Starting phenix.real_space_refine on Mon Feb 19 23:15:58 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ehf_28146/02_2024/8ehf_28146_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ehf_28146/02_2024/8ehf_28146.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.3 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ehf_28146/02_2024/8ehf_28146.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ehf_28146/02_2024/8ehf_28146.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ehf_28146/02_2024/8ehf_28146_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ehf_28146/02_2024/8ehf_28146_updated.pdb" } resolution = 3.3 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.007 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 7 Type Number sf(0) Gaussians Zn 2 6.06 5 P 62 5.49 5 Mg 1 5.21 5 S 106 5.16 5 C 16178 2.51 5 N 4612 2.21 5 O 5149 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "G GLU 32": "OE1" <-> "OE2" Residue "G GLU 72": "OE1" <-> "OE2" Residue "G GLU 204": "OE1" <-> "OE2" Residue "H GLU 17": "OE1" <-> "OE2" Residue "H GLU 32": "OE1" <-> "OE2" Residue "H GLU 97": "OE1" <-> "OE2" Residue "H GLU 181": "OE1" <-> "OE2" Residue "H GLU 204": "OE1" <-> "OE2" Residue "I GLU 84": "OE1" <-> "OE2" Residue "I GLU 126": "OE1" <-> "OE2" Residue "I GLU 218": "OE1" <-> "OE2" Residue "I GLU 278": "OE1" <-> "OE2" Residue "I GLU 379": "OE1" <-> "OE2" Residue "I GLU 386": "OE1" <-> "OE2" Residue "I GLU 477": "OE1" <-> "OE2" Residue "I GLU 504": "OE1" <-> "OE2" Residue "I GLU 541": "OE1" <-> "OE2" Residue "I GLU 641": "OE1" <-> "OE2" Residue "I GLU 705": "OE1" <-> "OE2" Residue "I GLU 778": "OE1" <-> "OE2" Residue "I GLU 949": "OE1" <-> "OE2" Residue "I GLU 963": "OE1" <-> "OE2" Residue "I GLU 968": "OE1" <-> "OE2" Residue "I GLU 1197": "OE1" <-> "OE2" Residue "I GLU 1289": "OE1" <-> "OE2" Residue "J GLU 69": "OE1" <-> "OE2" Residue "J GLU 171": "OE1" <-> "OE2" Residue "J GLU 199": "OE1" <-> "OE2" Residue "J GLU 225": "OE1" <-> "OE2" Residue "J GLU 414": "OE1" <-> "OE2" Residue "J GLU 443": "OE1" <-> "OE2" Residue "J GLU 497": "OE1" <-> "OE2" Residue "J GLU 663": "OE1" <-> "OE2" Residue "J GLU 811": "OE1" <-> "OE2" Residue "J GLU 818": "OE1" <-> "OE2" Residue "J GLU 874": "OE1" <-> "OE2" Residue "J GLU 1009": "OE1" <-> "OE2" Residue "J GLU 1293": "OE1" <-> "OE2" Residue "J GLU 1327": "OE1" <-> "OE2" Residue "J GLU 1334": "OE1" <-> "OE2" Residue "K GLU 53": "OE1" <-> "OE2" Time to flip residues: 0.08s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5238/modules/chem_data/mon_lib" Total number of atoms: 26110 Number of models: 1 Model: "" Number of chains: 10 Chain: "A" Number of atoms: 470 Number of conformers: 1 Conformer: "" Number of residues, atoms: 23, 470 Classifications: {'DNA': 23} Modifications used: {'5*END': 1} Link IDs: {'rna3p': 22} Chain breaks: 1 Chain: "B" Number of atoms: 608 Number of conformers: 1 Conformer: "" Number of residues, atoms: 30, 608 Classifications: {'DNA': 30} Link IDs: {'rna3p': 29} Chain: "R" Number of atoms: 214 Number of conformers: 1 Conformer: "" Number of residues, atoms: 10, 214 Classifications: {'RNA': 10} Modifications used: {'rna3p_pur': 5, 'rna3p_pyr': 5} Link IDs: {'rna3p': 9} Chain: "G" Number of atoms: 1679 Number of conformers: 1 Conformer: "" Number of residues, atoms: 218, 1679 Classifications: {'peptide': 218} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PCIS': 1, 'PTRANS': 8, 'TRANS': 208} Chain breaks: 1 Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 7 Unresolved non-hydrogen dihedrals: 5 Planarities with less than four sites: {'ARG:plan': 1} Unresolved non-hydrogen planarities: 5 Chain: "H" Number of atoms: 1698 Number of conformers: 1 Conformer: "" Number of residues, atoms: 220, 1698 Classifications: {'peptide': 220} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PCIS': 1, 'PTRANS': 7, 'TRANS': 211} Chain breaks: 1 Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 5 Unresolved non-hydrogen dihedrals: 3 Planarities with less than four sites: {'GLU:plan': 1} Unresolved non-hydrogen planarities: 4 Chain: "I" Number of atoms: 10381 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1316, 10381 Classifications: {'peptide': 1316} Link IDs: {'PCIS': 1, 'PTRANS': 54, 'TRANS': 1260} Chain breaks: 1 Chain: "J" Number of atoms: 10403 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1337, 10403 Classifications: {'peptide': 1337} Link IDs: {'PCIS': 1, 'PTRANS': 54, 'TRANS': 1281} Chain breaks: 2 Chain: "K" Number of atoms: 627 Number of conformers: 1 Conformer: "" Number of residues, atoms: 79, 627 Classifications: {'peptide': 79} Link IDs: {'PTRANS': 2, 'TRANS': 76} Chain: "I" Number of atoms: 27 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 27 Unusual residues: {'4QM': 1} Classifications: {'undetermined': 1} Chain: "J" Number of atoms: 3 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 3 Unusual residues: {' MG': 1, ' ZN': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 15499 SG CYS J 70 105.183 99.479 87.898 1.00 89.24 S ATOM 15513 SG CYS J 72 105.602 103.235 88.164 1.00 89.72 S ATOM 15621 SG CYS J 85 107.567 100.997 90.454 1.00 92.71 S ATOM 15645 SG CYS J 88 103.767 101.285 90.883 1.00 95.20 S ATOM 21333 SG CYS J 814 85.988 36.431 87.533 1.00 42.35 S ATOM 21898 SG CYS J 888 84.442 39.866 87.310 1.00 34.88 S ATOM 21949 SG CYS J 895 85.264 37.996 84.100 1.00 30.26 S ATOM 21970 SG CYS J 898 82.474 36.741 86.233 1.00 33.96 S Time building chain proxies: 15.44, per 1000 atoms: 0.59 Number of scatterers: 26110 At special positions: 0 Unit cell: (137.8, 156, 162.5, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 7 Type Number sf(0) Zn 2 29.99 S 106 16.00 P 62 15.00 Mg 1 11.99 O 5149 8.00 N 4612 7.00 C 16178 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: 10.89 Conformation dependent library (CDL) restraints added in 4.9 seconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN J1502 " pdb="ZN ZN J1502 " - pdb=" SG CYS J 72 " 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 J1503 " pdb="ZN ZN J1503 " - pdb=" SG CYS J 898 " pdb="ZN ZN J1503 " - pdb=" SG CYS J 814 " pdb="ZN ZN J1503 " - pdb=" SG CYS J 895 " pdb="ZN ZN J1503 " - pdb=" SG CYS J 888 " Number of angles added : 12 6300 Ramachandran restraints generated. 3150 Oldfield, 0 Emsley, 3150 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 5852 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 101 helices and 33 sheets defined 32.0% alpha, 12.3% beta 26 base pairs and 47 stacking pairs defined. Time for finding SS restraints: 13.23 Creating SS restraints... Processing helix chain 'G' and resid 36 through 49 Processing helix chain 'G' and resid 78 through 86 Processing helix chain 'G' and resid 112 through 114 No H-bonds generated for 'chain 'G' and resid 112 through 114' Processing helix chain 'G' and resid 213 through 230 removed outlier: 4.495A pdb=" N ALA G 230 " --> pdb=" O GLU G 226 " (cutoff:3.500A) Processing helix chain 'H' and resid 35 through 49 removed outlier: 3.588A pdb=" N SER H 49 " --> pdb=" O ARG H 45 " (cutoff:3.500A) Processing helix chain 'H' and resid 78 through 86 removed outlier: 3.566A pdb=" N LEU H 83 " --> pdb=" O LEU H 79 " (cutoff:3.500A) Processing helix chain 'H' and resid 112 through 114 No H-bonds generated for 'chain 'H' and resid 112 through 114' Processing helix chain 'H' and resid 213 through 229 removed outlier: 4.029A pdb=" N ARG H 218 " --> pdb=" O GLU H 214 " (cutoff:3.500A) removed outlier: 3.512A pdb=" N LEU H 228 " --> pdb=" O LEU H 224 " (cutoff:3.500A) removed outlier: 3.825A pdb=" N GLU H 229 " --> pdb=" O ALA H 225 " (cutoff:3.500A) Processing helix chain 'I' and resid 29 through 39 Processing helix chain 'I' and resid 43 through 45 No H-bonds generated for 'chain 'I' and resid 43 through 45' Processing helix chain 'I' and resid 49 through 56 Processing helix chain 'I' and resid 82 through 88 Processing helix chain 'I' and resid 206 through 212 Processing helix chain 'I' and resid 217 through 224 Processing helix chain 'I' and resid 243 through 246 Processing helix chain 'I' and resid 271 through 280 Processing helix chain 'I' and resid 289 through 294 removed outlier: 3.533A pdb=" N ILE I 292 " --> pdb=" O VAL I 289 " (cutoff:3.500A) removed outlier: 3.790A pdb=" N GLY I 294 " --> pdb=" O TYR I 291 " (cutoff:3.500A) Processing helix chain 'I' and resid 319 through 328 removed outlier: 3.746A pdb=" N SER I 328 " --> pdb=" O LYS I 324 " (cutoff:3.500A) Processing helix chain 'I' and resid 346 through 353 Processing helix chain 'I' and resid 359 through 370 Processing helix chain 'I' and resid 378 through 389 removed outlier: 4.159A pdb=" N PHE I 389 " --> pdb=" O PHE I 385 " (cutoff:3.500A) Processing helix chain 'I' and resid 399 through 408 Processing helix chain 'I' and resid 422 through 437 Processing helix chain 'I' and resid 456 through 481 removed outlier: 3.947A pdb=" N GLU I 461 " --> pdb=" O GLY I 457 " (cutoff:3.500A) removed outlier: 3.647A pdb=" N SER I 480 " --> pdb=" O LYS I 476 " (cutoff:3.500A) removed outlier: 4.143A pdb=" N LEU I 481 " --> pdb=" O GLU I 477 " (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 545 through 548 No H-bonds generated for 'chain 'I' and resid 545 through 548' Processing helix chain 'I' and resid 552 through 554 No H-bonds generated for 'chain 'I' and resid 552 through 554' Processing helix chain 'I' and resid 647 through 649 No H-bonds generated for 'chain 'I' and resid 647 through 649' Processing helix chain 'I' and resid 665 through 667 No H-bonds generated for 'chain 'I' and resid 665 through 667' 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 687 Processing helix chain 'I' and resid 705 through 711 removed outlier: 3.763A pdb=" N VAL I 710 " --> pdb=" O ARG I 706 " (cutoff:3.500A) Processing helix chain 'I' and resid 820 through 824 Processing helix chain 'I' and resid 859 through 862 No H-bonds generated for 'chain 'I' and resid 859 through 862' Processing helix chain 'I' and resid 943 through 947 Processing helix chain 'I' and resid 950 through 979 removed outlier: 3.687A pdb=" N GLU I 962 " --> pdb=" O LYS I 958 " (cutoff:3.500A) Processing helix chain 'I' and resid 1006 through 1036 Processing helix chain 'I' and resid 1082 through 1084 No H-bonds generated for 'chain 'I' and resid 1082 through 1084' Processing helix chain 'I' and resid 1100 through 1104 Proline residue: I1104 - end of helix Processing helix chain 'I' and resid 1110 through 1133 Processing helix chain 'I' and resid 1138 through 1149 Processing helix chain 'I' and resid 1161 through 1163 No H-bonds generated for 'chain 'I' and resid 1161 through 1163' Processing helix chain 'I' and resid 1168 through 1175 Processing helix chain 'I' and resid 1192 through 1201 Processing helix chain 'I' and resid 1272 through 1281 removed outlier: 3.515A pdb=" N TRP I1276 " --> pdb=" O GLU I1272 " (cutoff:3.500A) Processing helix chain 'I' and resid 1284 through 1291 Processing helix chain 'I' and resid 1299 through 1310 removed outlier: 3.915A pdb=" N LYS I1303 " --> pdb=" O ASN I1299 " (cutoff:3.500A) removed outlier: 3.730A pdb=" N MET I1304 " --> pdb=" O GLY I1300 " (cutoff:3.500A) Processing helix chain 'I' and resid 1321 through 1331 Processing helix chain 'J' and resid 27 through 33 Processing helix chain 'J' and resid 78 through 80 No H-bonds generated for 'chain 'J' and resid 78 through 80' Processing helix chain 'J' and resid 95 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 127 Processing helix chain 'J' and resid 132 through 139 Processing helix chain 'J' and resid 162 through 172 Processing helix chain 'J' and resid 181 through 191 removed outlier: 3.531A pdb=" N ILE J 185 " --> pdb=" O GLY J 181 " (cutoff:3.500A) Processing helix chain 'J' and resid 194 through 207 Processing helix chain 'J' and resid 211 through 229 Processing helix chain 'J' and resid 234 through 237 removed outlier: 3.666A pdb=" N MET J 237 " --> pdb=" O PRO J 234 " (cutoff:3.500A) No H-bonds generated for 'chain 'J' and resid 234 through 237' Processing helix chain 'J' and resid 247 through 249 No H-bonds generated for 'chain 'J' and resid 247 through 249' Processing helix chain 'J' and resid 264 through 284 Processing helix chain 'J' and resid 289 through 307 Processing helix chain 'J' and resid 338 through 341 No H-bonds generated for 'chain 'J' and resid 338 through 341' Processing helix chain 'J' and resid 370 through 376 removed outlier: 3.761A pdb=" N LEU J 374 " --> pdb=" O LYS J 370 " (cutoff:3.500A) removed outlier: 4.106A pdb=" N GLU J 375 " --> pdb=" O LYS J 371 " (cutoff:3.500A) Processing helix chain 'J' and resid 378 through 385 Processing helix chain 'J' and resid 394 through 403 Processing helix chain 'J' and resid 408 through 415 Processing helix chain 'J' and resid 431 through 433 No H-bonds generated for 'chain 'J' and resid 431 through 433' Processing helix chain 'J' and resid 451 through 457 removed outlier: 4.229A pdb=" N ALA J 455 " --> pdb=" O LEU J 452 " (cutoff:3.500A) Processing helix chain 'J' and resid 474 through 482 Processing helix chain 'J' and resid 486 through 488 No H-bonds generated for 'chain 'J' and resid 486 through 488' Processing helix chain 'J' and resid 506 through 513 Processing helix chain 'J' and resid 530 through 538 Processing helix chain 'J' and resid 574 through 581 removed outlier: 3.505A pdb=" N TRP J 580 " --> pdb=" O ARG J 576 " (cutoff:3.500A) removed outlier: 4.002A pdb=" N MET J 581 " --> pdb=" O ALA J 577 " (cutoff:3.500A) Processing helix chain 'J' and resid 598 through 612 Processing helix chain 'J' and resid 615 through 633 removed outlier: 3.692A pdb=" N ASP J 622 " --> pdb=" O VAL J 618 " (cutoff:3.500A) removed outlier: 3.630A pdb=" N TYR J 631 " --> pdb=" O THR J 627 " (cutoff:3.500A) Processing helix chain 'J' and resid 650 through 669 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 741 Processing helix chain 'J' and resid 769 through 803 removed outlier: 3.939A pdb=" N HIS J 777 " --> pdb=" O PHE J 773 " (cutoff:3.500A) removed outlier: 4.447A pdb=" N GLY J 778 " --> pdb=" O ILE J 774 " (cutoff:3.500A) removed outlier: 3.534A pdb=" N GLY J 782 " --> pdb=" O GLY J 778 " (cutoff:3.500A) removed outlier: 3.891A pdb=" N THR J 786 " --> pdb=" O GLY J 782 " (cutoff:3.500A) removed outlier: 3.798A pdb=" N THR J 790 " --> pdb=" O THR J 786 " (cutoff:3.500A) removed outlier: 4.690A pdb=" N ALA J 791 " --> pdb=" O ALA J 787 " (cutoff:3.500A) removed outlier: 3.806A pdb=" N ASN J 792 " --> pdb=" O LEU J 788 " (cutoff:3.500A) removed outlier: 3.853A pdb=" N TYR J 795 " --> pdb=" O ALA J 791 " (cutoff:3.500A) Processing helix chain 'J' and resid 835 through 839 Processing helix chain 'J' and resid 866 through 874 Processing helix chain 'J' and resid 885 through 887 No H-bonds generated for 'chain 'J' and resid 885 through 887' Processing helix chain 'J' and resid 915 through 928 Proline residue: J 926 - end of helix Processing helix chain 