Starting phenix.real_space_refine on Wed Feb 21 16:51:52 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7szj_25570/02_2024/7szj_25570_trim_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7szj_25570/02_2024/7szj_25570.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.11 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7szj_25570/02_2024/7szj_25570.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7szj_25570/02_2024/7szj_25570.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7szj_25570/02_2024/7szj_25570_trim_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7szj_25570/02_2024/7szj_25570_trim_updated.pdb" } resolution = 3.11 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= -0.001 sd= 0.114 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 106 5.49 5 Mg 1 5.21 5 S 128 5.16 5 C 19211 2.51 5 N 5523 2.21 5 O 6202 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A GLU 206": "OE1" <-> "OE2" Residue "C ASP 23": "OD1" <-> "OD2" Residue "C TYR 47": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 179": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 244": "OE1" <-> "OE2" Residue "C GLU 412": "OE1" <-> "OE2" Residue "C PHE 545": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 546": "OE1" <-> "OE2" Residue "C ASP 549": "OD1" <-> "OD2" Residue "C ASP 648": "OD1" <-> "OD2" Residue "C TYR 1053": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 1168": "OE1" <-> "OE2" Residue "D TYR 46": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ASP 129": "OD1" <-> "OD2" Residue "D TYR 144": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ASP 174": "OD1" <-> "OD2" Residue "D GLU 443": "OE1" <-> "OE2" Residue "D GLU 562": "OE1" <-> "OE2" Residue "D GLU 648": "OE1" <-> "OE2" Residue "D PHE 1274": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F GLU 104": "OE1" <-> "OE2" Residue "F PHE 256": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F ASP 403": "OD1" <-> "OD2" Residue "F TYR 425": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.09s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5238/modules/chem_data/mon_lib" Total number of atoms: 31173 Number of models: 1 Model: "" Number of chains: 10 Chain: "A" Number of atoms: 1794 Number of conformers: 1 Conformer: "" Number of residues, atoms: 231, 1794 Classifications: {'peptide': 231} Link IDs: {'PTRANS': 9, 'TRANS': 221} Chain: "B" Number of atoms: 1786 Number of conformers: 1 Conformer: "" Number of residues, atoms: 230, 1786 Classifications: {'peptide': 230} Link IDs: {'PTRANS': 9, 'TRANS': 220} Chain: "C" Number of atoms: 10570 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1340, 10570 Classifications: {'peptide': 1340} Modifications used: {'COO': 1} Link IDs: {'CIS': 2, 'PCIS': 1, 'PTRANS': 55, 'TRANS': 1281} Chain: "D" Number of atoms: 10382 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1340, 10382 Classifications: {'peptide': 1340} Incomplete info: {'truncation_to_alanine': 8} Link IDs: {'CIS': 4, 'PTRANS': 55, 'TRANS': 1280} Chain breaks: 2 Unresolved non-hydrogen bonds: 29 Unresolved non-hydrogen angles: 36 Unresolved non-hydrogen dihedrals: 22 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'GLU:plan': 2, 'ASN:plan1': 2, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 19 Chain: "E" Number of atoms: 605 Number of conformers: 1 Conformer: "" Number of residues, atoms: 76, 605 Classifications: {'peptide': 76} Link IDs: {'PTRANS': 2, 'TRANS': 73} Chain: "F" Number of atoms: 3799 Number of conformers: 1 Conformer: "" Number of residues, atoms: 466, 3799 Classifications: {'peptide': 466} Link IDs: {'PTRANS': 14, 'TRANS': 451} Chain breaks: 3 Chain: "X" Number of atoms: 1162 Number of conformers: 1 Conformer: "" Number of residues, atoms: 57, 1162 Classifications: {'DNA': 57} Link IDs: {'rna3p': 56} Chain breaks: 1 Chain: "Y" Number of atoms: 1013 Number of conformers: 1 Conformer: "" Number of residues, atoms: 49, 1013 Classifications: {'DNA': 49} Link IDs: {'rna3p': 48} Chain breaks: 1 Chain: "C" Number of atoms: 59 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 59 Unusual residues: {'RFP': 1} Classifications: {'undetermined': 1} Chain: "D" 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 14615 SG CYS D 70 64.628 116.508 81.516 1.00 34.65 S ATOM 14629 SG CYS D 72 64.329 116.955 85.439 1.00 36.54 S ATOM 14737 SG CYS D 85 63.760 119.837 83.215 1.00 39.22 S ATOM 14761 SG CYS D 88 67.167 118.538 83.641 1.00 40.02 S ATOM 20449 SG CYS D 814 101.537 96.654 28.039 1.00 28.16 S ATOM 21014 SG CYS D 888 102.173 96.436 31.666 1.00 23.24 S ATOM 21065 SG CYS D 895 100.123 93.940 30.058 1.00 14.89 S ATOM 21086 SG CYS D 898 103.580 94.008 29.413 1.00 15.21 S Time building chain proxies: 15.08, per 1000 atoms: 0.48 Number of scatterers: 31173 At special positions: 0 Unit cell: (192.64, 191.52, 165.76, 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 128 16.00 P 106 15.00 Mg 1 11.99 O 6202 8.00 N 5523 7.00 C 19211 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: 12.08 Conformation dependent library (CDL) restraints added in 5.5 seconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN D2002 " pdb="ZN ZN D2002 " - pdb=" SG CYS D 85 " pdb="ZN ZN D2002 " - pdb=" SG CYS D 88 " pdb="ZN ZN D2002 " - pdb=" SG CYS D 72 " pdb="ZN ZN D2002 " - pdb=" SG CYS D 70 " pdb=" ZN D2003 " pdb="ZN ZN D2003 " - pdb=" SG CYS D 898 " pdb="ZN ZN D2003 " - pdb=" SG CYS D 895 " pdb="ZN ZN D2003 " - pdb=" SG CYS D 888 " pdb="ZN ZN D2003 " - pdb=" SG CYS D 814 " Number of angles added : 12 7322 Ramachandran restraints generated. 3661 Oldfield, 0 Emsley, 3661 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 6836 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 127 helices and 32 sheets defined 38.4% alpha, 9.5% beta 23 base pairs and 69 stacking pairs defined. Time for finding SS restraints: 13.99 Creating SS restraints... Processing helix chain 'A' and resid 35 through 49 Processing helix chain 'A' and resid 78 through 87 removed outlier: 3.773A pdb=" N GLY A 87 " --> pdb=" O LEU A 83 " (cutoff:3.500A) Processing helix chain 'A' and resid 112 through 114 No H-bonds generated for 'chain 'A' and resid 112 through 114' Processing helix chain 'A' and resid 155 through 160 Processing helix chain 'A' and resid 213 through 232 removed outlier: 4.749A pdb=" N ALA A 230 " --> pdb=" O GLU A 226 " (cutoff:3.500A) removed outlier: 4.860A pdb=" N PHE A 231 " --> pdb=" O GLN A 227 " (cutoff:3.500A) Processing helix chain 'B' and resid 35 through 49 Processing helix chain 'B' and resid 78 through 86 Processing helix chain 'B' and resid 112 through 114 No H-bonds generated for 'chain 'B' and resid 112 through 114' Processing helix chain 'B' and resid 155 through 160 Processing helix chain 'B' and resid 213 through 232 removed outlier: 4.436A pdb=" N ALA B 230 " --> pdb=" O GLU B 226 " (cutoff:3.500A) removed outlier: 5.316A pdb=" N PHE B 231 " --> pdb=" O GLN B 227 " (cutoff:3.500A) removed outlier: 3.591A pdb=" N VAL B 232 " --> pdb=" O LEU B 228 " (cutoff:3.500A) Processing helix chain 'C' and resid 5 through 8 No H-bonds generated for 'chain 'C' and resid 5 through 8' Processing helix chain 'C' and resid 29 through 39 Processing helix chain 'C' and resid 49 through 56 Processing helix chain 'C' and resid 82 through 88 Processing helix chain 'C' and resid 164 through 166 No H-bonds generated for 'chain 'C' and resid 164 through 166' Processing helix chain 'C' and resid 207 through 213 Processing helix chain 'C' and resid 217 through 223 Processing helix chain 'C' and resid 243 through 246 Processing helix chain 'C' and resid 271 through 280 Processing helix chain 'C' and resid 289 through 294 removed outlier: 4.452A pdb=" N GLY C 294 " --> pdb=" O GLU C 290 " (cutoff:3.500A) Processing helix chain 'C' and resid 319 through 327 Processing helix chain 'C' and resid 346 through 353 Processing helix chain 'C' and resid 359 through 370 Processing helix chain 'C' and resid 378 through 389 removed outlier: 4.070A pdb=" N PHE C 389 " --> pdb=" O PHE C 385 " (cutoff:3.500A) Processing helix chain 'C' and resid 399 through 408 Processing helix chain 'C' and resid 422 through 436 Processing helix chain 'C' and resid 456 through 481 Processing helix chain 'C' and resid 495 through 507 Processing helix chain 'C' and resid 520 through 527 Processing helix chain 'C' and resid 540 through 542 No H-bonds generated for 'chain 'C' and resid 540 through 542' Processing helix chain 'C' and resid 552 through 554 No H-bonds generated for 'chain 'C' and resid 552 through 554' Processing helix chain 'C' and resid 608 through 613 removed outlier: 4.033A pdb=" N ASN C 613 " --> pdb=" O ILE C 609 " (cutoff:3.500A) Processing helix chain 'C' and resid 647 through 649 No H-bonds generated for 'chain 'C' and resid 647 through 649' Processing helix chain 'C' and resid 663 through 667 Processing helix chain 'C' and resid 671 through 673 No H-bonds generated for 'chain 'C' and resid 671 through 673' Processing helix chain 'C' and resid 676 through 688 removed outlier: 4.337A pdb=" N ARG C 687 " --> pdb=" O ALA C 683 " (cutoff:3.500A) removed outlier: 4.562A pdb=" N GLN C 688 " --> pdb=" O ASN C 684 " (cutoff:3.500A) Processing helix chain 'C' and resid 705 through 711 Processing helix chain 'C' and resid 821 through 824 No H-bonds generated for 'chain 'C' and resid 821 through 824' Processing helix chain 'C' and resid 897 through 906 Processing helix chain 'C' and resid 943 through 980 Processing helix chain 'C' and resid 986 through 991 Processing helix chain 'C' and resid 994 through 999 removed outlier: 4.528A pdb=" N LEU C 998 " --> pdb=" O ARG C 994 " (cutoff:3.500A) removed outlier: 3.762A pdb=" N GLU C 999 " --> pdb=" O ASP C 995 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 994 through 999' Processing helix chain 'C' and resid 1006 through 1037 Processing helix chain 'C' and resid 1082 through 1084 No H-bonds generated for 'chain 'C' and resid 1082 through 1084' Processing helix chain 'C' and resid 1100 through 1105 Proline residue: C1104 - end of helix Processing helix chain 'C' and resid 1110 through 1133 Processing helix chain 'C' and resid 1138 through 1150 Processing helix chain 'C' and resid 1167 through 1176 Processing helix chain 'C' and resid 1192 through 1201 Processing helix chain 'C' and resid 1239 through 1241 No H-bonds