Starting phenix.real_space_refine on Thu Feb 22 05:04:28 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6psq_20460/02_2024/6psq_20460_trim_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6psq_20460/02_2024/6psq_20460.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.4 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6psq_20460/02_2024/6psq_20460.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6psq_20460/02_2024/6psq_20460.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6psq_20460/02_2024/6psq_20460_trim_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6psq_20460/02_2024/6psq_20460_trim_updated.pdb" } resolution = 3.4 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.006 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 100 5.49 5 Mg 1 5.21 5 S 139 5.16 5 C 20260 2.51 5 N 5780 2.21 5 O 6494 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "J GLU 42": "OE1" <-> "OE2" Residue "J GLU 100": "OE1" <-> "OE2" Residue "J GLU 155": "OE1" <-> "OE2" Residue "J GLU 163": "OE1" <-> "OE2" Residue "J GLU 175": "OE1" <-> "OE2" Residue "J GLU 225": "OE1" <-> "OE2" Residue "J PHE 338": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J GLU 402": "OE1" <-> "OE2" Residue "J GLU 556": "OE1" <-> "OE2" Residue "J GLU 658": "OE1" <-> "OE2" Residue "J GLU 677": "OE1" <-> "OE2" Residue "J GLU 704": "OE1" <-> "OE2" Residue "J ARG 799": "NH1" <-> "NH2" Residue "J GLU 827": "OE1" <-> "OE2" Residue "J GLU 846": "OE1" <-> "OE2" Residue "J GLU 873": "OE1" <-> "OE2" Residue "J ARG 905": "NH1" <-> "NH2" Residue "J GLU 1066": "OE1" <-> "OE2" Residue "J GLU 1110": "OE1" <-> "OE2" Residue "J ASP 1133": "OD1" <-> "OD2" Residue "J GLU 1187": "OE1" <-> "OE2" Residue "J GLU 1188": "OE1" <-> "OE2" Residue "J GLU 1200": "OE1" <-> "OE2" Residue "J GLU 1202": "OE1" <-> "OE2" Residue "J GLU 1205": "OE1" <-> "OE2" Residue "J GLU 1291": "OE1" <-> "OE2" Residue "G GLU 29": "OE1" <-> "OE2" Residue "G GLU 136": "OE1" <-> "OE2" Residue "H GLU 17": "OE1" <-> "OE2" Residue "H GLU 32": "OE1" <-> "OE2" Residue "H GLU 60": "OE1" <-> "OE2" Residue "H GLU 122": "OE1" <-> "OE2" Residue "I GLU 50": "OE1" <-> "OE2" Residue "I TYR 70": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I GLU 84": "OE1" <-> "OE2" Residue "I GLU 187": "OE1" <-> "OE2" Residue "I GLU 218": "OE1" <-> "OE2" Residue "I GLU 226": "OE1" <-> "OE2" Residue "I GLU 240": "OE1" <-> "OE2" Residue "I GLU 264": "OE1" <-> "OE2" Residue "I GLU 286": "OE1" <-> "OE2" Residue "I GLU 308": "OE1" <-> "OE2" Residue "I ARG 332": "NH1" <-> "NH2" Residue "I GLU 349": "OE1" <-> "OE2" Residue "I GLU 379": "OE1" <-> "OE2" Residue "I GLU 778": "OE1" <-> "OE2" Residue "I GLU 820": "OE1" <-> "OE2" Residue "I GLU 859": "OE1" <-> "OE2" Residue "I GLU 940": "OE1" <-> "OE2" Residue "I GLU 962": "OE1" <-> "OE2" Residue "I GLU 987": "OE1" <-> "OE2" Residue "I GLU 1020": "OE1" <-> "OE2" Residue "I GLU 1167": "OE1" <-> "OE2" Residue "I GLU 1174": "OE1" <-> "OE2" Residue "I PHE 1187": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I GLU 1222": "OE1" <-> "OE2" Residue "K GLU 11": "OE1" <-> "OE2" Residue "K GLU 42": "OE1" <-> "OE2" Residue "K GLU 56": "OE1" <-> "OE2" Residue "K GLU 71": "OE1" <-> "OE2" Residue "K GLU 74": "OE1" <-> "OE2" Residue "L GLU 58": "OE1" <-> "OE2" Residue "L GLU 74": "OE1" <-> "OE2" Residue "L GLU 78": "OE1" <-> "OE2" Residue "L TYR 101": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L GLU 104": "OE1" <-> "OE2" Residue "L GLU 114": "OE1" <-> "OE2" Residue "L GLU 139": "OE1" <-> "OE2" Residue "L GLU 155": "OE1" <-> "OE2" Residue "L GLU 219": "OE1" <-> "OE2" Residue "L GLU 223": "OE1" <-> "OE2" Residue "L GLU 247": "OE1" <-> "OE2" Residue "L GLU 248": "OE1" <-> "OE2" Residue "L GLU 335": "OE1" <-> "OE2" Residue "L GLU 369": "OE1" <-> "OE2" Residue "L GLU 381": "OE1" <-> "OE2" Residue "L GLU 458": "OE1" <-> "OE2" Residue "L GLU 491": "OE1" <-> "OE2" Residue "L GLU 515": "OE1" <-> "OE2" Residue "L GLU 538": "OE1" <-> "OE2" Residue "L GLU 574": "OE1" <-> "OE2" Residue "M GLU 302": "OE1" <-> "OE2" 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: 32777 Number of models: 1 Model: "" Number of chains: 13 Chain: "J" Number of atoms: 10466 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1345, 10466 Classifications: {'peptide': 1345} Link IDs: {'CIS': 1, 'PCIS': 1, 'PTRANS': 54, 'TRANS': 1288} Chain breaks: 2 Chain: "N" Number of atoms: 571 Number of conformers: 1 Conformer: "" Number of residues, atoms: 72, 571 Classifications: {'peptide': 72} Link IDs: {'PTRANS': 4, 'TRANS': 67} Chain: "G" Number of atoms: 1764 Number of conformers: 1 Conformer: "" Number of residues, atoms: 230, 1764 Classifications: {'peptide': 230} Incomplete info: {'truncation_to_alanine': 5} Link IDs: {'CIS': 1, 'PTRANS': 9, 'TRANS': 219} Unresolved non-hydrogen bonds: 18 Unresolved non-hydrogen angles: 23 Unresolved non-hydrogen dihedrals: 13 Planarities with less than four sites: {'GLU:plan': 3, 'ASP:plan': 2} Unresolved non-hydrogen planarities: 18 Chain: "H" Number of atoms: 1682 Number of conformers: 1 Conformer: "" Number of residues, atoms: 219, 1682 Classifications: {'peptide': 219} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'PCIS': 1, 'PTRANS': 7, 'TRANS': 210} Chain breaks: 1 Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 4 Unresolved non-hydrogen chiralities: 2 Chain: "I" Number of atoms: 10549 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1339, 10549 Classifications: {'peptide': 1339} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'CIS': 3, 'PCIS': 2, 'PTRANS': 54, 'TRANS': 1279} Unresolved non-hydrogen bonds: 12 Unresolved non-hydrogen angles: 16 Unresolved non-hydrogen dihedrals: 11 Planarities with less than four sites: {'TYR:plan': 1, 'GLU:plan': 1} Unresolved non-hydrogen planarities: 11 Chain: "K" Number of atoms: 600 Number of conformers: 1 Conformer: "" Number of residues, atoms: 75, 600 Classifications: {'peptide': 75} Link IDs: {'PTRANS': 2, 'TRANS': 72} Chain: "L" Number of atoms: 4411 Number of conformers: 1 Conformer: "" Number of residues, atoms: 551, 4411 Classifications: {'peptide': 551} Incomplete info: {'truncation_to_alanine': 12} Link IDs: {'CIS': 3, 'PTRANS': 16, 'TRANS': 531} Chain breaks: 3 Unresolved non-hydrogen bonds: 35 Unresolved non-hydrogen angles: 44 Unresolved non-hydrogen dihedrals: 26 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'GLU:plan': 1, 'ASN:plan1': 2, 'ARG:plan': 1, 'ASP:plan': 3} Unresolved non-hydrogen planarities: 24 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: "O" Number of atoms: 1024 Number of conformers: 1 Conformer: "" Number of residues, atoms: 50, 1024 Classifications: {'DNA': 50} Link IDs: {'rna3p': 49} Chain: "P" Number of atoms: 1026 Number of conformers: 1 Conformer: "" Number of residues, atoms: 50, 1026 Classifications: {'DNA': 50} Link IDs: {'rna3p': 49} Chain: "J" Number of atoms: 84 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 84 Unusual residues: {' MG': 1, ' ZN': 2, '1N7': 3} Classifications: {'undetermined': 6} Link IDs: {None: 5} Unresolved non-hydrogen bonds: 48 Unresolved non-hydrogen angles: 72 Unresolved non-hydrogen dihedrals: 39 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {'1N7:plan-1': 3} Unresolved non-hydrogen planarities: 9 Chain: "N" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} 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 List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 449 SG CYS J 70 72.194 102.418 115.202 1.00 52.73 S ATOM 463 SG CYS J 72 74.047 104.963 116.597 1.00 56.38 S ATOM 571 SG CYS J 85 71.379 104.485 118.786 1.00 52.65 S ATOM 595 SG CYS J 88 69.971 105.038 115.019 1.00 47.70 S ATOM 6283 SG CYS J 814 66.416 41.755 89.956 1.00 33.33 S ATOM 6848 SG CYS J 888 66.534 45.280 88.537 1.00 31.08 S ATOM 6899 SG CYS J 895 69.451 43.632 89.446 1.00 21.00 S ATOM 6920 SG CYS J 898 68.518 41.514 86.838 1.00 26.18 S ATOM 10747 SG CYS N 37 49.312 56.215 28.935 1.00 68.32 S ATOM 10767 SG CYS N 40 46.948 57.222 26.641 1.00 71.01 S ATOM 10904 SG CYS N 58 50.262 58.391 26.383 1.00 56.63 S ATOM 10926 SG CYS N 61 47.517 59.375 29.831 1.00 60.81 S Time building chain proxies: 17.52, per 1000 atoms: 0.53 Number of scatterers: 32777 At special positions: 0 Unit cell: (157.3, 154.7, 167.7, 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 139 16.00 P 100 15.00 Mg 1 11.99 O 6494 8.00 N 5780 7.00 C 20260 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: 15.52 Conformation dependent library (CDL) restraints added in 6.2 seconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN J1502 " pdb="ZN ZN J1502 " - pdb=" SG CYS J 70 " pdb="ZN ZN J1502 " - pdb=" SG CYS J 85 " pdb="ZN ZN J1502 " - pdb=" SG CYS J 88 " pdb="ZN ZN J1502 " - pdb=" SG CYS J 72 " pdb=" ZN J1503 " pdb="ZN ZN J1503 " - pdb=" SG CYS J 895 " pdb="ZN ZN J1503 " - pdb=" SG CYS J 898 " pdb="ZN ZN J1503 " - pdb=" SG CYS J 888 " pdb="ZN ZN J1503 " - pdb=" SG CYS J 814 " 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 61 " pdb="ZN ZN N 101 " - pdb=" SG CYS N 37 " Number of angles added : 18 7752 Ramachandran restraints generated. 3876 Oldfield, 0 Emsley, 3876 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 7258 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 134 helices and 32 sheets defined 36.6% alpha, 8.2% beta 50 base pairs and 82 stacking pairs defined. Time for finding SS restraints: 15.78 Creating SS restraints... 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 117 No H-bonds generated for 'chain 'J' and resid 114 through 117' 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 171 Processing helix chain 'J' and resid 181 through 191 Processing helix chain 'J' and resid 194 through 206 Processing helix chain 'J' and resid 211 through 229 Processing helix chain 'J' and resid 234 through 237 removed outlier: 4.202A 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 250 Processing helix chain 'J' and resid 264 through 285 removed outlier: 3.541A pdb=" N ARG J 275 " --> pdb=" O ARG J 271 " (cutoff:3.500A) Processing helix chain 'J' and resid 289 through 307 Processing helix chain 'J' and resid 327 through 331 Processing helix chain 'J' and resid 370 through 376 Processing helix chain 'J' and resid 378 through 387 Processing helix chain 'J' and resid 394 through 403 Processing helix chain 'J' and resid 406 through 415 removed outlier: 3.870A pdb=" N ASP J 410 " --> pdb=" O ALA J 406 " (cutoff:3.500A) Processing helix chain 'J' and resid 451 through 457 removed outlier: 3.726A pdb=" N ALA J 455 " --> pdb=" O LEU J 452 " (cutoff:3.500A) removed outlier: 3.672A pdb=" N TYR J 457 " --> pdb=" O CYS J 454 " (cutoff:3.500A) Processing helix chain 'J' and resid 474 through 483 Processing helix chain 'J' and resid 505 through 513 Processing helix chain 'J' and resid 530 through 537 Processing helix chain 'J' and resid 574 through 582 removed outlier: 4.018A pdb=" N MET J 581 " --> pdb=" O ALA J 577 " (cutoff:3.500A) removed outlier: 4.929A pdb=" N ILE J 582 " --> pdb=" O ILE J 578 " (cutoff:3.500A) Processing helix chain 'J' and resid 589 through 591 No H-bonds generated for 'chain 'J' and resid 589 through 591' Processing helix chain 'J' and resid 599 through 612 removed outlier: 4.100A pdb=" N LEU J 605 " --> pdb=" O ILE J 601 " (cutoff:3.500A) Processing helix chain 'J' and resid 615 through 635 Processing helix chain 'J' and resid 650 through 670 Processing helix chain 'J' and resid 675 through 702 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 791 removed outlier: 4.130A pdb=" N HIS J 777 " --> pdb=" O PHE J 773 " (cutoff:3.500A) removed outlier: 4.368A pdb=" N GLY J 778 " --> pdb=" O ILE J 774 " (cutoff:3.500A) removed outlier: 4.030A pdb=" N ALA J 791 " --> pdb=" O ALA J 787 " (cutoff:3.500A) Processing helix chain 'J' and resid 795 through 803 removed outlier: 3.838A 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 873 Processing helix chain 'J' and resid 915 through 924 Processing helix chain 'J' and resid 926 through 928 No H-bonds generated for 'chain 'J' and resid 926 through 928' Processing helix chain 'J' and resid 1138 through 1146 Processing helix chain 'J' and resid 1217 through 1224 Processing helix chain 'J' and resid 1226 through 1242 Processing helix chain 'J' and resid 1251 through 1260 Processing helix chain 'J' and resid 1282 through 1294 Processing helix chain 'J' and resid 1309 through 1312 No H-bonds generated for 'chain 'J' and resid 1309 through 1312' Processing helix chain 'J' and resid 1328 through 1337 Processing helix chain 'J' and resid 1347 through 1352 removed outlier: 3.566A pdb=" N VAL J1351 " --> pdb=" O LEU J1347 " (cutoff:3.500A) Processing helix chain 'J' and resid 1361 through 1372 removed outlier: 3.635A pdb=" N ARG J1371 " --> pdb=" O ASP J1368 " (cutoff:3.500A) removed outlier: 3.583A pdb=" N ARG J1372 " --> pdb=" O ARG J1369 " (cutoff:3.500A) Processing helix chain 'N' and resid 4 through 25 removed outlier: 3.881A pdb=" N SER N 10 " --> pdb=" O ASP N 6 " (cutoff:3.500A) removed outlier: 4.424A pdb=" N ARG N 22 " --> pdb=" O THR N 18 " (cutoff:3.500A) removed outlier: 3.692A pdb=" N ILE N 23 " --> pdb=" O GLY N 19 " (cutoff:3.500A) Processing helix chain 'N' and resid 46 through 51 Processing helix chain 'N' and resid 59 through 71 removed outlier: 4.179A pdb=" N HIS N 71 " --> pdb=" O ARG N 67 " (cutoff:3.500A) Processing helix chain 'G' and resid 35 through 49 Processing helix chain 'G' and resid 78 through 85 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 156 through 158 No H-bonds generated for 'chain 'G' and resid 156 through 158' Processing helix chain 'G' and resid 213 through 233 Processing helix chain 'H' and resid 35 through 49 Processing helix chain 'H' and resid 79 through 86 Processing helix chain 'H' and resid 155 through 157 No H-bonds generated for 'chain 'H' and resid 155 through 157' Processing helix chain 'H' and resid 213 through 228 removed outlier: 3.845A pdb=" N LEU H 228 " --> pdb=" O LEU H 224 " (cutoff:3.500A) Processing helix chain 'I' and resid 29 through 38 Processing helix chain 'I' and resid 50 through 53 No H-bonds generated for 'chain 'I' and resid 50 through 53' Processing helix chain 'I' and resid 82 through 88 Processing helix chain 'I' and resid 206 through 213 Processing helix chain 'I' and resid 217 through 224 Processing helix chain 'I' and resid 243 through 246 Processing helix chain 'I' and resid 271 through 280 Processing helix chain 'I' and resid 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 388 Processing helix chain 'I' and resid 399 through 408 Processing helix chain 'I' and resid 422 through 437 Processing helix chain 'I' and resid 456 through 480 removed outlier: 4.284A pdb=" N ASN I 462 " --> pdb=" O GLU I 458 " (cutoff:3.500A) Processing helix chain 'I' and resid 496 through 507 Processing helix chain 'I' and resid 520 through 527 Processing helix chain 'I' and resid 608 through 613 removed outlier: 3.963A pdb=" N GLY I 612 " --> pdb=" O ALA I 608 " (cutoff:3.500A) removed outlier: 5.137A pdb=" N ASN I 613 " --> pdb=" O ILE I 609 " (cutoff:3.500A) No H-bonds generated for 'chain 'I' and resid 608 through 613' Processing helix chain 'I' and resid 647 through 649 No H-bonds generated for 'chain 'I' and resid 647 through 649' Processing helix chain 'I' and resid 657 through 660 removed outlier: 4.325A pdb=" N VAL I 660 " --> pdb=" O THR I 657 " (cutoff:3.500A) No H-bonds generated for 'chain 'I' and resid 657 through 660' Processing helix chain 'I' and resid 664 through 666 No H-bonds generated for 'chain 'I' and resid 664 through 666' 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: 3.998A pdb=" N GLN I 688 " --> pdb=" O ASN I 684 " (cutoff:3.500A) Processing helix chain 'I' and resid 704 through 711 Processing helix chain 'I' and resid 820 through 824 Processing helix chain 'I' and resid 859 through 862 Processing helix chain 'I' and resid 899 through 906 removed outlier: 3.519A pdb=" N PHE I 906 " --> pdb=" O LEU I 902 " (cutoff:3.500A) Processing helix chain 'I' and resid 943 through 978 Processing helix chain 'I' and resid 994 through 997 Processing helix chain 'I' and resid 1006 through 1036 Processing helix chain 'I' and resid 1100 through 1102 No H-bonds generated for 'chain 'I' and resid 1100 through 1102' Processing helix chain 'I' and resid 1110 through 1133 Processing helix chain 'I' and resid 1138 through 1150 Processing helix chain 'I' and resid 1170 through 1175 Processing helix chain 'I' and resid 1192 through 1201 Processing helix chain 'I' and resid 1239 through 1241 No H-bonds generated for 'chain 'I' and resid 1239 through 1241' Processing helix chain 'I' and resid 1273 through 1280 Processing helix chain 'I' and resid 1284 through 1291 Processing helix chain 'I' and resid 1300 through 1309 Processing helix chain 'I' and resid 1321 through 1332 Processing helix chain 'K' and resid 7 through 13 Processing helix chain 'K' and resid 16 through 31 removed outlier: 3.582A pdb=" N VAL K 20 " --> pdb=" O ARG K 16 " (cutoff:3.500A) removed outlier: 3.543A pdb=" N LEU K 21 " --> pdb=" O PHE K 17 " (cutoff:3.500A) Processing helix chain 'K' and resid 46 through 56 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 29 Processing helix chain 'L' and resid 38 through 51 removed outlier: 3.590A pdb=" N MET L 51 " --> pdb=" O MET L 47 " (cutoff:3.500A) Processing helix chain 'L' and resid 75 through 87 removed outlier: 3.534A pdb=" N ALA L 79 " --> pdb=" O ASP L 75 " (cutoff:3.500A) Processing helix chain 'L' and resid 97 through 107 Processing helix chain 'L' and resid 115 through 126 Processing helix chain 'L' and resid 129 through 135 Processing helix chain 'L' and resid 138 through 151 Processing helix chain 'L' and resid 158 through 161 removed outlier: 3.645A pdb=" N LEU L 161 " --> pdb=" O LEU L 158 " (cutoff:3.500A) No H-bonds generated for 'chain 'L' and resid 158 through 161' Processing helix chain 'L' and resid 214 through 232 Processing helix chain 'L' and resid 235 through 257 removed outlier: 4.175A pdb=" N ALA L 245 " --> pdb=" O ILE L 235 " (cutoff:3.500A) removed outlier: 5.043A pdb=" N GLN L 246 " --> pdb=" O ALA L 243 " (cutoff:3.500A) removed outlier: 4.014A pdb=" N GLU L 247 " --> pdb=" O THR L 244 " (cutoff:3.500A) removed outlier: 3.657A pdb=" N GLU L 248 " --> pdb=" O ALA L 245 " (cutoff:3.500A) removed outlier: 3.510A pdb=" N ILE L 249 " --> pdb=" O GLN L 246 " (cutoff:3.500A) removed outlier: 3.559A pdb=" N VAL L 255 " --> pdb=" O LEU L 252 " (cutoff:3.500A) Processing helix chain 'L' and resid 263 through 288 Processing helix chain 'L' and resid 299 through 304 Processing helix chain 'L' and resid 306 through 309 No H-bonds generated for 'chain 'L' and resid 306 through 309' Processing helix chain 'L' and resid 320 through 322 No H-bonds generated for 'chain 'L' and resid 320 through 322' Processing helix chain 'L' and resid 327 through 329 No H-bonds generated for 'chain 'L' and resid 327 through 329' Processing helix chain 'L' and resid 334 through 351 removed outlier: 3.563A pdb=" N GLN L 342 " --> pdb=" O HIS L 338 " (cutoff:3.500A) removed outlier: 4.245A pdb=" N GLU L 349 " --> pdb=" O GLN L 345 " (cutoff:3.500A) Processing helix chain 'L' and resid 355 through 394 removed outlier: 3.506A pdb=" N ALA L 375 " --> pdb=" O LYS L 371 " (cutoff:3.500A) removed outlier: 4.084A pdb=" N GLU L 378 " --> pdb=" O ARG L 374 " (cutoff:3.500A) removed outlier: 4.345A pdb=" N LEU L 386 " --> pdb=" O ALA L 382 " (cutoff:3.500A) removed outlier: 4.426A pdb=" N SER L 389 " --> pdb=" O ARG L 385 " (cutoff:3.500A) removed outlier: 4.133A pdb=" N LYS L 393 " --> pdb=" O SER L 389 " (cutoff:3.500A) removed outlier: 5.004A pdb=" N TYR L 394 " --> pdb=" O ILE L 390 " (cutoff:3.500A) Processing helix chain 'L' and resid 401 through 418 Processing helix chain 'L' and resid 427 through 445 Processing helix chain 'L' and resid 454 through 473 Processing helix chain 'L' and resid 480 through 486 removed outlier: 3.791A pdb=" N GLU L 485 " --> pdb=" O GLU L 481 " (cutoff:3.500A) Processing helix chain 'L' and resid 493 through 501 Processing helix chain 'L' and resid 519 through 521 No H-bonds generated for 'chain 'L' and resid 519 through 521' Processing helix chain 'L' and resid 531 through 549 removed outlier: 3.623A pdb=" N SER L 539 " --> pdb=" O ALA L 535 " (cutoff:3.500A) Processing helix chain 'L' and resid 553 through 562 Processing helix chain 'L' and resid 573 through 580 Processing helix chain 'L' and resid 584 through 599 Processing helix chain 'L' and resid 605 through 610 Processing helix chain 'M' and resid 257 