'J' and resid 1069 through 1071 No H-bonds generated for 'chain 'J' and resid 1069 through 1071' Processing helix chain 'J' and resid 1138 through 1146 Processing helix chain 'J' and resid 1219 through 1224 Processing helix chain 'J' and resid 1226 through 1244 removed outlier: 3.926A pdb=" N GLN J1244 " --> pdb=" O VAL J1240 " (cutoff:3.500A) Processing helix chain 'J' and resid 1250 through 1260 Processing helix chain 'J' and resid 1282 through 1294 Processing helix chain 'J' and resid 1311 through 1314 No H-bonds generated for 'chain 'J' and resid 1311 through 1314' Processing helix chain 'J' and resid 1319 through 1325 Processing helix chain 'J' and resid 1328 through 1338 removed outlier: 3.777A pdb=" N GLU J1334 " --> pdb=" O ARG J1330 " (cutoff:3.500A) Processing helix chain 'J' and resid 1348 through 1353 Processing helix chain 'J' and resid 1361 through 1371 Processing helix chain 'K' and resid 7 through 12 Processing helix chain 'K' and resid 18 through 31 Processing helix chain 'K' and resid 46 through 56 Processing helix chain 'K' and resid 61 through 79 Processing sheet with id= A, first strand: chain 'G' and resid 12 through 17 removed outlier: 6.839A pdb=" N THR G 27 " --> pdb=" O VAL G 14 " (cutoff:3.500A) removed outlier: 4.299A pdb=" N ILE G 16 " --> pdb=" O LYS G 25 " (cutoff:3.500A) removed outlier: 6.217A pdb=" N LYS G 25 " --> pdb=" O ILE G 16 " (cutoff:3.500A) Processing sheet with id= B, first strand: chain 'G' and resid 97 through 105 removed outlier: 3.642A pdb=" N GLU G 58 " --> pdb=" O LYS G 145 " (cutoff:3.500A) removed outlier: 6.197A pdb=" N GLN G 147 " --> pdb=" O VAL G 56 " (cutoff:3.500A) removed outlier: 5.264A pdb=" N VAL G 56 " --> pdb=" O GLN G 147 " (cutoff:3.500A) removed outlier: 6.673A pdb=" N GLY G 149 " --> pdb=" O CYS G 54 " (cutoff:3.500A) removed outlier: 5.679A pdb=" N CYS G 54 " --> pdb=" O GLY G 149 " (cutoff:3.500A) Processing sheet with id= C, first strand: chain 'G' and resid 151 through 153 removed outlier: 3.510A pdb=" N ALA G 175 " --> pdb=" O VAL G 153 " (cutoff:3.500A) Processing sheet with id= D, first strand: chain 'G' and resid 108 through 111 removed outlier: 3.871A pdb=" N CYS G 131 " --> pdb=" O VAL G 110 " (cutoff:3.500A) Processing sheet with id= E, first strand: chain 'H' and resid 12 through 19 removed outlier: 3.589A pdb=" N ARG H 12 " --> pdb=" O GLU H 29 " (cutoff:3.500A) removed outlier: 3.512A pdb=" N GLU H 29 " --> pdb=" O ARG H 12 " (cutoff:3.500A) removed outlier: 6.676A pdb=" N THR H 27 " --> pdb=" O VAL H 14 " (cutoff:3.500A) removed outlier: 4.231A pdb=" N ILE H 16 " --> pdb=" O LYS H 25 " (cutoff:3.500A) removed outlier: 4.658A pdb=" N LYS H 25 " --> pdb=" O ILE H 16 " (cutoff:3.500A) removed outlier: 5.389A pdb=" N GLN H 18 " --> pdb=" O HIS H 23 " (cutoff:3.500A) removed outlier: 7.219A pdb=" N HIS H 23 " --> pdb=" O GLN H 18 " (cutoff:3.500A) removed outlier: 3.606A pdb=" N ALA H 190 " --> pdb=" O LEU H 198 " (cutoff:3.500A) Processing sheet with id= F, first strand: chain 'H' and resid 97 through 101 removed outlier: 6.198A pdb=" N GLN H 147 " --> pdb=" O VAL H 56 " (cutoff:3.500A) removed outlier: 5.486A pdb=" N VAL H 56 " --> pdb=" O GLN H 147 " (cutoff:3.500A) removed outlier: 6.949A pdb=" N GLY H 149 " --> pdb=" O CYS H 54 " (cutoff:3.500A) removed outlier: 5.296A pdb=" N CYS H 54 " --> pdb=" O GLY H 149 " (cutoff:3.500A) Processing sheet with id= G, first strand: chain 'H' and resid 108 through 111 removed outlier: 3.607A pdb=" N CYS H 131 " --> pdb=" O VAL H 110 " (cutoff:3.500A) Processing sheet with id= H, first strand: chain 'I' and resid 93 through 95 Processing sheet with id= I, first strand: chain 'I' and resid 143 through 145 Processing sheet with id= J, first strand: chain 'I' and resid 148 through 151 Processing sheet with id= K, first strand: chain 'I' and resid 154 through 158 Processing sheet with id= L, first strand: chain 'I' and resid 184 through 187 Processing sheet with id= M, first strand: chain 'I' and resid 227 through 231 Processing sheet with id= N, first strand: chain 'I' and resid 603 through 606 Processing sheet with id= O, first strand: chain 'I' and resid 633 through 637 Processing sheet with id= P, first strand: chain 'I' and resid 749 through 752 removed outlier: 3.676A pdb=" N TYR I 726 " --> pdb=" O VAL I 733 " (cutoff:3.500A) removed outlier: 5.969A pdb=" N LYS I 735 " --> pdb=" O VAL I 724 " (cutoff:3.500A) removed outlier: 5.541A pdb=" N VAL I 724 " --> pdb=" O LYS I 735 " (cutoff:3.500A) Processing sheet with id= Q, first strand: chain 'I' and resid 1226 through 1232 removed outlier: 4.383A pdb=" N THR I1226 " --> pdb=" O PHE I 804 " (cutoff:3.500A) removed outlier: 6.601A pdb=" N ILE I1096 " --> pdb=" O ALA I 803 " (cutoff:3.500A) Processing sheet with id= R, first strand: chain 'I' and resid 66 through 75 removed outlier: 6.853A pdb=" N LYS I 99 " --> pdb=" O VAL I 71 " (cutoff:3.500A) removed outlier: 4.810A pdb=" N TYR I 73 " --> pdb=" O ARG I 97 " (cutoff:3.500A) removed outlier: 6.928A pdb=" N ARG I 97 " --> pdb=" O TYR I 73 " (cutoff:3.500A) removed outlier: 3.721A pdb=" N ASP I 116 " --> pdb=" O ILE I 104 " (cutoff:3.500A) Processing sheet with id= S, first strand: chain 'I' and resid 255 through 257 removed outlier: 6.496A pdb=" N ALA I 257 " --> pdb=" O VAL I 261 " (cutoff:3.500A) removed outlier: 5.100A pdb=" N VAL I 261 " --> pdb=" O ALA I 257 " (cutoff:3.500A) Processing sheet with id= T, first strand: chain 'I' and resid 816 through 819 removed outlier: 7.613A pdb=" N VAL I 818 " --> pdb=" O SER I1077 " (cutoff:3.500A) removed outlier: 4.166A pdb=" N ILE I1079 " --> pdb=" O VAL I 818 " (cutoff:3.500A) Processing sheet with id= U, first strand: chain 'I' and resid 830 through 841 removed outlier: 3.583A pdb=" N LYS I1048 " --> pdb=" O SER I 840 " (cutoff:3.500A) removed outlier: 3.927A pdb=" N ASP I 930 " --> pdb=" O TYR I1053 " (cutoff:3.500A) removed outlier: 6.630A pdb=" N ALA I1055 " --> pdb=" O VAL I 928 " (cutoff:3.500A) removed outlier: 5.701A pdb=" N VAL I 928 " --> pdb=" O ALA I1055 " (cutoff:3.500A) Processing sheet with id= V, first strand: chain 'J' and resid 103 through 106 removed outlier: 3.720A pdb=" N GLY J 103 " --> pdb=" O VAL J 244 " (cutoff:3.500A) Processing sheet with id= W, first strand: chain 'J' and resid 145 through 147 removed outlier: 3.667A pdb=" N ILE J 147 " --> pdb=" O ASP J 177 " (cutoff:3.500A) removed outlier: 4.394A pdb=" N ASP J 177 " --> pdb=" O ILE J 147 " (cutoff:3.500A) Processing sheet with id= X, first strand: chain 'J' and resid 350 through 354 Processing sheet with id= Y, first strand: chain 'J' and resid 548 through 556 Processing sheet with id= Z, first strand: chain 'J' and resid 820 through 822 Processing sheet with id= AA, first strand: chain 'J' and resid 957 through 961 removed outlier: 3.683A pdb=" N GLU J 981 " --> pdb=" O SER J 961 " (cutoff:3.500A) Processing sheet with id= AB, first strand: chain 'J' and resid 965 through 967 Processing sheet with id= AC, first strand: chain 'J' and resid 1034 through 1038 removed outlier: 3.631A pdb=" N LYS J1079 " --> pdb=" O ARG J1036 " (cutoff:3.500A) Processing sheet with id= AD, first strand: chain 'J' and resid 1046 through 1048 removed outlier: 4.268A pdb=" N VAL J1060 " --> pdb=" O THR J1047 " (cutoff:3.500A) Processing sheet with id= AE, first strand: chain 'J' and resid 1162 through 1165 Processing sheet with id= AF, first strand: chain 'J' and resid 1279 through 1281 removed outlier: 7.030A pdb=" N THR J1301 " --> pdb=" O VAL J1267 " (cutoff:3.500A) Processing sheet with id= AG, first strand: chain 'J' and resid 949 through 952 removed outlier: 3.791A pdb=" N ALA J1018 " --> pdb=" O ILE J 950 " (cutoff:3.500A) removed outlier: 6.316A pdb=" N VAL J 952 " --> pdb=" O THR J1016 " (cutoff:3.500A) removed outlier: 5.942A pdb=" N THR J1016 " --> pdb=" O VAL J 952 " (cutoff:3.500A) 791 hydrogen bonds defined for protein. 2277 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 65 hydrogen bonds 130 hydrogen bond angles 0 basepair planarities 26 basepair parallelities 47 stacking parallelities Total time for adding SS restraints: 10.44 Time building geometry restraints manager: 11.61 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.03 - 1.19: 17 1.19 - 1.35: 8784 1.35 - 1.51: 7219 1.51 - 1.66: 10419 1.66 - 1.82: 187 Bond restraints: 26626 Sorted by residual: bond pdb=" C VAL J 803 " pdb=" O VAL J 803 " ideal model delta sigma weight residual 1.236 1.070 0.167 9.70e-03 1.06e+04 2.96e+02 bond pdb=" C VAL J 808 " pdb=" O VAL J 808 " ideal model delta sigma weight residual 1.234 1.051 0.183 1.11e-02 8.12e+03 2.72e+02 bond pdb=" CA GLN J 805 " pdb=" C GLN J 805 " ideal model delta sigma weight residual 1.522 1.302 0.220 1.36e-02 5.41e+03 2.62e+02 bond pdb=" C ALA J 804 " pdb=" O ALA J 804 " ideal model delta sigma weight residual 1.236 1.035 0.202 1.33e-02 5.65e+03 2.30e+02 bond pdb=" C GLN J 805 " pdb=" O GLN J 805 " ideal model delta sigma weight residual 1.236 1.055 0.182 1.25e-02 6.40e+03 2.12e+02 ... (remaining 26621 not shown) Histogram of bond angle deviations from ideal: 92.89 - 101.12: 106 101.12 - 109.35: 2820 109.35 - 117.58: 17188 117.58 - 125.80: 15678 125.80 - 134.03: 443 Bond angle restraints: 36235 Sorted by residual: angle pdb=" C ARG I 18 " pdb=" N PRO I 19 " pdb=" CA PRO I 19 " ideal model delta sigma weight residual 119.76 132.27 -12.51 1.03e+00 9.43e-01 1.48e+02 angle pdb=" CA PRO I 19 " pdb=" C PRO I 19 " pdb=" O PRO I 19 " ideal model delta sigma weight residual 121.34 110.24 11.10 1.14e+00 7.69e-01 9.49e+01 angle pdb=" N VAL J 803 " pdb=" CA VAL J 803 " pdb=" CB VAL J 803 " ideal model delta sigma weight residual 110.64 122.17 -11.53 1.20e+00 6.94e-01 9.23e+01 angle pdb=" CG1 VAL J 803 " pdb=" CB VAL J 803 " pdb=" CG2 VAL J 803 " ideal model delta sigma weight residual 110.80 92.89 17.91 2.20e+00 2.07e-01 6.62e+01 angle pdb=" CA VAL J 808 " pdb=" C VAL J 808 " pdb=" N VAL J 809 " ideal model delta sigma weight residual 115.96 127.27 -11.31 1.43e+00 4.89e-01 6.25e+01 ... (remaining 36230 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 27.93: 15441 27.93 - 55.86: 759 55.86 - 83.80: 112 83.80 - 111.73: 11 111.73 - 139.66: 2 Dihedral angle restraints: 16325 sinusoidal: 7228 harmonic: 9097 Sorted by residual: dihedral pdb=" N VAL J 803 " pdb=" C VAL J 803 " pdb=" CA VAL J 803 " pdb=" CB VAL J 803 " ideal model delta harmonic sigma weight residual 123.40 137.61 -14.21 0 2.50e+00 1.60e-01 3.23e+01 dihedral pdb=" CA GLY J 852 " pdb=" C GLY J 852 " pdb=" N THR J 853 " pdb=" CA THR J 853 " ideal model delta harmonic sigma weight residual 180.00 -152.49 -27.51 0 5.00e+00 4.00e-02 3.03e+01 dihedral pdb=" CA SER J 503 " pdb=" C SER J 503 " pdb=" N GLN J 504 " pdb=" CA GLN J 504 " ideal model delta harmonic sigma weight residual 180.00 153.57 26.43 0 5.00e+00 4.00e-02 2.79e+01 ... (remaining 16322 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.179: 4134 0.179 - 0.359: 9 0.359 - 0.538: 3 0.538 - 0.718: 6 0.718 - 0.897: 1 Chirality restraints: 4153 Sorted by residual: chirality pdb=" CA GLN J 805 " pdb=" N GLN J 805 " pdb=" C GLN J 805 " pdb=" CB GLN J 805 " both_signs ideal model delta sigma weight residual False 2.51 1.61 0.90 2.00e-01 2.50e+01 2.01e+01 chirality pdb=" CA VAL J 803 " pdb=" N VAL J 803 " pdb=" C VAL J 803 " pdb=" CB VAL J 803 " both_signs ideal model delta sigma weight residual False 2.44 1.74 0.70 2.00e-01 2.50e+01 1.22e+01 chirality pdb=" CA ASP J 806 " pdb=" N ASP J 806 " pdb=" C ASP J 806 " pdb=" CB ASP J 806 " both_signs ideal model delta sigma weight residual False 2.51 1.83 0.68 2.00e-01 2.50e+01 1.16e+01 ... (remaining 4150 not shown) Planarity restraints: 4520 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ARG I 18 " 0.079 5.00e-02 4.00e+02 1.17e-01 2.18e+01 pdb=" N PRO I 19 " -0.202 5.00e-02 4.00e+02 pdb=" CA PRO I 19 " 0.072 5.00e-02 4.00e+02 pdb=" CD PRO I 19 " 0.051 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA VAL J 803 " 0.020 2.00e-02 2.50e+03 4.12e-02 1.70e+01 pdb=" C VAL J 803 " -0.071 2.00e-02 2.50e+03 pdb=" O VAL J 803 " 0.027 2.00e-02 2.50e+03 pdb=" N ALA J 804 " 0.024 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA THR J 810 " 0.021 2.00e-02 2.50e+03 4.10e-02 1.68e+01 pdb=" C THR J 810 " -0.071 2.00e-02 2.50e+03 pdb=" O THR J 810 " 0.026 2.00e-02 2.50e+03 pdb=" N GLU J 811 " 0.024 2.00e-02 2.50e+03 ... (remaining 4517 not shown) Histogram of nonbonded interaction distances: 2.04 - 2.61: 298 2.61 - 3.18: 21902 3.18 - 3.75: 40563 3.75 - 4.33: 56503 4.33 - 4.90: 94367 Nonbonded interactions: 213633 Sorted by model distance: nonbonded pdb=" OD1 ASP J 462 " pdb="MG MG J1501 " model vdw 2.037 2.170 nonbonded pdb=" OD1 ASP J 460 " pdb="MG MG J1501 " model vdw 2.129 2.170 nonbonded pdb=" NH2 ARG I1223 " pdb=" O PHE J 719 " model vdw 2.218 2.520 nonbonded pdb=" OD1 ASN J1268 " pdb=" OG1 THR J1301 " model vdw 2.224 2.440 nonbonded pdb=" O TYR I 810 " pdb=" OG SER I1077 " model vdw 2.232 2.440 ... (remaining 213628 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = (chain 'G' and (resid 8 through 135 or (resid 136 and (name N or name CA or name \ C or name O or name CB )) or resid 137 through 158 or resid 170 through 231)) selection = (chain 'H' and (resid 8 through 190 or (resid 191 and (name N or name CA or name \ C or name O or name CB )) or resid 192 through 231)) } 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: 0.990 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: 5.380 Check model and map are aligned: 0.410 Set scattering table: 0.270 Process input model: 83.460 Find NCS groups from input model: 1.020 Set up NCS constraints: 0.090 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.840 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 94.490 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8065 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 : 0.009 0.287 26626 Z= 0.559 Angle : 0.765 18.513 36235 Z= 0.443 Chirality : 0.055 0.897 4153 Planarity : 0.005 0.117 4520 Dihedral : 15.973 139.662 10473 Min Nonbonded Distance : 2.037 Molprobity Statistics. All-atom Clashscore : 7.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.41 % Favored : 93.59 % Rotamer: Outliers : 3.82 % Allowed : 10.01 % Favored : 86.17 % Cbeta Deviations : 0.21 % Peptide Plane: Cis-proline : 3.10 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.52 (0.14), residues: 3150 helix: 0.08 (0.16), residues: 1073 sheet: -1.05 (0.26), residues: 376 loop : -1.75 (0.14), residues: 1701 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP J 409 HIS 0.006 0.001 HIS G 23 PHE 0.022 0.002 PHE I 15 TYR 0.020 0.001 TYR G 177 ARG 0.008 0.000 ARG I 18 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6300 Ramachandran restraints generated. 3150 Oldfield, 0 Emsley, 3150 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6300 Ramachandran restraints generated. 