117 ILE Chi-restraints excluded: chain I residue 132 ASP Chi-restraints excluded: chain I residue 208 ILE Chi-restraints excluded: chain I residue 263 VAL Chi-restraints excluded: chain I residue 415 GLU Chi-restraints excluded: chain I residue 444 ASP Chi-restraints excluded: chain I residue 445 ILE Chi-restraints excluded: chain I residue 446 ASP Chi-restraints excluded: chain I residue 456 VAL Chi-restraints excluded: chain I residue 471 VAL Chi-restraints excluded: chain I residue 558 VAL Chi-restraints excluded: chain I residue 561 ILE Chi-restraints excluded: chain I residue 589 THR Chi-restraints excluded: chain I residue 609 ILE Chi-restraints excluded: chain I residue 639 LYS Chi-restraints excluded: chain I residue 655 VAL Chi-restraints excluded: chain I residue 663 VAL Chi-restraints excluded: chain I residue 685 MET Chi-restraints excluded: chain I residue 690 VAL Chi-restraints excluded: chain I residue 704 MET Chi-restraints excluded: chain I residue 727 VAL Chi-restraints excluded: chain I residue 740 GLU Chi-restraints excluded: chain I residue 748 ILE Chi-restraints excluded: chain I residue 753 LEU Chi-restraints excluded: chain I residue 779 ARG Chi-restraints excluded: chain I residue 796 LEU Chi-restraints excluded: chain I residue 799 ASN Chi-restraints excluded: chain I residue 802 VAL Chi-restraints excluded: chain I residue 811 ASN Chi-restraints excluded: chain I residue 817 LEU Chi-restraints excluded: chain I residue 835 GLU Chi-restraints excluded: chain I residue 845 LEU Chi-restraints excluded: chain I residue 878 THR Chi-restraints excluded: chain I residue 893 THR Chi-restraints excluded: chain I residue 896 THR Chi-restraints excluded: chain I residue 924 VAL Chi-restraints excluded: chain I residue 937 ASP Chi-restraints excluded: chain I residue 953 LEU Chi-restraints excluded: chain I residue 980 VAL Chi-restraints excluded: chain I residue 984 VAL Chi-restraints excluded: chain I residue 1046 VAL Chi-restraints excluded: chain I residue 1060 ILE Chi-restraints excluded: chain I residue 1082 ILE Chi-restraints excluded: chain I residue 1092 THR Chi-restraints excluded: chain I residue 1109 ILE Chi-restraints excluded: chain I residue 1117 LEU Chi-restraints excluded: chain I residue 1163 THR Chi-restraints excluded: chain I residue 1206 THR Chi-restraints excluded: chain I residue 1225 VAL Chi-restraints excluded: chain I residue 1250 SER Chi-restraints excluded: chain I residue 1290 MET Chi-restraints excluded: chain I residue 1296 ASP Chi-restraints excluded: chain I residue 1298 VAL Chi-restraints excluded: chain J residue 46 TYR Chi-restraints excluded: chain J residue 81 ARG Chi-restraints excluded: chain J residue 92 VAL Chi-restraints excluded: chain J residue 159 ILE Chi-restraints excluded: chain J residue 170 GLU Chi-restraints excluded: chain J residue 212 THR Chi-restraints excluded: chain J residue 227 PHE Chi-restraints excluded: chain J residue 279 LEU Chi-restraints excluded: chain J residue 343 LEU Chi-restraints excluded: chain J residue 357 VAL Chi-restraints excluded: chain J residue 365 GLN Chi-restraints excluded: chain J residue 399 LYS Chi-restraints excluded: chain J residue 401 VAL Chi-restraints excluded: chain J residue 428 THR Chi-restraints excluded: chain J residue 429 LEU Chi-restraints excluded: chain J residue 468 VAL Chi-restraints excluded: chain J residue 489 ASN Chi-restraints excluded: chain J residue 500 ILE Chi-restraints excluded: chain J residue 507 VAL Chi-restraints excluded: chain J residue 536 LEU Chi-restraints excluded: chain J residue 545 HIS Chi-restraints excluded: chain J residue 560 ASN Chi-restraints excluded: chain J residue 567 THR Chi-restraints excluded: chain J residue 571 ASP Chi-restraints excluded: chain J residue 594 GLN Chi-restraints excluded: chain J residue 614 LEU Chi-restraints excluded: chain J residue 740 LEU Chi-restraints excluded: chain J residue 757 THR Chi-restraints excluded: chain J residue 783 LEU Chi-restraints excluded: chain J residue 786 THR Chi-restraints excluded: chain J residue 792 ASN Chi-restraints excluded: chain J residue 803 VAL Chi-restraints excluded: chain J residue 835 LEU Chi-restraints excluded: chain J residue 839 VAL Chi-restraints excluded: chain J residue 847 ASP Chi-restraints excluded: chain J residue 869 CYS Chi-restraints excluded: chain J residue 1177 ILE Chi-restraints excluded: chain J residue 1209 VAL Chi-restraints excluded: chain J residue 1248 ILE Chi-restraints excluded: chain J residue 1255 VAL Chi-restraints excluded: chain J residue 1267 VAL Chi-restraints excluded: chain J residue 1286 LYS Chi-restraints excluded: chain J residue 1373 ARG Chi-restraints excluded: chain K residue 39 VAL Chi-restraints excluded: chain L residue 34 ASP Chi-restraints excluded: chain L residue 41 ILE Chi-restraints excluded: chain L residue 43 ASP Chi-restraints excluded: chain L residue 45 ILE Chi-restraints excluded: chain L residue 49 ASN Chi-restraints excluded: chain L residue 95 THR Chi-restraints excluded: chain L residue 98 VAL Chi-restraints excluded: chain L residue 341 LEU Chi-restraints excluded: chain L residue 344 LEU Chi-restraints excluded: chain L residue 386 LEU Chi-restraints excluded: chain L residue 449 THR Chi-restraints excluded: chain L residue 454 VAL Chi-restraints excluded: chain L residue 468 ARG Chi-restraints excluded: chain L residue 473 GLU Chi-restraints excluded: chain L residue 485 GLU Chi-restraints excluded: chain L residue 505 ILE Chi-restraints excluded: chain L residue 527 THR Chi-restraints excluded: chain L residue 552 THR Chi-restraints excluded: chain L residue 559 LEU Chi-restraints excluded: chain L residue 568 ASN Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 379 random chunks: chunk 305 optimal weight: 3.9990 chunk 207 optimal weight: 6.9990 chunk 5 optimal weight: 0.0970 chunk 272 optimal weight: 6.9990 chunk 151 optimal weight: 0.9980 chunk 312 optimal weight: 7.9990 chunk 253 optimal weight: 4.9990 chunk 0 optimal weight: 10.0000 chunk 187 optimal weight: 0.7980 chunk 328 optimal weight: 0.9990 chunk 92 optimal weight: 9.9990 overall best weight: 1.3782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: N 68 GLN ** M 268 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 526 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** I 618 GLN I 811 ASN I1268 GLN ** J 320 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 364 HIS J1279 GLN ** J1350 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 129 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 309 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 518 HIS Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7856 moved from start: 0.3267 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 32133 Z= 0.216 Angle : 0.613 11.249 43850 Z= 0.318 Chirality : 0.042 0.273 5031 Planarity : 0.004 0.058 5353 Dihedral : 17.854 179.359 5618 Min Nonbonded Distance : 2.081 Molprobity Statistics. All-atom Clashscore : 13.00 Ramachandran Plot: Outliers : 0.14 % Allowed : 5.73 % Favored : 94.13 % Rotamer: Outliers : 7.30 % Allowed : 25.31 % Favored : 67.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.37 % Cis-general : 0.28 % Twisted Proline : 0.00 % Twisted General : 0.06 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.91 (0.14), residues: 3698 helix: 0.58 (0.13), residues: 1565 sheet: -0.96 (0.26), residues: 365 loop : -1.64 (0.14), residues: 1768 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP I 807 HIS 0.004 0.001 HIS J 545 PHE 0.016 0.001 PHE L 259 TYR 0.016 0.001 TYR N 64 ARG 0.010 0.000 ARG I 272 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7396 Ramachandran restraints generated. 3698 Oldfield, 0 Emsley, 3698 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7396 Ramachandran restraints generated. 3698 Oldfield, 0 Emsley, 3698 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 617 residues out of total 3197 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 232 poor density : 385 time to evaluate : 3.532 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: N 18 THR cc_start: 0.8802 (t) cc_final: 0.8492 (p) REVERT: N 70 LYS cc_start: 0.8426 (tttt) cc_final: 0.8117 (pttp) REVERT: H 12 ARG cc_start: 0.7319 (OUTLIER) cc_final: 0.6791 (ptp-170) REVERT: H 191 ARG cc_start: 0.7218 (ptt-90) cc_final: 0.6970 (ptt-90) REVERT: I 309 LEU cc_start: 0.7910 (tp) cc_final: 0.7635 (tp) REVERT: I 319 LEU cc_start: 0.8077 (mp) cc_final: 0.7838 (mp) REVERT: I 337 PHE cc_start: 0.7896 (t80) cc_final: 0.7536 (t80) REVERT: I 639 LYS cc_start: 0.8061 (OUTLIER) cc_final: 0.7778 (mppt) REVERT: I 779 ARG cc_start: 0.7517 (OUTLIER) cc_final: 0.6683 (ttm-80) REVERT: I 796 LEU cc_start: 0.9031 (OUTLIER) cc_final: 0.8732 (mp) REVERT: I 867 GLU cc_start: 0.7581 (OUTLIER) cc_final: 0.7362 (pt0) REVERT: I 916 SER cc_start: 0.9220 (OUTLIER) cc_final: 0.8967 (p) REVERT: I 955 GLN cc_start: 0.8539 (tp40) cc_final: 0.8325 (tp-100) REVERT: I 1167 GLU cc_start: 0.7587 (OUTLIER) cc_final: 0.7359 (tp30) REVERT: I 1297 ASP cc_start: 0.7273 (t0) cc_final: 0.6914 (t0) REVERT: J 81 ARG cc_start: 0.7292 (OUTLIER) cc_final: 0.6687 (ttm170) REVERT: J 83 VAL cc_start: 0.7845 (p) cc_final: 0.7621 (m) REVERT: J 97 VAL cc_start: 0.8674 (p) cc_final: 0.8236 (m) REVERT: J 170 GLU cc_start: 0.7082 (OUTLIER) cc_final: 0.6882 (mm-30) REVERT: J 194 LEU cc_start: 0.8010 (mm) cc_final: 0.7659 (mt) REVERT: J 227 PHE cc_start: 0.8821 (OUTLIER) cc_final: 0.7462 (t80) REVERT: J 301 GLU cc_start: 0.7308 (tt0) cc_final: 0.7060 (tt0) REVERT: J 594 GLN cc_start: 0.8939 (OUTLIER) cc_final: 0.7778 (pp30) REVERT: J 602 SER cc_start: 0.7967 (m) cc_final: 0.7556 (p) REVERT: J 1146 GLU cc_start: 0.7702 (OUTLIER) cc_final: 0.6965 (mp0) REVERT: J 1149 ARG cc_start: 0.7361 (tpp-160) cc_final: 0.6987 (mmm160) REVERT: J 1189 MET cc_start: 0.5620 (mmp) cc_final: 0.5191 (mmm) REVERT: J 1253 ILE cc_start: 0.8486 (mm) cc_final: 0.8169 (mm) REVERT: J 1373 ARG cc_start: 0.7197 (OUTLIER) cc_final: 0.6943 (ttp-110) REVERT: L 33 GLU cc_start: 0.6641 (OUTLIER) cc_final: 0.6390 (pm20) REVERT: L 45 ILE cc_start: 0.8543 (OUTLIER) cc_final: 0.8281 (tt) REVERT: L 49 ASN cc_start: 0.6126 (OUTLIER) cc_final: 0.5918 (t0) REVERT: L 341 LEU cc_start: 0.1139 (OUTLIER) cc_final: 0.0859 (tm) REVERT: L 386 LEU cc_start: 0.9064 (OUTLIER) cc_final: 0.8651 (tp) REVERT: L 489 MET cc_start: 0.7376 (mpt) cc_final: 0.6951 (mmm) REVERT: L 554 ARG cc_start: 0.7268 (mtp85) cc_final: 0.6851 (ttt180) outliers start: 232 outliers final: 133 residues processed: 565 average time/residue: 1.3194 time to fit residues: 893.9877 Evaluate side-chains 510 residues out of total 3197 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 151 poor density : 359 time to evaluate : 3.369 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain N residue 72 TYR Chi-restraints excluded: chain M residue 260 LEU Chi-restraints excluded: chain M residue 300 LEU Chi-restraints excluded: chain G residue 26 VAL Chi-restraints excluded: chain G residue 56 VAL Chi-restraints excluded: chain G residue 74 VAL Chi-restraints excluded: chain G residue 90 VAL Chi-restraints excluded: chain G residue 92 VAL Chi-restraints excluded: chain G residue 118 ASP Chi-restraints excluded: chain G residue 160 HIS Chi-restraints excluded: chain G residue 168 ILE Chi-restraints excluded: chain G residue 171 LEU Chi-restraints excluded: chain G residue 173 VAL Chi-restraints excluded: chain G residue 199 ASP Chi-restraints excluded: chain H residue 12 ARG Chi-restraints excluded: chain H residue 14 VAL Chi-restraints excluded: chain H residue 18 GLN Chi-restraints excluded: chain H residue 19 VAL Chi-restraints excluded: chain H residue 27 THR Chi-restraints excluded: chain H residue 38 THR Chi-restraints excluded: chain H residue 43 LEU Chi-restraints excluded: chain H residue 98 VAL Chi-restraints excluded: chain H residue 99 ILE Chi-restraints excluded: chain H residue 120 ASP Chi-restraints excluded: chain H residue 124 VAL Chi-restraints excluded: chain H residue 144 ILE Chi-restraints excluded: chain H residue 174 ASP Chi-restraints excluded: chain H residue 178 SER Chi-restraints excluded: chain H residue 198 LEU Chi-restraints excluded: chain H residue 202 VAL Chi-restraints excluded: chain H residue 207 THR Chi-restraints excluded: chain H residue 231 PHE Chi-restraints excluded: chain I residue 2 VAL Chi-restraints excluded: chain I residue 79 VAL Chi-restraints excluded: chain I residue 104 ILE Chi-restraints excluded: chain I residue 117 ILE Chi-restraints excluded: chain I residue 229 ILE Chi-restraints excluded: chain I residue 263 VAL Chi-restraints excluded: chain I residue 415 GLU Chi-restraints excluded: chain I residue 446 ASP Chi-restraints excluded: chain I residue 456 VAL Chi-restraints excluded: chain I residue 471 VAL Chi-restraints excluded: chain I residue 484 LEU Chi-restraints excluded: chain I residue 550 VAL Chi-restraints excluded: chain I residue 558 VAL Chi-restraints excluded: chain I residue 589 THR Chi-restraints excluded: chain I residue 609 ILE Chi-restraints excluded: chain I residue 639 LYS Chi-restraints excluded: chain I residue 655 VAL Chi-restraints excluded: chain I residue 663 VAL Chi-restraints excluded: chain I residue 685 MET Chi-restraints excluded: chain I residue 690 VAL Chi-restraints excluded: chain I residue 704 MET Chi-restraints excluded: chain I residue 727 VAL Chi-restraints excluded: chain I residue 748 ILE Chi-restraints excluded: chain I residue 749 ASP Chi-restraints excluded: chain I residue 779 ARG Chi-restraints excluded: chain I residue 796 LEU Chi-restraints excluded: chain I residue 799 ASN Chi-restraints excluded: chain I residue 802 VAL Chi-restraints excluded: chain I residue 811 ASN Chi-restraints excluded: chain I residue 835 GLU Chi-restraints excluded: chain I residue 845 LEU Chi-restraints excluded: chain I residue 867 GLU Chi-restraints excluded: chain I residue 893 THR Chi-restraints excluded: chain I residue 896 THR Chi-restraints excluded: chain I residue 916 SER Chi-restraints excluded: chain I residue 924 VAL Chi-restraints excluded: chain I residue 937 ASP Chi-restraints excluded: chain I residue 971 LEU Chi-restraints excluded: chain I residue 980 VAL Chi-restraints excluded: chain I residue 984 VAL Chi-restraints excluded: chain I residue 1046 VAL Chi-restraints excluded: chain I residue 1060 ILE Chi-restraints excluded: chain I residue 1082 ILE Chi-restraints excluded: chain I residue 1109 ILE Chi-restraints excluded: chain I residue 1117 LEU Chi-restraints excluded: chain I residue 1159 VAL Chi-restraints excluded: chain I residue 1167 GLU Chi-restraints excluded: chain I residue 1206 THR Chi-restraints excluded: chain I residue 1225 VAL Chi-restraints excluded: chain I residue 1250 SER Chi-restraints excluded: chain I residue 1290 MET Chi-restraints excluded: chain I residue 1296 ASP Chi-restraints excluded: chain I residue 1298 VAL Chi-restraints excluded: chain J residue 46 TYR Chi-restraints excluded: chain J residue 81 ARG Chi-restraints excluded: chain J residue 92 VAL Chi-restraints excluded: chain J residue 159 ILE Chi-restraints excluded: chain J residue 170 GLU Chi-restraints excluded: chain J residue 212 THR Chi-restraints excluded: chain J residue 227 PHE Chi-restraints excluded: chain J residue 279 LEU Chi-restraints excluded: chain J residue 343 LEU Chi-restraints excluded: chain J residue 357 VAL Chi-restraints excluded: chain J residue 401 VAL Chi-restraints excluded: chain J residue 428 THR Chi-restraints excluded: chain J residue 429 LEU Chi-restraints excluded: chain J residue 468 VAL Chi-restraints excluded: chain J residue 489 ASN Chi-restraints excluded: chain J residue 500 ILE Chi-restraints excluded: chain J residue 507 VAL Chi-restraints excluded: chain J residue 536 LEU Chi-restraints excluded: chain J residue 545 HIS Chi-restraints excluded: chain J residue 560 ASN Chi-restraints excluded: chain J residue 567 THR Chi-restraints excluded: chain J residue 571 ASP Chi-restraints excluded: chain J residue 594 GLN Chi-restraints excluded: chain J residue 614 LEU Chi-restraints excluded: chain J residue 709 ARG Chi-restraints excluded: chain J residue 740 LEU Chi-restraints excluded: chain J residue 770 LEU Chi-restraints excluded: chain J residue 775 SER Chi-restraints excluded: chain J residue 783 LEU Chi-restraints excluded: chain J residue 786 THR Chi-restraints excluded: chain J residue 803 VAL Chi-restraints excluded: chain J residue 835 LEU Chi-restraints excluded: chain J residue 839 VAL Chi-restraints excluded: chain J residue 847 ASP Chi-restraints excluded: chain J residue 869 CYS Chi-restraints excluded: chain J residue 1146 GLU Chi-restraints excluded: chain J residue 1177 ILE Chi-restraints excluded: chain J residue 1209 VAL Chi-restraints excluded: chain J residue 1248 ILE Chi-restraints excluded: chain J residue 1255 VAL Chi-restraints excluded: chain J residue 1267 VAL Chi-restraints excluded: chain J residue 1286 LYS Chi-restraints excluded: chain J residue 1295 ASN Chi-restraints excluded: chain J residue 1373 ARG Chi-restraints excluded: chain K residue 10 VAL Chi-restraints excluded: chain K residue 39 VAL Chi-restraints excluded: chain L residue 33 GLU Chi-restraints excluded: chain L residue 34 ASP Chi-restraints excluded: chain L residue 45 ILE Chi-restraints excluded: chain L residue 49 ASN Chi-restraints excluded: chain L residue 95 THR Chi-restraints excluded: chain L residue 98 VAL Chi-restraints excluded: chain L residue 108 VAL Chi-restraints excluded: chain L residue 341 LEU Chi-restraints excluded: chain L residue 344 LEU Chi-restraints excluded: chain L residue 386 LEU Chi-restraints excluded: chain L residue 449 THR Chi-restraints excluded: chain L residue 454 VAL Chi-restraints excluded: chain L residue 468 ARG Chi-restraints excluded: chain L residue 473 GLU Chi-restraints excluded: chain L residue 485 GLU Chi-restraints excluded: chain L residue 505 ILE Chi-restraints excluded: chain L residue 552 THR Chi-restraints excluded: chain L residue 559 LEU Chi-restraints excluded: chain L residue 568 ASN Chi-restraints excluded: chain L residue 569 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 379 random chunks: chunk 123 optimal weight: 0.8980 chunk 329 optimal weight: 6.9990 chunk 72 optimal weight: 0.9980 chunk 215 optimal weight: 8.9990 chunk 90 optimal weight: 10.0000 chunk 366 optimal weight: 8.9990 chunk 304 optimal weight: 2.9990 chunk 169 optimal weight: 1.9990 chunk 30 optimal weight: 7.9990 chunk 121 optimal weight: 9.9990 chunk 192 optimal weight: 0.0060 overall best weight: 1.3800 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: N 68 GLN M 268 ASN I 437 ASN ** I 526 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** I 618 GLN I 811 ASN I 932 GLN ** J 320 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J1218 HIS ** J1350 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 129 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 309 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7850 moved from start: 0.3449 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 32133 Z= 0.216 Angle : 0.612 11.058 43850 Z= 0.316 Chirality : 0.042 0.258 5031 Planarity : 0.004 0.074 5353 Dihedral : 17.637 179.057 5602 Min Nonbonded Distance : 2.060 Molprobity Statistics. All-atom Clashscore : 12.71 Ramachandran Plot: Outliers : 0.14 % Allowed : 5.73 % Favored : 94.13 % Rotamer: Outliers : 6.71 % Allowed : 26.01 % Favored : 67.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.37 % Cis-general : 0.28 % Twisted Proline : 0.00 % Twisted General : 0.06 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.75 (0.14), residues: 3698 helix: 0.69 (0.13), residues: 1566 sheet: -0.89 (0.27), residues: 361 loop : -1.52 (0.14), residues: 1771 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP I 807 HIS 0.004 0.001 HIS J 545 PHE 0.023 0.001 PHE L 221 TYR 0.021 0.001 TYR L 148 ARG 0.013 0.000 ARG L 274 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7396 Ramachandran restraints generated. 3698 Oldfield, 0 Emsley, 3698 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7396 Ramachandran restraints generated. 