Starting phenix.real_space_refine on Thu Sep 26 11:49:32 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7yuy_34115/09_2024/7yuy_34115_neut.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7yuy_34115/09_2024/7yuy_34115.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.5 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7yuy_34115/09_2024/7yuy_34115.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7yuy_34115/09_2024/7yuy_34115.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7yuy_34115/09_2024/7yuy_34115_neut.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7yuy_34115/09_2024/7yuy_34115_neut.cif" } resolution = 3.5 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= 0.004 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: 5 Type Number sf(0) Gaussians P 1 5.49 5 S 72 5.16 5 C 8140 2.51 5 N 2035 2.21 5 O 2143 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 38 residue(s): 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5461/modules/chem_data/mon_lib" Total number of atoms: 12391 Number of models: 1 Model: "" Number of chains: 4 Chain: "F" Number of atoms: 12063 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1503, 12063 Classifications: {'peptide': 1503} Incomplete info: {'truncation_to_alanine': 51} Link IDs: {'PTRANS': 66, 'TRANS': 1436} Chain breaks: 10 Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 197 Unresolved non-hydrogen angles: 253 Unresolved non-hydrogen dihedrals: 171 Unresolved non-hydrogen chiralities: 19 Planarities with less than four sites: {'GLN:plan1': 4, 'ASP:plan': 1, 'TYR:plan': 2, 'TRP:plan': 1, 'HIS:plan': 1, 'PHE:plan': 7, 'GLU:plan': 2, 'ARG:plan': 2} Unresolved non-hydrogen planarities: 107 Chain: "A" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "C" Number of atoms: 45 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 45 Unusual residues: {'BGC': 4} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "F" Number of atoms: 255 Number of conformers: 1 Conformer: "" Number of residues, atoms: 25, 255 Unusual residues: {'C14': 1, 'D10': 6, 'D12': 3, 'DD9': 7, 'HP6': 7, 'XKP': 1} Classifications: {'undetermined': 25} Link IDs: {None: 24} Time building chain proxies: 7.48, per 1000 atoms: 0.60 Number of scatterers: 12391 At special positions: 0 Unit cell: (101.2, 115, 135.24, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 72 16.00 P 1 15.00 O 2143 8.00 N 2035 7.00 C 8140 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=2, symmetry=0 Simple disulfide: pdb=" SG CYS F 658 " - pdb=" SG CYS F 669 " distance=1.77 Simple disulfide: pdb=" SG CYS F1328 " - pdb=" SG CYS F1345 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 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 Links applied BETA1-3 " BGC C 1 " - " BGC C 2 " " BGC C 2 " - " BGC C 3 " " BGC C 3 " - " BGC C 4 " BETA1-4 " NAG A 1 " - " NAG A 2 " NAG-ASN " NAG A 1 " - " ASN F1849 " Time building additional restraints: 3.37 Conformation dependent library (CDL) restraints added in 1.5 seconds 2962 Ramachandran restraints generated. 1481 Oldfield, 0 Emsley, 1481 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2858 Finding SS restraints... Secondary structure from input PDB file: 72 helices and 4 sheets defined 60.7% alpha, 3.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.42 Creating SS restraints... Processing helix chain 'F' and resid 160 through 176 removed outlier: 4.118A pdb=" N ILE F 167 " --> pdb=" O GLN F 163 " (cutoff:3.500A) Processing helix chain 'F' and resid 178 through 196 removed outlier: 3.952A pdb=" N ASP F 187 " --> pdb=" O ARG F 183 " (cutoff:3.500A) removed outlier: 3.982A pdb=" N ARG F 196 " --> pdb=" O LEU F 192 " (cutoff:3.500A) Processing helix chain 'F' and resid 201 through 214 removed outlier: 3.733A pdb=" N LEU F 207 " --> pdb=" O ASP F 203 " (cutoff:3.500A) removed outlier: 3.621A pdb=" N ILE F 214 " --> pdb=" O HIS F 210 " (cutoff:3.500A) Processing helix chain 'F' and resid 219 through 229 removed outlier: 3.666A pdb=" N LYS F 223 " --> pdb=" O ALA F 219 " (cutoff:3.500A) removed outlier: 3.546A pdb=" N ALA F 227 " --> pdb=" O LYS F 223 " (cutoff:3.500A) Processing helix chain 'F' and resid 233 through 243 removed outlier: 3.530A pdb=" N GLY F 237 " --> pdb=" O ASP F 233 " (cutoff:3.500A) Processing helix chain 'F' and resid 282 through 293 removed outlier: 4.207A pdb=" N ARG F 288 " --> pdb=" O ALA F 284 " (cutoff:3.500A) Processing helix chain 'F' and resid 294 through 296 No H-bonds generated for 'chain 'F' and resid 294 through 296' Processing helix chain 'F' and resid 297 through 313 removed outlier: 3.645A pdb=" N VAL F 302 " --> pdb=" O PRO F 298 " (cutoff:3.500A) removed outlier: 4.087A pdb=" N ARG F 303 " --> pdb=" O LEU F 299 " (cutoff:3.500A) removed outlier: 3.533A pdb=" N HIS F 304 " --> pdb=" O GLU F 300 " (cutoff:3.500A) removed outlier: 3.592A pdb=" N LEU F 307 " --> pdb=" O ARG F 303 " (cutoff:3.500A) removed outlier: 3.578A pdb=" N TYR F 308 " --> pdb=" O HIS F 304 " (cutoff:3.500A) Processing helix chain 'F' and resid 321 through 337 removed outlier: 3.897A pdb=" N LEU F 325 " --> pdb=" O THR F 321 " (cutoff:3.500A) Processing helix chain 'F' and resid 339 through 344 removed outlier: 4.297A pdb=" N GLN F 343 " --> pdb=" O PRO F 339 " (cutoff:3.500A) removed outlier: 4.297A pdb=" N ARG F 344 " --> pdb=" O LEU F 340 " (cutoff:3.500A) No H-bonds generated for 'chain 'F' and resid 339 through 344' Processing helix chain 'F' and resid 351 through 357 removed outlier: 3.570A pdb=" N ASN F 355 " --> pdb=" O GLY F 351 " (cutoff:3.500A) removed outlier: 3.659A pdb=" N VAL F 357 " --> pdb=" O PHE F 353 " (cutoff:3.500A) Processing helix chain 'F' and resid 358 through 368 Processing helix chain 'F' and resid 389 through 394 Processing helix chain 'F' and resid 395 through 398 removed outlier: 3.647A pdb=" N TRP F 398 " --> pdb=" O GLN F 395 " (cutoff:3.500A) No H-bonds generated for 'chain 'F' and resid 395 through 398' Processing helix chain 'F' and resid 399 through 404 Processing helix chain 'F' and resid 419 through 428 removed outlier: 3.615A pdb=" N ARG F 422 " --> pdb=" O LEU F 419 " (cutoff:3.500A) removed outlier: 4.315A pdb=" N TYR F 423 " --> pdb=" O GLU F 420 " (cutoff:3.500A) removed outlier: 5.198A pdb=" N LEU F 424 " --> pdb=" O GLU F 421 " (cutoff:3.500A) removed outlier: 3.969A pdb=" N ARG F 425 " --> pdb=" O ARG F 422 " (cutoff:3.500A) removed outlier: 4.148A pdb=" N GLY F 427 " --> pdb=" O LEU F 424 " (cutoff:3.500A) removed outlier: 3.532A pdb=" N ASP F 428 " --> pdb=" O ARG F 425 " (cutoff:3.500A) Processing helix chain 'F' and resid 444 through 452 removed outlier: 3.806A pdb=" N LEU F 448 " --> pdb=" O THR F 444 " (cutoff:3.500A) removed outlier: 3.962A pdb=" N VAL F 449 " --> pdb=" O TRP F 445 " (cutoff:3.500A) removed outlier: 4.361A pdb=" N THR F 450 " --> pdb=" O LEU F 446 " (cutoff:3.500A) removed outlier: 3.556A pdb=" N PHE F 452 " --> pdb=" O LEU F 448 " (cutoff:3.500A) Processing helix chain 'F' and resid 459 through 470 removed outlier: 3.888A pdb=" N MET F 465 " --> pdb=" O SER F 461 " (cutoff:3.500A) removed outlier: 3.818A pdb=" N ASN F 470 " --> pdb=" O TYR F 466 " (cutoff:3.500A) Processing helix chain 'F' and resid 489 through 497 removed outlier: 3.792A pdb=" N TRP F 493 " --> pdb=" O ALA F 489 " (cutoff:3.500A) Processing helix chain 'F' and resid 498 through 515 removed outlier: 3.988A pdb=" N VAL F 502 " --> pdb=" O LEU F 498 " (cutoff:3.500A) removed outlier: 3.595A pdb=" N ALA F 503 " --> pdb=" O GLY F 499 " (cutoff:3.500A) removed outlier: 4.321A pdb=" N GLN F 507 " --> pdb=" O ALA F 503 " (cutoff:3.500A) removed outlier: 3.633A pdb=" N THR F 511 " --> pdb=" O GLN F 507 " (cutoff:3.500A) Processing helix chain 'F' and resid 525 through 551 removed outlier: 3.804A pdb=" N SER F 529 " --> pdb=" O ALA F 525 " (cutoff:3.500A) removed outlier: 3.801A pdb=" N TRP F 533 " --> pdb=" O SER F 529 " (cutoff:3.500A) removed outlier: 3.973A pdb=" N PHE F 534 " --> pdb=" O ARG F 530 " (cutoff:3.500A) removed outlier: 3.898A pdb=" N ILE F 537 " --> pdb=" O TRP F 533 " (cutoff:3.500A) removed outlier: 3.509A pdb=" N ILE F 538 " --> pdb=" O PHE F 534 " (cutoff:3.500A) Proline residue: F 545 - end of helix removed outlier: 3.634A pdb=" N PHE F 548 " --> pdb=" O GLY F 544 " (cutoff:3.500A) removed outlier: 3.571A pdb=" N ALA F 551 " --> pdb=" O ILE F 547 " (cutoff:3.500A) Processing helix chain 'F' and resid 559 through 581 removed outlier: 3.608A pdb=" N HIS F 563 " --> pdb=" O SER F 559 " (cutoff:3.500A) removed outlier: 4.147A pdb=" N VAL F 564 " --> pdb=" O THR F 560 " (cutoff:3.500A) removed outlier: 4.305A pdb=" N VAL F 565 " --> pdb=" O ALA F 561 " (cutoff:3.500A) removed outlier: 3.656A pdb=" N ALA F 566 " --> pdb=" O ALA F 562 " (cutoff:3.500A) removed outlier: 3.884A pdb=" N MET F 569 " --> pdb=" O VAL F 565 " (cutoff:3.500A) removed outlier: 3.587A pdb=" N PHE F 570 " --> pdb=" O ALA F 566 " (cutoff:3.500A) removed outlier: 3.784A pdb=" N PHE F 571 " --> pdb=" O ALA F 567 " (cutoff:3.500A) removed outlier: 3.713A pdb=" N VAL F 574 " --> pdb=" O PHE F 570 " (cutoff:3.500A) removed outlier: 3.602A pdb=" N ALA F 575 " --> pdb=" O PHE F 571 " (cutoff:3.500A) removed outlier: 4.213A pdb=" N ILE F 577 " --> pdb=" O ALA F 573 " (cutoff:3.500A) Processing helix chain 'F' and resid 584 through 588 removed outlier: 4.080A pdb=" N LEU F 588 " --> pdb=" O LEU F 585 " (cutoff:3.500A) Processing helix chain 'F' and resid 616 through 636 removed outlier: 4.103A pdb=" N TYR F 622 " --> pdb=" O ARG F 618 " (cutoff:3.500A) removed outlier: 3.804A pdb=" N LEU F 623 " --> pdb=" O TRP F 619 " (cutoff:3.500A) removed outlier: 3.743A pdb=" N VAL F 624 " --> pdb=" O MET F 620 " (cutoff:3.500A) removed outlier: 4.065A pdb=" N TRP F 625 " --> pdb=" O SER F 621 " (cutoff:3.500A) Processing helix chain 'F' and resid 641 through 644 Processing helix chain 'F' and resid 645 through 652 removed outlier: 3.600A pdb=" N ARG F 649 " --> pdb=" O ARG F 645 " (cutoff:3.500A) Processing helix chain 'F' and resid 671 through 683 removed outlier: 3.924A pdb=" N ILE F 675 " --> pdb=" O VAL F 671 " (cutoff:3.500A) Processing helix chain 'F' and resid 686 through 711 removed outlier: 3.910A pdb=" N LEU F 690 " --> pdb=" O ILE F 686 " (cutoff:3.500A) removed outlier: 4.009A pdb=" N ASP F 691 " --> pdb=" O LEU F 687 " (cutoff:3.500A) removed outlier: 4.727A pdb=" N THR F 692 " --> pdb=" O PHE F 688 " (cutoff:3.500A) removed outlier: 4.144A pdb=" N TYR F 693 " --> pdb=" O PHE F 689 " (cutoff:3.500A) removed outlier: 3.626A pdb=" N ILE F 697 " --> pdb=" O TYR F 693 " (cutoff:3.500A) removed outlier: 3.818A pdb=" N ILE F 698 " --> pdb=" O LEU F 694 " (cutoff:3.500A) removed outlier: 3.737A pdb=" N PHE F 703 " --> pdb=" O VAL F 699 " (cutoff:3.500A) removed outlier: 3.645A pdb=" N SER F 704 " --> pdb=" O ASN F 700 " (cutoff:3.500A) Processing helix chain 'F' and resid 718 through 723 removed outlier: 3.855A pdb=" N ILE F 722 " --> pdb=" O PRO F 718 " (cutoff:3.500A) removed outlier: 4.354A pdb=" N PHE F 723 " --> pdb=" O TRP F 719 " (cutoff:3.500A) No H-bonds generated for 'chain 'F' and resid 718 through 723' Processing helix chain 'F' and resid 726 through 734 removed outlier: 3.578A pdb=" N SER F 732 " --> pdb=" O LYS F 728 " (cutoff:3.500A) Processing helix chain 'F' and resid 747 through 764 removed outlier: 3.632A pdb=" N MET F 761 " --> pdb=" O ILE F 757 " (cutoff:3.500A) Processing helix chain 'F' and resid 768 through 773 removed outlier: 3.952A pdb=" N GLN F 773 " --> pdb=" O ILE F 769 " (cutoff:3.500A) Processing helix chain 'F' and resid 793 through 797 Processing helix chain 'F' and resid 813 through 825 Processing helix chain 'F' and resid 857 through 862 removed outlier: 3.938A pdb=" N ILE F 861 " --> pdb=" O LEU F 857 " (cutoff:3.500A) Processing helix chain 'F' and resid 871 through 880 Processing helix chain 'F' and resid 882 through 896 Processing helix chain 'F' and resid 933 through 946 removed outlier: 3.581A pdb=" N ARG F 946 " --> pdb=" O TRP F 942 " (cutoff:3.500A) Processing helix chain 'F' and resid 950 through 958 Processing helix chain 'F' and resid 958 through 972 removed outlier: 4.212A pdb=" N ARG F 962 " --> pdb=" O MET F 958 " (cutoff:3.500A) Processing helix chain 'F' and resid 973 through 979 removed outlier: 4.328A pdb=" N PHE F 979 " --> pdb=" O ILE F 975 " (cutoff:3.500A) Processing helix chain 'F' and resid 982 through 995 Processing helix chain 'F' and resid 1006 through 1010 removed outlier: 3.659A pdb=" N LYS F1009 " --> pdb=" O ARG F1006 " (cutoff:3.500A) Processing helix chain 'F' and resid 1011 through 1025 removed outlier: 3.768A pdb=" N GLU F1016 " --> pdb=" O PRO F1012 " (cutoff:3.500A) removed outlier: 3.800A pdb=" N ASN F1017 " --> pdb=" O HIS F1013 " (cutoff:3.500A) removed outlier: 3.710A pdb=" N ALA F1018 " --> pdb=" O GLU F1014 " (cutoff:3.500A) removed outlier: 3.564A pdb=" N LEU F1022 " --> pdb=" O ALA F1018 " (cutoff:3.500A) removed outlier: 3.501A pdb=" N ARG F1023 " --> pdb=" O GLU F1019 " (cutoff:3.500A) Processing helix chain 'F' and resid 1082 through 1089 removed outlier: 3.950A pdb=" N ALA F1089 " --> pdb=" O ASN F1085 " (cutoff:3.500A) Processing helix chain 'F' and resid 1109 through 1113 removed outlier: 3.734A pdb=" N LEU F1113 " --> pdb=" O GLU F1110 " (cutoff:3.500A) Processing helix chain 'F' and resid 1114 through 1119 removed outlier: 3.602A pdb=" N VAL F1118 " --> pdb=" O LYS F1114 " (cutoff:3.500A) removed outlier: 3.757A pdb=" N LEU F1119 " --> pdb=" O ILE F1115 " (cutoff:3.500A) No H-bonds generated for 'chain 'F' and resid 1114 through 1119' Processing helix chain 'F' and resid 1169 through 1187 removed outlier: 3.822A pdb=" N ILE F1187 " --> pdb=" O THR F1183 " (cutoff:3.500A) Processing helix chain 'F' and resid 1201 through 1206 removed outlier: 3.816A pdb=" N THR F1206 " --> pdb=" O THR F1202 " (cutoff:3.500A) Processing helix chain 'F' and resid 1223 through 1229 Processing helix chain 'F' and resid 1273 through 1280 removed outlier: 3.687A pdb=" N TYR F1277 " --> pdb=" O ARG F1273 " (cutoff:3.500A) removed outlier: 3.661A pdb=" N THR F1280 " --> pdb=" O TYR F1276 " (cutoff:3.500A) Processing helix chain 'F' and resid 1283 through 1292 Processing helix chain 'F' and resid 1294 through 1320 removed outlier: 3.831A pdb=" N HIS F1298 " --> pdb=" O HIS F1294 " (cutoff:3.500A) removed outlier: 3.603A pdb=" N ASN F1301 " --> pdb=" O PHE F1297 " (cutoff:3.500A) removed outlier: 3.936A pdb=" N LEU F1302 " --> pdb=" O HIS F1298 " (cutoff:3.500A) removed outlier: 3.704A pdb=" N PHE F1303 " --> pdb=" O LEU F1299 " (cutoff:3.500A) removed outlier: 3.869A pdb=" N GLN F1305 " --> pdb=" O ASN F1301 " (cutoff:3.500A) removed outlier: 3.726A pdb=" N GLN F1309 " --> pdb=" O GLN F1305 " (cutoff:3.500A) removed outlier: 3.666A pdb=" N MET F1310 " --> pdb=" O LEU F1306 " (cutoff:3.500A) removed outlier: 4.194A pdb=" N PHE F1311 " --> pdb=" O SER F1307 " (cutoff:3.500A) removed outlier: 3.660A pdb=" N MET F1312 " --> pdb=" O LEU F1308 " (cutoff:3.500A) removed outlier: 3.515A pdb=" N LEU F1313 " --> pdb=" O GLN F1309 " (cutoff:3.500A) removed outlier: 3.603A pdb=" N VAL F1316 " --> pdb=" O MET F1312 " (cutoff:3.500A) removed outlier: 3.856A pdb=" N ASN F1317 " --> pdb=" O LEU F1313 " (cutoff:3.500A) Processing helix chain 'F' and resid 1348 through 1353 Processing helix chain 'F' and resid 1353 through 1365 removed outlier: 3.719A pdb=" N ARG F1357 " --> pdb=" O ASP F1353 " (cutoff:3.500A) removed outlier: 3.842A pdb=" N LEU F1360 " --> pdb=" O ARG F1356 " (cutoff:3.500A) removed outlier: 3.984A pdb=" N SER F1361 " --> pdb=" O ARG F1357 " (cutoff:3.500A) removed outlier: 3.520A pdb=" N PHE F1363 " --> pdb=" O THR F1359 " (cutoff:3.500A) removed outlier: 3.572A pdb=" N ILE F1364 " --> pdb=" O LEU F1360 " (cutoff:3.500A) removed outlier: 3.692A pdb=" N VAL F1365 " --> pdb=" O SER F1361 " (cutoff:3.500A) Processing helix chain 'F' and resid 1371 through 1379 removed outlier: 4.184A pdb=" N VAL F1375 " --> pdb=" O VAL F1371 " (cutoff:3.500A) removed outlier: 3.925A pdb=" N GLN F1376 " --> pdb=" O PRO F1372 " (cutoff:3.500A) Processing helix chain 'F' and resid 1382 through 1393 Processing helix chain 'F' and resid 1398 through 1406 Processing helix chain 'F' and resid 1407 through 1418 removed outlier: 3.834A pdb=" N SER F1411 " --> pdb=" O GLN F1407 " (cutoff:3.500A) Processing helix chain 'F' and resid 1437 through 1446 removed outlier: 3.854A pdb=" N PHE F1445 " --> pdb=" O LEU F1441 " (cutoff:3.500A) Processing helix chain 'F' and resid 1450 through 1467 removed outlier: 3.788A pdb=" N ARG F1455 " --> pdb=" O TYR F1451 " (cutoff:3.500A) removed outlier: 3.924A pdb=" N MET F1459 " --> pdb=" O ARG F1455 " (cutoff:3.500A) removed outlier: 3.705A pdb=" N LEU F1460 " --> pdb=" O SER F1456 " (cutoff:3.500A) removed outlier: 3.595A pdb=" N HIS F1467 " --> pdb=" O GLY F1463 " (cutoff:3.500A) Processing helix chain 'F' and resid 1469 through 1471 No H-bonds generated for 'chain 'F' and resid 1469 through 1471' Processing helix chain 'F' and resid 1472 through 1481 removed outlier: 3.929A pdb=" N TRP F1476 " --> pdb=" O LEU F1472 " (cutoff:3.500A) removed outlier: 3.584A pdb=" N ALA F1477 " --> pdb=" O LEU F1473 " (cutoff:3.500A) removed outlier: 4.068A pdb=" N SER F1478 " --> pdb=" O TRP F1474 " (cutoff:3.500A) Processing helix chain 'F' and resid 1497 through 1512 Processing helix chain 'F' and resid 1565 through 1584 removed outlier: 3.547A pdb=" N TYR F1571 " --> pdb=" O PRO F1567 " (cutoff:3.500A) removed outlier: 4.007A pdb=" N ALA F1572 " --> pdb=" O CYS F1568 " (cutoff:3.500A) removed outlier: 3.704A pdb=" N CYS F1575 " --> pdb=" O TYR F1571 " (cutoff:3.500A) removed outlier: 3.592A pdb=" N ALA F1578 " --> pdb=" O GLY F1574 " (cutoff:3.500A) removed outlier: 3.631A pdb=" N ILE F1582 " --> pdb=" O ALA F1578 " (cutoff:3.500A) removed outlier: 3.601A pdb=" N ASN F1583 " --> pdb=" O PHE F1579 " (cutoff:3.500A) Processing helix chain 'F' and resid 1598 through 1626 removed outlier: 4.129A pdb=" N ILE F1602 " --> pdb=" O SER F1598 " (cutoff:3.500A) removed outlier: 3.529A pdb=" N ILE F1603 " --> pdb=" O VAL F1599 " (cutoff:3.500A) removed outlier: 3.834A pdb=" N ALA F1608 " --> pdb=" O ILE F1604 " (cutoff:3.500A) Proline residue: F1609 - end of helix Processing helix chain 'F' and resid 1639 through 1665 removed outlier: 3.536A pdb=" N HIS F1654 " --> pdb=" O ALA F1650 " (cutoff:3.500A) removed outlier: 3.621A pdb=" N MET F1661 " --> pdb=" O PHE F1657 " (cutoff:3.500A) removed outlier: 3.563A pdb=" N TRP F1662 " --> pdb=" O PHE F1658 " (cutoff:3.500A) Processing helix chain 'F' and resid 1669 through 1697 removed outlier: 3.937A pdb=" N ILE F1674 " --> pdb=" O VAL F1670 " (cutoff:3.500A) removed outlier: 4.648A pdb=" N GLY F1675 " --> pdb=" O ARG F1671 " (cutoff:3.500A) removed outlier: 3.558A pdb=" N THR F1678 " --> pdb=" O ILE F1674 " (cutoff:3.500A) Processing helix chain 'F' and resid 1725 through 1751 removed outlier: 3.802A pdb=" N LYS F1733 " --> pdb=" O GLU F1729 " (cutoff:3.500A) removed outlier: 3.792A pdb=" N ALA F1741 " --> pdb=" O LEU F1737 " (cutoff:3.500A) removed outlier: 3.774A pdb=" N ALA F1742 " --> pdb=" O SER F1738 " (cutoff:3.500A) removed outlier: 4.138A pdb=" N GLY F1747 " --> pdb=" O ASP F1743 " (cutoff:3.500A) removed outlier: 4.000A pdb=" N HIS F1748 " --> pdb=" O PHE F1744 " (cutoff:3.500A) Processing helix chain 'F' and resid 1754 through 1758 Processing helix chain 'F' and resid 1763 through 1775 Processing helix chain 'F' and resid 1786 through 1821 removed outlier: 4.046A pdb=" N SER F1802 " --> pdb=" O LYS F1798 " (cutoff:3.500A) removed outlier: 4.359A pdb=" N LEU F1803 " --> pdb=" O LYS F1799 " (cutoff:3.500A) removed outlier: 3.685A pdb=" N LEU F1808 " --> pdb=" O TYR F1804 " (cutoff:3.500A) removed outlier: 3.933A pdb=" N ALA F1809 " --> pdb=" O PHE F1805 " (cutoff:3.500A) Proline residue: F1818 - end of helix Processing sheet with id=AA1, first strand: chain 'F' and resid 371 through 372 Processing sheet with id=AA2, first strand: chain 'F' and resid 779 through 781 Processing sheet with id=AA3, first strand: chain 'F' and resid 999 through 1004 removed outlier: 6.797A pdb=" N PHE F 842 " --> pdb=" O LYS F 999 " (cutoff:3.500A) removed outlier: 8.073A pdb=" N LEU F1001 " --> pdb=" O PHE F 842 " (cutoff:3.500A) removed outlier: 5.805A pdb=" N VAL F 844 " --> pdb=" O LEU F1001 " (cutoff:3.500A) removed outlier: 7.197A pdb=" N SER F1003 " --> pdb=" O VAL F 844 " (cutoff:3.500A) removed outlier: 7.151A pdb=" N THR F 846 " --> pdb=" O SER F1003 " (cutoff:3.500A) removed outlier: 6.422A pdb=" N THR F 843 " --> pdb=" O GLN F1099 " (cutoff:3.500A) removed outlier: 6.902A pdb=" N ALA F1149 " --> pdb=" O ASN F1200 " (cutoff:3.500A) removed outlier: 7.507A pdb=" N LYS F1237 " --> pdb=" O ALA F1149 " (cutoff:3.500A) removed outlier: 4.183A pdb=" N VAL F1151 " --> pdb=" O LYS F1237 " (cutoff:3.500A) removed outlier: 5.872A pdb=" N CYS F1239 " --> pdb=" O VAL F1151 " (cutoff:3.500A) removed outlier: 4.771A pdb=" N ALA F1153 " --> pdb=" O CYS F1239 " (cutoff:3.500A) removed outlier: 7.727A pdb=" N TYR F1241 " --> pdb=" O ALA F1153 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'F' and resid 1030 through 1032 removed outlier: 3.878A pdb=" N PHE F1068 " --> pdb=" O LEU F1051 " (cutoff:3.500A) 498 hydrogen bonds defined for protein. 