3150 Oldfield, 0 Emsley, 3150 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 507 residues out of total 2699 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 103 poor density : 404 time to evaluate : 3.009 Fit side-chains REVERT: H 17 GLU cc_start: 0.7606 (tm-30) cc_final: 0.7391 (tt0) REVERT: H 103 ASN cc_start: 0.8165 (m-40) cc_final: 0.7849 (p0) REVERT: H 145 LYS cc_start: 0.8807 (tttm) cc_final: 0.8592 (tttm) REVERT: I 33 ASP cc_start: 0.7659 (m-30) cc_final: 0.7430 (m-30) REVERT: I 70 TYR cc_start: 0.8516 (t80) cc_final: 0.8300 (t80) REVERT: I 191 LYS cc_start: 0.8672 (mptt) cc_final: 0.8287 (mtmt) REVERT: I 214 ASN cc_start: 0.8296 (t0) cc_final: 0.8029 (t0) REVERT: I 370 MET cc_start: 0.9031 (mmm) cc_final: 0.8714 (mmm) REVERT: I 470 ARG cc_start: 0.7997 (mtt180) cc_final: 0.7666 (mtt180) REVERT: I 490 GLN cc_start: 0.7768 (tm-30) cc_final: 0.7486 (tp-100) REVERT: I 518 ASN cc_start: 0.8429 (OUTLIER) cc_final: 0.7843 (p0) REVERT: I 524 ILE cc_start: 0.8968 (tp) cc_final: 0.8496 (tp) REVERT: I 538 LEU cc_start: 0.9257 (OUTLIER) cc_final: 0.8926 (pt) REVERT: I 681 MET cc_start: 0.8418 (mtt) cc_final: 0.8078 (mtp) REVERT: I 850 ILE cc_start: 0.8700 (OUTLIER) cc_final: 0.8426 (mm) REVERT: I 1085 MET cc_start: 0.9111 (OUTLIER) cc_final: 0.8783 (mmm) REVERT: I 1119 MET cc_start: 0.8042 (tpt) cc_final: 0.7309 (ttt) REVERT: I 1154 ASP cc_start: 0.7727 (p0) cc_final: 0.6801 (p0) REVERT: I 1170 MET cc_start: 0.8761 (mmt) cc_final: 0.8408 (mmt) REVERT: I 1188 ASP cc_start: 0.8405 (t0) cc_final: 0.8010 (t0) REVERT: I 1273 MET cc_start: 0.8918 (mtp) cc_final: 0.8660 (mtp) REVERT: I 1310 ASP cc_start: 0.7201 (t0) cc_final: 0.6816 (t0) REVERT: J 765 GLU cc_start: 0.8309 (OUTLIER) cc_final: 0.7238 (pp20) REVERT: J 847 ASP cc_start: 0.8227 (OUTLIER) cc_final: 0.7900 (p0) REVERT: J 889 ASP cc_start: 0.8190 (OUTLIER) cc_final: 0.7855 (m-30) REVERT: J 895 CYS cc_start: 0.8028 (OUTLIER) cc_final: 0.7792 (p) REVERT: J 954 ASN cc_start: 0.6745 (m-40) cc_final: 0.6513 (m-40) REVERT: J 996 LYS cc_start: 0.8031 (tptt) cc_final: 0.7750 (mptt) REVERT: J 999 TYR cc_start: 0.6739 (t80) cc_final: 0.6531 (t80) REVERT: J 1025 MET cc_start: 0.5698 (mtm) cc_final: 0.5295 (mtm) REVERT: J 1189 MET cc_start: 0.7233 (mmt) cc_final: 0.6877 (tmm) REVERT: K 35 LYS cc_start: 0.8389 (mmtp) cc_final: 0.8131 (mptt) outliers start: 103 outliers final: 55 residues processed: 490 average time/residue: 0.3834 time to fit residues: 294.4939 Evaluate side-chains 397 residues out of total 2699 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 63 poor density : 334 time to evaluate : 2.922 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 19 VAL Chi-restraints excluded: chain G residue 23 HIS Chi-restraints excluded: chain H residue 19 VAL Chi-restraints excluded: chain H residue 28 LEU Chi-restraints excluded: chain H residue 90 VAL Chi-restraints excluded: chain H residue 100 LEU Chi-restraints excluded: chain H residue 146 VAL Chi-restraints excluded: chain H residue 188 GLU Chi-restraints excluded: chain H residue 198 LEU Chi-restraints excluded: chain I residue 11 ILE Chi-restraints excluded: chain I residue 17 LYS Chi-restraints excluded: chain I residue 28 LEU Chi-restraints excluded: chain I residue 81 ASP Chi-restraints excluded: chain I residue 122 VAL Chi-restraints excluded: chain I residue 127 ILE Chi-restraints excluded: chain I residue 221 LEU Chi-restraints excluded: chain I residue 228 VAL Chi-restraints excluded: chain I residue 287 VAL Chi-restraints excluded: chain I residue 377 THR Chi-restraints excluded: chain I residue 518 ASN Chi-restraints excluded: chain I residue 538 LEU Chi-restraints excluded: chain I residue 539 THR Chi-restraints excluded: chain I residue 550 VAL Chi-restraints excluded: chain I residue 615 VAL Chi-restraints excluded: chain I residue 635 THR Chi-restraints excluded: chain I residue 663 VAL Chi-restraints excluded: chain I residue 697 LYS Chi-restraints excluded: chain I residue 850 ILE Chi-restraints excluded: chain I residue 924 VAL Chi-restraints excluded: chain I residue 964 LEU Chi-restraints excluded: chain I residue 1056 VAL Chi-restraints excluded: chain I residue 1085 MET Chi-restraints excluded: chain I residue 1159 VAL Chi-restraints excluded: chain I residue 1225 VAL Chi-restraints excluded: chain I residue 1240 ASP Chi-restraints excluded: chain I residue 1254 VAL Chi-restraints excluded: chain I residue 1295 SER Chi-restraints excluded: chain I residue 1298 VAL Chi-restraints excluded: chain J residue 139 LEU Chi-restraints excluded: chain J residue 176 PHE Chi-restraints excluded: chain J residue 347 VAL Chi-restraints excluded: chain J residue 354 VAL Chi-restraints excluded: chain J residue 357 VAL Chi-restraints excluded: chain J residue 430 HIS Chi-restraints excluded: chain J residue 468 VAL Chi-restraints excluded: chain J residue 501 VAL Chi-restraints excluded: chain J residue 507 VAL Chi-restraints excluded: chain J residue 706 VAL Chi-restraints excluded: chain J residue 708 ASN Chi-restraints excluded: chain J residue 757 THR Chi-restraints excluded: chain J residue 765 GLU Chi-restraints excluded: chain J residue 805 GLN Chi-restraints excluded: chain J residue 825 VAL Chi-restraints excluded: chain J residue 826 ILE Chi-restraints excluded: chain J residue 831 VAL Chi-restraints excluded: chain J residue 847 ASP Chi-restraints excluded: chain J residue 857 LEU Chi-restraints excluded: chain J residue 889 ASP Chi-restraints excluded: chain J residue 895 CYS Chi-restraints excluded: chain J residue 967 VAL Chi-restraints excluded: chain J residue 1146 GLU Chi-restraints excluded: chain K residue 59 ILE Chi-restraints excluded: chain K residue 66 VAL Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 320 random chunks: chunk 270 optimal weight: 0.7980 chunk 242 optimal weight: 3.9990 chunk 134 optimal weight: 1.9990 chunk 82 optimal weight: 10.0000 chunk 163 optimal weight: 0.9990 chunk 129 optimal weight: 0.9990 chunk 250 optimal weight: 2.9990 chunk 97 optimal weight: 0.1980 chunk 152 optimal weight: 2.9990 chunk 186 optimal weight: 9.9990 chunk 290 optimal weight: 1.9990 overall best weight: 0.9986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: I 41 GLN ** I 618 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 955 GLN J 94 GLN J 229 GLN J 489 ASN J 805 GLN J1218 HIS Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8026 moved from start: 0.0713 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 26626 Z= 0.195 Angle : 0.535 8.121 36235 Z= 0.281 Chirality : 0.041 0.179 4153 Planarity : 0.004 0.059 4520 Dihedral : 15.017 140.071 4381 Min Nonbonded Distance : 1.985 Molprobity Statistics. All-atom Clashscore : 8.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.68 % Favored : 94.32 % Rotamer: Outliers : 4.00 % Allowed : 13.39 % Favored : 82.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.10 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.11 (0.15), residues: 3150 helix: 0.53 (0.16), residues: 1079 sheet: -0.72 (0.27), residues: 366 loop : -1.62 (0.14), residues: 1705 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP I1276 HIS 0.004 0.001 HIS G 23 PHE 0.024 0.001 PHE I 337 TYR 0.014 0.001 TYR G 177 ARG 0.008 0.000 ARG I 368 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6300 Ramachandran restraints generated. 3150 Oldfield, 0 Emsley, 3150 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6300 Ramachandran restraints generated. 3150 Oldfield, 0 Emsley, 3150 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 473 residues out of total 2699 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 108 poor density : 365 time to evaluate : 3.043 Fit side-chains REVERT: G 18 GLN cc_start: 0.8436 (mm-40) cc_final: 0.8049 (mm-40) REVERT: H 17 GLU cc_start: 0.7733 (tm-30) cc_final: 0.7414 (tm-30) REVERT: H 145 LYS cc_start: 0.8881 (tttm) cc_final: 0.8563 (tttm) REVERT: H 206 GLU cc_start: 0.7373 (mt-10) cc_final: 0.7136 (tt0) REVERT: I 33 ASP cc_start: 0.7686 (m-30) cc_final: 0.7379 (m-30) REVERT: I 70 TYR cc_start: 0.8413 (t80) cc_final: 0.8172 (t80) REVERT: I 173 ASN cc_start: 0.8336 (p0) cc_final: 0.8005 (p0) REVERT: I 189 ASP cc_start: 0.7836 (m-30) cc_final: 0.7378 (m-30) REVERT: I 191 LYS cc_start: 0.8700 (mptt) cc_final: 0.8288 (mtmt) REVERT: I 195 PHE cc_start: 0.8773 (m-80) cc_final: 0.8394 (m-80) REVERT: I 214 ASN cc_start: 0.8149 (t0) cc_final: 0.7881 (t0) REVERT: I 231 GLU cc_start: 0.7354 (mm-30) cc_final: 0.6416 (tp30) REVERT: I 376 PRO cc_start: 0.8717 (Cg_endo) cc_final: 0.8477 (Cg_exo) REVERT: I 518 ASN cc_start: 0.8335 (OUTLIER) cc_final: 0.7551 (p0) REVERT: I 538 LEU cc_start: 0.9222 (OUTLIER) cc_final: 0.8942 (pt) REVERT: I 992 LEU cc_start: 0.2086 (OUTLIER) cc_final: 0.1881 (mt) REVERT: I 1085 MET cc_start: 0.9103 (OUTLIER) cc_final: 0.8550 (mmp) REVERT: I 1119 MET cc_start: 0.8011 (tpt) cc_final: 0.7321 (ttt) REVERT: I 1154 ASP cc_start: 0.7544 (p0) cc_final: 0.6619 (p0) REVERT: I 1170 MET cc_start: 0.8754 (mmt) cc_final: 0.8464 (mmp) REVERT: I 1273 MET cc_start: 0.8760 (mtp) cc_final: 0.8499 (mtp) REVERT: I 1310 ASP cc_start: 0.7085 (t0) cc_final: 0.6702 (t0) REVERT: J 225 GLU cc_start: 0.7604 (mm-30) cc_final: 0.7390 (mm-30) REVERT: J 765 GLU cc_start: 0.8365 (OUTLIER) cc_final: 0.7149 (pp20) REVERT: J 847 ASP cc_start: 0.7882 (OUTLIER) cc_final: 0.7668 (p0) REVERT: J 889 ASP cc_start: 0.8233 (OUTLIER) cc_final: 0.7873 (m-30) REVERT: J 954 ASN cc_start: 0.6826 (m-40) cc_final: 0.6594 (m-40) REVERT: J 996 LYS cc_start: 0.7985 (tptt) cc_final: 0.7719 (mptt) REVERT: J 999 TYR cc_start: 0.6916 (t80) cc_final: 0.6590 (t80) REVERT: J 1025 MET cc_start: 0.5592 (mtm) cc_final: 0.5311 (mtm) REVERT: J 1040 MET cc_start: 0.6241 (mmm) cc_final: 0.5823 (tpp) REVERT: J 1189 MET cc_start: 0.7254 (mmt) cc_final: 0.6578 (tmm) REVERT: K 29 GLN cc_start: 0.8845 (mt0) cc_final: 0.8498 (mt0) REVERT: K 35 LYS cc_start: 0.8411 (mmtp) cc_final: 0.8163 (mptt) outliers start: 108 outliers final: 67 residues processed: 446 average time/residue: 0.3934 time to fit residues: 275.7535 Evaluate side-chains 409 residues out of total 2699 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 74 poor density : 335 time to evaluate : 3.352 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 19 VAL Chi-restraints excluded: chain G residue 23 HIS Chi-restraints excluded: chain G residue 50 SER Chi-restraints excluded: chain G residue 90 VAL Chi-restraints excluded: chain G residue 118 ASP Chi-restraints excluded: chain G residue 127 GLN Chi-restraints excluded: chain G residue 198 LEU Chi-restraints excluded: chain H residue 19 VAL Chi-restraints excluded: chain H residue 28 LEU Chi-restraints excluded: chain H residue 100 LEU Chi-restraints excluded: chain H residue 146 VAL Chi-restraints excluded: chain H residue 174 ASP Chi-restraints excluded: chain H residue 176 CYS Chi-restraints excluded: chain H residue 188 GLU Chi-restraints excluded: chain H residue 198 LEU Chi-restraints excluded: chain I residue 11 ILE Chi-restraints excluded: chain I residue 28 LEU Chi-restraints excluded: chain I residue 47 TYR Chi-restraints excluded: chain I residue 122 VAL Chi-restraints excluded: chain I residue 221 LEU Chi-restraints excluded: chain I residue 228 VAL Chi-restraints excluded: chain I residue 287 VAL Chi-restraints excluded: chain I residue 377 THR Chi-restraints excluded: chain I residue 503 LYS Chi-restraints excluded: chain I residue 518 ASN Chi-restraints excluded: chain I residue 538 LEU Chi-restraints excluded: chain I residue 539 THR Chi-restraints excluded: chain I residue 615 VAL Chi-restraints excluded: chain I residue 622 ASN Chi-restraints excluded: chain I residue 623 LEU Chi-restraints excluded: chain I residue 635 THR Chi-restraints excluded: chain I residue 650 VAL Chi-restraints excluded: chain I residue 651 ASP Chi-restraints excluded: chain I residue 697 LYS Chi-restraints excluded: chain I residue 924 VAL Chi-restraints excluded: chain I residue 964 LEU Chi-restraints excluded: chain I residue 989 LEU Chi-restraints excluded: chain I residue 990 ASP Chi-restraints excluded: chain I residue 992 LEU Chi-restraints excluded: chain I residue 1047 LEU Chi-restraints excluded: chain I residue 1056 VAL Chi-restraints excluded: chain I residue 1085 MET Chi-restraints excluded: chain I residue 1159 VAL Chi-restraints excluded: chain I residue 1225 VAL Chi-restraints excluded: chain I residue 1240 ASP Chi-restraints excluded: chain I residue 1254 VAL Chi-restraints excluded: chain I residue 1295 SER Chi-restraints excluded: chain I residue 1298 VAL Chi-restraints excluded: chain I residue 1319 MET Chi-restraints excluded: chain J residue 119 SER Chi-restraints excluded: chain J residue 176 PHE Chi-restraints excluded: chain J residue 285 LEU Chi-restraints excluded: chain J residue 347 VAL Chi-restraints excluded: chain J residue 410 ASP Chi-restraints excluded: chain J residue 416 ILE Chi-restraints excluded: chain J residue 424 ASN Chi-restraints excluded: chain J residue 430 HIS Chi-restraints excluded: chain J residue 468 VAL Chi-restraints excluded: chain J residue 501 VAL Chi-restraints excluded: chain J residue 507 VAL Chi-restraints excluded: chain J residue 765 GLU Chi-restraints excluded: chain J residue 805 GLN Chi-restraints excluded: chain J residue 816 THR Chi-restraints excluded: chain J residue 826 ILE Chi-restraints excluded: chain J residue 847 ASP Chi-restraints excluded: chain J residue 857 LEU Chi-restraints excluded: chain J residue 882 VAL Chi-restraints excluded: chain J residue 889 ASP Chi-restraints excluded: chain J residue 974 VAL Chi-restraints excluded: chain J residue 1035 VAL Chi-restraints excluded: chain J residue 1146 GLU Chi-restraints excluded: chain J residue 1267 VAL Chi-restraints excluded: chain K residue 59 ILE Chi-restraints excluded: chain K residue 66 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 320 random chunks: chunk 161 optimal weight: 3.9990 chunk 90 optimal weight: 8.9990 chunk 241 optimal weight: 2.9990 chunk 197 optimal weight: 2.9990 chunk 80 optimal weight: 20.0000 chunk 291 optimal weight: 0.6980 chunk 314 optimal weight: 0.2980 chunk 259 optimal weight: 4.9990 chunk 288 optimal weight: 1.9990 chunk 99 optimal weight: 0.6980 chunk 233 optimal weight: 5.9990 overall best weight: 1.3384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 103 ASN I 41 GLN ** I 618 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 229 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8039 moved from start: 0.0947 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.047 26626 Z= 0.229 Angle : 0.530 8.251 36235 Z= 0.278 Chirality : 0.042 0.178 4153 Planarity : 0.004 0.055 4520 Dihedral : 14.773 138.708 4356 Min Nonbonded Distance : 1.960 Molprobity Statistics. All-atom Clashscore : 9.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.25 % Favored : 93.75 % Rotamer: Outliers : 4.49 % Allowed : 14.46 % Favored : 81.