generated for 'chain 'C' and resid 1239 through 1241' Processing helix chain 'C' and resid 1272 through 1280 Processing helix chain 'C' and resid 1284 through 1292 Processing helix chain 'C' and resid 1298 through 1310 Processing helix chain 'C' and resid 1321 through 1332 Processing helix chain 'D' and resid 27 through 33 Processing helix chain 'D' and resid 95 through 99 Processing helix chain 'D' and resid 115 through 118 No H-bonds generated for 'chain 'D' and resid 115 through 118' Processing helix chain 'D' and resid 123 through 127 Processing helix chain 'D' and resid 132 through 139 Processing helix chain 'D' and resid 162 through 171 Processing helix chain 'D' and resid 182 through 191 Processing helix chain 'D' and resid 194 through 207 Processing helix chain 'D' and resid 211 through 229 Processing helix chain 'D' and resid 234 through 237 Processing helix chain 'D' and resid 247 through 249 No H-bonds generated for 'chain 'D' and resid 247 through 249' Processing helix chain 'D' and resid 264 through 285 Processing helix chain 'D' and resid 289 through 307 Processing helix chain 'D' and resid 327 through 331 removed outlier: 3.818A pdb=" N ILE D 331 " --> pdb=" O LEU D 327 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 327 through 331' Processing helix chain 'D' and resid 337 through 340 No H-bonds generated for 'chain 'D' and resid 337 through 340' Processing helix chain 'D' and resid 370 through 387 Proline residue: D 379 - end of helix Processing helix chain 'D' and resid 394 through 403 Processing helix chain 'D' and resid 406 through 415 Processing helix chain 'D' and resid 431 through 433 No H-bonds generated for 'chain 'D' and resid 431 through 433' Processing helix chain 'D' and resid 451 through 457 removed outlier: 4.222A pdb=" N ALA D 455 " --> pdb=" O LEU D 452 " (cutoff:3.500A) Processing helix chain 'D' and resid 474 through 482 Processing helix chain 'D' and resid 505 through 513 Processing helix chain 'D' and resid 530 through 538 Processing helix chain 'D' and resid 574 through 581 removed outlier: 3.899A pdb=" N MET D 581 " --> pdb=" O ALA D 577 " (cutoff:3.500A) Processing helix chain 'D' and resid 598 through 611 Processing helix chain 'D' and resid 615 through 635 Processing helix chain 'D' and resid 641 through 643 No H-bonds generated for 'chain 'D' and resid 641 through 643' Processing helix chain 'D' and resid 650 through 670 removed outlier: 3.567A pdb=" N SER D 670 " --> pdb=" O GLU D 666 " (cutoff:3.500A) Processing helix chain 'D' and resid 675 through 702 Processing helix chain 'D' and resid 721 through 727 Processing helix chain 'D' and resid 734 through 741 Processing helix chain 'D' and resid 769 through 803 removed outlier: 3.961A pdb=" N HIS D 777 " --> pdb=" O PHE D 773 " (cutoff:3.500A) removed outlier: 4.388A pdb=" N GLY D 778 " --> pdb=" O ILE D 774 " (cutoff:3.500A) removed outlier: 4.414A pdb=" N ALA D 791 " --> pdb=" O ALA D 787 " (cutoff:3.500A) Processing helix chain 'D' and resid 835 through 839 Processing helix chain 'D' and resid 866 through 874 Processing helix chain 'D' and resid 885 through 887 No H-bonds generated for 'chain 'D' and resid 885 through 887' Processing helix chain 'D' and resid 896 through 899 No H-bonds generated for 'chain 'D' and resid 896 through 899' Processing helix chain 'D' and resid 915 through 929 Proline residue: D 926 - end of helix removed outlier: 5.822A pdb=" N GLN D 929 " --> pdb=" O GLU D 925 " (cutoff:3.500A) Processing helix chain 'D' and resid 1138 through 1146 Processing helix chain 'D' and resid 1217 through 1224 Processing helix chain 'D' and resid 1227 through 1244 removed outlier: 4.433A pdb=" N GLN D1244 " --> pdb=" O VAL D1240 " (cutoff:3.500A) Processing helix chain 'D' and resid 1250 through 1261 Processing helix chain 'D' and resid 1280 through 1292 Processing helix chain 'D' and resid 1309 through 1314 Processing helix chain 'D' and resid 1319 through 1325 removed outlier: 3.871A pdb=" N PHE D1325 " --> pdb=" O SER D1321 " (cutoff:3.500A) Processing helix chain 'D' and resid 1328 through 1338 Processing helix chain 'D' and resid 1347 through 1353 Processing helix chain 'D' and resid 1360 through 1372 removed outlier: 3.578A pdb=" N TYR D1363 " --> pdb=" O GLY D1360 " (cutoff:3.500A) removed outlier: 4.194A pdb=" N ALA D1364 " --> pdb=" O THR D1361 " (cutoff:3.500A) Processing helix chain 'E' and resid 7 through 12 Processing helix chain 'E' and resid 18 through 31 Processing helix chain 'E' and resid 46 through 56 removed outlier: 3.517A pdb=" N GLU E 56 " --> pdb=" O ARG E 52 " (cutoff:3.500A) Processing helix chain 'E' and resid 61 through 76 Processing helix chain 'F' and resid 97 through 107 Processing helix chain 'F' and resid 113 through 136 removed outlier: 3.659A pdb=" N ILE F 117 " --> pdb=" O ARG F 113 " (cutoff:3.500A) Processing helix chain 'F' and resid 140 through 153 Processing helix chain 'F' and resid 158 through 161 No H-bonds generated for 'chain 'F' and resid 158 through 161' Processing helix chain 'F' and resid 214 through 233 Processing helix chain 'F' and resid 244 through 257 Processing helix chain 'F' and resid 263 through 295 removed outlier: 4.672A pdb=" N GLN F 294 " --> pdb=" O LEU F 290 " (cutoff:3.500A) Processing helix chain 'F' and resid 299 through 306 Processing helix chain 'F' and resid 314 through 320 Processing helix chain 'F' and resid 325 through 351 removed outlier: 4.487A pdb=" N ASP F 332 " --> pdb=" O GLU F 328 " (cutoff:3.500A) removed outlier: 4.762A pdb=" N VAL F 333 " --> pdb=" O LYS F 329 " (cutoff:3.500A) removed outlier: 4.421A pdb=" N GLU F 335 " --> pdb=" O HIS F 331 " (cutoff:3.500A) removed outlier: 5.503A pdb=" N GLU F 336 " --> pdb=" O ASP F 332 " (cutoff:3.500A) Processing helix chain 'F' and resid 355 through 392 removed outlier: 5.308A pdb=" N ARG F 385 " --> pdb=" O GLU F 381 " (cutoff:3.500A) removed outlier: 5.188A pdb=" N LEU F 386 " --> pdb=" O ALA F 382 " (cutoff:3.500A) Processing helix chain 'F' and resid 401 through 417 Processing helix chain 'F' and resid 427 through 445 Processing helix chain 'F' and resid 454 through 474 Processing helix chain 'F' and resid 480 through 486 Processing helix chain 'F' and resid 493 through 499 Processing helix chain 'F' and resid 519 through 522 removed outlier: 3.621A pdb=" N PHE F 522 " --> pdb=" O LEU F 519 " (cutoff:3.500A) No H-bonds generated for 'chain 'F' and resid 519 through 522' Processing helix chain 'F' and resid 531 through 550 Processing helix chain 'F' and resid 554 through 562 Processing helix chain 'F' and resid 573 through 579 Processing helix chain 'F' and resid 585 through 599 Processing helix chain 'F' and resid 605 through 610 Processing sheet with id= A, first strand: chain 'A' and resid 23 through 28 removed outlier: 3.541A pdb=" N ALA A 24 " --> pdb=" O MET A 205 " (cutoff:3.500A) removed outlier: 3.510A pdb=" N ARG A 182 " --> pdb=" O GLU A 206 " (cutoff:3.500A) Processing sheet with id= B, first strand: chain 'A' and resid 97 through 105 removed outlier: 3.610A pdb=" N GLU A 60 " --> pdb=" O ARG A 143 " (cutoff:3.500A) removed outlier: 3.898A pdb=" N GLU A 58 " --> pdb=" O LYS A 145 " (cutoff:3.500A) removed outlier: 6.540A pdb=" N GLN A 147 " --> pdb=" O VAL A 56 " (cutoff:3.500A) removed outlier: 5.921A pdb=" N VAL A 56 " --> pdb=" O GLN A 147 " (cutoff:3.500A) removed outlier: 6.983A pdb=" N GLY A 149 " --> pdb=" O CYS A 54 " (cutoff:3.500A) removed outlier: 5.359A pdb=" N CYS A 54 " --> pdb=" O GLY A 149 " (cutoff:3.500A) Processing sheet with id= C, first strand: chain 'A' and resid 108 through 111 removed outlier: 3.562A pdb=" N CYS A 131 " --> pdb=" O VAL A 110 " (cutoff:3.500A) Processing sheet with id= D, first strand: chain 'B' and resid 24 through 28 Processing sheet with id= E, first strand: chain 'B' and resid 170 through 172 removed outlier: 7.078A pdb=" N LYS B 145 " --> pdb=" O THR B 57 " (cutoff:3.500A) removed outlier: 4.677A pdb=" N VAL B 59 " --> pdb=" O ARG B 143 " (cutoff:3.500A) removed outlier: 6.777A pdb=" N ARG B 143 " --> pdb=" O VAL B 59 " (cutoff:3.500A) removed outlier: 5.203A pdb=" N ILE B 61 " --> pdb=" O SER B 141 " (cutoff:3.500A) removed outlier: 7.917A pdb=" N SER B 141 " --> pdb=" O ILE B 61 " (cutoff:3.500A) Processing sheet with id= F, first strand: chain 'B' and resid 90 through 92 Processing sheet with id= G, first strand: chain 'B' and resid 108 through 111 removed outlier: 3.632A pdb=" N GLY B 108 " --> pdb=" O LEU B 133 " (cutoff:3.500A) Processing sheet with id= H, first strand: chain 'C' and resid 93 through 95 Processing sheet with id= I, first strand: chain 'C' and resid 115 through 117 removed outlier: 3.784A pdb=" N LYS C 115 " --> pdb=" O ILE C 104 " (cutoff:3.500A) removed outlier: 3.971A pdb=" N SER C 72 " --> pdb=" O LYS C 99 " (cutoff:3.500A) removed outlier: 6.208A pdb=" N ARG C 101 " --> pdb=" O TYR C 70 " (cutoff:3.500A) removed outlier: 5.350A pdb=" N TYR C 70 " --> pdb=" O ARG C 101 " (cutoff:3.500A) removed outlier: 7.139A pdb=" N VAL C 103 " --> pdb=" O LEU C 68 " (cutoff:3.500A) removed outlier: 5.306A pdb=" N LEU C 68 " --> pdb=" O VAL C 103 " (cutoff:3.500A) Processing sheet with id= J, first strand: chain 'C' and resid 143 through 145 Processing sheet with id= K, first strand: chain 'C' and resid 148 through 151 Processing sheet with id= L, first strand: chain 'C' and resid 154 through 158 removed outlier: 3.555A pdb=" N ASN C 173 " --> pdb=" O ASP C 158 " (cutoff:3.500A) removed outlier: 3.608A pdb=" N LEU C 184 " --> pdb=" O ILE C 176 " (cutoff:3.500A) Processing sheet with id= M, first strand: chain 'C' and resid 238 through 240 Processing sheet with id= N, first strand: chain 'C' and resid 603 through 606 Processing sheet with id= O, first strand: chain 'C' and resid 634 through 637 removed outlier: 3.555A pdb=" N SER C 643 " --> pdb=" O CYS C 636 " (cutoff:3.500A) Processing sheet with id= P, first strand: chain 'C' and resid 749 through 752 removed outlier: 3.512A pdb=" N TYR C 726 " --> pdb=" O VAL C 733 " (cutoff:3.500A) removed outlier: 6.314A pdb=" N LYS C 735 " --> pdb=" O VAL C 724 " (cutoff:3.500A) removed outlier: 5.927A pdb=" N VAL C 724 " --> pdb=" O LYS C 735 " (cutoff:3.500A) Processing sheet with id= Q, first strand: chain 'C' and resid 1226 through 1232 removed outlier: 4.455A pdb=" N THR