Starting phenix.real_space_refine on Wed Feb 21 07:59:39 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8igr_35438/02_2024/8igr_35438.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8igr_35438/02_2024/8igr_35438.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.1 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8igr_35438/02_2024/8igr_35438.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8igr_35438/02_2024/8igr_35438.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8igr_35438/02_2024/8igr_35438.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8igr_35438/02_2024/8igr_35438.pdb" } resolution = 3.1 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.003 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 122 5.49 5 Mg 1 5.21 5 S 127 5.16 5 C 18481 2.51 5 N 5336 2.21 5 O 5974 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "G ASP 15": "OD1" <-> "OD2" Residue "G GLU 17": "OE1" <-> "OE2" Residue "G GLU 32": "OE1" <-> "OE2" Residue "G GLU 97": "OE1" <-> "OE2" Residue "G ASP 259": "OD1" <-> "OD2" Residue "H ASP 62": "OD1" <-> "OD2" Residue "I GLU 84": "OE1" <-> "OE2" Residue "I TYR 123": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I TYR 172": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I ASP 199": "OD1" <-> "OD2" Residue "I ASP 354": "OD1" <-> "OD2" Residue "I TYR 367": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I GLU 374": "OE1" <-> "OE2" Residue "I GLU 472": "OE1" <-> "OE2" Residue "I ASP 549": "OD1" <-> "OD2" Residue "I ASP 651": "OD1" <-> "OD2" Residue "I ASP 739": "OD1" <-> "OD2" Residue "I TYR 751": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I ASP 853": "OD1" <-> "OD2" Residue "I GLU 867": "OE1" <-> "OE2" Residue "I ASP 912": "OD1" <-> "OD2" Residue "I GLU 1143": "OE1" <-> "OE2" Residue "J ASP 54": "OD1" <-> "OD2" Residue "J ASP 304": "OD1" <-> "OD2" Residue "J PHE 437": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J GLU 497": "OE1" <-> "OE2" Residue "J GLU 656": "OE1" <-> "OE2" Residue "J ASP 785": "OD1" <-> "OD2" Residue "J GLU 1281": "OE1" <-> "OE2" Residue "L ASP 96": "OD1" <-> "OD2" Residue "L TYR 421": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L ASP 516": "OD1" <-> "OD2" Residue "L PHE 563": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L GLU 574": "OE1" <-> "OE2" Residue "A GLU 14": "OE1" <-> "OE2" 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: 30043 Number of models: 1 Model: "" Number of chains: 13 Chain: "G" Number of atoms: 2254 Number of conformers: 1 Conformer: "" Number of residues, atoms: 293, 2254 Classifications: {'peptide': 293} Incomplete info: {'truncation_to_alanine': 4} Link IDs: {'PTRANS': 11, 'TRANS': 281} Chain breaks: 1 Unresolved non-hydrogen bonds: 13 Unresolved non-hydrogen angles: 17 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLU:plan': 2, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 11 Chain: "H" Number of atoms: 1678 Number of conformers: 1 Conformer: "" Number of residues, atoms: 219, 1678 Classifications: {'peptide': 219} Incomplete info: {'truncation_to_alanine': 4} Link IDs: {'PCIS': 1, 'PTRANS': 7, 'TRANS': 210} Chain breaks: 1 Unresolved non-hydrogen bonds: 10 Unresolved non-hydrogen angles: 13 Unresolved non-hydrogen dihedrals: 7 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'GLU:plan': 1} Unresolved non-hydrogen planarities: 4 Chain: "I" Number of atoms: 9176 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1167, 9176 Classifications: {'peptide': 1167} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 52, 'TRANS': 1114} Chain breaks: 2 Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 7 Unresolved non-hydrogen dihedrals: 5 Planarities with less than four sites: {'ARG:plan': 1} Unresolved non-hydrogen planarities: 5 Chain: "J" Number of atoms: 9022 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1154, 9022 Classifications: {'peptide': 1154} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PCIS': 1, 'PTRANS': 46, 'TRANS': 1106} Chain breaks: 1 Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 7 Unresolved non-hydrogen dihedrals: 5 Planarities with less than four sites: {'ARG:plan': 1} Unresolved non-hydrogen planarities: 5 Chain: "K" 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: "L" Number of atoms: 2500 Number of conformers: 1 Conformer: "" Number of residues, atoms: 309, 2500 Classifications: {'peptide': 309} Link IDs: {'PTRANS': 10, 'TRANS': 298} Chain breaks: 1 Chain: "A" Number of atoms: 583 Number of conformers: 1 Conformer: "" Number of residues, atoms: 74, 583 Classifications: {'peptide': 74} Link IDs: {'PTRANS': 1, 'TRANS': 72} Chain: "B" Number of atoms: 577 Number of conformers: 1 Conformer: "" Number of residues, atoms: 73, 577 Classifications: {'peptide': 73} Link IDs: {'PTRANS': 1, 'TRANS': 71} Chain: "C" Number of atoms: 587 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 74, 584 Classifications: {'peptide': 74} Link IDs: {'PTRANS': 1, 'TRANS': 72} Conformer: "B" Number of residues, atoms: 74, 584 Classifications: {'peptide': 74} Link IDs: {'PTRANS': 1, 'TRANS': 72} bond proxies already assigned to first conformer: 588 Chain: "D" Number of atoms: 557 Number of conformers: 1 Conformer: "" Number of residues, atoms: 71, 557 Classifications: {'peptide': 71} Link IDs: {'PTRANS': 1, 'TRANS': 69} Chain: "N" Number of atoms: 1247 Number of conformers: 1 Conformer: "" Number of residues, atoms: 61, 1247 Classifications: {'DNA': 61} Link IDs: {'rna3p': 60} Chain: "T" Number of atoms: 1254 Number of conformers: 1 Conformer: "" Number of residues, atoms: 61, 1254 Classifications: {'DNA': 61} Link IDs: {'rna3p': 60} Chain: "J" Number of atoms: 3 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 3 Unusual residues: {' MG': 1, ' ZN': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 13557 SG CYS J 70 62.328 117.543 61.629 1.00 64.95 S ATOM 13571 SG CYS J 72 63.204 121.129 62.066 1.00 59.35 S ATOM 13679 SG CYS J 85 60.786 120.084 59.277 1.00 60.83 S ATOM 13703 SG CYS J 88 64.424 118.649 59.164 1.00 54.04 S ATOM 19385 SG CYS J 814 61.934 51.403 52.012 1.00 24.88 S ATOM 19950 SG CYS J 888 64.250 54.281 52.863 1.00 15.26 S ATOM 20001 SG CYS J 895 62.069 52.638 55.617 1.00 17.04 S ATOM 20022 SG CYS J 898 65.034 50.894 54.292 1.00 17.85 S Time building chain proxies: 15.62, per 1000 atoms: 0.52 Number of scatterers: 30043 At special positions: 0 Unit cell: (151.13, 168.98, 149.94, 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 127 16.00 P 122 15.00 Mg 1 11.99 O 5974 8.00 N 5336 7.00 C 18481 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: 12.03 Conformation dependent library (CDL) restraints added in 5.4 seconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN J2002 " pdb="ZN ZN J2002 " - pdb=" SG CYS J 70 " pdb="ZN ZN J2002 " - pdb=" SG CYS J 85 " pdb="ZN ZN J2002 " - pdb=" SG CYS J 72 " pdb="ZN ZN J2002 " - pdb=" SG CYS J 88 " pdb=" ZN J2003 " pdb="ZN ZN J2003 " - pdb=" SG CYS J 895 " pdb="ZN ZN J2003 " - pdb=" SG CYS J 898 " pdb="ZN ZN J2003 " - pdb=" SG CYS J 888 " pdb="ZN ZN J2003 " - pdb=" SG CYS J 814 " Number of angles added : 12 6956 Ramachandran restraints generated. 3478 Oldfield, 0 Emsley, 3478 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 6526 Finding SS restraints... Secondary structure from input PDB file: 143 helices and 42 sheets defined 48.4% alpha, 13.2% beta 47 base pairs and 90 stacking pairs defined. Time for finding SS restraints: 11.61 Creating SS restraints... Processing helix chain 'G' and resid 34 through 50 removed outlier: 3.512A pdb=" N THR G 38 " --> pdb=" O GLY G 34 " (cutoff:3.500A) removed outlier: 3.639A pdb=" N SER G 49 " --> pdb=" O ARG G 45 " (cutoff:3.500A) Processing helix chain 'G' and resid 77 through 86 Processing helix chain 'G' and resid 154 through 159 Processing helix chain 'G' and resid 212 through 234 removed outlier: 3.989A pdb=" N LEU G 234 " --> pdb=" O ALA G 230 " (cutoff:3.500A) Processing helix chain 'G' and resid 256 through 260 Processing helix chain 'G' and resid 263 through 273 Processing helix chain 'G' and resid 277 through 282 Processing helix chain 'G' and resid 285 through 291 removed outlier: 3.755A pdb=" N LYS G 291 " --> pdb=" O VAL G 287 " (cutoff:3.500A) Processing helix chain 'G' and resid 296 through 310 Processing helix chain 'H' and resid 34 through 50 Processing helix chain 'H' and resid 77 through 87 Processing helix chain 'H' and resid 212 through 228 removed outlier: 3.514A pdb=" N LEU H 228 " --> pdb=" O LEU H 224 " (cutoff:3.500A) Processing helix chain 'I' and resid 4 through 9 Processing helix chain 'I' and resid 28 through 40 removed outlier: 3.650A pdb=" N SER I 34 " --> pdb=" O ILE I 30 " (cutoff:3.500A) Processing helix chain 'I' and resid 47 through 57 Processing helix chain 'I' and resid 81 through 89 Processing helix chain 'I' and resid 206 through 213 removed outlier: 3.649A pdb=" N LEU I 210 " --> pdb=" O ALA I 206 " (cutoff:3.500A) Processing helix chain 'I' and resid 216 through 224 Processing helix chain 'I' and resid 347 through 354 Processing helix chain 'I' and resid 358 through 371 Processing helix chain 'I' and resid 377 through 389 removed outlier: 3.981A pdb=" N PHE I 389 " --> pdb=" O PHE I 385 " (cutoff:3.500A) Processing helix chain 'I' and resid 398 through 409 Processing helix chain 'I' and resid 421 through 438 Processing helix chain 'I' and resid 455 through 480 removed outlier: 4.462A pdb=" N ALA I 474 " --> pdb=" O ARG I 470 " (cutoff:3.500A) Processing helix chain 'I' and resid 494 through 508 removed outlier: 4.637A pdb=" N ILE I 498 " --> pdb=" O ASN I 494 " (cutoff:3.500A) Processing helix chain 'I' and resid 519 through 528 Processing helix chain 'I' and resid 544 through 549 removed outlier: 3.617A pdb=" N ARG I 548 " --> pdb=" O GLY I 544 " (cutoff:3.500A) Processing helix chain 'I' and resid 551 through 555 removed outlier: 3.506A pdb=" N TYR I 555 " --> pdb=" O PRO I 552 " (cutoff:3.500A) Processing helix chain 'I' and resid 608 through 612 removed outlier: 3.838A pdb=" N GLY I 612 " --> pdb=" O ALA I 608 " (cutoff:3.500A) No H-bonds generated for 'chain 'I' and resid 608 through 612' Processing helix chain 'I' and resid 648 through 650 No H-bonds generated for 'chain 'I' and resid 648 through 650' Processing helix chain 'I' and resid 664 through 668 removed outlier: 3.529A pdb=" N ILE I 668 " --> pdb=" O ALA I 665 " (cutoff:3.500A) Processing helix chain 'I' and resid 670 through 674 Processing helix chain 'I' and resid 675 through 687 Processing helix chain 'I' and resid 704 through 712 Processing helix chain 'I' and resid 738 through 741 Processing helix chain 'I' and resid 820 through 825 Processing helix chain 'I' and resid 859 through 863 Processing helix chain 'I' and resid 899 through 906 Processing helix chain 'I' and resid 942 through 967 Processing helix chain 'I' and resid 1022 through 1038 Processing helix chain 'I' and resid 1101 through 1106 removed outlier: 4.377A pdb=" N SER I1105 " --> pdb=" O LEU I1101 " (cutoff:3.500A) removed outlier: 3.908A pdb=" N ARG I1106 " --> pdb=" O GLY I1102 " (cutoff:3.500A) No H-bonds generated for 'chain 'I' and resid 1101 through 1106' Processing helix chain 'I' and resid 1109 through 1134 Processing helix chain 'I' and resid 1137 through 1151 removed outlier: 3.604A pdb=" N LEU I1141 " --> pdb=" O GLU I1137 " (cutoff:3.500A) removed outlier: 3.791A pdb=" N LEU I1151 " --> pdb=" O ARG I1147 " (cutoff:3.500A) Processing helix chain 'I' and resid 1160 through 1164 removed outlier: 3.684A pdb=" N THR I1163 " --> pdb=" O ASP I1160 " (cutoff:3.500A) Processing helix chain 'I' and resid 1165 through 1176 Processing helix chain 'I' and resid 1191 through 1202 Processing helix chain 'I' and resid 1271 through 1281 Processing helix chain 'I' and resid 1283 through 1293 Processing helix chain 'I' and resid 1297 through 1310 removed outlier: 3.816A pdb=" N THR I1302 " --> pdb=" O VAL I1298 " (cutoff:3.500A) Processing helix chain 'I' and resid 1320 through 1333 removed outlier: 3.595A pdb=" N ASN I1324 " --> pdb=" O PRO I1320 " (cutoff:3.500A) Processing helix chain 'J' and resid 26 through 33 Processing helix chain 'J' and resid 58 through 63 Processing helix chain 'J' and resid 77 through 81 Processing helix chain 'J' and resid 95 through 100 Processing helix chain 'J' and resid 113 through 118 Processing helix chain 'J' and resid 122 through 129 Processing helix chain 'J' and resid 131 through 140 Processing helix chain 'J' and resid 161 through 172 removed outlier: 3.795A pdb=" N GLU J 170 " --> pdb=" O LEU J 166 " (cutoff:3.500A) removed outlier: 3.522A pdb=" N GLU J 171 " --> pdb=" O ASP J 167 " (cutoff:3.500A) Processing helix chain 'J' and resid 180 through 192 removed outlier: 3.833A pdb=" N ALA J 184 " --> pdb=" O MET J 180 " (cutoff:3.500A) Processing helix chain 'J' and resid 193 through 207 Processing helix chain 'J' and resid 210 through 230 removed outlier: 3.723A pdb=" N SER J 230 " --> pdb=" O ALA J 226 " (cutoff:3.500A) Processing helix chain 'J' and resid 233 through 236 Processing helix chain 'J' and resid 246 through 250 Processing helix chain 'J' and resid 263 through 286 removed outlier: 3.956A pdb=" N ASP J 267 " --> pdb=" O SER J 263 " (cutoff:3.500A) Processing helix chain 'J' and resid 288 through 308 Processing helix chain 'J' and resid 336 through 341 Processing helix chain 'J' and resid 370 through 377 Processing helix chain 'J' and resid 377 through 388 Processing helix chain 'J' and resid 393 through 404 Processing helix chain 'J' and resid 405 through 416 removed outlier: 3.820A pdb=" N TRP J 409 " --> pdb=" O GLU J 405 " (cutoff:3.500A) removed outlier: 3.814A pdb=" N ASP J 410 " --> pdb=" O ALA J 406 " (cutoff:3.500A) Processing helix chain 'J' and resid 430 through 432 No H-bonds generated for 'chain 'J' and resid 430 through 432' Processing helix chain 'J' and resid 450 through 452 No H-bonds generated for 'chain 'J' and resid 450 through 452' Processing helix chain 'J' and resid 453 through 458 Processing helix chain 'J' and resid 473 through 483 Processing helix chain 'J' and resid 504 through 515 Processing helix chain 'J' and resid 529 through 539 Processing helix chain 'J' and resid 573 through 581 removed outlier: 3.858A pdb=" N MET J 581 " --> pdb=" O ALA J 577 " (cutoff:3.500A) Processing helix chain 'J' and resid 588 through 593 removed outlier: 3.581A pdb=" N ILE J 591 " --> pdb=" O PRO J 588 " (cutoff:3.500A) Processing helix chain 'J' and resid 597 through 612 Processing helix chain 'J' and resid 613 through 636 removed outlier: 3.712A pdb=" N THR J 617 " --> pdb=" O GLY J 613 " (cutoff:3.500A) removed outlier: 3.748A pdb=" N GLY J 636 " --> pdb=" O ALA J 632 " (cutoff:3.500A) Processing helix chain 'J' and resid 649 through 670 Processing helix chain 'J' and resid 674 through 703 removed outlier: 3.938A pdb=" N THR J 703 " --> pdb=" O ASP J 699 " (cutoff:3.500A) Processing helix chain 'J' and resid 720 through 728 Processing helix chain 'J' and resid 733 through 741 Processing helix chain 'J' and resid 768 through 788 removed outlier: 3.714A pdb=" N GLY J 778 " --> pdb=" O ILE J 774 " (cutoff:3.500A) removed outlier: 3.560A pdb=" N LYS J 781 " --> pdb=" O HIS J 777 " (cutoff:3.500A) Processing helix chain 'J' and resid 789 through 805 Processing helix chain 'J' and resid 865 through 876 Processing helix chain 'J' and resid 884 through 888 Processing helix chain 'J' and resid 896 through 900 Processing helix chain 'J' and resid 914 through 925 Processing helix chain 'J' and resid 926 through 929 Processing helix chain 'J' and resid 1138 through 1147 Processing helix chain 'J' and resid 1216 through 1224 Processing helix chain 'J' and resid 1225 through 1244 Processing helix chain 'J' and resid 1249 through 1261 removed outlier: 4.223A pdb=" N ILE J1253 " --> pdb=" O ASN J1249 " (cutoff:3.500A) Processing helix chain 'J' and resid 1282 through 1292 Processing helix chain 'J' and resid 1308 through 1315 Processing helix chain 'J' and resid 1318 through 1324 removed outlier: 3.565A pdb=" N ALA J1322 " --> pdb=" O SER J1318 " (cutoff:3.500A) Processing helix chain 'J' and resid 1327 through 1339 removed outlier: 3.724A pdb=" N VAL J1331 " --> pdb=" O GLU J1327 " (cutoff:3.500A) Processing helix chain 'J' and resid 1346 through 1353 Processing helix chain 'J' and resid 1361 through 1374 removed outlier: 4.602A pdb=" N TYR J1365 " --> pdb=" O THR J1361 " (cutoff:3.500A) Processing helix chain 'K' and resid 7 through 14 Processing helix chain 'K' and resid 17 through 32 Processing helix chain 'K' and resid 45 through 56 Processing helix chain 'K' and resid 60 through 76 removed outlier: 3.678A pdb=" N GLU K 76 " --> pdb=" O GLN K 72 " (cutoff:3.500A) Processing helix chain 'L' and resid 96 through 106 Processing helix chain 'L' and resid 114 through 136 removed outlier: 3.659A pdb=" N ASP L 118 " --> pdb=" O GLU L 114 " (cutoff:3.500A) Processing helix chain 'L' and resid 137 through 153 Processing helix chain 'L' and resid 366 through 374 Processing helix chain 'L' and resid 376 through 383 Processing helix chain 'L' and resid 383 through 390 removed outlier: 3.549A pdb=" N VAL L 387 " --> pdb=" O ASN L 383 " (cutoff:3.500A) removed outlier: 3.505A pdb=" N ILE L 388 " --> pdb=" O LEU L 384 " (cutoff:3.500A) Processing helix chain 'L' and resid 391 through 395 removed outlier: 3.874A pdb=" N THR L 395 " --> pdb=" O LYS L 392 " (cutoff:3.500A) Processing helix chain 'L' and resid 400 through 419 Processing helix chain 'L' and resid 420 through 424 removed outlier: 3.706A pdb=" N ARG L 423 " --> pdb=" O GLU L 420 " (cutoff:3.500A) Processing helix chain 'L' and resid 426 through 447 removed outlier: 3.749A pdb=" N TYR L 430 " --> pdb=" O LYS L 426 " (cutoff:3.500A) removed outlier: 3.971A pdb=" N TRP L 433 " --> pdb=" O THR L 429 " (cutoff:3.500A) removed outlier: 3.652A pdb=" N TRP L 434 " --> pdb=" O TYR L 430 " (cutoff:3.500A) Processing helix chain 'L' and resid 453 through 475 removed outlier: 3.597A pdb=" N GLN L 472 " --> pdb=" O ARG L 468 " (cutoff:3.500A) Processing helix chain 'L' and resid 482 through 487 removed outlier: 3.542A pdb=" N ARG L 486 " --> pdb=" O GLU L 482 " (cutoff:3.500A) Processing helix chain 'L' and resid 491 through 500 removed outlier: 3.972A pdb=" N ARG L 495 " --> pdb=" O GLU L 491 " (cutoff:3.500A) Processing helix chain 'L' and resid 518 through 523 removed outlier: 3.851A pdb=" N ILE L 523 " --> pdb=" O GLY L 520 " (cutoff:3.500A) Processing helix chain 'L' and resid 530 through 549 Processing helix chain 'L' and resid 552 through 563 Processing helix chain 'L' and resid 572 through 581 Processing helix chain 'L' and resid 583 through 599 Processing helix chain 'L' and resid 604 through 610 Processing helix chain 'A' and resid 8 through 25 Processing helix chain 'A' and resid 25 through 34 Processing helix chain 'A' and resid 36 through 47 removed outlier: 3.846A pdb=" N ARG A 45 " --> pdb=" O SER A 41 " (cutoff:3.500A) Processing helix chain 'A' and resid 47 through 60 removed outlier: 3.941A pdb=" N TRP A 60 " --> pdb=" O ALA A 56 " (cutoff:3.500A) Processing helix chain 'A' and resid 63 through 78 Processing helix chain 'B' and resid 7 through 25 Processing helix chain 'B' and resid 25 through 33 Processing helix chain 'B' and resid 36 through 38 No H-bonds generated for 'chain 'B' and resid 36 through 38' Processing helix chain 'B' and resid 39 through 58 removed outlier: 3.759A pdb=" N ILE B 48 " --> pdb=" O LYS B 44 " (cutoff:3.500A) Proline residue: B 49 - end of helix Processing helix chain 'B' and resid 64 through 78 removed outlier: 3.914A pdb=" N ALA B 68 " --> pdb=" O ASP B 64 " (cutoff:3.500A) removed outlier: 3.636A pdb=" N ILE B 77 " --> pdb=" O GLN B 73 " (cutoff:3.500A) Processing helix chain 'C' and resid 7 through 25 Processing helix chain 'C' and resid 25 through 34 Processing helix chain 'C' and resid 36 through 47 removed outlier: 3.732A pdb=" N ARG C 45 " --> pdb=" O SER C 41 " (cutoff:3.500A) Processing helix chain 'C' and resid 47 through 59 Processing helix chain 'C' and resid 64 through 79 Processing helix chain 'D' and resid 9 through 25 Processing helix chain 'D' and resid 25 through 34 Processing helix chain 'D' and resid 39 through 59 Proline residue: D 49 - end of helix Processing helix chain 'D' and resid 61 through 78 Processing sheet with id=AA1, first strand: chain 'G' and resid 13 through 17 removed outlier: 3.975A pdb=" N THR G 27 " --> pdb=" O VAL G 14 " (cutoff:3.500A) removed outlier: 4.551A pdb=" N ILE G 16 " --> pdb=" O LYS G 25 " (cutoff:3.500A) removed outlier: 6.159A pdb=" N LYS G 25 " --> pdb=" O ILE G 16 " (cutoff:3.500A) removed outlier: 6.536A pdb=" N ASP G 199 " --> pdb=" O PRO G 30 " (cutoff:3.500A) removed outlier: 4.493A pdb=" N LEU G 198 " --> pdb=" O ALA G 190 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'G' and resid 52 through 53 Processing sheet with id=AA3, first strand: chain 'G' and resid 115 through 116 removed outlier: 4.371A pdb=" N THR G 101 " --> pdb=" O THR G 116 " (cutoff:3.500A) removed outlier: 7.235A pdb=" N SER G 141 " --> pdb=" O ILE G 61 " (cutoff:3.500A) removed outlier: 4.734A pdb=" N ILE G 61 " --> pdb=" O SER G 141 " (cutoff:3.500A) removed outlier: 6.548A pdb=" N ARG G 143 " --> pdb=" O VAL G 59 " (cutoff:3.500A) removed outlier: 4.486A pdb=" N VAL G 59 " --> pdb=" O ARG G 143 " (cutoff:3.500A) removed outlier: 6.712A pdb=" N LYS G 145 " --> pdb=" O THR G 57 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'G' and resid 90 through 92 Processing sheet with id=AA5, first strand: chain 'G' and resid 108 through 111 removed outlier: 6.488A pdb=" N GLY G 108 " --> pdb=" O HIS G 132 " (cutoff:3.500A) removed outlier: 4.730A pdb=" N HIS G 132 " --> pdb=" O GLY G 108 " (cutoff:3.500A) removed outlier: 6.712A pdb=" N VAL G 110 " --> pdb=" O ILE G 130 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'H' and resid 15 through 18 removed outlier: 4.053A pdb=" N ASP H 15 " --> pdb=" O THR H 27 " (cutoff:3.500A) removed outlier: 4.060A pdb=" N GLU H 17 " --> pdb=" O LYS H 25 " (cutoff:3.500A) removed outlier: 5.964A pdb=" N HIS H 23 " --> pdb=" O THR H 207 " (cutoff:3.500A) removed outlier: 7.516A pdb=" N THR H 207 " --> pdb=" O HIS H 23 " (cutoff:3.500A) removed outlier: 5.458A pdb=" N LYS H 25 " --> pdb=" O MET H 205 " (cutoff:3.500A) removed outlier: 7.427A pdb=" N MET H 205 " --> pdb=" O LYS H 25 " (cutoff:3.500A) removed outlier: 5.501A pdb=" N THR H 27 " --> pdb=" O ILE H 203 " (cutoff:3.500A) removed outlier: 7.269A pdb=" N ILE H 203 " --> pdb=" O THR H 27 " (cutoff:3.500A) removed outlier: 5.442A pdb=" N GLU H 29 " --> pdb=" O LEU H 201 " (cutoff:3.500A) removed outlier: 7.588A pdb=" N LEU H 201 " --> pdb=" O GLU H 29 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'H' and resid 53 through 61 removed outlier: 6.617A pdb=" N LYS H 145 " --> pdb=" O THR H 57 " (cutoff:3.500A) removed outlier: 4.245A pdb=" N VAL H 59 " --> pdb=" O ARG H 143 " (cutoff:3.500A) removed outlier: 6.554A pdb=" N ARG H 143 " --> pdb=" O VAL H 59 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'H' and resid 90 through 91 Processing sheet with id=AA9, first strand: chain 'H' and resid 104 through 105 Processing sheet with id=AB1, first strand: chain 'H' and resid 109 through 111 Processing sheet with id=AB2, first strand: chain 'H' and resid 152 through 153 Processing sheet with id=AB3, first strand: chain 'I' and resid 13 through 14 removed outlier: 6.666A pdb=" N LYS I 13 " --> pdb=" O ALA I1183 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'I' and resid 59 through 60 removed outlier: 6.071A pdb=" N SER I 66 " --> pdb=" O TYR I 105 " (cutoff:3.500A) removed outlier: 6.924A pdb=" N TYR I 105 " --> pdb=" O SER I 66 " (cutoff:3.500A) removed outlier: 5.125A pdb=" N LEU I 68 " --> pdb=" O VAL I 103 " (cutoff:3.500A) removed outlier: 6.972A pdb=" N VAL I 103 " --> pdb=" O LEU I 68 " (cutoff:3.500A) removed outlier: 5.443A pdb=" N TYR I 70 " --> pdb=" O ARG I 101 " (cutoff:3.500A) removed outlier: 6.576A pdb=" N ARG I 101 " --> pdb=" O TYR I 70 " (cutoff:3.500A) removed outlier: 3.730A pdb=" N SER I 72 " --> pdb=" O LYS I 99 " (cutoff:3.500A) removed outlier: 6.948A pdb=" N ALA I 94 " --> pdb=" O GLY I 125 " (cutoff:3.500A) removed outlier: 7.252A pdb=" N GLY I 125 " --> pdb=" O ALA I 94 " (cutoff:3.500A) removed outlier: 7.128A pdb=" N LEU I 96 " --> pdb=" O TYR I 123 " (cutoff:3.500A) removed outlier: 4.570A pdb=" N TYR I 123 " --> pdb=" O LEU I 96 " (cutoff:3.500A) removed outlier: 6.338A pdb=" N VAL I 98 " --> pdb=" O GLU I 121 " (cutoff:3.500A) removed outlier: 4.542A pdb=" N GLU I 121 " --> pdb=" O VAL I 98 " (cutoff:3.500A) removed outlier: 6.676A pdb=" N LEU I 100 " --> pdb=" O GLU I 119 " (cutoff:3.500A) removed outlier: 4.354A pdb=" N GLU I 119 " --> pdb=" O LEU I 100 " (cutoff:3.500A) removed outlier: 6.297A pdb=" N LEU I 102 " --> pdb=" O ILE I 117 " (cutoff:3.500A) removed outlier: 4.287A pdb=" N ILE I 117 " --> pdb=" O LEU I 102 " (cutoff:3.500A) removed outlier: 6.634A pdb=" N ILE I 104 " --> pdb=" O LYS I 115 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'I' and