through 260 Processing helix chain 'M' and resid 264 through 273 Processing helix chain 'M' and resid 286 through 290 Processing helix chain 'M' and resid 297 through 309 Processing sheet with id= A, first strand: chain 'J' and resid 103 through 106 Processing sheet with id= B, first strand: chain 'J' and resid 446 through 448 removed outlier: 7.581A pdb=" N ILE J 447 " --> pdb=" O ARG J 352 " (cutoff:3.500A) removed outlier: 6.397A pdb=" N VAL J 354 " --> pdb=" O ILE J 447 " (cutoff:3.500A) Processing sheet with id= C, first strand: chain 'J' and resid 548 through 556 Processing sheet with id= D, first strand: chain 'J' and resid 820 through 823 Processing sheet with id= E, first strand: chain 'J' and resid 957 through 961 Processing sheet with id= F, first strand: chain 'J' and resid 1034 through 1038 Processing sheet with id= G, first strand: chain 'J' and resid 1047 through 1051 Processing sheet with id= H, first strand: chain 'J' and resid 1162 through 1165 removed outlier: 3.749A pdb=" N ILE J1177 " --> pdb=" O TYR J1186 " (cutoff:3.500A) removed outlier: 4.536A pdb=" N TYR J1186 " --> pdb=" O ILE J1177 " (cutoff:3.500A) Processing sheet with id= I, first strand: chain 'J' and resid 1279 through 1281 removed outlier: 6.458A pdb=" N THR J1301 " --> pdb=" O VAL J1267 " (cutoff:3.500A) Processing sheet with id= J, first strand: chain 'G' and resid 26 through 28 Processing sheet with id= K, first strand: chain 'G' and resid 90 through 92 Processing sheet with id= L, first strand: chain 'G' and resid 97 through 105 Processing sheet with id= M, first strand: chain 'G' and resid 151 through 153 Processing sheet with id= N, first strand: chain 'G' and resid 108 through 111 Processing sheet with id= O, first strand: chain 'H' and resid 23 through 28 removed outlier: 3.520A pdb=" N ARG H 182 " --> pdb=" O GLU H 206 " (cutoff:3.500A) Processing sheet with id= P, first strand: chain 'H' and resid 99 through 101 removed outlier: 6.234A pdb=" N GLN H 147 " --> pdb=" O VAL H 56 " (cutoff:3.500A) removed outlier: 5.683A pdb=" N VAL H 56 " --> pdb=" O GLN H 147 " (cutoff:3.500A) removed outlier: 6.400A pdb=" N GLY H 149 " --> pdb=" O CYS H 54 " (cutoff:3.500A) removed outlier: 5.238A pdb=" N CYS H 54 " --> pdb=" O GLY H 149 " (cutoff:3.500A) Processing sheet with id= Q, first strand: chain 'I' and resid 66 through 70 Processing sheet with id= R, first strand: chain 'I' and resid 73 through 75 Processing sheet with id= S, first strand: chain 'I' and resid 93 through 95 Processing sheet with id= T, first strand: chain 'I' and resid 143 through 145 Processing sheet with id= U, first strand: chain 'I' and resid 154 through 157 Processing sheet with id= V, first strand: chain 'I' and resid 184 through 187 Processing sheet with id= W, first strand: chain 'I' and resid 227 through 230 Processing sheet with id= X, first strand: chain 'I' and resid 603 through 606 Processing sheet with id= Y, first strand: chain 'I' and resid 749 through 752 removed outlier: 3.704A pdb=" N TYR I 726 " --> pdb=" O VAL I 733 " (cutoff:3.500A) removed outlier: 6.287A pdb=" N LYS I 735 " --> pdb=" O VAL I 724 " (cutoff:3.500A) removed outlier: 5.502A pdb=" N VAL I 724 " --> pdb=" O LYS I 735 " (cutoff:3.500A) Processing sheet with id= Z, first strand: chain 'I' and resid 1226 through 1232 removed outlier: 4.365A pdb=" N THR I1226 " --> pdb=" O PHE I 804 " (cutoff:3.500A) removed outlier: 6.540A pdb=" N ILE I1096 " --> pdb=" O ALA I 803 " (cutoff:3.500A) Processing sheet with id= AA, first strand: chain 'I' and resid 876 through 878 removed outlier: 7.746A pdb=" N SER I 925 " --> pdb=" O LYS I1057 " (cutoff:3.500A) removed outlier: 4.391A pdb=" N LYS I1057 " --> pdb=" O SER I 925 " (cutoff:3.500A) removed outlier: 3.700A pdb=" N THR I 927 " --> pdb=" O ALA I1055 " (cutoff:3.500A) removed outlier: 6.599A pdb=" N TYR I1053 " --> pdb=" O ILE I 929 " (cutoff:3.500A) removed outlier: 4.177A pdb=" N VAL I 931 " --> pdb=" O LYS I1051 " (cutoff:3.500A) removed outlier: 6.477A pdb=" N LYS I1051 " --> pdb=" O VAL I 931 " (cutoff:3.500A) removed outlier: 4.401A pdb=" N VAL I 933 " --> pdb=" O ILE I1049 " (cutoff:3.500A) removed outlier: 6.275A pdb=" N ILE I1049 " --> pdb=" O VAL I 933 " (cutoff:3.500A) removed outlier: 5.130A pdb=" N THR I 935 " --> pdb=" O LEU I1047 " (cutoff:3.500A) removed outlier: 8.196A pdb=" N LEU I1047 " --> pdb=" O THR I 935 " (cutoff:3.500A) removed outlier: 6.576A pdb=" N SER I 840 " --> pdb=" O LEU I1047 " (cutoff:3.500A) removed outlier: 4.552A pdb=" N ILE I1049 " --> pdb=" O CYS I 838 " (cutoff:3.500A) removed outlier: 6.462A pdb=" N CYS I 838 " --> pdb=" O ILE I1049 " (cutoff:3.500A) removed outlier: 4.448A pdb=" N LYS I1051 " --> pdb=" O LEU I 836 " (cutoff:3.500A) removed outlier: 6.464A pdb=" N LEU I 836 " --> pdb=" O LYS I1051 " (cutoff:3.500A) removed outlier: 4.160A pdb=" N TYR I1053 " --> pdb=" O GLN I 834 " (cutoff:3.500A) removed outlier: 5.713A pdb=" N GLN I 834 " --> pdb=" O TYR I1053 " (cutoff:3.500A) removed outlier: 4.510A pdb=" N ALA I1055 " --> pdb=" O HIS I 832 " (cutoff:3.500A) removed outlier: 5.810A pdb=" N HIS I 832 " --> pdb=" O ALA I1055 " (cutoff:3.500A) removed outlier: 4.850A pdb=" N LYS I1057 " --> pdb=" O THR I 830 " (cutoff:3.500A) removed outlier: 5.885A pdb=" N THR I 830 " --> pdb=" O LYS I1057 " (cutoff:3.500A) Processing sheet with id= AB, first strand: chain 'I' and resid 887 through 889 Processing sheet with id= AC, first strand: chain 'I' and resid 1065 through 1067 Processing sheet with id= AD, first strand: chain 'I' and resid 255 through 257 removed outlier: 6.194A pdb=" N ALA I 257 " --> pdb=" O VAL I 261 " (cutoff:3.500A) removed outlier: 4.588A pdb=" N VAL I 261 " --> pdb=" O ALA I 257 " (cutoff:3.500A) Processing sheet with id= AE, first strand: chain 'I' and resid 634 through 639 removed outlier: 3.795A pdb=" N SER I 638 " --> pdb=" O GLU I 641 " (cutoff:3.500A) removed outlier: 6.507A pdb=" N GLU I 641 " --> pdb=" O SER I 638 " (cutoff:3.500A) Processing sheet with id= AF, first strand: chain 'I' and resid 816 through 819 removed outlier: 7.345A pdb=" N VAL I 818 " --> pdb=" O SER I1077 " (cutoff:3.500A) removed outlier: 4.109A pdb=" N ILE I1079 " --> pdb=" O VAL I 818 " (cutoff:3.500A) 1039 hydrogen bonds defined for protein. 2961 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 120 hydrogen bonds 236 hydrogen bond angles 0 basepair planarities 50 basepair parallelities 82 stacking parallelities Total time for adding SS restraints: 14.60 Time building geometry restraints manager: 15.71 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.12 - 1.26: 5483 1.26 - 1.40: 7646 1.40 - 1.55: 19837 1.55 - 1.69: 257 1.69 - 1.83: 252 Bond restraints: 33475 Sorted by residual: bond pdb=" C19 1N7 J1504 " pdb=" C3 1N7 J1504 " ideal model delta sigma weight residual 1.532 1.827 -0.295 2.00e-02 2.50e+03 2.18e+02 bond pdb=" C19 1N7 J1506 " pdb=" C3 1N7 J1506 " ideal model delta sigma weight residual 1.532 1.824 -0.292 2.00e-02 2.50e+03 2.13e+02 bond pdb=" C19 1N7 J1505 " pdb=" C3 1N7 J1505 " ideal model delta sigma weight residual 1.532 1.821 -0.289 2.00e-02 2.50e+03 2.09e+02 bond pdb=" C19 1N7 I1401 " pdb=" C3 1N7 I1401 " 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 J1504 " pdb=" C4 1N7 J1504 " ideal model delta sigma weight residual 1.532 1.730 -0.198 2.00e-02 2.50e+03 9.76e+01 ... (remaining 33470 not shown) Histogram of bond angle deviations from ideal: 94.21 - 102.19: 265 102.19 - 110.17: 8279 110.17 - 118.15: 18002 118.15 - 126.13: 18511 126.13 - 134.11: 605 Bond angle restraints: 45662 Sorted by residual: angle pdb=" C ARG J 362 " pdb=" N LEU J 363 " pdb=" CA LEU J 363 " ideal model delta sigma weight residual 122.56 106.98 15.58 1.72e+00 3.38e-01 8.21e+01 angle pdb=" C ILE I1082 " pdb=" CA ILE I1082 " pdb=" CB ILE I1082 " ideal model delta sigma weight residual 112.04 102.96 9.08 1.31e+00 5.83e-01 4.80e+01 angle pdb=" N ILE I1079 " pdb=" CA ILE I1079 " pdb=" C ILE I1079 " ideal model delta sigma weight residual 106.53 97.39 9.14 1.41e+00 5.03e-01 4.21e+01 angle pdb=" N PRO I1081 " pdb=" CA PRO I1081 " pdb=" CB PRO I1081 " ideal model delta sigma weight residual 103.25 96.55 6.70 1.05e+00 9.07e-01 4.07e+01 angle pdb=" N PRO I1081 " pdb=" CD PRO I1081 " pdb=" CG PRO I1081 " ideal model delta sigma weight residual 103.20 94.21 8.99 1.50e+00 4.44e-01 3.59e+01 ... (remaining 45657 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 30.18: 18754 30.18 - 60.37: 1761 60.37 - 90.55: 87 90.55 - 120.74: 3 120.74 - 150.92: 4 Dihedral angle restraints: 20609 sinusoidal: 9359 harmonic: 11250 Sorted by residual: dihedral pdb=" CA ASP I 199 " pdb=" C ASP I 199 " pdb=" N ARG I 200 " pdb=" CA ARG I 200 " ideal model delta harmonic sigma weight residual -180.00 -135.04 -44.96 0 5.00e+00 4.00e-02 8.08e+01 dihedral pdb=" CA PRO I 897 " pdb=" C PRO I 897 " pdb=" N GLU I 898 " pdb=" CA GLU I 898 " ideal model delta harmonic sigma weight residual 180.00 -143.30 -36.70 0 5.00e+00 4.00e-02 5.39e+01 dihedral pdb=" CA GLN I1134 " pdb=" C GLN I1134 " pdb=" N GLN I1135 " pdb=" CA GLN I1135 " ideal model delta harmonic sigma weight residual -180.00 -143.67 -36.33 0 5.00e+00 4.00e-02 5.28e+01 ... (remaining 20606 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.069: 4381 0.069 - 0.137: 798 0.137 - 0.206: 51 0.206 - 0.275: 8 0.275 - 0.344: 2 Chirality restraints: 5240 Sorted by residual: chirality pdb=" CA ILE I1079 " pdb=" N ILE I1079 " pdb=" C ILE I1079 " pdb=" CB ILE I1079 " both_signs ideal model delta sigma weight residual False 2.43 2.78 -0.34 2.00e-01 2.50e+01 2.95e+00 chirality pdb=" C19 1N7 J1506 " pdb=" C18 1N7 J1506 " pdb=" C2 1N7 J1506 " pdb=" C3 1N7 J1506 " both_signs ideal model delta sigma weight residual False -2.53 -2.87 0.33 2.00e-01 2.50e+01 2.79e+00 chirality pdb=" C19 1N7 J1504 " pdb=" C18 1N7 J1504 " pdb=" C2 1N7 J1504 " pdb=" C3 1N7 J1504 " both_signs ideal model delta sigma weight residual False -2.53 -2.78 0.25 2.00e-01 2.50e+01 1.58e+00 ... (remaining 5237 not shown) Planarity restraints: 5595 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ASN I1080 " -0.044 5.00e-02 4.00e+02 7.12e-02 8.12e+00 pdb=" N PRO I1081 " 0.123 5.00e-02 4.00e+02 pdb=" CA PRO I1081 " -0.036 5.00e-02 4.00e+02 pdb=" CD PRO I1081 " -0.044 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C LYS J 850 " 0.042 5.00e-02 4.00e+02 6.36e-02 6.48e+00 pdb=" N PRO J 851 " -0.110 5.00e-02 4.00e+02 pdb=" CA PRO J 851 " 0.033 5.00e-02 4.00e+02 pdb=" CD PRO J 851 " 0.035 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ASN I 519 " 0.042 5.00e-02 4.00e+02 6.33e-02 6.41e+00 pdb=" N PRO I 520 " -0.109 5.00e-02 4.00e+02 pdb=" CA PRO I 520 " 0.032 5.00e-02 4.00e+02 pdb=" CD PRO I 520 " 0.035 5.00e-02 4.00e+02 ... (remaining 5592 not shown) Histogram of nonbonded interaction distances: 1.99 - 2.58: 462 2.58 - 3.16: 29795 3.16 - 3.74: 52178 3.74 - 4.32: 73910 4.32 - 4.90: 118212 Nonbonded interactions: 274557 Sorted by model distance: nonbonded pdb=" OD1 ASP J 464 " pdb="MG MG J1501 " model vdw 1.995 2.170 nonbonded pdb=" OH TYR I 301 " pdb=" O ARG I 332 " model vdw 2.001 2.440 nonbonded pdb=" O LEU J 361 " pdb=" OH TYR J 626 " model vdw 2.007 2.440 nonbonded pdb=" O ILE I 11 " pdb=" OH TYR I1149 " model vdw 2.034 2.440 nonbonded pdb=" O ARG G 45 " pdb=" OG SER G 49 " model vdw 2.034 2.440 ... (remaining 274552 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 and (name N or name CA or name C or name O or name CB ) \ ) or resid 6 through 158 or resid 171 through 233 or (resid 234 and (name N or n \ ame CA or name C or name O or name CB )))) selection = (chain 'H' and (resid 5 through 232 or (resid 233 through 234 and (name N or nam \ e CA or name C or name O or name CB )))) } 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: 0.840 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 5.950 Check model and map are aligned: 0.460 Set scattering table: 0.280 Process input model: 105.240 Find NCS groups from input model: 1.230 Set up NCS constraints: 0.130 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:3.140 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 117.290 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7818 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 0.295 33475 Z= 0.662 Angle : 0.997 15.582 45662 Z= 0.576 Chirality : 0.051 0.344 5240 Planarity : 0.005 0.071 5595 Dihedral : 20.449 150.923 13351 Min Nonbonded Distance : 1.995 Molprobity Statistics. All-atom Clashscore : 40.42 Ramachandran Plot: Outliers : 0.28 % Allowed : 10.24 % Favored : 89.47 % Rotamer: Outliers : 13.45 % Allowed : 21.69 % Favored : 64.86 % Cbeta Deviations : 0.06 % Peptide Plane: Cis-proline : 3.25 % Cis-general : 0.21 % Twisted Proline : 1.30 % Twisted General : 0.21 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -4.43 (0.11), residues: 3876 helix: -2.34 (0.10), residues: 1545 sheet: -3.38 (0.21), residues: 429 loop : -3.38 (0.12), residues: 1902 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP L 434 HIS 0.009 0.002 HIS J 430 PHE 0.026 0.003 PHE I 514 TYR 0.022 0.003 TYR G 177 ARG 0.011 0.001 ARG J 576 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7752 Ramachandran restraints generated. 3876 Oldfield, 0 Emsley, 3876 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7752 Ramachandran restraints generated. 3876 Oldfield, 0 Emsley, 3876 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 930 residues out of total 3346 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 447 poor density : 483 time to evaluate : 3.982 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: J 69 GLU cc_start: 0.7698 (tt0) cc_final: 0.7412 (mt-10) REVERT: J 77 ARG cc_start: 0.7397 (mpp-170) cc_final: 0.6725 (mpt180) REVERT: J 86 GLU cc_start: 0.7908 (pm20) cc_final: 0.7684 (pm20) REVERT: J 137 ARG cc_start: 0.7552 (mtp180) cc_final: 0.7080 (mtm-85) REVERT: J 306 LEU cc_start: 0.9403 (OUTLIER) cc_final: 0.9124 (tp) REVERT: J 339 ARG cc_start: 0.4934 (mmm160) cc_final: 0.3917 (mmt-90) REVERT: J 375 GLU cc_start: 0.8372 (tp30) cc_final: 0.7942 (tp30) REVERT: J 400 MET cc_start: 0.8237 (mtp) cc_final: 0.7992 (ttm) REVERT: J 557 LYS cc_start: 0.7748 (OUTLIER) cc_final: 0.7031 (pttt) REVERT: J 591 ILE cc_start: 0.8969 (OUTLIER) cc_final: 0.8647 (tp) REVERT: J 661 VAL cc_start: 0.8607 (OUTLIER) cc_final: 0.8352 (t) REVERT: J 1101 LEU cc_start: 0.5654 (OUTLIER) cc_final: 0.5428 (mp) REVERT: J 1144 LEU cc_start: 0.8930 (OUTLIER) cc_final: 0.8657 (tt) REVERT: J 1194 ARG cc_start: 0.5649 (mpt180) cc_final: 0.4334 (mmm-85) REVERT: J 1236 GLU cc_start: 0.7341 (OUTLIER) cc_final: 0.7040 (mp0) REVERT: J 1304 ARG cc_start: 0.7140 (OUTLIER) cc_final: 0.6200 (tpt90) REVERT: J 1310 THR cc_start: 0.8875 (OUTLIER) cc_final: 0.8557 (m) REVERT: N 17 MET cc_start: 0.6730 (OUTLIER) cc_final: 0.6472 (mtt) REVERT: N 21 ASN cc_start: 0.7912 (OUTLIER) cc_final: 0.7411 (m-40) REVERT: G 15 ASP cc_start: 0.6907 (OUTLIER) cc_final: 0.6554 (m-30) REVERT: G 33 ARG cc_start: 0.7063 (OUTLIER) cc_final: 0.6138 (ttp-170) REVERT: G 157 THR cc_start: 0.7739 (m) cc_final: 0.7386 (m) REVERT: G 158 ARG cc_start: 0.7720 (OUTLIER) cc_final: 0.6651 (ttm-80) REVERT: I 200 ARG cc_start: 0.7070 (mmm160) cc_final: 0.6817 (ptt90) REVERT: I 268 ARG cc_start: 0.4424 (OUTLIER) cc_final: 0.4182 (ttm170) REVERT: I 284 LEU cc_start: 0.6834 (OUTLIER) cc_final: 0.6572 (mp) REVERT: I 301 TYR cc_start: 0.5044 (OUTLIER) cc_final: 0.3823 (m-10) REVERT: I 503 LYS cc_start: 0.8447 (ttpp) cc_final: 0.8195 (ptmm) REVERT: I 514 PHE cc_start: 0.8169 (OUTLIER) cc_final: 0.7595 (m-10) REVERT: I 892 GLU cc_start: 0.6287 (tt0) cc_final: 0.6086 (pm20) REVERT: I 1016 GLU cc_start: 0.6653 (OUTLIER) cc_final: 0.6225 (tm-30) REVERT: I 1041 ASP cc_start: 0.7638 (OUTLIER) cc_final: 0.7247 (m-30) REVERT: K 42 GLU cc_start: 0.8222 (OUTLIER) cc_final: 0.6399 (pp20) REVERT: K 74 GLU cc_start: 0.6279 (mt-10) cc_final: 0.6058 (mt-10) REVERT: L 24 TYR cc_start: 0.7014 (OUTLIER) cc_final: 0.5007 (t80) REVERT: L 144 LEU cc_start: 0.4461 (OUTLIER) cc_final: 0.4220 (pp) REVERT: L 273 MET cc_start: 0.4296 (OUTLIER) cc_final: 0.2654 (tpp) REVERT: L 379 MET cc_start: 0.7237 (tpp) cc_final: 0.6562 (tpp) REVERT: L 559 LEU cc_start: 0.9013 (OUTLIER) cc_final: 0.8438 (mp) REVERT: L 561 MET cc_start: 0.7922 (ttm) cc_final: 0.7578 (mtp) REVERT: M 297 LYS cc_start: 0.6093 (OUTLIER) cc_final: 0.5752 (pttp) outliers start: 447 outliers final: 309 residues processed: 874 average time/residue: 0.4896 time to fit residues: 670.3711 Evaluate side-chains 700 residues out of total 3346 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 335 poor density : 365 time to evaluate : 4.384 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain J residue 24 LEU Chi-restraints excluded: chain J residue 37 GLU Chi-restraints excluded: chain J residue 46 TYR Chi-restraints excluded: chain J residue 56 LEU Chi-restraints excluded: chain J residue 65 VAL Chi-restraints excluded: chain J residue 90 VAL Chi-restraints excluded: chain J residue 93 THR Chi-restraints excluded: chain J residue 95 THR Chi-restraints excluded: chain J residue 120 LEU Chi-restraints excluded: chain J residue 146 VAL Chi-restraints excluded: chain J residue 161 THR Chi-restraints excluded: chain J residue 199 GLU Chi-restraints excluded: chain J residue 201 LEU Chi-restraints excluded: chain J residue 212 THR Chi-restraints excluded: chain J residue 217 LEU Chi-restraints excluded: chain J residue 241 VAL Chi-restraints excluded: chain J residue 244 VAL Chi-restraints excluded: chain J residue 264 ASP Chi-restraints excluded: chain J residue 289 ASP Chi-restraints excluded: chain J residue 292 VAL Chi-restraints excluded: chain J residue 306 LEU Chi-restraints excluded: chain J residue 324 LEU Chi-restraints excluded: chain J residue 326 SER Chi-restraints excluded: chain J residue 357 VAL Chi-restraints excluded: chain J residue 365 GLN Chi-restraints excluded: chain J residue 374 LEU Chi-restraints excluded: chain J residue 393 THR Chi-restraints excluded: chain J residue 416 ILE Chi-restraints excluded: chain J residue 434 ILE Chi-restraints excluded: chain J residue 442 ILE Chi-restraints excluded: chain J residue 466 MET Chi-restraints excluded: chain J residue 468 VAL Chi-restraints excluded: chain J residue 473 THR Chi-restraints excluded: chain J residue 474 LEU Chi-restraints excluded: chain J residue 478 LEU Chi-restraints excluded: chain J residue 489 ASN Chi-restraints excluded: chain J residue 492 SER Chi-restraints excluded: chain J residue 506 VAL Chi-restraints excluded: chain J residue 517 CYS Chi-restraints excluded: chain J residue 526 VAL Chi-restraints excluded: chain J residue 543 SER Chi-restraints excluded: chain J residue 545 HIS Chi-restraints excluded: chain J residue 548 VAL Chi-restraints excluded: chain J residue 550 VAL Chi-restraints excluded: chain J residue 553 THR Chi-restraints excluded: chain J residue 557 LYS Chi-restraints excluded: chain J residue 558 ASP Chi-restraints excluded: chain J residue 571 ASP Chi-restraints excluded: chain J residue 572 THR Chi-restraints excluded: chain J residue 576 ARG Chi-restraints excluded: chain J residue 578 ILE Chi-restraints excluded: chain J residue 591 ILE Chi-restraints excluded: chain J residue 592 VAL Chi-restraints excluded: chain J residue 601 ILE Chi-restraints excluded: chain J residue 638 SER Chi-restraints excluded: chain J residue 661 VAL Chi-restraints excluded: chain J residue 674 THR Chi-restraints excluded: chain J residue 683 ILE Chi-restraints excluded: chain J residue 685 ILE Chi-restraints excluded: chain J residue 706 VAL Chi-restraints excluded: chain J residue 708 ASN Chi-restraints excluded: chain J residue 717 VAL Chi-restraints excluded: chain J residue 722 ILE Chi-restraints excluded: chain J residue 744 ARG Chi-restraints excluded: chain J residue 762 ASN Chi-restraints excluded: chain J residue 770 LEU Chi-restraints excluded: chain J residue 783 LEU Chi-restraints excluded: chain J residue 788 LEU Chi-restraints excluded: chain J residue 796 LEU Chi-restraints excluded: chain J residue 797 THR Chi-restraints excluded: chain J residue 801 VAL Chi-restraints excluded: chain J residue 803 VAL Chi-restraints excluded: chain J residue 816 THR Chi-restraints excluded: chain J residue 825 VAL Chi-restraints excluded: chain J residue 835 LEU Chi-restraints excluded: chain J residue 869 CYS Chi-restraints excluded: chain J residue 878 ASP Chi-restraints excluded: chain J residue 882 VAL Chi-restraints excluded: chain J residue 891 ASP Chi-restraints excluded: chain J residue 894 