C1226 " --> pdb=" O PHE C 804 " (cutoff:3.500A) removed outlier: 6.757A pdb=" N ILE C1096 " --> pdb=" O ALA C 803 " (cutoff:3.500A) Processing sheet with id= R, first strand: chain 'C' and resid 1065 through 1067 Processing sheet with id= S, first strand: chain 'C' and resid 816 through 819 removed outlier: 7.364A pdb=" N VAL C 818 " --> pdb=" O SER C1077 " (cutoff:3.500A) removed outlier: 4.078A pdb=" N ILE C1079 " --> pdb=" O VAL C 818 " (cutoff:3.500A) Processing sheet with id= T, first strand: chain 'C' and resid 830 through 841 removed outlier: 4.031A pdb=" N ASP C 930 " --> pdb=" O TYR C1053 " (cutoff:3.500A) removed outlier: 6.711A pdb=" N ALA C1055 " --> pdb=" O VAL C 928 " (cutoff:3.500A) removed outlier: 6.097A pdb=" N VAL C 928 " --> pdb=" O ALA C1055 " (cutoff:3.500A) Processing sheet with id= U, first strand: chain 'D' and resid 103 through 106 Processing sheet with id= V, first strand: chain 'D' and resid 350 through 354 Processing sheet with id= W, first strand: chain 'D' and resid 547 through 556 Processing sheet with id= X, first strand: chain 'D' and resid 706 through 708 Processing sheet with id= Y, first strand: chain 'D' and resid 820 through 822 Processing sheet with id= Z, first strand: chain 'D' and resid 957 through 961 removed outlier: 3.552A pdb=" N GLU D 981 " --> pdb=" O SER D 961 " (cutoff:3.500A) removed outlier: 4.443A pdb=" N THR D 980 " --> pdb=" O VAL D 997 " (cutoff:3.500A) Processing sheet with id= AA, first strand: chain 'D' and resid 965 through 967 Processing sheet with id= AB, first strand: chain 'D' and resid 1035 through 1038 removed outlier: 3.636A pdb=" N THR D1038 " --> pdb=" O ALA D1077 " (cutoff:3.500A) Processing sheet with id= AC, first strand: chain 'D' and resid 1162 through 1165 Processing sheet with id= AD, first strand: chain 'D' and resid 1277 through 1279 Processing sheet with id= AE, first strand: chain 'D' and resid 825 through 827 removed outlier: 3.695A pdb=" N GLU D 833 " --> pdb=" O VAL D 825 " (cutoff:3.500A) removed outlier: 6.427A pdb=" N GLU D 827 " --> pdb=" O VAL D 831 " (cutoff:3.500A) removed outlier: 4.748A pdb=" N VAL D 831 " --> pdb=" O GLU D 827 " (cutoff:3.500A) Processing sheet with id= AF, first strand: chain 'D' and resid 949 through 952 removed outlier: 3.597A pdb=" N ILE D 950 " --> pdb=" O ALA D1018 " (cutoff:3.500A) removed outlier: 4.015A pdb=" N ALA D1018 " --> pdb=" O ILE D 950 " (cutoff:3.500A) removed outlier: 6.235A pdb=" N VAL D 952 " --> pdb=" O THR D1016 " (cutoff:3.500A) removed outlier: 6.057A pdb=" N THR D1016 " --> pdb=" O VAL D 952 " (cutoff:3.500A) No H-bonds generated for sheet with id= AF 1071 hydrogen bonds defined for protein. 3102 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 57 hydrogen bonds 114 hydrogen bond angles 0 basepair planarities 23 basepair parallelities 69 stacking parallelities Total time for adding SS restraints: 11.63 Time building geometry restraints manager: 13.06 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.17 - 1.30: 5190 1.30 - 1.43: 7911 1.43 - 1.56: 18315 1.56 - 1.69: 217 1.69 - 1.81: 225 Bond restraints: 31858 Sorted by residual: bond pdb=" C6 RFP C3001 " pdb=" O3 RFP C3001 " ideal model delta sigma weight residual 1.339 1.531 -0.192 2.00e-02 2.50e+03 9.24e+01 bond pdb=" C6 RFP C3001 " pdb=" C7 RFP C3001 " ideal model delta sigma weight residual 1.387 1.570 -0.183 2.00e-02 2.50e+03 8.35e+01 bond pdb=" C10 RFP C3001 " pdb=" C4 RFP C3001 " ideal model delta sigma weight residual 1.411 1.572 -0.161 2.00e-02 2.50e+03 6.52e+01 bond pdb=" C1 RFP C3001 " pdb=" C9 RFP C3001 " ideal model delta sigma weight residual 1.411 1.570 -0.159 2.00e-02 2.50e+03 6.36e+01 bond pdb=" C10 RFP C3001 " pdb=" C5 RFP C3001 " ideal model delta sigma weight residual 1.431 1.590 -0.159 2.00e-02 2.50e+03 6.34e+01 ... (remaining 31853 not shown) Histogram of bond angle deviations from ideal: 97.76 - 105.00: 855 105.00 - 112.25: 16507 112.25 - 119.50: 10729 119.50 - 126.75: 14804 126.75 - 134.00: 575 Bond angle restraints: 43470 Sorted by residual: angle pdb=" N PHE D1274 " pdb=" CA PHE D1274 " pdb=" CB PHE D1274 " ideal model delta sigma weight residual 114.17 109.49 4.68 1.14e+00 7.69e-01 1.69e+01 angle pdb=" N ASP F 581 " pdb=" CA ASP F 581 " pdb=" CB ASP F 581 " ideal model delta sigma weight residual 114.17 110.21 3.96 1.14e+00 7.69e-01 1.21e+01 angle pdb=" C41 RFP C3001 " pdb=" N3 RFP C3001 " pdb=" N2 RFP C3001 " ideal model delta sigma weight residual 112.16 122.28 -10.12 3.00e+00 1.11e-01 1.14e+01 angle pdb=" C7 RFP C3001 " pdb=" C6 RFP C3001 " pdb=" O3 RFP C3001 " ideal model delta sigma weight residual 121.50 131.59 -10.09 3.00e+00 1.11e-01 1.13e+01 angle pdb=" N LEU C1161 " pdb=" CA LEU C1161 " pdb=" C LEU C1161 " ideal model delta sigma weight residual 111.00 120.28 -9.28 2.80e+00 1.28e-01 1.10e+01 ... (remaining 43465 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.37: 18628 35.37 - 70.74: 709 70.74 - 106.11: 30 106.11 - 141.48: 7 141.48 - 176.85: 2 Dihedral angle restraints: 19376 sinusoidal: 8772 harmonic: 10604 Sorted by residual: dihedral pdb=" CA LEU D1344 " pdb=" C LEU D1344 " pdb=" N ARG D1345 " pdb=" CA ARG D1345 " ideal model delta harmonic sigma weight residual 180.00 140.07 39.93 0 5.00e+00 4.00e-02 6.38e+01 dihedral pdb=" CA SER C1295 " pdb=" C SER C1295 " pdb=" N ASP C1296 " pdb=" CA ASP C1296 " ideal model delta harmonic sigma weight residual -180.00 -152.94 -27.06 0 5.00e+00 4.00e-02 2.93e+01 dihedral pdb=" CA ILE C 39 " pdb=" C ILE C 39 " pdb=" N GLU C 40 " pdb=" CA GLU C 40 " ideal model delta harmonic sigma weight residual 180.00 153.15 26.85 0 5.00e+00 4.00e-02 2.88e+01 ... (remaining 19373 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.067: 4460 0.067 - 0.133: 482 0.133 - 0.200: 7 0.200 - 0.266: 2 0.266 - 0.333: 1 Chirality restraints: 4952 Sorted by residual: chirality pdb=" C22 RFP C3001 " pdb=" C21 RFP C3001 " pdb=" C23 RFP C3001 " pdb=" C32 RFP C3001 " both_signs ideal model delta sigma weight residual False 2.47 2.80 -0.33 2.00e-01 2.50e+01 2.76e+00 chirality pdb=" C24 RFP C3001 " pdb=" C23 RFP C3001 " pdb=" C25 RFP C3001 " pdb=" C33 RFP C3001 " both_signs ideal model delta sigma weight residual False 2.56 2.79 -0.24 2.00e-01 2.50e+01 1.40e+00 chirality pdb=" C20 RFP C3001 " pdb=" C19 RFP C3001 " pdb=" C21 RFP C3001 " pdb=" C31 RFP C3001 " both_signs ideal model delta sigma weight residual False -2.56 -2.77 0.21 2.00e-01 2.50e+01 1.11e+00 ... (remaining 4949 not shown) Planarity restraints: 5309 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C LYS C 697 " 0.040 5.00e-02 4.00e+02 6.08e-02 5.92e+00 pdb=" N PRO C 698 " -0.105 5.00e-02 4.00e+02 pdb=" CA PRO C 698 " 0.031 5.00e-02 4.00e+02 pdb=" CD PRO C 698 " 0.034 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C SER A 178 " 0.030 5.00e-02 4.00e+02 4.56e-02 3.32e+00 pdb=" N PRO A 179 " -0.079 5.00e-02 4.00e+02 pdb=" CA PRO A 179 " 0.023 5.00e-02 4.00e+02 pdb=" CD PRO A 179 " 0.025 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CG GLU F 104 " -0.009 2.00e-02 2.50e+03 1.82e-02 3.30e+00 pdb=" CD GLU F 104 " 0.031 2.00e-02 2.50e+03 pdb=" OE1 GLU F 104 " -0.011 2.00e-02 2.50e+03 pdb=" OE2 GLU F 104 " -0.011 2.00e-02 2.50e+03 ... (remaining 5306 not shown) Histogram of nonbonded interaction distances: 1.98 - 2.56: 252 2.56 - 3.15: 26289 3.15 - 3.73: 46283 3.73 - 4.32: 64515 4.32 - 4.90: 108761 Nonbonded interactions: 246100 Sorted by model distance: nonbonded pdb=" O LYS D 964 " pdb=" OG1 THR D 976 " model vdw 1.979 2.440 nonbonded pdb=" OE1 GLU D1030 " pdb=" OH TYR D1099 " model vdw 1.996 2.440 nonbonded pdb=" OG1 THR C 91 " pdb=" O ILE C 138 " model vdw 2.015 2.440 nonbonded pdb=" OG1 THR C 843 " pdb=" O GLY C 846 " model vdw 2.024 2.440 nonbonded pdb=" O LEU C 397 " pdb=" OG SER C 398 " model vdw 2.060 2.440 ... (remaining 246095 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 'A' and resid 7 through 235) selection = (chain 'B' and resid 7 through 235) } 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=0.30 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: 4.050 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: 11.560 Check model and map are aligned: 0.480 Set scattering table: 0.290 Process input model: 90.520 Find NCS groups from input model: 1.120 Set up NCS constraints: 0.100 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:2.800 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 110.950 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7957 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 : 0.005 0.192 31858 Z= 0.311 Angle : 0.528 10.124 43470 Z= 0.277 Chirality : 0.040 0.333 4952 Planarity : 0.004 0.061 5309 Dihedral : 17.127 176.854 12540 Min Nonbonded Distance : 1.979 Molprobity Statistics. All-atom Clashscore : 29.92 Ramachandran Plot: Outliers : 0.05 % Allowed : 6.80 % Favored : 93.14 % Rotamer: Outliers : 0.00 % Allowed : 0.13 % Favored : 99.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.69 % Cis-general : 0.17 % Twisted Proline : 0.00 % Twisted General : 0.03 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.24 (0.14), residues: 3661 helix: 2.13 (0.14), residues: 1461 sheet: -0.30 (0.27), residues: 390 loop : -1.48 (0.14), residues: 1810 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP F 326 HIS 0.008 0.001 HIS D 545 PHE 0.019 0.001 PHE C 514 TYR 0.013 0.001 TYR D 631 ARG 0.006 0.000 ARG F 476 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7322 Ramachandran restraints generated. 3661 Oldfield, 0 Emsley, 3661 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7322 Ramachandran restraints generated. 