resid 136 through 137 Processing sheet with id=AB6, first strand: chain 'I' and resid 451 through 454 Processing sheet with id=AB7, first strand: chain 'I' and resid 154 through 157 Processing sheet with id=AB8, first strand: chain 'I' and resid 580 through 581 removed outlier: 5.485A pdb=" N GLU I 602 " --> pdb=" O LYS I 593 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'I' and resid 580 through 581 Processing sheet with id=AC1, first strand: chain 'I' and resid 716 through 717 removed outlier: 6.328A pdb=" N ALA I 716 " --> pdb=" O LEU I 783 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'I' and resid 748 through 752 removed outlier: 6.773A pdb=" N ARG I 731 " --> pdb=" O VAL I 727 " (cutoff:3.500A) removed outlier: 4.824A pdb=" N VAL I 727 " --> pdb=" O ARG I 731 " (cutoff:3.500A) removed outlier: 6.508A pdb=" N VAL I 733 " --> pdb=" O GLN I 725 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'I' and resid 757 through 758 Processing sheet with id=AC4, first strand: chain 'I' and resid 789 through 790 Processing sheet with id=AC5, first strand: chain 'I' and resid 1066 through 1067 removed outlier: 4.297A pdb=" N THR I1226 " --> pdb=" O PHE I 804 " (cutoff:3.500A) removed outlier: 8.895A pdb=" N ILE I1096 " --> pdb=" O ASN I 799 " (cutoff:3.500A) removed outlier: 6.390A pdb=" N ARG I 801 " --> pdb=" O ILE I1096 " (cutoff:3.500A) removed outlier: 7.689A pdb=" N LEU I1098 " --> pdb=" O ARG I 801 " (cutoff:3.500A) removed outlier: 6.248A pdb=" N ALA I 803 " --> pdb=" O LEU I1098 " (cutoff:3.500A) removed outlier: 6.767A pdb=" N ILE I 816 " --> pdb=" O LYS I1078 " (cutoff:3.500A) removed outlier: 7.803A pdb=" N ASN I1080 " --> pdb=" O ILE I 816 " (cutoff:3.500A) removed outlier: 6.734A pdb=" N VAL I 818 " --> pdb=" O ASN I1080 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'I' and resid 1066 through 1067 Processing sheet with id=AC7, first strand: chain 'I' and resid 830 through 831 Processing sheet with id=AC8, first strand: chain 'I' and resid 846 through 847 removed outlier: 6.093A pdb=" N GLN I 834 " --> pdb=" O TYR I1053 " (cutoff:3.500A) removed outlier: 4.322A pdb=" N TYR I1053 " --> pdb=" O GLN I 834 " (cutoff:3.500A) removed outlier: 6.254A pdb=" N LEU I 836 " --> pdb=" O LYS I1051 " (cutoff:3.500A) removed outlier: 4.491A pdb=" N LYS I1051 " --> pdb=" O LEU I 836 " (cutoff:3.500A) removed outlier: 6.646A pdb=" N CYS I 838 " --> pdb=" O ILE I1049 " (cutoff:3.500A) removed outlier: 4.457A pdb=" N ILE I1049 " --> pdb=" O CYS I 838 " (cutoff:3.500A) removed outlier: 6.624A pdb=" N SER I 840 " --> pdb=" O LEU I1047 " (cutoff:3.500A) removed outlier: 3.674A pdb=" N ASP I 930 " --> pdb=" O TYR I1053 " (cutoff:3.500A) removed outlier: 6.726A pdb=" N ALA I1055 " --> pdb=" O VAL I 928 " (cutoff:3.500A) removed outlier: 6.101A pdb=" N VAL I 928 " --> pdb=" O ALA I1055 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'I' and resid 882 through 884 removed outlier: 6.601A pdb=" N LEU I 918 " --> pdb=" O LEU I 883 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'I' and resid 887 through 889 Processing sheet with id=AD2, first strand: chain 'I' and resid 1268 through 1270 removed outlier: 3.578A pdb=" N GLN I1268 " --> pdb=" O VAL J 347 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'I' and resid 1335 through 1339 Processing sheet with id=AD4, first strand: chain 'J' and resid 34 through 37 removed outlier: 7.432A pdb=" N HIS J 104 " --> pdb=" O PHE J 35 " (cutoff:3.500A) removed outlier: 4.431A pdb=" N GLU J 37 " --> pdb=" O HIS J 104 " (cutoff:3.500A) removed outlier: 7.617A pdb=" N GLU J 106 " --> pdb=" O GLU J 37 " (cutoff:3.500A) removed outlier: 9.934A pdb=" N LEU J 107 " --> pdb=" O PRO J 243 " (cutoff:3.500A) removed outlier: 10.399A pdb=" N SER J 109 " --> pdb=" O VAL J 241 " (cutoff:3.500A) removed outlier: 7.160A pdb=" N VAL J 241 " --> pdb=" O SER J 109 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'J' and resid 159 through 160 Processing sheet with id=AD6, first strand: chain 'J' and resid 252 through 255 removed outlier: 6.512A pdb=" N PHE J 260 " --> pdb=" O ILE L 505 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'J' and resid 350 through 356 removed outlier: 6.176A pdb=" N CYS J 366 " --> pdb=" O VAL J 440 " (cutoff:3.500A) removed outlier: 6.816A pdb=" N ILE J 442 " --> pdb=" O CYS J 366 " (cutoff:3.500A) removed outlier: 6.001A pdb=" N LEU J 368 " --> pdb=" O ILE J 442 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'J' and resid 526 through 527 Processing sheet with id=AD9, first strand: chain 'J' and resid 706 through 707 removed outlier: 3.787A pdb=" N ILE J 707 " --> pdb=" O GLU J 714 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'J' and resid 809 through 811 removed outlier: 6.111A pdb=" N VAL J 894 " --> pdb=" O VAL J 809 " (cutoff:3.500A) removed outlier: 3.711A pdb=" N GLU J 811 " --> pdb=" O VAL J 894 " (cutoff:3.500A) No H-bonds generated for sheet with id=AE1 Processing sheet with id=AE2, first strand: chain 'J' and resid 820 through 822 Processing sheet with id=AE3, first strand: chain 'J' and resid 825 through 826 removed outlier: 6.903A pdb=" N VAL J 825 " --> pdb=" O LYS J 832 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'J' and resid 848 through 849 removed outlier: 3.591A pdb=" N VAL J 848 " --> pdb=" O VAL J 858 " (cutoff:3.500A) Processing sheet with id=AE5, first strand: chain 'J' and resid 1187 through 1189 Processing sheet with id=AE6, first strand: chain 'J' and resid 1279 through 1281 removed outlier: 6.725A pdb=" N THR J1301 " --> pdb=" O VAL J1267 " (cutoff:3.500A) 1313 hydrogen bonds defined for protein. 3753 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 112 hydrogen bonds 224 hydrogen bond angles 0 basepair planarities 47 basepair parallelities 90 stacking parallelities Total time for adding SS restraints: 16.02 Time building geometry restraints manager: 12.89 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.32: 5010 1.32 - 1.44: 7889 1.44 - 1.57: 17372 1.57 - 1.69: 242 1.69 - 1.81: 225 Bond restraints: 30738 Sorted by residual: bond pdb=" N ILE I 59 " pdb=" CA ILE I 59 " ideal model delta sigma weight residual 1.456 1.493 -0.037 1.14e-02 7.69e+03 1.05e+01 bond pdb=" N VAL I 196 " pdb=" CA VAL I 196 " ideal model delta sigma weight residual 1.458 1.494 -0.036 1.12e-02 7.97e+03 1.02e+01 bond pdb=" N PHE I 57 " pdb=" CA PHE I 57 " ideal model delta sigma weight residual 1.459 1.492 -0.033 1.04e-02 9.25e+03 1.02e+01 bond pdb=" C PRO J 51 " pdb=" O PRO J 51 " ideal model delta sigma weight residual 1.233 1.195 0.038 1.19e-02 7.06e+03 1.01e+01 bond pdb=" N VAL I 56 " pdb=" CA VAL I 56 " ideal model delta sigma weight residual 1.459 1.498 -0.039 1.25e-02 6.40e+03 9.78e+00 ... (remaining 30733 not shown) Histogram of bond angle deviations from ideal: 97.59 - 104.88: 856 104.88 - 112.17: 15662 112.17 - 119.46: 10770 119.46 - 126.76: 14111 126.76 - 134.05: 626 Bond angle restraints: 42025 Sorted by residual: angle pdb=" N ARG J 53 " pdb=" CA ARG J 53 " pdb=" C ARG J 53 " ideal model delta sigma weight residual 111.07 116.02 -4.95 1.07e+00 8.73e-01 2.14e+01 angle pdb=" N VAL H 192 " pdb=" CA VAL H 192 " pdb=" C VAL H 192 " ideal model delta sigma weight residual 110.21 105.22 4.99 1.13e+00 7.83e-01 1.95e+01 angle pdb=" CA ARG J 53 " pdb=" C ARG J 53 " pdb=" O ARG J 53 " ideal model delta sigma weight residual 120.82 116.20 4.62 1.05e+00 9.07e-01 1.94e+01 angle pdb=" C THR I 91 " pdb=" CA THR I 91 " pdb=" CB THR I 91 " ideal model delta sigma weight residual 110.22 103.45 6.77 1.67e+00 3.59e-01 1.64e+01 angle pdb=" N GLN I 490 " pdb=" CA GLN I 490 " pdb=" C GLN I 490 " ideal model delta sigma weight residual 114.56 109.56 5.00 1.27e+00 6.20e-01 1.55e+01 ... (remaining 42020 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 34.98: 17368 34.98 - 69.95: 1202 69.95 - 104.93: 66 104.93 - 139.91: 2 139.91 - 174.88: 1 Dihedral angle restraints: 18639 sinusoidal: 8531 harmonic: 10108 Sorted by residual: dihedral pdb=" C ASP I 199 " pdb=" N ASP I 199 " pdb=" CA ASP I 199 " pdb=" CB ASP I 199 " ideal model delta harmonic sigma weight residual -122.60 -136.42 13.82 0 2.50e+00 1.60e-01 3.06e+01 dihedral pdb=" N ASP I 199 " pdb=" C ASP I 199 " pdb=" CA ASP I 199 " pdb=" CB ASP I 199 " ideal model delta harmonic sigma weight residual 122.80 136.23 -13.43 0 2.50e+00 1.60e-01 2.89e+01 dihedral pdb=" CA TRP I 807 " pdb=" C TRP I 807 " pdb=" N ASN I 808 " pdb=" CA ASN I 808 " ideal model delta harmonic sigma weight residual 180.00 154.02 25.98 0 5.00e+00 4.00e-02 2.70e+01 ... (remaining 18636 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.100: 4612 0.100 - 0.200: 190 0.200 - 0.301: 2 0.301 - 0.401: 1 0.401 - 0.501: 1 Chirality restraints: 4806 Sorted by residual: chirality pdb=" CA ASP I 199 " pdb=" N ASP I 199 " pdb=" C ASP I 199 " pdb=" CB ASP I 199 " both_signs ideal model delta sigma weight residual False 2.51 2.01 0.50 2.00e-01 2.50e+01 6.27e+00 chirality pdb=" CA PHE I 57 " pdb=" N PHE I 57 " pdb=" C PHE I 57 " pdb=" CB PHE I 57 " both_signs ideal model delta sigma weight residual False 2.51 2.19 0.32 2.00e-01 2.50e+01 2.51e+00 chirality pdb=" CA THR I 91 " pdb=" N THR I 91 " pdb=" C THR I 91 " pdb=" CB THR I 91 " both_signs ideal model delta sigma weight residual False 2.53 2.81 -0.28 2.00e-01 2.50e+01 1.97e+00 ... (remaining 4803 not shown) Planarity restraints: 5039 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA VAL I 196 " 0.009 2.00e-02 2.50e+03 1.80e-02 3.25e+00 pdb=" C VAL I 196 " -0.031 2.00e-02 2.50e+03 pdb=" O VAL I 196 " 0.011 2.00e-02 2.50e+03 pdb=" N ARG I 197 " 0.011 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C SER J 492 " -0.029 5.00e-02 4.00e+02 4.43e-02 3.14e+00 pdb=" N PRO J 493 " 0.077 5.00e-02 4.00e+02 pdb=" CA PRO J 493 " -0.023 5.00e-02 4.00e+02 pdb=" CD PRO J 493 " -0.025 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA ASN J 45 " -0.009 2.00e-02 2.50e+03 1.73e-02 3.00e+00 pdb=" C ASN J 45 " 0.030 2.00e-02 2.50e+03 pdb=" O ASN J 45 " -0.011 2.00e-02 2.50e+03 pdb=" N TYR J 46 " -0.010 2.00e-02 2.50e+03 ... (remaining 5036 not shown) Histogram of nonbonded interaction distances: 1.79 - 2.41: 71 2.41 - 3.03: 18232 3.03 - 3.65: 45282 3.65 - 4.28: 71263 4.28 - 4.90: 116679 Nonbonded interactions: 251527 Sorted by model distance: nonbonded pdb=" OD1 ASP J 462 " pdb="MG MG J2001 " model vdw 1.787 2.170 nonbonded pdb=" NZ LYS I 890 " pdb=" O SER I 911 " model vdw 2.212 2.520 nonbonded pdb=" O TYR I 346 " pdb=" OG1 THR I 350 " model vdw 2.218 2.440 nonbonded pdb=" O VAL L 130 " pdb=" OG SER L 133 " model vdw 2.219 2.440 nonbonded pdb=" OD1 ASP A 36 " pdb=" N LYS A 37 " model vdw 2.225 2.520 ... (remaining 251522 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 8 through 71 or resid 73 through 78)) selection = (chain 'B' and (resid 8 through 71 or resid 73 through 78)) selection = (chain 'C' and (resid 8 through 71 or resid 73 through 78)) selection = (chain 'D' and (resid 8 through 71 or resid 73 through 78)) } 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=0.13 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.490 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 4.160 Check model and map are aligned: 0.450 Set scattering table: 0.270 Process input model: 95.970 Find NCS groups from input model: 1.150 Set up NCS constraints: 0.120 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.770 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 105.410 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8189 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 0.053 30738 Z= 0.297 Angle : 0.616 7.522 42025 Z= 0.351 Chirality : 0.044 0.501 4806 Planarity : 0.005 0.046 5039 Dihedral : 20.464 174.883 12113 Min Nonbonded Distance : 1.787 Molprobity Statistics. All-atom Clashscore : 5.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.64 % Favored : 93.36 % Rotamer: Outliers : 0.60 % Allowed : 19.80 % Favored : 79.60 % Cbeta Deviations : 0.03 % Peptide Plane: Cis-proline : 1.49 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.49 (0.14), residues: 3478 helix: 0.75 (0.13), residues: 1545 sheet: -0.97 (0.24), residues: 385 loop : -1.22 (0.15), residues: 1548 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP D 43 HIS 0.007 0.001 HIS I1023 PHE 0.025 0.002 PHE J 227 TYR 0.017 0.002 TYR G 177 ARG 0.006 0.000 ARG I 779 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6956 Ramachandran restraints generated. 3478 Oldfield, 0 Emsley, 3478 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6956 Ramachandran restraints generated. 