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.10 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.98 (0.15), residues: 3150 helix: 0.66 (0.16), residues: 1089 sheet: -0.66 (0.27), residues: 383 loop : -1.58 (0.14), residues: 1678 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP J 409 HIS 0.005 0.001 HIS G 23 PHE 0.024 0.001 PHE I 337 TYR 0.019 0.001 TYR I 123 ARG 0.011 0.000 ARG J 133 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6300 Ramachandran restraints generated. 3150 Oldfield, 0 Emsley, 3150 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6300 Ramachandran restraints generated. 3150 Oldfield, 0 Emsley, 3150 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 479 residues out of total 2699 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 121 poor density : 358 time to evaluate : 3.035 Fit side-chains REVERT: G 18 GLN cc_start: 0.8426 (mm-40) cc_final: 0.8210 (mm-40) REVERT: G 177 TYR cc_start: 0.8768 (OUTLIER) cc_final: 0.8437 (m-80) REVERT: H 17 GLU cc_start: 0.7887 (tm-30) cc_final: 0.7578 (tm-30) REVERT: H 145 LYS cc_start: 0.8887 (tttm) cc_final: 0.8589 (tttm) REVERT: I 33 ASP cc_start: 0.7836 (m-30) cc_final: 0.7552 (m-30) REVERT: I 70 TYR cc_start: 0.8437 (t80) cc_final: 0.8128 (t80) REVERT: I 72 SER cc_start: 0.8756 (t) cc_final: 0.8555 (p) REVERT: I 173 ASN cc_start: 0.8369 (p0) cc_final: 0.8029 (p0) REVERT: I 189 ASP cc_start: 0.8067 (OUTLIER) cc_final: 0.7629 (m-30) REVERT: I 191 LYS cc_start: 0.8711 (mptt) cc_final: 0.8256 (mtmt) REVERT: I 195 PHE cc_start: 0.8805 (m-80) cc_final: 0.8399 (m-80) REVERT: I 214 ASN cc_start: 0.8176 (t0) cc_final: 0.7835 (t0) REVERT: I 231 GLU cc_start: 0.7187 (mm-30) cc_final: 0.6428 (tp30) REVERT: I 376 PRO cc_start: 0.8756 (Cg_endo) cc_final: 0.8446 (Cg_exo) REVERT: I 490 GLN cc_start: 0.7668 (tp40) cc_final: 0.7404 (tp-100) REVERT: I 518 ASN cc_start: 0.8291 (OUTLIER) cc_final: 0.7351 (p0) REVERT: I 524 ILE cc_start: 0.8830 (tp) cc_final: 0.8415 (tp) REVERT: I 538 LEU cc_start: 0.9243 (OUTLIER) cc_final: 0.8918 (pt) REVERT: I 1085 MET cc_start: 0.9102 (OUTLIER) cc_final: 0.8799 (mmm) REVERT: I 1119 MET cc_start: 0.8023 (tpt) cc_final: 0.7337 (ttt) REVERT: I 1170 MET cc_start: 0.8762 (mmt) cc_final: 0.8476 (mmp) REVERT: I 1273 MET cc_start: 0.8765 (mtp) cc_final: 0.8398 (mtp) REVERT: I 1310 ASP cc_start: 0.7159 (t0) cc_final: 0.6943 (t0) REVERT: J 248 ASP cc_start: 0.7982 (t0) cc_final: 0.7618 (t0) REVERT: J 625 MET cc_start: 0.9043 (ttp) cc_final: 0.8825 (ttp) REVERT: J 765 GLU cc_start: 0.8408 (OUTLIER) cc_final: 0.7083 (pp20) REVERT: J 889 ASP cc_start: 0.8123 (OUTLIER) cc_final: 0.7745 (m-30) REVERT: J 954 ASN cc_start: 0.6933 (m-40) cc_final: 0.6713 (m-40) REVERT: J 999 TYR cc_start: 0.6952 (t80) cc_final: 0.6635 (t80) REVERT: J 1040 MET cc_start: 0.6227 (mmm) cc_final: 0.5924 (tpp) REVERT: J 1174 ARG cc_start: 0.7606 (mtp85) cc_final: 0.7298 (mtp85) REVERT: J 1189 MET cc_start: 0.7021 (mmt) cc_final: 0.6672 (tmm) REVERT: J 1258 ARG cc_start: 0.8721 (OUTLIER) cc_final: 0.8439 (ttt-90) REVERT: J 1371 ARG cc_start: 0.7762 (mtm110) cc_final: 0.7273 (ptp-170) REVERT: K 35 LYS cc_start: 0.8421 (mmtp) cc_final: 0.8143 (mptt) outliers start: 121 outliers final: 80 residues processed: 449 average time/residue: 0.3848 time to fit residues: 273.1150 Evaluate side-chains 417 residues out of total 2699 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 88 poor density : 329 time to evaluate : 3.159 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 19 VAL Chi-restraints excluded: chain G residue 23 HIS Chi-restraints excluded: chain G residue 50 SER Chi-restraints excluded: chain G residue 90 VAL Chi-restraints excluded: chain G residue 118 ASP Chi-restraints excluded: chain G residue 127 GLN Chi-restraints excluded: chain G residue 177 TYR Chi-restraints excluded: chain G residue 198 LEU Chi-restraints excluded: chain H residue 19 VAL Chi-restraints excluded: chain H residue 28 LEU Chi-restraints excluded: chain H residue 144 ILE Chi-restraints excluded: chain H residue 146 VAL Chi-restraints excluded: chain H residue 174 ASP Chi-restraints excluded: chain H residue 176 CYS Chi-restraints excluded: chain H residue 188 GLU Chi-restraints excluded: chain H residue 198 LEU Chi-restraints excluded: chain I residue 11 ILE Chi-restraints excluded: chain I residue 21 VAL Chi-restraints excluded: chain I residue 28 LEU Chi-restraints excluded: chain I residue 47 TYR Chi-restraints excluded: chain I residue 98 VAL Chi-restraints excluded: chain I residue 104 ILE Chi-restraints excluded: chain I residue 189 ASP Chi-restraints excluded: chain I residue 221 LEU Chi-restraints excluded: chain I residue 228 VAL Chi-restraints excluded: chain I residue 287 VAL Chi-restraints excluded: chain I residue 320 ASP Chi-restraints excluded: chain I residue 377 THR Chi-restraints excluded: chain I residue 484 LEU Chi-restraints excluded: chain I residue 503 LYS Chi-restraints excluded: chain I residue 518 ASN Chi-restraints excluded: chain I residue 538 LEU Chi-restraints excluded: chain I residue 539 THR Chi-restraints excluded: chain I residue 547 VAL Chi-restraints excluded: chain I residue 615 VAL Chi-restraints excluded: chain I residue 620 ASN Chi-restraints excluded: chain I residue 623 LEU Chi-restraints excluded: chain I residue 635 THR Chi-restraints excluded: chain I residue 650 VAL Chi-restraints excluded: chain I residue 651 ASP Chi-restraints excluded: chain I residue 697 LYS Chi-restraints excluded: chain I residue 765 ILE Chi-restraints excluded: chain I residue 924 VAL Chi-restraints excluded: chain I residue 946 LEU Chi-restraints excluded: chain I residue 964 LEU Chi-restraints excluded: chain I residue 989 LEU Chi-restraints excluded: chain I residue 990 ASP Chi-restraints excluded: chain I residue 1047 LEU Chi-restraints excluded: chain I residue 1056 VAL Chi-restraints excluded: chain I residue 1085 MET Chi-restraints excluded: chain I residue 1159 VAL Chi-restraints excluded: chain I residue 1225 VAL Chi-restraints excluded: chain I residue 1240 ASP Chi-restraints excluded: chain I residue 1254 VAL Chi-restraints excluded: chain I residue 1295 SER Chi-restraints excluded: chain I residue 1298 VAL Chi-restraints excluded: chain I residue 1319 MET Chi-restraints excluded: chain J residue 176 PHE Chi-restraints excluded: chain J residue 212 THR Chi-restraints excluded: chain J residue 285 LEU Chi-restraints excluded: chain J residue 347 VAL Chi-restraints excluded: chain J residue 354 VAL Chi-restraints excluded: chain J residue 374 LEU Chi-restraints excluded: chain J residue 408 VAL Chi-restraints excluded: chain J residue 410 ASP Chi-restraints excluded: chain J residue 416 ILE Chi-restraints excluded: chain J residue 424 ASN Chi-restraints excluded: chain J residue 430 HIS Chi-restraints excluded: chain J residue 468 VAL Chi-restraints excluded: chain J residue 501 VAL Chi-restraints excluded: chain J residue 507 VAL Chi-restraints excluded: chain J residue 591 ILE Chi-restraints excluded: chain J residue 765 GLU Chi-restraints excluded: chain J residue 805 GLN Chi-restraints excluded: chain J residue 816 THR Chi-restraints excluded: chain J residue 826 ILE Chi-restraints excluded: chain J residue 831 VAL Chi-restraints excluded: chain J residue 844 THR Chi-restraints excluded: chain J residue 882 VAL Chi-restraints excluded: chain J residue 889 ASP Chi-restraints excluded: chain J residue 974 VAL Chi-restraints excluded: chain J residue 1035 VAL Chi-restraints excluded: chain J residue 1095 MET Chi-restraints excluded: chain J residue 1146 GLU Chi-restraints excluded: chain J residue 1258 ARG Chi-restraints excluded: chain J residue 1267 VAL Chi-restraints excluded: chain K residue 59 ILE Chi-restraints excluded: chain K residue 66 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 320 random chunks: chunk 287 optimal weight: 20.0000 chunk 218 optimal weight: 0.1980 chunk 151 optimal weight: 5.9990 chunk 32 optimal weight: 2.9990 chunk 138 optimal weight: 6.9990 chunk 195 optimal weight: 10.0000 chunk 292 optimal weight: 8.9990 chunk 309 optimal weight: 3.9990 chunk 152 optimal weight: 1.9990 chunk 276 optimal weight: 4.9990 chunk 83 optimal weight: 7.9990 overall best weight: 2.8388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 103 ASN ** I 618 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 955 GLN J 229 GLN J 320 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8098 moved from start: 0.1124 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.071 26626 Z= 0.423 Angle : 0.616 8.536 36235 Z= 0.320 Chirality : 0.045 0.181 4153 Planarity : 0.004 0.054 4520 Dihedral : 14.891 139.241 4349 Min Nonbonded Distance : 1.931 Molprobity Statistics. All-atom Clashscore : 10.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.79 % Favored : 93.21 % Rotamer: Outliers : 5.15 % Allowed : 15.02 % Favored : 79.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.10 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.10 (0.15), residues: 3150 helix: 0.48 (0.16), residues: 1090 sheet: -0.69 (0.27), residues: 382 loop : -1.59 (0.14), residues: 1678 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP J 409 HIS 0.008 0.001 HIS G 23 PHE 0.023 0.002 PHE I 337 TYR 0.019 0.002 TYR G 177 ARG 0.010 0.001 ARG J 133 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6300 Ramachandran restraints generated. 3150 Oldfield, 0 Emsley, 3150 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6300 Ramachandran restraints generated. 3150 Oldfield, 0 Emsley, 3150 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 481 residues out of total 2699 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 139 poor density : 342 time to evaluate : 2.429 Fit side-chains revert: symmetry clash REVERT: G 18 GLN cc_start: 0.8516 (mm-40) cc_final: 0.8268 (mm-40) REVERT: G 93 GLN cc_start: 0.7413 (mm-40) cc_final: 0.6967 (mm-40) REVERT: H 17 GLU cc_start: 0.7963 (tm-30) cc_final: 0.7625 (tm-30) REVERT: H 103 ASN cc_start: 0.8205 (OUTLIER) cc_final: 0.7939 (p0) REVERT: I 33 ASP cc_start: 0.7914 (m-30) cc_final: 0.7626 (m-30) REVERT: I 189 ASP cc_start: 0.8117 (OUTLIER) cc_final: 0.7699 (m-30) REVERT: I 191 LYS cc_start: 0.8742 (mptt) cc_final: 0.8494 (mmtp) REVERT: I 195 PHE cc_start: 0.8871 (m-80) cc_final: 0.8510 (m-80) REVERT: I 214 ASN cc_start: 0.8367 (t0) cc_final: 0.8089 (t0) REVERT: I 231 GLU cc_start: 0.7268 (mm-30) cc_final: 0.6562 (tp30) REVERT: I 490 GLN cc_start: 0.7662 (tp40) cc_final: 0.7404 (tp-100) REVERT: I 518 ASN cc_start: 0.8402 (OUTLIER) cc_final: 0.7453 (p0) REVERT: I 524 ILE cc_start: 0.8927 (tp) cc_final: 0.8580 (tp) REVERT: I 538 LEU cc_start: 0.9319 (OUTLIER) cc_final: 0.8978 (pt) REVERT: I 1085 MET cc_start: 0.9117 (OUTLIER) cc_final: 0.8825 (mmm) REVERT: I 1119 MET cc_start: 0.8082 (tpt) cc_final: 0.7361 (ttt) REVERT: I 1170 MET cc_start: 0.8813 (mmt) cc_final: 0.8532 (mmp) REVERT: I 1273 MET cc_start: 0.8681 (mtp) cc_final: 0.8418 (mtp) REVERT: J 81 ARG cc_start: 0.7834 (tmm-80) cc_final: 0.7449 (ttp-170) REVERT: J 889 ASP cc_start: 0.8009 (OUTLIER) cc_final: 0.7620 (m-30) REVERT: J 954 ASN cc_start: 0.6930 (m-40) cc_final: 0.6691 (m-40) REVERT: J 999 TYR cc_start: 0.7035 (t80) cc_final: 0.6738 (t80) REVERT: J 1168 GLU cc_start: 0.5926 (OUTLIER) cc_final: 0.5480 (mt-10) REVERT: J 1189 MET cc_start: 0.7062 (mmt) cc_final: 0.6640 (tmm) REVERT: J 1258 ARG cc_start: 0.8773 (OUTLIER) cc_final: 0.8488 (ttt-90) REVERT: J 1290 ARG cc_start: 0.7930 (mtm110) cc_final: 0.7615 (mtp180) REVERT: J 1371 ARG cc_start: 0.7861 (mtm110) cc_final: 0.7246 (ptp-170) REVERT: K 35 LYS cc_start: 0.8512 (mmtp) cc_final: 0.8199 (mptt) outliers start: 139 outliers final: 102 residues processed: 446 average time/residue: 0.3933 time to fit residues: 275.5934 Evaluate side-chains 434 residues out of total 2699 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 110 poor density : 324 time to evaluate : 2.783 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 19 VAL Chi-restraints excluded: chain G residue 23 HIS Chi-restraints excluded: chain G residue 49 SER Chi-restraints excluded: chain G residue 50 SER Chi-restraints excluded: chain G residue 90 VAL Chi-restraints excluded: chain G residue 98 VAL Chi-restraints excluded: chain G residue 118 ASP Chi-restraints excluded: chain G residue 127 GLN Chi-restraints excluded: chain G residue 198 LEU Chi-restraints excluded: chain G residue 205 MET Chi-restraints excluded: chain H residue 19 VAL Chi-restraints excluded: chain H residue 28 LEU Chi-restraints excluded: chain H residue 90 VAL Chi-restraints excluded: chain H residue 100 LEU Chi-restraints excluded: chain H residue 103 ASN Chi-restraints excluded: chain H residue 144 ILE Chi-restraints excluded: chain H residue 146 VAL Chi-restraints excluded: chain H residue 174 ASP Chi-restraints excluded: chain H residue 176 CYS Chi-restraints excluded: chain H residue 188 GLU Chi-restraints excluded: chain H residue 198 LEU Chi-restraints excluded: chain I residue 11 ILE Chi-restraints excluded: chain I residue 21 VAL Chi-restraints excluded: chain I residue 47 TYR Chi-restraints excluded: chain I residue 98 VAL Chi-restraints excluded: chain I residue 104 ILE Chi-restraints excluded: chain I residue 122 VAL Chi-restraints excluded: chain I residue 189 ASP Chi-restraints excluded: chain I residue 208 ILE Chi-restraints excluded: chain I residue 221 LEU Chi-restraints excluded: chain I residue 228 VAL Chi-restraints excluded: chain I residue 287 VAL Chi-restraints excluded: chain I residue 320 ASP Chi-restraints excluded: chain I residue 475 VAL Chi-restraints excluded: chain I residue 484 LEU Chi-restraints excluded: chain I residue 503 LYS Chi-restraints excluded: chain I residue 516 ASP Chi-restraints excluded: chain I residue 518 ASN Chi-restraints excluded: chain I residue 525 THR Chi-restraints excluded: chain I residue 538 LEU Chi-restraints excluded: chain I residue 539 THR Chi-restraints excluded: chain I residue 547 VAL Chi-restraints excluded: chain I residue 581 THR Chi-restraints excluded: chain I residue 606 LEU Chi-restraints excluded: chain I residue 615 VAL Chi-restraints excluded: chain I residue 622 ASN Chi-restraints excluded: chain I residue 623 LEU Chi-restraints excluded: chain I residue 635 THR Chi-restraints excluded: chain I residue 650 VAL Chi-restraints excluded: chain I residue 651 ASP Chi-restraints excluded: chain I residue 653 MET Chi-restraints excluded: chain I residue 663 VAL Chi-restraints excluded: chain I residue 697 LYS Chi-restraints excluded: chain I residue 765 ILE Chi-restraints excluded: chain I residue 918 LEU Chi-restraints excluded: chain I residue 924 VAL Chi-restraints excluded: chain I residue 946 LEU Chi-restraints excluded: chain I residue 964 LEU Chi-restraints excluded: chain I residue 989 LEU Chi-restraints excluded: chain I residue 990 ASP Chi-restraints excluded: chain I residue 1056 VAL Chi-restraints excluded: chain I residue 1085 MET