3698 Oldfield, 0 Emsley, 3698 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 590 residues out of total 3197 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 213 poor density : 377 time to evaluate : 3.469 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: N 18 THR cc_start: 0.8811 (t) cc_final: 0.8497 (p) REVERT: N 70 LYS cc_start: 0.8457 (tttt) cc_final: 0.8162 (pttp) REVERT: H 12 ARG cc_start: 0.7252 (OUTLIER) cc_final: 0.6655 (ptp-170) REVERT: H 116 THR cc_start: 0.7495 (OUTLIER) cc_final: 0.7094 (m) REVERT: H 191 ARG cc_start: 0.7231 (ptt-90) cc_final: 0.6798 (ptt-90) REVERT: H 199 ASP cc_start: 0.7569 (t70) cc_final: 0.7205 (m-30) REVERT: I 289 VAL cc_start: 0.8517 (OUTLIER) cc_final: 0.8159 (m) REVERT: I 309 LEU cc_start: 0.7972 (tp) cc_final: 0.7770 (tp) REVERT: I 319 LEU cc_start: 0.8037 (mp) cc_final: 0.7812 (mp) REVERT: I 337 PHE cc_start: 0.7886 (t80) cc_final: 0.7518 (t80) REVERT: I 568 ASN cc_start: 0.8374 (OUTLIER) cc_final: 0.8106 (p0) REVERT: I 639 LYS cc_start: 0.8040 (OUTLIER) cc_final: 0.7775 (mppt) REVERT: I 779 ARG cc_start: 0.7520 (OUTLIER) cc_final: 0.6711 (ttm-80) REVERT: I 796 LEU cc_start: 0.9040 (OUTLIER) cc_final: 0.8754 (mp) REVERT: I 800 MET cc_start: 0.8009 (OUTLIER) cc_final: 0.6903 (mtm) REVERT: I 867 GLU cc_start: 0.7598 (OUTLIER) cc_final: 0.7366 (pt0) REVERT: I 916 SER cc_start: 0.9216 (OUTLIER) cc_final: 0.8990 (p) REVERT: I 955 GLN cc_start: 0.8554 (tp40) cc_final: 0.8350 (tp-100) REVERT: I 1167 GLU cc_start: 0.7597 (OUTLIER) cc_final: 0.7368 (tp30) REVERT: J 81 ARG cc_start: 0.7288 (OUTLIER) cc_final: 0.6632 (ttm170) REVERT: J 83 VAL cc_start: 0.7852 (p) cc_final: 0.7614 (m) REVERT: J 97 VAL cc_start: 0.8687 (p) cc_final: 0.8236 (m) REVERT: J 170 GLU cc_start: 0.7061 (OUTLIER) cc_final: 0.6859 (mm-30) REVERT: J 194 LEU cc_start: 0.7843 (mm) cc_final: 0.7487 (mt) REVERT: J 227 PHE cc_start: 0.8843 (OUTLIER) cc_final: 0.7474 (t80) REVERT: J 301 GLU cc_start: 0.7253 (tt0) cc_final: 0.7044 (tt0) REVERT: J 399 LYS cc_start: 0.8494 (OUTLIER) cc_final: 0.7888 (mptt) REVERT: J 500 ILE cc_start: 0.8189 (OUTLIER) cc_final: 0.7758 (mp) REVERT: J 594 GLN cc_start: 0.8935 (OUTLIER) cc_final: 0.7791 (pp30) REVERT: J 602 SER cc_start: 0.8000 (m) cc_final: 0.7552 (p) REVERT: J 911 LYS cc_start: 0.8821 (OUTLIER) cc_final: 0.8525 (tttt) REVERT: J 1149 ARG cc_start: 0.7439 (tpp-160) cc_final: 0.7100 (mmm160) REVERT: J 1189 MET cc_start: 0.5627 (mmp) cc_final: 0.5283 (mmm) REVERT: J 1253 ILE cc_start: 0.8489 (mm) cc_final: 0.8171 (mm) REVERT: J 1355 ARG cc_start: 0.8338 (OUTLIER) cc_final: 0.7331 (ptm-80) REVERT: L 33 GLU cc_start: 0.6655 (OUTLIER) cc_final: 0.6343 (pm20) REVERT: L 45 ILE cc_start: 0.8423 (OUTLIER) cc_final: 0.8189 (tt) REVERT: L 276 MET cc_start: 0.4501 (mtt) cc_final: 0.4128 (tpt) REVERT: L 341 LEU cc_start: 0.1122 (OUTLIER) cc_final: 0.0838 (tm) REVERT: L 386 LEU cc_start: 0.9055 (OUTLIER) cc_final: 0.8639 (tp) REVERT: L 489 MET cc_start: 0.7267 (mpt) cc_final: 0.6905 (mmm) REVERT: L 554 ARG cc_start: 0.7279 (mtp85) cc_final: 0.6863 (ttt180) outliers start: 213 outliers final: 140 residues processed: 546 average time/residue: 1.3683 time to fit residues: 893.8805 Evaluate side-chains 519 residues out of total 3197 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 163 poor density : 356 time to evaluate : 3.451 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain N residue 59 VAL Chi-restraints excluded: chain N residue 72 TYR Chi-restraints excluded: chain M residue 300 LEU Chi-restraints excluded: chain G residue 26 VAL Chi-restraints excluded: chain G residue 56 VAL Chi-restraints excluded: chain G residue 74 VAL Chi-restraints excluded: chain G residue 90 VAL Chi-restraints excluded: chain G residue 92 VAL Chi-restraints excluded: chain G residue 118 ASP Chi-restraints excluded: chain G residue 160 HIS Chi-restraints excluded: chain G residue 168 ILE Chi-restraints excluded: chain G residue 173 VAL Chi-restraints excluded: chain G residue 199 ASP Chi-restraints excluded: chain H residue 12 ARG Chi-restraints excluded: chain H residue 14 VAL Chi-restraints excluded: chain H residue 19 VAL Chi-restraints excluded: chain H residue 27 THR Chi-restraints excluded: chain H residue 43 LEU Chi-restraints excluded: chain H residue 98 VAL Chi-restraints excluded: chain H residue 99 ILE Chi-restraints excluded: chain H residue 116 THR Chi-restraints excluded: chain H residue 120 ASP Chi-restraints excluded: chain H residue 124 VAL Chi-restraints excluded: chain H residue 140 ILE Chi-restraints excluded: chain H residue 144 ILE Chi-restraints excluded: chain H residue 156 SER Chi-restraints excluded: chain H residue 174 ASP Chi-restraints excluded: chain H residue 178 SER Chi-restraints excluded: chain H residue 198 LEU Chi-restraints excluded: chain H residue 202 VAL Chi-restraints excluded: chain H residue 207 THR Chi-restraints excluded: chain H residue 231 PHE Chi-restraints excluded: chain I residue 2 VAL Chi-restraints excluded: chain I residue 56 VAL Chi-restraints excluded: chain I residue 60 GLN Chi-restraints excluded: chain I residue 79 VAL Chi-restraints excluded: chain I residue 104 ILE Chi-restraints excluded: chain I residue 229 ILE Chi-restraints excluded: chain I residue 263 VAL Chi-restraints excluded: chain I residue 289 VAL Chi-restraints excluded: chain I residue 296 VAL Chi-restraints excluded: chain I residue 415 GLU Chi-restraints excluded: chain I residue 446 ASP Chi-restraints excluded: chain I residue 456 VAL Chi-restraints excluded: chain I residue 471 VAL Chi-restraints excluded: chain I residue 483 ASP Chi-restraints excluded: chain I residue 484 LEU Chi-restraints excluded: chain I residue 550 VAL Chi-restraints excluded: chain I residue 558 VAL Chi-restraints excluded: chain I residue 568 ASN Chi-restraints excluded: chain I residue 589 THR Chi-restraints excluded: chain I residue 609 ILE Chi-restraints excluded: chain I residue 639 LYS Chi-restraints excluded: chain I residue 648 ASP Chi-restraints excluded: chain I residue 655 VAL Chi-restraints excluded: chain I residue 663 VAL Chi-restraints excluded: chain I residue 685 MET Chi-restraints excluded: chain I residue 690 VAL Chi-restraints excluded: chain I residue 704 MET Chi-restraints excluded: chain I residue 727 VAL Chi-restraints excluded: chain I residue 740 GLU Chi-restraints excluded: chain I residue 748 ILE Chi-restraints excluded: chain I residue 779 ARG Chi-restraints excluded: chain I residue 796 LEU Chi-restraints excluded: chain I residue 799 ASN Chi-restraints excluded: chain I residue 800 MET Chi-restraints excluded: chain I residue 802 VAL Chi-restraints excluded: chain I residue 811 ASN Chi-restraints excluded: chain I residue 835 GLU Chi-restraints excluded: chain I residue 839 VAL Chi-restraints excluded: chain I residue 845 LEU Chi-restraints excluded: chain I residue 867 GLU Chi-restraints excluded: chain I residue 893 THR Chi-restraints excluded: chain I residue 896 THR Chi-restraints excluded: chain I residue 916 SER Chi-restraints excluded: chain I residue 924 VAL Chi-restraints excluded: chain I residue 937 ASP Chi-restraints excluded: chain I residue 971 LEU Chi-restraints excluded: chain I residue 980 VAL Chi-restraints excluded: chain I residue 984 VAL Chi-restraints excluded: chain I residue 1046 VAL Chi-restraints excluded: chain I residue 1060 ILE Chi-restraints excluded: chain I residue 1082 ILE Chi-restraints excluded: chain I residue 1109 ILE Chi-restraints excluded: chain I residue 1117 LEU Chi-restraints excluded: chain I residue 1159 VAL Chi-restraints excluded: chain I residue 1163 THR Chi-restraints excluded: chain I residue 1167 GLU Chi-restraints excluded: chain I residue 1206 THR Chi-restraints excluded: chain I residue 1225 VAL Chi-restraints excluded: chain I residue 1250 SER Chi-restraints excluded: chain I residue 1296 ASP Chi-restraints excluded: chain I residue 1298 VAL Chi-restraints excluded: chain J residue 46 TYR Chi-restraints excluded: chain J residue 81 ARG Chi-restraints excluded: chain J residue 92 VAL Chi-restraints excluded: chain J residue 159 ILE Chi-restraints excluded: chain J residue 170 GLU Chi-restraints excluded: chain J residue 224 LEU Chi-restraints excluded: chain J residue 227 PHE Chi-restraints excluded: chain J residue 279 LEU Chi-restraints excluded: chain J residue 343 LEU Chi-restraints excluded: chain J residue 357 VAL Chi-restraints excluded: chain J residue 399 LYS Chi-restraints excluded: chain J residue 401 VAL Chi-restraints excluded: chain J residue 428 THR Chi-restraints excluded: chain J residue 429 LEU Chi-restraints excluded: chain J residue 468 VAL Chi-restraints excluded: chain J residue 489 ASN Chi-restraints excluded: chain J residue 500 ILE Chi-restraints excluded: chain J residue 507 VAL Chi-restraints excluded: chain J residue 536 LEU Chi-restraints excluded: chain J residue 545 HIS Chi-restraints excluded: chain J residue 567 THR Chi-restraints excluded: chain J residue 594 GLN Chi-restraints excluded: chain J residue 614 LEU Chi-restraints excluded: chain J residue 709 ARG Chi-restraints excluded: chain J residue 740 LEU Chi-restraints excluded: chain J residue 770 LEU Chi-restraints excluded: chain J residue 775 SER Chi-restraints excluded: chain J residue 783 LEU Chi-restraints excluded: chain J residue 786 THR Chi-restraints excluded: chain J residue 803 VAL Chi-restraints excluded: chain J residue 835 LEU Chi-restraints excluded: chain J residue 839 VAL Chi-restraints excluded: chain J residue 847 ASP Chi-restraints excluded: chain J residue 869 CYS Chi-restraints excluded: chain J residue 911 LYS Chi-restraints excluded: chain J residue 1177 ILE Chi-restraints excluded: chain J residue 1205 GLU Chi-restraints excluded: chain J residue 1248 ILE Chi-restraints excluded: chain J residue 1255 VAL Chi-restraints excluded: chain J residue 1267 VAL Chi-restraints excluded: chain J residue 1286 LYS Chi-restraints excluded: chain J residue 1295 ASN Chi-restraints excluded: chain J residue 