3478 Oldfield, 0 Emsley, 3478 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 437 residues out of total 2988 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 419 time to evaluate : 4.028 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 24 LEU cc_start: 0.7908 (tp) cc_final: 0.7490 (tp) outliers start: 18 outliers final: 4 residues processed: 431 average time/residue: 0.5003 time to fit residues: 326.8439 Evaluate side-chains 305 residues out of total 2988 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 301 time to evaluate : 3.485 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 186 ASN Chi-restraints excluded: chain G residue 252 ILE Chi-restraints excluded: chain I residue 56 VAL Chi-restraints excluded: chain I residue 799 ASN Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 358 random chunks: chunk 302 optimal weight: 3.9990 chunk 271 optimal weight: 10.0000 chunk 150 optimal weight: 3.9990 chunk 92 optimal weight: 8.9990 chunk 183 optimal weight: 1.9990 chunk 144 optimal weight: 3.9990 chunk 280 optimal weight: 10.0000 chunk 108 optimal weight: 3.9990 chunk 170 optimal weight: 7.9990 chunk 208 optimal weight: 4.9990 chunk 325 optimal weight: 20.0000 overall best weight: 3.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: G 117 HIS G 268 ASN H 186 ASN I 165 HIS J1218 HIS L 406 GLN A 8 ASN C 8 ASN ** D 73 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8252 moved from start: 0.1676 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.062 30738 Z= 0.341 Angle : 0.628 7.909 42025 Z= 0.334 Chirality : 0.043 0.184 4806 Planarity : 0.004 0.045 5039 Dihedral : 18.287 178.611 5224 Min Nonbonded Distance : 1.997 Molprobity Statistics. All-atom Clashscore : 7.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.75 % Favored : 94.25 % Rotamer: Outliers : 3.22 % Allowed : 20.67 % Favored : 76.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.49 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.07 (0.14), residues: 3478 helix: 1.28 (0.13), residues: 1572 sheet: -0.62 (0.26), residues: 376 loop : -1.06 (0.16), residues: 1530 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP B 43 HIS 0.014 0.001 HIS I 165 PHE 0.031 0.002 PHE B 51 TYR 0.020 0.002 TYR G 177 ARG 0.006 0.000 ARG J 259 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6956 Ramachandran restraints generated. 3478 Oldfield, 0 Emsley, 3478 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6956 Ramachandran restraints generated. 3478 Oldfield, 0 Emsley, 3478 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 407 residues out of total 2988 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 96 poor density : 311 time to evaluate : 3.569 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: I 596 ASP cc_start: 0.6086 (p0) cc_final: 0.5842 (p0) REVERT: C 40 ILE cc_start: 0.8663 (mm) cc_final: 0.8282 (mm) outliers start: 96 outliers final: 54 residues processed: 382 average time/residue: 0.4352 time to fit residues: 263.6290 Evaluate side-chains 345 residues out of total 2988 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 54 poor density : 291 time to evaluate : 3.584 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 19 VAL Chi-restraints excluded: chain G residue 118 ASP Chi-restraints excluded: chain G residue 153 VAL Chi-restraints excluded: chain G residue 177 TYR Chi-restraints excluded: chain G residue 186 ASN Chi-restraints excluded: chain G residue 252 ILE Chi-restraints excluded: chain H residue 14 VAL Chi-restraints excluded: chain H residue 100 LEU Chi-restraints excluded: chain H residue 103 ASN Chi-restraints excluded: chain H residue 146 VAL Chi-restraints excluded: chain H residue 174 ASP Chi-restraints excluded: chain I residue 56 VAL Chi-restraints excluded: chain I residue 90 VAL Chi-restraints excluded: chain I residue 132 ASP Chi-restraints excluded: chain I residue 137 VAL Chi-restraints excluded: chain I residue 216 THR Chi-restraints excluded: chain I residue 377 THR Chi-restraints excluded: chain I residue 398 SER Chi-restraints excluded: chain I residue 417 SER Chi-restraints excluded: chain I residue 502 VAL Chi-restraints excluded: chain I residue 514 PHE Chi-restraints excluded: chain I residue 651 ASP Chi-restraints excluded: chain I residue 714 VAL Chi-restraints excluded: chain I residue 827 ARG Chi-restraints excluded: chain I residue 878 THR Chi-restraints excluded: chain I residue 951 MET Chi-restraints excluded: chain I residue 1056 VAL Chi-restraints excluded: chain I residue 1151 LEU Chi-restraints excluded: chain I residue 1227 VAL Chi-restraints excluded: chain I residue 1293 VAL Chi-restraints excluded: chain J residue 46 TYR Chi-restraints excluded: chain J residue 48 THR Chi-restraints excluded: chain J residue 180 MET Chi-restraints excluded: chain J residue 192 MET Chi-restraints excluded: chain J residue 701 LEU Chi-restraints excluded: chain J residue 803 VAL Chi-restraints excluded: chain J residue 1178 THR Chi-restraints excluded: chain J residue 1209 VAL Chi-restraints excluded: chain J residue 1298 VAL Chi-restraints excluded: chain K residue 11 GLU Chi-restraints excluded: chain L residue 95 THR Chi-restraints excluded: chain L residue 105 MET Chi-restraints excluded: chain L residue 457 ILE Chi-restraints excluded: chain L residue 552 THR Chi-restraints excluded: chain A residue 26 THR Chi-restraints excluded: chain A residue 66 ASP Chi-restraints excluded: chain A residue 73 GLN Chi-restraints excluded: chain B residue 26 THR Chi-restraints excluded: chain B residue 55 LEU Chi-restraints excluded: chain B residue 64 ASP Chi-restraints excluded: chain C residue 64 ASP Chi-restraints excluded: chain D residue 17 LEU Chi-restraints excluded: chain D residue 26 THR Chi-restraints excluded: chain D residue 52 SER Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 358 random chunks: chunk 180 optimal weight: 10.0000 chunk 100 optimal weight: 9.9990 chunk 270 optimal weight: 1.9990 chunk 221 optimal weight: 7.9990 chunk 89 optimal weight: 3.9990 chunk 325 optimal weight: 20.0000 chunk 351 optimal weight: 10.0000 chunk 290 optimal weight: 9.9990 chunk 322 optimal weight: 8.9990 chunk 111 optimal weight: 6.9990 chunk 261 optimal weight: 9.9990 overall best weight: 5.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: I 582 ASN J 294 ASN J 364 HIS J 739 GLN L 406 GLN L 455 HIS C 8 ASN C 73 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8317 moved from start: 0.2094 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.086 30738 Z= 0.514 Angle : 0.680 9.283 42025 Z= 0.359 Chirality : 0.045 0.185 4806 Planarity : 0.005 0.049 5039 Dihedral : 18.296 178.118 5222 Min Nonbonded Distance : 1.966 Molprobity Statistics. All-atom Clashscore : 8.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.04 % Favored : 93.96 % Rotamer: Outliers : 4.60 % Allowed : 20.54 % Favored : 74.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.49 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.05 (0.14), residues: 3478 helix: 1.26 (0.13), residues: 1568 sheet: -0.61 (0.25), residues: 376 loop : -1.09 (0.16), residues: 1534 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP B 43 HIS 0.007 0.001 HIS I 165 PHE 0.040 0.002 PHE B 51 TYR 0.021 0.002 TYR G 177 ARG 0.006 0.001 ARG I 528 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6956 Ramachandran restraints generated. 3478 Oldfield, 0 Emsley, 3478 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6956 Ramachandran restraints generated. 3478 Oldfield, 0 Emsley, 3478 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 449 residues out of total 2988 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 137 poor density : 312 time to evaluate : 3.634 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: G 283 GLN cc_start: 0.7973 (OUTLIER) cc_final: 0.7425 (mp10) REVERT: H 218 ARG cc_start: 0.8172 (OUTLIER) cc_final: 0.7450 (ptp90) REVERT: I 592 ARG cc_start: 0.8769 (OUTLIER) cc_final: 0.8337 (ptm160) REVERT: I 637 ARG cc_start: 0.8762 (OUTLIER) cc_final: 0.8039 (ptt-90) REVERT: J 160 LEU cc_start: 0.8841 (OUTLIER) cc_final: 0.8310 (mt) REVERT: J 1165 PHE cc_start: 0.7381 (OUTLIER) cc_final: 0.6374 (m-10) REVERT: C 40 ILE cc_start: 0.8626 (mm) cc_final: 0.8411 (mm) outliers start: 137 outliers final: 82 residues processed: 423 average time/residue: 0.4782 time to fit residues: 324.5627 Evaluate side-chains 381 residues out of total 2988 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 88 poor density : 293 time to evaluate : 3.641 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 19 VAL Chi-restraints excluded: chain G residue 54 CYS Chi-restraints excluded: chain G residue 118 ASP Chi-restraints excluded: chain G residue 186 ASN Chi-restraints excluded: chain G residue 252 ILE Chi-restraints excluded: chain G residue 257 VAL Chi-restraints excluded: chain G residue 283 GLN Chi-restraints excluded: chain H residue 14 VAL Chi-restraints excluded: chain H residue 16 ILE Chi-restraints excluded: chain H residue 64 VAL Chi-restraints excluded: chain H residue 98 VAL Chi-restraints excluded: chain H residue 100 LEU Chi-restraints excluded: chain H residue 103 ASN Chi-restraints excluded: chain H residue 146 VAL Chi-restraints excluded: chain H residue 156 SER Chi-restraints excluded: chain H residue 183 ILE Chi-restraints excluded: chain H residue 188 GLU Chi-restraints excluded: chain H residue 218 ARG Chi-restraints excluded: chain I residue 2 VAL Chi-restraints excluded: chain I residue 21 VAL Chi-restraints excluded: chain I residue 56 VAL Chi-restraints excluded: chain I residue 62 TYR Chi-restraints excluded: chain I residue 90 VAL Chi-restraints excluded: chain I residue 132 ASP Chi-restraints excluded: chain I residue 216 THR Chi-restraints excluded: chain I residue 377 THR Chi-restraints excluded: chain I residue 398 SER Chi-restraints excluded: chain I residue 417 SER Chi-restraints excluded: chain I residue 499 SER Chi-restraints excluded: chain I residue 502 VAL Chi-restraints excluded: chain I residue 512 SER Chi-restraints excluded: chain I residue 514 PHE Chi-restraints excluded: chain I residue 562 GLU Chi-restraints excluded: chain I residue 573 ASN Chi-restraints excluded: chain I residue 592 ARG Chi-restraints excluded: chain I residue 637 ARG Chi-restraints excluded: chain I residue 651 ASP Chi-restraints excluded: chain I residue 714 VAL Chi-restraints excluded: chain I residue 799 ASN Chi-restraints excluded: chain I residue 827 ARG Chi-restraints excluded: chain I residue 878 THR Chi-restraints excluded: chain I residue 951 MET Chi-restraints excluded: chain I residue 1054 LEU Chi-restraints excluded: chain I residue 1151 LEU Chi-restraints excluded: chain I residue 1163 THR Chi-restraints excluded: chain I residue 1225 VAL Chi-restraints excluded: chain I residue 1227 VAL Chi-restraints excluded: chain I residue 1293 VAL Chi-restraints excluded: chain J residue 46 TYR Chi-restraints excluded: chain J residue 48 THR Chi-restraints excluded: chain J residue 160 LEU Chi-restraints excluded: chain J residue 192 MET Chi-restraints excluded: chain J residue 198 CYS Chi-restraints excluded: chain J residue 408 VAL Chi-restraints excluded: chain J residue 410 ASP Chi-restraints excluded: chain J residue 545 HIS Chi-restraints excluded: chain J residue 596 LEU Chi-restraints excluded: chain J residue 722 ILE Chi-restraints excluded: chain J residue 803 VAL Chi-restraints excluded: chain J residue 1165 PHE Chi-restraints excluded: chain J residue 1209 VAL Chi-restraints excluded: chain J residue 1258 ARG Chi-restraints excluded: chain J residue 1298 VAL Chi-restraints excluded: chain J residue 1320 ILE Chi-restraints excluded: chain K residue 11 GLU Chi-restraints excluded: chain L residue 95 THR Chi-restraints excluded: chain L residue 105 MET Chi-restraints excluded: chain L residue 442 SER Chi-restraints excluded: chain L residue 457 ILE Chi-restraints excluded: chain L residue 469 GLN Chi-restraints excluded: chain L residue 552 THR Chi-restraints excluded: chain L residue 559 LEU Chi-restraints excluded: chain A residue 26 THR Chi-restraints excluded: chain A residue 66 ASP Chi-restraints excluded: chain A residue 73 GLN Chi-restraints excluded: chain B residue 17 LEU Chi-restraints excluded: chain B residue 26 THR Chi-restraints excluded: chain B residue 55 LEU Chi-restraints excluded: chain B residue 58 LEU Chi-restraints excluded: chain B residue 64 ASP Chi-restraints excluded: chain B residue 74 VAL Chi-restraints excluded: chain C residue 29 THR Chi-restraints excluded: chain C residue 55 LEU Chi-restraints excluded: chain C residue 64 ASP Chi-restraints excluded: chain C residue 74 VAL Chi-restraints excluded: chain D residue 17 LEU Chi-restraints excluded: chain D residue 52 SER Chi-restraints excluded: chain D residue 63 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 358 random chunks: chunk 321 optimal weight: 3.9990 chunk 244 optimal weight: 2.9990 chunk 169 optimal weight: 1.9990 chunk 36 optimal weight: 7.9990 chunk 155 optimal weight: 0.9980 chunk 218 optimal weight: 1.9990 chunk 326 optimal weight: 5.9990 chunk 346 optimal weight: 10.0000 chunk 170 optimal weight: 1.9990 chunk 309 optimal weight: 2.9990 chunk 93 optimal weight: 0.8980 overall best weight: 1.5786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** I 519 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 811 ASN J 200 GLN J 365 GLN J 489 ASN J 651 HIS C 8 ASN C 73 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8240 moved from start: 0.2379 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 30738 Z= 0.202 Angle : 0.567 8.448 42025 Z= 0.301 Chirality : 0.040 0.164 4806 Planarity : 0.004 0.046 5039 Dihedral : 18.097 178.736 5222 Min Nonbonded Distance : 2.010 Molprobity Statistics. All-atom Clashscore : 8.