Chi-restraints excluded: chain I residue 1159 VAL Chi-restraints excluded: chain I residue 1225 VAL Chi-restraints excluded: chain I residue 1240 ASP Chi-restraints excluded: chain I residue 1254 VAL Chi-restraints excluded: chain I residue 1295 SER Chi-restraints excluded: chain I residue 1298 VAL Chi-restraints excluded: chain I residue 1319 MET Chi-restraints excluded: chain J residue 48 THR Chi-restraints excluded: chain J residue 119 SER Chi-restraints excluded: chain J residue 176 PHE Chi-restraints excluded: chain J residue 198 CYS Chi-restraints excluded: chain J residue 212 THR Chi-restraints excluded: chain J residue 285 LEU Chi-restraints excluded: chain J residue 347 VAL Chi-restraints excluded: chain J residue 352 ARG Chi-restraints excluded: chain J residue 354 VAL Chi-restraints excluded: chain J residue 374 LEU Chi-restraints excluded: chain J residue 401 VAL Chi-restraints excluded: chain J residue 408 VAL Chi-restraints excluded: chain J residue 416 ILE Chi-restraints excluded: chain J residue 424 ASN Chi-restraints excluded: chain J residue 430 HIS Chi-restraints excluded: chain J residue 468 VAL Chi-restraints excluded: chain J residue 501 VAL Chi-restraints excluded: chain J residue 507 VAL Chi-restraints excluded: chain J residue 547 ARG Chi-restraints excluded: chain J residue 706 VAL Chi-restraints excluded: chain J residue 708 ASN Chi-restraints excluded: chain J residue 755 ILE Chi-restraints excluded: chain J residue 757 THR Chi-restraints excluded: chain J residue 765 GLU Chi-restraints excluded: chain J residue 805 GLN Chi-restraints excluded: chain J residue 816 THR Chi-restraints excluded: chain J residue 826 ILE Chi-restraints excluded: chain J residue 831 VAL Chi-restraints excluded: chain J residue 844 THR Chi-restraints excluded: chain J residue 857 LEU Chi-restraints excluded: chain J residue 882 VAL Chi-restraints excluded: chain J residue 889 ASP Chi-restraints excluded: chain J residue 967 VAL Chi-restraints excluded: chain J residue 974 VAL Chi-restraints excluded: chain J residue 1035 VAL Chi-restraints excluded: chain J residue 1146 GLU Chi-restraints excluded: chain J residue 1168 GLU Chi-restraints excluded: chain J residue 1258 ARG Chi-restraints excluded: chain J residue 1267 VAL Chi-restraints excluded: chain K residue 59 ILE Chi-restraints excluded: chain K residue 66 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 320 random chunks: chunk 257 optimal weight: 0.7980 chunk 175 optimal weight: 0.8980 chunk 4 optimal weight: 6.9990 chunk 230 optimal weight: 2.9990 chunk 127 optimal weight: 2.9990 chunk 263 optimal weight: 8.9990 chunk 213 optimal weight: 0.9990 chunk 0 optimal weight: 10.0000 chunk 157 optimal weight: 0.5980 chunk 277 optimal weight: 20.0000 chunk 78 optimal weight: 10.0000 overall best weight: 1.2584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: G 137 ASN H 132 HIS ** I 618 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 955 GLN J 229 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8051 moved from start: 0.1207 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 26626 Z= 0.224 Angle : 0.533 8.391 36235 Z= 0.279 Chirality : 0.042 0.177 4153 Planarity : 0.004 0.056 4520 Dihedral : 14.746 139.190 4346 Min Nonbonded Distance : 1.975 Molprobity Statistics. All-atom Clashscore : 9.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.78 % Favored : 94.22 % Rotamer: Outliers : 4.75 % Allowed : 16.31 % Favored : 78.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.10 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.88 (0.15), residues: 3150 helix: 0.74 (0.16), residues: 1081 sheet: -0.61 (0.26), residues: 390 loop : -1.50 (0.14), residues: 1679 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP J 409 HIS 0.004 0.001 HIS G 23 PHE 0.022 0.001 PHE I 337 TYR 0.019 0.001 TYR I 123 ARG 0.010 0.000 ARG J 133 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6300 Ramachandran restraints generated. 3150 Oldfield, 0 Emsley, 3150 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6300 Ramachandran restraints generated. 3150 Oldfield, 0 Emsley, 3150 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 486 residues out of total 2699 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 128 poor density : 358 time to evaluate : 3.038 Fit side-chains revert: symmetry clash REVERT: G 93 GLN cc_start: 0.7287 (mm-40) cc_final: 0.6838 (mm-40) REVERT: H 17 GLU cc_start: 0.7958 (tm-30) cc_final: 0.7666 (tm-30) REVERT: H 103 ASN cc_start: 0.8015 (m-40) cc_final: 0.7719 (p0) REVERT: I 33 ASP cc_start: 0.7791 (m-30) cc_final: 0.7507 (m-30) REVERT: I 173 ASN cc_start: 0.8363 (p0) cc_final: 0.8016 (p0) REVERT: I 189 ASP cc_start: 0.8084 (OUTLIER) cc_final: 0.7653 (m-30) REVERT: I 191 LYS cc_start: 0.8738 (mptt) cc_final: 0.8485 (mmtp) REVERT: I 195 PHE cc_start: 0.8806 (m-80) cc_final: 0.8484 (m-80) REVERT: I 214 ASN cc_start: 0.8355 (t0) cc_final: 0.8094 (t0) REVERT: I 231 GLU cc_start: 0.7276 (mm-30) cc_final: 0.6589 (tp30) REVERT: I 490 GLN cc_start: 0.7611 (tp40) cc_final: 0.7364 (tp-100) REVERT: I 518 ASN cc_start: 0.8082 (OUTLIER) cc_final: 0.7733 (p0) REVERT: I 524 ILE cc_start: 0.8828 (tp) cc_final: 0.8394 (tp) REVERT: I 538 LEU cc_start: 0.9277 (OUTLIER) cc_final: 0.8942 (pt) REVERT: I 957 LYS cc_start: 0.7571 (mtmt) cc_final: 0.7103 (mttm) REVERT: I 1085 MET cc_start: 0.9113 (OUTLIER) cc_final: 0.8816 (mmm) REVERT: I 1119 MET cc_start: 0.8041 (tpt) cc_final: 0.7349 (ttt) REVERT: I 1134 GLN cc_start: 0.8379 (OUTLIER) cc_final: 0.7074 (pp30) REVERT: I 1273 MET cc_start: 0.8670 (mtp) cc_final: 0.8349 (mtp) REVERT: J 81 ARG cc_start: 0.7724 (tmm-80) cc_final: 0.7452 (ttp-170) REVERT: J 155 GLU cc_start: 0.7467 (mp0) cc_final: 0.7115 (mm-30) REVERT: J 352 ARG cc_start: 0.8671 (OUTLIER) cc_final: 0.8256 (ptm160) REVERT: J 547 ARG cc_start: 0.8270 (OUTLIER) cc_final: 0.8044 (mmt90) REVERT: J 724 MET cc_start: 0.8614 (mtm) cc_final: 0.8344 (mtm) REVERT: J 889 ASP cc_start: 0.8019 (OUTLIER) cc_final: 0.7717 (m-30) REVERT: J 954 ASN cc_start: 0.7096 (m-40) cc_final: 0.6855 (m-40) REVERT: J 999 TYR cc_start: 0.6843 (t80) cc_final: 0.6603 (t80) REVERT: J 1168 GLU cc_start: 0.5783 (OUTLIER) cc_final: 0.5336 (mt-10) REVERT: J 1189 MET cc_start: 0.7110 (mmt) cc_final: 0.6683 (tmm) REVERT: J 1258 ARG cc_start: 0.8702 (OUTLIER) cc_final: 0.8422 (ttt-90) REVERT: J 1281 GLU cc_start: 0.8282 (OUTLIER) cc_final: 0.7997 (tt0) REVERT: J 1290 ARG cc_start: 0.7869 (mtm110) cc_final: 0.7543 (mtp180) REVERT: J 1307 LEU cc_start: 0.9360 (OUTLIER) cc_final: 0.9005 (mp) REVERT: J 1371 ARG cc_start: 0.7652 (mtm110) cc_final: 0.7193 (ptp-170) REVERT: K 35 LYS cc_start: 0.8415 (mmtp) cc_final: 0.8145 (mptt) outliers start: 128 outliers final: 90 residues processed: 452 average time/residue: 0.3965 time to fit residues: 281.8401 Evaluate side-chains 437 residues out of total 2699 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 102 poor density : 335 time to evaluate : 3.196 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 19 VAL Chi-restraints excluded: chain G residue 23 HIS Chi-restraints excluded: chain G residue 50 SER Chi-restraints excluded: chain G residue 90 VAL Chi-restraints excluded: chain G residue 98 VAL Chi-restraints excluded: chain G residue 118 ASP Chi-restraints excluded: chain G residue 127 GLN Chi-restraints excluded: chain G residue 198 LEU Chi-restraints excluded: chain G residue 205 MET Chi-restraints excluded: chain G residue 207 THR Chi-restraints excluded: chain H residue 19 VAL Chi-restraints excluded: chain H residue 28 LEU Chi-restraints excluded: chain H residue 90 VAL Chi-restraints excluded: chain H residue 100 LEU Chi-restraints excluded: chain H residue 144 ILE Chi-restraints excluded: chain H residue 146 VAL Chi-restraints excluded: chain H residue 174 ASP Chi-restraints excluded: chain H residue 176 CYS Chi-restraints excluded: chain H residue 188 GLU Chi-restraints excluded: chain H residue 198 LEU Chi-restraints excluded: chain I residue 11 ILE Chi-restraints excluded: chain I residue 28 LEU Chi-restraints excluded: chain I residue 47 TYR Chi-restraints excluded: chain I residue 98 VAL Chi-restraints excluded: chain I residue 104 ILE Chi-restraints excluded: chain I residue 122 VAL Chi-restraints excluded: chain I residue 189 ASP Chi-restraints excluded: chain I residue 228 VAL Chi-restraints excluded: chain I residue 287 VAL Chi-restraints excluded: chain I residue 320 ASP Chi-restraints excluded: chain I residue 377 THR Chi-restraints excluded: chain I residue 503 LYS Chi-restraints excluded: chain I residue 518 ASN Chi-restraints excluded: chain I residue 538 LEU Chi-restraints excluded: chain I residue 547 VAL Chi-restraints excluded: chain I residue 609 ILE Chi-restraints excluded: chain I residue 615 VAL Chi-restraints excluded: chain I residue 622 ASN Chi-restraints excluded: chain I residue 623 LEU Chi-restraints excluded: chain I residue 635 THR Chi-restraints excluded: chain I residue 650 VAL Chi-restraints excluded: chain I residue 651 ASP Chi-restraints excluded: chain I residue 681 MET Chi-restraints excluded: chain I residue 697 LYS Chi-restraints excluded: chain I residue 765 ILE Chi-restraints excluded: chain I residue 870 ILE Chi-restraints excluded: chain I residue 918 LEU Chi-restraints excluded: chain I residue 924 VAL Chi-restraints excluded: chain I residue 946 LEU Chi-restraints excluded: chain I residue 964 LEU Chi-restraints excluded: chain I residue 989 LEU Chi-restraints excluded: chain I residue 990 ASP Chi-restraints excluded: chain I residue 1056 VAL Chi-restraints excluded: chain I residue 1085 MET Chi-restraints excluded: chain I residue 1134 GLN Chi-restraints excluded: chain I residue 1154 ASP Chi-restraints excluded: chain I residue 1159 VAL Chi-restraints excluded: chain I residue 1225 VAL Chi-restraints excluded: chain I residue 1240 ASP Chi-restraints excluded: chain I residue 1254 VAL Chi-restraints excluded: chain I residue 1295 SER Chi-restraints excluded: chain I residue 1298 VAL Chi-restraints excluded: chain I residue 1319 MET Chi-restraints excluded: chain J residue 83 VAL Chi-restraints excluded: chain J residue 119 SER Chi-restraints excluded: chain J residue 176 PHE Chi-restraints excluded: chain J residue 198 CYS Chi-restraints excluded: chain J residue 212 THR Chi-restraints excluded: chain J residue 285 LEU Chi-restraints excluded: chain J residue 347 VAL Chi-restraints excluded: chain J residue 352 ARG Chi-restraints excluded: chain J residue 354 VAL Chi-restraints excluded: chain J residue 374 LEU Chi-restraints excluded: chain J residue 416 ILE Chi-restraints excluded: chain J residue 424 ASN Chi-restraints excluded: chain J residue 430 HIS Chi-restraints excluded: chain J residue 468 VAL Chi-restraints excluded: chain J residue 501 VAL Chi-restraints excluded: chain J residue 507 VAL Chi-restraints excluded: chain J residue 547 ARG Chi-restraints excluded: chain J residue 591 ILE Chi-restraints excluded: chain J residue 706 VAL Chi-restraints excluded: chain J residue 765 GLU Chi-restraints excluded: chain J residue 805 GLN Chi-restraints excluded: chain J residue 816 THR Chi-restraints excluded: chain J residue 826 ILE Chi-restraints excluded: chain J residue 831 VAL Chi-restraints excluded: chain J residue 844 THR Chi-restraints excluded: chain J residue 857 LEU Chi-restraints excluded: chain J residue 882 VAL Chi-restraints excluded: chain J residue 889 ASP Chi-restraints excluded: chain J residue 967 VAL Chi-restraints excluded: chain J residue 974 VAL Chi-restraints excluded: chain J residue 1035 VAL Chi-restraints excluded: chain J residue 1095 MET Chi-restraints excluded: chain J residue 1146 GLU Chi-restraints excluded: chain J residue 1168 GLU Chi-restraints excluded: chain J residue 1258 ARG Chi-restraints excluded: chain J residue 1267 VAL Chi-restraints excluded: chain J residue 1281 GLU Chi-restraints excluded: chain J residue 1307 LEU Chi-restraints excluded: chain K residue 59 ILE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 320 random chunks: chunk 104 optimal weight: 3.9990 chunk 278 optimal weight: 0.9990 chunk 61 optimal weight: 3.9990 chunk 181 optimal weight: 0.9990 chunk 76 optimal weight: 4.9990 chunk 309 optimal weight: 0.0870 chunk 257 optimal weight: 6.9990 chunk 143 optimal weight: 0.9980 chunk 25 optimal weight: 5.9990 chunk 102 optimal weight: 0.5980 chunk 162 optimal weight: 0.3980 overall best weight: 0.6160 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: G 137 ASN I 41 GLN I 554 HIS ** I 618 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 229 GLN J1259 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8008 moved from start: 0.1402 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.036 26626 Z= 0.154 Angle : 0.500 8.424 36235 Z= 0.262 Chirality : 0.041 0.185 4153 Planarity : 0.003 0.055 4520 Dihedral : 14.558 138.868 4342 Min Nonbonded Distance : 2.000 Molprobity Statistics. All-atom Clashscore : 8.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.30 % Favored : 94.70 % Rotamer: Outliers : 4.26 % Allowed : 17.06 % Favored : 78.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.10 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.66 (0.15), residues: 3150 helix: 0.93 (0.16), residues: 1084 sheet: -0.45 (0.26), residues: 397 loop : -1.40 (0.14), residues: 1669 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP J 33 HIS 0.003 0.001 HIS J 865 PHE 0.020 0.001 PHE I 337 TYR 0.020 0.001 TYR I 123 ARG 0.015 0.000 ARG J 133 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6300 Ramachandran restraints generated. 3150 Oldfield, 0 Emsley, 3150 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6300 Ramachandran restraints generated. 