3661 Oldfield, 0 Emsley, 3661 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 289 residues out of total 3153 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 289 time to evaluate : 3.167 Fit side-chains revert: symmetry clash REVERT: A 51 MET cc_start: 0.9007 (mmp) cc_final: 0.8481 (mmp) REVERT: C 1315 MET cc_start: 0.8477 (ptt) cc_final: 0.8249 (ptt) REVERT: D 697 MET cc_start: 0.8668 (ttp) cc_final: 0.8446 (ttp) outliers start: 0 outliers final: 0 residues processed: 289 average time/residue: 0.4589 time to fit residues: 206.3776 Evaluate side-chains 251 residues out of total 3153 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 251 time to evaluate : 3.333 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 376 random chunks: chunk 317 optimal weight: 3.9990 chunk 284 optimal weight: 2.9990 chunk 158 optimal weight: 2.9990 chunk 97 optimal weight: 0.6980 chunk 192 optimal weight: 1.9990 chunk 152 optimal weight: 4.9990 chunk 294 optimal weight: 0.9980 chunk 114 optimal weight: 0.8980 chunk 179 optimal weight: 1.9990 chunk 219 optimal weight: 2.9990 chunk 341 optimal weight: 0.6980 overall best weight: 1.0582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 23 HIS C 69 GLN ** C 406 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 157 GLN D 294 ASN D 667 GLN D1197 ASN F 294 GLN ** F 342 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 406 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7943 moved from start: 0.1103 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.064 31858 Z= 0.241 Angle : 0.598 10.484 43470 Z= 0.312 Chirality : 0.043 0.174 4952 Planarity : 0.004 0.057 5309 Dihedral : 16.317 178.459 5261 Min Nonbonded Distance : 2.123 Molprobity Statistics. All-atom Clashscore : 9.51 Ramachandran Plot: Outliers : 0.03 % Allowed : 5.60 % Favored : 94.37 % Rotamer: Outliers : 0.57 % Allowed : 7.92 % Favored : 91.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.69 % Cis-general : 0.17 % Twisted Proline : 0.00 % Twisted General : 0.06 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.12 (0.14), residues: 3661 helix: 1.90 (0.14), residues: 1451 sheet: -0.29 (0.26), residues: 409 loop : -1.44 (0.14), residues: 1801 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP F 433 HIS 0.006 0.001 HIS D 545 PHE 0.015 0.001 PHE C 514 TYR 0.018 0.001 TYR D 46 ARG 0.005 0.000 ARG F 281 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7322 Ramachandran restraints generated. 3661 Oldfield, 0 Emsley, 3661 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7322 Ramachandran restraints generated. 3661 Oldfield, 0 Emsley, 3661 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 298 residues out of total 3153 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 280 time to evaluate : 3.559 Fit side-chains revert: symmetry clash REVERT: A 51 MET cc_start: 0.8956 (mmp) cc_final: 0.8255 (mmp) REVERT: C 1315 MET cc_start: 0.8506 (ptt) cc_final: 0.8172 (ptt) REVERT: D 697 MET cc_start: 0.8707 (ttp) cc_final: 0.8314 (ttp) REVERT: D 802 ASP cc_start: 0.7003 (m-30) cc_final: 0.6738 (m-30) REVERT: D 1189 MET cc_start: 0.7533 (tpt) cc_final: 0.7264 (mmm) outliers start: 18 outliers final: 12 residues processed: 290 average time/residue: 0.4691 time to fit residues: 216.8045 Evaluate side-chains 261 residues out of total 3153 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 249 time to evaluate : 3.529 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 14 VAL Chi-restraints excluded: chain A residue 208 ASN Chi-restraints excluded: chain B residue 54 CYS Chi-restraints excluded: chain B residue 64 VAL Chi-restraints excluded: chain B residue 101 THR Chi-restraints excluded: chain C residue 315 MET Chi-restraints excluded: chain C residue 353 VAL Chi-restraints excluded: chain C residue 498 ILE Chi-restraints excluded: chain C residue 727 VAL Chi-restraints excluded: chain C residue 949 GLU Chi-restraints excluded: chain D residue 46 TYR Chi-restraints excluded: chain E residue 30 MET Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 376 random chunks: chunk 189 optimal weight: 4.9990 chunk 105 optimal weight: 0.5980 chunk 284 optimal weight: 8.9990 chunk 232 optimal weight: 2.9990 chunk 94 optimal weight: 0.0000 chunk 342 optimal weight: 8.9990 chunk 369 optimal weight: 10.0000 chunk 304 optimal weight: 2.9990 chunk 339 optimal weight: 10.0000 chunk 116 optimal weight: 2.9990 chunk 274 optimal weight: 8.9990 overall best weight: 1.9190 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 526 HIS C 952 GLN ** D1098 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D1197 ASN D1367 GLN ** F 147 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 342 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7994 moved from start: 0.1300 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.070 31858 Z= 0.348 Angle : 0.630 10.512 43470 Z= 0.327 Chirality : 0.044 0.203 4952 Planarity : 0.005 0.059 5309 Dihedral : 16.388 178.375 5261 Min Nonbonded Distance : 2.049 Molprobity Statistics. All-atom Clashscore : 9.04 Ramachandran Plot: Outliers : 0.05 % Allowed : 6.09 % Favored : 93.85 % Rotamer: Outliers : 1.40 % Allowed : 11.76 % Favored : 86.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.69 % Cis-general : 0.17 % Twisted Proline : 0.00 % Twisted General : 0.06 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.21 (0.14), residues: 3661 helix: 1.56 (0.14), residues: 1457 sheet: -0.38 (0.25), residues: 426 loop : -1.60 (0.14), residues: 1778 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP F 433 HIS 0.006 0.001 HIS D 469 PHE 0.018 0.002 PHE C 514 TYR 0.015 0.002 TYR D 46 ARG 0.006 0.001 ARG D1173 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7322 Ramachandran restraints generated. 3661 Oldfield, 0 Emsley, 3661 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7322 Ramachandran restraints generated. 3661 Oldfield, 0 Emsley, 3661 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 301 residues out of total 3153 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 44 poor density : 257 time to evaluate : 3.467 Fit side-chains revert: symmetry clash REVERT: A 51 MET cc_start: 0.8819 (mmp) cc_final: 0.8398 (mmp) REVERT: A 129 VAL cc_start: 0.8833 (OUTLIER) cc_final: 0.8628 (t) REVERT: C 1315 MET cc_start: 0.8565 (ptt) cc_final: 0.8123 (ptt) REVERT: D 129 ASP cc_start: 0.7296 (t0) cc_final: 0.6954 (t0) REVERT: D 664 ILE cc_start: 0.7639 (mm) cc_final: 0.7369 (tt) REVERT: D 697 MET cc_start: 0.8783 (ttp) cc_final: 0.8451 (ttp) REVERT: D 1189 MET cc_start: 0.7559 (tpt) cc_final: 0.7187 (mmm) REVERT: F 342 GLN cc_start: 0.5458 (OUTLIER) cc_final: 0.5177 (mm-40) outliers start: 44 outliers final: 25 residues processed: 288 average time/residue: 0.4582 time to fit residues: 209.6922 Evaluate side-chains 270 residues out of total 3153 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 243 time to evaluate : 3.388 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 93 GLN Chi-restraints excluded: chain A residue 129 VAL Chi-restraints excluded: chain A residue 208 ASN Chi-restraints excluded: chain B residue 19 VAL Chi-restraints excluded: chain B residue 54 CYS Chi-restraints excluded: chain B residue 64 VAL Chi-restraints excluded: chain B residue 101 THR Chi-restraints excluded: chain B residue 202 VAL Chi-restraints excluded: chain C residue 127 ILE Chi-restraints excluded: chain C residue 170 VAL Chi-restraints excluded: chain C residue 315 MET Chi-restraints excluded: chain C residue 353 VAL Chi-restraints excluded: chain C residue 468 LEU Chi-restraints excluded: chain C residue 498 ILE Chi-restraints excluded: chain C residue 727 VAL Chi-restraints excluded: chain C residue 924 VAL Chi-restraints excluded: chain C residue 949 GLU Chi-restraints excluded: chain C residue 1186 VAL Chi-restraints excluded: chain C residue 1225 VAL Chi-restraints excluded: chain D residue 46 TYR Chi-restraints excluded: chain D residue 159 ILE Chi-restraints excluded: chain D residue 357 VAL Chi-restraints excluded: chain D residue 714 GLU Chi-restraints excluded: chain D residue 786 THR Chi-restraints excluded: chain D residue 901 ARG Chi-restraints excluded: chain D residue 1038 THR Chi-restraints excluded: chain F residue 342 GLN Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 376 random chunks: chunk 337 optimal weight: 9.9990 chunk 257 optimal weight: 4.9990 chunk 177 optimal weight: 0.9980 chunk 37 optimal weight: 4.9990 chunk 163 optimal weight: 2.9990 chunk 229 optimal weight: 0.6980 chunk 343 optimal weight: 20.0000 chunk 363 optimal weight: 9.9990 chunk 179 optimal weight: 2.9990 chunk 325 optimal weight: 20.0000 chunk 97 optimal weight: 1.9990 overall best weight: 1.9386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 147 GLN ** D1098 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D1197 ASN ** F 147 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 342 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8001 moved from start: 0.1520 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.065 31858 Z= 0.345 Angle : 0.625 10.265 43470 Z= 0.326 Chirality : 0.044 0.198 4952 Planarity : 0.005 0.059 5309 Dihedral : 16.360 176.598 5261 Min Nonbonded Distance : 2.017 Molprobity Statistics. All-atom Clashscore : 8.48 Ramachandran Plot: Outliers : 0.05 % Allowed : 6.34 % Favored : 93.61 % Rotamer: Outliers : 2.45 % Allowed : 14.40 % Favored : 83.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.69 % Cis-general : 0.17 % Twisted Proline : 0.00 % Twisted General : 0.06 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.39 (0.14), residues: 3661 helix: 1.39 (0.14), residues: 1459 sheet: -0.50 (0.25), residues: 433 loop : -1.67 (0.14), residues: 1769 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP F 433 HIS 0.010 0.001 HIS C 526 PHE 0.018 0.002 PHE A 35 TYR 0.014 0.002 TYR D 46 ARG 0.007 0.001 ARG A 218 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7322 Ramachandran restraints generated. 3661 Oldfield, 0 Emsley, 3661 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7322 Ramachandran restraints generated. 