VAL Chi-restraints excluded: chain J residue 903 LEU Chi-restraints excluded: chain J residue 909 ILE Chi-restraints excluded: chain J residue 918 ILE Chi-restraints excluded: chain J residue 928 THR Chi-restraints excluded: chain J residue 931 THR Chi-restraints excluded: chain J residue 952 VAL Chi-restraints excluded: chain J residue 968 ASN Chi-restraints excluded: chain J residue 1028 ILE Chi-restraints excluded: chain J residue 1060 VAL Chi-restraints excluded: chain J residue 1081 VAL Chi-restraints excluded: chain J residue 1101 LEU Chi-restraints excluded: chain J residue 1116 SER Chi-restraints excluded: chain J residue 1120 THR Chi-restraints excluded: chain J residue 1144 LEU Chi-restraints excluded: chain J residue 1148 ARG Chi-restraints excluded: chain J residue 1155 ILE Chi-restraints excluded: chain J residue 1164 SER Chi-restraints excluded: chain J residue 1177 ILE Chi-restraints excluded: chain J residue 1181 ASP Chi-restraints excluded: chain J residue 1196 LEU Chi-restraints excluded: chain J residue 1198 VAL Chi-restraints excluded: chain J residue 1206 ARG Chi-restraints excluded: chain J residue 1220 ILE Chi-restraints excluded: chain J residue 1223 LEU Chi-restraints excluded: chain J residue 1230 THR Chi-restraints excluded: chain J residue 1236 GLU Chi-restraints excluded: chain J residue 1240 VAL Chi-restraints excluded: chain J residue 1243 LEU Chi-restraints excluded: chain J residue 1256 ILE Chi-restraints excluded: chain J residue 1257 VAL Chi-restraints excluded: chain J residue 1258 ARG Chi-restraints excluded: chain J residue 1261 LEU Chi-restraints excluded: chain J residue 1262 ARG Chi-restraints excluded: chain J residue 1266 ILE Chi-restraints excluded: chain J residue 1267 VAL Chi-restraints excluded: chain J residue 1273 ASP Chi-restraints excluded: chain J residue 1304 ARG Chi-restraints excluded: chain J residue 1307 LEU Chi-restraints excluded: chain J residue 1310 THR Chi-restraints excluded: chain J residue 1332 LEU Chi-restraints excluded: chain J residue 1333 THR Chi-restraints excluded: chain J residue 1342 ASP Chi-restraints excluded: chain J residue 1344 LEU Chi-restraints excluded: chain J residue 1356 LEU Chi-restraints excluded: chain N residue 10 SER Chi-restraints excluded: chain N residue 15 LEU Chi-restraints excluded: chain N residue 17 MET Chi-restraints excluded: chain N residue 21 ASN Chi-restraints excluded: chain N residue 27 ILE Chi-restraints excluded: chain N residue 61 CYS Chi-restraints excluded: chain G residue 5 VAL Chi-restraints excluded: chain G residue 6 THR Chi-restraints excluded: chain G residue 13 LEU Chi-restraints excluded: chain G residue 15 ASP Chi-restraints excluded: chain G residue 29 GLU Chi-restraints excluded: chain G residue 33 ARG Chi-restraints excluded: chain G residue 39 LEU Chi-restraints excluded: chain G residue 75 GLN Chi-restraints excluded: chain G residue 79 LEU Chi-restraints excluded: chain G residue 82 LEU Chi-restraints excluded: chain G residue 92 VAL Chi-restraints excluded: chain G residue 98 VAL Chi-restraints excluded: chain G residue 100 LEU Chi-restraints excluded: chain G residue 105 SER Chi-restraints excluded: chain G residue 124 VAL Chi-restraints excluded: chain G residue 130 ILE Chi-restraints excluded: chain G residue 133 LEU Chi-restraints excluded: chain G residue 140 ILE Chi-restraints excluded: chain G residue 144 ILE Chi-restraints excluded: chain G residue 146 VAL Chi-restraints excluded: chain G residue 153 VAL Chi-restraints excluded: chain G residue 158 ARG Chi-restraints excluded: chain G residue 171 LEU Chi-restraints excluded: chain G residue 177 TYR Chi-restraints excluded: chain G residue 182 ARG Chi-restraints excluded: chain G residue 192 VAL Chi-restraints excluded: chain G residue 196 THR Chi-restraints excluded: chain G residue 198 LEU Chi-restraints excluded: chain G residue 200 LYS Chi-restraints excluded: chain G residue 211 ILE Chi-restraints excluded: chain G residue 214 GLU Chi-restraints excluded: chain G residue 231 PHE Chi-restraints excluded: chain H residue 16 ILE Chi-restraints excluded: chain H residue 19 VAL Chi-restraints excluded: chain H residue 28 LEU Chi-restraints excluded: chain H residue 38 THR Chi-restraints excluded: chain H residue 57 THR Chi-restraints excluded: chain H residue 61 ILE Chi-restraints excluded: chain H residue 83 LEU Chi-restraints excluded: chain H residue 98 VAL Chi-restraints excluded: chain H residue 99 ILE Chi-restraints excluded: chain H residue 115 ILE Chi-restraints excluded: chain H residue 140 ILE Chi-restraints excluded: chain H residue 146 VAL Chi-restraints excluded: chain H residue 172 LEU Chi-restraints excluded: chain H residue 183 ILE Chi-restraints excluded: chain H residue 203 ILE Chi-restraints excluded: chain H residue 217 ILE Chi-restraints excluded: chain I residue 33 ASP Chi-restraints excluded: chain I residue 37 LYS Chi-restraints excluded: chain I residue 67 GLU Chi-restraints excluded: chain I residue 91 THR Chi-restraints excluded: chain I residue 114 VAL Chi-restraints excluded: chain I residue 127 ILE Chi-restraints excluded: chain I residue 133 ASN Chi-restraints excluded: chain I residue 138 ILE Chi-restraints excluded: chain I residue 147 SER Chi-restraints excluded: chain I residue 177 ILE Chi-restraints excluded: chain I residue 220 ILE Chi-restraints excluded: chain I residue 256 GLU Chi-restraints excluded: chain I residue 268 ARG Chi-restraints excluded: chain I residue 284 LEU Chi-restraints excluded: chain I residue 286 GLU Chi-restraints excluded: chain I residue 287 VAL Chi-restraints excluded: chain I residue 289 VAL Chi-restraints excluded: chain I residue 296 VAL Chi-restraints excluded: chain I residue 301 TYR Chi-restraints excluded: chain I residue 317 LEU Chi-restraints excluded: chain I residue 319 LEU Chi-restraints excluded: chain I residue 347 ILE Chi-restraints excluded: chain I residue 391 SER Chi-restraints excluded: chain I residue 398 SER Chi-restraints excluded: chain I residue 417 SER Chi-restraints excluded: chain I residue 435 ILE Chi-restraints excluded: chain I residue 466 VAL Chi-restraints excluded: chain I residue 471 VAL Chi-restraints excluded: chain I residue 475 VAL Chi-restraints excluded: chain I residue 487 LEU Chi-restraints excluded: chain I residue 514 PHE Chi-restraints excluded: chain I residue 521 LEU Chi-restraints excluded: chain I residue 524 ILE Chi-restraints excluded: chain I residue 525 THR Chi-restraints excluded: chain I residue 531 SER Chi-restraints excluded: chain I residue 539 THR Chi-restraints excluded: chain I residue 553 THR Chi-restraints excluded: chain I residue 558 VAL Chi-restraints excluded: chain I residue 561 ILE Chi-restraints excluded: chain I residue 563 THR Chi-restraints excluded: chain I residue 573 ASN Chi-restraints excluded: chain I residue 576 SER Chi-restraints excluded: chain I residue 581 THR Chi-restraints excluded: chain I residue 583 GLU Chi-restraints excluded: chain I residue 589 THR Chi-restraints excluded: chain I residue 596 ASP Chi-restraints excluded: chain I residue 600 THR Chi-restraints excluded: chain I residue 602 GLU Chi-restraints excluded: chain I residue 604 HIS Chi-restraints excluded: chain I residue 609 ILE Chi-restraints excluded: chain I residue 633 LEU Chi-restraints excluded: chain I residue 634 VAL Chi-restraints excluded: chain I residue 635 THR Chi-restraints excluded: chain I residue 643 SER Chi-restraints excluded: chain I residue 658 GLN Chi-restraints excluded: chain I residue 659 GLN Chi-restraints excluded: chain I residue 662 SER Chi-restraints excluded: chain I residue 690 VAL Chi-restraints excluded: chain I residue 699 LEU Chi-restraints excluded: chain I residue 717 VAL Chi-restraints excluded: chain I residue 736 VAL Chi-restraints excluded: chain I residue 750 ILE Chi-restraints excluded: chain I residue 754 THR Chi-restraints excluded: chain I residue 764 CYS Chi-restraints excluded: chain I residue 765 ILE Chi-restraints excluded: chain I residue 773 LEU Chi-restraints excluded: chain I residue 777 VAL Chi-restraints excluded: chain I residue 783 LEU Chi-restraints excluded: chain I residue 799 ASN Chi-restraints excluded: chain I residue 800 MET Chi-restraints excluded: chain I residue 816 ILE Chi-restraints excluded: chain I residue 819 SER Chi-restraints excluded: chain I residue 839 VAL Chi-restraints excluded: chain I residue 843 THR Chi-restraints excluded: chain I residue 905 ILE Chi-restraints excluded: chain I residue 911 SER Chi-restraints excluded: chain I residue 919 ARG Chi-restraints excluded: chain I residue 935 THR Chi-restraints excluded: chain I residue 939 VAL Chi-restraints excluded: chain I residue 1003 THR Chi-restraints excluded: chain I residue 1014 LEU Chi-restraints excluded: chain I residue 1016 GLU Chi-restraints excluded: chain I residue 1041 ASP Chi-restraints excluded: chain I residue 1073 LYS Chi-restraints excluded: chain I residue 1083 GLU Chi-restraints excluded: chain I residue 1092 THR Chi-restraints excluded: chain I residue 1096 ILE Chi-restraints excluded: chain I residue 1097 VAL Chi-restraints excluded: chain I residue 1107 MET Chi-restraints excluded: chain I residue 1135 GLN Chi-restraints excluded: chain I residue 1159 VAL Chi-restraints excluded: chain I residue 1165 SER Chi-restraints excluded: chain I residue 1182 ILE Chi-restraints excluded: chain I residue 1186 VAL Chi-restraints excluded: chain I residue 1198 LEU Chi-restraints excluded: chain I residue 1201 LEU Chi-restraints excluded: chain I residue 1206 THR Chi-restraints excluded: chain I residue 1210 ILE Chi-restraints excluded: chain I residue 1240 ASP Chi-restraints excluded: chain I residue 1247 SER Chi-restraints excluded: chain I residue 1253 LEU Chi-restraints excluded: chain I residue 1254 VAL Chi-restraints excluded: chain I residue 1255 THR Chi-restraints excluded: chain I residue 1289 GLU Chi-restraints excluded: chain I residue 1295 SER Chi-restraints excluded: chain I residue 1296 ASP Chi-restraints excluded: chain I residue 1322 SER Chi-restraints excluded: chain I residue 1327 LEU Chi-restraints excluded: chain K residue 4 VAL Chi-restraints excluded: chain K residue 13 ILE Chi-restraints excluded: chain K residue 42 GLU Chi-restraints excluded: chain K residue 46 THR Chi-restraints excluded: chain K residue 52 ARG Chi-restraints excluded: chain K residue 54 ILE Chi-restraints excluded: chain K residue 66 VAL Chi-restraints excluded: chain L residue 23 THR Chi-restraints excluded: chain L residue 24 TYR Chi-restraints excluded: chain L residue 41 ILE Chi-restraints excluded: chain L residue 94 THR Chi-restraints excluded: chain L residue 118 ASP Chi-restraints excluded: chain L residue 127 ILE Chi-restraints excluded: chain L residue 144 LEU Chi-restraints excluded: chain L residue 162 ILE Chi-restraints excluded: chain L residue 229 VAL Chi-restraints excluded: chain L residue 231 THR Chi-restraints excluded: chain L residue 235 ILE Chi-restraints excluded: chain L residue 255 VAL Chi-restraints excluded: chain L residue 262 VAL Chi-restraints excluded: chain L residue 273 MET Chi-restraints excluded: chain L residue 275 VAL Chi-restraints excluded: chain L residue 314 THR Chi-restraints excluded: chain L residue 330 LEU Chi-restraints excluded: chain L residue 337 VAL Chi-restraints excluded: chain L residue 338 HIS Chi-restraints excluded: chain L residue 366 SER Chi-restraints excluded: chain L residue 386 LEU Chi-restraints excluded: chain L residue 389 SER Chi-restraints excluded: chain L residue 395 THR Chi-restraints excluded: chain L residue 405 ILE Chi-restraints excluded: chain L residue 439 ILE Chi-restraints excluded: chain L residue 442 SER Chi-restraints excluded: chain L residue 454 VAL Chi-restraints excluded: chain L residue 467 SER Chi-restraints excluded: chain L residue 494 ILE Chi-restraints excluded: chain L residue 498 LEU Chi-restraints excluded: chain L residue 511 ILE Chi-restraints excluded: chain L residue 517 SER Chi-restraints excluded: chain L residue 519 LEU Chi-restraints excluded: chain L residue 530 LEU Chi-restraints excluded: chain L residue 547 VAL Chi-restraints excluded: chain L residue 559 LEU Chi-restraints excluded: chain L residue 587 ILE Chi-restraints excluded: chain M residue 262 LEU Chi-restraints excluded: chain M residue 285 THR Chi-restraints excluded: chain M residue 289 LEU Chi-restraints excluded: chain M residue 297 LYS Chi-restraints excluded: chain M residue 306 VAL Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 397 random chunks: chunk 335 optimal weight: 2.9990 chunk 300 optimal weight: 5.9990 chunk 166 optimal weight: 0.8980 chunk 102 optimal weight: 5.9990 chunk 202 optimal weight: 3.9990 chunk 160 optimal weight: 0.2980 chunk 311 optimal weight: 0.8980 chunk 120 optimal weight: 1.9990 chunk 189 optimal weight: 0.7980 chunk 231 optimal weight: 0.7980 chunk 360 optimal weight: 4.9990 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: J 80 HIS ** J 266 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 450 HIS J 477 GLN J 680 ASN ** J 720 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 777 HIS J 875 ASN ** J1049 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J1218 HIS J1227 HIS ** J1244 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J1249 ASN N 71 HIS G 132 HIS H 37 HIS H 84 ASN I 31 GLN ** I 150 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** I 276 GLN ** I 519 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 618 GLN I 799 ASN I 811 ASN I 834 GLN I1116 HIS I1134 GLN ** I1136 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I1209 GLN I1237 HIS I1264 GLN K 61 ASN L 323 ASN ** L 362 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 406 GLN L 409 ASN L 446 GLN L 461 ASN L 518 HIS M 268 ASN M 283 GLN M 320 ASN Total number of N/Q/H flips: 34 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7712 moved from start: 0.1926 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.061 33475 Z= 0.213 Angle : 0.676 9.727 45662 Z= 0.355 Chirality : 0.044 0.198 5240 Planarity : 0.005 0.076 5595 Dihedral : 18.617 151.681 6259 Min Nonbonded Distance : 1.990 Molprobity Statistics. All-atom Clashscore : 16.63 Ramachandran Plot: Outliers : 0.13 % Allowed : 7.07 % Favored : 92.80 % Rotamer: Outliers : 7.55 % Allowed : 24.46 % Favored : 67.99 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.25 % Cis-general : 0.21 % Twisted Proline : 0.65 % Twisted General : 0.11 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.96 (0.12), residues: 3876 helix: -0.89 (0.12), residues: 1570 sheet: -2.82 (0.22), residues: 418 loop : -2.73 (0.13), residues: 1888 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP I 807 HIS 0.006 0.001 HIS I 273 PHE 0.015 0.002 PHE I 906 TYR 0.014 0.001 TYR G 177 ARG 0.008 0.001 ARG J1149 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7752 Ramachandran restraints generated. 3876 Oldfield, 0 Emsley, 3876 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7752 Ramachandran restraints generated. 3876 Oldfield, 0 Emsley, 3876 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 699 residues out of total 3346 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 251 poor density : 448 time to evaluate : 3.652 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: J 69 GLU cc_start: 0.7751 (tt0) cc_final: 0.7297 (mt-10) REVERT: J 133 ARG cc_start: 0.6877 (tpt170) cc_final: 0.6657 (tpp-160) REVERT: J 169 LEU cc_start: 0.7358 (tt) cc_final: 0.7151 (tt) REVERT: J 290 ILE cc_start: 0.7167 (OUTLIER) cc_final: 0.6945 (mt) REVERT: J 375 GLU cc_start: 0.8338 (tp30) cc_final: 0.7841 (tp30) REVERT: J 557 LYS cc_start: 0.7548 (ptmt) cc_final: 0.7043 (pttt) REVERT: J 625 MET cc_start: 0.8976 (ttp) cc_final: 0.8597 (ttp) REVERT: J 1134 ILE cc_start: 0.7714 (OUTLIER) cc_final: 0.7380 (pt) REVERT: J 1135 THR cc_start: 0.8108 (OUTLIER) cc_final: 0.7907 (m) REVERT: J 1194 ARG cc_start: 0.5144 (mpt180) cc_final: 0.4425 (mmm-85) REVERT: J 1266 ILE cc_start: 0.7036 (OUTLIER) cc_final: 0.6587 (mm) REVERT: N 48 ARG cc_start: 0.8483 (OUTLIER) cc_final: 0.8243 (tpt-90) REVERT: G 200 LYS cc_start: 0.7887 (OUTLIER) cc_final: 0.7571 (ptmt) REVERT: G 231 PHE cc_start: 0.8364 (OUTLIER) cc_final: 0.8101 (t80) REVERT: H 69 SER cc_start: 0.8404 (OUTLIER) cc_final: 0.7908 (m) REVERT: H 183 ILE cc_start: 0.8671 (OUTLIER) cc_final: 0.8404 (tt) REVERT: I 200 ARG cc_start: 0.6999 (mmm160) cc_final: 0.6549 (ptt90) REVERT: I 240 GLU cc_start: 0.6012 (tm-30) cc_final: 0.5782 (tm-30) REVERT: I 304 GLU cc_start: 0.6728 (mm-30) cc_final: 0.6278 (mp0) REVERT: I 315 MET cc_start: 0.5640 (mmm) cc_final: 0.5407 (tpt) REVERT: I 514 PHE cc_start: 0.8105 (OUTLIER) cc_final: 0.7696 (m-10) REVERT: I 528 ARG cc_start: 0.8368 (OUTLIER) cc_final: 0.7478 (mtp85) REVERT: I 569 ILE cc_start: 0.8957 (mt) cc_final: 0.8598 (tt) REVERT: I 659 GLN cc_start: 0.8824 (OUTLIER) cc_final: 0.8443 (tt0) REVERT: I 800 MET cc_start: 0.8372 (OUTLIER) cc_final: 0.8117 (mtm) REVERT: I 1016 GLU cc_start: 0.6675 (tm-30) cc_final: 0.6430 (tm-30) REVERT: I 1082 ILE cc_start: 0.8465 (mt) cc_final: 0.8245 (mt) REVERT: I 1106 ARG cc_start: 0.6532 (OUTLIER) cc_final: 0.6157 (mtt180) REVERT: I 1211 ARG cc_start: 0.7996 (OUTLIER) cc_final: 0.7791 (ptp-170) REVERT: I 1253 LEU cc_start: 0.9224 (OUTLIER) cc_final: 0.8721 (tp) REVERT: K 30 MET cc_start: 0.8500 (mtm) cc_final: 0.8276 (mtp) REVERT: K 42 GLU cc_start: 0.7881 (OUTLIER) cc_final: 0.6444 (pp20) REVERT: K 74 GLU cc_start: 0.6259 (mt-10) cc_final: 0.6039 (mt-10) REVERT: L 116 GLU cc_start: 0.6750 (mm-30) cc_final: 0.6449 (pt0) REVERT: L 273 MET cc_start: 0.3419 (OUTLIER) cc_final: 0.2922 (tpp) REVERT: L 277 MET cc_start: 0.4550 (tpp) cc_final: 0.4046 (mmt) REVERT: L 561 MET cc_start: 0.7824 (ttm) cc_final: 0.7528 (mtp) REVERT: M 297 LYS cc_start: 0.5714 (OUTLIER) cc_final: 0.5306 (pttp) REVERT: M 300 LEU cc_start: 0.5329 (OUTLIER) cc_final: 0.5088 (tp) REVERT: M 316 MET cc_start: 0.3898 (mmt) cc_final: 0.2232 (tmm) outliers start: 251 outliers final: 127 residues processed: 657 average time/residue: 0.4685 time to fit residues: 489.1985 Evaluate side-chains 521 residues out of total 3346 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 147 poor density : 374 time to evaluate : 3.752 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain J residue 24 LEU Chi-restraints excluded: chain J residue 46 TYR Chi-restraints excluded: chain J residue 56 LEU Chi-restraints excluded: chain J residue 65 VAL Chi-restraints excluded: chain J residue 76 LYS Chi-restraints excluded: chain J residue 93 THR Chi-restraints excluded: chain J residue 95 THR Chi-restraints excluded: chain J residue 146 VAL Chi-restraints excluded: chain J residue 152 THR Chi-restraints excluded: chain J residue 159 ILE Chi-restraints excluded: chain J residue 199 GLU Chi-restraints excluded: chain J residue 205 LEU Chi-restraints excluded: chain J residue 244 VAL Chi-restraints excluded: chain J residue 290 ILE Chi-restraints excluded: chain J residue 292 VAL Chi-restraints excluded: chain J residue 324 LEU Chi-restraints excluded: chain J residue 416 ILE Chi-restraints excluded: chain J residue 442 ILE Chi-restraints excluded: chain J residue 478 LEU Chi-restraints excluded: chain J residue 489 ASN Chi-restraints excluded: chain J residue 506 VAL Chi-restraints excluded: chain J residue 545 HIS Chi-restraints excluded: chain J residue 558 ASP Chi-restraints excluded: chain J residue 567 THR Chi-restraints excluded: chain J residue 706 VAL Chi-restraints excluded: chain J residue 707 ILE Chi-restraints excluded: chain J residue 708 ASN Chi-restraints excluded: chain J residue 717 VAL Chi-restraints excluded: chain J residue 762 ASN Chi-restraints excluded: chain J residue 769 VAL Chi-restraints excluded: chain J residue 770 LEU Chi-restraints excluded: chain J residue 783 LEU Chi-restraints excluded: chain J residue 796 LEU Chi-restraints excluded: chain J residue 797 THR Chi-restraints excluded: chain J residue 803 VAL Chi-restraints excluded: chain J residue 825 VAL Chi-restraints excluded: chain J residue 835 LEU Chi-restraints excluded: chain J residue 839 VAL Chi-restraints excluded: chain J residue 878 ASP Chi-restraints excluded: chain J residue 903 LEU Chi-restraints excluded: chain J residue 918 ILE Chi-restraints excluded: chain J residue 928 THR Chi-restraints excluded: chain J residue 931 THR Chi-restraints excluded: chain J residue 968 ASN Chi-restraints excluded: chain J residue 1028 ILE Chi-restraints excluded: chain