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.92 % Favored : 95.08 % Rotamer: Outliers : 3.66 % Allowed : 22.15 % Favored : 74.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.49 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.30 (0.14), residues: 3478 helix: 1.51 (0.13), residues: 1564 sheet: -0.54 (0.26), residues: 373 loop : -0.97 (0.16), residues: 1541 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP B 43 HIS 0.004 0.001 HIS I1070 PHE 0.040 0.002 PHE B 51 TYR 0.020 0.001 TYR G 177 ARG 0.010 0.000 ARG D 72 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6956 Ramachandran restraints generated. 3478 Oldfield, 0 Emsley, 3478 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6956 Ramachandran restraints generated. 3478 Oldfield, 0 Emsley, 3478 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 419 residues out of total 2988 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 109 poor density : 310 time to evaluate : 5.642 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: G 283 GLN cc_start: 0.7947 (OUTLIER) cc_final: 0.7406 (mp10) REVERT: H 218 ARG cc_start: 0.8045 (OUTLIER) cc_final: 0.7660 (mtm-85) REVERT: I 592 ARG cc_start: 0.8695 (OUTLIER) cc_final: 0.8282 (ptm160) REVERT: I 596 ASP cc_start: 0.6316 (p0) cc_final: 0.5938 (p0) REVERT: J 160 LEU cc_start: 0.8766 (OUTLIER) cc_final: 0.8221 (mt) REVERT: J 1165 PHE cc_start: 0.7268 (OUTLIER) cc_final: 0.6316 (m-10) REVERT: C 40 ILE cc_start: 0.8523 (mm) cc_final: 0.8281 (mm) outliers start: 109 outliers final: 61 residues processed: 402 average time/residue: 0.4363 time to fit residues: 279.1429 Evaluate side-chains 360 residues out of total 2988 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 66 poor density : 294 time to evaluate : 3.114 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 19 VAL Chi-restraints excluded: chain G residue 118 ASP Chi-restraints excluded: chain G residue 153 VAL Chi-restraints excluded: chain G residue 177 TYR Chi-restraints excluded: chain G residue 186 ASN Chi-restraints excluded: chain G residue 252 ILE Chi-restraints excluded: chain G residue 257 VAL Chi-restraints excluded: chain G residue 283 GLN Chi-restraints excluded: chain G residue 292 THR Chi-restraints excluded: chain H residue 14 VAL Chi-restraints excluded: chain H residue 64 VAL Chi-restraints excluded: chain H residue 100 LEU Chi-restraints excluded: chain H residue 103 ASN Chi-restraints excluded: chain H residue 146 VAL Chi-restraints excluded: chain H residue 183 ILE Chi-restraints excluded: chain H residue 218 ARG Chi-restraints excluded: chain I residue 21 VAL Chi-restraints excluded: chain I residue 90 VAL Chi-restraints excluded: chain I residue 132 ASP Chi-restraints excluded: chain I residue 137 VAL Chi-restraints excluded: chain I residue 216 THR Chi-restraints excluded: chain I residue 398 SER Chi-restraints excluded: chain I residue 417 SER Chi-restraints excluded: chain I residue 471 VAL Chi-restraints excluded: chain I residue 499 SER Chi-restraints excluded: chain I residue 512 SER Chi-restraints excluded: chain I residue 514 PHE Chi-restraints excluded: chain I residue 575 LEU Chi-restraints excluded: chain I residue 592 ARG Chi-restraints excluded: chain I residue 651 ASP Chi-restraints excluded: chain I residue 799 ASN Chi-restraints excluded: chain I residue 1054 LEU Chi-restraints excluded: chain I residue 1056 VAL Chi-restraints excluded: chain I residue 1075 VAL Chi-restraints excluded: chain I residue 1151 LEU Chi-restraints excluded: chain I residue 1227 VAL Chi-restraints excluded: chain I residue 1289 GLU Chi-restraints excluded: chain I residue 1296 ASP Chi-restraints excluded: chain J residue 46 TYR Chi-restraints excluded: chain J residue 160 LEU Chi-restraints excluded: chain J residue 192 MET Chi-restraints excluded: chain J residue 198 CYS Chi-restraints excluded: chain J residue 545 HIS Chi-restraints excluded: chain J residue 612 LEU Chi-restraints excluded: chain J residue 708 ASN Chi-restraints excluded: chain J residue 803 VAL Chi-restraints excluded: chain J residue 849 LEU Chi-restraints excluded: chain J residue 1165 PHE Chi-restraints excluded: chain J residue 1209 VAL Chi-restraints excluded: chain J residue 1258 ARG Chi-restraints excluded: chain J residue 1298 VAL Chi-restraints excluded: chain K residue 13 ILE Chi-restraints excluded: chain L residue 105 MET Chi-restraints excluded: chain L residue 429 THR Chi-restraints excluded: chain L residue 442 SER Chi-restraints excluded: chain L residue 457 ILE Chi-restraints excluded: chain A residue 26 THR Chi-restraints excluded: chain A residue 66 ASP Chi-restraints excluded: chain A residue 73 GLN Chi-restraints excluded: chain B residue 26 THR Chi-restraints excluded: chain B residue 55 LEU Chi-restraints excluded: chain B residue 58 LEU Chi-restraints excluded: chain B residue 64 ASP Chi-restraints excluded: chain C residue 64 ASP Chi-restraints excluded: chain C residue 74 VAL Chi-restraints excluded: chain D residue 52 SER Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 358 random chunks: chunk 288 optimal weight: 9.9990 chunk 196 optimal weight: 8.9990 chunk 5 optimal weight: 0.6980 chunk 257 optimal weight: 1.9990 chunk 142 optimal weight: 2.9990 chunk 295 optimal weight: 9.9990 chunk 239 optimal weight: 0.0070 chunk 0 optimal weight: 10.0000 chunk 176 optimal weight: 4.9990 chunk 310 optimal weight: 6.9990 chunk 87 optimal weight: 0.7980 overall best weight: 1.3002 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** I 519 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 811 ASN I 932 GLN I1134 GLN J 651 HIS J 929 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8220 moved from start: 0.2597 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 30738 Z= 0.190 Angle : 0.543 8.501 42025 Z= 0.289 Chirality : 0.040 0.151 4806 Planarity : 0.004 0.046 5039 Dihedral : 17.916 179.867 5221 Min Nonbonded Distance : 1.996 Molprobity Statistics. All-atom Clashscore : 8.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.95 % Favored : 95.05 % Rotamer: Outliers : 3.72 % Allowed : 22.25 % Favored : 74.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.49 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.45 (0.15), residues: 3478 helix: 1.63 (0.13), residues: 1567 sheet: -0.50 (0.25), residues: 392 loop : -0.88 (0.16), residues: 1519 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP D 43 HIS 0.004 0.001 HIS I1070 PHE 0.041 0.001 PHE B 51 TYR 0.019 0.001 TYR G 177 ARG 0.009 0.000 ARG D 72 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6956 Ramachandran restraints generated. 3478 Oldfield, 0 Emsley, 3478 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6956 Ramachandran restraints generated. 3478 Oldfield, 0 Emsley, 3478 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 422 residues out of total 2988 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 111 poor density : 311 time to evaluate : 3.072 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: G 283 GLN cc_start: 0.7912 (OUTLIER) cc_final: 0.7399 (mp10) REVERT: H 218 ARG cc_start: 0.8054 (OUTLIER) cc_final: 0.7734 (mtm-85) REVERT: I 592 ARG cc_start: 0.8722 (OUTLIER) cc_final: 0.8375 (ptm160) REVERT: I 596 ASP cc_start: 0.6413 (p0) cc_final: 0.6119 (p0) REVERT: J 160 LEU cc_start: 0.8762 (OUTLIER) cc_final: 0.8231 (mt) REVERT: J 1165 PHE cc_start: 0.7218 (OUTLIER) cc_final: 0.6312 (m-10) REVERT: B 54 LEU cc_start: 0.8854 (OUTLIER) cc_final: 0.8541 (tt) outliers start: 111 outliers final: 65 residues processed: 401 average time/residue: 0.4400 time to fit residues: 278.5937 Evaluate side-chains 373 residues out of total 2988 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 71 poor density : 302 time to evaluate : 3.135 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 19 VAL Chi-restraints excluded: chain G residue 118 ASP Chi-restraints excluded: chain G residue 153 VAL Chi-restraints excluded: chain G residue 186 ASN Chi-restraints excluded: chain G residue 252 ILE Chi-restraints excluded: chain G residue 257 VAL Chi-restraints excluded: chain G residue 283 GLN Chi-restraints excluded: chain G residue 292 THR Chi-restraints excluded: chain H residue 14 VAL Chi-restraints excluded: chain H residue 64 VAL Chi-restraints excluded: chain H residue 98 VAL Chi-restraints excluded: chain H residue 100 LEU Chi-restraints excluded: chain H residue 103 ASN Chi-restraints excluded: chain H residue 146 VAL Chi-restraints excluded: chain H residue 156 SER Chi-restraints excluded: chain H residue 183 ILE Chi-restraints excluded: chain H residue 218 ARG Chi-restraints excluded: chain I residue 2 VAL Chi-restraints excluded: chain I residue 21 VAL Chi-restraints excluded: chain I residue 56 VAL Chi-restraints excluded: chain I residue 69 GLN Chi-restraints excluded: chain I residue 90 VAL Chi-restraints excluded: chain I residue 132 ASP Chi-restraints excluded: chain I residue 137 VAL Chi-restraints excluded: chain I residue 216 THR Chi-restraints excluded: chain I residue 371 ARG Chi-restraints excluded: chain I residue 377 THR Chi-restraints excluded: chain I residue 398 SER Chi-restraints excluded: chain I residue 417 SER Chi-restraints excluded: chain I residue 471 VAL Chi-restraints excluded: chain I residue 499 SER Chi-restraints excluded: chain I residue 512 SER Chi-restraints excluded: chain I residue 514 PHE Chi-restraints excluded: chain I residue 592 ARG Chi-restraints excluded: chain I residue 714 VAL Chi-restraints excluded: chain I residue 799 ASN Chi-restraints excluded: chain I residue 823 VAL Chi-restraints excluded: chain I residue 827 ARG Chi-restraints excluded: chain I residue 912 ASP Chi-restraints excluded: chain I residue 1054 LEU Chi-restraints excluded: chain I residue 1056 VAL Chi-restraints excluded: chain I residue 1151 LEU Chi-restraints excluded: chain I residue 1225 VAL Chi-restraints excluded: chain I residue 1227 VAL Chi-restraints excluded: chain I residue 1289 GLU Chi-restraints excluded: chain I residue 1293 VAL Chi-restraints excluded: chain I residue 1296 ASP Chi-restraints excluded: chain J residue 46 TYR Chi-restraints excluded: chain J residue 160 LEU Chi-restraints excluded: chain J residue 192 MET Chi-restraints excluded: chain J residue 545 HIS Chi-restraints excluded: chain J residue 569 LEU Chi-restraints excluded: chain J residue 707 ILE Chi-restraints excluded: chain J residue 708 ASN Chi-restraints excluded: chain J residue 803 VAL Chi-restraints excluded: chain J residue 849 LEU Chi-restraints excluded: chain J residue 1165 PHE Chi-restraints excluded: chain J residue 1298 VAL Chi-restraints excluded: chain L residue 105 MET Chi-restraints excluded: chain L residue 442 SER Chi-restraints excluded: chain L residue 457 ILE Chi-restraints excluded: chain L residue 552 THR Chi-restraints excluded: chain A residue 26 THR Chi-restraints excluded: chain A residue 73 GLN Chi-restraints excluded: chain B residue 29 THR Chi-restraints excluded: chain B residue 54 LEU Chi-restraints excluded: chain B residue 58 LEU Chi-restraints excluded: chain B residue 64 ASP Chi-restraints excluded: chain C residue 64 ASP Chi-restraints excluded: chain C residue 74 VAL Chi-restraints excluded: chain D residue 63 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 358 random chunks: chunk 116 optimal weight: 0.6980 chunk 311 optimal weight: 3.9990 chunk 68 optimal weight: 6.9990 chunk 203 optimal weight: 5.9990 chunk 85 optimal weight: 10.0000 chunk 346 optimal weight: 10.0000 chunk 287 optimal weight: 4.9990 chunk 160 optimal weight: 5.9990 chunk 28 optimal weight: 7.9990 chunk 114 optimal weight: 0.9990 chunk 181 optimal weight: 20.0000 overall best weight: 3.3388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: I 798 GLN I 811 ASN ** I 965 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 365 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 651 HIS L 383 ASN C 73 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8267 moved from start: 0.2649 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.060 30738 Z= 0.314 Angle : 0.589 9.176 42025 Z= 0.311 Chirality : 0.041 0.162 4806 Planarity : 0.004 0.047 5039 Dihedral : 17.945 179.752 5221 Min Nonbonded Distance : 1.972 Molprobity Statistics. All-atom Clashscore : 8.