1355 ARG Chi-restraints excluded: chain K residue 10 VAL Chi-restraints excluded: chain K residue 39 VAL Chi-restraints excluded: chain K residue 74 GLU Chi-restraints excluded: chain L residue 9 LEU Chi-restraints excluded: chain L residue 33 GLU Chi-restraints excluded: chain L residue 34 ASP Chi-restraints excluded: chain L residue 42 GLU Chi-restraints excluded: chain L residue 45 ILE Chi-restraints excluded: chain L residue 95 THR Chi-restraints excluded: chain L residue 108 VAL Chi-restraints excluded: chain L residue 320 ILE Chi-restraints excluded: chain L residue 341 LEU Chi-restraints excluded: chain L residue 344 LEU Chi-restraints excluded: chain L residue 355 ILE Chi-restraints excluded: chain L residue 386 LEU Chi-restraints excluded: chain L residue 449 THR Chi-restraints excluded: chain L residue 454 VAL Chi-restraints excluded: chain L residue 468 ARG Chi-restraints excluded: chain L residue 473 GLU Chi-restraints excluded: chain L residue 485 GLU Chi-restraints excluded: chain L residue 505 ILE Chi-restraints excluded: chain L residue 526 THR Chi-restraints excluded: chain L residue 527 THR Chi-restraints excluded: chain L residue 552 THR Chi-restraints excluded: chain L residue 559 LEU Chi-restraints excluded: chain L residue 568 ASN Chi-restraints excluded: chain L residue 569 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 379 random chunks: chunk 353 optimal weight: 7.9990 chunk 41 optimal weight: 8.9990 chunk 208 optimal weight: 2.9990 chunk 267 optimal weight: 0.8980 chunk 207 optimal weight: 0.8980 chunk 308 optimal weight: 1.9990 chunk 204 optimal weight: 4.9990 chunk 365 optimal weight: 0.0020 chunk 228 optimal weight: 4.9990 chunk 222 optimal weight: 3.9990 chunk 168 optimal weight: 10.0000 overall best weight: 1.3592 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: N 68 GLN ** I 526 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** I 582 ASN I 618 GLN I 811 ASN I 932 GLN I1017 GLN J 157 GLN ** J 320 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J1350 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 129 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 309 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 406 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7847 moved from start: 0.3578 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 32133 Z= 0.213 Angle : 0.613 11.336 43850 Z= 0.316 Chirality : 0.042 0.249 5031 Planarity : 0.004 0.074 5353 Dihedral : 17.461 179.031 5588 Min Nonbonded Distance : 2.060 Molprobity Statistics. All-atom Clashscore : 12.69 Ramachandran Plot: Outliers : 0.14 % Allowed : 5.57 % Favored : 94.29 % Rotamer: Outliers : 6.68 % Allowed : 26.73 % Favored : 66.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.37 % Cis-general : 0.28 % Twisted Proline : 0.00 % Twisted General : 0.06 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.66 (0.14), residues: 3698 helix: 0.74 (0.13), residues: 1571 sheet: -0.82 (0.27), residues: 361 loop : -1.46 (0.14), residues: 1766 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP I 807 HIS 0.004 0.001 HIS J 545 PHE 0.019 0.001 PHE L 259 TYR 0.014 0.001 TYR L 148 ARG 0.013 0.000 ARG L 274 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7396 Ramachandran restraints generated. 3698 Oldfield, 0 Emsley, 3698 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7396 Ramachandran restraints generated. 3698 Oldfield, 0 Emsley, 3698 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 589 residues out of total 3197 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 212 poor density : 377 time to evaluate : 3.907 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: N 18 THR cc_start: 0.8815 (t) cc_final: 0.8494 (p) REVERT: N 70 LYS cc_start: 0.8502 (tttt) cc_final: 0.8208 (pttp) REVERT: G 35 PHE cc_start: 0.8515 (m-80) cc_final: 0.8121 (m-80) REVERT: H 12 ARG cc_start: 0.7192 (OUTLIER) cc_final: 0.6648 (ptp-170) REVERT: H 17 GLU cc_start: 0.7187 (OUTLIER) cc_final: 0.6928 (pt0) REVERT: H 75 GLN cc_start: 0.8222 (tm-30) cc_final: 0.7715 (tt0) REVERT: H 116 THR cc_start: 0.7492 (OUTLIER) cc_final: 0.7096 (m) REVERT: H 199 ASP cc_start: 0.7573 (t70) cc_final: 0.7237 (m-30) REVERT: I 289 VAL cc_start: 0.8534 (OUTLIER) cc_final: 0.8177 (m) REVERT: I 319 LEU cc_start: 0.8046 (mp) cc_final: 0.7815 (mp) REVERT: I 337 PHE cc_start: 0.7906 (t80) cc_final: 0.7539 (t80) REVERT: I 525 THR cc_start: 0.8984 (t) cc_final: 0.8701 (p) REVERT: I 568 ASN cc_start: 0.8391 (OUTLIER) cc_final: 0.8114 (p0) REVERT: I 639 LYS cc_start: 0.8043 (OUTLIER) cc_final: 0.7746 (mppt) REVERT: I 779 ARG cc_start: 0.7517 (OUTLIER) cc_final: 0.6718 (ttm-80) REVERT: I 796 LEU cc_start: 0.9039 (OUTLIER) cc_final: 0.8763 (mp) REVERT: I 800 MET cc_start: 0.8002 (mmm) cc_final: 0.6927 (mtm) REVERT: I 867 GLU cc_start: 0.7604 (OUTLIER) cc_final: 0.7370 (pt0) REVERT: I 878 THR cc_start: 0.8535 (p) cc_final: 0.8189 (t) REVERT: I 1167 GLU cc_start: 0.7597 (OUTLIER) cc_final: 0.7373 (tp30) REVERT: J 81 ARG cc_start: 0.7276 (OUTLIER) cc_final: 0.6617 (ttm170) REVERT: J 83 VAL cc_start: 0.7864 (p) cc_final: 0.7608 (m) REVERT: J 97 VAL cc_start: 0.8686 (p) cc_final: 0.8236 (m) REVERT: J 170 GLU cc_start: 0.7042 (OUTLIER) cc_final: 0.6838 (mm-30) REVERT: J 194 LEU cc_start: 0.7813 (mm) cc_final: 0.7561 (mt) REVERT: J 227 PHE cc_start: 0.8835 (OUTLIER) cc_final: 0.7460 (t80) REVERT: J 301 GLU cc_start: 0.7242 (tt0) cc_final: 0.7010 (tt0) REVERT: J 399 LYS cc_start: 0.8486 (OUTLIER) cc_final: 0.7884 (mptt) REVERT: J 500 ILE cc_start: 0.8181 (OUTLIER) cc_final: 0.7860 (mp) REVERT: J 515 ARG cc_start: 0.8078 (OUTLIER) cc_final: 0.5970 (tpt90) REVERT: J 594 GLN cc_start: 0.8937 (OUTLIER) cc_final: 0.7739 (pp30) REVERT: J 911 LYS cc_start: 0.8822 (OUTLIER) cc_final: 0.8526 (tttt) REVERT: J 1149 ARG cc_start: 0.7380 (tpp-160) cc_final: 0.7034 (mmm160) REVERT: J 1253 ILE cc_start: 0.8487 (OUTLIER) cc_final: 0.8159 (mm) REVERT: L 33 GLU cc_start: 0.6693 (OUTLIER) cc_final: 0.6294 (pm20) REVERT: L 49 ASN cc_start: 0.6135 (OUTLIER) cc_final: 0.5930 (t0) REVERT: L 274 ARG cc_start: 0.5083 (mmm160) cc_final: 0.4707 (mmm-85) REVERT: L 276 MET cc_start: 0.4487 (mtt) cc_final: 0.4048 (tpt) REVERT: L 341 LEU cc_start: 0.1124 (OUTLIER) cc_final: 0.0864 (tm) REVERT: L 363 ARG cc_start: 0.7680 (tmm160) cc_final: 0.7317 (ttp-170) REVERT: L 386 LEU cc_start: 0.9050 (OUTLIER) cc_final: 0.8635 (tp) REVERT: L 489 MET cc_start: 0.7244 (mpt) cc_final: 0.6890 (mmm) REVERT: L 554 ARG cc_start: 0.7242 (mtp85) cc_final: 0.6687 (ttt180) outliers start: 212 outliers final: 133 residues processed: 542 average time/residue: 1.3613 time to fit residues: 880.9058 Evaluate side-chains 508 residues out of total 3197 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 156 poor density : 352 time to evaluate : 3.424 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain N residue 59 VAL Chi-restraints excluded: chain N residue 72 TYR Chi-restraints excluded: chain M residue 300 LEU Chi-restraints excluded: chain G residue 26 VAL Chi-restraints excluded: chain G residue 56 VAL Chi-restraints excluded: chain G residue 74 VAL Chi-restraints excluded: chain G residue 90 VAL Chi-restraints excluded: chain G residue 118 ASP Chi-restraints excluded: chain G residue 127 GLN Chi-restraints excluded: chain G residue 160 HIS Chi-restraints excluded: chain G residue 168 ILE Chi-restraints excluded: chain G residue 173 VAL Chi-restraints excluded: chain G residue 199 ASP Chi-restraints excluded: chain H residue 12 ARG Chi-restraints excluded: chain H residue 14 VAL Chi-restraints excluded: chain H residue 17 GLU Chi-restraints excluded: chain H residue 27 THR Chi-restraints excluded: chain H residue 43 LEU Chi-restraints excluded: chain H residue 72 GLU Chi-restraints excluded: chain H residue 98 VAL Chi-restraints excluded: chain H residue 99 ILE Chi-restraints excluded: chain H residue 116 THR Chi-restraints excluded: chain H residue 120 ASP Chi-restraints excluded: chain H residue 124 VAL Chi-restraints excluded: chain H residue 140 ILE Chi-restraints excluded: chain H residue 144 ILE Chi-restraints excluded: chain H residue 156 SER Chi-restraints excluded: chain H residue 174 ASP Chi-restraints excluded: chain H residue 178 SER Chi-restraints excluded: chain H residue 198 LEU Chi-restraints excluded: chain H residue 231 PHE Chi-restraints excluded: chain I residue 2 VAL Chi-restraints excluded: chain I residue 56 VAL Chi-restraints excluded: chain I residue 60 GLN Chi-restraints excluded: chain I residue 79 VAL Chi-restraints excluded: chain I residue 104 ILE Chi-restraints excluded: chain I residue 132 ASP Chi-restraints excluded: chain I residue 208 ILE Chi-restraints excluded: chain I residue 229 ILE Chi-restraints excluded: chain I residue 263 VAL Chi-restraints excluded: chain I residue 289 VAL Chi-restraints excluded: chain I residue 296 VAL Chi-restraints excluded: chain I residue 415 GLU Chi-restraints excluded: chain I residue 446 ASP Chi-restraints excluded: chain I residue 456 VAL Chi-restraints excluded: chain I residue 471 VAL Chi-restraints excluded: chain I residue 508 SER Chi-restraints excluded: chain I residue 550 VAL Chi-restraints excluded: chain I residue 558 VAL Chi-restraints excluded: chain I residue 568 ASN Chi-restraints excluded: chain I residue 589 THR Chi-restraints excluded: chain I residue 596 ASP Chi-restraints excluded: chain I residue 609 ILE Chi-restraints excluded: chain I residue 639 LYS Chi-restraints excluded: chain I residue 655 VAL Chi-restraints excluded: chain I residue 656 SER Chi-restraints excluded: chain I residue 657 THR Chi-restraints excluded: chain I residue 663 VAL Chi-restraints excluded: chain I residue 685 MET Chi-restraints excluded: chain I residue 690 VAL Chi-restraints excluded: chain I residue 704 MET Chi-restraints excluded: chain I residue 727 VAL Chi-restraints excluded: chain I residue 740 GLU Chi-restraints excluded: chain I residue 748 ILE Chi-restraints excluded: chain I residue 749 ASP Chi-restraints excluded: chain I residue 779 ARG Chi-restraints excluded: chain I