1458 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 3.80 Time building geometry restraints manager: 3.72 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: 2020 1.32 - 1.44: 3475 1.44 - 1.57: 7069 1.57 - 1.69: 3 1.69 - 1.81: 115 Bond restraints: 12682 Sorted by residual: bond pdb=" C17 XKP F1925 " pdb=" C22 XKP F1925 " ideal model delta sigma weight residual 1.524 1.306 0.218 2.00e-02 2.50e+03 1.19e+02 bond pdb=" C8 XKP F1925 " pdb=" O2 XKP F1925 " ideal model delta sigma weight residual 1.409 1.451 -0.042 2.00e-02 2.50e+03 4.51e+00 bond pdb=" O5 XKP F1925 " pdb=" P XKP F1925 " ideal model delta sigma weight residual 1.647 1.606 0.041 2.00e-02 2.50e+03 4.23e+00 bond pdb=" C3 XKP F1925 " pdb=" C4 XKP F1925 " ideal model delta sigma weight residual 1.535 1.495 0.040 2.00e-02 2.50e+03 4.02e+00 bond pdb=" C LEU F 642 " pdb=" N PRO F 643 " ideal model delta sigma weight residual 1.334 1.349 -0.015 8.40e-03 1.42e+04 3.33e+00 ... (remaining 12677 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.27: 16629 2.27 - 4.53: 422 4.53 - 6.80: 52 6.80 - 9.07: 10 9.07 - 11.33: 3 Bond angle restraints: 17116 Sorted by residual: angle pdb=" N VAL F 318 " pdb=" CA VAL F 318 " pdb=" C VAL F 318 " ideal model delta sigma weight residual 112.90 104.78 8.12 9.60e-01 1.09e+00 7.15e+01 angle pdb=" C ARG F 869 " pdb=" CA ARG F 869 " pdb=" CB ARG F 869 " ideal model delta sigma weight residual 116.54 108.36 8.18 1.15e+00 7.56e-01 5.06e+01 angle pdb=" CA ARG F 869 " pdb=" C ARG F 869 " pdb=" N VAL F 870 " ideal model delta sigma weight residual 119.52 115.38 4.14 7.90e-01 1.60e+00 2.74e+01 angle pdb=" N ILE F 734 " pdb=" CA ILE F 734 " pdb=" C ILE F 734 " ideal model delta sigma weight residual 113.71 109.08 4.63 9.50e-01 1.11e+00 2.37e+01 angle pdb=" C SER F 281 " pdb=" CA SER F 281 " pdb=" CB SER F 281 " ideal model delta sigma weight residual 115.79 110.49 5.30 1.19e+00 7.06e-01 1.98e+01 ... (remaining 17111 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 28.79: 7268 28.79 - 57.57: 308 57.57 - 86.35: 22 86.35 - 115.14: 3 115.14 - 143.92: 5 Dihedral angle restraints: 7606 sinusoidal: 3189 harmonic: 4417 Sorted by residual: dihedral pdb=" CB CYS F1328 " pdb=" SG CYS F1328 " pdb=" SG CYS F1345 " pdb=" CB CYS F1345 " ideal model delta sinusoidal sigma weight residual 93.00 134.43 -41.43 1 1.00e+01 1.00e-02 2.40e+01 dihedral pdb=" CB CYS F 658 " pdb=" SG CYS F 658 " pdb=" SG CYS F 669 " pdb=" CB CYS F 669 " ideal model delta sinusoidal sigma weight residual -86.00 -126.36 40.36 1 1.00e+01 1.00e-02 2.28e+01 dihedral pdb=" CA PHE F1657 " pdb=" C PHE F1657 " pdb=" N PHE F1658 " pdb=" CA PHE F1658 " ideal model delta harmonic sigma weight residual 180.00 157.87 22.13 0 5.00e+00 4.00e-02 1.96e+01 ... (remaining 7603 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.216: 1890 0.216 - 0.432: 3 0.432 - 0.649: 0 0.649 - 0.865: 0 0.865 - 1.081: 1 Chirality restraints: 1894 Sorted by residual: chirality pdb=" C1 NAG A 1 " pdb=" ND2 ASN F1849 " pdb=" C2 NAG A 1 " pdb=" O5 NAG A 1 " both_signs ideal model delta sigma weight residual False -2.40 -3.48 1.08 2.00e-01 2.50e+01 2.92e+01 chirality pdb=" C1 BGC C 3 " pdb=" O3 BGC C 2 " pdb=" C2 BGC C 3 " pdb=" O5 BGC C 3 " both_signs ideal model delta sigma weight residual False -2.40 -2.32 -0.08 2.00e-02 2.50e+03 1.58e+01 chirality pdb=" C1 NAG A 2 " pdb=" O4 NAG A 1 " pdb=" C2 NAG A 2 " pdb=" O5 NAG A 2 " both_signs ideal model delta sigma weight residual False -2.40 -2.33 -0.07 2.00e-02 2.50e+03 1.19e+01 ... (remaining 1891 not shown) Planarity restraints: 2123 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C2 NAG A 1 " 0.278 2.00e-02 2.50e+03 2.33e-01 6.77e+02 pdb=" C7 NAG A 1 " -0.074 2.00e-02 2.50e+03 pdb=" C8 NAG A 1 " 0.183 2.00e-02 2.50e+03 pdb=" N2 NAG A 1 " -0.393 2.00e-02 2.50e+03 pdb=" O7 NAG A 1 " 0.006 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C2 NAG A 2 " -0.136 2.00e-02 2.50e+03 1.12e-01 1.56e+02 pdb=" C7 NAG A 2 " 0.037 2.00e-02 2.50e+03 pdb=" C8 NAG A 2 " -0.101 2.00e-02 2.50e+03 pdb=" N2 NAG A 2 " 0.179 2.00e-02 2.50e+03 pdb=" O7 NAG A 2 " 0.021 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB ASN F1849 " 0.063 2.00e-02 2.50e+03 5.99e-02 4.49e+01 pdb=" CG ASN F1849 " -0.020 2.00e-02 2.50e+03 pdb=" OD1 ASN F1849 " -0.021 2.00e-02 2.50e+03 pdb=" ND2 ASN F1849 " -0.091 2.00e-02 2.50e+03 pdb=" C1 NAG A 1 " 0.070 2.00e-02 2.50e+03 ... (remaining 2120 not shown) Histogram of nonbonded interaction distances: 2.08 - 2.64: 159 2.64 - 3.21: 11238 3.21 - 3.77: 16802 3.77 - 4.34: 22815 4.34 - 4.90: 38412 Nonbonded interactions: 89426 Sorted by model distance: nonbonded pdb=" O4 BGC C 3 " pdb=" O5 BGC C 4 " model vdw 2.081 3.040 nonbonded pdb=" O3 NAG A 2 " pdb=" O7 NAG A 2 " model vdw 2.103 3.040 nonbonded pdb=" O2 BGC C 1 " pdb=" O2 BGC C 2 " model vdw 2.139 3.040 nonbonded pdb=" O MET F 458 " pdb=" OH TYR F 633 " model vdw 2.227 3.040 nonbonded pdb=" NH1 ARG F 344 " pdb=" O GLU F 346 " model vdw 2.231 3.120 ... (remaining 89421 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue 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: 2.820 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: 0.000 Extract box with map and model: 0.000 Check model and map are aligned: 0.000 Set scattering table: 0.000 Process input model: 29.250 Find NCS groups from input model: 0.130 Set up NCS constraints: 0.050 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.890 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 35.140 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8337 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 : 0.006 0.218 12682 Z= 0.419 Angle : 0.873 11.334 17116 Z= 0.504 Chirality : 0.054 1.081 1894 Planarity : 0.007 0.233 2122 Dihedral : 15.055 143.924 4742 Min Nonbonded Distance : 2.081 Molprobity Statistics. All-atom Clashscore : 7.73 Ramachandran Plot: Outliers : 0.20 % Allowed : 9.66 % Favored : 90.14 % Rotamer: Outliers : 0.32 % Allowed : 0.47 % Favored : 99.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -2.51 (0.22), residues: 1481 helix: -0.61 (0.18), residues: 842 sheet: -2.90 (0.69), residues: 56 loop : -3.15 (0.24), residues: 583 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP F 625 HIS 0.011 0.001 HIS F 384 PHE 0.025 0.002 PHE F 796 TYR 0.019 0.001 TYR F1093 ARG 0.005 0.000 ARG F 940 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2962 Ramachandran restraints generated. 1481 Oldfield, 0 Emsley, 1481 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2962 Ramachandran restraints generated. 1481 Oldfield, 0 Emsley, 1481 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 171 residues out of total 1320 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 167 time to evaluate : 1.431 Fit side-chains REVERT: F 241 MET cc_start: 0.8325 (ttm) cc_final: 0.8112 (ttp) REVERT: F 493 TRP cc_start: 0.8117 (m-10) cc_final: 0.7530 (m100) REVERT: F 1362 ILE cc_start: 0.9253 (tp) cc_final: 0.8915 (tp) REVERT: F 1498 ASP cc_start: 0.6231 (p0) cc_final: 0.5891 (t0) REVERT: F 1766 PHE cc_start: 0.7364 (m-80) cc_final: 0.7065 (m-80) outliers start: 4 outliers final: 2 residues processed: 169 average time/residue: 0.2795 time to fit residues: 66.3753 Evaluate side-chains 132 residues out of total 1320 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 130 time to evaluate : 1.370 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain F residue 669 CYS Chi-restraints excluded: chain F residue 670 LYS Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 150 random chunks: chunk 126 optimal weight: 0.0000 chunk 113 optimal weight: 10.0000 chunk 63 optimal weight: 0.9990 chunk 38 optimal weight: 0.8980 chunk 76 optimal weight: 4.9990 chunk 60 optimal weight: 8.9990 chunk 117 optimal weight: 0.8980 chunk 45 optimal weight: 0.0070 chunk 71 optimal weight: 0.9990 chunk 87 optimal weight: 0.7980 chunk 136 optimal weight: 0.0170 overall best weight: 0.3440 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: F 316 ASN F1107 ASN F1238 HIS ** F1647 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F1859 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8265 moved from start: 0.1140 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.052 12682 Z= 0.165 Angle : 0.619 6.608 17116 Z= 0.312 Chirality : 0.042 0.165 1894 Planarity : 0.004 0.041 2122 Dihedral : 9.091 117.100 1959 Min Nonbonded Distance : 2.565 Molprobity Statistics. All-atom Clashscore : 4.03 Ramachandran Plot: Outliers : 0.20 % Allowed : 8.91 % Favored : 90.88 % Rotamer: Outliers : 0.95 % Allowed : 8.27 % Favored : 90.