J residue 1134 ILE Chi-restraints excluded: chain J residue 1135 THR Chi-restraints excluded: chain J residue 1148 ARG Chi-restraints excluded: chain J residue 1160 SER Chi-restraints excluded: chain J residue 1181 ASP Chi-restraints excluded: chain J residue 1196 LEU Chi-restraints excluded: chain J residue 1223 LEU Chi-restraints excluded: chain J residue 1249 ASN Chi-restraints excluded: chain J residue 1257 VAL Chi-restraints excluded: chain J residue 1261 LEU Chi-restraints excluded: chain J residue 1262 ARG Chi-restraints excluded: chain J residue 1266 ILE Chi-restraints excluded: chain J residue 1273 ASP Chi-restraints excluded: chain J residue 1307 LEU Chi-restraints excluded: chain J residue 1332 LEU Chi-restraints excluded: chain J residue 1342 ASP Chi-restraints excluded: chain N residue 27 ILE Chi-restraints excluded: chain N residue 48 ARG Chi-restraints excluded: chain G residue 6 THR Chi-restraints excluded: chain G residue 9 LEU Chi-restraints excluded: chain G residue 29 GLU Chi-restraints excluded: chain G residue 117 HIS Chi-restraints excluded: chain G residue 133 LEU Chi-restraints excluded: chain G residue 177 TYR Chi-restraints excluded: chain G residue 192 VAL Chi-restraints excluded: chain G residue 200 LYS Chi-restraints excluded: chain G residue 211 ILE Chi-restraints excluded: chain G residue 231 PHE Chi-restraints excluded: chain H residue 29 GLU Chi-restraints excluded: chain H residue 38 THR Chi-restraints excluded: chain H residue 49 SER Chi-restraints excluded: chain H residue 61 ILE Chi-restraints excluded: chain H residue 65 LEU Chi-restraints excluded: chain H residue 69 SER Chi-restraints excluded: chain H residue 102 LEU Chi-restraints excluded: chain H residue 134 THR Chi-restraints excluded: chain H residue 139 SER Chi-restraints excluded: chain H residue 146 VAL Chi-restraints excluded: chain H residue 183 ILE Chi-restraints excluded: chain I residue 37 LYS Chi-restraints excluded: chain I residue 114 VAL Chi-restraints excluded: chain I residue 117 ILE Chi-restraints excluded: chain I residue 138 ILE Chi-restraints excluded: chain I residue 263 VAL Chi-restraints excluded: chain I residue 319 LEU Chi-restraints excluded: chain I residue 442 VAL Chi-restraints excluded: chain I residue 456 VAL Chi-restraints excluded: chain I residue 514 PHE Chi-restraints excluded: chain I residue 521 LEU Chi-restraints excluded: chain I residue 528 ARG Chi-restraints excluded: chain I residue 558 VAL Chi-restraints excluded: chain I residue 563 THR Chi-restraints excluded: chain I residue 576 SER Chi-restraints excluded: chain I residue 589 THR Chi-restraints excluded: chain I residue 594 VAL Chi-restraints excluded: chain I residue 606 LEU Chi-restraints excluded: chain I residue 609 ILE Chi-restraints excluded: chain I residue 633 LEU Chi-restraints excluded: chain I residue 659 GLN Chi-restraints excluded: chain I residue 699 LEU Chi-restraints excluded: chain I residue 750 ILE Chi-restraints excluded: chain I residue 799 ASN Chi-restraints excluded: chain I residue 800 MET Chi-restraints excluded: chain I residue 913 VAL Chi-restraints excluded: chain I residue 919 ARG Chi-restraints excluded: chain I residue 939 VAL Chi-restraints excluded: chain I residue 1003 THR Chi-restraints excluded: chain I residue 1014 LEU Chi-restraints excluded: chain I residue 1083 GLU Chi-restraints excluded: chain I residue 1092 THR Chi-restraints excluded: chain I residue 1106 ARG Chi-restraints excluded: chain I residue 1135 GLN Chi-restraints excluded: chain I residue 1165 SER Chi-restraints excluded: chain I residue 1198 LEU Chi-restraints excluded: chain I residue 1211 ARG Chi-restraints excluded: chain I residue 1240 ASP Chi-restraints excluded: chain I residue 1253 LEU Chi-restraints excluded: chain I residue 1254 VAL Chi-restraints excluded: chain I residue 1296 ASP Chi-restraints excluded: chain I residue 1327 LEU Chi-restraints excluded: chain K residue 4 VAL Chi-restraints excluded: chain K residue 13 ILE Chi-restraints excluded: chain K residue 42 GLU Chi-restraints excluded: chain L residue 31 LEU Chi-restraints excluded: chain L residue 94 THR Chi-restraints excluded: chain L residue 96 ASP Chi-restraints excluded: chain L residue 118 ASP Chi-restraints excluded: chain L residue 144 LEU Chi-restraints excluded: chain L residue 162 ILE Chi-restraints excluded: chain L residue 231 THR Chi-restraints excluded: chain L residue 235 ILE Chi-restraints excluded: chain L residue 255 VAL Chi-restraints excluded: chain L residue 262 VAL Chi-restraints excluded: chain L residue 273 MET Chi-restraints excluded: chain L residue 357 GLN Chi-restraints excluded: chain L residue 386 LEU Chi-restraints excluded: chain L residue 429 THR Chi-restraints excluded: chain L residue 547 VAL Chi-restraints excluded: chain M residue 262 LEU Chi-restraints excluded: chain M residue 268 ASN Chi-restraints excluded: chain M residue 297 LYS Chi-restraints excluded: chain M residue 300 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 397 random chunks: chunk 200 optimal weight: 7.9990 chunk 111 optimal weight: 0.0870 chunk 300 optimal weight: 0.7980 chunk 245 optimal weight: 0.9980 chunk 99 optimal weight: 10.0000 chunk 361 optimal weight: 10.0000 chunk 390 optimal weight: 10.0000 chunk 321 optimal weight: 7.9990 chunk 358 optimal weight: 0.0770 chunk 123 optimal weight: 9.9990 chunk 289 optimal weight: 0.5980 overall best weight: 0.5116 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: J 45 ASN J 294 ASN J 320 ASN ** J 720 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J1049 GLN ** J1366 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 150 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 519 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 766 ASN I 811 ASN I 894 GLN I1136 GLN ** L 362 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 406 GLN ** M 268 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** M 283 GLN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7666 moved from start: 0.2772 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 33475 Z= 0.172 Angle : 0.610 9.535 45662 Z= 0.319 Chirality : 0.042 0.188 5240 Planarity : 0.004 0.081 5595 Dihedral : 17.753 154.929 5872 Min Nonbonded Distance : 2.007 Molprobity Statistics. All-atom Clashscore : 13.91 Ramachandran Plot: Outliers : 0.13 % Allowed : 6.50 % Favored : 93.37 % Rotamer: Outliers : 6.38 % Allowed : 24.82 % Favored : 68.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.25 % Cis-general : 0.21 % Twisted Proline : 0.00 % Twisted General : 0.08 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.04 (0.13), residues: 3876 helix: -0.03 (0.13), residues: 1560 sheet: -2.31 (0.23), residues: 411 loop : -2.31 (0.13), residues: 1905 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP L 434 HIS 0.007 0.001 HIS G 160 PHE 0.013 0.001 PHE I 906 TYR 0.015 0.001 TYR J 589 ARG 0.007 0.000 ARG J1373 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7752 Ramachandran restraints generated. 3876 Oldfield, 0 Emsley, 3876 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7752 Ramachandran restraints generated. 3876 Oldfield, 0 Emsley, 3876 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 649 residues out of total 3346 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 212 poor density : 437 time to evaluate : 3.778 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: J 69 GLU cc_start: 0.7591 (tt0) cc_final: 0.7002 (mt-10) REVERT: J 169 LEU cc_start: 0.7339 (tt) cc_final: 0.7070 (tt) REVERT: J 375 GLU cc_start: 0.8231 (tp30) cc_final: 0.7761 (tp30) REVERT: J 625 MET cc_start: 0.8795 (ttp) cc_final: 0.8484 (ttt) REVERT: J 1095 MET cc_start: 0.1969 (ttp) cc_final: 0.1535 (ttm) REVERT: J 1143 ASP cc_start: 0.7305 (t0) cc_final: 0.7073 (t0) REVERT: J 1189 MET cc_start: 0.4153 (mmm) cc_final: 0.3301 (mmm) REVERT: J 1194 ARG cc_start: 0.4798 (mpt180) cc_final: 0.4309 (mmm-85) REVERT: J 1266 ILE cc_start: 0.6841 (OUTLIER) cc_final: 0.6457 (mm) REVERT: G 137 ASN cc_start: 0.8492 (p0) cc_final: 0.8249 (p0) REVERT: G 231 PHE cc_start: 0.8327 (OUTLIER) cc_final: 0.7832 (t80) REVERT: H 69 SER cc_start: 0.8503 (OUTLIER) cc_final: 0.8021 (m) REVERT: I 11 ILE cc_start: 0.8492 (OUTLIER) cc_final: 0.8280 (mt) REVERT: I 200 ARG cc_start: 0.6885 (mmm160) cc_final: 0.6240 (ptt90) REVERT: I 521 LEU cc_start: 0.9068 (OUTLIER) cc_final: 0.8813 (tp) REVERT: I 569 ILE cc_start: 0.9024 (mt) cc_final: 0.8700 (tt) REVERT: I 572 ILE cc_start: 0.9300 (OUTLIER) cc_final: 0.8915 (mt) REVERT: I 609 ILE cc_start: 0.8617 (OUTLIER) cc_final: 0.8336 (pt) REVERT: I 800 MET cc_start: 0.8380 (OUTLIER) cc_final: 0.8013 (mtm) REVERT: I 922 ASN cc_start: 0.7970 (OUTLIER) cc_final: 0.7673 (m-40) REVERT: I 1020 GLU cc_start: 0.7389 (tm-30) cc_final: 0.7112 (tm-30) REVERT: I 1041 ASP cc_start: 0.7433 (OUTLIER) cc_final: 0.7199 (m-30) REVERT: K 30 MET cc_start: 0.8536 (mtm) cc_final: 0.8269 (mtp) REVERT: K 42 GLU cc_start: 0.7692 (OUTLIER) cc_final: 0.6252 (pp20) REVERT: L 116 GLU cc_start: 0.6719 (mm-30) cc_final: 0.6153 (pt0) REVERT: L 269 LEU cc_start: 0.6316 (mt) cc_final: 0.5156 (pp) REVERT: L 271 ASN cc_start: 0.6647 (t0) cc_final: 0.6161 (t0) REVERT: L 273 MET cc_start: 0.3582 (OUTLIER) cc_final: 0.2761 (tpp) REVERT: L 343 LYS cc_start: 0.4124 (OUTLIER) cc_final: 0.3867 (mmmt) REVERT: L 377 LYS cc_start: 0.7689 (tttt) cc_final: 0.6919 (ttmm) REVERT: L 417 ASP cc_start: 0.6545 (m-30) cc_final: 0.6096 (m-30) REVERT: L 545 HIS cc_start: 0.7073 (t70) cc_final: 0.6605 (t70) REVERT: L 561 MET cc_start: 0.7751 (ttm) cc_final: 0.7524 (mtp) REVERT: M 316 MET cc_start: 0.3616 (mmt) cc_final: 0.2201 (tmm) outliers start: 212 outliers final: 104 residues processed: 609 average time/residue: 0.4446 time to fit residues: 439.1115 Evaluate side-chains 483 residues out of total 3346 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 117 poor density : 366 time to evaluate : 4.008 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain J residue 26 SER Chi-restraints excluded: chain J residue 46 TYR Chi-restraints excluded: chain J residue 56 LEU Chi-restraints excluded: chain J residue 65 VAL Chi-restraints excluded: chain J residue 76 LYS Chi-restraints excluded: chain J residue 93 THR Chi-restraints excluded: chain J residue 135 ILE Chi-restraints excluded: chain J residue 146 VAL Chi-restraints excluded: chain J residue 159 ILE Chi-restraints excluded: chain J residue 192 MET Chi-restraints excluded: chain J residue 205 LEU Chi-restraints excluded: chain J residue 264 ASP Chi-restraints excluded: chain J residue 292 VAL Chi-restraints excluded: chain J residue 408 VAL Chi-restraints excluded: chain J residue 416 ILE Chi-restraints excluded: chain J residue 442 ILE Chi-restraints excluded: chain J residue 506 VAL Chi-restraints excluded: chain J residue 508 LEU Chi-restraints excluded: chain J residue 513 MET Chi-restraints excluded: chain J residue 545 HIS Chi-restraints excluded: chain J residue 558 ASP Chi-restraints excluded: chain J residue 571 ASP Chi-restraints excluded: chain J residue 596 LEU Chi-restraints excluded: chain J residue 706 VAL Chi-restraints excluded: chain J residue 707 ILE Chi-restraints excluded: chain J residue 708 ASN Chi-restraints excluded: chain J residue 717 VAL Chi-restraints excluded: chain J residue 722 ILE Chi-restraints excluded: chain J residue 740 LEU Chi-restraints excluded: chain J residue 762 ASN Chi-restraints excluded: chain J residue 770 LEU Chi-restraints excluded: chain J residue 797 THR Chi-restraints excluded: chain J residue 839 VAL Chi-restraints excluded: chain J residue 903 LEU Chi-restraints excluded: chain J residue 918 ILE Chi-restraints excluded: chain J residue 974 VAL Chi-restraints excluded: chain J residue 991 THR Chi-restraints excluded: chain J residue 1135 THR Chi-restraints excluded: chain J residue 1148 ARG Chi-restraints excluded: chain J residue 1181 ASP Chi-restraints excluded: chain J residue 1184 ASP Chi-restraints excluded: chain J residue 1196 LEU Chi-restraints excluded: chain J residue 1261 LEU Chi-restraints excluded: chain J residue 1266 ILE Chi-restraints excluded: chain J residue 1273 ASP Chi-restraints excluded: chain J residue 1301 THR Chi-restraints excluded: chain J residue 1332 LEU Chi-restraints excluded: chain J residue 1342 ASP Chi-restraints excluded: chain N residue 27 ILE Chi-restraints excluded: chain G residue 6 THR Chi-restraints excluded: chain G residue 29 GLU Chi-restraints excluded: chain G residue 130 ILE Chi-restraints excluded: chain G residue 177 TYR Chi-restraints excluded: chain G residue 192 VAL Chi-restraints excluded: chain G residue 211 ILE Chi-restraints excluded: chain G residue 231 PHE Chi-restraints excluded: chain H residue 27 THR Chi-restraints excluded: chain H residue 38 THR Chi-restraints excluded: chain H residue 65 LEU Chi-restraints excluded: chain H residue 69 SER Chi-restraints excluded: chain H residue 102 LEU Chi-restraints excluded: chain H residue 134 THR Chi-restraints excluded: chain H residue 139 SER Chi-restraints excluded: chain H residue 141 SER Chi-restraints excluded: chain I residue 11 ILE Chi-restraints excluded: chain I residue 37 LYS Chi-restraints excluded: chain I residue 105 TYR Chi-restraints excluded: chain I residue 117 ILE Chi-restraints excluded: chain I residue 138 ILE Chi-restraints excluded: chain I residue 203 LYS Chi-restraints excluded: chain I residue 296 VAL Chi-restraints excluded: chain I residue 442 VAL Chi-restraints excluded: chain I residue 456 VAL Chi-restraints excluded: chain I residue 471 VAL Chi-restraints excluded: chain I residue 498 ILE Chi-restraints excluded: chain I residue 521 LEU Chi-restraints excluded: chain I residue 523 GLU Chi-restraints excluded: chain I residue 524 ILE Chi-restraints excluded: chain I residue 558 VAL Chi-restraints excluded: chain I residue 572 ILE Chi-restraints excluded: chain I residue 606 LEU Chi-restraints excluded: chain I residue 609 ILE Chi-restraints excluded: chain I residue 633 LEU Chi-restraints excluded: chain I residue 750 ILE Chi-restraints excluded: chain I residue 773 LEU Chi-restraints excluded: chain I residue 785 ASP 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 913 VAL Chi-restraints excluded: chain I residue 922 ASN Chi-restraints excluded: chain I residue 939 VAL Chi-restraints excluded: chain I residue 973 SER Chi-restraints excluded: chain I residue 1014 LEU Chi-restraints excluded: chain I residue 1041 ASP Chi-restraints excluded: chain I residue 1083 GLU Chi-restraints excluded: chain I residue 1092 THR Chi-restraints excluded: chain I residue 1167 GLU Chi-restraints excluded: chain I residue 1240 ASP Chi-restraints excluded: chain I residue 1254 VAL Chi-restraints excluded: chain I residue 1296 ASP Chi-restraints excluded: chain I residue 1332 SER Chi-restraints excluded: chain K residue 4 VAL Chi-restraints excluded: chain K residue 13 ILE Chi-restraints excluded: chain K residue 42 GLU Chi-restraints excluded: chain L residue 31 LEU Chi-restraints excluded: chain L residue 94 THR Chi-restraints excluded: chain L residue 118 ASP Chi-restraints excluded: chain L residue 144 LEU Chi-restraints excluded: chain L residue 162 ILE Chi-restraints excluded: chain L residue 231 THR Chi-restraints excluded: chain L residue 262 VAL Chi-restraints excluded: chain L residue 273 MET Chi-restraints excluded: chain L residue 343 LYS Chi-restraints excluded: chain L residue 604 SER Chi-restraints excluded: chain M residue 262 LEU Chi-restraints excluded: chain M residue 292 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 397 random chunks: chunk 356 optimal weight: 6.9990 chunk 271 optimal weight: 4.9990 chunk 187 optimal weight: 0.0970 chunk 39 optimal weight: 0.9980 chunk 172 optimal weight: 0.7980 chunk 242 optimal weight: 3.9990 chunk 362 optimal weight: 2.9990 chunk 383 optimal weight: 6.9990 chunk 189 optimal weight: 0.7980 chunk 343 optimal weight: 8.9990 chunk 103 optimal weight: 8.9990 overall best weight: 1.1380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: J 320 ASN J1195 GLN ** J1244 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J1249 ASN ** I 150 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** I 894 GLN I1264 GLN ** L 362 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** M 268 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7691 moved from start: 0.2990 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 33475 Z= 0.198 Angle : 0.598 9.335 45662 Z= 0.312 Chirality : 0.042 0.205 5240 Planarity : 0.004 0.083 5595 Dihedral : 17.289 156.395 5785 Min Nonbonded Distance : 1.978 Molprobity Statistics. All-atom Clashscore : 13.43 Ramachandran Plot: Outliers : 0.13 % Allowed : 6.48 % Favored : 93.40 % Rotamer: Outliers : 5.93 % Allowed : 25.06 % Favored : 69.01 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.25 % Cis-general : 0.21 % Twisted Proline : 0.00 % Twisted General : 0.05 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.72 (0.13), residues: 3876 helix: 0.23 (0.13), residues: 1573 sheet: -2.09 (0.23), residues: 417 loop : -2.15 (0.13), residues: 1886 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP I 807 HIS 0.008 0.001 HIS G 160 PHE 0.016 0.001 PHE N 52 TYR 0.016 0.001 TYR G 177 ARG 0.006 0.000 ARG J1373 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7752 Ramachandran restraints generated. 3876 Oldfield, 0 Emsley, 3876 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7752 Ramachandran restraints generated. 