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.66 % Favored : 94.34 % Rotamer: Outliers : 3.62 % Allowed : 22.82 % Favored : 73.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.49 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.41 (0.15), residues: 3478 helix: 1.57 (0.13), residues: 1572 sheet: -0.51 (0.25), residues: 395 loop : -0.89 (0.16), residues: 1511 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP D 43 HIS 0.005 0.001 HIS G 23 PHE 0.050 0.002 PHE B 51 TYR 0.015 0.001 TYR J 679 ARG 0.008 0.000 ARG D 72 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6956 Ramachandran restraints generated. 3478 Oldfield, 0 Emsley, 3478 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6956 Ramachandran restraints generated. 3478 Oldfield, 0 Emsley, 3478 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 417 residues out of total 2988 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 108 poor density : 309 time to evaluate : 3.586 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: G 283 GLN cc_start: 0.8053 (OUTLIER) cc_final: 0.7492 (mp10) REVERT: H 218 ARG cc_start: 0.8061 (OUTLIER) cc_final: 0.7681 (mtm-85) REVERT: I 592 ARG cc_start: 0.8730 (OUTLIER) cc_final: 0.8360 (ptm160) REVERT: I 596 ASP cc_start: 0.6465 (p0) cc_final: 0.6165 (p0) REVERT: I 637 ARG cc_start: 0.8655 (OUTLIER) cc_final: 0.7969 (ptt-90) REVERT: J 160 LEU cc_start: 0.8808 (OUTLIER) cc_final: 0.8269 (mt) REVERT: J 227 PHE cc_start: 0.8579 (OUTLIER) cc_final: 0.8312 (t80) REVERT: J 1165 PHE cc_start: 0.7289 (OUTLIER) cc_final: 0.6351 (m-10) REVERT: B 54 LEU cc_start: 0.8839 (OUTLIER) cc_final: 0.8583 (tt) outliers start: 108 outliers final: 83 residues processed: 396 average time/residue: 0.4481 time to fit residues: 279.7027 Evaluate side-chains 391 residues out of total 2988 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 91 poor density : 300 time to evaluate : 3.509 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 19 VAL Chi-restraints excluded: chain G residue 54 CYS Chi-restraints excluded: chain G residue 118 ASP Chi-restraints excluded: chain G residue 145 LYS Chi-restraints excluded: chain G residue 153 VAL Chi-restraints excluded: chain G residue 186 ASN Chi-restraints excluded: chain G residue 252 ILE Chi-restraints excluded: chain G residue 257 VAL Chi-restraints excluded: chain G residue 283 GLN Chi-restraints excluded: chain G residue 292 THR Chi-restraints excluded: chain H residue 14 VAL Chi-restraints excluded: chain H residue 16 ILE Chi-restraints excluded: chain H residue 64 VAL Chi-restraints excluded: chain H residue 98 VAL Chi-restraints excluded: chain H residue 100 LEU Chi-restraints excluded: chain H residue 103 ASN Chi-restraints excluded: chain H residue 146 VAL Chi-restraints excluded: chain H residue 156 SER Chi-restraints excluded: chain H residue 183 ILE Chi-restraints excluded: chain H residue 218 ARG Chi-restraints excluded: chain I residue 2 VAL Chi-restraints excluded: chain I residue 21 VAL Chi-restraints excluded: chain I residue 56 VAL Chi-restraints excluded: chain I residue 62 TYR Chi-restraints excluded: chain I residue 90 VAL Chi-restraints excluded: chain I residue 132 ASP Chi-restraints excluded: chain I residue 137 VAL Chi-restraints excluded: chain I residue 216 THR Chi-restraints excluded: chain I residue 377 THR Chi-restraints excluded: chain I residue 398 SER Chi-restraints excluded: chain I residue 417 SER Chi-restraints excluded: chain I residue 471 VAL Chi-restraints excluded: chain I residue 499 SER Chi-restraints excluded: chain I residue 512 SER Chi-restraints excluded: chain I residue 514 PHE Chi-restraints excluded: chain I residue 575 LEU Chi-restraints excluded: chain I residue 592 ARG Chi-restraints excluded: chain I residue 637 ARG Chi-restraints excluded: chain I residue 651 ASP Chi-restraints excluded: chain I residue 714 VAL Chi-restraints excluded: chain I residue 799 ASN Chi-restraints excluded: chain I residue 823 VAL Chi-restraints excluded: chain I residue 827 ARG Chi-restraints excluded: chain I residue 912 ASP Chi-restraints excluded: chain I residue 1054 LEU Chi-restraints excluded: chain I residue 1056 VAL Chi-restraints excluded: chain I residue 1075 VAL Chi-restraints excluded: chain I residue 1151 LEU Chi-restraints excluded: chain I residue 1225 VAL Chi-restraints excluded: chain I residue 1227 VAL Chi-restraints excluded: chain I residue 1289 GLU Chi-restraints excluded: chain I residue 1293 VAL Chi-restraints excluded: chain I residue 1296 ASP Chi-restraints excluded: chain J residue 44 ILE Chi-restraints excluded: chain J residue 46 TYR Chi-restraints excluded: chain J residue 160 LEU Chi-restraints excluded: chain J residue 192 MET Chi-restraints excluded: chain J residue 198 CYS Chi-restraints excluded: chain J residue 227 PHE Chi-restraints excluded: chain J residue 545 HIS Chi-restraints excluded: chain J residue 569 LEU Chi-restraints excluded: chain J residue 594 GLN Chi-restraints excluded: chain J residue 596 LEU Chi-restraints excluded: chain J residue 612 LEU Chi-restraints excluded: chain J residue 707 ILE Chi-restraints excluded: chain J residue 708 ASN Chi-restraints excluded: chain J residue 803 VAL Chi-restraints excluded: chain J residue 826 ILE Chi-restraints excluded: chain J residue 839 VAL Chi-restraints excluded: chain J residue 849 LEU Chi-restraints excluded: chain J residue 1163 VAL Chi-restraints excluded: chain J residue 1165 PHE Chi-restraints excluded: chain J residue 1258 ARG Chi-restraints excluded: chain J residue 1298 VAL Chi-restraints excluded: chain L residue 95 THR Chi-restraints excluded: chain L residue 105 MET Chi-restraints excluded: chain L residue 442 SER Chi-restraints excluded: chain L residue 457 ILE Chi-restraints excluded: chain L residue 552 THR Chi-restraints excluded: chain L residue 559 LEU Chi-restraints excluded: chain A residue 26 THR Chi-restraints excluded: chain A residue 63 VAL Chi-restraints excluded: chain A residue 73 GLN Chi-restraints excluded: chain B residue 17 LEU Chi-restraints excluded: chain B residue 54 LEU Chi-restraints excluded: chain B residue 58 LEU Chi-restraints excluded: chain B residue 64 ASP Chi-restraints excluded: chain C residue 26 THR Chi-restraints excluded: chain C residue 64 ASP Chi-restraints excluded: chain C residue 74 VAL Chi-restraints excluded: chain D residue 63 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 358 random chunks: chunk 333 optimal weight: 9.9990 chunk 39 optimal weight: 4.9990 chunk 197 optimal weight: 5.9990 chunk 252 optimal weight: 0.9980 chunk 195 optimal weight: 7.9990 chunk 291 optimal weight: 10.0000 chunk 193 optimal weight: 2.9990 chunk 345 optimal weight: 30.0000 chunk 215 optimal weight: 2.9990 chunk 210 optimal weight: 5.9990 chunk 159 optimal weight: 1.9990 overall best weight: 2.7988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** I 519 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 811 ASN J 651 HIS C 8 ASN C 73 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8258 moved from start: 0.2751 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.055 30738 Z= 0.275 Angle : 0.585 14.783 42025 Z= 0.306 Chirality : 0.041 0.200 4806 Planarity : 0.004 0.044 5039 Dihedral : 17.924 179.817 5221 Min Nonbonded Distance : 1.990 Molprobity Statistics. All-atom Clashscore : 8.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.29 % Favored : 94.71 % Rotamer: Outliers : 3.86 % Allowed : 23.39 % Favored : 72.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.49 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.41 (0.15), residues: 3478 helix: 1.55 (0.13), residues: 1573 sheet: -0.48 (0.25), residues: 393 loop : -0.88 (0.16), residues: 1512 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP B 43 HIS 0.004 0.001 HIS G 23 PHE 0.049 0.002 PHE B 51 TYR 0.018 0.001 TYR L 137 ARG 0.007 0.000 ARG A 72 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6956 Ramachandran restraints generated. 3478 Oldfield, 0 Emsley, 3478 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6956 Ramachandran restraints generated. 3478 Oldfield, 0 Emsley, 3478 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 424 residues out of total 2988 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 115 poor density : 309 time to evaluate : 3.469 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: G 283 GLN cc_start: 0.8048 (OUTLIER) cc_final: 0.7495 (mp10) REVERT: H 218 ARG cc_start: 0.8050 (OUTLIER) cc_final: 0.7679 (mtm-85) REVERT: I 592 ARG cc_start: 0.8735 (OUTLIER) cc_final: 0.8395 (ptm160) REVERT: I 596 ASP cc_start: 0.6535 (p0) cc_final: 0.6249 (p0) REVERT: I 637 ARG cc_start: 0.8635 (OUTLIER) cc_final: 0.8033 (ptt-90) REVERT: I 648 ASP cc_start: 0.6083 (p0) cc_final: 0.5787 (p0) REVERT: J 160 LEU cc_start: 0.8816 (OUTLIER) cc_final: 0.8292 (mt) REVERT: J 227 PHE cc_start: 0.8621 (OUTLIER) cc_final: 0.8344 (t80) REVERT: J 1165 PHE cc_start: 0.7266 (OUTLIER) cc_final: 0.6326 (m-10) outliers start: 115 outliers final: 86 residues processed: 407 average time/residue: 0.4454 time to fit residues: 288.1163 Evaluate side-chains 394 residues out of total 2988 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 93 poor density : 301 time to evaluate : 3.570 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 19 VAL Chi-restraints excluded: chain G residue 54 CYS Chi-restraints excluded: chain G residue 118 ASP Chi-restraints excluded: chain G residue 145 LYS Chi-restraints excluded: chain G residue 153 VAL Chi-restraints excluded: chain G residue 186 ASN Chi-restraints excluded: chain G residue 252 ILE Chi-restraints excluded: chain G residue 257 VAL Chi-restraints excluded: chain G residue 275 ILE Chi-restraints excluded: chain G residue 283 GLN Chi-restraints excluded: chain G residue 292 THR Chi-restraints excluded: chain H residue 14 VAL Chi-restraints excluded: chain H residue 16 ILE Chi-restraints excluded: chain H residue 64 VAL Chi-restraints excluded: chain H residue 98 VAL Chi-restraints excluded: chain H residue 100 LEU Chi-restraints excluded: chain H residue 146 VAL Chi-restraints excluded: chain H residue 156 SER Chi-restraints excluded: chain H residue 174 ASP Chi-restraints excluded: chain H residue 183 ILE Chi-restraints excluded: chain H residue 218 ARG Chi-restraints excluded: chain I residue 2 VAL Chi-restraints excluded: chain I residue 21 VAL Chi-restraints excluded: chain I residue 56 VAL Chi-restraints excluded: chain I residue 62 TYR Chi-restraints excluded: chain I residue 90 VAL Chi-restraints excluded: chain I residue 132 ASP Chi-restraints excluded: chain I residue 137 VAL Chi-restraints excluded: chain I residue 216 THR Chi-restraints excluded: chain I residue 219 GLN Chi-restraints excluded: chain I residue 377 THR Chi-restraints excluded: chain I residue 398 SER Chi-restraints excluded: chain I residue 400 VAL Chi-restraints excluded: chain I residue 417 SER Chi-restraints excluded: chain I residue 471 VAL Chi-restraints excluded: chain I residue 499 SER Chi-restraints excluded: chain I residue 512 SER Chi-restraints excluded: chain I residue 514 PHE Chi-restraints excluded: chain I residue 575 LEU Chi-restraints excluded: chain I residue 592 ARG Chi-restraints excluded: chain I residue 637 ARG Chi-restraints excluded: chain I residue 651 ASP Chi-restraints excluded: chain I residue 714 VAL Chi-restraints excluded: chain I residue 799 ASN Chi-restraints excluded: chain I residue 823 VAL Chi-restraints excluded: chain I residue 827 ARG Chi-restraints excluded: chain I residue 912 ASP Chi-restraints