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.84 (0.22), residues: 1481 helix: -0.00 (0.19), residues: 846 sheet: -2.01 (0.81), residues: 49 loop : -3.05 (0.24), residues: 586 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP F 625 HIS 0.007 0.001 HIS F1238 PHE 0.013 0.001 PHE F 467 TYR 0.021 0.001 TYR F 875 ARG 0.004 0.000 ARG F1064 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2962 Ramachandran restraints generated. 1481 Oldfield, 0 Emsley, 1481 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2962 Ramachandran restraints generated. 1481 Oldfield, 0 Emsley, 1481 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 167 residues out of total 1320 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 155 time to evaluate : 1.237 Fit side-chains REVERT: F 493 TRP cc_start: 0.8115 (m-10) cc_final: 0.7437 (m100) REVERT: F 978 MET cc_start: 0.7085 (mmt) cc_final: 0.6871 (mmt) REVERT: F 1362 ILE cc_start: 0.9130 (tp) cc_final: 0.8889 (tp) REVERT: F 1444 ARG cc_start: 0.8320 (ttp-110) cc_final: 0.8109 (ttp80) REVERT: F 1498 ASP cc_start: 0.6098 (p0) cc_final: 0.5889 (t0) REVERT: F 1610 ILE cc_start: 0.8510 (mm) cc_final: 0.8281 (mt) outliers start: 12 outliers final: 6 residues processed: 163 average time/residue: 0.2541 time to fit residues: 58.6253 Evaluate side-chains 143 residues out of total 1320 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 137 time to evaluate : 1.204 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain F residue 473 THR Chi-restraints excluded: chain F residue 846 THR Chi-restraints excluded: chain F residue 1084 ASP Chi-restraints excluded: chain F residue 1689 CYS Chi-restraints excluded: chain F residue 1749 VAL Chi-restraints excluded: chain F residue 1806 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 150 random chunks: chunk 75 optimal weight: 0.7980 chunk 42 optimal weight: 0.9990 chunk 113 optimal weight: 0.9980 chunk 92 optimal weight: 30.0000 chunk 37 optimal weight: 6.9990 chunk 136 optimal weight: 10.0000 chunk 147 optimal weight: 20.0000 chunk 121 optimal weight: 6.9990 chunk 135 optimal weight: 0.8980 chunk 46 optimal weight: 5.9990 chunk 109 optimal weight: 4.9990 overall best weight: 1.7384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: F1088 HIS F1107 ASN F1647 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8301 moved from start: 0.1320 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.059 12682 Z= 0.226 Angle : 0.604 9.863 17116 Z= 0.301 Chirality : 0.042 0.178 1894 Planarity : 0.004 0.035 2122 Dihedral : 8.175 107.935 1954 Min Nonbonded Distance : 2.543 Molprobity Statistics. All-atom Clashscore : 3.62 Ramachandran Plot: Outliers : 0.20 % Allowed : 9.32 % Favored : 90.48 % Rotamer: Outliers : 1.26 % Allowed : 11.51 % Favored : 87.23 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.60 (0.22), residues: 1481 helix: 0.25 (0.19), residues: 845 sheet: -1.88 (0.82), residues: 49 loop : -3.04 (0.24), residues: 587 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP F 625 HIS 0.005 0.001 HIS F 384 PHE 0.019 0.001 PHE F1766 TYR 0.015 0.001 TYR F1330 ARG 0.006 0.000 ARG F1154 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2962 Ramachandran restraints generated. 1481 Oldfield, 0 Emsley, 1481 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2962 Ramachandran restraints generated. 1481 Oldfield, 0 Emsley, 1481 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 157 residues out of total 1320 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 141 time to evaluate : 1.370 Fit side-chains REVERT: F 493 TRP cc_start: 0.8138 (m-10) cc_final: 0.7463 (m100) REVERT: F 1346 TYR cc_start: 0.8305 (OUTLIER) cc_final: 0.6771 (p90) REVERT: F 1362 ILE cc_start: 0.9142 (tp) cc_final: 0.8923 (tp) REVERT: F 1498 ASP cc_start: 0.6146 (p0) cc_final: 0.5862 (t0) REVERT: F 1610 ILE cc_start: 0.8531 (mm) cc_final: 0.8283 (mt) REVERT: F 1729 GLU cc_start: 0.7397 (pp20) cc_final: 0.6935 (tm-30) outliers start: 16 outliers final: 10 residues processed: 155 average time/residue: 0.2732 time to fit residues: 60.6201 Evaluate side-chains 144 residues out of total 1320 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 133 time to evaluate : 1.319 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain F residue 387 ILE Chi-restraints excluded: chain F residue 412 THR Chi-restraints excluded: chain F residue 438 THR Chi-restraints excluded: chain F residue 846 THR Chi-restraints excluded: chain F residue 1084 ASP Chi-restraints excluded: chain F residue 1346 TYR Chi-restraints excluded: chain F residue 1371 VAL Chi-restraints excluded: chain F residue 1596 VAL Chi-restraints excluded: chain F residue 1689 CYS Chi-restraints excluded: chain F residue 1691 THR Chi-restraints excluded: chain F residue 1773 TRP Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 150 random chunks: chunk 134 optimal weight: 0.9990 chunk 102 optimal weight: 0.9990 chunk 70 optimal weight: 10.0000 chunk 15 optimal weight: 0.6980 chunk 65 optimal weight: 4.9990 chunk 91 optimal weight: 5.9990 chunk 136 optimal weight: 0.9990 chunk 144 optimal weight: 0.9990 chunk 71 optimal weight: 0.8980 chunk 129 optimal weight: 7.9990 chunk 39 optimal weight: 4.9990 overall best weight: 0.9186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: F1107 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8270 moved from start: 0.1628 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.031 12682 Z= 0.154 Angle : 0.575 15.553 17116 Z= 0.281 Chirality : 0.041 0.174 1894 Planarity : 0.003 0.039 2122 Dihedral : 7.335 98.809 1954 Min Nonbonded Distance : 2.555 Molprobity Statistics. All-atom Clashscore : 3.66 Ramachandran Plot: Outliers : 0.20 % Allowed : 8.85 % Favored : 90.95 % Rotamer: Outliers : 2.05 % Allowed : 13.48 % Favored : 84.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.31 (0.23), residues: 1481 helix: 0.51 (0.19), residues: 843 sheet: -2.18 (0.71), residues: 59 loop : -2.91 (0.24), residues: 579 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP F 625 HIS 0.005 0.001 HIS F1647 PHE 0.012 0.001 PHE F 548 TYR 0.014 0.001 TYR F1330 ARG 0.009 0.000 ARG F1154 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2962 Ramachandran restraints generated. 1481 Oldfield, 0 Emsley, 1481 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2962 Ramachandran restraints generated. 