3661 Oldfield, 0 Emsley, 3661 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 335 residues out of total 3153 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 77 poor density : 258 time to evaluate : 3.586 Fit side-chains revert: symmetry clash REVERT: A 129 VAL cc_start: 0.8837 (OUTLIER) cc_final: 0.8634 (t) REVERT: B 180 VAL cc_start: 0.8981 (OUTLIER) cc_final: 0.8698 (t) REVERT: C 799 ASN cc_start: 0.8803 (OUTLIER) cc_final: 0.8250 (p0) REVERT: C 800 MET cc_start: 0.8723 (OUTLIER) cc_final: 0.7847 (mtp) REVERT: C 1315 MET cc_start: 0.8606 (ptt) cc_final: 0.8143 (ptt) REVERT: D 81 ARG cc_start: 0.7360 (OUTLIER) cc_final: 0.6855 (mtm-85) REVERT: D 129 ASP cc_start: 0.7262 (t0) cc_final: 0.6888 (t0) REVERT: D 227 PHE cc_start: 0.8723 (OUTLIER) cc_final: 0.7682 (t80) REVERT: D 664 ILE cc_start: 0.7584 (mm) cc_final: 0.7355 (tt) REVERT: D 697 MET cc_start: 0.8813 (ttp) cc_final: 0.8520 (ttp) REVERT: D 724 MET cc_start: 0.8583 (ttp) cc_final: 0.8300 (mtm) REVERT: D 1189 MET cc_start: 0.7372 (tpt) cc_final: 0.7042 (mmm) REVERT: F 342 GLN cc_start: 0.5452 (OUTLIER) cc_final: 0.5172 (mm-40) outliers start: 77 outliers final: 46 residues processed: 316 average time/residue: 0.4298 time to fit residues: 219.8780 Evaluate side-chains 300 residues out of total 3153 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 53 poor density : 247 time to evaluate : 3.286 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 16 ILE Chi-restraints excluded: chain A residue 19 VAL Chi-restraints excluded: chain A residue 74 VAL Chi-restraints excluded: chain A residue 93 GLN Chi-restraints excluded: chain A residue 129 VAL Chi-restraints excluded: chain A residue 202 VAL Chi-restraints excluded: chain A residue 208 ASN Chi-restraints excluded: chain B residue 19 VAL Chi-restraints excluded: chain B residue 54 CYS Chi-restraints excluded: chain B residue 64 VAL Chi-restraints excluded: chain B residue 101 THR Chi-restraints excluded: chain B residue 180 VAL Chi-restraints excluded: chain B residue 202 VAL Chi-restraints excluded: chain C residue 30 ILE Chi-restraints excluded: chain C residue 117 ILE Chi-restraints excluded: chain C residue 127 ILE Chi-restraints excluded: chain C residue 170 VAL Chi-restraints excluded: chain C residue 199 ASP Chi-restraints excluded: chain C residue 315 MET Chi-restraints excluded: chain C residue 353 VAL Chi-restraints excluded: chain C residue 468 LEU Chi-restraints excluded: chain C residue 498 ILE Chi-restraints excluded: chain C residue 581 THR Chi-restraints excluded: chain C residue 727 VAL Chi-restraints excluded: chain C residue 799 ASN Chi-restraints excluded: chain C residue 800 MET Chi-restraints excluded: chain C residue 924 VAL Chi-restraints excluded: chain C residue 949 GLU Chi-restraints excluded: chain C residue 1072 ASN Chi-restraints excluded: chain C residue 1186 VAL Chi-restraints excluded: chain C residue 1225 VAL Chi-restraints excluded: chain D residue 46 TYR Chi-restraints excluded: chain D residue 81 ARG Chi-restraints excluded: chain D residue 146 VAL Chi-restraints excluded: chain D residue 159 ILE Chi-restraints excluded: chain D residue 227 PHE Chi-restraints excluded: chain D residue 356 THR Chi-restraints excluded: chain D residue 357 VAL Chi-restraints excluded: chain D residue 468 VAL Chi-restraints excluded: chain D residue 518 VAL Chi-restraints excluded: chain D residue 545 HIS Chi-restraints excluded: chain D residue 714 GLU Chi-restraints excluded: chain D residue 786 THR Chi-restraints excluded: chain D residue 901 ARG Chi-restraints excluded: chain D residue 931 THR Chi-restraints excluded: chain D residue 1038 THR Chi-restraints excluded: chain D residue 1061 VAL Chi-restraints excluded: chain D residue 1246 VAL Chi-restraints excluded: chain D residue 1255 VAL Chi-restraints excluded: chain D residue 1327 GLU Chi-restraints excluded: chain E residue 39 VAL Chi-restraints excluded: chain F residue 107 THR Chi-restraints excluded: chain F residue 342 GLN Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 376 random chunks: chunk 302 optimal weight: 0.9980 chunk 206 optimal weight: 0.5980 chunk 5 optimal weight: 2.9990 chunk 270 optimal weight: 1.9990 chunk 149 optimal weight: 7.9990 chunk 310 optimal weight: 4.9990 chunk 251 optimal weight: 1.9990 chunk 0 optimal weight: 4.9990 chunk 185 optimal weight: 3.9990 chunk 326 optimal weight: 20.0000 chunk 91 optimal weight: 0.6980 overall best weight: 1.2584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 406 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 490 GLN D1098 GLN ** F 147 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 342 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7966 moved from start: 0.1696 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.048 31858 Z= 0.246 Angle : 0.561 8.537 43470 Z= 0.294 Chirality : 0.042 0.168 4952 Planarity : 0.004 0.059 5309 Dihedral : 16.313 176.547 5261 Min Nonbonded Distance : 2.036 Molprobity Statistics. All-atom Clashscore : 7.99 Ramachandran Plot: Outliers : 0.03 % Allowed : 5.74 % Favored : 94.24 % Rotamer: Outliers : 1.94 % Allowed : 15.87 % Favored : 82.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.69 % Cis-general : 0.17 % Twisted Proline : 0.00 % Twisted General : 0.06 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.24 (0.14), residues: 3661 helix: 1.55 (0.14), residues: 1453 sheet: -0.44 (0.25), residues: 441 loop : -1.61 (0.14), residues: 1767 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP F 326 HIS 0.005 0.001 HIS C 526 PHE 0.012 0.001 PHE A 35 TYR 0.014 0.001 TYR D 46 ARG 0.004 0.000 ARG A 218 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7322 Ramachandran restraints generated. 3661 Oldfield, 0 Emsley, 3661 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7322 Ramachandran restraints generated. 3661 Oldfield, 0 Emsley, 3661 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 321 residues out of total 3153 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 61 poor density : 260 time to evaluate : 3.249 Fit side-chains revert: symmetry clash REVERT: C 799 ASN cc_start: 0.8769 (OUTLIER) cc_final: 0.8309 (p0) REVERT: C 1315 MET cc_start: 0.8593 (ptt) cc_final: 0.8056 (ptt) REVERT: D 81 ARG cc_start: 0.7325 (OUTLIER) cc_final: 0.6822 (mtm-85) REVERT: D 129 ASP cc_start: 0.7190 (t0) cc_final: 0.6919 (t0) REVERT: D 485 MET cc_start: 0.8888 (tpp) cc_final: 0.8654 (tpt) REVERT: D 664 ILE cc_start: 0.7512 (mm) cc_final: 0.7267 (tt) REVERT: D 697 MET cc_start: 0.8771 (ttp) cc_final: 0.8462 (ttp) REVERT: D 724 MET cc_start: 0.8568 (ttp) cc_final: 0.8314 (mtm) REVERT: D 1189 MET cc_start: 0.7363 (tpt) cc_final: 0.6971 (mmm) REVERT: F 104 GLU cc_start: 0.7485 (mp0) cc_final: 0.7259 (mp0) REVERT: F 342 GLN cc_start: 0.5597 (OUTLIER) cc_final: 0.5228 (mm-40) REVERT: F 583 THR cc_start: 0.7209 (OUTLIER) cc_final: 0.7007 (t) outliers start: 61 outliers final: 37 residues processed: 309 average time/residue: 0.4334 time to fit residues: 214.9035 Evaluate side-chains 291 residues out of total 3153 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 41 poor density : 250 time to evaluate : 3.429 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 19 VAL Chi-restraints excluded: chain A residue 74 VAL Chi-restraints excluded: chain A residue 93 GLN Chi-restraints excluded: chain A residue 202 VAL Chi-restraints excluded: chain A residue 208 ASN Chi-restraints excluded: chain B residue 19 VAL Chi-restraints excluded: chain B residue 54 CYS Chi-restraints excluded: chain B residue 64 VAL Chi-restraints excluded: chain B residue 101 THR Chi-restraints excluded: chain C residue 127 ILE Chi-restraints excluded: chain C residue 199 ASP Chi-restraints excluded: chain C residue 315 MET Chi-restraints excluded: chain C residue 353 VAL Chi-restraints excluded: chain C residue 468 LEU Chi-restraints excluded: chain C residue 498 ILE Chi-restraints excluded: chain C residue 519 ASN Chi-restraints excluded: chain C residue 727 VAL Chi-restraints excluded: chain C residue 739 ASP Chi-restraints excluded: chain C residue 799 ASN Chi-restraints excluded: chain C residue 949 GLU Chi-restraints excluded: chain C residue 1072 ASN Chi-restraints excluded: chain C residue 1124 ILE Chi-restraints excluded: chain C residue 1186 VAL Chi-restraints excluded: chain D residue 46 TYR Chi-restraints excluded: chain D residue 81 ARG Chi-restraints excluded: chain D residue 146 VAL Chi-restraints excluded: chain D residue 159 ILE Chi-restraints excluded: chain D residue 468 VAL Chi-restraints excluded: chain D residue 545 HIS Chi-restraints excluded: chain D residue 569 LEU Chi-restraints excluded: chain D residue 714 GLU Chi-restraints excluded: chain D residue 762 ASN Chi-restraints excluded: chain D residue 786 THR Chi-restraints excluded: chain D residue 831 VAL Chi-restraints excluded: chain D residue 901 ARG Chi-restraints excluded: chain D residue 1038 THR Chi-restraints excluded: chain D residue 1061 VAL Chi-restraints excluded: chain D residue 1327 GLU Chi-restraints excluded: chain F residue 107 THR Chi-restraints excluded: chain F residue 342 GLN Chi-restraints excluded: chain F residue 583 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 376 random chunks: chunk 122 optimal weight: 0.0670 chunk 327 optimal weight: 6.9990 chunk 71 optimal weight: 20.0000 chunk 213 optimal weight: 2.9990 chunk 89 optimal weight: 0.6980 chunk 363 optimal weight: 10.0000 chunk 301 optimal weight: 2.9990 chunk 168 optimal weight: 0.3980 chunk 30 optimal weight: 5.9990 chunk 120 optimal weight: 2.9990 chunk 190 optimal weight: 3.9990 overall best weight: 1.4322 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 406 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 157 GLN D 200 GLN ** F 147 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 342 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7980 moved from start: 0.1786 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.053 31858 Z= 0.268 Angle : 0.573 8.235 43470 Z= 0.300 Chirality : 0.042 0.175 4952 Planarity : 0.004 0.060 5309 Dihedral : 16.332 175.220 5261 Min Nonbonded Distance : 2.025 Molprobity Statistics. All-atom Clashscore : 8.15 Ramachandran Plot: Outliers : 0.03 % Allowed : 6.04 % Favored : 93.94 % Rotamer: Outliers : 2.61 % Allowed : 16.03 % Favored : 81.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.69 % Cis-general : 0.17 % Twisted Proline : 0.00 % Twisted General : 0.06 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.25 (0.14), residues: 3661 helix: 1.53 (0.14), residues: 1451 sheet: -0.44 (0.25), residues: 441 loop : -1.62 (0.14), residues: 1769 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP F 433 HIS 0.005 0.001 HIS D 469 PHE 0.016 0.001 PHE A 35 TYR 0.014 0.001 TYR D 46 ARG 0.004 0.000 ARG A 45 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7322 Ramachandran restraints generated. 3661 Oldfield, 0 Emsley, 3661 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7322 Ramachandran restraints generated. 