3150 Oldfield, 0 Emsley, 3150 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 473 residues out of total 2699 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 115 poor density : 358 time to evaluate : 3.025 Fit side-chains revert: symmetry clash REVERT: H 17 GLU cc_start: 0.7732 (tm-30) cc_final: 0.7481 (tm-30) REVERT: H 103 ASN cc_start: 0.7787 (m-40) cc_final: 0.7502 (p0) REVERT: H 145 LYS cc_start: 0.8835 (tttm) cc_final: 0.8443 (tttm) REVERT: I 33 ASP cc_start: 0.7749 (m-30) cc_final: 0.7454 (m-30) REVERT: I 173 ASN cc_start: 0.8302 (p0) cc_final: 0.7939 (p0) REVERT: I 189 ASP cc_start: 0.8074 (OUTLIER) cc_final: 0.7669 (m-30) REVERT: I 191 LYS cc_start: 0.8743 (mptt) cc_final: 0.8478 (mmtp) REVERT: I 195 PHE cc_start: 0.8768 (m-80) cc_final: 0.8382 (m-80) REVERT: I 214 ASN cc_start: 0.8324 (t0) cc_final: 0.8095 (t0) REVERT: I 321 LEU cc_start: 0.7377 (mp) cc_final: 0.6887 (tt) REVERT: I 369 MET cc_start: 0.8763 (tmm) cc_final: 0.8549 (tmm) REVERT: I 490 GLN cc_start: 0.7511 (tp40) cc_final: 0.7289 (tp-100) REVERT: I 518 ASN cc_start: 0.7950 (OUTLIER) cc_final: 0.7671 (p0) REVERT: I 538 LEU cc_start: 0.9206 (OUTLIER) cc_final: 0.8890 (pt) REVERT: I 957 LYS cc_start: 0.7466 (mtmt) cc_final: 0.7129 (mttm) REVERT: I 1085 MET cc_start: 0.9115 (OUTLIER) cc_final: 0.8836 (mmm) REVERT: I 1108 ASN cc_start: 0.8766 (p0) cc_final: 0.8220 (p0) REVERT: I 1134 GLN cc_start: 0.8373 (OUTLIER) cc_final: 0.7060 (pp30) REVERT: I 1273 MET cc_start: 0.8621 (mtp) cc_final: 0.8224 (mtp) REVERT: J 81 ARG cc_start: 0.7640 (tmm-80) cc_final: 0.7394 (ttp-110) REVERT: J 155 GLU cc_start: 0.7432 (mp0) cc_final: 0.7114 (mm-30) REVERT: J 352 ARG cc_start: 0.8658 (OUTLIER) cc_final: 0.8072 (ptm160) REVERT: J 497 GLU cc_start: 0.7593 (mm-30) cc_final: 0.7334 (mt-10) REVERT: J 724 MET cc_start: 0.8430 (mtm) cc_final: 0.8157 (mtm) REVERT: J 765 GLU cc_start: 0.8464 (OUTLIER) cc_final: 0.7033 (pp20) REVERT: J 889 ASP cc_start: 0.8094 (OUTLIER) cc_final: 0.7749 (m-30) REVERT: J 954 ASN cc_start: 0.7015 (m-40) cc_final: 0.6804 (m-40) REVERT: J 999 TYR cc_start: 0.6786 (t80) cc_final: 0.6535 (t80) REVERT: J 1066 GLU cc_start: 0.3023 (OUTLIER) cc_final: 0.2411 (pm20) REVERT: J 1174 ARG cc_start: 0.7484 (mtp85) cc_final: 0.7182 (mtp-110) REVERT: J 1189 MET cc_start: 0.7042 (mmt) cc_final: 0.6680 (tmm) REVERT: J 1258 ARG cc_start: 0.8618 (OUTLIER) cc_final: 0.8415 (ttt90) REVERT: J 1281 GLU cc_start: 0.8197 (OUTLIER) cc_final: 0.7962 (tt0) REVERT: J 1290 ARG cc_start: 0.7785 (mtm110) cc_final: 0.7404 (mtp180) REVERT: J 1371 ARG cc_start: 0.7571 (mtm110) cc_final: 0.7127 (ptp-170) REVERT: K 29 GLN cc_start: 0.8834 (mt0) cc_final: 0.8471 (mt0) REVERT: K 59 ILE cc_start: 0.8403 (OUTLIER) cc_final: 0.8198 (tt) outliers start: 115 outliers final: 82 residues processed: 449 average time/residue: 0.4029 time to fit residues: 284.9799 Evaluate side-chains 434 residues out of total 2699 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 94 poor density : 340 time to evaluate : 3.025 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 19 VAL Chi-restraints excluded: chain G residue 90 VAL Chi-restraints excluded: chain G residue 98 VAL Chi-restraints excluded: chain G residue 118 ASP Chi-restraints excluded: chain G residue 127 GLN Chi-restraints excluded: chain G residue 198 LEU Chi-restraints excluded: chain G residue 205 MET Chi-restraints excluded: chain G residue 207 THR Chi-restraints excluded: chain H residue 28 LEU Chi-restraints excluded: chain H residue 90 VAL Chi-restraints excluded: chain H residue 144 ILE Chi-restraints excluded: chain H residue 146 VAL Chi-restraints excluded: chain H residue 173 VAL Chi-restraints excluded: chain H residue 174 ASP Chi-restraints excluded: chain H residue 188 GLU Chi-restraints excluded: chain H residue 198 LEU Chi-restraints excluded: chain I residue 11 ILE Chi-restraints excluded: chain I residue 28 LEU Chi-restraints excluded: chain I residue 47 TYR Chi-restraints excluded: chain I residue 98 VAL Chi-restraints excluded: chain I residue 104 ILE Chi-restraints excluded: chain I residue 122 VAL Chi-restraints excluded: chain I residue 142 GLU Chi-restraints excluded: chain I residue 189 ASP Chi-restraints excluded: chain I residue 228 VAL Chi-restraints excluded: chain I residue 234 ASP Chi-restraints excluded: chain I residue 287 VAL Chi-restraints excluded: chain I residue 320 ASP Chi-restraints excluded: chain I residue 377 THR Chi-restraints excluded: chain I residue 484 LEU Chi-restraints excluded: chain I residue 503 LYS Chi-restraints excluded: chain I residue 518 ASN Chi-restraints excluded: chain I residue 538 LEU Chi-restraints excluded: chain I residue 539 THR Chi-restraints excluded: chain I residue 547 VAL Chi-restraints excluded: chain I residue 615 VAL Chi-restraints excluded: chain I residue 620 ASN Chi-restraints excluded: chain I residue 623 LEU Chi-restraints excluded: chain I residue 635 THR Chi-restraints excluded: chain I residue 650 VAL Chi-restraints excluded: chain I residue 663 VAL Chi-restraints excluded: chain I residue 697 LYS Chi-restraints excluded: chain I residue 765 ILE Chi-restraints excluded: chain I residue 870 ILE Chi-restraints excluded: chain I residue 924 VAL Chi-restraints excluded: chain I residue 946 LEU Chi-restraints excluded: chain I residue 964 LEU Chi-restraints excluded: chain I residue 989 LEU Chi-restraints excluded: chain I residue 1085 MET Chi-restraints excluded: chain I residue 1134 GLN Chi-restraints excluded: chain I residue 1154 ASP Chi-restraints excluded: chain I residue 1159 VAL Chi-restraints excluded: chain I residue 1225 VAL Chi-restraints excluded: chain I residue 1240 ASP Chi-restraints excluded: chain I residue 1295 SER Chi-restraints excluded: chain I residue 1298 VAL Chi-restraints excluded: chain I residue 1319 MET Chi-restraints excluded: chain J residue 83 VAL Chi-restraints excluded: chain J residue 176 PHE Chi-restraints excluded: chain J residue 198 CYS Chi-restraints excluded: chain J residue 212 THR Chi-restraints excluded: chain J residue 285 LEU Chi-restraints excluded: chain J residue 352 ARG Chi-restraints excluded: chain J residue 354 VAL Chi-restraints excluded: chain J residue 357 VAL Chi-restraints excluded: chain J residue 410 ASP Chi-restraints excluded: chain J residue 416 ILE Chi-restraints excluded: chain J residue 424 ASN Chi-restraints excluded: chain J residue 430 HIS Chi-restraints excluded: chain J residue 468 VAL Chi-restraints excluded: chain J residue 501 VAL Chi-restraints excluded: chain J residue 507 VAL Chi-restraints excluded: chain J residue 706 VAL Chi-restraints excluded: chain J residue 708 ASN Chi-restraints excluded: chain J residue 765 GLU Chi-restraints excluded: chain J residue 805 GLN Chi-restraints excluded: chain J residue 816 THR Chi-restraints excluded: chain J residue 826 ILE Chi-restraints excluded: chain J residue 831 VAL Chi-restraints excluded: chain J residue 844 THR Chi-restraints excluded: chain J residue 857 LEU Chi-restraints excluded: chain J residue 882 VAL Chi-restraints excluded: chain J residue 889 ASP Chi-restraints excluded: chain J residue 967 VAL Chi-restraints excluded: chain J residue 974 VAL Chi-restraints excluded: chain J residue 1035 VAL Chi-restraints excluded: chain J residue 1066 GLU Chi-restraints excluded: chain J residue 1095 MET Chi-restraints excluded: chain J residue 1146 GLU Chi-restraints excluded: chain J residue 1258 ARG Chi-restraints excluded: chain J residue 1267 VAL Chi-restraints excluded: chain J residue 1281 GLU Chi-restraints excluded: chain J residue 1307 LEU Chi-restraints excluded: chain K residue 59 ILE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 320 random chunks: chunk 298 optimal weight: 0.9980 chunk 34 optimal weight: 0.9990 chunk 176 optimal weight: 6.9990 chunk 226 optimal weight: 1.9990 chunk 175 optimal weight: 0.9980 chunk 260 optimal weight: 8.9990 chunk 172 optimal weight: 0.7980 chunk 308 optimal weight: 2.9990 chunk 193 optimal weight: 0.0060 chunk 188 optimal weight: 5.9990 chunk 142 optimal weight: 1.9990 overall best weight: 0.7598 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: G 137 ASN ** I 618 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 799 ASN J 229 GLN J1044 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8004 moved from start: 0.1531 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.093 26626 Z= 0.170 Angle : 0.514 9.249 36235 Z= 0.267 Chirality : 0.041 0.231 4153 Planarity : 0.003 0.056 4520 Dihedral : 14.458 138.933 4336 Min Nonbonded Distance : 1.979 Molprobity Statistics. All-atom Clashscore : 9.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.46 % Favored : 94.54 % Rotamer: Outliers : 4.23 % Allowed : 17.61 % Favored : 78.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.10 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.54 (0.15), residues: 3150 helix: 1.03 (0.16), residues: 1083 sheet: -0.33 (0.26), residues: 393 loop : -1.33 (0.14), residues: 1674 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP J 33 HIS 0.004 0.001 HIS G 23 PHE 0.019 0.001 PHE I 337 TYR 0.018 0.001 TYR I 123 ARG 0.012 0.000 ARG J 133 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6300 Ramachandran restraints generated. 3150 Oldfield, 0 Emsley, 3150 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6300 Ramachandran restraints generated. 3150 Oldfield, 0 Emsley, 3150 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 466 residues out of total 2699 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 114 poor density : 352 time to evaluate : 3.310 Fit side-chains revert: symmetry clash REVERT: H 17 GLU cc_start: 0.7740 (tm-30) cc_final: 0.7471 (tm-30) REVERT: H 103 ASN cc_start: 0.7858 (m-40) cc_final: 0.7646 (m-40) REVERT: I 33 ASP cc_start: 0.7747 (m-30) cc_final: 0.7469 (m-30) REVERT: I 173 ASN cc_start: 0.8288 (p0) cc_final: 0.7937 (p0) REVERT: I 189 ASP cc_start: 0.8076 (OUTLIER) cc_final: 0.7698 (m-30) REVERT: I 191 LYS cc_start: 0.8760 (mptt) cc_final: 0.8485 (mmtp) REVERT: I 195 PHE cc_start: 0.8790 (m-80) cc_final: 0.8426 (m-80) REVERT: I 200 ARG cc_start: 0.7722 (mmm-85) cc_final: 0.7511 (mmm-85) REVERT: I 214 ASN cc_start: 0.8338 (t0) cc_final: 0.8115 (t0) REVERT: I 321 LEU cc_start: 0.7357 (mp) cc_final: 0.6862 (tt) REVERT: I 369 MET cc_start: 0.8778 (tmm) cc_final: 0.8575 (tmm) REVERT: I 376 PRO cc_start: 0.8558 (Cg_endo) cc_final: 0.8301 (Cg_exo) REVERT: I 490 GLN cc_start: 0.7463 (tp40) cc_final: 0.7218 (tp-100) REVERT: I 518 ASN cc_start: 0.8002 (OUTLIER) cc_final: 0.7643 (p0) REVERT: I 538 LEU cc_start: 0.9190 (OUTLIER) cc_final: 0.8886 (pt) REVERT: I 957 LYS cc_start: 0.7430 (mtmt) cc_final: 0.7118 (mttm) REVERT: I 1085 MET cc_start: 0.9122 (OUTLIER) cc_final: 0.8843 (mmm) REVERT: I 1108 ASN cc_start: 0.8811 (p0) cc_final: 0.8328 (p0) REVERT: I 1134 GLN cc_start: 0.8309 (OUTLIER) cc_final: 0.6998 (pp30) REVERT: I 1273 MET cc_start: 0.8588 (mtp) cc_final: 0.8205 (mtp) REVERT: J 81 ARG cc_start: 0.7649 (tmm-80) cc_final: 0.7430 (ttp-110) REVERT: J 352 ARG cc_start: 0.8641 (OUTLIER) cc_final: 0.8030 (ptm160) REVERT: J 497 GLU cc_start: 0.7573 (mm-30) cc_final: 0.7334 (mt-10) REVERT: J 765 GLU cc_start: 0.8448 (OUTLIER) cc_final: 0.7026 (pp20) REVERT: J 847 ASP cc_start: 0.8156 (OUTLIER) cc_final: 0.7770 (p0) REVERT: J 889 ASP cc_start: 0.8030 (OUTLIER) cc_final: 0.7697 (m-30) REVERT: J 999 TYR cc_start: 0.6637 (t80) cc_final: 0.6361 (t80) REVERT: J 1066 GLU cc_start: 0.3048 (OUTLIER) cc_final: 0.2451 (pm20) REVERT: J 1189 MET cc_start: 0.7059 (mmt) cc_final: 0.6643 (tmm) REVERT: J 1281 GLU cc_start: 0.8188 (OUTLIER) cc_final: 0.7958 (tt0) REVERT: J 1371 ARG cc_start: 0.7572 (mtm110) cc_final: 0.7124 (ptp-170) REVERT: K 74 GLU cc_start: 0.6818 (mm-30) cc_final: 0.6606 (mt-10) outliers start: 114 outliers final: 83 residues processed: 439 average time/residue: 0.3916 time to fit residues: 270.0241 Evaluate side-chains 426 residues out of total 2699 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 94 poor density : 332 time to evaluate : 2.938 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 19 VAL Chi-restraints excluded: chain G residue 90 VAL Chi-restraints excluded: chain G residue 98 VAL Chi-restraints excluded: chain G residue 118 ASP Chi-restraints excluded: chain G residue 127 GLN Chi-restraints excluded: chain G residue 198 LEU Chi-restraints excluded: chain G residue 205 MET Chi-restraints excluded: chain G residue 207 THR Chi-restraints excluded: chain H residue 28 LEU Chi-restraints excluded: chain H residue 90 VAL Chi-restraints excluded: chain H residue 144 ILE Chi-restraints excluded: chain H residue 146 VAL Chi-restraints excluded: chain H residue 174 ASP Chi-restraints excluded: chain H residue 188 GLU Chi-restraints excluded: chain H residue 198 LEU Chi-restraints excluded: chain I residue 11 ILE Chi-restraints excluded: chain I residue 28 LEU Chi-restraints excluded: chain I residue 47 TYR Chi-restraints excluded: chain I residue 98 VAL Chi-restraints excluded: chain I residue 104 ILE Chi-restraints excluded: chain I residue 122 VAL Chi-restraints excluded: chain I residue 189 ASP Chi-restraints excluded: chain I residue 228 VAL Chi-restraints excluded: chain I residue 234 ASP Chi-restraints excluded: chain I residue 287 VAL Chi-restraints excluded: chain I residue 320 ASP Chi-restraints excluded: chain I residue 377 THR Chi-restraints excluded: chain I residue 503 LYS Chi-restraints excluded: chain I residue 518 ASN Chi-restraints excluded: chain I residue 538 LEU Chi-restraints excluded: chain I residue 539 THR Chi-restraints excluded: chain I residue 547 VAL Chi-restraints excluded: chain I residue 615 VAL Chi-restraints excluded: chain I residue 620 ASN Chi-restraints excluded: chain I residue 623 LEU Chi-restraints excluded: chain I residue 635 THR Chi-restraints excluded: chain I residue 650 VAL Chi-restraints excluded: chain I residue 651 ASP Chi-restraints excluded: chain I residue 663 VAL Chi-restraints excluded: chain I residue 697 LYS Chi-restraints excluded: chain I residue 765 ILE Chi-restraints excluded: chain I residue 870 ILE Chi-restraints excluded: chain I residue 924 VAL Chi-restraints excluded: chain I residue 946 LEU Chi-restraints excluded: chain I residue 989 LEU Chi-restraints excluded: chain I residue 990 ASP Chi-restraints excluded: chain I residue 1056 VAL Chi-restraints excluded: chain I residue 1085 MET Chi-restraints excluded: chain I residue 1134 GLN Chi-restraints excluded: chain I residue 1159 VAL Chi-restraints excluded: chain I residue 1225 VAL Chi-restraints excluded: chain I residue 1240 ASP Chi-restraints excluded: chain I residue 1295 SER Chi-restraints excluded: chain I residue 1298 VAL Chi-restraints excluded: chain J residue 83 VAL Chi-restraints excluded: chain J residue 119 SER Chi-restraints excluded: chain J residue 176 PHE Chi-restraints excluded: chain J residue 198 CYS Chi-restraints excluded: chain J residue 212 THR Chi-restraints excluded: chain J residue 227 PHE Chi-restraints excluded: chain J residue 347 VAL Chi-restraints excluded: chain J residue 352 ARG Chi-restraints excluded: chain J residue 354 VAL Chi-restraints excluded: chain J residue 410 ASP Chi-restraints excluded: chain J residue 416 ILE Chi-restraints excluded: chain J residue 424 ASN Chi-restraints excluded: chain J residue 430 HIS Chi-restraints excluded: chain J residue 468 VAL Chi-restraints excluded: chain J residue 501 VAL Chi-restraints excluded: chain J residue 507 VAL Chi-restraints excluded: chain J residue 525 MET Chi-restraints excluded: chain J residue 547 ARG Chi-restraints excluded: chain J residue 706 VAL Chi-restraints excluded: chain J residue 708 ASN Chi-restraints excluded: chain J residue 765 GLU Chi-restraints excluded: chain J residue 805 GLN Chi-restraints excluded: chain J residue 816 THR Chi-restraints excluded: chain J residue 826 ILE Chi-restraints excluded: chain J residue 831 VAL Chi-restraints excluded: chain J residue 844 THR Chi-restraints excluded: chain J residue 847 ASP Chi-restraints excluded: chain J residue 857 LEU Chi-restraints excluded: chain J residue 882 VAL Chi-restraints excluded: chain J residue 889 ASP Chi-restraints excluded: chain J residue 967 VAL Chi-restraints excluded: chain J residue 974 VAL Chi-restraints excluded: chain J residue 1035 VAL Chi-restraints excluded: chain J residue 1066 GLU Chi-restraints excluded: chain J residue 1095 MET Chi-restraints excluded: chain J residue 1146 GLU Chi-restraints excluded: chain J residue 1267 VAL Chi-restraints excluded: chain J residue 1281 GLU Chi-restraints excluded: chain J residue 1307 LEU Chi-restraints excluded: chain K residue 59 ILE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 320 random chunks: chunk 190 optimal weight: 1.9990 chunk 123 optimal weight: 0.9990 chunk 184 optimal weight: 5.9990 chunk 92 optimal weight: 5.9990 chunk 60 optimal weight: 20.0000 chunk 59 optimal weight: 6.9990 chunk 196 optimal weight: 10.0000 chunk 210 optimal weight: 8.9990 chunk 152 optimal weight: 2.9990 chunk 28 optimal weight: 5.9990 chunk 242 optimal weight: 6.9990 overall best weight: 3.