1481 Oldfield, 0 Emsley, 1481 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 168 residues out of total 1320 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 142 time to evaluate : 1.365 Fit side-chains revert: symmetry clash REVERT: F 230 LEU cc_start: 0.8944 (OUTLIER) cc_final: 0.8585 (pp) REVERT: F 348 MET cc_start: 0.8895 (mtt) cc_final: 0.8672 (mtt) REVERT: F 493 TRP cc_start: 0.8115 (m-10) cc_final: 0.7438 (m100) REVERT: F 1346 TYR cc_start: 0.8342 (OUTLIER) cc_final: 0.6870 (p90) REVERT: F 1610 ILE cc_start: 0.8486 (mm) cc_final: 0.8230 (mt) REVERT: F 1729 GLU cc_start: 0.7439 (pp20) cc_final: 0.6987 (tm-30) outliers start: 26 outliers final: 16 residues processed: 161 average time/residue: 0.2628 time to fit residues: 60.4992 Evaluate side-chains 149 residues out of total 1320 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 131 time to evaluate : 1.305 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain F residue 230 LEU Chi-restraints excluded: chain F residue 430 VAL Chi-restraints excluded: chain F residue 432 ASP Chi-restraints excluded: chain F residue 526 GLN Chi-restraints excluded: chain F residue 541 ILE Chi-restraints excluded: chain F residue 795 PHE Chi-restraints excluded: chain F residue 846 THR Chi-restraints excluded: chain F residue 936 THR Chi-restraints excluded: chain F residue 1015 LEU Chi-restraints excluded: chain F residue 1084 ASP Chi-restraints excluded: chain F residue 1144 THR Chi-restraints excluded: chain F residue 1346 TYR Chi-restraints excluded: chain F residue 1371 VAL Chi-restraints excluded: chain F residue 1374 VAL Chi-restraints excluded: chain F residue 1596 VAL Chi-restraints excluded: chain F residue 1689 CYS Chi-restraints excluded: chain F residue 1773 TRP Chi-restraints excluded: chain F residue 1806 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 150 random chunks: chunk 120 optimal weight: 0.0040 chunk 82 optimal weight: 3.9990 chunk 2 optimal weight: 3.9990 chunk 107 optimal weight: 0.0270 chunk 59 optimal weight: 30.0000 chunk 123 optimal weight: 40.0000 chunk 100 optimal weight: 4.9990 chunk 0 optimal weight: 10.0000 chunk 74 optimal weight: 0.0060 chunk 130 optimal weight: 30.0000 chunk 36 optimal weight: 30.0000 overall best weight: 1.6070 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: F 779 GLN F1107 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8295 moved from start: 0.1725 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 12682 Z= 0.204 Angle : 0.574 10.381 17116 Z= 0.286 Chirality : 0.042 0.196 1894 Planarity : 0.003 0.036 2122 Dihedral : 7.049 99.570 1954 Min Nonbonded Distance : 2.534 Molprobity Statistics. All-atom Clashscore : 3.71 Ramachandran Plot: Outliers : 0.20 % Allowed : 8.78 % Favored : 91.02 % Rotamer: Outliers : 2.52 % Allowed : 14.89 % Favored : 82.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.16 (0.23), residues: 1481 helix: 0.59 (0.19), residues: 847 sheet: -1.34 (0.84), residues: 48 loop : -2.87 (0.24), residues: 586 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP F 625 HIS 0.004 0.001 HIS F1647 PHE 0.020 0.001 PHE F1766 TYR 0.015 0.001 TYR F1330 ARG 0.008 0.000 ARG F1154 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2962 Ramachandran restraints generated. 1481 Oldfield, 0 Emsley, 1481 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2962 Ramachandran restraints generated. 1481 Oldfield, 0 Emsley, 1481 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 167 residues out of total 1320 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 135 time to evaluate : 1.454 Fit side-chains revert: symmetry clash REVERT: F 230 LEU cc_start: 0.8965 (OUTLIER) cc_final: 0.8625 (pp) REVERT: F 348 MET cc_start: 0.8895 (mtt) cc_final: 0.8623 (mtt) REVERT: F 493 TRP cc_start: 0.8079 (m-10) cc_final: 0.7400 (m100) REVERT: F 1308 LEU cc_start: 0.9167 (tp) cc_final: 0.8952 (tt) REVERT: F 1346 TYR cc_start: 0.8379 (OUTLIER) cc_final: 0.6754 (p90) REVERT: F 1610 ILE cc_start: 0.8541 (mm) cc_final: 0.8257 (mt) REVERT: F 1729 GLU cc_start: 0.7454 (pp20) cc_final: 0.6993 (tm-30) outliers start: 32 outliers final: 19 residues processed: 158 average time/residue: 0.2697 time to fit residues: 60.7884 Evaluate side-chains 152 residues out of total 1320 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 131 time to evaluate : 1.317 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain F residue 230 LEU Chi-restraints excluded: chain F residue 387 ILE Chi-restraints excluded: chain F residue 412 THR Chi-restraints excluded: chain F residue 430 VAL Chi-restraints excluded: chain F residue 432 ASP Chi-restraints excluded: chain F residue 541 ILE Chi-restraints excluded: chain F residue 776 LEU Chi-restraints excluded: chain F residue 795 PHE Chi-restraints excluded: chain F residue 846 THR Chi-restraints excluded: chain F residue 936 THR Chi-restraints excluded: chain F residue 1084 ASP Chi-restraints excluded: chain F residue 1130 VAL Chi-restraints excluded: chain F residue 1144 THR Chi-restraints excluded: chain F residue 1346 TYR Chi-restraints excluded: chain F residue 1371 VAL Chi-restraints excluded: chain F residue 1374 VAL Chi-restraints excluded: chain F residue 1689 CYS Chi-restraints excluded: chain F residue 1691 THR Chi-restraints excluded: chain F residue 1749 VAL Chi-restraints excluded: chain F residue 1773 TRP Chi-restraints excluded: chain F residue 1806 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 150 random chunks: chunk 48 optimal weight: 0.9990 chunk 130 optimal weight: 40.0000 chunk 28 optimal weight: 4.9990 chunk 85 optimal weight: 3.9990 chunk 35 optimal weight: 7.9990 chunk 145 optimal weight: 9.9990 chunk 120 optimal weight: 4.9990 chunk 67 optimal weight: 9.9990 chunk 12 optimal weight: 0.9980 chunk 76 optimal weight: 1.9990 chunk 139 optimal weight: 0.8980 overall best weight: 1.7786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: F1107 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8303 moved from start: 0.1817 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 12682 Z= 0.213 Angle : 0.572 7.829 17116 Z= 0.286 Chirality : 0.042 0.177 1894 Planarity : 0.003 0.038 2122 Dihedral : 6.963 100.488 1954 Min Nonbonded Distance : 2.549 Molprobity Statistics. All-atom Clashscore : 3.71 Ramachandran Plot: Outliers : 0.20 % Allowed : 9.18 % Favored : 90.61 % Rotamer: Outliers : 2.44 % Allowed : 16.08 % Favored : 81.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.01 (0.23), residues: 1481 helix: 0.73 (0.19), residues: 848 sheet: -1.18 (0.85), residues: 48 loop : -2.84 (0.24), residues: 585 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP F 625 HIS 0.004 0.001 HIS F1647 PHE 0.029 0.001 PHE F 887 TYR 0.016 0.001 TYR F1292 ARG 0.008 0.000 ARG F1154 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2962 Ramachandran restraints generated. 1481 Oldfield, 0 Emsley, 1481 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2962 Ramachandran restraints generated. 