3876 Oldfield, 0 Emsley, 3876 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 584 residues out of total 3346 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 197 poor density : 387 time to evaluate : 3.704 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: J 306 LEU cc_start: 0.9347 (OUTLIER) cc_final: 0.9129 (tp) REVERT: J 375 GLU cc_start: 0.8247 (tp30) cc_final: 0.7763 (tp30) REVERT: J 625 MET cc_start: 0.8762 (ttp) cc_final: 0.8437 (ttt) REVERT: J 796 LEU cc_start: 0.8951 (OUTLIER) cc_final: 0.8713 (tm) REVERT: J 985 ILE cc_start: 0.4891 (OUTLIER) cc_final: 0.4456 (tt) REVERT: J 1098 GLN cc_start: 0.2688 (OUTLIER) cc_final: 0.2484 (mp10) REVERT: J 1189 MET cc_start: 0.4354 (mmm) cc_final: 0.3897 (mmm) REVERT: J 1197 ASN cc_start: 0.6836 (m-40) cc_final: 0.6382 (m-40) REVERT: J 1266 ILE cc_start: 0.7055 (OUTLIER) cc_final: 0.6665 (mm) REVERT: N 21 ASN cc_start: 0.7636 (OUTLIER) cc_final: 0.7093 (m-40) REVERT: G 158 ARG cc_start: 0.7682 (OUTLIER) cc_final: 0.6943 (ttm-80) REVERT: G 231 PHE cc_start: 0.8266 (OUTLIER) cc_final: 0.7848 (t80) REVERT: H 69 SER cc_start: 0.8511 (OUTLIER) cc_final: 0.8014 (m) REVERT: H 206 GLU cc_start: 0.8228 (OUTLIER) cc_final: 0.7964 (mt-10) REVERT: I 200 ARG cc_start: 0.6846 (mmm160) cc_final: 0.6231 (ptt90) REVERT: I 521 LEU cc_start: 0.9070 (OUTLIER) cc_final: 0.8845 (tp) REVERT: I 609 ILE cc_start: 0.8561 (OUTLIER) cc_final: 0.8307 (pt) REVERT: I 800 MET cc_start: 0.8384 (OUTLIER) cc_final: 0.8073 (mtm) REVERT: I 1041 ASP cc_start: 0.7466 (OUTLIER) cc_final: 0.7228 (m-30) REVERT: I 1253 LEU cc_start: 0.9220 (OUTLIER) cc_final: 0.8729 (tp) REVERT: K 13 ILE cc_start: 0.7981 (OUTLIER) cc_final: 0.7756 (tt) REVERT: K 30 MET cc_start: 0.8568 (mtm) cc_final: 0.8222 (mtp) REVERT: L 271 ASN cc_start: 0.6657 (t0) cc_final: 0.6159 (t0) REVERT: L 273 MET cc_start: 0.3193 (tpp) cc_final: 0.2966 (ttt) REVERT: L 436 ARG cc_start: 0.7461 (ptp-110) cc_final: 0.7044 (ptp-170) REVERT: L 474 MET cc_start: 0.7638 (tmm) cc_final: 0.6598 (tmm) REVERT: L 477 GLU cc_start: 0.5887 (tp30) cc_final: 0.5654 (mm-30) REVERT: L 508 GLU cc_start: 0.7883 (OUTLIER) cc_final: 0.7464 (mt-10) REVERT: L 545 HIS cc_start: 0.6949 (t70) cc_final: 0.6467 (t70) REVERT: L 561 MET cc_start: 0.7814 (ttm) cc_final: 0.7553 (mtp) REVERT: M 297 LYS cc_start: 0.5457 (OUTLIER) cc_final: 0.5100 (pptt) REVERT: M 316 MET cc_start: 0.3598 (mmt) cc_final: 0.2216 (tmm) outliers start: 197 outliers final: 125 residues processed: 548 average time/residue: 0.4559 time to fit residues: 404.1117 Evaluate side-chains 496 residues out of total 3346 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 143 poor density : 353 time to evaluate : 3.742 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain J residue 26 SER Chi-restraints excluded: chain J residue 46 TYR Chi-restraints excluded: chain J residue 56 LEU Chi-restraints excluded: chain J residue 65 VAL Chi-restraints excluded: chain J residue 76 LYS Chi-restraints excluded: chain J residue 90 VAL Chi-restraints excluded: chain J residue 93 THR Chi-restraints excluded: chain J residue 135 ILE Chi-restraints excluded: chain J residue 146 VAL Chi-restraints excluded: chain J residue 159 ILE Chi-restraints excluded: chain J residue 205 LEU Chi-restraints excluded: chain J residue 264 ASP Chi-restraints excluded: chain J residue 292 VAL Chi-restraints excluded: chain J residue 306 LEU Chi-restraints excluded: chain J residue 324 LEU Chi-restraints excluded: chain J residue 416 ILE Chi-restraints excluded: chain J residue 442 ILE Chi-restraints excluded: chain J residue 478 LEU Chi-restraints excluded: chain J residue 489 ASN Chi-restraints excluded: chain J residue 506 VAL Chi-restraints excluded: chain J residue 508 LEU Chi-restraints excluded: chain J residue 513 MET Chi-restraints excluded: chain J residue 545 HIS Chi-restraints excluded: chain J residue 558 ASP Chi-restraints excluded: chain J residue 571 ASP Chi-restraints excluded: chain J residue 596 LEU Chi-restraints excluded: chain J residue 706 VAL Chi-restraints excluded: chain J residue 707 ILE Chi-restraints excluded: chain J residue 708 ASN Chi-restraints excluded: chain J residue 722 ILE Chi-restraints excluded: chain J residue 740 LEU Chi-restraints excluded: chain J residue 762 ASN Chi-restraints excluded: chain J residue 770 LEU Chi-restraints excluded: chain J residue 786 THR Chi-restraints excluded: chain J residue 788 LEU Chi-restraints excluded: chain J residue 796 LEU Chi-restraints excluded: chain J residue 807 LEU Chi-restraints excluded: chain J residue 825 VAL Chi-restraints excluded: chain J residue 839 VAL Chi-restraints excluded: chain J residue 862 THR Chi-restraints excluded: chain J residue 878 ASP Chi-restraints excluded: chain J residue 882 VAL Chi-restraints excluded: chain J residue 903 LEU Chi-restraints excluded: chain J residue 918 ILE Chi-restraints excluded: chain J residue 928 THR Chi-restraints excluded: chain J residue 974 VAL Chi-restraints excluded: chain J residue 985 ILE Chi-restraints excluded: chain J residue 991 THR Chi-restraints excluded: chain J residue 1054 THR Chi-restraints excluded: chain J residue 1098 GLN Chi-restraints excluded: chain J residue 1135 THR Chi-restraints excluded: chain J residue 1160 SER Chi-restraints excluded: chain J residue 1181 ASP Chi-restraints excluded: chain J residue 1186 TYR Chi-restraints excluded: chain J residue 1196 LEU Chi-restraints excluded: chain J residue 1249 ASN Chi-restraints excluded: chain J residue 1261 LEU Chi-restraints excluded: chain J residue 1266 ILE Chi-restraints excluded: chain J residue 1280 VAL Chi-restraints excluded: chain J residue 1297 LYS Chi-restraints excluded: chain J residue 1301 THR Chi-restraints excluded: chain J residue 1307 LEU Chi-restraints excluded: chain J residue 1332 LEU Chi-restraints excluded: chain J residue 1342 ASP Chi-restraints excluded: chain N residue 21 ASN Chi-restraints excluded: chain N residue 27 ILE Chi-restraints excluded: chain G residue 6 THR Chi-restraints excluded: chain G residue 9 LEU Chi-restraints excluded: chain G residue 61 ILE Chi-restraints excluded: chain G residue 130 ILE Chi-restraints excluded: chain G residue 158 ARG Chi-restraints excluded: chain G residue 171 LEU Chi-restraints excluded: chain G residue 177 TYR Chi-restraints excluded: chain G residue 192 VAL Chi-restraints excluded: chain G residue 231 PHE Chi-restraints excluded: chain H residue 38 THR Chi-restraints excluded: chain H residue 51 MET Chi-restraints excluded: chain H residue 65 LEU Chi-restraints excluded: chain H residue 69 SER Chi-restraints excluded: chain H residue 102 LEU Chi-restraints excluded: chain H residue 134 THR Chi-restraints excluded: chain H residue 139 SER Chi-restraints excluded: chain H residue 146 VAL Chi-restraints excluded: chain H residue 206 GLU Chi-restraints excluded: chain I residue 33 ASP Chi-restraints excluded: chain I residue 37 LYS Chi-restraints excluded: chain I residue 105 TYR Chi-restraints excluded: chain I residue 117 ILE Chi-restraints excluded: chain I residue 127 ILE Chi-restraints excluded: chain I residue 138 ILE Chi-restraints excluded: chain I residue 203 LYS Chi-restraints excluded: chain I residue 282 VAL Chi-restraints excluded: chain I residue 296 VAL Chi-restraints excluded: chain I residue 297 VAL Chi-restraints excluded: chain I residue 442 VAL Chi-restraints excluded: chain I residue 456 VAL Chi-restraints excluded: chain I residue 471 VAL Chi-restraints excluded: chain I residue 498 ILE Chi-restraints excluded: chain I residue 521 LEU Chi-restraints excluded: chain I residue 523 GLU Chi-restraints excluded: chain I residue 558 VAL Chi-restraints excluded: chain I residue 573 ASN Chi-restraints excluded: chain I residue 589 THR Chi-restraints excluded: chain I residue 594 VAL Chi-restraints excluded: chain I residue 606 LEU Chi-restraints excluded: chain I residue 609 ILE Chi-restraints excluded: chain I residue 633 LEU Chi-restraints excluded: chain I residue 750 ILE Chi-restraints excluded: chain I residue 773 LEU Chi-restraints excluded: chain I residue 785 ASP Chi-restraints excluded: chain I residue 799 ASN Chi-restraints excluded: chain I residue 800 MET Chi-restraints excluded: chain I residue 839 VAL Chi-restraints excluded: chain I residue 913 VAL Chi-restraints excluded: chain I residue 939 VAL Chi-restraints excluded: chain I residue 973 SER Chi-restraints excluded: chain I residue 1014 LEU Chi-restraints excluded: chain I residue 1041 ASP Chi-restraints excluded: chain I residue 1083 GLU Chi-restraints excluded: chain I residue 1092 THR Chi-restraints excluded: chain I residue 1240 ASP Chi-restraints excluded: chain I residue 1253 LEU Chi-restraints excluded: chain I residue 1254 VAL Chi-restraints excluded: chain I residue 1296 ASP Chi-restraints excluded: chain I residue 1315 MET Chi-restraints excluded: chain I residue 1332 SER Chi-restraints excluded: chain K residue 4 VAL Chi-restraints excluded: chain K residue 13 ILE Chi-restraints excluded: chain K residue 66 VAL Chi-restraints excluded: chain L residue 31 LEU Chi-restraints excluded: chain L residue 94 THR Chi-restraints excluded: chain L residue 118 ASP Chi-restraints excluded: chain L residue 144 LEU Chi-restraints excluded: chain L residue 162 ILE Chi-restraints excluded: chain L residue 262 VAL Chi-restraints excluded: chain L residue 275 VAL Chi-restraints excluded: chain L residue 429 THR Chi-restraints excluded: chain L residue 508 GLU Chi-restraints excluded: chain L residue 604 SER Chi-restraints excluded: chain M residue 262 LEU Chi-restraints excluded: chain M residue 263 THR Chi-restraints excluded: chain M residue 292 THR Chi-restraints excluded: chain M residue 297 LYS Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 397 random chunks: chunk 319 optimal weight: 0.9990 chunk 217 optimal weight: 7.9990 chunk 5 optimal weight: 0.9990 chunk 285 optimal weight: 7.9990 chunk 158 optimal weight: 6.9990 chunk 327 optimal weight: 9.9990 chunk 265 optimal weight: 0.6980 chunk 0 optimal weight: 7.9990 chunk 195 optimal weight: 3.9990 chunk 344 optimal weight: 2.9990 chunk 96 optimal weight: 20.0000 overall best weight: 1.9388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: J 951 GLN ** J1195 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J1244 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J1249 ASN ** L 362 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** M 283 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7726 moved from start: 0.3049 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.055 33475 Z= 0.258 Angle : 0.617 9.925 45662 Z= 0.321 Chirality : 0.042 0.168 5240 Planarity : 0.004 0.073 5595 Dihedral : 17.132 157.426 5765 Min Nonbonded Distance : 1.951 Molprobity Statistics. All-atom Clashscore : 13.88 Ramachandran Plot: Outliers : 0.13 % Allowed : 6.84 % Favored : 93.03 % Rotamer: Outliers : 6.29 % Allowed : 25.39 % Favored : 68.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.25 % Cis-general : 0.21 % Twisted Proline : 0.00 % Twisted General : 0.05 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.51 (0.13), residues: 3876 helix: 0.38 (0.13), residues: 1558 sheet: -1.92 (0.24), residues: 434 loop : -2.00 (0.14), residues: 1884 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP I 807 HIS 0.008 0.001 HIS G 160 PHE 0.015 0.001 PHE N 52 TYR 0.020 0.001 TYR J 165 ARG 0.006 0.000 ARG I 473 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7752 Ramachandran restraints generated. 3876 Oldfield, 0 Emsley, 3876 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7752 Ramachandran restraints generated. 3876 Oldfield, 0 Emsley, 3876 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 570 residues out of total 3346 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 209 poor density : 361 time to evaluate : 3.814 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: J 250 ARG cc_start: 0.8840 (OUTLIER) cc_final: 0.8580 (ptt90) REVERT: J 609 TYR cc_start: 0.8544 (t80) cc_final: 0.8308 (t80) REVERT: J 625 MET cc_start: 0.8776 (ttp) cc_final: 0.8435 (ttp) REVERT: J 796 LEU cc_start: 0.8991 (OUTLIER) cc_final: 0.8756 (tm) REVERT: J 985 ILE cc_start: 0.4890 (OUTLIER) cc_final: 0.4539 (tt) REVERT: J 1005 LYS cc_start: 0.3121 (OUTLIER) cc_final: 0.2634 (pttp) REVERT: J 1197 ASN cc_start: 0.6842 (m-40) cc_final: 0.6483 (m-40) REVERT: J 1220 ILE cc_start: 0.8994 (OUTLIER) cc_final: 0.8717 (mm) REVERT: N 21 ASN cc_start: 0.7789 (OUTLIER) cc_final: 0.7221 (m-40) REVERT: G 231 PHE cc_start: 0.8152 (OUTLIER) cc_final: 0.7745 (t80) REVERT: H 69 SER cc_start: 0.8509 (OUTLIER) cc_final: 0.8018 (m) REVERT: H 206 GLU cc_start: 0.8327 (OUTLIER) cc_final: 0.8072 (mt-10) REVERT: I 200 ARG cc_start: 0.6914 (mmm160) cc_final: 0.6266 (ptt90) REVERT: I 202 ARG cc_start: 0.8087 (OUTLIER) cc_final: 0.7815 (mtp-110) REVERT: I 322 LEU cc_start: 0.6688 (pp) cc_final: 0.6238 (tp) REVERT: I 492 MET cc_start: 0.6356 (pmm) cc_final: 0.6077 (pmm) REVERT: I 521 LEU cc_start: 0.9112 (OUTLIER) cc_final: 0.8873 (tp) REVERT: I 541 GLU cc_start: 0.6193 (OUTLIER) cc_final: 0.5777 (mp0) REVERT: I 609 ILE cc_start: 0.8529 (OUTLIER) cc_final: 0.8312 (pt) REVERT: I 637 ARG cc_start: 0.8384 (OUTLIER) cc_final: 0.8137 (ptt-90) REVERT: I 693 LEU cc_start: 0.8673 (OUTLIER) cc_final: 0.8459 (tt) REVERT: I 1041 ASP cc_start: 0.7639 (OUTLIER) cc_final: 0.7371 (m-30) REVERT: I 1253 LEU cc_start: 0.9249 (OUTLIER) cc_final: 0.8724 (tp) REVERT: K 13 ILE cc_start: 0.8024 (tt) cc_final: 0.7778 (tt) REVERT: K 30 MET cc_start: 0.8574 (mtm) cc_final: 0.8270 (mtp) REVERT: L 271 ASN cc_start: 0.6862 (t0) cc_final: 0.6403 (t0) REVERT: L 417 ASP cc_start: 0.6516 (m-30) cc_final: 0.6161 (m-30) REVERT: L 474 MET cc_start: 0.7584 (tmm) cc_final: 0.6675 (tmm) REVERT: L 508 GLU cc_start: 0.7855 (OUTLIER) cc_final: 0.7425 (mt-10) REVERT: L 545 HIS cc_start: 0.6879 (t70) cc_final: 0.6398 (t70) REVERT: L 561 MET cc_start: 0.7871 (ttm) cc_final: 0.7546 (mtp) REVERT: M 297 LYS cc_start: 0.5523 (OUTLIER) cc_final: 0.5176 (pptt) REVERT: M 316 MET cc_start: 0.3688 (mmt) cc_final: 0.2216 (tmm) REVERT: M 319 GLU cc_start: 0.3992 (OUTLIER) cc_final: 0.3513 (tm-30) outliers start: 209 outliers final: 139 residues processed: 536 average time/residue: 0.4527 time to fit residues: 397.5563 Evaluate side-chains 500 residues out of total 3346 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 159 poor density : 341 time to evaluate : 3.813 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain J residue 26 SER Chi-restraints excluded: chain J residue 46 TYR Chi-restraints excluded: chain J residue 56 LEU Chi-restraints excluded: chain J residue 65 VAL Chi-restraints excluded: chain J residue 76 LYS Chi-restraints excluded: chain J residue 90 VAL Chi-restraints excluded: chain J residue 93 THR Chi-restraints excluded: chain J residue 135 ILE Chi-restraints excluded: chain J residue 146 VAL Chi-restraints excluded: chain J residue 147 ILE Chi-restraints excluded: chain J residue 159 ILE Chi-restraints excluded: chain J residue 205 LEU Chi-restraints excluded: chain J residue 250 ARG Chi-restraints excluded: chain J residue 264 ASP Chi-restraints excluded: chain J residue 292 VAL Chi-restraints excluded: chain J residue 324 LEU Chi-restraints excluded: chain J residue 363 LEU Chi-restraints excluded: chain J residue 408 VAL Chi-restraints excluded: chain J residue 416 ILE Chi-restraints excluded: chain J residue 442 ILE Chi-restraints excluded: chain J residue 478 LEU Chi-restraints excluded: chain J residue 489 ASN Chi-restraints excluded: chain J residue 506 VAL Chi-restraints excluded: chain J residue 508 LEU Chi-restraints excluded: chain J residue 513 MET Chi-restraints excluded: chain J residue 543 SER Chi-restraints excluded: chain J residue 544 LEU Chi-restraints excluded: chain J residue 545 HIS Chi-restraints excluded: chain J residue 553 THR Chi-restraints excluded: chain J residue 558 ASP Chi-restraints excluded: chain J residue 567 THR Chi-restraints excluded: chain J residue 571 ASP Chi-restraints excluded: chain J residue 596 LEU Chi-restraints excluded: chain J residue 612 LEU Chi-restraints excluded: chain J residue 706 VAL Chi-restraints excluded: chain J residue 707 ILE Chi-restraints excluded: chain J residue 708 ASN Chi-restraints excluded: chain J residue 722 ILE Chi-restraints excluded: chain J residue 740 LEU Chi-restraints excluded: chain J residue 762 ASN Chi-restraints excluded: chain J residue 770 LEU Chi-restraints excluded: chain J residue 786 THR Chi-restraints excluded: chain J residue 788 LEU Chi-restraints excluded: chain J residue 790 THR Chi-restraints excluded: chain J residue 796 LEU Chi-restraints excluded: chain J residue 807 LEU Chi-restraints excluded: chain J residue 825 VAL Chi-restraints excluded: chain J residue 839 VAL Chi-restraints excluded: chain J residue 862 THR Chi-restraints excluded: chain J residue 869 CYS Chi-restraints excluded: chain J residue 878 ASP Chi-restraints excluded: chain J residue 903 LEU Chi-restraints excluded: chain J residue 918 ILE Chi-restraints excluded: chain J residue 928 THR Chi-restraints excluded: chain J residue 931 THR Chi-restraints excluded: chain J residue 974 VAL Chi-restraints excluded: chain J residue 985 ILE Chi-restraints excluded: chain J residue 991 THR Chi-restraints excluded: chain J residue 1005 LYS Chi-restraints excluded: chain J residue 1054 THR Chi-restraints excluded: chain J residue 1135 THR Chi-restraints excluded: chain J residue 1160 SER Chi-restraints excluded: chain J residue 1181 ASP Chi-restraints excluded: chain J residue 1196 LEU Chi-restraints excluded: chain J residue 1198 VAL Chi-restraints excluded: chain J residue 1220 ILE Chi-restraints excluded: chain J residue 1249 ASN Chi-restraints excluded: chain J residue 1261 LEU Chi-restraints excluded: chain J residue 1262 ARG Chi-restraints excluded: chain J residue 1266 ILE Chi-restraints excluded: chain J residue 1280 VAL Chi-restraints excluded: chain J residue 1297 LYS Chi-restraints excluded: chain J residue 1301 THR Chi-restraints excluded: chain J residue 1307 LEU Chi-restraints excluded: chain J residue 1342 ASP Chi-restraints excluded: chain N residue 21 ASN Chi-restraints excluded: chain N residue 27 ILE Chi-restraints excluded: chain G residue 6 THR Chi-restraints excluded: chain G residue 9 LEU Chi-restraints excluded: chain G residue 61 ILE Chi-restraints excluded: chain G residue 130 ILE Chi-restraints excluded: chain G residue 171 LEU Chi-restraints excluded: chain G residue 177 TYR Chi-restraints excluded: chain G residue 192 VAL Chi-restraints excluded: chain G residue 202 VAL Chi-restraints excluded: chain G residue 231 PHE Chi-restraints excluded: chain H residue 38 THR Chi-restraints excluded: chain H residue 51 MET Chi-restraints excluded: chain H residue 65 LEU Chi-restraints excluded: chain H residue 69 SER Chi-restraints excluded: chain H residue 102 LEU Chi-restraints excluded: chain H residue 139 SER Chi-restraints excluded: chain H residue 141 SER Chi-restraints excluded: chain H residue 146 VAL Chi-restraints excluded: chain H residue 153 VAL Chi-restraints excluded: chain H residue 206 GLU Chi-restraints excluded: chain I residue 33 ASP Chi-restraints excluded: chain I residue 37 LYS Chi-restraints excluded: chain I residue 105 TYR Chi-restraints excluded: chain I residue 117 ILE Chi-restraints excluded: chain I residue 127 ILE Chi-restraints excluded: chain I residue 138 ILE Chi-restraints excluded: chain I residue 182 SER Chi-restraints excluded: chain I residue 202 ARG Chi-restraints excluded: chain I residue 203 LYS Chi-restraints excluded: chain I residue 282 VAL Chi-restraints excluded: chain I residue 296 VAL Chi-restraints excluded: chain I residue 297 VAL Chi-restraints excluded: chain I residue 442 VAL Chi-restraints excluded: chain I residue 456 VAL Chi-restraints excluded: chain I residue 471 VAL Chi-restraints excluded: chain I residue 498 ILE Chi-restraints excluded: chain I residue 521 LEU Chi-restraints excluded: chain I residue 523 GLU Chi-restraints excluded: chain I residue 541 GLU Chi-restraints excluded: chain I residue 573 ASN Chi-restraints excluded: chain I residue 583 GLU Chi-restraints excluded: chain I residue 589 THR Chi-restraints excluded: chain I residue 594 VAL Chi-restraints excluded: chain I residue 606 LEU Chi-restraints excluded: chain I residue 609 ILE Chi-restraints excluded: chain I residue 633 LEU Chi-restraints excluded: chain I residue 637 ARG Chi-restraints excluded: chain I residue 693 LEU Chi-restraints excluded: chain I residue 750 ILE Chi-restraints excluded: chain I residue 773 LEU Chi-restraints excluded: chain I residue 785 ASP Chi-restraints excluded: chain I residue 799 ASN Chi-restraints excluded: chain I residue 839 VAL Chi-restraints excluded: chain I residue 913 VAL Chi-restraints excluded: chain I residue 939 VAL Chi-restraints excluded: chain I residue 973 SER Chi-restraints excluded: chain I residue 1014 LEU Chi-restraints excluded: chain I residue 1041 ASP Chi-restraints excluded: chain I residue 1083 GLU Chi-restraints excluded: chain I residue 1092 THR Chi-restraints excluded: chain I residue 1240 ASP Chi-restraints excluded: chain I residue 1253 LEU Chi-restraints excluded: chain I residue 1254 VAL Chi-restraints excluded: chain I residue 1296 ASP Chi-restraints excluded: chain I residue 1315 MET Chi-restraints excluded: chain I residue 1332 SER Chi-restraints excluded: chain K residue 66 VAL Chi-restraints excluded: chain L residue 31 LEU Chi-restraints excluded: chain L residue 94 THR Chi-restraints excluded: chain L residue 118 ASP Chi-restraints excluded: chain L residue 144 LEU Chi-restraints excluded: chain L residue 162 ILE Chi-restraints excluded: chain L residue 262 VAL Chi-restraints excluded: chain L residue 275 VAL Chi-restraints excluded: chain L residue 386 LEU Chi-restraints excluded: chain L residue 429 THR Chi-restraints excluded: chain L residue 508 GLU Chi-restraints excluded: chain L residue 604 SER Chi-restraints excluded: chain M residue 262 LEU Chi-restraints excluded: chain M residue 263 THR Chi-restraints excluded: chain M residue 292 THR Chi-restraints excluded: chain M residue 297 LYS Chi-restraints excluded: chain M residue 319 GLU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 397 random chunks: chunk 129 optimal weight: 7.9990 chunk 345 optimal weight: 5.9990 chunk 75 optimal weight: 1.9990 chunk 225 optimal weight: 9.9990 chunk 94 optimal weight: 0.2980 chunk 384 optimal weight: 2.9990 chunk 318 optimal weight: 0.9990 chunk 177 optimal weight: 3.9990 chunk 31 optimal weight: 0.0980 chunk 127 optimal weight: 9.9990 chunk 201 optimal weight: 5.9990 overall best weight: 1.2786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** J1244 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J1249 ASN ** I 46 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 362 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7701 moved from start: 0.3295 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 33475 Z= 0.201 Angle : 0.588 9.302 45662 Z= 0.306 Chirality : 0.041 0.164 5240 Planarity : 0.004 0.068 5595 Dihedral : 16.915 158.134 5756 Min Nonbonded Distance : 1.981 Molprobity Statistics. All-atom Clashscore : 13.39 Ramachandran Plot: Outliers : 0.13 % Allowed : 6.58 % Favored : 93.29 % Rotamer: Outliers : 5.54 % Allowed : 26.29 % Favored : 68.