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: G 137 ASN H 103 ASN I 86 GLN ** I 618 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 620 ASN I 799 ASN J 229 GLN J1044 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8113 moved from start: 0.1561 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.074 26626 Z= 0.516 Angle : 0.669 10.877 36235 Z= 0.344 Chirality : 0.047 0.239 4153 Planarity : 0.005 0.055 4520 Dihedral : 14.699 139.083 4334 Min Nonbonded Distance : 1.925 Molprobity Statistics. All-atom Clashscore : 10.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.95 % Favored : 93.05 % Rotamer: Outliers : 4.86 % Allowed : 17.50 % Favored : 77.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.10 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.95 (0.15), residues: 3150 helix: 0.54 (0.16), residues: 1088 sheet: -0.59 (0.26), residues: 395 loop : -1.46 (0.14), residues: 1667 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP J 409 HIS 0.009 0.001 HIS G 23 PHE 0.021 0.002 PHE I 337 TYR 0.023 0.002 TYR G 177 ARG 0.013 0.001 ARG J 133 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6300 Ramachandran restraints generated. 3150 Oldfield, 0 Emsley, 3150 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6300 Ramachandran restraints generated. 3150 Oldfield, 0 Emsley, 3150 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 467 residues out of total 2699 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 131 poor density : 336 time to evaluate : 3.229 Fit side-chains revert: symmetry clash REVERT: G 93 GLN cc_start: 0.7304 (mm-40) cc_final: 0.6907 (mm-40) REVERT: G 185 TYR cc_start: 0.8775 (p90) cc_final: 0.8410 (p90) REVERT: H 17 GLU cc_start: 0.7825 (tm-30) cc_final: 0.7440 (tm-30) REVERT: H 102 LEU cc_start: 0.8985 (tp) cc_final: 0.8752 (tp) REVERT: H 103 ASN cc_start: 0.8249 (OUTLIER) cc_final: 0.7975 (p0) REVERT: I 33 ASP cc_start: 0.7915 (m-30) cc_final: 0.7621 (m-30) REVERT: I 189 ASP cc_start: 0.8150 (m-30) cc_final: 0.7783 (m-30) REVERT: I 191 LYS cc_start: 0.8810 (mptt) cc_final: 0.8517 (mmtp) REVERT: I 195 PHE cc_start: 0.8895 (m-80) cc_final: 0.8586 (m-80) REVERT: I 239 MET cc_start: 0.3358 (OUTLIER) cc_final: 0.2993 (tmm) REVERT: I 376 PRO cc_start: 0.8656 (Cg_endo) cc_final: 0.8394 (Cg_exo) REVERT: I 524 ILE cc_start: 0.8938 (tp) cc_final: 0.8555 (tp) REVERT: I 525 THR cc_start: 0.9246 (OUTLIER) cc_final: 0.8970 (m) REVERT: I 538 LEU cc_start: 0.9340 (OUTLIER) cc_final: 0.9031 (pt) REVERT: I 696 ASP cc_start: 0.7983 (t70) cc_final: 0.7770 (t70) REVERT: I 814 ASP cc_start: 0.8005 (m-30) cc_final: 0.7578 (m-30) REVERT: I 1085 MET cc_start: 0.9136 (OUTLIER) cc_final: 0.8844 (mmm) REVERT: I 1134 GLN cc_start: 0.8512 (OUTLIER) cc_final: 0.7107 (pp30) REVERT: I 1216 ARG cc_start: 0.8824 (OUTLIER) cc_final: 0.8462 (ptt180) REVERT: J 81 ARG cc_start: 0.7666 (tmm-80) cc_final: 0.7412 (ttp-110) REVERT: J 199 GLU cc_start: 0.7710 (mt-10) cc_final: 0.7472 (pt0) REVERT: J 275 ARG cc_start: 0.7462 (mmp80) cc_final: 0.7257 (mmt180) REVERT: J 627 THR cc_start: 0.9484 (OUTLIER) cc_final: 0.9232 (m) REVERT: J 707 ILE cc_start: 0.8545 (tp) cc_final: 0.8215 (mm) REVERT: J 724 MET cc_start: 0.8492 (mtm) cc_final: 0.8207 (mtm) REVERT: J 889 ASP cc_start: 0.8082 (OUTLIER) cc_final: 0.7766 (m-30) REVERT: J 999 TYR cc_start: 0.6624 (t80) cc_final: 0.6336 (t80) REVERT: J 1168 GLU cc_start: 0.5970 (OUTLIER) cc_final: 0.5545 (mt-10) REVERT: J 1189 MET cc_start: 0.7147 (mmt) cc_final: 0.6670 (tmm) REVERT: J 1281 GLU cc_start: 0.8372 (OUTLIER) cc_final: 0.8161 (tt0) REVERT: J 1371 ARG cc_start: 0.7725 (mtm110) cc_final: 0.7449 (ttp80) outliers start: 131 outliers final: 91 residues processed: 440 average time/residue: 0.3995 time to fit residues: 278.5149 Evaluate side-chains 426 residues out of total 2699 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 102 poor density : 324 time to evaluate : 2.774 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 19 VAL Chi-restraints excluded: chain G residue 90 VAL Chi-restraints excluded: chain G residue 98 VAL Chi-restraints excluded: chain G residue 118 ASP Chi-restraints excluded: chain G residue 198 LEU Chi-restraints excluded: chain G residue 205 MET Chi-restraints excluded: chain H residue 28 LEU Chi-restraints excluded: chain H residue 90 VAL Chi-restraints excluded: chain H residue 100 LEU Chi-restraints excluded: chain H residue 103 ASN Chi-restraints excluded: chain H residue 144 ILE Chi-restraints excluded: chain H residue 146 VAL Chi-restraints excluded: chain H residue 173 VAL Chi-restraints excluded: chain H residue 174 ASP Chi-restraints excluded: chain H residue 188 GLU Chi-restraints excluded: chain H residue 198 LEU Chi-restraints excluded: chain I residue 11 ILE Chi-restraints excluded: chain I residue 21 VAL Chi-restraints excluded: chain I residue 47 TYR Chi-restraints excluded: chain I residue 72 SER Chi-restraints excluded: chain I residue 98 VAL Chi-restraints excluded: chain I residue 122 VAL Chi-restraints excluded: chain I residue 228 VAL Chi-restraints excluded: chain I residue 234 ASP Chi-restraints excluded: chain I residue 239 MET Chi-restraints excluded: chain I residue 287 VAL Chi-restraints excluded: chain I residue 320 ASP Chi-restraints excluded: chain I residue 503 LYS Chi-restraints excluded: chain I residue 518 ASN Chi-restraints excluded: chain I residue 525 THR Chi-restraints excluded: chain I residue 538 LEU Chi-restraints excluded: chain I residue 539 THR Chi-restraints excluded: chain I residue 547 VAL Chi-restraints excluded: chain I residue 561 ILE Chi-restraints excluded: chain I residue 615 VAL Chi-restraints excluded: chain I residue 622 ASN Chi-restraints excluded: chain I residue 623 LEU Chi-restraints excluded: chain I residue 635 THR Chi-restraints excluded: chain I residue 650 VAL Chi-restraints excluded: chain I residue 651 ASP Chi-restraints excluded: chain I residue 663 VAL Chi-restraints excluded: chain I residue 681 MET Chi-restraints excluded: chain I residue 697 LYS Chi-restraints excluded: chain I residue 765 ILE Chi-restraints excluded: chain I residue 802 VAL Chi-restraints excluded: chain I residue 870 ILE Chi-restraints excluded: chain I residue 924 VAL Chi-restraints excluded: chain I residue 946 LEU Chi-restraints excluded: chain I residue 989 LEU Chi-restraints excluded: chain I residue 990 ASP Chi-restraints excluded: chain I residue 1056 VAL Chi-restraints excluded: chain I residue 1085 MET Chi-restraints excluded: chain I residue 1092 THR Chi-restraints excluded: chain I residue 1134 GLN Chi-restraints excluded: chain I residue 1159 VAL Chi-restraints excluded: chain I residue 1216 ARG Chi-restraints excluded: chain I residue 1225 VAL Chi-restraints excluded: chain I residue 1240 ASP Chi-restraints excluded: chain I residue 1295 SER Chi-restraints excluded: chain I residue 1298 VAL Chi-restraints excluded: chain I residue 1319 MET Chi-restraints excluded: chain J residue 83 VAL Chi-restraints excluded: chain J residue 119 SER Chi-restraints excluded: chain J residue 176 PHE Chi-restraints excluded: chain J residue 198 CYS Chi-restraints excluded: chain J residue 212 THR Chi-restraints excluded: chain J residue 285 LEU Chi-restraints excluded: chain J residue 347 VAL Chi-restraints excluded: chain J residue 352 ARG Chi-restraints excluded: chain J residue 354 VAL Chi-restraints excluded: chain J residue 374 LEU Chi-restraints excluded: chain J residue 408 VAL Chi-restraints excluded: chain J residue 410 ASP Chi-restraints excluded: chain J residue 416 ILE Chi-restraints excluded: chain J residue 424 ASN Chi-restraints excluded: chain J residue 430 HIS Chi-restraints excluded: chain J residue 468 VAL Chi-restraints excluded: chain J residue 501 VAL Chi-restraints excluded: chain J residue 507 VAL Chi-restraints excluded: chain J residue 627 THR Chi-restraints excluded: chain J residue 706 VAL Chi-restraints excluded: chain J residue 708 ASN Chi-restraints excluded: chain J residue 755 ILE Chi-restraints excluded: chain J residue 765 GLU Chi-restraints excluded: chain J residue 805 GLN Chi-restraints excluded: chain J residue 816 THR Chi-restraints excluded: chain J residue 826 ILE Chi-restraints excluded: chain J residue 831 VAL Chi-restraints excluded: chain J residue 844 THR Chi-restraints excluded: chain J residue 857 LEU Chi-restraints excluded: chain J residue 882 VAL Chi-restraints excluded: chain J residue 889 ASP Chi-restraints excluded: chain J residue 967 VAL Chi-restraints excluded: chain J residue 974 VAL Chi-restraints excluded: chain J residue 1035 VAL Chi-restraints excluded: chain J residue 1095 MET Chi-restraints excluded: chain J residue 1146 GLU Chi-restraints excluded: chain J residue 1168 GLU Chi-restraints excluded: chain J residue 1267 VAL Chi-restraints excluded: chain J residue 1281 GLU Chi-restraints excluded: chain J residue 1307 LEU Chi-restraints excluded: chain K residue 59 ILE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 320 random chunks: chunk 280 optimal weight: 8.9990 chunk 295 optimal weight: 2.9990 chunk 269 optimal weight: 0.4980 chunk 287 optimal weight: 9.9990 chunk 172 optimal weight: 0.7980 chunk 125 optimal weight: 1.9990 chunk 225 optimal weight: 0.6980 chunk 88 optimal weight: 0.8980 chunk 259 optimal weight: 0.9990 chunk 271 optimal weight: 3.9990 chunk 286 optimal weight: 0.7980 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: G 103 ASN G 137 ASN I 46 GLN ** I 618 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 799 ASN I 955 GLN J 229 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8026 moved from start: 0.1607 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 26626 Z= 0.171 Angle : 0.535 9.992 36235 Z= 0.278 Chirality : 0.041 0.210 4153 Planarity : 0.004 0.056 4520 Dihedral : 14.517 139.379 4334 Min Nonbonded Distance : 2.001 Molprobity Statistics. All-atom Clashscore : 9.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.33 % Favored : 94.67 % Rotamer: Outliers : 3.45 % Allowed : 18.95 % Favored : 77.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.10 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.64 (0.15), residues: 3150 helix: 0.84 (0.16), residues: 1093 sheet: -0.23 (0.27), residues: 372 loop : -1.36 (0.14), residues: 1685 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP J 33 HIS 0.003 0.001 HIS J 865 PHE 0.019 0.001 PHE I 337 TYR 0.019 0.001 TYR I 123 ARG 0.012 0.000 ARG J 133 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6300 Ramachandran restraints generated. 3150 Oldfield, 0 Emsley, 3150 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6300 Ramachandran restraints generated. 3150 Oldfield, 0 Emsley, 3150 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 438 residues out of total 2699 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 93 poor density : 345 time to evaluate : 3.048 Fit side-chains revert: symmetry clash REVERT: G 93 GLN cc_start: 0.7313 (mm-40) cc_final: 0.6945 (mm-40) REVERT: H 17 GLU cc_start: 0.7789 (tm-30) cc_final: 0.7457 (tm-30) REVERT: H 23 HIS cc_start: 0.8437 (t-90) cc_final: 0.8161 (t-90) REVERT: H 103 ASN cc_start: 0.8021 (m-40) cc_final: 0.7669 (p0) REVERT: I 33 ASP cc_start: 0.7772 (m-30) cc_final: 0.7484 (m-30) REVERT: I 173 ASN cc_start: 0.8312 (p0) cc_final: 0.7948 (p0) REVERT: I 189 ASP cc_start: 0.8116 (m-30) cc_final: 0.7731 (m-30) REVERT: I 191 LYS cc_start: 0.8782 (mptt) cc_final: 0.8488 (mmtp) REVERT: I 195 PHE cc_start: 0.8808 (m-80) cc_final: 0.8474 (m-80) REVERT: I 200 ARG cc_start: 0.7827 (mmm-85) cc_final: 0.7597 (mmm-85) REVERT: I 321 LEU cc_start: 0.7599 (mp) cc_final: 0.7214 (tt) REVERT: I 376 PRO cc_start: 0.8509 (Cg_endo) cc_final: 0.8257 (Cg_exo) REVERT: I 538 LEU cc_start: 0.9235 (OUTLIER) cc_final: 0.8931 (pt) REVERT: I 696 ASP cc_start: 0.7840 (t70) cc_final: 0.7466 (t70) REVERT: I 957 LYS cc_start: 0.7526 (mtmt) cc_final: 0.7063 (mttm) REVERT: I 1085 MET cc_start: 0.9116 (OUTLIER) cc_final: 0.8832 (mmm) REVERT: I 1108 ASN cc_start: 0.8777 (p0) cc_final: 0.8232 (p0) REVERT: I 1134 GLN cc_start: 0.8426 (OUTLIER) cc_final: 0.6973 (pp30) REVERT: I 1216 ARG cc_start: 0.8724 (OUTLIER) cc_final: 0.7689 (ptt90) REVERT: J 81 ARG cc_start: 0.7525 (tmm-80) cc_final: 0.7289 (ttp-110) REVERT: J 153 ASN cc_start: 0.6441 (OUTLIER) cc_final: 0.5658 (p0) REVERT: J 352 ARG cc_start: 0.8661 (OUTLIER) cc_final: 0.8203 (ptm160) REVERT: J 497 GLU cc_start: 0.7524 (mm-30) cc_final: 0.7280 (mt-10) REVERT: J 606 ASN cc_start: 0.8414 (t0) cc_final: 0.8212 (t0) REVERT: J 724 MET cc_start: 0.8484 (mtm) cc_final: 0.8194 (mtm) REVERT: J 889 ASP cc_start: 0.8152 (OUTLIER) cc_final: 0.7860 (m-30) REVERT: J 999 TYR cc_start: 0.6563 (t80) cc_final: 0.6290 (t80) REVERT: J 1371 ARG cc_start: 0.7568 (mtm110) cc_final: 0.7124 (ptp-170) REVERT: K 74 GLU cc_start: 0.6978 (mm-30) cc_final: 0.6722 (mt-10) outliers start: 93 outliers final: 81 residues processed: 419 average time/residue: 0.3761 time to fit residues: 247.2002 Evaluate side-chains 420 residues out of total 2699 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 88 poor density : 332 time to evaluate : 2.756 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 19 VAL Chi-restraints excluded: chain G residue 90 VAL Chi-restraints excluded: chain G residue 118 ASP Chi-restraints excluded: chain G residue 198 LEU Chi-restraints excluded: chain G residue 207 THR Chi-restraints excluded: chain H residue 28 LEU Chi-restraints excluded: chain H residue 90 VAL Chi-restraints excluded: chain H residue 144 ILE Chi-restraints excluded: chain H residue 146 VAL Chi-restraints excluded: chain H residue 173 VAL Chi-restraints excluded: chain H residue 174 ASP Chi-restraints excluded: chain H residue 188 GLU Chi-restraints excluded: chain H residue 198 LEU Chi-restraints excluded: chain I residue 11 ILE Chi-restraints excluded: chain I residue 28 LEU Chi-restraints excluded: chain I residue 47 TYR Chi-restraints