1481 Oldfield, 0 Emsley, 1481 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 164 residues out of total 1320 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 133 time to evaluate : 1.335 Fit side-chains revert: symmetry clash REVERT: F 230 LEU cc_start: 0.8961 (OUTLIER) cc_final: 0.8627 (pp) REVERT: F 348 MET cc_start: 0.8877 (mtt) cc_final: 0.8616 (mtt) REVERT: F 493 TRP cc_start: 0.8123 (m-10) cc_final: 0.7420 (m100) REVERT: F 526 GLN cc_start: 0.8054 (tt0) cc_final: 0.7814 (mt0) REVERT: F 1308 LEU cc_start: 0.9150 (tp) cc_final: 0.8881 (tt) REVERT: F 1346 TYR cc_start: 0.8428 (OUTLIER) cc_final: 0.6831 (p90) REVERT: F 1362 ILE cc_start: 0.9045 (tp) cc_final: 0.8833 (tp) REVERT: F 1610 ILE cc_start: 0.8551 (mm) cc_final: 0.8248 (mt) REVERT: F 1729 GLU cc_start: 0.7402 (pp20) cc_final: 0.6899 (tm-30) outliers start: 31 outliers final: 21 residues processed: 156 average time/residue: 0.2752 time to fit residues: 61.0501 Evaluate side-chains 151 residues out of total 1320 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 128 time to evaluate : 1.366 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain F residue 230 LEU Chi-restraints excluded: chain F residue 387 ILE Chi-restraints excluded: chain F residue 412 THR Chi-restraints excluded: chain F residue 430 VAL Chi-restraints excluded: chain F residue 432 ASP Chi-restraints excluded: chain F residue 444 THR Chi-restraints excluded: chain F residue 541 ILE Chi-restraints excluded: chain F residue 776 LEU Chi-restraints excluded: chain F residue 795 PHE Chi-restraints excluded: chain F residue 846 THR Chi-restraints excluded: chain F residue 936 THR Chi-restraints excluded: chain F residue 1015 LEU Chi-restraints excluded: chain F residue 1084 ASP Chi-restraints excluded: chain F residue 1130 VAL Chi-restraints excluded: chain F residue 1144 THR Chi-restraints excluded: chain F residue 1148 VAL Chi-restraints excluded: chain F residue 1346 TYR Chi-restraints excluded: chain F residue 1371 VAL Chi-restraints excluded: chain F residue 1374 VAL Chi-restraints excluded: chain F residue 1689 CYS Chi-restraints excluded: chain F residue 1691 THR Chi-restraints excluded: chain F residue 1773 TRP Chi-restraints excluded: chain F residue 1806 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 150 random chunks: chunk 16 optimal weight: 5.9990 chunk 82 optimal weight: 0.9990 chunk 105 optimal weight: 3.9990 chunk 122 optimal weight: 6.9990 chunk 81 optimal weight: 4.9990 chunk 144 optimal weight: 2.9990 chunk 90 optimal weight: 0.8980 chunk 88 optimal weight: 0.0040 chunk 66 optimal weight: 0.0770 chunk 89 optimal weight: 8.9990 chunk 57 optimal weight: 0.4980 overall best weight: 0.4952 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: F1107 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8237 moved from start: 0.2148 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.027 12682 Z= 0.132 Angle : 0.538 12.841 17116 Z= 0.267 Chirality : 0.040 0.172 1894 Planarity : 0.003 0.036 2122 Dihedral : 6.380 96.351 1954 Min Nonbonded Distance : 2.561 Molprobity Statistics. All-atom Clashscore : 3.54 Ramachandran Plot: Outliers : 0.20 % Allowed : 7.97 % Favored : 91.83 % Rotamer: Outliers : 2.13 % Allowed : 17.10 % Favored : 80.77 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -0.76 (0.23), residues: 1481 helix: 0.93 (0.19), residues: 847 sheet: -0.34 (1.00), residues: 39 loop : -2.76 (0.24), residues: 595 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP F1468 HIS 0.004 0.001 HIS F1088 PHE 0.016 0.001 PHE F1766 TYR 0.014 0.001 TYR F1330 ARG 0.008 0.000 ARG F1154 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2962 Ramachandran restraints generated. 1481 Oldfield, 0 Emsley, 1481 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2962 Ramachandran restraints generated. 1481 Oldfield, 0 Emsley, 1481 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 176 residues out of total 1320 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 149 time to evaluate : 1.308 Fit side-chains revert: symmetry clash REVERT: F 230 LEU cc_start: 0.8863 (OUTLIER) cc_final: 0.8541 (pp) REVERT: F 493 TRP cc_start: 0.8111 (m-10) cc_final: 0.7411 (m100) REVERT: F 816 GLU cc_start: 0.7861 (tt0) cc_final: 0.7480 (tt0) REVERT: F 987 GLU cc_start: 0.8498 (tp30) cc_final: 0.8193 (tp30) REVERT: F 1019 GLU cc_start: 0.8642 (tp30) cc_final: 0.8429 (tp30) REVERT: F 1346 TYR cc_start: 0.8401 (OUTLIER) cc_final: 0.6837 (p90) REVERT: F 1365 VAL cc_start: 0.9185 (OUTLIER) cc_final: 0.8913 (t) REVERT: F 1610 ILE cc_start: 0.8465 (mm) cc_final: 0.8160 (mt) outliers start: 27 outliers final: 13 residues processed: 167 average time/residue: 0.2649 time to fit residues: 63.0096 Evaluate side-chains 149 residues out of total 1320 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 133 time to evaluate : 1.328 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain F residue 230 LEU Chi-restraints excluded: chain F residue 430 VAL Chi-restraints excluded: chain F residue 432 ASP Chi-restraints excluded: chain F residue 444 THR Chi-restraints excluded: chain F residue 776 LEU Chi-restraints excluded: chain F residue 795 PHE Chi-restraints excluded: chain F residue 846 THR Chi-restraints excluded: chain F residue 936 THR Chi-restraints excluded: chain F residue 1148 VAL Chi-restraints excluded: chain F residue 1341 VAL Chi-restraints excluded: chain F residue 1346 TYR Chi-restraints excluded: chain F residue 1365 VAL Chi-restraints excluded: chain F residue 1371 VAL Chi-restraints excluded: chain F residue 1374 VAL Chi-restraints excluded: chain F residue 1596 VAL Chi-restraints excluded: chain F residue 1750 ILE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 150 random chunks: chunk 86 optimal weight: 3.9990 chunk 43 optimal weight: 0.6980 chunk 28 optimal weight: 4.9990 chunk 91 optimal weight: 6.9990 chunk 98 optimal weight: 4.9990 chunk 71 optimal weight: 1.9990 chunk 13 optimal weight: 3.9990 chunk 113 optimal weight: 9.9990 chunk 131 optimal weight: 20.0000 chunk 138 optimal weight: 8.9990 chunk 126 optimal weight: 6.9990 overall best weight: 3.1388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: F 526 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8342 moved from start: 0.1975 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.050 12682 Z= 0.336 Angle : 0.641 11.483 17116 Z= 0.321 Chirality : 0.045 0.180 1894 Planarity : 0.004 0.041 2122 Dihedral : 7.039 106.529 1954 Min Nonbonded Distance : 2.524 Molprobity Statistics. All-atom Clashscore : 4.11 Ramachandran Plot: Outliers : 0.20 % Allowed : 9.25 % Favored : 90.55 % Rotamer: Outliers : 2.05 % Allowed : 18.05 % Favored : 79.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -0.83 (0.23), residues: 1481 helix: 0.85 (0.19), residues: 852 sheet: -1.08 (0.85), residues: 48 loop : -2.75 (0.25), residues: 581 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP F 625 HIS 0.005 0.001 HIS F 384 PHE 0.018 0.002 PHE F1766 TYR 0.027 0.002 TYR F1093 ARG 0.007 0.000 ARG F1154 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2962 Ramachandran restraints generated. 1481 Oldfield, 0 Emsley, 1481 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2962 Ramachandran restraints generated. 