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.25 % Cis-general : 0.21 % Twisted Proline : 0.00 % Twisted General : 0.05 % 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: -1.31 (0.13), residues: 3876 helix: 0.54 (0.13), residues: 1573 sheet: -1.80 (0.24), residues: 437 loop : -1.90 (0.14), residues: 1866 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP I 807 HIS 0.008 0.001 HIS G 160 PHE 0.013 0.001 PHE N 52 TYR 0.016 0.001 TYR G 177 ARG 0.007 0.000 ARG G 143 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7752 Ramachandran restraints generated. 3876 Oldfield, 0 Emsley, 3876 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7752 Ramachandran restraints generated. 3876 Oldfield, 0 Emsley, 3876 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 560 residues out of total 3346 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 184 poor density : 376 time to evaluate : 3.668 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: J 250 ARG cc_start: 0.8821 (OUTLIER) cc_final: 0.8564 (ptt90) REVERT: J 609 TYR cc_start: 0.8505 (t80) cc_final: 0.8273 (t80) REVERT: J 625 MET cc_start: 0.8746 (ttp) cc_final: 0.8505 (ttt) REVERT: J 796 LEU cc_start: 0.8982 (OUTLIER) cc_final: 0.8732 (tm) REVERT: J 830 ASP cc_start: 0.4322 (OUTLIER) cc_final: 0.4106 (m-30) REVERT: J 985 ILE cc_start: 0.4881 (OUTLIER) cc_final: 0.4547 (tt) REVERT: J 1184 ASP cc_start: 0.6158 (OUTLIER) cc_final: 0.5926 (p0) REVERT: J 1197 ASN cc_start: 0.6302 (m-40) cc_final: 0.5932 (m-40) REVERT: G 158 ARG cc_start: 0.7506 (OUTLIER) cc_final: 0.6741 (ttm-80) REVERT: H 69 SER cc_start: 0.8489 (OUTLIER) cc_final: 0.7980 (m) REVERT: H 206 GLU cc_start: 0.8223 (OUTLIER) cc_final: 0.7965 (mt-10) REVERT: I 200 ARG cc_start: 0.6882 (mmm160) cc_final: 0.6206 (ptt90) REVERT: I 202 ARG cc_start: 0.8045 (OUTLIER) cc_final: 0.7782 (mtm-85) REVERT: I 278 GLU cc_start: 0.6399 (pt0) cc_final: 0.6175 (mt-10) REVERT: I 322 LEU cc_start: 0.6639 (pp) cc_final: 0.6120 (tp) REVERT: I 492 MET cc_start: 0.6220 (pmm) cc_final: 0.5727 (pmm) REVERT: I 514 PHE cc_start: 0.8136 (OUTLIER) cc_final: 0.7902 (m-10) REVERT: I 521 LEU cc_start: 0.9073 (OUTLIER) cc_final: 0.8864 (tp) REVERT: I 541 GLU cc_start: 0.6092 (OUTLIER) cc_final: 0.5709 (mp0) REVERT: I 572 ILE cc_start: 0.9196 (OUTLIER) cc_final: 0.8813 (mt) REVERT: I 609 ILE cc_start: 0.8549 (pt) cc_final: 0.8342 (pt) REVERT: I 1034 ARG cc_start: 0.7961 (tmm-80) cc_final: 0.7654 (ttp-170) REVERT: I 1041 ASP cc_start: 0.7733 (OUTLIER) cc_final: 0.7478 (m-30) REVERT: I 1253 LEU cc_start: 0.9199 (OUTLIER) cc_final: 0.8651 (tp) REVERT: K 13 ILE cc_start: 0.7944 (OUTLIER) cc_final: 0.7694 (tt) REVERT: K 30 MET cc_start: 0.8493 (mtm) cc_final: 0.8197 (mtp) REVERT: K 42 GLU cc_start: 0.7594 (OUTLIER) cc_final: 0.6161 (pp20) REVERT: L 271 ASN cc_start: 0.6661 (t0) cc_final: 0.6325 (t0) REVERT: L 436 ARG cc_start: 0.7490 (ptp-110) cc_final: 0.7004 (ptp-110) REVERT: L 474 MET cc_start: 0.7624 (tmm) cc_final: 0.6920 (tmm) REVERT: L 508 GLU cc_start: 0.7850 (OUTLIER) cc_final: 0.7422 (mt-10) REVERT: L 545 HIS cc_start: 0.6938 (t70) cc_final: 0.6454 (t70) REVERT: L 561 MET cc_start: 0.7857 (ttm) cc_final: 0.7553 (mtp) REVERT: M 297 LYS cc_start: 0.5581 (OUTLIER) cc_final: 0.5247 (pptt) REVERT: M 316 MET cc_start: 0.3590 (mmt) cc_final: 0.2189 (tmm) REVERT: M 319 GLU cc_start: 0.3976 (OUTLIER) cc_final: 0.3471 (tm-30) outliers start: 184 outliers final: 128 residues processed: 530 average time/residue: 0.4448 time to fit residues: 383.9041 Evaluate side-chains 499 residues out of total 3346 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 148 poor density : 351 time to evaluate : 3.412 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain J residue 46 TYR Chi-restraints excluded: chain J residue 56 LEU Chi-restraints excluded: chain J residue 65 VAL Chi-restraints excluded: chain J residue 76 LYS Chi-restraints excluded: chain J residue 90 VAL Chi-restraints excluded: chain J residue 93 THR Chi-restraints excluded: chain J residue 135 ILE Chi-restraints excluded: chain J residue 146 VAL Chi-restraints excluded: chain J residue 147 ILE Chi-restraints excluded: chain J residue 159 ILE Chi-restraints excluded: chain J residue 205 LEU Chi-restraints excluded: chain J residue 212 THR Chi-restraints excluded: chain J residue 250 ARG Chi-restraints excluded: chain J residue 264 ASP Chi-restraints excluded: chain J residue 292 VAL Chi-restraints excluded: chain J residue 324 LEU Chi-restraints excluded: chain J residue 332 LYS Chi-restraints excluded: chain J residue 363 LEU Chi-restraints excluded: chain J residue 416 ILE Chi-restraints excluded: chain J residue 442 ILE Chi-restraints excluded: chain J residue 478 LEU Chi-restraints excluded: chain J residue 489 ASN Chi-restraints excluded: chain J residue 506 VAL Chi-restraints excluded: chain J residue 508 LEU Chi-restraints excluded: chain J residue 513 MET Chi-restraints excluded: chain J residue 543 SER Chi-restraints excluded: chain J residue 545 HIS Chi-restraints excluded: chain J residue 553 THR Chi-restraints excluded: chain J residue 567 THR Chi-restraints excluded: chain J residue 571 ASP Chi-restraints excluded: chain J residue 596 LEU Chi-restraints excluded: chain J residue 612 LEU Chi-restraints excluded: chain J residue 706 VAL Chi-restraints excluded: chain J residue 707 ILE Chi-restraints excluded: chain J residue 708 ASN Chi-restraints excluded: chain J residue 740 LEU Chi-restraints excluded: chain J residue 762 ASN Chi-restraints excluded: chain J residue 770 LEU Chi-restraints excluded: chain J residue 786 THR Chi-restraints excluded: chain J residue 788 LEU Chi-restraints excluded: chain J residue 790 THR Chi-restraints excluded: chain J residue 796 LEU Chi-restraints excluded: chain J residue 807 LEU Chi-restraints excluded: chain J residue 825 VAL Chi-restraints excluded: chain J residue 830 ASP Chi-restraints excluded: chain J residue 839 VAL Chi-restraints excluded: chain J residue 862 THR Chi-restraints excluded: chain J residue 869 CYS Chi-restraints excluded: chain J residue 878 ASP Chi-restraints excluded: chain J residue 903 LEU Chi-restraints excluded: chain J residue 918 ILE Chi-restraints excluded: chain J residue 928 THR Chi-restraints excluded: chain J residue 931 THR Chi-restraints excluded: chain J residue 974 VAL Chi-restraints excluded: chain J residue 985 ILE Chi-restraints excluded: chain J residue 991 THR Chi-restraints excluded: chain J residue 1160 SER Chi-restraints excluded: chain J residue 1181 ASP Chi-restraints excluded: chain J residue 1184 ASP Chi-restraints excluded: chain J residue 1186 TYR Chi-restraints excluded: chain J residue 1196 LEU Chi-restraints excluded: chain J residue 1261 LEU Chi-restraints excluded: chain J residue 1262 ARG Chi-restraints excluded: chain J residue 1266 ILE Chi-restraints excluded: chain J residue 1280 VAL Chi-restraints excluded: chain J residue 1297 LYS Chi-restraints excluded: chain J residue 1307 LEU Chi-restraints excluded: chain J residue 1342 ASP Chi-restraints excluded: chain N residue 27 ILE Chi-restraints excluded: chain G residue 6 THR Chi-restraints excluded: chain G residue 9 LEU Chi-restraints excluded: chain G residue 39 LEU Chi-restraints excluded: chain G residue 61 ILE Chi-restraints excluded: chain G residue 130 ILE Chi-restraints excluded: chain G residue 137 ASN Chi-restraints excluded: chain G residue 158 ARG Chi-restraints excluded: chain G residue 177 TYR Chi-restraints excluded: chain G residue 192 VAL Chi-restraints excluded: chain G residue 202 VAL Chi-restraints excluded: chain H residue 38 THR Chi-restraints excluded: chain H residue 51 MET Chi-restraints excluded: chain H residue 65 LEU Chi-restraints excluded: chain H residue 69 SER Chi-restraints excluded: chain H residue 102 LEU Chi-restraints excluded: chain H residue 134 THR Chi-restraints excluded: chain H residue 139 SER Chi-restraints excluded: chain H residue 146 VAL Chi-restraints excluded: chain H residue 153 VAL Chi-restraints excluded: chain H residue 206 GLU Chi-restraints excluded: chain I residue 37 LYS Chi-restraints excluded: chain I residue 105 TYR Chi-restraints excluded: chain I residue 127 ILE Chi-restraints excluded: chain I residue 138 ILE Chi-restraints excluded: chain I residue 182 SER Chi-restraints excluded: chain I residue 202 ARG Chi-restraints excluded: chain I residue 203 LYS Chi-restraints excluded: chain I residue 282 VAL Chi-restraints excluded: chain I residue 296 VAL Chi-restraints excluded: chain I residue 297 VAL Chi-restraints excluded: chain I residue 309 LEU Chi-restraints excluded: chain I residue 456 VAL Chi-restraints excluded: chain I residue 471 VAL Chi-restraints excluded: chain I residue 498 ILE Chi-restraints excluded: chain I residue 513 GLN Chi-restraints excluded: chain I residue 514 PHE Chi-restraints excluded: chain I residue 521 LEU Chi-restraints excluded: chain I residue 523 GLU Chi-restraints excluded: chain I residue 541 GLU Chi-restraints excluded: chain I residue 572 ILE Chi-restraints excluded: chain I residue 583 GLU Chi-restraints excluded: chain I residue 589 THR Chi-restraints excluded: chain I residue 594 VAL Chi-restraints excluded: chain I residue 606 LEU Chi-restraints excluded: chain I residue 633 LEU Chi-restraints excluded: chain I residue 659 GLN Chi-restraints excluded: chain I residue 773 LEU Chi-restraints excluded: chain I residue 785 ASP Chi-restraints excluded: chain I residue 839 VAL Chi-restraints excluded: chain I residue 878 THR Chi-restraints excluded: chain I residue 913 VAL Chi-restraints excluded: chain I residue 939 VAL Chi-restraints excluded: chain I residue 960 LEU Chi-restraints excluded: chain I residue 973 SER Chi-restraints excluded: chain I residue 1014 LEU Chi-restraints excluded: chain I residue 1041 ASP Chi-restraints excluded: chain I residue 1083 GLU Chi-restraints excluded: chain I residue 1240 ASP Chi-restraints excluded: chain I residue 1253 LEU Chi-restraints excluded: chain I residue 1254 VAL Chi-restraints excluded: chain I residue 1296 ASP Chi-restraints excluded: chain I residue 1332 SER Chi-restraints excluded: chain K residue 13 ILE Chi-restraints excluded: chain K residue 42 GLU Chi-restraints excluded: chain K residue 66 VAL Chi-restraints excluded: chain L residue 31 LEU Chi-restraints excluded: chain L residue 94 THR Chi-restraints excluded: chain L residue 118 ASP Chi-restraints excluded: chain L residue 144 LEU Chi-restraints excluded: chain L residue 262 VAL Chi-restraints excluded: chain L residue 381 GLU Chi-restraints excluded: chain L residue 388 ILE Chi-restraints excluded: chain L residue 395 THR Chi-restraints excluded: chain L residue 429 THR Chi-restraints excluded: chain L residue 508 GLU Chi-restraints excluded: chain L residue 604 SER Chi-restraints excluded: chain M residue 263 THR Chi-restraints excluded: chain M residue 297 LYS Chi-restraints excluded: chain M residue 319 GLU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 397 random chunks: chunk 370 optimal weight: 10.0000 chunk 43 optimal weight: 0.9990 chunk 218 optimal weight: 9.9990 chunk 280 optimal weight: 0.8980 chunk 217 optimal weight: 8.9990 chunk 323 optimal weight: 2.9990 chunk 214 optimal weight: 0.0980 chunk 382 optimal weight: 7.9990 chunk 239 optimal weight: 7.9990 chunk 233 optimal weight: 0.3980 chunk 176 optimal weight: 6.9990 overall best weight: 1.0784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: J1010 GLN ** J1244 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 46 GLN ** L 362 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7689 moved from start: 0.3490 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 33475 Z= 0.188 Angle : 0.583 9.487 45662 Z= 0.302 Chirality : 0.041 0.161 5240 Planarity : 0.004 0.068 5595 Dihedral : 16.741 158.658 5741 Min Nonbonded Distance : 1.984 Molprobity Statistics. All-atom Clashscore : 12.89 Ramachandran Plot: Outliers : 0.13 % Allowed : 6.48 % Favored : 93.40 % Rotamer: Outliers : 5.63 % Allowed : 26.26 % Favored : 68.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.25 % Cis-general : 0.21 % Twisted Proline : 0.00 % Twisted General : 0.05 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.13 (0.13), residues: 3876 helix: 0.67 (0.13), residues: 1570 sheet: -1.64 (0.24), residues: 437 loop : -1.80 (0.14), residues: 1869 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP I 807 HIS 0.009 0.001 HIS G 160 PHE 0.021 0.001 PHE L 165 TYR 0.019 0.001 TYR L 143 ARG 0.004 0.000 ARG G 143 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7752 Ramachandran restraints generated. 3876 Oldfield, 0 Emsley, 3876 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7752 Ramachandran restraints generated. 3876 Oldfield, 0 Emsley, 3876 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 560 residues out of total 3346 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 187 poor density : 373 time to evaluate : 3.972 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: J 56 LEU cc_start: 0.8771 (OUTLIER) cc_final: 0.8545 (mt) REVERT: J 345 LYS cc_start: 0.8328 (OUTLIER) cc_final: 0.8005 (mttp) REVERT: J 479 GLU cc_start: 0.7948 (mt-10) cc_final: 0.7688 (mt-10) REVERT: J 609 TYR cc_start: 0.8497 (t80) cc_final: 0.8260 (t80) REVERT: J 625 MET cc_start: 0.8740 (ttp) cc_final: 0.8514 (ttp) REVERT: J 796 LEU cc_start: 0.8984 (OUTLIER) cc_final: 0.8737 (tm) REVERT: J 836 ARG cc_start: 0.7387 (ttt-90) cc_final: 0.6788 (mtp-110) REVERT: J 985 ILE cc_start: 0.4871 (OUTLIER) cc_final: 0.4547 (tt) REVERT: J 1197 ASN cc_start: 0.6117 (m-40) cc_final: 0.5775 (m-40) REVERT: J 1220 ILE cc_start: 0.8884 (OUTLIER) cc_final: 0.8573 (mm) REVERT: J 1258 ARG cc_start: 0.8564 (OUTLIER) cc_final: 0.8199 (ttt180) REVERT: G 158 ARG cc_start: 0.7513 (OUTLIER) cc_final: 0.6730 (ttm-80) REVERT: H 69 SER cc_start: 0.8439 (OUTLIER) cc_final: 0.7917 (m) REVERT: H 206 GLU cc_start: 0.8052 (OUTLIER) cc_final: 0.7781 (mt-10) REVERT: I 202 ARG cc_start: 0.7945 (OUTLIER) cc_final: 0.7688 (mtm-85) REVERT: I 238 GLN cc_start: 0.2905 (mm-40) cc_final: 0.2642 (mm-40) REVERT: I 278 GLU cc_start: 0.6467 (pt0) cc_final: 0.6221 (mt-10) REVERT: I 322 LEU cc_start: 0.6694 (pp) cc_final: 0.6135 (tp) REVERT: I 453 ILE cc_start: 0.8845 (mt) cc_final: 0.8522 (pt) REVERT: I 478 ARG cc_start: 0.7595 (tpt90) cc_final: 0.7310 (tpt90) REVERT: I 521 LEU cc_start: 0.9060 (OUTLIER) cc_final: 0.8852 (tp) REVERT: I 541 GLU cc_start: 0.6047 (OUTLIER) cc_final: 0.5743 (mp0) REVERT: I 572 ILE cc_start: 0.9198 (OUTLIER) cc_final: 0.8816 (mt) REVERT: I 609 ILE cc_start: 0.8570 (pt) cc_final: 0.8354 (pt) REVERT: I 637 ARG cc_start: 0.8312 (OUTLIER) cc_final: 0.8057 (ptt-90) REVERT: I 1034 ARG cc_start: 0.7970 (tmm-80) cc_final: 0.7752 (ttp-170) REVERT: I 1041 ASP cc_start: 0.7614 (OUTLIER) cc_final: 0.7356 (m-30) REVERT: I 1253 LEU cc_start: 0.9222 (OUTLIER) cc_final: 0.8735 (tp) REVERT: K 13 ILE cc_start: 0.7921 (OUTLIER) cc_final: 0.7690 (tt) REVERT: K 30 MET cc_start: 0.8475 (mtm) cc_final: 0.8179 (mtp) REVERT: L 271 ASN cc_start: 0.6821 (t0) cc_final: 0.6470 (t0) REVERT: L 435 ILE cc_start: 0.7646 (OUTLIER) cc_final: 0.7370 (mt) REVERT: L 436 ARG cc_start: 0.7487 (ptp-110) cc_final: 0.6894 (ptp-110) REVERT: L 508 GLU cc_start: 0.7852 (OUTLIER) cc_final: 0.7426 (mt-10) REVERT: L 545 HIS cc_start: 0.6928 (t70) cc_final: 0.6457 (t70) REVERT: L 561 MET cc_start: 0.7874 (ttm) cc_final: 0.7554 (mtp) REVERT: M 297 LYS cc_start: 0.5750 (OUTLIER) cc_final: 0.5536 (pptt) REVERT: M 319 GLU cc_start: 0.3937 (OUTLIER) cc_final: 0.3384 (tm-30) outliers start: 187 outliers final: 130 residues processed: 530 average time/residue: 0.4440 time to fit residues: 382.8516 Evaluate side-chains 499 residues out of total 3346 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 151 poor density : 348 time to evaluate : 3.834 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain J residue 46 TYR Chi-restraints excluded: chain J residue 56 LEU Chi-restraints excluded: chain J residue 65 VAL Chi-restraints excluded: chain J residue 76 LYS Chi-restraints excluded: chain J residue 90 VAL Chi-restraints excluded: chain J residue 93 THR Chi-restraints excluded: chain J residue 109 SER Chi-restraints excluded: chain J residue 135 ILE Chi-restraints excluded: chain J residue 146 VAL Chi-restraints excluded: chain J residue 147 ILE Chi-restraints excluded: chain J residue 159 ILE Chi-restraints excluded: chain J residue 205 LEU Chi-restraints excluded: chain J residue 212 THR Chi-restraints excluded: chain J residue 264 ASP Chi-restraints excluded: chain J residue 292 VAL Chi-restraints excluded: chain J residue 324 LEU Chi-restraints excluded: chain J residue 332 LYS Chi-restraints excluded: chain J residue 345 LYS Chi-restraints excluded: chain J residue 363 LEU Chi-restraints excluded: chain J residue 416 ILE Chi-restraints excluded: chain J residue 442 ILE Chi-restraints excluded: chain J residue 489 ASN Chi-restraints excluded: chain J residue 506 VAL Chi-restraints excluded: chain J residue 508 LEU Chi-restraints excluded: chain J residue 543 SER Chi-restraints excluded: chain J residue 545 HIS Chi-restraints excluded: chain J residue 553 THR Chi-restraints excluded: chain J residue 567 THR Chi-restraints excluded: chain J residue 571 ASP Chi-restraints excluded: chain J residue 596 LEU Chi-restraints excluded: chain J residue 612 LEU Chi-restraints excluded: chain J residue 706 VAL Chi-restraints excluded: chain J residue 707 ILE Chi-restraints excluded: chain J residue 708 ASN Chi-restraints excluded: chain J residue 740 LEU Chi-restraints excluded: chain J residue 762 ASN Chi-restraints excluded: chain J residue 770 LEU Chi-restraints excluded: chain J residue 786 THR Chi-restraints excluded: chain J residue 788 LEU Chi-restraints excluded: chain J residue 796 LEU Chi-restraints excluded: chain J residue 807 LEU Chi-restraints excluded: chain J residue 825 VAL Chi-restraints excluded: chain J residue 839 VAL Chi-restraints excluded: chain J residue 862 THR Chi-restraints excluded: chain J residue 878 ASP Chi-restraints excluded: chain J residue 903 LEU Chi-restraints excluded: chain J residue 918 ILE Chi-restraints excluded: chain J residue 928 THR Chi-restraints excluded: chain J residue 931 THR Chi-restraints excluded: chain J residue 985 ILE Chi-restraints excluded: chain J residue 991 THR Chi-restraints excluded: chain J residue 1098 GLN Chi-restraints excluded: chain J residue 1160 SER Chi-restraints excluded: chain J residue 1181 ASP Chi-restraints excluded: chain J residue 1196 LEU Chi-restraints excluded: chain J residue 1198 VAL Chi-restraints excluded: chain J residue 1220 ILE Chi-restraints excluded: chain J residue 1258 ARG Chi-restraints excluded: chain J residue 1261 LEU Chi-restraints excluded: chain J residue 1266 ILE Chi-restraints excluded: chain J residue 1280 VAL Chi-restraints excluded: chain J residue 1297 LYS Chi-restraints excluded: chain J residue 1301 THR Chi-restraints excluded: chain J residue 1307 LEU Chi-restraints excluded: chain J residue 1342 ASP Chi-restraints excluded: chain N residue 18 THR Chi-restraints excluded: chain G residue 6 THR Chi-restraints excluded: chain G residue 9 LEU Chi-restraints excluded: chain G residue 39 LEU Chi-restraints excluded: chain G residue 61 ILE Chi-restraints excluded: chain G residue 130 ILE Chi-restraints excluded: chain G residue 158 ARG Chi-restraints excluded: chain G residue 171 LEU Chi-restraints excluded: chain G residue 177 TYR Chi-restraints excluded: chain G residue 192 VAL Chi-restraints excluded: chain G residue 202 VAL Chi-restraints excluded: chain H residue 38 THR Chi-restraints excluded: chain H residue 51 MET Chi-restraints excluded: chain H residue 65 LEU Chi-restraints excluded: chain H residue 69 SER Chi-restraints excluded: chain H residue 134 THR Chi-restraints excluded: chain H residue 139 SER Chi-restraints excluded: chain H residue 146 VAL Chi-restraints excluded: chain H residue 153 VAL Chi-restraints excluded: chain H residue 206 GLU Chi-restraints excluded: chain I residue 33 ASP Chi-restraints excluded: chain I residue 37 LYS Chi-restraints excluded: chain I residue 105 TYR Chi-restraints excluded: chain I residue 127 ILE Chi-restraints excluded: chain I residue 138 ILE Chi-restraints excluded: chain I residue 182 SER Chi-restraints excluded: chain I residue 202 ARG Chi-restraints excluded: chain I residue 203 LYS Chi-restraints excluded: chain I residue 282 VAL Chi-restraints excluded: chain I residue 296 VAL Chi-restraints excluded: chain I residue 297 VAL Chi-restraints excluded: chain I residue 309 LEU Chi-restraints excluded: chain I residue 426 ILE Chi-restraints excluded: chain I residue 442 VAL Chi-restraints excluded: chain I