residue 796 LEU Chi-restraints excluded: chain I residue 799 ASN Chi-restraints excluded: chain I residue 817 LEU Chi-restraints excluded: chain I residue 835 GLU Chi-restraints excluded: chain I residue 839 VAL Chi-restraints excluded: chain I residue 845 LEU Chi-restraints excluded: chain I residue 867 GLU Chi-restraints excluded: chain I residue 893 THR Chi-restraints excluded: chain I residue 896 THR Chi-restraints excluded: chain I residue 924 VAL Chi-restraints excluded: chain I residue 971 LEU Chi-restraints excluded: chain I residue 980 VAL Chi-restraints excluded: chain I residue 984 VAL Chi-restraints excluded: chain I residue 1037 THR Chi-restraints excluded: chain I residue 1046 VAL Chi-restraints excluded: chain I residue 1060 ILE Chi-restraints excluded: chain I residue 1082 ILE Chi-restraints excluded: chain I residue 1109 ILE Chi-restraints excluded: chain I residue 1117 LEU Chi-restraints excluded: chain I residue 1143 GLU Chi-restraints excluded: chain I residue 1159 VAL Chi-restraints excluded: chain I residue 1163 THR Chi-restraints excluded: chain I residue 1167 GLU Chi-restraints excluded: chain I residue 1206 THR Chi-restraints excluded: chain I residue 1225 VAL Chi-restraints excluded: chain I residue 1250 SER Chi-restraints excluded: chain I residue 1296 ASP Chi-restraints excluded: chain I residue 1298 VAL Chi-restraints excluded: chain J residue 46 TYR Chi-restraints excluded: chain J residue 81 ARG Chi-restraints excluded: chain J residue 92 VAL Chi-restraints excluded: chain J residue 159 ILE Chi-restraints excluded: chain J residue 170 GLU Chi-restraints excluded: chain J residue 224 LEU Chi-restraints excluded: chain J residue 227 PHE Chi-restraints excluded: chain J residue 279 LEU Chi-restraints excluded: chain J residue 343 LEU Chi-restraints excluded: chain J residue 357 VAL Chi-restraints excluded: chain J residue 399 LYS Chi-restraints excluded: chain J residue 428 THR Chi-restraints excluded: chain J residue 429 LEU Chi-restraints excluded: chain J residue 468 VAL Chi-restraints excluded: chain J residue 489 ASN Chi-restraints excluded: chain J residue 500 ILE Chi-restraints excluded: chain J residue 507 VAL Chi-restraints excluded: chain J residue 515 ARG Chi-restraints excluded: chain J residue 536 LEU Chi-restraints excluded: chain J residue 545 HIS Chi-restraints excluded: chain J residue 594 GLN Chi-restraints excluded: chain J residue 709 ARG Chi-restraints excluded: chain J residue 740 LEU Chi-restraints excluded: chain J residue 757 THR Chi-restraints excluded: chain J residue 770 LEU Chi-restraints excluded: chain J residue 775 SER Chi-restraints excluded: chain J residue 783 LEU Chi-restraints excluded: chain J residue 786 THR Chi-restraints excluded: chain J residue 803 VAL Chi-restraints excluded: chain J residue 835 LEU Chi-restraints excluded: chain J residue 839 VAL Chi-restraints excluded: chain J residue 847 ASP Chi-restraints excluded: chain J residue 911 LYS Chi-restraints excluded: chain J residue 1177 ILE Chi-restraints excluded: chain J residue 1205 GLU Chi-restraints excluded: chain J residue 1253 ILE Chi-restraints excluded: chain J residue 1255 VAL Chi-restraints excluded: chain J residue 1265 THR Chi-restraints excluded: chain J residue 1267 VAL Chi-restraints excluded: chain J residue 1295 ASN Chi-restraints excluded: chain K residue 10 VAL Chi-restraints excluded: chain K residue 39 VAL Chi-restraints excluded: chain K residue 74 GLU Chi-restraints excluded: chain L residue 9 LEU Chi-restraints excluded: chain L residue 33 GLU Chi-restraints excluded: chain L residue 49 ASN Chi-restraints excluded: chain L residue 98 VAL Chi-restraints excluded: chain L residue 108 VAL Chi-restraints excluded: chain L residue 320 ILE Chi-restraints excluded: chain L residue 341 LEU Chi-restraints excluded: chain L residue 344 LEU Chi-restraints excluded: chain L residue 355 ILE Chi-restraints excluded: chain L residue 386 LEU Chi-restraints excluded: chain L residue 449 THR Chi-restraints excluded: chain L residue 454 VAL Chi-restraints excluded: chain L residue 468 ARG Chi-restraints excluded: chain L residue 473 GLU Chi-restraints excluded: chain L residue 485 GLU Chi-restraints excluded: chain L residue 505 ILE Chi-restraints excluded: chain L residue 526 THR Chi-restraints excluded: chain L residue 552 THR Chi-restraints excluded: chain L residue 559 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 379 random chunks: chunk 225 optimal weight: 4.9990 chunk 145 optimal weight: 6.9990 chunk 218 optimal weight: 0.9990 chunk 110 optimal weight: 0.9990 chunk 71 optimal weight: 1.9990 chunk 70 optimal weight: 0.6980 chunk 232 optimal weight: 7.9990 chunk 248 optimal weight: 4.9990 chunk 180 optimal weight: 1.9990 chunk 34 optimal weight: 0.2980 chunk 287 optimal weight: 10.0000 overall best weight: 0.9986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** I 526 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** I 582 ASN I 618 GLN I 811 ASN ** J 320 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J1350 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 49 ASN ** L 129 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 309 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 406 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7823 moved from start: 0.3759 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 32133 Z= 0.186 Angle : 0.607 13.174 43850 Z= 0.313 Chirality : 0.041 0.237 5031 Planarity : 0.004 0.076 5353 Dihedral : 17.299 179.094 5573 Min Nonbonded Distance : 2.048 Molprobity Statistics. All-atom Clashscore : 12.64 Ramachandran Plot: Outliers : 0.11 % Allowed : 5.35 % Favored : 94.54 % Rotamer: Outliers : 6.01 % Allowed : 27.58 % Favored : 66.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.37 % Cis-general : 0.28 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.52 (0.14), residues: 3698 helix: 0.81 (0.13), residues: 1578 sheet: -0.65 (0.27), residues: 356 loop : -1.35 (0.15), residues: 1764 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP I 807 HIS 0.003 0.001 HIS J 545 PHE 0.022 0.001 PHE L 259 TYR 0.013 0.001 TYR H 177 ARG 0.012 0.000 ARG L 274 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7396 Ramachandran restraints generated. 3698 Oldfield, 0 Emsley, 3698 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7396 Ramachandran restraints generated. 3698 Oldfield, 0 Emsley, 3698 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 578 residues out of total 3197 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 191 poor density : 387 time to evaluate : 3.738 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: N 70 LYS cc_start: 0.8508 (tttt) cc_final: 0.8232 (pttp) REVERT: G 33 ARG cc_start: 0.7893 (tpp-160) cc_final: 0.7605 (tpp-160) REVERT: G 35 PHE cc_start: 0.8416 (m-80) cc_final: 0.8057 (m-80) REVERT: H 12 ARG cc_start: 0.7119 (OUTLIER) cc_final: 0.6355 (ptp-170) REVERT: H 17 GLU cc_start: 0.7097 (OUTLIER) cc_final: 0.6839 (pt0) REVERT: H 199 ASP cc_start: 0.7578 (t70) cc_final: 0.7245 (m-30) REVERT: I 254 ASP cc_start: 0.6024 (OUTLIER) cc_final: 0.4958 (p0) REVERT: I 289 VAL cc_start: 0.8498 (OUTLIER) cc_final: 0.8144 (m) REVERT: I 319 LEU cc_start: 0.8055 (mp) cc_final: 0.7838 (mp) REVERT: I 337 PHE cc_start: 0.7868 (t80) cc_final: 0.7488 (t80) REVERT: I 481 LEU cc_start: 0.7799 (mt) cc_final: 0.7543 (mt) REVERT: I 525 THR cc_start: 0.8973 (t) cc_final: 0.8701 (p) REVERT: I 639 LYS cc_start: 0.7999 (OUTLIER) cc_final: 0.7708 (mppt) REVERT: I 779 ARG cc_start: 0.7494 (OUTLIER) cc_final: 0.6616 (ttm-80) REVERT: I 796 LEU cc_start: 0.9022 (OUTLIER) cc_final: 0.8792 (mp) REVERT: I 800 MET cc_start: 0.7926 (OUTLIER) cc_final: 0.6889 (mtm) REVERT: I 867 GLU cc_start: 0.7609 (OUTLIER) cc_final: 0.7372 (pt0) REVERT: I 1167 GLU cc_start: 0.7586 (OUTLIER) cc_final: 0.7357 (tp30) REVERT: I 1219 GLU cc_start: 0.7627 (pt0) cc_final: 0.7162 (pt0) REVERT: J 97 VAL cc_start: 0.8652 (p) cc_final: 0.8220 (m) REVERT: J 194 LEU cc_start: 0.7745 (mm) cc_final: 0.7530 (mt) REVERT: J 227 PHE cc_start: 0.8811 (OUTLIER) cc_final: 0.7368 (t80) REVERT: J 301 GLU cc_start: 0.7220 (tt0) cc_final: 0.7005 (tt0) REVERT: J 500 ILE cc_start: 0.8186 (OUTLIER) cc_final: 0.7861 (mp) REVERT: J 515 ARG cc_start: 0.8034 (OUTLIER) cc_final: 0.5958 (tpt90) REVERT: J 634 ARG cc_start: 0.7869 (mtp180) cc_final: 0.7565 (mtp85) REVERT: J 911 LYS cc_start: 0.8801 (OUTLIER) cc_final: 0.8516 (tttt) REVERT: J 1149 ARG cc_start: 0.7287 (tpp-160) cc_final: 0.6977 (mmm160) REVERT: J 1253 ILE cc_start: 0.8465 (mm) cc_final: 0.8215 (mm) REVERT: J 1355 ARG cc_start: 0.8274 (OUTLIER) cc_final: 0.7052 (ptm-80) REVERT: L 274 ARG cc_start: 0.5229 (mmm160) cc_final: 0.4783 (mmm-85) REVERT: L 276 MET cc_start: 0.4617 (mtt) cc_final: 0.4096 (tpt) REVERT: L 341 LEU cc_start: 0.1101 (OUTLIER) cc_final: 0.0850 (tm) REVERT: L 386 LEU cc_start: 0.9012 (OUTLIER) cc_final: 0.8602 (tp) REVERT: L 456 MET cc_start: 0.8156 (tpp) cc_final: 0.7853 (tpt) REVERT: L 489 MET cc_start: 0.7131 (mpt) cc_final: 0.6815 (mmm) REVERT: L 554 ARG cc_start: 0.7226 (mtp85) cc_final: 0.6734 (ttt180) outliers start: 191 outliers final: 122 residues processed: 536 average time/residue: 1.3506 time to fit residues: 864.2508 Evaluate side-chains 495 residues out of total 3197 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 139 poor density : 356 time to evaluate : 3.503 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain N residue 59 VAL Chi-restraints excluded: chain N residue 72 TYR Chi-restraints excluded: chain M residue 300 LEU Chi-restraints excluded: chain G residue 56 VAL Chi-restraints excluded: chain G residue 90 VAL Chi-restraints excluded: chain G residue 95 LYS Chi-restraints excluded: chain G residue 127 GLN Chi-restraints excluded: chain G residue 160 HIS Chi-restraints excluded: chain G residue 168 ILE Chi-restraints excluded: chain G residue 173 VAL Chi-restraints excluded: chain G residue 199 ASP Chi-restraints excluded: chain H residue 12 ARG Chi-restraints excluded: chain H residue 14 VAL Chi-restraints excluded: chain H residue 16 ILE Chi-restraints excluded: chain H residue 17 GLU Chi-restraints excluded: chain H residue 27 THR Chi-restraints excluded: chain H residue 43 LEU Chi-restraints excluded: chain H residue 98 VAL Chi-restraints excluded: chain H residue 99 ILE Chi-restraints excluded: chain H residue 116 THR Chi-restraints excluded: chain H residue 124 VAL Chi-restraints excluded: chain H residue 140 ILE Chi-restraints excluded: chain H residue 144 ILE Chi-restraints excluded: chain H residue 156 SER Chi-restraints excluded: chain H residue 178 SER Chi-restraints excluded: chain H residue 198 LEU Chi-restraints excluded: chain H residue 231 PHE Chi-restraints excluded: chain I residue 2 VAL Chi-restraints excluded: chain I residue 56 VAL Chi-restraints excluded: chain I residue 60 GLN Chi-restraints excluded: chain I residue 79 VAL Chi-restraints excluded: chain I residue 104 ILE Chi-restraints excluded: chain I residue 208 ILE Chi-restraints excluded: chain I residue 229 ILE Chi-restraints excluded: chain I residue 253 PHE Chi-restraints excluded: chain I residue 254 ASP Chi-restraints excluded: chain I residue 263 VAL Chi-restraints excluded: chain I residue 289 VAL Chi-restraints excluded: chain I residue 296 VAL Chi-restraints excluded: chain I residue 456 VAL Chi-restraints excluded: chain I residue 471 VAL Chi-restraints excluded: chain I residue 484 LEU Chi-restraints excluded: chain I residue 508 SER Chi-restraints excluded: chain I residue 550 VAL Chi-restraints excluded: chain I residue 558 VAL Chi-restraints excluded: chain I residue 589 THR Chi-restraints excluded: chain I residue 609 ILE Chi-restraints excluded: chain I residue 638 SER Chi-restraints excluded: chain I residue 639 LYS Chi-restraints excluded: chain I residue 655 VAL Chi-restraints excluded: chain I residue 656 SER Chi-restraints excluded: chain I residue 657 THR Chi-restraints excluded: chain I residue 685 MET Chi-restraints excluded: chain I residue 704 MET Chi-restraints excluded: chain I residue 727 VAL Chi-restraints excluded: chain I residue 748 ILE Chi-restraints excluded: chain I residue 779 ARG Chi-restraints excluded: chain I residue 796 LEU Chi-restraints excluded: chain I residue 799 ASN Chi-restraints excluded: chain I residue 800 MET Chi-restraints excluded: chain I residue 835 GLU Chi-restraints excluded: chain I residue 839 VAL Chi-restraints excluded: chain I residue 845 LEU Chi-restraints excluded: chain I residue 867 GLU Chi-restraints excluded: chain I residue 893 THR Chi-restraints excluded: chain I residue 896 THR Chi-restraints excluded: chain I residue 924 VAL Chi-restraints excluded: chain I residue 971 LEU Chi-restraints excluded: chain I residue 979 LEU Chi-restraints excluded: chain I residue 980 VAL Chi-restraints excluded: chain I residue 984 VAL Chi-restraints excluded: chain I residue 1037 THR Chi-restraints excluded: chain I residue 1046 VAL Chi-restraints excluded: chain I residue 1060 ILE Chi-restraints excluded: chain I residue 1082 ILE Chi-restraints excluded: chain I residue 1092 THR Chi-restraints excluded: chain I residue 1117 LEU Chi-restraints excluded: chain I residue 1143 GLU Chi-restraints excluded: chain I residue 1159 VAL Chi-restraints excluded: chain I residue 1163 THR Chi-restraints excluded: chain I residue 1167 GLU Chi-restraints excluded: chain I residue 1206 THR Chi-restraints excluded: chain I residue 1225 VAL Chi-restraints excluded: chain I residue 1250 SER Chi-restraints excluded: chain I residue 1296 ASP Chi-restraints excluded: chain I residue 1298 VAL Chi-restraints excluded: chain J residue 46 TYR Chi-restraints excluded: chain J residue 92 VAL Chi-restraints excluded: chain J residue 159 ILE Chi-restraints excluded: chain J residue 212 THR Chi-restraints excluded: chain J residue 224 LEU Chi-restraints excluded: chain J residue 227 PHE Chi-restraints excluded: chain J residue 279 LEU Chi-restraints excluded: chain J residue 329 ASP Chi-restraints excluded: chain J residue 343 LEU Chi-restraints excluded: chain J residue 357 VAL Chi-restraints excluded: chain J residue 428 THR Chi-restraints excluded: chain J residue 429 LEU Chi-restraints excluded: chain J residue 468 VAL Chi-restraints excluded: chain J residue 500 ILE Chi-restraints excluded: chain J residue 515 ARG Chi-restraints excluded: chain J residue 536 LEU Chi-restraints excluded: chain J residue 545 HIS Chi-restraints excluded: chain J residue 567 THR Chi-restraints excluded: chain J residue 709 ARG Chi-restraints excluded: chain J residue 740 LEU Chi-restraints excluded: chain J residue 757 THR Chi-restraints excluded: chain J residue 770 LEU Chi-restraints excluded: chain J residue 775 SER Chi-restraints excluded: chain J residue 783 LEU Chi-restraints excluded: chain J residue 786 THR Chi-restraints excluded: chain J residue 835 LEU Chi-restraints excluded: chain J residue 839 VAL Chi-restraints excluded: chain J residue 847 ASP Chi-restraints excluded: chain J residue 911 LYS Chi-restraints excluded: chain J residue 1177 ILE Chi-restraints excluded: chain J residue 1255 VAL Chi-restraints excluded: chain J residue 1267 VAL Chi-restraints excluded: chain J residue 1295 ASN Chi-restraints excluded: chain J residue 1355 ARG Chi-restraints excluded: chain K residue 39 VAL Chi-restraints excluded: chain K residue 74 GLU Chi-restraints excluded: chain L residue 9 LEU Chi-restraints excluded: chain L residue 98 VAL Chi-restraints excluded: chain L residue 108 VAL Chi-restraints excluded: chain L residue 320 ILE Chi-restraints excluded: chain L residue 341 LEU Chi-restraints excluded: chain L residue 344 LEU Chi-restraints excluded: chain L residue 355 ILE Chi-restraints excluded: chain L residue 386 LEU Chi-restraints excluded: chain L residue 449 THR Chi-restraints excluded: chain L residue 468 ARG Chi-restraints excluded: chain L residue 473 GLU Chi-restraints excluded: chain L residue 485 GLU Chi-restraints excluded: chain L residue 505 ILE Chi-restraints excluded: chain L residue 552 THR Chi-restraints excluded: chain L residue 559 LEU Chi-restraints excluded: chain L residue 568 ASN Chi-restraints excluded: chain L residue 569 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 379 random chunks: chunk 332 optimal weight: 9.9990 chunk 349 optimal weight: 0.8980 chunk 319 optimal weight: 7.9990 chunk 340 optimal weight: 0.4980 chunk 204 optimal weight: 2.9990 chunk 148 optimal weight: 0.8980 chunk 267 optimal weight: 4.9990 chunk 104 optimal weight: 5.9990 chunk 307 optimal weight: 0.0980 chunk 321 optimal weight: 0.7980 chunk 339 optimal weight: 10.0000 overall best weight: 0.6380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: G 147 GLN ** I 193 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 510 GLN ** I 526 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** I 582 ASN I 618 GLN I 811 ASN J 594 GLN ** J1350 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 129 GLN ** L 309 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 362 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 406 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 518 HIS Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7791 moved from start: 0.4034 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 32133 Z= 0.166 Angle : 0.598 11.245 43850 Z= 0.307 Chirality : 0.041 0.226 5031 Planarity : 0.004 0.059 5353 Dihedral : 17.067 179.541 5555 Min Nonbonded Distance : 2.051 Molprobity Statistics. All-atom Clashscore : 12.42 Ramachandran Plot: Outliers : 0.08 % Allowed : 5.16 % Favored : 94.75 % Rotamer: Outliers : 4.53 % Allowed : 29.31 % Favored : 66.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.37 % Cis-general : 0.28 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.35 (0.14), residues: 3698 helix: 1.00 (0.13), residues: 1567 sheet: -0.61 (0.28), residues: 344 loop : -1.29 (0.15), residues: 1787 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP I 807 HIS 0.003 0.001 HIS I 604 PHE 0.022 0.001 PHE L 259 TYR 0.022 0.001 TYR N 35 ARG 0.011 0.000 ARG L 274 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7396 Ramachandran restraints generated. 3698 Oldfield, 0 Emsley, 3698 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7396 Ramachandran restraints generated. 3698 Oldfield, 0 Emsley, 3698 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 528 residues out of total 3197 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 144 poor density : 384 time to evaluate : 3.717 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: N 70 LYS cc_start: 0.8549 (tttt) cc_final: 0.8299 (pttp) REVERT: G 35 PHE cc_start: 0.8294 (m-80) cc_final: 0.7984 (m-80) REVERT: G 92 VAL cc_start: 0.8523 (m) cc_final: 0.8229 (t) REVERT: H 12 ARG cc_start: 0.6997 (OUTLIER) cc_final: 0.6344 (ptp-170) REVERT: H 75 GLN cc_start: 0.8218 (tm-30) cc_final: 0.7511 (pt0) REVERT: H 199 ASP cc_start: 0.7529 (t70) cc_final: 0.7236 (t0) REVERT: I 238 GLN cc_start: 0.5384 (tt0) cc_final: 0.5015 (tm-30) REVERT: I 289 VAL cc_start: 0.8475 (OUTLIER) cc_final: 0.8159 (m) REVERT: I 337 PHE cc_start: 0.7880 (t80) cc_final: 0.7516 (t80) REVERT: I 473 ARG cc_start: 0.7609 (ttp80) cc_final: 0.7158 (ttp80) REVERT: I 525 THR cc_start: 0.8969 (t) cc_final: 0.8706 (p) REVERT: I 779 ARG cc_start: 0.7536 (OUTLIER) cc_final: 0.6698 (ttm-80) REVERT: I 800 MET cc_start: 0.7891 (OUTLIER) cc_final: 0.6902 (mtm) REVERT: I 1026 GLU cc_start: 0.7790 (OUTLIER) cc_final: 0.7568 (tp30) REVERT: I 1167 GLU cc_start: 0.7568 (OUTLIER) cc_final: 0.7333 (tp30) REVERT: J 97 VAL cc_start: 0.8575 (p) cc_final: 0.8181 (m) REVERT: J 194 LEU cc_start: 0.7593 (mm) cc_final: 0.7351 (mt) REVERT: J 227 PHE cc_start: 0.8801 (OUTLIER) cc_final: 0.7316 (t80) REVERT: J 466 MET cc_start: 0.8574 (OUTLIER) cc_final: 0.8362 (ttp) REVERT: J 500 ILE cc_start: 0.8110 (OUTLIER) cc_final: 0.7788 (mp) REVERT: J 634 ARG cc_start: 0.7850 (mtp180) cc_final: 0.7494 (mtp85) REVERT: J 1149 ARG cc_start: 0.7249 (tpp-160) cc_final: 0.6970 (mmm160) REVERT: J 1189 MET cc_start: 0.5326 (mmp) cc_final: 0.4813 (mmm) REVERT: J 1253 ILE cc_start: 0.8483 (OUTLIER) cc_final: 0.8168 (mm) REVERT: J 1314 LEU cc_start: 0.8134 (mp) cc_final: 0.7905 (mt) REVERT: J 1326 GLN cc_start: 0.8439 (mt0) cc_final: 0.7825 (mt0) REVERT: K 72 GLN cc_start: 0.6946 (tp40) cc_final: 0.5871 (mt0) REVERT: L 33 GLU cc_start: 0.6652 (OUTLIER) cc_final: 0.6388 (pm20) REVERT: L 274 ARG cc_start: 0.5407 (mmm160) cc_final: 0.4934 (mmm-85) REVERT: L 276 MET cc_start: 0.4426 (mtt) cc_final: 0.4090 (tpt) REVERT: L 341 LEU cc_start: 0.0958 (OUTLIER) cc_final: 0.0698 (tm) REVERT: L 386 LEU cc_start: 0.8955 (OUTLIER) cc_final: 0.8571 (tp) REVERT: L 456 MET cc_start: 0.8162 (tpp) cc_final: 0.7843 (mmm) REVERT: L 489 MET cc_start: 0.7298 (mpt) cc_final: 0.6884 (mmm) REVERT: L 554 ARG cc_start: 0.7240 (mtp85) cc_final: 0.6777 (ttt180) REVERT: L 561 MET cc_start: 0.8021 (tmm) cc_final: 0.7727 (ttp) outliers start: 144 outliers final: 97 residues processed: 495 average time/residue: 1.4086 time to fit residues: 829.6126 Evaluate side-chains 458 residues out of total 3197 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 110 poor density : 348 time to evaluate : 3.560 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain N residue 59 VAL Chi-restraints excluded: chain M residue 300 LEU Chi-restraints excluded: chain G residue 56 VAL Chi-restraints excluded: chain G residue 90 VAL Chi-restraints excluded: chain G residue 95 LYS Chi-restraints excluded: chain G residue 118 ASP Chi-restraints excluded: chain G residue 127 GLN Chi-restraints excluded: chain G residue 160 HIS Chi-restraints excluded: chain G residue 168 ILE Chi-restraints excluded: chain G residue 173 VAL Chi-restraints excluded: chain H residue 12 ARG Chi-restraints excluded: chain H residue 27 THR Chi-restraints excluded: chain H residue 43 LEU Chi-restraints excluded: chain H residue 99 ILE Chi-restraints excluded: chain H residue 116 THR Chi-restraints excluded: chain H residue 124 VAL Chi-restraints excluded: chain H residue 140 ILE Chi-restraints excluded: chain H residue 144 ILE Chi-restraints excluded: chain H residue 178 SER Chi-restraints excluded: chain H residue 198 LEU Chi-restraints excluded: chain H residue 231 PHE Chi-restraints excluded: chain I residue 2 VAL Chi-restraints excluded: chain I residue 60 GLN Chi-restraints excluded: chain I residue 104 ILE Chi-restraints excluded: chain I residue 229 ILE Chi-restraints excluded: chain I residue 254 ASP Chi-restraints excluded: chain I residue 289 VAL Chi-restraints excluded: chain I residue 296 VAL Chi-restraints excluded: chain I residue 456 VAL Chi-restraints excluded: chain I residue 508 SER Chi-restraints excluded: chain I residue 550 VAL Chi-restraints excluded: chain I residue 558 VAL Chi-restraints excluded: chain I residue 589 THR Chi-restraints excluded: chain I residue 609 ILE Chi-restraints excluded: chain I residue 638 SER Chi-restraints excluded: chain I residue 656 SER Chi-restraints excluded: chain I residue 657 THR Chi-restraints excluded: chain I residue 685 MET Chi-restraints excluded: chain I residue 704 MET Chi-restraints excluded: chain I residue 727 VAL Chi-restraints excluded: chain I residue 748 ILE Chi-restraints excluded: chain I residue 779 ARG Chi-restraints excluded: chain I residue 799 ASN Chi-restraints excluded: chain I residue 800 MET Chi-restraints excluded: chain I residue 811 ASN Chi-restraints excluded: chain I residue 835 GLU Chi-restraints excluded: chain I residue 839 VAL Chi-restraints excluded: chain I residue 845 LEU Chi-restraints excluded: chain I residue 893 THR Chi-restraints excluded: chain I residue 896 THR Chi-restraints excluded: chain I residue 924 VAL Chi-restraints excluded: chain I residue 980 VAL Chi-restraints excluded: chain I residue 984 VAL Chi-restraints excluded: chain I residue 1026 GLU Chi-restraints excluded: chain I residue 1046 VAL Chi-restraints excluded: chain I residue 1060 ILE Chi-restraints excluded: chain I residue 1082 ILE Chi-restraints excluded: chain I residue 1092 THR Chi-restraints excluded: chain I residue 1117 LEU Chi-restraints excluded: chain I residue 1143 GLU Chi-restraints excluded: chain I residue 1163 THR Chi-restraints excluded: chain I residue 1167 GLU Chi-restraints excluded: chain I residue 1206 THR Chi-restraints excluded: chain I residue 1250 SER Chi-restraints excluded: chain I residue 1296 ASP Chi-restraints excluded: chain I residue 1298 VAL Chi-restraints excluded: chain J residue 46 TYR Chi-restraints excluded: chain J residue 92 VAL Chi-restraints excluded: chain J residue 159 ILE Chi-restraints excluded: chain J residue 212 THR Chi-restraints excluded: chain J residue 224 LEU Chi-restraints excluded: chain J residue 227 PHE Chi-restraints excluded: chain J residue 279 LEU Chi-restraints excluded: chain J residue 343 LEU Chi-restraints excluded: chain J residue 428 THR Chi-restraints excluded: chain J residue 429 LEU Chi-restraints excluded: chain J residue 466 MET Chi-restraints excluded: chain J residue 468 VAL Chi-restraints excluded: chain J residue 500 ILE Chi-restraints excluded: chain J residue 536 LEU Chi-restraints excluded: chain J residue 545 HIS Chi-restraints excluded: chain J residue 709 ARG Chi-restraints excluded: chain J residue 740 LEU Chi-restraints excluded: chain J residue 775 SER Chi-restraints excluded: chain J residue 783 LEU Chi-restraints excluded: chain J residue 835 LEU Chi-restraints excluded: chain J residue 839 VAL Chi-restraints excluded: chain J residue 847 ASP Chi-restraints excluded: chain J residue 1177 ILE Chi-restraints excluded: chain J residue 1253 ILE Chi-restraints excluded: chain J residue 1265 THR Chi-restraints excluded: chain J residue 1267 VAL Chi-restraints excluded: chain K residue 74 GLU Chi-restraints excluded: chain L residue 33 GLU Chi-restraints excluded: chain L residue 98 VAL Chi-restraints excluded: chain L residue 108 VAL Chi-restraints excluded: chain L residue 320 ILE Chi-restraints excluded: chain L residue 341 LEU Chi-restraints excluded: chain L residue 344 LEU Chi-restraints excluded: chain L residue 355 ILE Chi-restraints excluded: chain L residue 386 LEU Chi-restraints excluded: chain L residue 399 LEU Chi-restraints excluded: chain L residue 449 THR Chi-restraints excluded: chain L residue 468 ARG Chi-restraints excluded: chain L residue 485 GLU Chi-restraints excluded: chain L residue 505 ILE Chi-restraints excluded: chain L residue 552 THR Chi-restraints excluded: chain L residue 559 LEU Chi-restraints excluded: chain L residue 568 ASN Chi-restraints excluded: chain L residue 569 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 379 random chunks: chunk 223 optimal weight: 2.9990 chunk 359 optimal weight: 1.9990 chunk 219 optimal weight: 0.8980 chunk 170 optimal weight: 4.9990 chunk 250 optimal weight: 3.9990 chunk 377 optimal weight: 4.9990 chunk 347 optimal weight: 5.9990 chunk 300 optimal weight: 0.3980 chunk 31 optimal weight: 3.9990 chunk 232 optimal weight: 3.9990 chunk 184 optimal weight: 0.8980 overall best weight: 1.4384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** I 526 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** I 582 ASN I 618 GLN I 932 GLN ** J 94 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 229 GLN ** J 309 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 594 GLN ** J1350 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 54 GLN ** L 283 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 309 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 362 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 406 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 518 HIS Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7798 moved from start: 0.4054 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.268 32133 Z= 0.256 Angle : 0.709 59.166 43850 Z= 0.385 Chirality : 0.042 0.256 5031 Planarity : 0.004 0.095 5353 Dihedral : 17.044 179.541 5537 Min Nonbonded Distance : 1.894 Molprobity Statistics. All-atom Clashscore : 13.73 Ramachandran Plot: Outliers : 0.08 % Allowed : 5.08 % Favored : 94.84 % Rotamer: Outliers : 3.97 % Allowed : 29.85 % Favored : 66.18 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.37 % Cis-general : 0.28 % Twisted Proline : 0.00 % Twisted General : 0.03 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.36 (0.14), residues: 3698 helix: 0.99 (0.13), residues: 1567 sheet: -0.67 (0.27), residues: 354 loop : -1.28 (0.15), residues: 1777 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP I 807 HIS 0.003 0.001 HIS I 447 PHE 0.020 0.001 PHE L 259 TYR 0.017 0.001 TYR N 35 ARG 0.013 0.000 ARG I 272 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7396 Ramachandran restraints generated. 3698 Oldfield, 0 Emsley, 3698 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7396 Ramachandran restraints generated. 