excluded: chain I residue 72 SER Chi-restraints excluded: chain I residue 122 VAL Chi-restraints excluded: chain I residue 228 VAL Chi-restraints excluded: chain I residue 234 ASP Chi-restraints excluded: chain I residue 287 VAL Chi-restraints excluded: chain I residue 320 ASP Chi-restraints excluded: chain I residue 503 LYS Chi-restraints excluded: chain I residue 518 ASN Chi-restraints excluded: chain I residue 538 LEU Chi-restraints excluded: chain I residue 539 THR Chi-restraints excluded: chain I residue 547 VAL Chi-restraints excluded: chain I residue 615 VAL Chi-restraints excluded: chain I residue 622 ASN Chi-restraints excluded: chain I residue 623 LEU Chi-restraints excluded: chain I residue 635 THR Chi-restraints excluded: chain I residue 650 VAL Chi-restraints excluded: chain I residue 663 VAL Chi-restraints excluded: chain I residue 681 MET Chi-restraints excluded: chain I residue 697 LYS Chi-restraints excluded: chain I residue 765 ILE Chi-restraints excluded: chain I residue 799 ASN Chi-restraints excluded: chain I residue 870 ILE Chi-restraints excluded: chain I residue 918 LEU Chi-restraints excluded: chain I residue 924 VAL Chi-restraints excluded: chain I residue 946 LEU Chi-restraints excluded: chain I residue 964 LEU Chi-restraints excluded: chain I residue 989 LEU Chi-restraints excluded: chain I residue 990 ASP Chi-restraints excluded: chain I residue 1056 VAL Chi-restraints excluded: chain I residue 1085 MET Chi-restraints excluded: chain I residue 1134 GLN Chi-restraints excluded: chain I residue 1159 VAL Chi-restraints excluded: chain I residue 1216 ARG Chi-restraints excluded: chain I residue 1225 VAL Chi-restraints excluded: chain I residue 1240 ASP Chi-restraints excluded: chain I residue 1295 SER Chi-restraints excluded: chain I residue 1298 VAL Chi-restraints excluded: chain J residue 48 THR Chi-restraints excluded: chain J residue 83 VAL Chi-restraints excluded: chain J residue 153 ASN Chi-restraints excluded: chain J residue 166 LEU Chi-restraints excluded: chain J residue 176 PHE Chi-restraints excluded: chain J residue 198 CYS Chi-restraints excluded: chain J residue 347 VAL Chi-restraints excluded: chain J residue 352 ARG Chi-restraints excluded: chain J residue 354 VAL Chi-restraints excluded: chain J residue 408 VAL Chi-restraints excluded: chain J residue 410 ASP Chi-restraints excluded: chain J residue 416 ILE Chi-restraints excluded: chain J residue 424 ASN Chi-restraints excluded: chain J residue 430 HIS Chi-restraints excluded: chain J residue 468 VAL Chi-restraints excluded: chain J residue 501 VAL Chi-restraints excluded: chain J residue 507 VAL Chi-restraints excluded: chain J residue 706 VAL Chi-restraints excluded: chain J residue 708 ASN Chi-restraints excluded: chain J residue 765 GLU Chi-restraints excluded: chain J residue 805 GLN Chi-restraints excluded: chain J residue 816 THR Chi-restraints excluded: chain J residue 826 ILE Chi-restraints excluded: chain J residue 831 VAL Chi-restraints excluded: chain J residue 857 LEU Chi-restraints excluded: chain J residue 882 VAL Chi-restraints excluded: chain J residue 889 ASP Chi-restraints excluded: chain J residue 967 VAL Chi-restraints excluded: chain J residue 974 VAL Chi-restraints excluded: chain J residue 1035 VAL Chi-restraints excluded: chain J residue 1095 MET Chi-restraints excluded: chain J residue 1146 GLU Chi-restraints excluded: chain J residue 1267 VAL Chi-restraints excluded: chain J residue 1307 LEU Chi-restraints excluded: chain K residue 59 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 320 random chunks: chunk 188 optimal weight: 9.9990 chunk 303 optimal weight: 0.9990 chunk 185 optimal weight: 9.9990 chunk 144 optimal weight: 3.9990 chunk 211 optimal weight: 0.9990 chunk 318 optimal weight: 4.9990 chunk 293 optimal weight: 8.9990 chunk 253 optimal weight: 4.9990 chunk 26 optimal weight: 5.9990 chunk 196 optimal weight: 6.9990 chunk 155 optimal weight: 0.1980 overall best weight: 2.2388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: G 137 ASN H 103 ASN I 41 GLN ** I 618 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 799 ASN J 229 GLN J 954 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8071 moved from start: 0.1609 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.061 26626 Z= 0.344 Angle : 0.591 9.957 36235 Z= 0.304 Chirality : 0.044 0.236 4153 Planarity : 0.004 0.055 4520 Dihedral : 14.554 139.293 4334 Min Nonbonded Distance : 1.931 Molprobity Statistics. All-atom Clashscore : 10.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.25 % Favored : 93.75 % Rotamer: Outliers : 3.82 % Allowed : 18.87 % Favored : 77.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.10 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.75 (0.15), residues: 3150 helix: 0.71 (0.16), residues: 1096 sheet: -0.43 (0.26), residues: 397 loop : -1.37 (0.15), residues: 1657 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP J 409 HIS 0.005 0.001 HIS G 23 PHE 0.019 0.001 PHE I 337 TYR 0.017 0.001 TYR G 177 ARG 0.012 0.000 ARG J 133 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6300 Ramachandran restraints generated. 3150 Oldfield, 0 Emsley, 3150 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6300 Ramachandran restraints generated. 3150 Oldfield, 0 Emsley, 3150 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 436 residues out of total 2699 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 103 poor density : 333 time to evaluate : 3.194 Fit side-chains REVERT: G 93 GLN cc_start: 0.7258 (mm-40) cc_final: 0.6883 (mm-40) REVERT: H 17 GLU cc_start: 0.7819 (tm-30) cc_final: 0.7460 (tm-30) REVERT: H 23 HIS cc_start: 0.8502 (t-90) cc_final: 0.8226 (t-90) REVERT: H 97 GLU cc_start: 0.8217 (pp20) cc_final: 0.7857 (pp20) REVERT: H 103 ASN cc_start: 0.8082 (OUTLIER) cc_final: 0.7777 (p0) REVERT: I 33 ASP cc_start: 0.7851 (m-30) cc_final: 0.7560 (m-30) REVERT: I 173 ASN cc_start: 0.8399 (p0) cc_final: 0.7805 (p0) REVERT: I 189 ASP cc_start: 0.8136 (m-30) cc_final: 0.7748 (m-30) REVERT: I 191 LYS cc_start: 0.8801 (mptt) cc_final: 0.8512 (mmtp) REVERT: I 195 PHE cc_start: 0.8855 (m-80) cc_final: 0.8525 (m-80) REVERT: I 200 ARG cc_start: 0.7886 (mmm-85) cc_final: 0.7658 (mmm-85) REVERT: I 321 LEU cc_start: 0.7715 (mp) cc_final: 0.7317 (tt) REVERT: I 376 PRO cc_start: 0.8635 (Cg_endo) cc_final: 0.8319 (Cg_exo) REVERT: I 524 ILE cc_start: 0.8863 (tp) cc_final: 0.8451 (tp) REVERT: I 538 LEU cc_start: 0.9299 (OUTLIER) cc_final: 0.8955 (pt) REVERT: I 696 ASP cc_start: 0.7747 (t70) cc_final: 0.7425 (t70) REVERT: I 799 ASN cc_start: 0.8841 (OUTLIER) cc_final: 0.8215 (m110) REVERT: I 1085 MET cc_start: 0.9128 (OUTLIER) cc_final: 0.8839 (mmm) REVERT: I 1108 ASN cc_start: 0.8850 (p0) cc_final: 0.8285 (p0) REVERT: I 1134 GLN cc_start: 0.8475 (OUTLIER) cc_final: 0.7016 (pp30) REVERT: I 1203 ASP cc_start: 0.7161 (m-30) cc_final: 0.6891 (m-30) REVERT: I 1216 ARG cc_start: 0.8820 (OUTLIER) cc_final: 0.8475 (ptt180) REVERT: J 81 ARG cc_start: 0.7539 (tmm-80) cc_final: 0.7301 (ttp-110) REVERT: J 153 ASN cc_start: 0.6417 (OUTLIER) cc_final: 0.5782 (p0) REVERT: J 352 ARG cc_start: 0.8675 (OUTLIER) cc_final: 0.8336 (ptm160) REVERT: J 497 GLU cc_start: 0.7600 (mm-30) cc_final: 0.7377 (mt-10) REVERT: J 532 GLU cc_start: 0.8306 (OUTLIER) cc_final: 0.7856 (tt0) REVERT: J 606 ASN cc_start: 0.8446 (t0) cc_final: 0.8233 (t0) REVERT: J 724 MET cc_start: 0.8507 (mtm) cc_final: 0.8209 (mtm) REVERT: J 889 ASP cc_start: 0.8142 (OUTLIER) cc_final: 0.7836 (m-30) REVERT: J 999 TYR cc_start: 0.6565 (t80) cc_final: 0.6282 (t80) REVERT: J 1371 ARG cc_start: 0.7632 (mtm110) cc_final: 0.7359 (ttp80) REVERT: K 74 GLU cc_start: 0.6959 (mm-30) cc_final: 0.6646 (mt-10) outliers start: 103 outliers final: 89 residues processed: 417 average time/residue: 0.4004 time to fit residues: 261.9329 Evaluate side-chains 427 residues out of total 2699 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 99 poor density : 328 time to evaluate : 2.994 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 19 VAL Chi-restraints excluded: chain G residue 50 SER Chi-restraints excluded: chain G residue 90 VAL Chi-restraints excluded: chain G residue 98 VAL Chi-restraints excluded: chain G residue 118 ASP Chi-restraints excluded: chain G residue 198 LEU Chi-restraints excluded: chain G residue 205 MET Chi-restraints excluded: chain G residue 207 THR Chi-restraints excluded: chain H residue 28 LEU Chi-restraints excluded: chain H residue 90 VAL Chi-restraints excluded: chain H residue 103 ASN Chi-restraints excluded: chain H residue 144 ILE Chi-restraints excluded: chain H residue 146 VAL Chi-restraints excluded: chain H residue 173 VAL Chi-restraints excluded: chain H residue 174 ASP Chi-restraints excluded: chain H residue 188 GLU Chi-restraints excluded: chain H residue 198 LEU Chi-restraints excluded: chain I residue 11 ILE Chi-restraints excluded: chain I residue 28 LEU Chi-restraints excluded: chain I residue 47 TYR Chi-restraints excluded: chain I residue 72 SER Chi-restraints excluded: chain I residue 98 VAL Chi-restraints excluded: chain I residue 122 VAL Chi-restraints excluded: chain I residue 142 GLU Chi-restraints excluded: chain I residue 228 VAL Chi-restraints excluded: chain I residue 234 ASP Chi-restraints excluded: chain I residue 287 VAL Chi-restraints excluded: chain I residue 320 ASP Chi-restraints excluded: chain I residue 503 LYS Chi-restraints excluded: chain I residue 518 ASN Chi-restraints excluded: chain I residue 538 LEU Chi-restraints excluded: chain I residue 539 THR Chi-restraints excluded: chain I residue 547 VAL Chi-restraints excluded: chain I residue 615 VAL Chi-restraints excluded: chain I residue 622 ASN Chi-restraints excluded: chain I residue 623 LEU Chi-restraints excluded: chain I residue 635 THR Chi-restraints excluded: chain I residue 650 VAL Chi-restraints excluded: chain I residue 651 ASP Chi-restraints excluded: chain I residue 663 VAL Chi-restraints excluded: chain I residue 681 MET Chi-restraints excluded: chain I residue 697 LYS Chi-restraints excluded: chain I residue 765 ILE Chi-restraints excluded: chain I residue 799 ASN Chi-restraints excluded: chain I residue 870 ILE Chi-restraints excluded: chain I residue 918 LEU Chi-restraints excluded: chain I residue 924 VAL Chi-restraints excluded: chain I residue 946 LEU Chi-restraints excluded: chain I residue 964 LEU Chi-restraints excluded: chain I residue 989 LEU Chi-restraints excluded: chain I residue 990 ASP Chi-restraints excluded: chain I residue 1056 VAL Chi-restraints excluded: chain I residue 1085 MET Chi-restraints excluded: chain I residue 1106 ARG Chi-restraints excluded: chain I residue 1134 GLN Chi-restraints excluded: chain I residue 1159 VAL Chi-restraints excluded: chain I residue 1216 ARG Chi-restraints excluded: chain I residue 1225 VAL Chi-restraints excluded: chain I residue 1240 ASP Chi-restraints excluded: chain I residue 1295 SER Chi-restraints excluded: chain I residue 1298 VAL Chi-restraints excluded: chain I residue 1319 MET Chi-restraints excluded: chain J residue 48 THR Chi-restraints excluded: chain J residue 83 VAL Chi-restraints excluded: chain J residue 153 ASN Chi-restraints excluded: chain J residue 166 LEU Chi-restraints excluded: chain J residue 176 PHE Chi-restraints excluded: chain J residue 198 CYS Chi-restraints excluded: chain J residue 347 VAL Chi-restraints excluded: chain J residue 352 ARG Chi-restraints excluded: chain J residue 354 VAL Chi-restraints excluded: chain J residue 374 LEU Chi-restraints excluded: chain J residue 408 VAL Chi-restraints excluded: chain J residue 410 ASP Chi-restraints excluded: chain J residue 416 ILE Chi-restraints excluded: chain J residue 424 ASN Chi-restraints excluded: chain J residue 430 HIS Chi-restraints excluded: chain J residue 468 VAL Chi-restraints excluded: chain J residue 501 VAL Chi-restraints excluded: chain J residue 507 VAL Chi-restraints excluded: chain J residue 532 GLU Chi-restraints excluded: chain J residue 706 VAL Chi-restraints excluded: chain J residue 708 ASN Chi-restraints excluded: chain J residue 765 GLU Chi-restraints excluded: chain J residue 805 GLN Chi-restraints excluded: chain J residue 816 THR Chi-restraints excluded: chain J residue 826 ILE Chi-restraints excluded: chain J residue 831 VAL Chi-restraints excluded: chain J residue 857 LEU Chi-restraints excluded: chain J residue 882 VAL Chi-restraints excluded: chain J residue 889 ASP Chi-restraints excluded: chain J residue 967 VAL Chi-restraints excluded: chain J residue 974 VAL Chi-restraints excluded: chain J residue 1035 VAL Chi-restraints excluded: chain J residue 1095 MET Chi-restraints excluded: chain J residue 1146 GLU Chi-restraints excluded: chain J residue 1267 VAL Chi-restraints excluded: chain J residue 1307 LEU Chi-restraints excluded: chain K residue 59 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 320 random chunks: chunk 201 optimal weight: 0.0050 chunk 270 optimal weight: 2.9990 chunk 77 optimal weight: 10.0000 chunk 234 optimal weight: 1.9990 chunk 37 optimal weight: 0.7980 chunk 70 optimal weight: 0.9980 chunk 254 optimal weight: 0.8980 chunk 106 optimal weight: 0.9980 chunk 261 optimal weight: 0.9990 chunk 32 optimal weight: 6.9990 chunk 46 optimal weight: 0.9980 overall best weight: 0.7394 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: G 137 ASN H 103 ASN ** I 618 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 799 ASN J 229 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3824 r_free = 0.3824 target = 0.166163 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3299 r_free = 0.3299 target = 0.120406 restraints weight = 30859.226| |-----------------------------------------------------------------------------| r_work (start): 0.3271 rms_B_bonded: 2.72 r_work: 0.2898 rms_B_bonded: 3.47 restraints_weight: 0.5000 r_work (final): 0.2898 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8354 moved from start: 0.1714 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 26626 Z= 0.168 Angle : 0.534 10.114 36235 Z= 0.277 Chirality : 0.041 0.207 4153 Planarity : 0.004 0.056 4520 Dihedral : 14.448 139.265 4334 Min Nonbonded Distance : 1.997 Molprobity Statistics. All-atom Clashscore : 9.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.24 % Favored : 94.76 % Rotamer: Outliers : 3.45 % Allowed : 19.35 % Favored : 77.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.10 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.54 (0.15), residues: 3150 helix: 0.91 (0.16), residues: 1092 sheet: -0.15 (0.27), residues: 370 loop : -1.30 (0.14), residues: 1688 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP J 33 HIS 0.003 0.001 HIS J 865 PHE 0.020 0.001 PHE I 337 TYR 0.018 0.001 TYR I 123 ARG 0.012 0.000 ARG J 133 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 6089.62 seconds wall clock time: 111 minutes 26.64 seconds (6686.64 seconds total)