residue 456 VAL Chi-restraints excluded: chain I residue 471 VAL Chi-restraints excluded: chain I residue 498 ILE Chi-restraints excluded: chain I residue 521 LEU Chi-restraints excluded: chain I residue 523 GLU Chi-restraints excluded: chain I residue 541 GLU Chi-restraints excluded: chain I residue 572 ILE Chi-restraints excluded: chain I residue 581 THR Chi-restraints excluded: chain I residue 583 GLU Chi-restraints excluded: chain I residue 589 THR Chi-restraints excluded: chain I residue 594 VAL Chi-restraints excluded: chain I residue 606 LEU Chi-restraints excluded: chain I residue 633 LEU Chi-restraints excluded: chain I residue 637 ARG Chi-restraints excluded: chain I residue 659 GLN Chi-restraints excluded: chain I residue 773 LEU Chi-restraints excluded: chain I residue 785 ASP Chi-restraints excluded: chain I residue 839 VAL Chi-restraints excluded: chain I residue 913 VAL Chi-restraints excluded: chain I residue 939 VAL Chi-restraints excluded: chain I residue 960 LEU Chi-restraints excluded: chain I residue 973 SER Chi-restraints excluded: chain I residue 1041 ASP Chi-restraints excluded: chain I residue 1083 GLU Chi-restraints excluded: chain I residue 1162 SER Chi-restraints excluded: chain I residue 1240 ASP Chi-restraints excluded: chain I residue 1253 LEU Chi-restraints excluded: chain I residue 1254 VAL Chi-restraints excluded: chain I residue 1296 ASP Chi-restraints excluded: chain I residue 1315 MET Chi-restraints excluded: chain I residue 1332 SER Chi-restraints excluded: chain K residue 13 ILE Chi-restraints excluded: chain K residue 66 VAL Chi-restraints excluded: chain L residue 31 LEU Chi-restraints excluded: chain L residue 94 THR Chi-restraints excluded: chain L residue 118 ASP Chi-restraints excluded: chain L residue 144 LEU Chi-restraints excluded: chain L residue 262 VAL Chi-restraints excluded: chain L residue 275 VAL Chi-restraints excluded: chain L residue 381 GLU Chi-restraints excluded: chain L residue 386 LEU Chi-restraints excluded: chain L residue 388 ILE Chi-restraints excluded: chain L residue 395 THR Chi-restraints excluded: chain L residue 429 THR Chi-restraints excluded: chain L residue 435 ILE Chi-restraints excluded: chain L residue 508 GLU Chi-restraints excluded: chain L residue 604 SER Chi-restraints excluded: chain M residue 262 LEU Chi-restraints excluded: chain M residue 263 THR Chi-restraints excluded: chain M residue 285 THR Chi-restraints excluded: chain M residue 297 LYS Chi-restraints excluded: chain M residue 319 GLU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 397 random chunks: chunk 236 optimal weight: 0.9980 chunk 152 optimal weight: 5.9990 chunk 228 optimal weight: 0.6980 chunk 115 optimal weight: 7.9990 chunk 75 optimal weight: 2.9990 chunk 74 optimal weight: 2.9990 chunk 243 optimal weight: 0.9980 chunk 260 optimal weight: 0.9990 chunk 189 optimal weight: 4.9990 chunk 35 optimal weight: 5.9990 chunk 300 optimal weight: 0.8980 overall best weight: 0.9182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: J 320 ASN ** J1244 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J1279 GLN H 66 HIS ** L 362 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7676 moved from start: 0.3662 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 33475 Z= 0.178 Angle : 0.576 13.572 45662 Z= 0.297 Chirality : 0.041 0.169 5240 Planarity : 0.004 0.067 5595 Dihedral : 16.620 158.881 5737 Min Nonbonded Distance : 1.994 Molprobity Statistics. All-atom Clashscore : 12.45 Ramachandran Plot: Outliers : 0.13 % Allowed : 6.45 % Favored : 93.42 % Rotamer: Outliers : 5.08 % Allowed : 26.84 % Favored : 68.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.25 % Cis-general : 0.21 % Twisted Proline : 0.00 % Twisted General : 0.05 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.99 (0.14), residues: 3876 helix: 0.77 (0.13), residues: 1571 sheet: -1.53 (0.24), residues: 439 loop : -1.71 (0.14), residues: 1866 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP J 868 HIS 0.008 0.001 HIS G 160 PHE 0.013 0.001 PHE N 52 TYR 0.018 0.001 TYR J 679 ARG 0.005 0.000 ARG I 557 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7752 Ramachandran restraints generated. 3876 Oldfield, 0 Emsley, 3876 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7752 Ramachandran restraints generated. 3876 Oldfield, 0 Emsley, 3876 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 537 residues out of total 3346 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 169 poor density : 368 time to evaluate : 4.173 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: J 148 GLU cc_start: 0.7135 (mt-10) cc_final: 0.6873 (tt0) REVERT: J 250 ARG cc_start: 0.8793 (OUTLIER) cc_final: 0.8570 (ptt90) REVERT: J 345 LYS cc_start: 0.8312 (OUTLIER) cc_final: 0.8006 (mttp) REVERT: J 442 ILE cc_start: 0.8858 (OUTLIER) cc_final: 0.8462 (pt) REVERT: J 479 GLU cc_start: 0.7877 (mt-10) cc_final: 0.7663 (mt-10) REVERT: J 625 MET cc_start: 0.8721 (ttp) cc_final: 0.8498 (ttt) REVERT: J 796 LEU cc_start: 0.8929 (OUTLIER) cc_final: 0.8702 (tm) REVERT: J 985 ILE cc_start: 0.4864 (OUTLIER) cc_final: 0.4564 (tt) REVERT: J 1095 MET cc_start: 0.0988 (ttp) cc_final: 0.0460 (ttp) REVERT: J 1197 ASN cc_start: 0.5960 (m-40) cc_final: 0.5623 (m-40) REVERT: J 1258 ARG cc_start: 0.8584 (OUTLIER) cc_final: 0.8236 (ttt180) REVERT: G 158 ARG cc_start: 0.7494 (OUTLIER) cc_final: 0.6751 (ttm-80) REVERT: H 69 SER cc_start: 0.8360 (OUTLIER) cc_final: 0.7820 (m) REVERT: H 206 GLU cc_start: 0.7989 (OUTLIER) cc_final: 0.7739 (mt-10) REVERT: I 202 ARG cc_start: 0.7881 (OUTLIER) cc_final: 0.7648 (mtm-85) REVERT: I 322 LEU cc_start: 0.6813 (pp) cc_final: 0.6079 (tp) REVERT: I 330 HIS cc_start: 0.5090 (m170) cc_final: 0.4772 (m170) REVERT: I 478 ARG cc_start: 0.7563 (tpt90) cc_final: 0.7271 (tpt90) REVERT: I 541 GLU cc_start: 0.5977 (OUTLIER) cc_final: 0.5716 (mp0) REVERT: I 572 ILE cc_start: 0.9159 (OUTLIER) cc_final: 0.8717 (mt) REVERT: I 609 ILE cc_start: 0.8567 (pt) cc_final: 0.8350 (pt) REVERT: I 637 ARG cc_start: 0.8326 (OUTLIER) cc_final: 0.8066 (ptt-90) REVERT: I 922 ASN cc_start: 0.7956 (OUTLIER) cc_final: 0.7555 (m-40) REVERT: I 1020 GLU cc_start: 0.7981 (tm-30) cc_final: 0.7668 (tm-30) REVERT: I 1024 GLU cc_start: 0.7454 (OUTLIER) cc_final: 0.7081 (mp0) REVERT: I 1041 ASP cc_start: 0.7647 (OUTLIER) cc_final: 0.7386 (m-30) REVERT: I 1253 LEU cc_start: 0.9223 (OUTLIER) cc_final: 0.8732 (tp) REVERT: K 13 ILE cc_start: 0.7899 (OUTLIER) cc_final: 0.7663 (tt) REVERT: K 30 MET cc_start: 0.8500 (mtm) cc_final: 0.8264 (mtp) REVERT: K 42 GLU cc_start: 0.7365 (OUTLIER) cc_final: 0.6379 (pp20) REVERT: K 55 GLU cc_start: 0.7879 (mt-10) cc_final: 0.7649 (mt-10) REVERT: L 271 ASN cc_start: 0.6765 (t0) cc_final: 0.6400 (t0) REVERT: L 435 ILE cc_start: 0.7629 (OUTLIER) cc_final: 0.7336 (mt) REVERT: L 436 ARG cc_start: 0.7451 (ptp-110) cc_final: 0.6843 (ptp-110) REVERT: L 508 GLU cc_start: 0.7850 (OUTLIER) cc_final: 0.7423 (mt-10) REVERT: L 545 HIS cc_start: 0.6893 (t70) cc_final: 0.6457 (t70) REVERT: L 561 MET cc_start: 0.7863 (ttm) cc_final: 0.7554 (mtp) REVERT: M 297 LYS cc_start: 0.5743 (OUTLIER) cc_final: 0.5526 (pptt) REVERT: M 319 GLU cc_start: 0.3964 (OUTLIER) cc_final: 0.3374 (tm-30) outliers start: 169 outliers final: 119 residues processed: 509 average time/residue: 0.4657 time to fit residues: 384.5139 Evaluate side-chains 483 residues out of total 3346 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 142 poor density : 341 time to evaluate : 3.565 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain J residue 26 SER Chi-restraints excluded: chain J residue 46 TYR Chi-restraints excluded: chain J residue 65 VAL Chi-restraints excluded: chain J residue 93 THR Chi-restraints excluded: chain J residue 109 SER Chi-restraints excluded: chain J residue 135 ILE Chi-restraints excluded: chain J residue 146 VAL Chi-restraints excluded: chain J residue 147 ILE Chi-restraints excluded: chain J residue 159 ILE Chi-restraints excluded: chain J residue 205 LEU Chi-restraints excluded: chain J residue 212 THR Chi-restraints excluded: chain J residue 250 ARG Chi-restraints excluded: chain J residue 264 ASP Chi-restraints excluded: chain J residue 292 VAL Chi-restraints excluded: chain J residue 324 LEU Chi-restraints excluded: chain J residue 332 LYS Chi-restraints excluded: chain J residue 345 LYS Chi-restraints excluded: chain J residue 363 LEU Chi-restraints excluded: chain J residue 416 ILE Chi-restraints excluded: chain J residue 442 ILE Chi-restraints excluded: chain J residue 478 LEU Chi-restraints excluded: chain J residue 489 ASN Chi-restraints excluded: chain J residue 506 VAL Chi-restraints excluded: chain J residue 543 SER Chi-restraints excluded: chain J residue 545 HIS Chi-restraints excluded: chain J residue 553 THR Chi-restraints excluded: chain J residue 567 THR Chi-restraints excluded: chain J residue 571 ASP Chi-restraints excluded: chain J residue 596 LEU Chi-restraints excluded: chain J residue 612 LEU Chi-restraints excluded: chain J residue 706 VAL Chi-restraints excluded: chain J residue 707 ILE Chi-restraints excluded: chain J residue 708 ASN Chi-restraints excluded: chain J residue 740 LEU Chi-restraints excluded: chain J residue 762 ASN Chi-restraints excluded: chain J residue 770 LEU Chi-restraints excluded: chain J residue 786 THR Chi-restraints excluded: chain J residue 788 LEU Chi-restraints excluded: chain J residue 796 LEU Chi-restraints excluded: chain J residue 807 LEU Chi-restraints excluded: chain J residue 825 VAL Chi-restraints excluded: chain J residue 839 VAL Chi-restraints excluded: chain J residue 862 THR Chi-restraints excluded: chain J residue 903 LEU Chi-restraints excluded: chain J residue 918 ILE Chi-restraints excluded: chain J residue 928 THR Chi-restraints excluded: chain J residue 974 VAL Chi-restraints excluded: chain J residue 985 ILE Chi-restraints excluded: chain J residue 991 THR Chi-restraints excluded: chain J residue 1078 LEU Chi-restraints excluded: chain J residue 1181 ASP Chi-restraints excluded: chain J residue 1196 LEU Chi-restraints excluded: chain J residue 1258 ARG Chi-restraints excluded: chain J residue 1261 LEU Chi-restraints excluded: chain J residue 1266 ILE Chi-restraints excluded: chain J residue 1280 VAL Chi-restraints excluded: chain J residue 1297 LYS Chi-restraints excluded: chain J residue 1301 THR Chi-restraints excluded: chain J residue 1307 LEU Chi-restraints excluded: chain J residue 1342 ASP Chi-restraints excluded: chain G residue 6 THR Chi-restraints excluded: chain G residue 9 LEU Chi-restraints excluded: chain G residue 61 ILE Chi-restraints excluded: chain G residue 130 ILE Chi-restraints excluded: chain G residue 158 ARG Chi-restraints excluded: chain G residue 171 LEU Chi-restraints excluded: chain G residue 177 TYR Chi-restraints excluded: chain G residue 192 VAL Chi-restraints excluded: chain G residue 202 VAL Chi-restraints excluded: chain H residue 38 THR Chi-restraints excluded: chain H residue 51 MET Chi-restraints excluded: chain H residue 65 LEU Chi-restraints excluded: chain H residue 69 SER Chi-restraints excluded: chain H residue 134 THR Chi-restraints excluded: chain H residue 139 SER Chi-restraints excluded: chain H residue 146 VAL Chi-restraints excluded: chain H residue 153 VAL Chi-restraints excluded: chain H residue 206 GLU Chi-restraints excluded: chain I residue 33 ASP Chi-restraints excluded: chain I residue 37 LYS Chi-restraints excluded: chain I residue 105 TYR Chi-restraints excluded: chain I residue 127 ILE Chi-restraints excluded: chain I residue 182 SER Chi-restraints excluded: chain I residue 202 ARG Chi-restraints excluded: chain I residue 282 VAL Chi-restraints excluded: chain I residue 296 VAL Chi-restraints excluded: chain I residue 297 VAL Chi-restraints excluded: chain I residue 309 LEU Chi-restraints excluded: chain I residue 426 ILE Chi-restraints excluded: chain I residue 442 VAL Chi-restraints excluded: chain I residue 456 VAL Chi-restraints excluded: chain I residue 471 VAL Chi-restraints excluded: chain I residue 498 ILE Chi-restraints excluded: chain I residue 513 GLN Chi-restraints excluded: chain I residue 523 GLU Chi-restraints excluded: chain I residue 541 GLU Chi-restraints excluded: chain I residue 572 ILE Chi-restraints excluded: chain I residue 581 THR Chi-restraints excluded: chain I residue 583 GLU Chi-restraints excluded: chain I residue 594 VAL Chi-restraints excluded: chain I residue 606 LEU Chi-restraints excluded: chain I residue 633 LEU Chi-restraints excluded: chain I residue 637 ARG Chi-restraints excluded: chain I residue 659 GLN Chi-restraints excluded: chain I residue 768 MET Chi-restraints excluded: chain I residue 773 LEU Chi-restraints excluded: chain I residue 785 ASP Chi-restraints excluded: chain I residue 799 ASN Chi-restraints excluded: chain I residue 839 VAL Chi-restraints excluded: chain I residue 913 VAL Chi-restraints excluded: chain I residue 922 ASN Chi-restraints excluded: chain I residue 939 VAL Chi-restraints excluded: chain I residue 960 LEU Chi-restraints excluded: chain I residue 973 SER Chi-restraints excluded: chain I residue 1024 GLU Chi-restraints excluded: chain I residue 1041 ASP Chi-restraints excluded: chain I residue 1083 GLU Chi-restraints excluded: chain I residue 1162 SER Chi-restraints excluded: chain I residue 1240 ASP Chi-restraints excluded: chain I residue 1253 LEU Chi-restraints excluded: chain I residue 1254 VAL Chi-restraints excluded: chain I residue 1296 ASP Chi-restraints excluded: chain I residue 1332 SER Chi-restraints excluded: chain K residue 13 ILE Chi-restraints excluded: chain K residue 42 GLU Chi-restraints excluded: chain K residue 66 VAL Chi-restraints excluded: chain L residue 31 LEU Chi-restraints excluded: chain L residue 94 THR Chi-restraints excluded: chain L residue 105 MET Chi-restraints excluded: chain L residue 118 ASP Chi-restraints excluded: chain L residue 262 VAL Chi-restraints excluded: chain L residue 330 LEU Chi-restraints excluded: chain L residue 381 GLU Chi-restraints excluded: chain L residue 429 THR Chi-restraints excluded: chain L residue 435 ILE Chi-restraints excluded: chain L residue 508 GLU Chi-restraints excluded: chain L residue 604 SER Chi-restraints excluded: chain M residue 262 LEU Chi-restraints excluded: chain M residue 263 THR Chi-restraints excluded: chain M residue 285 THR Chi-restraints excluded: chain M residue 297 LYS Chi-restraints excluded: chain M residue 319 GLU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 397 random chunks: chunk 348 optimal weight: 5.9990 chunk 366 optimal weight: 0.0570 chunk 334 optimal weight: 8.9990 chunk 356 optimal weight: 3.9990 chunk 214 optimal weight: 4.9990 chunk 155 optimal weight: 10.0000 chunk 279 optimal weight: 2.9990 chunk 109 optimal weight: 10.0000 chunk 322 optimal weight: 0.9990 chunk 337 optimal weight: 9.9990 chunk 355 optimal weight: 6.9990 overall best weight: 2.6106 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: J 320 ASN ** J1244 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J1268 ASN H 147 GLN I 46 GLN L 301 ASN ** L 362 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7753 moved from start: 0.3471 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.065 33475 Z= 0.318 Angle : 0.650 13.317 45662 Z= 0.334 Chirality : 0.043 0.209 5240 Planarity : 0.004 0.066 5595 Dihedral : 16.704 158.720 5729 Min Nonbonded Distance : 1.945 Molprobity Statistics. All-atom Clashscore : 13.63 Ramachandran Plot: Outliers : 0.13 % Allowed : 7.38 % Favored : 92.49 % Rotamer: Outliers : 5.26 % Allowed : 27.05 % Favored : 67.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.25 % Cis-general : 0.21 % Twisted Proline : 0.00 % Twisted General : 0.05 % 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: -1.14 (0.13), residues: 3876 helix: 0.57 (0.13), residues: 1572 sheet: -1.48 (0.24), residues: 462 loop : -1.74 (0.14), residues: 1842 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP I 807 HIS 0.009 0.001 HIS G 160 PHE 0.016 0.002 PHE N 52 TYR 0.027 0.002 TYR L 143 ARG 0.006 0.001 ARG I 107 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7752 Ramachandran restraints generated. 3876 Oldfield, 0 Emsley, 3876 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7752 Ramachandran restraints generated. 3876 Oldfield, 0 Emsley, 3876 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 523 residues out of total 3346 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 175 poor density : 348 time to evaluate : 3.711 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: J 56 LEU cc_start: 0.8777 (OUTLIER) cc_final: 0.8345 (mt) REVERT: J 148 GLU cc_start: 0.7146 (mt-10) cc_final: 0.6858 (tt0) REVERT: J 250 ARG cc_start: 0.8888 (OUTLIER) cc_final: 0.8576 (ptt90) REVERT: J 479 GLU cc_start: 0.7929 (mt-10) cc_final: 0.7694 (mt-10) REVERT: J 625 MET cc_start: 0.8760 (ttp) cc_final: 0.8434 (ttp) REVERT: J 796 LEU cc_start: 0.9034 (OUTLIER) cc_final: 0.8802 (tm) REVERT: J 1095 MET cc_start: 0.1040 (ttp) cc_final: 0.0423 (ttp) REVERT: J 1197 ASN cc_start: 0.6115 (m-40) cc_final: 0.5793 (m-40) REVERT: J 1258 ARG cc_start: 0.8663 (OUTLIER) cc_final: 0.8311 (ttt180) REVERT: J 1262 ARG cc_start: 0.8154 (OUTLIER) cc_final: 0.7891 (ptt180) REVERT: H 48 LEU cc_start: 0.8956 (OUTLIER) cc_final: 0.8665 (mp) REVERT: H 69 SER cc_start: 0.8208 (OUTLIER) cc_final: 0.7854 (m) REVERT: H 206 GLU cc_start: 0.8304 (OUTLIER) cc_final: 0.8006 (mt-10) REVERT: I 83 GLN cc_start: 0.8022 (mp-120) cc_final: 0.7747 (mm-40) REVERT: I 158 ASP cc_start: 0.7429 (OUTLIER) cc_final: 0.7212 (m-30) REVERT: I 202 ARG cc_start: 0.8099 (OUTLIER) cc_final: 0.7779 (mtp-110) REVERT: I 322 LEU cc_start: 0.6869 (pp) cc_final: 0.6067 (tp) REVERT: I 515 MET cc_start: 0.8706 (ttp) cc_final: 0.8485 (ttp) REVERT: I 541 GLU cc_start: 0.6049 (OUTLIER) cc_final: 0.5784 (mp0) REVERT: I 637 ARG cc_start: 0.8333 (OUTLIER) cc_final: 0.8074 (ptt-90) REVERT: I 1020 GLU cc_start: 0.8006 (tm-30) cc_final: 0.7692 (tm-30) REVERT: I 1024 GLU cc_start: 0.7514 (OUTLIER) cc_final: 0.7109 (mp0) REVERT: I 1041 ASP cc_start: 0.7866 (OUTLIER) cc_final: 0.7524 (m-30) REVERT: I 1253 LEU cc_start: 0.9272 (OUTLIER) cc_final: 0.8813 (tp) REVERT: K 13 ILE cc_start: 0.7905 (OUTLIER) cc_final: 0.7623 (tt) REVERT: K 30 MET cc_start: 0.8534 (mtm) cc_final: 0.8149 (mtp) REVERT: K 42 GLU cc_start: 0.7812 (OUTLIER) cc_final: 0.6490 (pp20) REVERT: L 271 ASN cc_start: 0.6795 (t0) cc_final: 0.6313 (t0) REVERT: L 379 MET cc_start: 0.7995 (mmm) cc_final: 0.7625 (mmm) REVERT: L 435 ILE cc_start: 0.7759 (OUTLIER) cc_final: 0.7465 (mt) REVERT: L 508 GLU cc_start: 0.7864 (OUTLIER) cc_final: 0.7412 (mt-10) REVERT: L 545 HIS cc_start: 0.7062 (t70) cc_final: 0.6764 (t-90) REVERT: L 561 MET cc_start: 0.7964 (ttm) cc_final: 0.7585 (mtp) REVERT: M 297 LYS cc_start: 0.5491 (OUTLIER) cc_final: 0.5204 (pptt) REVERT: M 316 MET cc_start: 0.3441 (mpp) cc_final: 0.1982 (ppp) REVERT: M 319 GLU cc_start: 0.4073 (OUTLIER) cc_final: 0.3568 (tm-30) outliers start: 175 outliers final: 140 residues processed: 490 average time/residue: 0.4387 time to fit residues: 352.4493 Evaluate side-chains 493 residues out of total 3346 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 161 poor density : 332 time to evaluate : 3.685 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain J residue 26 SER Chi-restraints excluded: chain J residue 46 TYR Chi-restraints excluded: chain J residue 56 LEU Chi-restraints excluded: chain J residue 65 VAL Chi-restraints excluded: chain J residue 90 VAL Chi-restraints excluded: chain J residue 93 THR Chi-restraints excluded: chain J residue 109 SER Chi-restraints excluded: chain J residue 135 ILE Chi-restraints excluded: chain J residue 146 VAL Chi-restraints excluded: chain J residue 147 ILE Chi-restraints excluded: chain J residue 159 ILE Chi-restraints excluded: chain J residue 205 LEU Chi-restraints excluded: chain J residue 212 THR Chi-restraints excluded: chain J residue 242 LEU Chi-restraints excluded: chain J residue 250 ARG Chi-restraints excluded: chain J residue 264 ASP Chi-restraints excluded: chain J residue 292 VAL Chi-restraints excluded: chain J residue 324 LEU Chi-restraints excluded: chain J residue 332 LYS Chi-restraints excluded: chain J residue 345 LYS Chi-restraints excluded: chain J residue 363 LEU Chi-restraints excluded: chain J residue 402 GLU Chi-restraints excluded: chain J residue 408 VAL Chi-restraints excluded: chain J residue 416 ILE Chi-restraints excluded: chain J residue 442 ILE Chi-restraints excluded: chain