3698 Oldfield, 0 Emsley, 3698 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 473 residues out of total 3197 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 126 poor density : 347 time to evaluate : 3.447 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: N 70 LYS cc_start: 0.8546 (tttt) cc_final: 0.8303 (pttp) REVERT: G 35 PHE cc_start: 0.8298 (m-80) cc_final: 0.7991 (m-80) REVERT: G 92 VAL cc_start: 0.8520 (m) cc_final: 0.8233 (t) REVERT: H 12 ARG cc_start: 0.7006 (OUTLIER) cc_final: 0.6391 (ptp-170) REVERT: H 75 GLN cc_start: 0.8187 (tm-30) cc_final: 0.7518 (pt0) REVERT: H 199 ASP cc_start: 0.7539 (t70) cc_final: 0.7243 (t0) REVERT: I 238 GLN cc_start: 0.5391 (tt0) cc_final: 0.5015 (tm-30) REVERT: I 289 VAL cc_start: 0.8490 (OUTLIER) cc_final: 0.8107 (m) REVERT: I 319 LEU cc_start: 0.8083 (mp) cc_final: 0.7841 (mp) REVERT: I 337 PHE cc_start: 0.7879 (t80) cc_final: 0.7515 (t80) REVERT: I 473 ARG cc_start: 0.7603 (ttp80) cc_final: 0.7204 (ttp80) REVERT: I 525 THR cc_start: 0.8968 (t) cc_final: 0.8704 (p) REVERT: I 779 ARG cc_start: 0.7486 (OUTLIER) cc_final: 0.6658 (ttm-80) REVERT: I 800 MET cc_start: 0.7918 (OUTLIER) cc_final: 0.6910 (mtm) REVERT: I 1026 GLU cc_start: 0.7800 (OUTLIER) cc_final: 0.7567 (tp30) REVERT: I 1167 GLU cc_start: 0.7567 (OUTLIER) cc_final: 0.7335 (tp30) REVERT: J 97 VAL cc_start: 0.8606 (p) cc_final: 0.8203 (m) REVERT: J 194 LEU cc_start: 0.7598 (mm) cc_final: 0.7352 (mt) REVERT: J 227 PHE cc_start: 0.8797 (OUTLIER) cc_final: 0.7317 (t80) REVERT: J 466 MET cc_start: 0.8577 (OUTLIER) cc_final: 0.8370 (ttp) REVERT: J 500 ILE cc_start: 0.8123 (OUTLIER) cc_final: 0.7796 (mp) REVERT: J 634 ARG cc_start: 0.7747 (mtp180) cc_final: 0.7509 (mtp85) REVERT: J 1149 ARG cc_start: 0.7253 (tpp-160) cc_final: 0.6968 (mmm160) REVERT: J 1189 MET cc_start: 0.5330 (mmp) cc_final: 0.4813 (mmm) REVERT: J 1253 ILE cc_start: 0.8485 (OUTLIER) cc_final: 0.8175 (mm) REVERT: J 1314 LEU cc_start: 0.8135 (mp) cc_final: 0.7913 (mt) REVERT: J 1326 GLN cc_start: 0.8448 (mt0) cc_final: 0.7832 (mt0) REVERT: K 72 GLN cc_start: 0.6813 (tp40) cc_final: 0.5752 (mt0) REVERT: L 33 GLU cc_start: 0.6652 (OUTLIER) cc_final: 0.6390 (pm20) REVERT: L 274 ARG cc_start: 0.5364 (mmm160) cc_final: 0.4939 (mmm-85) REVERT: L 276 MET cc_start: 0.4436 (mtt) cc_final: 0.4088 (tpt) REVERT: L 386 LEU cc_start: 0.8962 (OUTLIER) cc_final: 0.8577 (tp) REVERT: L 456 MET cc_start: 0.8171 (tpp) cc_final: 0.7845 (mmm) REVERT: L 489 MET cc_start: 0.7298 (mpt) cc_final: 0.6886 (mmm) REVERT: L 554 ARG cc_start: 0.7245 (mtp85) cc_final: 0.6778 (ttt180) REVERT: L 561 MET cc_start: 0.8040 (tmm) cc_final: 0.7731 (ttp) outliers start: 126 outliers final: 103 residues processed: 444 average time/residue: 1.4146 time to fit residues: 749.7986 Evaluate side-chains 457 residues out of total 3197 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 115 poor density : 342 time to evaluate : 3.647 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain N residue 59 VAL Chi-restraints excluded: chain N residue 72 TYR Chi-restraints excluded: chain M residue 300 LEU Chi-restraints excluded: chain G residue 56 VAL Chi-restraints excluded: chain G residue 90 VAL Chi-restraints excluded: chain G residue 95 LYS Chi-restraints excluded: chain G residue 118 ASP Chi-restraints excluded: chain G residue 127 GLN Chi-restraints excluded: chain G residue 160 HIS Chi-restraints excluded: chain G residue 168 ILE Chi-restraints excluded: chain G residue 173 VAL Chi-restraints excluded: chain H residue 12 ARG Chi-restraints excluded: chain H residue 27 THR Chi-restraints excluded: chain H residue 43 LEU Chi-restraints excluded: chain H residue 99 ILE Chi-restraints excluded: chain H residue 116 THR Chi-restraints excluded: chain H residue 124 VAL Chi-restraints excluded: chain H residue 140 ILE Chi-restraints excluded: chain H residue 144 ILE Chi-restraints excluded: chain H residue 178 SER Chi-restraints excluded: chain H residue 198 LEU Chi-restraints excluded: chain H residue 231 PHE Chi-restraints excluded: chain I residue 2 VAL Chi-restraints excluded: chain I residue 60 GLN Chi-restraints excluded: chain I residue 104 ILE Chi-restraints excluded: chain I residue 229 ILE Chi-restraints excluded: chain I residue 254 ASP Chi-restraints excluded: chain I residue 255 ILE Chi-restraints excluded: chain I residue 289 VAL Chi-restraints excluded: chain I residue 296 VAL Chi-restraints excluded: chain I residue 456 VAL Chi-restraints excluded: chain I residue 508 SER Chi-restraints excluded: chain I residue 550 VAL Chi-restraints excluded: chain I residue 558 VAL Chi-restraints excluded: chain I residue 589 THR Chi-restraints excluded: chain I residue 609 ILE Chi-restraints excluded: chain I residue 638 SER Chi-restraints excluded: chain I residue 656 SER Chi-restraints excluded: chain I residue 685 MET Chi-restraints excluded: chain I residue 704 MET Chi-restraints excluded: chain I residue 727 VAL Chi-restraints excluded: chain I residue 748 ILE Chi-restraints excluded: chain I residue 779 ARG Chi-restraints excluded: chain I residue 799 ASN Chi-restraints excluded: chain I residue 800 MET Chi-restraints excluded: chain I residue 811 ASN Chi-restraints excluded: chain I residue 835 GLU Chi-restraints excluded: chain I residue 839 VAL Chi-restraints excluded: chain I residue 845 LEU Chi-restraints excluded: chain I residue 893 THR Chi-restraints excluded: chain I residue 896 THR Chi-restraints excluded: chain I residue 924 VAL Chi-restraints excluded: chain I residue 971 LEU Chi-restraints excluded: chain I residue 980 VAL Chi-restraints excluded: chain I residue 984 VAL Chi-restraints excluded: chain I residue 1026 GLU Chi-restraints excluded: chain I residue 1046 VAL Chi-restraints excluded: chain I residue 1060 ILE Chi-restraints excluded: chain I residue 1082 ILE Chi-restraints excluded: chain I residue 1092 THR Chi-restraints excluded: chain I residue 1117 LEU Chi-restraints excluded: chain I residue 1143 GLU Chi-restraints excluded: chain I residue 1163 THR Chi-restraints excluded: chain I residue 1167 GLU Chi-restraints excluded: chain I residue 1206 THR Chi-restraints excluded: chain I residue 1250 SER Chi-restraints excluded: chain I residue 1296 ASP Chi-restraints excluded: chain I residue 1298 VAL Chi-restraints excluded: chain J residue 46 TYR Chi-restraints excluded: chain J residue 92 VAL Chi-restraints excluded: chain J residue 159 ILE Chi-restraints excluded: chain J residue 212 THR Chi-restraints excluded: chain J residue 224 LEU Chi-restraints excluded: chain J residue 227 PHE Chi-restraints excluded: chain J residue 279 LEU Chi-restraints excluded: chain J residue 343 LEU Chi-restraints excluded: chain J residue 428 THR Chi-restraints excluded: chain J residue 429 LEU Chi-restraints excluded: chain J residue 466 MET Chi-restraints excluded: chain J residue 468 VAL Chi-restraints excluded: chain J residue 500 ILE Chi-restraints excluded: chain J residue 536 LEU Chi-restraints excluded: chain J residue 545 HIS Chi-restraints excluded: chain J residue 709 ARG Chi-restraints excluded: chain J residue 740 LEU Chi-restraints excluded: chain J residue 775 SER Chi-restraints excluded: chain J residue 783 LEU Chi-restraints excluded: chain J residue 835 LEU Chi-restraints excluded: chain J residue 839 VAL Chi-restraints excluded: chain J residue 847 ASP Chi-restraints excluded: chain J residue 1177 ILE Chi-restraints excluded: chain J residue 1248 ILE Chi-restraints excluded: chain J residue 1253 ILE Chi-restraints excluded: chain J residue 1265 THR Chi-restraints excluded: chain J residue 1267 VAL Chi-restraints excluded: chain K residue 74 GLU Chi-restraints excluded: chain L residue 33 GLU Chi-restraints excluded: chain L residue 54 GLN Chi-restraints excluded: chain L residue 98 VAL Chi-restraints excluded: chain L residue 108 VAL Chi-restraints excluded: chain L residue 117 ILE Chi-restraints excluded: chain L residue 320 ILE Chi-restraints excluded: chain L residue 344 LEU Chi-restraints excluded: chain L residue 355 ILE Chi-restraints excluded: chain L residue 386 LEU Chi-restraints excluded: chain L residue 399 LEU Chi-restraints excluded: chain L residue 449 THR Chi-restraints excluded: chain L residue 468 ARG Chi-restraints excluded: chain L residue 485 GLU Chi-restraints excluded: chain L residue 505 ILE Chi-restraints excluded: chain L residue 532 LEU Chi-restraints excluded: chain L residue 552 THR Chi-restraints excluded: chain L residue 559 LEU Chi-restraints excluded: chain L residue 568 ASN Chi-restraints excluded: chain L residue 569 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 379 random chunks: chunk 238 optimal weight: 0.9980 chunk 320 optimal weight: 9.9990 chunk 92 optimal weight: 9.9990 chunk 277 optimal weight: 6.9990 chunk 44 optimal weight: 2.9990 chunk 83 optimal weight: 1.9990 chunk 301 optimal weight: 0.9990 chunk 126 optimal weight: 0.9980 chunk 309 optimal weight: 1.9990 chunk 38 optimal weight: 5.9990 chunk 55 optimal weight: 0.9980 overall best weight: 1.1984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** I 214 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 526 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** I 582 ASN I 618 GLN ** I 811 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 932 GLN ** J 94 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 158 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 229 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 594 GLN ** J1350 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 283 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 309 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 362 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 406 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 518 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3998 r_free = 0.3998 target = 0.164677 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3536 r_free = 0.3536 target = 0.124203 restraints weight = 42918.349| |-----------------------------------------------------------------------------| r_work (start): 0.3512 rms_B_bonded: 1.89 r_work: 0.3274 rms_B_bonded: 2.78 restraints_weight: 0.5000 r_work: 0.3146 rms_B_bonded: 4.58 restraints_weight: 0.2500 r_work (final): 0.3146 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8184 moved from start: 0.4058 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.268 32133 Z= 0.254 Angle : 0.699 47.207 43850 Z= 0.389 Chirality : 0.042 0.255 5031 Planarity : 0.004 0.095 5353 Dihedral : 17.044 179.541 5537 Min Nonbonded Distance : 1.849 Molprobity Statistics. All-atom Clashscore : 14.25 Ramachandran Plot: Outliers : 0.08 % Allowed : 5.08 % Favored : 94.84 % Rotamer: Outliers : 3.68 % Allowed : 30.29 % Favored : 66.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.37 % Cis-general : 0.28 % Twisted Proline : 0.00 % Twisted General : 0.03 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.36 (0.14), residues: 3698 helix: 0.99 (0.13), residues: 1567 sheet: -0.67 (0.27), residues: 354 loop : -1.28 (0.15), residues: 1777 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP I 807 HIS 0.003 0.001 HIS I 447 PHE 0.020 0.001 PHE L 259 TYR 0.016 0.001 TYR N 35 ARG 0.013 0.000 ARG I 272 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 13920.95 seconds wall clock time: 246 minutes 42.18 seconds (14802.18 seconds total)