3661 Oldfield, 0 Emsley, 3661 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 333 residues out of total 3153 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 82 poor density : 251 time to evaluate : 3.330 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 129 VAL cc_start: 0.8829 (OUTLIER) cc_final: 0.8621 (t) REVERT: C 145 ILE cc_start: 0.9012 (OUTLIER) cc_final: 0.8695 (mm) REVERT: C 799 ASN cc_start: 0.8880 (OUTLIER) cc_final: 0.8368 (p0) REVERT: C 800 MET cc_start: 0.8716 (OUTLIER) cc_final: 0.7799 (mtp) REVERT: C 1315 MET cc_start: 0.8665 (ptt) cc_final: 0.8103 (ptt) REVERT: D 81 ARG cc_start: 0.7331 (OUTLIER) cc_final: 0.6832 (mtm-85) REVERT: D 227 PHE cc_start: 0.8718 (OUTLIER) cc_final: 0.7684 (t80) REVERT: D 664 ILE cc_start: 0.7524 (mm) cc_final: 0.7278 (tt) REVERT: D 697 MET cc_start: 0.8775 (ttp) cc_final: 0.8488 (ttp) REVERT: D 724 MET cc_start: 0.8553 (ttp) cc_final: 0.8337 (mtm) REVERT: D 1189 MET cc_start: 0.7413 (tpt) cc_final: 0.6986 (mmm) REVERT: F 342 GLN cc_start: 0.5594 (OUTLIER) cc_final: 0.5203 (mm-40) REVERT: F 583 THR cc_start: 0.7226 (OUTLIER) cc_final: 0.7022 (t) outliers start: 82 outliers final: 54 residues processed: 317 average time/residue: 0.4393 time to fit residues: 226.3489 Evaluate side-chains 308 residues out of total 3153 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 62 poor density : 246 time to evaluate : 3.455 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 16 ILE Chi-restraints excluded: chain A residue 19 VAL Chi-restraints excluded: chain A residue 74 VAL Chi-restraints excluded: chain A residue 93 GLN Chi-restraints excluded: chain A residue 129 VAL Chi-restraints excluded: chain A residue 168 ILE Chi-restraints excluded: chain A residue 202 VAL Chi-restraints excluded: chain A residue 208 ASN Chi-restraints excluded: chain B residue 19 VAL Chi-restraints excluded: chain B residue 54 CYS Chi-restraints excluded: chain B residue 64 VAL Chi-restraints excluded: chain B residue 101 THR Chi-restraints excluded: chain B residue 129 VAL Chi-restraints excluded: chain B residue 183 ILE Chi-restraints excluded: chain B residue 202 VAL Chi-restraints excluded: chain C residue 30 ILE Chi-restraints excluded: chain C residue 127 ILE Chi-restraints excluded: chain C residue 145 ILE Chi-restraints excluded: chain C residue 170 VAL Chi-restraints excluded: chain C residue 199 ASP Chi-restraints excluded: chain C residue 315 MET Chi-restraints excluded: chain C residue 353 VAL Chi-restraints excluded: chain C residue 468 LEU Chi-restraints excluded: chain C residue 492 MET Chi-restraints excluded: chain C residue 498 ILE Chi-restraints excluded: chain C residue 519 ASN Chi-restraints excluded: chain C residue 727 VAL Chi-restraints excluded: chain C residue 739 ASP Chi-restraints excluded: chain C residue 799 ASN Chi-restraints excluded: chain C residue 800 MET Chi-restraints excluded: chain C residue 949 GLU Chi-restraints excluded: chain C residue 1124 ILE Chi-restraints excluded: chain C residue 1186 VAL Chi-restraints excluded: chain C residue 1225 VAL Chi-restraints excluded: chain D residue 46 TYR Chi-restraints excluded: chain D residue 70 CYS Chi-restraints excluded: chain D residue 81 ARG Chi-restraints excluded: chain D residue 146 VAL Chi-restraints excluded: chain D residue 159 ILE Chi-restraints excluded: chain D residue 227 PHE Chi-restraints excluded: chain D residue 356 THR Chi-restraints excluded: chain D residue 357 VAL Chi-restraints excluded: chain D residue 468 VAL Chi-restraints excluded: chain D residue 545 HIS Chi-restraints excluded: chain D residue 569 LEU Chi-restraints excluded: chain D residue 714 GLU Chi-restraints excluded: chain D residue 762 ASN Chi-restraints excluded: chain D residue 786 THR Chi-restraints excluded: chain D residue 831 VAL Chi-restraints excluded: chain D residue 901 ARG Chi-restraints excluded: chain D residue 931 THR Chi-restraints excluded: chain D residue 1038 THR Chi-restraints excluded: chain D residue 1061 VAL Chi-restraints excluded: chain D residue 1246 VAL Chi-restraints excluded: chain D residue 1314 LEU Chi-restraints excluded: chain D residue 1327 GLU Chi-restraints excluded: chain E residue 39 VAL Chi-restraints excluded: chain F residue 104 GLU Chi-restraints excluded: chain F residue 107 THR Chi-restraints excluded: chain F residue 342 GLN Chi-restraints excluded: chain F residue 552 THR Chi-restraints excluded: chain F residue 583 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 376 random chunks: chunk 350 optimal weight: 3.9990 chunk 41 optimal weight: 2.9990 chunk 207 optimal weight: 0.0010 chunk 265 optimal weight: 4.9990 chunk 205 optimal weight: 2.9990 chunk 306 optimal weight: 4.9990 chunk 203 optimal weight: 0.0070 chunk 362 optimal weight: 6.9990 chunk 226 optimal weight: 2.9990 chunk 220 optimal weight: 0.9980 chunk 167 optimal weight: 2.9990 overall best weight: 1.4008 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 406 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 200 GLN ** F 147 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 342 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7976 moved from start: 0.1888 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.049 31858 Z= 0.263 Angle : 0.566 7.911 43470 Z= 0.297 Chirality : 0.042 0.176 4952 Planarity : 0.004 0.060 5309 Dihedral : 16.282 174.572 5261 Min Nonbonded Distance : 2.029 Molprobity Statistics. All-atom Clashscore : 7.88 Ramachandran Plot: Outliers : 0.03 % Allowed : 5.71 % Favored : 94.26 % Rotamer: Outliers : 2.51 % Allowed : 16.57 % Favored : 80.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.69 % Cis-general : 0.17 % Twisted Proline : 0.00 % Twisted General : 0.06 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.24 (0.14), residues: 3661 helix: 1.53 (0.14), residues: 1451 sheet: -0.44 (0.24), residues: 446 loop : -1.60 (0.14), residues: 1764 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP C 807 HIS 0.005 0.001 HIS D 469 PHE 0.015 0.001 PHE A 35 TYR 0.014 0.001 TYR D 46 ARG 0.004 0.000 ARG A 45 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7322 Ramachandran restraints generated. 3661 Oldfield, 0 Emsley, 3661 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7322 Ramachandran restraints generated. 3661 Oldfield, 0 Emsley, 3661 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 333 residues out of total 3153 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 79 poor density : 254 time to evaluate : 3.224 Fit side-chains revert: symmetry clash REVERT: A 129 VAL cc_start: 0.8841 (OUTLIER) cc_final: 0.8630 (t) REVERT: C 145 ILE cc_start: 0.9005 (OUTLIER) cc_final: 0.8682 (mm) REVERT: C 799 ASN cc_start: 0.8837 (OUTLIER) cc_final: 0.8382 (p0) REVERT: C 1315 MET cc_start: 0.8668 (ptt) cc_final: 0.8105 (ptt) REVERT: C 1340 GLU cc_start: 0.7805 (mm-30) cc_final: 0.7425 (mm-30) REVERT: D 81 ARG cc_start: 0.7276 (OUTLIER) cc_final: 0.6763 (mtm-85) REVERT: D 129 ASP cc_start: 0.7165 (t0) cc_final: 0.6872 (t0) REVERT: D 227 PHE cc_start: 0.8706 (OUTLIER) cc_final: 0.7644 (t80) REVERT: D 664 ILE cc_start: 0.7506 (mm) cc_final: 0.7263 (tt) REVERT: D 697 MET cc_start: 0.8769 (ttp) cc_final: 0.8481 (ttp) REVERT: D 724 MET cc_start: 0.8551 (ttp) cc_final: 0.8336 (mtm) REVERT: D 1189 MET cc_start: 0.7388 (tpt) cc_final: 0.6704 (tpp) REVERT: F 104 GLU cc_start: 0.7499 (OUTLIER) cc_final: 0.7295 (mp0) REVERT: F 342 GLN cc_start: 0.5796 (OUTLIER) cc_final: 0.5281 (mm-40) outliers start: 79 outliers final: 58 residues processed: 318 average time/residue: 0.4299 time to fit residues: 220.5901 Evaluate side-chains 311 residues out of total 3153 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 65 poor density : 246 time to evaluate : 3.204 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 16 ILE Chi-restraints excluded: chain A residue 19 VAL Chi-restraints excluded: chain A residue 74 VAL Chi-restraints excluded: chain A residue 93 GLN Chi-restraints excluded: chain A residue 129 VAL Chi-restraints excluded: chain A residue 168 ILE Chi-restraints excluded: chain A residue 202 VAL Chi-restraints excluded: chain A residue 208 ASN Chi-restraints excluded: chain B residue 19 VAL Chi-restraints excluded: chain B residue 54 CYS Chi-restraints excluded: chain B residue 64 VAL Chi-restraints excluded: chain B residue 101 THR Chi-restraints excluded: chain B residue 129 VAL Chi-restraints excluded: chain B residue 183 ILE Chi-restraints excluded: chain B residue 202 VAL Chi-restraints excluded: chain C residue 30 ILE Chi-restraints excluded: chain C residue 127 ILE Chi-restraints excluded: chain C residue 145 ILE Chi-restraints excluded: chain C residue 170 VAL Chi-restraints excluded: chain C residue 199 ASP Chi-restraints excluded: chain C residue 315 MET Chi-restraints excluded: chain C residue 353 VAL Chi-restraints excluded: chain C residue 444 ASP Chi-restraints excluded: chain C residue 468 LEU Chi-restraints excluded: chain C residue 492 MET Chi-restraints excluded: chain C residue 498 ILE Chi-restraints excluded: chain C residue 519 ASN Chi-restraints excluded: chain C residue 727 VAL Chi-restraints excluded: chain C residue 739 ASP Chi-restraints excluded: chain C residue 799 ASN Chi-restraints excluded: chain C residue 924 VAL Chi-restraints excluded: chain C residue 949 GLU Chi-restraints excluded: chain C residue 1072 ASN Chi-restraints excluded: chain C residue 1124 ILE Chi-restraints excluded: chain C residue 1186 VAL Chi-restraints excluded: chain C residue 1225 VAL Chi-restraints excluded: chain C residue 1292 THR Chi-restraints excluded: chain D residue 46 TYR Chi-restraints excluded: chain D residue 70 CYS Chi-restraints excluded: chain D residue 81 ARG Chi-restraints excluded: chain D residue 146 VAL Chi-restraints excluded: chain D residue 159 ILE Chi-restraints excluded: chain D residue 227 PHE Chi-restraints excluded: chain D residue 356 THR Chi-restraints excluded: chain D residue 357 VAL Chi-restraints excluded: chain D residue 468 VAL Chi-restraints excluded: chain D residue 545 HIS Chi-restraints excluded: chain D residue 569 LEU Chi-restraints excluded: chain D residue 714 GLU Chi-restraints excluded: chain D residue 762 ASN Chi-restraints excluded: chain D residue 786 THR Chi-restraints excluded: chain D residue 831 VAL Chi-restraints excluded: chain D residue 901 ARG Chi-restraints excluded: chain D residue 931 THR Chi-restraints excluded: chain D residue 1038 THR Chi-restraints excluded: chain D residue 1061 VAL Chi-restraints excluded: chain D residue 1246 VAL Chi-restraints excluded: chain D residue 1255 VAL Chi-restraints excluded: chain D residue 1314 LEU Chi-restraints excluded: chain D residue 1327 GLU Chi-restraints excluded: chain E residue 39 VAL Chi-restraints excluded: chain F residue 104 GLU Chi-restraints excluded: chain F residue 107 THR Chi-restraints excluded: chain F residue 342 GLN Chi-restraints excluded: chain F residue 552 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 376 random chunks: chunk 224 optimal weight: 0.6980 chunk 144 optimal weight: 20.0000 chunk 216 optimal weight: 0.9980 chunk 109 optimal weight: 0.8980 chunk 71 optimal weight: 7.9990 chunk 70 optimal weight: 7.9990 chunk 230 optimal weight: 2.9990 chunk 246 optimal weight: 9.9990 chunk 179 optimal weight: 0.7980 chunk 33 optimal weight: 0.7980 chunk 284 optimal weight: 8.9990 overall best weight: 0.8380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 406 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 200 GLN ** F 147 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 342 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7939 moved from start: 0.2040 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 31858 Z= 0.186 Angle : 0.526 8.150 43470 Z= 0.277 Chirality : 0.040 0.166 4952 Planarity : 0.004 0.060 5309 Dihedral : 16.157 174.314 5261 Min Nonbonded Distance : 2.027 Molprobity Statistics. All-atom Clashscore : 7.65 Ramachandran Plot: Outliers : 0.03 % Allowed : 5.38 % Favored : 94.59 % Rotamer: Outliers : 2.13 % Allowed : 17.20 % Favored : 80.