J residue 478 LEU Chi-restraints excluded: chain J residue 489 ASN Chi-restraints excluded: chain J residue 506 VAL Chi-restraints excluded: chain J residue 543 SER Chi-restraints excluded: chain J residue 544 LEU Chi-restraints excluded: chain J residue 545 HIS Chi-restraints excluded: chain J residue 553 THR Chi-restraints excluded: chain J residue 567 THR Chi-restraints excluded: chain J residue 571 ASP Chi-restraints excluded: chain J residue 596 LEU Chi-restraints excluded: chain J residue 612 LEU Chi-restraints excluded: chain J residue 706 VAL Chi-restraints excluded: chain J residue 707 ILE Chi-restraints excluded: chain J residue 708 ASN Chi-restraints excluded: chain J residue 740 LEU Chi-restraints excluded: chain J residue 762 ASN Chi-restraints excluded: chain J residue 770 LEU Chi-restraints excluded: chain J residue 786 THR Chi-restraints excluded: chain J residue 788 LEU Chi-restraints excluded: chain J residue 796 LEU Chi-restraints excluded: chain J residue 807 LEU Chi-restraints excluded: chain J residue 825 VAL Chi-restraints excluded: chain J residue 839 VAL Chi-restraints excluded: chain J residue 862 THR Chi-restraints excluded: chain J residue 878 ASP Chi-restraints excluded: chain J residue 903 LEU Chi-restraints excluded: chain J residue 918 ILE Chi-restraints excluded: chain J residue 928 THR Chi-restraints excluded: chain J residue 931 THR Chi-restraints excluded: chain J residue 974 VAL Chi-restraints excluded: chain J residue 991 THR Chi-restraints excluded: chain J residue 1078 LEU Chi-restraints excluded: chain J residue 1098 GLN Chi-restraints excluded: chain J residue 1181 ASP Chi-restraints excluded: chain J residue 1196 LEU Chi-restraints excluded: chain J residue 1198 VAL Chi-restraints excluded: chain J residue 1258 ARG Chi-restraints excluded: chain J residue 1261 LEU Chi-restraints excluded: chain J residue 1262 ARG Chi-restraints excluded: chain J residue 1266 ILE Chi-restraints excluded: chain J residue 1280 VAL Chi-restraints excluded: chain J residue 1297 LYS Chi-restraints excluded: chain J residue 1301 THR Chi-restraints excluded: chain J residue 1307 LEU Chi-restraints excluded: chain J residue 1342 ASP Chi-restraints excluded: chain N residue 30 HIS Chi-restraints excluded: chain G residue 6 THR Chi-restraints excluded: chain G residue 39 LEU Chi-restraints excluded: chain G residue 61 ILE Chi-restraints excluded: chain G residue 130 ILE Chi-restraints excluded: chain G residue 171 LEU Chi-restraints excluded: chain G residue 177 TYR Chi-restraints excluded: chain G residue 192 VAL Chi-restraints excluded: chain G residue 202 VAL Chi-restraints excluded: chain G residue 217 ILE Chi-restraints excluded: chain H residue 38 THR Chi-restraints excluded: chain H residue 48 LEU Chi-restraints excluded: chain H residue 51 MET Chi-restraints excluded: chain H residue 65 LEU Chi-restraints excluded: chain H residue 69 SER Chi-restraints excluded: chain H residue 134 THR Chi-restraints excluded: chain H residue 139 SER Chi-restraints excluded: chain H residue 146 VAL Chi-restraints excluded: chain H residue 153 VAL Chi-restraints excluded: chain H residue 206 GLU Chi-restraints excluded: chain I residue 33 ASP Chi-restraints excluded: chain I residue 37 LYS Chi-restraints excluded: chain I residue 105 TYR Chi-restraints excluded: chain I residue 107 ARG Chi-restraints excluded: chain I residue 127 ILE Chi-restraints excluded: chain I residue 133 ASN Chi-restraints excluded: chain I residue 158 ASP Chi-restraints excluded: chain I residue 182 SER Chi-restraints excluded: chain I residue 202 ARG Chi-restraints excluded: chain I residue 282 VAL Chi-restraints excluded: chain I residue 296 VAL Chi-restraints excluded: chain I residue 297 VAL Chi-restraints excluded: chain I residue 309 LEU Chi-restraints excluded: chain I residue 426 ILE Chi-restraints excluded: chain I residue 442 VAL Chi-restraints excluded: chain I residue 456 VAL Chi-restraints excluded: chain I residue 498 ILE Chi-restraints excluded: chain I residue 513 GLN Chi-restraints excluded: chain I residue 523 GLU Chi-restraints excluded: chain I residue 541 GLU Chi-restraints excluded: chain I residue 573 ASN Chi-restraints excluded: chain I residue 583 GLU Chi-restraints excluded: chain I residue 594 VAL Chi-restraints excluded: chain I residue 606 LEU Chi-restraints excluded: chain I residue 633 LEU Chi-restraints excluded: chain I residue 637 ARG Chi-restraints excluded: chain I residue 659 GLN Chi-restraints excluded: chain I residue 693 LEU Chi-restraints excluded: chain I residue 717 VAL Chi-restraints excluded: chain I residue 750 ILE Chi-restraints excluded: chain I residue 768 MET Chi-restraints excluded: chain I residue 773 LEU Chi-restraints excluded: chain I residue 785 ASP Chi-restraints excluded: chain I residue 799 ASN Chi-restraints excluded: chain I residue 839 VAL Chi-restraints excluded: chain I residue 878 THR Chi-restraints excluded: chain I residue 913 VAL Chi-restraints excluded: chain I residue 939 VAL Chi-restraints excluded: chain I residue 960 LEU Chi-restraints excluded: chain I residue 973 SER Chi-restraints excluded: chain I residue 1024 GLU Chi-restraints excluded: chain I residue 1041 ASP Chi-restraints excluded: chain I residue 1083 GLU Chi-restraints excluded: chain I residue 1162 SER Chi-restraints excluded: chain I residue 1240 ASP Chi-restraints excluded: chain I residue 1253 LEU Chi-restraints excluded: chain I residue 1254 VAL Chi-restraints excluded: chain I residue 1296 ASP Chi-restraints excluded: chain I residue 1315 MET Chi-restraints excluded: chain I residue 1332 SER Chi-restraints excluded: chain K residue 13 ILE Chi-restraints excluded: chain K residue 42 GLU Chi-restraints excluded: chain K residue 66 VAL Chi-restraints excluded: chain L residue 31 LEU Chi-restraints excluded: chain L residue 56 MET Chi-restraints excluded: chain L residue 94 THR Chi-restraints excluded: chain L residue 118 ASP Chi-restraints excluded: chain L residue 262 VAL Chi-restraints excluded: chain L residue 275 VAL Chi-restraints excluded: chain L residue 330 LEU Chi-restraints excluded: chain L residue 381 GLU Chi-restraints excluded: chain L residue 395 THR Chi-restraints excluded: chain L residue 429 THR Chi-restraints excluded: chain L residue 435 ILE Chi-restraints excluded: chain L residue 508 GLU Chi-restraints excluded: chain L residue 576 VAL Chi-restraints excluded: chain L residue 604 SER Chi-restraints excluded: chain M residue 262 LEU Chi-restraints excluded: chain M residue 263 THR Chi-restraints excluded: chain M residue 297 LYS Chi-restraints excluded: chain M residue 319 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 397 random chunks: chunk 234 optimal weight: 7.9990 chunk 377 optimal weight: 1.9990 chunk 230 optimal weight: 1.9990 chunk 178 optimal weight: 2.9990 chunk 262 optimal weight: 0.7980 chunk 395 optimal weight: 10.0000 chunk 364 optimal weight: 1.9990 chunk 314 optimal weight: 2.9990 chunk 32 optimal weight: 7.9990 chunk 243 optimal weight: 0.8980 chunk 193 optimal weight: 7.9990 overall best weight: 1.5386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** J1244 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I1061 GLN ** L 362 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7718 moved from start: 0.3641 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 33475 Z= 0.224 Angle : 0.607 13.550 45662 Z= 0.312 Chirality : 0.042 0.190 5240 Planarity : 0.004 0.067 5595 Dihedral : 16.620 158.342 5729 Min Nonbonded Distance : 1.972 Molprobity Statistics. All-atom Clashscore : 12.99 Ramachandran Plot: Outliers : 0.13 % Allowed : 6.60 % Favored : 93.27 % Rotamer: Outliers : 4.96 % Allowed : 27.32 % Favored : 67.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.25 % Cis-general : 0.21 % Twisted Proline : 0.00 % Twisted General : 0.05 % 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: -1.03 (0.13), residues: 3876 helix: 0.67 (0.13), residues: 1573 sheet: -1.40 (0.24), residues: 451 loop : -1.70 (0.14), residues: 1852 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP I 807 HIS 0.009 0.001 HIS G 160 PHE 0.015 0.001 PHE N 52 TYR 0.017 0.001 TYR G 177 ARG 0.004 0.000 ARG I 919 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7752 Ramachandran restraints generated. 3876 Oldfield, 0 Emsley, 3876 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7752 Ramachandran restraints generated. 3876 Oldfield, 0 Emsley, 3876 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 508 residues out of total 3346 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 165 poor density : 343 time to evaluate : 4.374 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: J 56 LEU cc_start: 0.8687 (OUTLIER) cc_final: 0.8470 (mt) REVERT: J 625 MET cc_start: 0.8744 (ttp) cc_final: 0.8529 (ttp) REVERT: J 796 LEU cc_start: 0.9023 (OUTLIER) cc_final: 0.8789 (tm) REVERT: J 985 ILE cc_start: 0.4874 (OUTLIER) cc_final: 0.4515 (tt) REVERT: J 1095 MET cc_start: 0.1046 (ttp) cc_final: 0.0698 (ttp) REVERT: J 1197 ASN cc_start: 0.6096 (m-40) cc_final: 0.5752 (m-40) REVERT: J 1258 ARG cc_start: 0.8604 (OUTLIER) cc_final: 0.8262 (ttt180) REVERT: H 69 SER cc_start: 0.8364 (OUTLIER) cc_final: 0.7815 (m) REVERT: H 206 GLU cc_start: 0.8237 (OUTLIER) cc_final: 0.7970 (mt-10) REVERT: I 202 ARG cc_start: 0.8012 (OUTLIER) cc_final: 0.7715 (mtm-85) REVERT: I 322 LEU cc_start: 0.6895 (pp) cc_final: 0.6088 (tp) REVERT: I 478 ARG cc_start: 0.7602 (tpt90) cc_final: 0.7284 (tpt90) REVERT: I 515 MET cc_start: 0.8625 (ttp) cc_final: 0.8382 (ttp) REVERT: I 541 GLU cc_start: 0.6065 (OUTLIER) cc_final: 0.5821 (mp0) REVERT: I 637 ARG cc_start: 0.8283 (OUTLIER) cc_final: 0.8060 (ptt-90) REVERT: I 1020 GLU cc_start: 0.8007 (tm-30) cc_final: 0.7690 (tm-30) REVERT: I 1024 GLU cc_start: 0.7785 (OUTLIER) cc_final: 0.7196 (mp0) REVERT: I 1034 ARG cc_start: 0.7894 (tmm-80) cc_final: 0.7505 (ttp80) REVERT: I 1041 ASP cc_start: 0.7801 (OUTLIER) cc_final: 0.7455 (m-30) REVERT: I 1253 LEU cc_start: 0.9252 (OUTLIER) cc_final: 0.8829 (tp) REVERT: K 13 ILE cc_start: 0.8005 (OUTLIER) cc_final: 0.7764 (tt) REVERT: K 30 MET cc_start: 0.8437 (mtm) cc_final: 0.8118 (mtp) REVERT: K 42 GLU cc_start: 0.7792 (OUTLIER) cc_final: 0.6509 (pp20) REVERT: L 379 MET cc_start: 0.8023 (mmm) cc_final: 0.7722 (mmm) REVERT: L 435 ILE cc_start: 0.7715 (OUTLIER) cc_final: 0.7459 (mt) REVERT: L 436 ARG cc_start: 0.7395 (ptp-110) cc_final: 0.6786 (ptp-110) REVERT: L 508 GLU cc_start: 0.7839 (OUTLIER) cc_final: 0.7417 (mt-10) REVERT: L 545 HIS cc_start: 0.7036 (t70) cc_final: 0.6736 (t-90) REVERT: L 561 MET cc_start: 0.7942 (ttm) cc_final: 0.7619 (mtp) REVERT: M 316 MET cc_start: 0.3475 (mpp) cc_final: 0.2161 (ppp) REVERT: M 319 GLU cc_start: 0.4043 (OUTLIER) cc_final: 0.3454 (tm-30) outliers start: 165 outliers final: 136 residues processed: 476 average time/residue: 0.4556 time to fit residues: 353.6415 Evaluate side-chains 489 residues out of total 3346 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 153 poor density : 336 time to evaluate : 3.748 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain J residue 26 SER Chi-restraints excluded: chain J residue 46 TYR Chi-restraints excluded: chain J residue 56 LEU Chi-restraints excluded: chain J residue 65 VAL Chi-restraints excluded: chain J residue 90 VAL Chi-restraints excluded: chain J residue 93 THR Chi-restraints excluded: chain J residue 109 SER Chi-restraints excluded: chain J residue 135 ILE Chi-restraints excluded: chain J residue 146 VAL Chi-restraints excluded: chain J residue 147 ILE Chi-restraints excluded: chain J residue 159 ILE Chi-restraints excluded: chain J residue 205 LEU Chi-restraints excluded: chain J residue 212 THR Chi-restraints excluded: chain J residue 242 LEU Chi-restraints excluded: chain J residue 264 ASP Chi-restraints excluded: chain J residue 292 VAL Chi-restraints excluded: chain J residue 324 LEU Chi-restraints excluded: chain J residue 332 LYS Chi-restraints excluded: chain J residue 363 LEU Chi-restraints excluded: chain J residue 402 GLU Chi-restraints excluded: chain J residue 408 VAL Chi-restraints excluded: chain J residue 416 ILE Chi-restraints excluded: chain J residue 442 ILE Chi-restraints excluded: chain J residue 478 LEU Chi-restraints excluded: chain J residue 489 ASN Chi-restraints excluded: chain J residue 506 VAL Chi-restraints excluded: chain J residue 543 SER Chi-restraints excluded: chain J residue 544 LEU Chi-restraints excluded: chain J residue 545 HIS Chi-restraints excluded: chain J residue 553 THR Chi-restraints excluded: chain J residue 567 THR Chi-restraints excluded: chain J residue 571 ASP Chi-restraints excluded: chain J residue 596 LEU Chi-restraints excluded: chain J residue 612 LEU Chi-restraints excluded: chain J residue 706 VAL Chi-restraints excluded: chain J residue 707 ILE Chi-restraints excluded: chain J residue 708 ASN Chi-restraints excluded: chain J residue 740 LEU Chi-restraints excluded: chain J residue 762 ASN Chi-restraints excluded: chain J residue 770 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 796 LEU Chi-restraints excluded: chain J residue 807 LEU Chi-restraints excluded: chain J residue 825 VAL Chi-restraints excluded: chain J residue 839 VAL Chi-restraints excluded: chain J residue 862 THR Chi-restraints excluded: chain J residue 878 ASP Chi-restraints excluded: chain J residue 903 LEU Chi-restraints excluded: chain J residue 918 ILE Chi-restraints excluded: chain J residue 928 THR Chi-restraints excluded: chain J residue 974 VAL Chi-restraints excluded: chain J residue 985 ILE Chi-restraints excluded: chain J residue 991 THR Chi-restraints excluded: chain J residue 1054 THR Chi-restraints excluded: chain J residue 1078 LEU Chi-restraints excluded: chain J residue 1098 GLN Chi-restraints excluded: chain J residue 1160 SER Chi-restraints excluded: chain J residue 1181 ASP Chi-restraints excluded: chain J residue 1196 LEU Chi-restraints excluded: chain J residue 1198 VAL Chi-restraints excluded: chain J residue 1258 ARG Chi-restraints excluded: chain J residue 1261 LEU Chi-restraints excluded: chain J residue 1266 ILE Chi-restraints excluded: chain J residue 1280 VAL Chi-restraints excluded: chain J residue 1297 LYS Chi-restraints excluded: chain J residue 1301 THR Chi-restraints excluded: chain J residue 1307 LEU Chi-restraints excluded: chain J residue 1342 ASP Chi-restraints excluded: chain N residue 2 SER Chi-restraints excluded: chain N residue 30 HIS Chi-restraints excluded: chain G residue 6 THR Chi-restraints excluded: chain G residue 9 LEU Chi-restraints excluded: chain G residue 39 LEU Chi-restraints excluded: chain G residue 61 ILE Chi-restraints excluded: chain G residue 130 ILE Chi-restraints excluded: chain G residue 171 LEU Chi-restraints excluded: chain G residue 177 TYR Chi-restraints excluded: chain G residue 192 VAL Chi-restraints excluded: chain G residue 202 VAL Chi-restraints excluded: chain H residue 38 THR Chi-restraints excluded: chain H residue 51 MET Chi-restraints excluded: chain H residue 65 LEU Chi-restraints excluded: chain H residue 69 SER Chi-restraints excluded: chain H residue 134 THR Chi-restraints excluded: chain H residue 139 SER Chi-restraints excluded: chain H residue 146 VAL Chi-restraints excluded: chain H residue 153 VAL Chi-restraints excluded: chain H residue 206 GLU Chi-restraints excluded: chain I residue 33 ASP Chi-restraints excluded: chain I residue 37 LYS Chi-restraints excluded: chain I residue 105 TYR Chi-restraints excluded: chain I residue 127 ILE Chi-restraints excluded: chain I residue 133 ASN Chi-restraints excluded: chain I residue 182 SER Chi-restraints excluded: chain I residue 202 ARG Chi-restraints excluded: chain I residue 282 VAL Chi-restraints excluded: chain I residue 296 VAL Chi-restraints excluded: chain I residue 297 VAL Chi-restraints excluded: chain I residue 426 ILE Chi-restraints excluded: chain I residue 442 VAL Chi-restraints excluded: chain I residue 456 VAL Chi-restraints excluded: chain I residue 498 ILE Chi-restraints excluded: chain I residue 523 GLU Chi-restraints excluded: chain I residue 541 GLU Chi-restraints excluded: chain I residue 583 GLU Chi-restraints excluded: chain I residue 594 VAL Chi-restraints excluded: chain I residue 633 LEU Chi-restraints excluded: chain I residue 637 ARG Chi-restraints excluded: chain I residue 659 GLN Chi-restraints excluded: chain I residue 693 LEU Chi-restraints excluded: chain I residue 717 VAL Chi-restraints excluded: chain I residue 768 MET Chi-restraints excluded: chain I residue 773 LEU Chi-restraints excluded: chain I residue 785 ASP Chi-restraints excluded: chain I residue 799 ASN Chi-restraints excluded: chain I residue 839 VAL Chi-restraints excluded: chain I residue 878 THR Chi-restraints excluded: chain I residue 913 VAL Chi-restraints excluded: chain I residue 939 VAL Chi-restraints excluded: chain I residue 960 LEU Chi-restraints excluded: chain I residue 973 SER Chi-restraints excluded: chain I residue 1024 GLU Chi-restraints excluded: chain I residue 1041 ASP Chi-restraints excluded: chain I residue 1083 GLU Chi-restraints excluded: chain I residue 1138 VAL Chi-restraints excluded: chain I residue 1162 SER Chi-restraints excluded: chain I residue 1240 ASP Chi-restraints excluded: chain I residue 1253 LEU Chi-restraints excluded: chain I residue 1254 VAL Chi-restraints excluded: chain I residue 1296 ASP Chi-restraints excluded: chain I residue 1332 SER Chi-restraints excluded: chain K residue 13 ILE Chi-restraints excluded: chain K residue 42 GLU Chi-restraints excluded: chain K residue 66 VAL Chi-restraints excluded: chain L residue 31 LEU Chi-restraints excluded: chain L residue 56 MET Chi-restraints excluded: chain L residue 94 THR Chi-restraints excluded: chain L residue 118 ASP Chi-restraints excluded: chain L residue 166 VAL Chi-restraints excluded: chain L residue 262 VAL Chi-restraints excluded: chain L residue 275 VAL Chi-restraints excluded: chain L residue 330 LEU Chi-restraints excluded: chain L residue 381 GLU Chi-restraints excluded: chain L residue 395 THR Chi-restraints excluded: chain L residue 429 THR Chi-restraints excluded: chain L residue 435 ILE Chi-restraints excluded: chain L residue 508 GLU Chi-restraints excluded: chain L residue 604 SER Chi-restraints excluded: chain M residue 262 LEU Chi-restraints excluded: chain M residue 263 THR Chi-restraints excluded: chain M residue 319 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 397 random chunks: chunk 250 optimal weight: 1.9990 chunk 335 optimal weight: 7.9990 chunk 96 optimal weight: 5.9990 chunk 290 optimal weight: 0.1980 chunk 46 optimal weight: 0.9980 chunk 87 optimal weight: 5.9990 chunk 315 optimal weight: 4.9990 chunk 132 optimal weight: 0.7980 chunk 323 optimal weight: 0.8980 chunk 39 optimal weight: 0.8980 chunk 58 optimal weight: 1.9990 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: J 477 GLN ** J1244 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J1279 GLN I1313 HIS ** L 362 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4006 r_free = 0.4006 target = 0.162633 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3555 r_free = 0.3555 target = 0.125341 restraints weight = 50284.637| |-----------------------------------------------------------------------------| r_work (start): 0.3520 rms_B_bonded: 2.43 r_work: 0.3217 rms_B_bonded: 3.16 restraints_weight: 0.5000 r_work (final): 0.3217 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8021 moved from start: 0.3919 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 33475 Z= 0.174 Angle : 0.583 13.169 45662 Z= 0.299 Chirality : 0.041 0.170 5240 Planarity : 0.004 0.070 5595 Dihedral : 16.470 158.296 5729 Min Nonbonded Distance : 2.005 Molprobity Statistics. All-atom Clashscore : 12.54 Ramachandran Plot: Outliers : 0.13 % Allowed : 6.58 % Favored : 93.29 % Rotamer: Outliers : 4.12 % Allowed : 28.13 % Favored : 67.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.25 % Cis-general : 0.21 % Twisted Proline : 0.00 % Twisted General : 0.05 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.82 (0.14), residues: 3876 helix: 0.86 (0.13), residues: 1568 sheet: -1.26 (0.24), residues: 453 loop : -1.62 (0.14), residues: 1855 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP L 434 HIS 0.009 0.001 HIS G 160 PHE 0.015 0.001 PHE N 52 TYR 0.018 0.001 TYR J 679 ARG 0.006 0.000 ARG G 143 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 8143.84 seconds wall clock time: 147 minutes 26.27 seconds (8846.27 seconds total)