excluded: chain I residue 1054 LEU Chi-restraints excluded: chain I residue 1056 VAL Chi-restraints excluded: chain I residue 1075 VAL Chi-restraints excluded: chain I residue 1151 LEU Chi-restraints excluded: chain I residue 1163 THR Chi-restraints excluded: chain I residue 1225 VAL Chi-restraints excluded: chain I residue 1227 VAL Chi-restraints excluded: chain I residue 1289 GLU Chi-restraints excluded: chain I residue 1293 VAL Chi-restraints excluded: chain I residue 1296 ASP Chi-restraints excluded: chain J residue 46 TYR Chi-restraints excluded: chain J residue 48 THR Chi-restraints excluded: chain J residue 160 LEU Chi-restraints excluded: chain J residue 183 GLU Chi-restraints excluded: chain J residue 192 MET Chi-restraints excluded: chain J residue 227 PHE Chi-restraints excluded: chain J residue 527 LEU Chi-restraints excluded: chain J residue 545 HIS Chi-restraints excluded: chain J residue 569 LEU Chi-restraints excluded: chain J residue 594 GLN Chi-restraints excluded: chain J residue 596 LEU Chi-restraints excluded: chain J residue 612 LEU Chi-restraints excluded: chain J residue 707 ILE Chi-restraints excluded: chain J residue 708 ASN Chi-restraints excluded: chain J residue 803 VAL Chi-restraints excluded: chain J residue 839 VAL Chi-restraints excluded: chain J residue 849 LEU Chi-restraints excluded: chain J residue 1163 VAL Chi-restraints excluded: chain J residue 1165 PHE Chi-restraints excluded: chain J residue 1258 ARG Chi-restraints excluded: chain J residue 1298 VAL Chi-restraints excluded: chain L residue 95 THR Chi-restraints excluded: chain L residue 105 MET Chi-restraints excluded: chain L residue 442 SER Chi-restraints excluded: chain L residue 457 ILE Chi-restraints excluded: chain L residue 552 THR Chi-restraints excluded: chain A residue 26 THR Chi-restraints excluded: chain A residue 63 VAL Chi-restraints excluded: chain B residue 17 LEU Chi-restraints excluded: chain B residue 58 LEU Chi-restraints excluded: chain B residue 64 ASP Chi-restraints excluded: chain C residue 64 ASP Chi-restraints excluded: chain C residue 74 VAL Chi-restraints excluded: chain D residue 17 LEU Chi-restraints excluded: chain D residue 26 THR Chi-restraints excluded: chain D residue 63 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 358 random chunks: chunk 213 optimal weight: 6.9990 chunk 137 optimal weight: 2.9990 chunk 206 optimal weight: 1.9990 chunk 103 optimal weight: 0.9990 chunk 67 optimal weight: 10.0000 chunk 66 optimal weight: 0.6980 chunk 219 optimal weight: 3.9990 chunk 235 optimal weight: 7.9990 chunk 170 optimal weight: 0.0470 chunk 32 optimal weight: 5.9990 chunk 271 optimal weight: 9.9990 overall best weight: 1.3484 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** I 519 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 811 ASN J 651 HIS C 8 ASN ** C 73 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8223 moved from start: 0.2899 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.078 30738 Z= 0.192 Angle : 0.574 13.192 42025 Z= 0.300 Chirality : 0.040 0.203 4806 Planarity : 0.004 0.043 5039 Dihedral : 17.836 179.562 5221 Min Nonbonded Distance : 2.012 Molprobity Statistics. All-atom Clashscore : 8.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.12 % Favored : 94.88 % Rotamer: Outliers : 2.95 % Allowed : 24.40 % Favored : 72.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.49 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.48 (0.15), residues: 3478 helix: 1.60 (0.13), residues: 1575 sheet: -0.37 (0.26), residues: 384 loop : -0.84 (0.16), residues: 1519 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP D 43 HIS 0.003 0.001 HIS G 23 PHE 0.046 0.001 PHE B 51 TYR 0.021 0.001 TYR L 137 ARG 0.013 0.000 ARG D 72 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6956 Ramachandran restraints generated. 3478 Oldfield, 0 Emsley, 3478 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6956 Ramachandran restraints generated. 3478 Oldfield, 0 Emsley, 3478 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 397 residues out of total 2988 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 88 poor density : 309 time to evaluate : 3.577 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: G 283 GLN cc_start: 0.8089 (OUTLIER) cc_final: 0.7573 (mp10) REVERT: H 218 ARG cc_start: 0.8017 (OUTLIER) cc_final: 0.7707 (mtm-85) REVERT: I 592 ARG cc_start: 0.8737 (OUTLIER) cc_final: 0.8396 (ptm160) REVERT: I 648 ASP cc_start: 0.5968 (p0) cc_final: 0.5755 (p0) REVERT: J 160 LEU cc_start: 0.8770 (OUTLIER) cc_final: 0.8263 (mt) REVERT: J 227 PHE cc_start: 0.8580 (OUTLIER) cc_final: 0.8287 (t80) REVERT: J 1165 PHE cc_start: 0.7178 (OUTLIER) cc_final: 0.6238 (m-10) outliers start: 88 outliers final: 70 residues processed: 389 average time/residue: 0.4533 time to fit residues: 282.4954 Evaluate side-chains 374 residues out of total 2988 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 76 poor density : 298 time to evaluate : 3.385 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 19 VAL Chi-restraints excluded: chain G residue 118 ASP Chi-restraints excluded: chain G residue 145 LYS Chi-restraints excluded: chain G residue 153 VAL Chi-restraints excluded: chain G residue 186 ASN Chi-restraints excluded: chain G residue 252 ILE Chi-restraints excluded: chain G residue 257 VAL Chi-restraints excluded: chain G residue 275 ILE Chi-restraints excluded: chain G residue 283 GLN Chi-restraints excluded: chain G residue 292 THR Chi-restraints excluded: chain H residue 14 VAL Chi-restraints excluded: chain H residue 64 VAL Chi-restraints excluded: chain H residue 146 VAL Chi-restraints excluded: chain H residue 156 SER Chi-restraints excluded: chain H residue 183 ILE Chi-restraints excluded: chain H residue 218 ARG Chi-restraints excluded: chain I residue 2 VAL Chi-restraints excluded: chain I residue 21 VAL Chi-restraints excluded: chain I residue 62 TYR Chi-restraints excluded: chain I residue 90 VAL Chi-restraints excluded: chain I residue 132 ASP Chi-restraints excluded: chain I residue 137 VAL Chi-restraints excluded: chain I residue 398 SER Chi-restraints excluded: chain I residue 400 VAL Chi-restraints excluded: chain I residue 471 VAL Chi-restraints excluded: chain I residue 499 SER Chi-restraints excluded: chain I residue 512 SER Chi-restraints excluded: chain I residue 514 PHE Chi-restraints excluded: chain I residue 592 ARG Chi-restraints excluded: chain I residue 651 ASP Chi-restraints excluded: chain I residue 714 VAL Chi-restraints excluded: chain I residue 799 ASN Chi-restraints excluded: chain I residue 823 VAL Chi-restraints excluded: chain I residue 827 ARG Chi-restraints excluded: chain I residue 912 ASP Chi-restraints excluded: chain I residue 1054 LEU Chi-restraints excluded: chain I residue 1056 VAL Chi-restraints excluded: chain I residue 1075 VAL Chi-restraints excluded: chain I residue 1151 LEU Chi-restraints excluded: chain I residue 1163 THR Chi-restraints excluded: chain I residue 1225 VAL Chi-restraints excluded: chain I residue 1227 VAL Chi-restraints excluded: chain I residue 1289 GLU Chi-restraints excluded: chain I residue 1296 ASP Chi-restraints excluded: chain J residue 46 TYR Chi-restraints excluded: chain J residue 48 THR Chi-restraints excluded: chain J residue 160 LEU Chi-restraints excluded: chain J residue 183 GLU Chi-restraints excluded: chain J residue 192 MET Chi-restraints excluded: chain J residue 198 CYS Chi-restraints excluded: chain J residue 227 PHE Chi-restraints excluded: chain J residue 410 ASP Chi-restraints excluded: chain J residue 527 LEU Chi-restraints excluded: chain J residue 545 HIS Chi-restraints excluded: chain J residue 569 LEU Chi-restraints excluded: chain J residue 594 GLN Chi-restraints excluded: chain J residue 596 LEU Chi-restraints excluded: chain J residue 707 ILE Chi-restraints excluded: chain J residue 708 ASN Chi-restraints excluded: chain J residue 803 VAL Chi-restraints excluded: chain J residue 826 ILE Chi-restraints excluded: chain J residue 839 VAL Chi-restraints excluded: chain J residue 849 LEU Chi-restraints excluded: chain J residue 1163 VAL Chi-restraints excluded: chain J residue 1165 PHE Chi-restraints excluded: chain J residue 1298 VAL Chi-restraints excluded: chain L residue 105 MET Chi-restraints excluded: chain L residue 442 SER Chi-restraints excluded: chain L residue 457 ILE Chi-restraints excluded: chain L residue 552 THR Chi-restraints excluded: chain L residue 559 LEU Chi-restraints excluded: chain B residue 58 LEU Chi-restraints excluded: chain C residue 26 THR Chi-restraints excluded: chain C residue 64 ASP Chi-restraints excluded: chain C residue 74 VAL Chi-restraints excluded: chain D residue 63 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 358 random chunks: chunk 313 optimal weight: 9.9990 chunk 330 optimal weight: 8.9990 chunk 301 optimal weight: 3.9990 chunk 321 optimal weight: 1.9990 chunk 193 optimal weight: 5.9990 chunk 140 optimal weight: 0.1980 chunk 252 optimal weight: 9.9990 chunk 98 optimal weight: 0.2980 chunk 290 optimal weight: 10.0000 chunk 304 optimal weight: 0.9980 chunk 320 optimal weight: 8.9990 overall best weight: 1.4984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** I 519 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 811 ASN I 955 GLN J 651 HIS C 8 ASN ** C 73 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8218 moved from start: 0.3017 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 30738 Z= 0.200 Angle : 0.580 12.183 42025 Z= 0.300 Chirality : 0.040 0.196 4806 Planarity : 0.004 0.046 5039 Dihedral : 17.744 179.072 5221 Min Nonbonded Distance : 2.013 Molprobity Statistics. All-atom Clashscore : 8.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.12 % Favored : 94.88 % Rotamer: Outliers : 3.05 % Allowed : 24.77 % Favored : 72.18 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.49 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.52 (0.15), residues: 3478 helix: 1.63 (0.13), residues: 1569 sheet: -0.38 (0.25), residues: 393 loop : -0.81 (0.16), residues: 1516 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP B 43 HIS 0.003 0.001 HIS G 23 PHE 0.042 0.001 PHE B 51 TYR 0.024 0.001 TYR L 137 ARG 0.015 0.000 ARG D 72 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6956 Ramachandran restraints generated. 3478 Oldfield, 0 Emsley, 3478 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6956 Ramachandran restraints generated. 3478 Oldfield, 0 Emsley, 3478 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 395 residues out of total 2988 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 91 poor density : 304 time to evaluate : 3.575 Fit side-chains revert: symmetry clash REVERT: G 283 GLN cc_start: 0.8080 (OUTLIER) cc_final: 0.7591 (mp10) REVERT: H 218 ARG cc_start: 0.7966 (OUTLIER) cc_final: 0.7688 (mtm-85) REVERT: I 592 ARG cc_start: 0.8725 (OUTLIER) cc_final: 0.8433 (ptm160) REVERT: I 648 ASP cc_start: 0.5971 (p0) cc_final: 0.5736 (p0) REVERT: J 160 LEU cc_start: 0.8808 (OUTLIER) cc_final: 0.8308 (mt) REVERT: J 227 PHE cc_start: 0.8568 (OUTLIER) cc_final: 0.8258 (t80) REVERT: J 1165 PHE cc_start: 0.7171 (OUTLIER) cc_final: 0.6242 (m-10) REVERT: L 489 MET cc_start: 0.7793 (mmm) cc_final: 0.7591 (mmm) REVERT: A 27 GLU cc_start: 0.7645 (OUTLIER) cc_final: 0.7349 (mm-30) outliers start: 91 outliers final: 75 residues processed: 385 average time/residue: 0.4406 time to fit residues: 271.2911 Evaluate side-chains 380 residues out of total 2988 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 82 poor density : 298 time to evaluate : 3.231 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 19 VAL Chi-restraints excluded: chain G residue 118 ASP Chi-restraints excluded: chain G residue 145 LYS Chi-restraints excluded: chain G residue 153 VAL Chi-restraints excluded: chain G residue 186 ASN Chi-restraints excluded: chain G residue 252 ILE Chi-restraints excluded: chain G residue 257 VAL Chi-restraints excluded: chain G residue 275 ILE Chi-restraints excluded: chain G residue 283 GLN Chi-restraints excluded: chain G residue 292 THR Chi-restraints excluded: chain H residue 14 VAL Chi-restraints excluded: chain H residue 64 VAL Chi-restraints excluded: chain H residue 103 ASN Chi-restraints excluded: chain H residue 146 VAL Chi-restraints excluded: chain H residue 156 SER Chi-restraints excluded: chain H residue 174 ASP Chi-restraints excluded: chain H residue 183 ILE Chi-restraints excluded: chain H residue 218 ARG Chi-restraints excluded: chain I residue 2 VAL Chi-restraints excluded: chain I residue 21 VAL Chi-restraints excluded: chain I residue 62 TYR Chi-restraints excluded: chain I residue 90 VAL Chi-restraints excluded: chain I residue 132 ASP Chi-restraints excluded: chain I residue 137 VAL Chi-restraints excluded: chain I residue 377 THR Chi-restraints excluded: chain I residue 398 SER Chi-restraints excluded: chain I residue 400 VAL Chi-restraints excluded: chain I residue 417 SER Chi-restraints excluded: chain I residue 471 VAL Chi-restraints excluded: chain I residue 499 SER Chi-restraints excluded: chain I residue 512 SER Chi-restraints excluded: chain I residue 514 PHE Chi-restraints excluded: chain I residue 561 ILE Chi-restraints excluded: chain I residue 575 LEU Chi-restraints excluded: chain I residue 592 ARG Chi-restraints excluded: chain I residue 651 ASP Chi-restraints excluded: chain I residue 714 VAL Chi-restraints excluded: chain I residue 799 ASN Chi-restraints excluded: chain I residue 823 VAL Chi-restraints excluded: chain I residue 827 ARG Chi-restraints excluded: chain I residue 912 ASP Chi-restraints excluded: chain I residue 958 LYS Chi-restraints excluded: chain I residue 1054 LEU Chi-restraints excluded: chain I residue 1056 VAL Chi-restraints excluded: chain I residue 1075 VAL Chi-restraints excluded: chain I residue 1151 LEU Chi-restraints excluded: chain I residue 1163 THR Chi-restraints excluded: chain I residue 1225 VAL Chi-restraints excluded: chain I residue 1227 VAL Chi-restraints excluded: chain I residue 1289 GLU Chi-restraints excluded: chain I residue 1296 ASP Chi-restraints excluded: chain J residue 46 TYR Chi-restraints excluded: chain J residue 48 THR Chi-restraints excluded: chain J residue 160 LEU Chi-restraints excluded: chain J residue 192 MET Chi-restraints excluded: chain J residue 227 PHE Chi-restraints excluded: chain J residue 410 ASP Chi-restraints excluded: chain J residue 527 LEU Chi-restraints excluded: chain J residue 545 HIS Chi-restraints excluded: chain J residue 569 LEU Chi-restraints excluded: chain J residue 594 GLN Chi-restraints excluded: chain J residue 596 LEU Chi-restraints excluded: chain J residue 707 ILE Chi-restraints excluded: chain J residue 708 ASN Chi-restraints excluded: chain J residue 764 ARG Chi-restraints excluded: chain J residue 803 VAL Chi-restraints excluded: chain J residue 826 ILE Chi-restraints excluded: chain J residue 839 VAL Chi-restraints excluded: chain J residue 849 LEU Chi-restraints excluded: chain J residue 1163 VAL Chi-restraints excluded: chain J residue 1165 PHE Chi-restraints excluded: chain J residue 1298 VAL Chi-restraints excluded: chain L residue 442 SER Chi-restraints excluded: chain L residue 457 ILE Chi-restraints excluded: chain L residue 552 THR Chi-restraints excluded: chain L residue 559 LEU Chi-restraints excluded: chain A residue 27 GLU Chi-restraints excluded: chain A residue 63 VAL Chi-restraints excluded: chain B residue 17 LEU Chi-restraints excluded: chain C residue 64 ASP Chi-restraints excluded: chain C residue 74 VAL Chi-restraints excluded: chain D residue 63 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 358 random chunks: chunk 211 optimal weight: 0.9980 chunk 340 optimal weight: 8.9990 chunk 207 optimal weight: 5.9990 chunk 161 optimal weight: 4.9990 chunk 236 optimal weight: 7.9990 chunk 356 optimal weight: 10.0000 chunk 328 optimal weight: 0.9990 chunk 284 optimal weight: 2.9990 chunk 29 optimal weight: 9.9990 chunk 219 optimal weight: 8.9990 chunk 174 optimal weight: 6.9990 overall best weight: 3.1988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: I 811 ASN J 365 GLN J 651 HIS A 73 GLN C 8 ASN ** C 73 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8258 moved from start: 0.2999 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.060 30738 Z= 0.303 Angle : 0.620 12.278 42025 Z= 0.321 Chirality : 0.042 0.190 4806 Planarity : 0.004 0.046 5039 Dihedral : 17.771 179.357 5221 Min Nonbonded Distance : 1.979 Molprobity Statistics. All-atom Clashscore : 8.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.64 % Favored : 94.36 % Rotamer: Outliers : 3.05 % Allowed : 24.77 % Favored : 72.18 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.49 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.43 (0.15), residues: 3478 helix: 1.55 (0.13), residues: 1571 sheet: -0.44 (0.25), residues: 393 loop : -0.84 (0.16), residues: 1514 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP B 47 HIS 0.004 0.001 HIS G 23 PHE 0.023 0.002 PHE I 57 TYR 0.024 0.001 TYR L 137 ARG 0.015 0.000 ARG D 72 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6956 Ramachandran restraints generated. 3478 Oldfield, 0 Emsley, 3478 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6956 Ramachandran restraints generated. 3478 Oldfield, 0 Emsley, 3478 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 384 residues out of total 2988 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 91 poor density : 293 time to evaluate : 3.527 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: G 283 GLN cc_start: 0.8108 (OUTLIER) cc_final: 0.7613 (mp10) REVERT: H 218 ARG cc_start: 0.7989 (OUTLIER) cc_final: 0.7670 (mtm-85) REVERT: I 592 ARG cc_start: 0.8716 (OUTLIER) cc_final: 0.8393 (ptm160) REVERT: I 637 ARG cc_start: 0.8602 (OUTLIER) cc_final: 0.8027 (ptt-90) REVERT: I 648 ASP cc_start: 0.6058 (p0) cc_final: 0.5778 (p0) REVERT: J 160 LEU cc_start: 0.8831 (OUTLIER) cc_final: 0.8324 (mt) REVERT: J 227 PHE cc_start: 0.8615 (OUTLIER) cc_final: 0.8314 (t80) REVERT: J 1165 PHE cc_start: 0.7214 (OUTLIER) cc_final: 0.6255 (m-10) outliers start: 91 outliers final: 79 residues processed: 374 average time/residue: 0.4396 time to fit residues: 260.6659 Evaluate side-chains 376 residues out of total 2988 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 86 poor density : 290 time to evaluate : 3.420 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 19 VAL Chi-restraints excluded: chain G residue 118 ASP Chi-restraints excluded: chain G residue 145 LYS Chi-restraints excluded: chain G residue 153 VAL Chi-restraints excluded: chain G residue 186 ASN Chi-restraints excluded: chain G residue 252 ILE Chi-restraints excluded: chain G residue 257 VAL Chi-restraints excluded: chain G residue 275 ILE Chi-restraints excluded: chain G residue 283 GLN Chi-restraints excluded: chain G residue 292 THR Chi-restraints excluded: chain H residue 14 VAL Chi-restraints excluded: chain H residue 64 VAL Chi-restraints excluded: chain H residue 103 ASN Chi-restraints excluded: chain H residue 146 VAL Chi-restraints excluded: chain H residue 156 SER Chi-restraints excluded: chain H residue 174 ASP Chi-restraints excluded: chain H residue 183 ILE Chi-restraints excluded: chain H residue 218 ARG Chi-restraints excluded: chain I residue 2 VAL Chi-restraints excluded: chain I residue 21 VAL Chi-restraints excluded: chain I residue 62 TYR Chi-restraints excluded: chain I residue 90 VAL Chi-restraints excluded: chain I residue 132 ASP Chi-restraints excluded: chain I residue 137 VAL Chi-restraints excluded: chain I residue 219 GLN Chi-restraints excluded: chain I residue 377 THR Chi-restraints excluded: chain I residue 398 SER Chi-restraints excluded: chain I residue 400 VAL Chi-restraints excluded: chain I residue 417 SER Chi-restraints excluded: chain I residue 471 VAL Chi-restraints excluded: chain I residue 499 SER Chi-restraints excluded: chain I residue 512 SER Chi-restraints excluded: chain I residue 514 PHE Chi-restraints excluded: chain I residue 561 ILE Chi-restraints excluded: chain I residue 575 LEU Chi-restraints excluded: chain I residue 592 ARG Chi-restraints excluded: chain I residue 637 ARG Chi-restraints excluded: chain I residue 651 ASP Chi-restraints excluded: chain I residue 714 VAL Chi-restraints excluded: chain I residue 799 ASN Chi-restraints excluded: chain I residue 823 VAL Chi-restraints excluded: chain I residue 827 ARG Chi-restraints excluded: chain I residue 912 ASP Chi-restraints excluded: chain I residue 1054 LEU Chi-restraints excluded: chain I residue 1056 VAL Chi-restraints excluded: chain I residue 1075 VAL Chi-restraints excluded: chain I residue 1151 LEU Chi-restraints excluded: chain I residue 1163 THR Chi-restraints excluded: chain I residue 1225 VAL Chi-restraints excluded: chain I residue 1227 VAL Chi-restraints excluded: chain I residue 1289 GLU Chi-restraints excluded: chain I residue 1296 ASP Chi-restraints excluded: chain J residue 46 TYR Chi-restraints excluded: chain J residue 48 THR Chi-restraints excluded: chain J residue 160 LEU Chi-restraints excluded: chain J residue 192 MET Chi-restraints excluded: chain J residue 198 CYS Chi-restraints excluded: chain J residue 227 PHE Chi-restraints excluded: chain J residue 410 ASP Chi-restraints excluded: chain J residue 527 LEU Chi-restraints excluded: chain J residue 545 HIS Chi-restraints excluded: chain J residue 569 LEU Chi-restraints excluded: chain J residue 594 GLN Chi-restraints excluded: chain J residue 596 LEU Chi-restraints excluded: chain J residue 707 ILE Chi-restraints excluded: chain J residue 708 ASN Chi-restraints excluded: chain J residue 764 ARG Chi-restraints excluded: chain J residue 803 VAL Chi-restraints excluded: chain J residue 826 ILE Chi-restraints excluded: chain J residue 839 VAL Chi-restraints excluded: chain J residue 849 LEU Chi-restraints excluded: chain J residue 1163 VAL Chi-restraints excluded: chain J residue 1165 PHE Chi-restraints excluded: chain J residue 1258 ARG Chi-restraints excluded: chain J residue 1298 VAL Chi-restraints excluded: chain L residue 413 MET Chi-restraints excluded: chain L residue 442 SER Chi-restraints excluded: chain L residue 457 ILE Chi-restraints excluded: chain L residue 552 THR Chi-restraints excluded: chain L residue 559 LEU Chi-restraints excluded: chain A residue 63 VAL Chi-restraints excluded: chain B residue 64 ASP Chi-restraints excluded: chain C residue 64 ASP Chi-restraints excluded: chain C residue 74 VAL Chi-restraints excluded: chain D residue 26 THR Chi-restraints excluded: chain D residue 63 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 358 random chunks: chunk 225 optimal weight: 5.9990 chunk 302 optimal weight: 0.9980 chunk 87 optimal weight: 0.8980 chunk 261 optimal weight: 9.9990 chunk 41 optimal weight: 4.9990 chunk 78 optimal weight: 0.7980 chunk 284 optimal weight: 2.9990 chunk 119 optimal weight: 0.9990 chunk 292 optimal weight: 20.0000 chunk 36 optimal weight: 8.9990 chunk 52 optimal weight: 4.9990 overall best weight: 1.3384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** I 519 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 811 ASN J 365 GLN J 651 HIS A 73 GLN C 8 ASN ** C 73 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3450 r_free = 0.3450 target = 0.084708 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.2889 r_free = 0.2889 target = 0.057656 restraints weight = 68422.331| |-----------------------------------------------------------------------------| r_work (start): 0.2861 rms_B_bonded: 2.57 r_work: 0.2710 rms_B_bonded: 3.20 restraints_weight: 0.5000 r_work (final): 0.2710 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2713 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2713 r_free = 0.2713 target_work(ls_wunit_k1) = 0.051 | | occupancies: max = 1.00 min = 0.13 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2712 r_free = 0.2712 target_work(ls_wunit_k1) = 0.051 | | occupancies: max = 1.00 min = 0.18 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2712 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8520 moved from start: 0.3119 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.057 30738 Z= 0.194 Angle : 0.587 11.993 42025 Z= 0.305 Chirality : 0.040 0.193 4806 Planarity : 0.004 0.047 5039 Dihedral : 17.697 179.087 5221 Min Nonbonded Distance : 2.016 Molprobity Statistics. All-atom Clashscore : 8.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.77 % Favored : 95.23 % Rotamer: Outliers : 3.05 % Allowed : 24.87 % Favored : 72.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.49 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.51 (0.15), residues: 3478 helix: 1.63 (0.13), residues: 1566 sheet: -0.40 (0.25), residues: 393 loop : -0.82 (0.16), residues: 1519 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP I 807 HIS 0.003 0.001 HIS G 23 PHE 0.018 0.001 PHE B 51 TYR 0.027 0.001 TYR L 143 ARG 0.015 0.000 ARG D 72 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 6509.69 seconds wall clock time: 118 minutes 56.20 seconds (7136.20 seconds total)