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.69 % Cis-general : 0.17 % Twisted Proline : 0.00 % Twisted General : 0.03 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.09 (0.14), residues: 3661 helix: 1.69 (0.14), residues: 1450 sheet: -0.29 (0.25), residues: 432 loop : -1.55 (0.14), residues: 1779 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP F 315 HIS 0.004 0.001 HIS D 104 PHE 0.011 0.001 PHE D1274 TYR 0.014 0.001 TYR D 46 ARG 0.009 0.000 ARG A 218 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7322 Ramachandran restraints generated. 3661 Oldfield, 0 Emsley, 3661 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7322 Ramachandran restraints generated. 3661 Oldfield, 0 Emsley, 3661 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 325 residues out of total 3153 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 67 poor density : 258 time to evaluate : 3.513 Fit side-chains revert: symmetry clash REVERT: C 799 ASN cc_start: 0.8697 (OUTLIER) cc_final: 0.8257 (p0) REVERT: C 800 MET cc_start: 0.8686 (OUTLIER) cc_final: 0.7736 (mtp) REVERT: C 1315 MET cc_start: 0.8618 (ptt) cc_final: 0.8027 (ptt) REVERT: C 1340 GLU cc_start: 0.7731 (mm-30) cc_final: 0.7334 (mm-30) REVERT: D 129 ASP cc_start: 0.7172 (t0) cc_final: 0.6911 (t0) REVERT: D 151 MET cc_start: 0.7282 (ptp) cc_final: 0.6471 (ptt) REVERT: D 227 PHE cc_start: 0.8634 (OUTLIER) cc_final: 0.7587 (t80) REVERT: D 485 MET cc_start: 0.8881 (tpp) cc_final: 0.8652 (tpt) REVERT: D 697 MET cc_start: 0.8679 (ttp) cc_final: 0.8335 (ttp) REVERT: D 714 GLU cc_start: 0.7996 (OUTLIER) cc_final: 0.7792 (mt-10) REVERT: D 1189 MET cc_start: 0.7350 (tpt) cc_final: 0.6619 (tpp) REVERT: D 1195 GLN cc_start: 0.7532 (mp10) cc_final: 0.7223 (mp10) REVERT: F 342 GLN cc_start: 0.5987 (OUTLIER) cc_final: 0.5484 (mm-40) outliers start: 67 outliers final: 45 residues processed: 312 average time/residue: 0.4263 time to fit residues: 214.2328 Evaluate side-chains 298 residues out of total 3153 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 50 poor density : 248 time to evaluate : 3.251 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 16 ILE Chi-restraints excluded: chain A residue 19 VAL Chi-restraints excluded: chain A residue 93 GLN Chi-restraints excluded: chain A residue 168 ILE Chi-restraints excluded: chain A residue 202 VAL Chi-restraints excluded: chain B residue 19 VAL Chi-restraints excluded: chain B residue 54 CYS Chi-restraints excluded: chain B residue 64 VAL Chi-restraints excluded: chain B residue 90 VAL Chi-restraints excluded: chain B residue 101 THR Chi-restraints excluded: chain B residue 129 VAL Chi-restraints excluded: chain B residue 183 ILE Chi-restraints excluded: chain B residue 202 VAL Chi-restraints excluded: chain C residue 30 ILE Chi-restraints excluded: chain C residue 127 ILE Chi-restraints excluded: chain C residue 170 VAL Chi-restraints excluded: chain C residue 315 MET Chi-restraints excluded: chain C residue 492 MET Chi-restraints excluded: chain C residue 498 ILE Chi-restraints excluded: chain C residue 519 ASN Chi-restraints excluded: chain C residue 542 ARG Chi-restraints excluded: chain C residue 558 VAL Chi-restraints excluded: chain C residue 631 GLU Chi-restraints excluded: chain C residue 739 ASP Chi-restraints excluded: chain C residue 799 ASN Chi-restraints excluded: chain C residue 800 MET Chi-restraints excluded: chain C residue 949 GLU Chi-restraints excluded: chain C residue 1072 ASN Chi-restraints excluded: chain C residue 1124 ILE Chi-restraints excluded: chain C residue 1186 VAL Chi-restraints excluded: chain D residue 46 TYR Chi-restraints excluded: chain D residue 70 CYS Chi-restraints excluded: chain D residue 146 VAL Chi-restraints excluded: chain D residue 159 ILE Chi-restraints excluded: chain D residue 227 PHE Chi-restraints excluded: chain D residue 356 THR Chi-restraints excluded: chain D residue 357 VAL Chi-restraints excluded: chain D residue 468 VAL Chi-restraints excluded: chain D residue 714 GLU Chi-restraints excluded: chain D residue 762 ASN Chi-restraints excluded: chain D residue 831 VAL Chi-restraints excluded: chain D residue 901 ARG Chi-restraints excluded: chain D residue 931 THR Chi-restraints excluded: chain D residue 1038 THR Chi-restraints excluded: chain D residue 1246 VAL Chi-restraints excluded: chain D residue 1327 GLU Chi-restraints excluded: chain E residue 39 VAL Chi-restraints excluded: chain F residue 107 THR Chi-restraints excluded: chain F residue 342 GLN Chi-restraints excluded: chain F residue 552 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 376 random chunks: chunk 329 optimal weight: 9.9990 chunk 347 optimal weight: 0.9980 chunk 316 optimal weight: 2.9990 chunk 337 optimal weight: 3.9990 chunk 203 optimal weight: 0.2980 chunk 147 optimal weight: 8.9990 chunk 265 optimal weight: 4.9990 chunk 103 optimal weight: 0.9990 chunk 305 optimal weight: 10.0000 chunk 319 optimal weight: 0.0770 chunk 336 optimal weight: 8.9990 overall best weight: 1.0742 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 208 ASN ** C 406 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 128 ASN ** F 147 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 342 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7953 moved from start: 0.2079 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 31858 Z= 0.218 Angle : 0.544 7.801 43470 Z= 0.285 Chirality : 0.041 0.169 4952 Planarity : 0.004 0.059 5309 Dihedral : 16.179 174.719 5261 Min Nonbonded Distance : 2.037 Molprobity Statistics. All-atom Clashscore : 7.71 Ramachandran Plot: Outliers : 0.03 % Allowed : 5.68 % Favored : 94.29 % Rotamer: Outliers : 2.23 % Allowed : 17.42 % Favored : 80.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.69 % Cis-general : 0.17 % Twisted Proline : 0.00 % Twisted General : 0.03 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.10 (0.14), residues: 3661 helix: 1.66 (0.14), residues: 1450 sheet: -0.33 (0.24), residues: 444 loop : -1.54 (0.14), residues: 1767 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP C 807 HIS 0.004 0.001 HIS D 469 PHE 0.011 0.001 PHE A 35 TYR 0.013 0.001 TYR D 46 ARG 0.005 0.000 ARG C1033 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7322 Ramachandran restraints generated. 3661 Oldfield, 0 Emsley, 3661 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7322 Ramachandran restraints generated. 3661 Oldfield, 0 Emsley, 3661 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 320 residues out of total 3153 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 70 poor density : 250 time to evaluate : 3.540 Fit side-chains revert: symmetry clash REVERT: C 145 ILE cc_start: 0.8981 (OUTLIER) cc_final: 0.8666 (mm) REVERT: C 799 ASN cc_start: 0.8777 (OUTLIER) cc_final: 0.8310 (p0) REVERT: C 800 MET cc_start: 0.8701 (OUTLIER) cc_final: 0.7777 (mtp) REVERT: C 1315 MET cc_start: 0.8626 (ptt) cc_final: 0.8027 (ptt) REVERT: D 129 ASP cc_start: 0.7246 (t0) cc_final: 0.6950 (t0) REVERT: D 151 MET cc_start: 0.7247 (ptp) cc_final: 0.6425 (ptt) REVERT: D 227 PHE cc_start: 0.8703 (OUTLIER) cc_final: 0.7675 (t80) REVERT: D 485 MET cc_start: 0.8833 (tpp) cc_final: 0.8603 (tpt) REVERT: D 697 MET cc_start: 0.8738 (ttp) cc_final: 0.8447 (ttp) REVERT: D 714 GLU cc_start: 0.8012 (OUTLIER) cc_final: 0.7805 (mt-10) REVERT: D 1189 MET cc_start: 0.7350 (tpt) cc_final: 0.6638 (tpp) REVERT: F 297 MET cc_start: 0.3326 (mtp) cc_final: 0.2906 (mtm) REVERT: F 342 GLN cc_start: 0.5758 (OUTLIER) cc_final: 0.5345 (mm-40) outliers start: 70 outliers final: 49 residues processed: 309 average time/residue: 0.4384 time to fit residues: 219.3609 Evaluate side-chains 304 residues out of total 3153 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 55 poor density : 249 time to evaluate : 3.584 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 16 ILE Chi-restraints excluded: chain A residue 19 VAL Chi-restraints excluded: chain A residue 93 GLN Chi-restraints excluded: chain A residue 168 ILE Chi-restraints excluded: chain A residue 202 VAL Chi-restraints excluded: chain A residue 208 ASN Chi-restraints excluded: chain B residue 19 VAL Chi-restraints excluded: chain B residue 54 CYS Chi-restraints excluded: chain B residue 64 VAL Chi-restraints excluded: chain B residue 90 VAL Chi-restraints excluded: chain B residue 101 THR Chi-restraints excluded: chain B residue 129 VAL Chi-restraints excluded: chain B residue 183 ILE Chi-restraints excluded: chain B residue 202 VAL Chi-restraints excluded: chain C residue 30 ILE Chi-restraints excluded: chain C residue 127 ILE Chi-restraints excluded: chain C residue 145 ILE Chi-restraints excluded: chain C residue 170 VAL Chi-restraints excluded: chain C residue 315 MET Chi-restraints excluded: chain C residue 492 MET Chi-restraints excluded: chain C residue 498 ILE Chi-restraints excluded: chain C residue 519 ASN Chi-restraints excluded: chain C residue 542 ARG Chi-restraints excluded: chain C residue 558 VAL Chi-restraints excluded: chain C residue 631 GLU Chi-restraints excluded: chain C residue 739 ASP Chi-restraints excluded: chain C residue 799 ASN Chi-restraints excluded: chain C residue 800 MET Chi-restraints excluded: chain C residue 949 GLU Chi-restraints excluded: chain C residue 1072 ASN Chi-restraints excluded: chain C residue 1124 ILE Chi-restraints excluded: chain C residue 1186 VAL Chi-restraints excluded: chain D residue 46 TYR Chi-restraints excluded: chain D residue 70 CYS Chi-restraints excluded: chain D residue 146 VAL Chi-restraints excluded: chain D residue 159 ILE Chi-restraints excluded: chain D residue 227 PHE Chi-restraints excluded: chain D residue 356 THR Chi-restraints excluded: chain D residue 357 VAL Chi-restraints excluded: chain D residue 468 VAL Chi-restraints excluded: chain D residue 714 GLU Chi-restraints excluded: chain D residue 762 ASN Chi-restraints excluded: chain D residue 786 THR Chi-restraints excluded: chain D residue 831 VAL Chi-restraints excluded: chain D residue 901 ARG Chi-restraints excluded: chain D residue 931 THR Chi-restraints excluded: chain D residue 1038 THR Chi-restraints excluded: chain D residue 1246 VAL Chi-restraints excluded: chain D residue 1314 LEU Chi-restraints excluded: chain D residue 1327 GLU Chi-restraints excluded: chain E residue 39 VAL Chi-restraints excluded: chain F residue 107 THR Chi-restraints excluded: chain F residue 342 GLN Chi-restraints excluded: chain F residue 443 ILE Chi-restraints excluded: chain F residue 552 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 376 random chunks: chunk 221 optimal weight: 0.8980 chunk 357 optimal weight: 0.1980 chunk 217 optimal weight: 0.8980 chunk 169 optimal weight: 1.9990 chunk 248 optimal weight: 4.9990 chunk 374 optimal weight: 10.0000 chunk 344 optimal weight: 0.9980 chunk 298 optimal weight: 1.9990 chunk 30 optimal weight: 5.9990 chunk 230 optimal weight: 2.9990 chunk 182 optimal weight: 0.5980 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 406 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 147 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 342 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7926 moved from start: 0.2204 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 31858 Z= 0.173 Angle : 0.522 8.071 43470 Z= 0.274 Chirality : 0.040 0.184 4952 Planarity : 0.004 0.060 5309 Dihedral : 16.137 174.856 5261 Min Nonbonded Distance : 2.042 Molprobity Statistics. All-atom Clashscore : 7.67 Ramachandran Plot: Outliers : 0.03 % Allowed : 5.05 % Favored : 94.92 % Rotamer: Outliers : 1.94 % Allowed : 17.77 % Favored : 80.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.69 % Cis-general : 0.17 % Twisted Proline : 0.00 % Twisted General : 0.03 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.02 (0.14), residues: 3661 helix: 1.72 (0.14), residues: 1456 sheet: -0.20 (0.25), residues: 435 loop : -1.52 (0.14), residues: 1770 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP D 33 HIS 0.003 0.001 HIS D 104 PHE 0.012 0.001 PHE F 256 TYR 0.013 0.001 TYR D 46 ARG 0.005 0.000 ARG C1033 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7322 Ramachandran restraints generated. 3661 Oldfield, 0 Emsley, 3661 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7322 Ramachandran restraints generated. 3661 Oldfield, 0 Emsley, 3661 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 317 residues out of total 3153 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 61 poor density : 256 time to evaluate : 3.652 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: C 124 MET cc_start: 0.7563 (mtm) cc_final: 0.7274 (mtm) REVERT: C 145 ILE cc_start: 0.8957 (OUTLIER) cc_final: 0.8652 (mm) REVERT: C 799 ASN cc_start: 0.8668 (OUTLIER) cc_final: 0.8232 (p0) REVERT: C 800 MET cc_start: 0.8692 (OUTLIER) cc_final: 0.7718 (mtp) REVERT: C 1315 MET cc_start: 0.8597 (ptt) cc_final: 0.8045 (ptt) REVERT: D 129 ASP cc_start: 0.7303 (t0) cc_final: 0.7031 (t0) REVERT: D 151 MET cc_start: 0.7394 (ptp) cc_final: 0.6567 (ptt) REVERT: D 227 PHE cc_start: 0.8645 (OUTLIER) cc_final: 0.7642 (t80) REVERT: D 485 MET cc_start: 0.8850 (tpp) cc_final: 0.8633 (tpt) REVERT: D 697 MET cc_start: 0.8653 (ttp) cc_final: 0.8291 (ttp) REVERT: D 714 GLU cc_start: 0.8000 (OUTLIER) cc_final: 0.7795 (mt-10) REVERT: D 1040 MET cc_start: 0.4090 (ppp) cc_final: 0.3533 (ppp) REVERT: D 1189 MET cc_start: 0.7375 (tpt) cc_final: 0.6690 (tpp) REVERT: D 1195 GLN cc_start: 0.7430 (mp10) cc_final: 0.7113 (mp10) REVERT: F 297 MET cc_start: 0.3144 (mtp) cc_final: 0.2725 (mtm) REVERT: F 342 GLN cc_start: 0.5907 (OUTLIER) cc_final: 0.5431 (mm-40) outliers start: 61 outliers final: 50 residues processed: 306 average time/residue: 0.4326 time to fit residues: 214.3356 Evaluate side-chains 307 residues out of total 3153 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 56 poor density : 251 time to evaluate : 3.417 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 16 ILE Chi-restraints excluded: chain A residue 19 VAL Chi-restraints excluded: chain A residue 93 GLN Chi-restraints excluded: chain A residue 168 ILE Chi-restraints excluded: chain A residue 202 VAL Chi-restraints excluded: chain B residue 19 VAL Chi-restraints excluded: chain B residue 54 CYS Chi-restraints excluded: chain B residue 64 VAL Chi-restraints excluded: chain B residue 90 VAL Chi-restraints excluded: chain B residue 101 THR Chi-restraints excluded: chain B residue 129 VAL Chi-restraints excluded: chain B residue 183 ILE Chi-restraints excluded: chain B residue 202 VAL Chi-restraints excluded: chain C residue 127 ILE Chi-restraints excluded: chain C residue 145 ILE Chi-restraints excluded: chain C residue 170 VAL Chi-restraints excluded: chain C residue 468 LEU Chi-restraints excluded: chain C residue 492 MET Chi-restraints excluded: chain C residue 498 ILE Chi-restraints excluded: chain C residue 519 ASN Chi-restraints excluded: chain C residue 542 ARG Chi-restraints excluded: chain C residue 558 VAL Chi-restraints excluded: chain C residue 631 GLU Chi-restraints excluded: chain C residue 727 VAL Chi-restraints excluded: chain C residue 739 ASP Chi-restraints excluded: chain C residue 799 ASN Chi-restraints excluded: chain C residue 800 MET Chi-restraints excluded: chain C residue 949 GLU Chi-restraints excluded: chain C residue 1072 ASN Chi-restraints excluded: chain C residue 1124 ILE Chi-restraints excluded: chain C residue 1186 VAL Chi-restraints excluded: chain C residue 1225 VAL Chi-restraints excluded: chain C residue 1232 MET Chi-restraints excluded: chain D residue 46 TYR Chi-restraints excluded: chain D residue 70 CYS Chi-restraints excluded: chain D residue 146 VAL Chi-restraints excluded: chain D residue 159 ILE Chi-restraints excluded: chain D residue 227 PHE Chi-restraints excluded: chain D residue 356 THR Chi-restraints excluded: chain D residue 357 VAL Chi-restraints excluded: chain D residue 468 VAL Chi-restraints excluded: chain D residue 714 GLU Chi-restraints excluded: chain D residue 762 ASN Chi-restraints excluded: chain D residue 786 THR Chi-restraints excluded: chain D residue 831 VAL Chi-restraints excluded: chain D residue 901 ARG Chi-restraints excluded: chain D residue 931 THR Chi-restraints excluded: chain D residue 1038 THR Chi-restraints excluded: chain D residue 1190 ILE Chi-restraints excluded: chain D residue 1246 VAL Chi-restraints excluded: chain D residue 1314 LEU Chi-restraints excluded: chain D residue 1327 GLU Chi-restraints excluded: chain E residue 39 VAL Chi-restraints excluded: chain F residue 107 THR Chi-restraints excluded: chain F residue 342 GLN Chi-restraints excluded: chain F residue 552 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 376 random chunks: chunk 236 optimal weight: 1.9990 chunk 317 optimal weight: 6.9990 chunk 91 optimal weight: 3.9990 chunk 275 optimal weight: 20.0000 chunk 44 optimal weight: 4.9990 chunk 82 optimal weight: 0.8980 chunk 298 optimal weight: 1.9990 chunk 125 optimal weight: 1.9990 chunk 306 optimal weight: 2.9990 chunk 37 optimal weight: 4.9990 chunk 55 optimal weight: 1.9990 overall best weight: 1.7788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 208 ASN ** C 406 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 147 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 331 HIS ** F 342 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4037 r_free = 0.4037 target = 0.180209 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3498 r_free = 0.3498 target = 0.131695 restraints weight = 36052.929| |-----------------------------------------------------------------------------| r_work (start): 0.3458 rms_B_bonded: 2.94 r_work: 0.3012 rms_B_bonded: 4.55 restraints_weight: 0.5000 r_work (final): 0.3012 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2995 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2995 r_free = 0.2995 target_work(ls_wunit_k1) = 0.093 | | occupancies: max = 1.00 min = 0.30 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2995 r_free = 0.2995 target_work(ls_wunit_k1) = 0.093 | | occupancies: max = 1.00 min = 0.37 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2995 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8279 moved from start: 0.2123 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.057 31858 Z= 0.315 Angle : 0.593 8.208 43470 Z= 0.308 Chirality : 0.043 0.189 4952 Planarity : 0.004 0.059 5309 Dihedral : 16.264 175.087 5261 Min Nonbonded Distance : 2.019 Molprobity Statistics. All-atom Clashscore : 8.20 Ramachandran Plot: Outliers : 0.05 % Allowed : 6.34 % Favored : 93.61 % Rotamer: Outliers : 2.19 % Allowed : 17.77 % Favored : 80.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.69 % Cis-general : 0.17 % Twisted Proline : 0.00 % Twisted General : 0.06 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.20 (0.14), residues: 3661 helix: 1.55 (0.14), residues: 1450 sheet: -0.26 (0.25), residues: 432 loop : -1.59 (0.14), residues: 1779 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP D 115 HIS 0.006 0.001 HIS D 430 PHE 0.016 0.002 PHE A 35 TYR 0.014 0.001 TYR C1281 ARG 0.007 0.000 ARG A 45 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 6163.74 seconds wall clock time: 112 minutes 44.45 seconds (6764.45 seconds total)