1481 Oldfield, 0 Emsley, 1481 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 159 residues out of total 1320 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 133 time to evaluate : 1.339 Fit side-chains revert: symmetry clash REVERT: F 230 LEU cc_start: 0.8978 (OUTLIER) cc_final: 0.8675 (pp) REVERT: F 348 MET cc_start: 0.8840 (mtt) cc_final: 0.8513 (mtt) REVERT: F 493 TRP cc_start: 0.8158 (m-10) cc_final: 0.7418 (m100) REVERT: F 957 PHE cc_start: 0.9238 (OUTLIER) cc_final: 0.8903 (t80) REVERT: F 1346 TYR cc_start: 0.8547 (OUTLIER) cc_final: 0.7032 (p90) REVERT: F 1365 VAL cc_start: 0.9283 (OUTLIER) cc_final: 0.9049 (t) REVERT: F 1610 ILE cc_start: 0.8551 (mm) cc_final: 0.8237 (mt) REVERT: F 1729 GLU cc_start: 0.7518 (pp20) cc_final: 0.6935 (tm-30) outliers start: 26 outliers final: 19 residues processed: 151 average time/residue: 0.2710 time to fit residues: 58.2440 Evaluate side-chains 153 residues out of total 1320 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 130 time to evaluate : 1.236 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain F residue 230 LEU Chi-restraints excluded: chain F residue 412 THR Chi-restraints excluded: chain F residue 430 VAL Chi-restraints excluded: chain F residue 432 ASP Chi-restraints excluded: chain F residue 776 LEU Chi-restraints excluded: chain F residue 845 LEU Chi-restraints excluded: chain F residue 846 THR Chi-restraints excluded: chain F residue 936 THR Chi-restraints excluded: chain F residue 957 PHE Chi-restraints excluded: chain F residue 1130 VAL Chi-restraints excluded: chain F residue 1148 VAL Chi-restraints excluded: chain F residue 1341 VAL Chi-restraints excluded: chain F residue 1346 TYR Chi-restraints excluded: chain F residue 1365 VAL Chi-restraints excluded: chain F residue 1371 VAL Chi-restraints excluded: chain F residue 1374 VAL Chi-restraints excluded: chain F residue 1478 SER Chi-restraints excluded: chain F residue 1596 VAL Chi-restraints excluded: chain F residue 1653 VAL Chi-restraints excluded: chain F residue 1689 CYS Chi-restraints excluded: chain F residue 1730 LEU Chi-restraints excluded: chain F residue 1806 LEU Chi-restraints excluded: chain F residue 1855 MET Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 150 random chunks: chunk 134 optimal weight: 0.8980 chunk 138 optimal weight: 5.9990 chunk 81 optimal weight: 0.7980 chunk 58 optimal weight: 9.9990 chunk 105 optimal weight: 0.9990 chunk 41 optimal weight: 3.9990 chunk 121 optimal weight: 0.6980 chunk 127 optimal weight: 10.0000 chunk 88 optimal weight: 3.9990 chunk 142 optimal weight: 4.9990 chunk 86 optimal weight: 0.9980 overall best weight: 0.8782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: F1107 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8274 moved from start: 0.2203 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.042 12682 Z= 0.157 Angle : 0.568 12.286 17116 Z= 0.282 Chirality : 0.041 0.171 1894 Planarity : 0.003 0.039 2122 Dihedral : 6.606 100.326 1954 Min Nonbonded Distance : 2.554 Molprobity Statistics. All-atom Clashscore : 3.83 Ramachandran Plot: Outliers : 0.20 % Allowed : 7.90 % Favored : 91.90 % Rotamer: Outliers : 1.89 % Allowed : 18.28 % Favored : 79.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -0.58 (0.23), residues: 1481 helix: 1.06 (0.19), residues: 852 sheet: -0.26 (1.00), residues: 39 loop : -2.70 (0.24), residues: 590 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP F 445 HIS 0.005 0.001 HIS F 384 PHE 0.016 0.001 PHE F 548 TYR 0.034 0.001 TYR F 875 ARG 0.010 0.000 ARG F1154 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2962 Ramachandran restraints generated. 1481 Oldfield, 0 Emsley, 1481 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2962 Ramachandran restraints generated. 1481 Oldfield, 0 Emsley, 1481 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 160 residues out of total 1320 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 136 time to evaluate : 1.381 Fit side-chains REVERT: F 230 LEU cc_start: 0.8899 (OUTLIER) cc_final: 0.8551 (pp) REVERT: F 493 TRP cc_start: 0.8137 (m-10) cc_final: 0.7406 (m100) REVERT: F 1019 GLU cc_start: 0.8682 (tp30) cc_final: 0.8473 (tp30) REVERT: F 1346 TYR cc_start: 0.8504 (OUTLIER) cc_final: 0.7000 (p90) REVERT: F 1610 ILE cc_start: 0.8496 (mm) cc_final: 0.8180 (mt) REVERT: F 1729 GLU cc_start: 0.7470 (pp20) cc_final: 0.6915 (tm-30) outliers start: 24 outliers final: 18 residues processed: 154 average time/residue: 0.2769 time to fit residues: 61.4521 Evaluate side-chains 152 residues out of total 1320 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 132 time to evaluate : 1.302 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain F residue 230 LEU Chi-restraints excluded: chain F residue 412 THR Chi-restraints excluded: chain F residue 430 VAL Chi-restraints excluded: chain F residue 432 ASP Chi-restraints excluded: chain F residue 446 LEU Chi-restraints excluded: chain F residue 776 LEU Chi-restraints excluded: chain F residue 795 PHE Chi-restraints excluded: chain F residue 845 LEU Chi-restraints excluded: chain F residue 846 THR Chi-restraints excluded: chain F residue 936 THR Chi-restraints excluded: chain F residue 1144 THR Chi-restraints excluded: chain F residue 1148 VAL Chi-restraints excluded: chain F residue 1341 VAL Chi-restraints excluded: chain F residue 1346 TYR Chi-restraints excluded: chain F residue 1371 VAL Chi-restraints excluded: chain F residue 1374 VAL Chi-restraints excluded: chain F residue 1691 THR Chi-restraints excluded: chain F residue 1806 LEU Chi-restraints excluded: chain F residue 1815 ILE Chi-restraints excluded: chain F residue 1855 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 150 random chunks: chunk 67 optimal weight: 9.9990 chunk 99 optimal weight: 1.9990 chunk 149 optimal weight: 3.9990 chunk 137 optimal weight: 8.9990 chunk 118 optimal weight: 0.8980 chunk 12 optimal weight: 2.9990 chunk 91 optimal weight: 2.9990 chunk 72 optimal weight: 6.9990 chunk 94 optimal weight: 0.9980 chunk 126 optimal weight: 4.9990 chunk 36 optimal weight: 30.0000 overall best weight: 1.9786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: F1107 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8306 moved from start: 0.2200 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.035 12682 Z= 0.232 Angle : 0.595 11.755 17116 Z= 0.296 Chirality : 0.042 0.175 1894 Planarity : 0.004 0.045 2122 Dihedral : 6.683 103.881 1954 Min Nonbonded Distance : 2.484 Molprobity Statistics. All-atom Clashscore : 4.39 Ramachandran Plot: Outliers : 0.20 % Allowed : 8.64 % Favored : 91.15 % Rotamer: Outliers : 1.81 % Allowed : 18.83 % Favored : 79.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -0.57 (0.23), residues: 1481 helix: 1.05 (0.19), residues: 858 sheet: -0.02 (1.01), residues: 38 loop : -2.72 (0.25), residues: 585 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.001 TRP F 445 HIS 0.006 0.001 HIS F 384 PHE 0.018 0.001 PHE F1766 TYR 0.027 0.001 TYR F 875 ARG 0.010 0.000 ARG F1154 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2962 Ramachandran restraints generated. 1481 Oldfield, 0 Emsley, 1481 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2962 Ramachandran restraints generated. 1481 Oldfield, 0 Emsley, 1481 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 155 residues out of total 1320 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 132 time to evaluate : 1.263 Fit side-chains REVERT: F 230 LEU cc_start: 0.8934 (OUTLIER) cc_final: 0.8586 (pp) REVERT: F 493 TRP cc_start: 0.8139 (m-10) cc_final: 0.7376 (m100) REVERT: F 957 PHE cc_start: 0.9184 (OUTLIER) cc_final: 0.8846 (t80) REVERT: F 1019 GLU cc_start: 0.8713 (tp30) cc_final: 0.8463 (tp30) REVERT: F 1308 LEU cc_start: 0.9125 (tp) cc_final: 0.8854 (tt) REVERT: F 1346 TYR cc_start: 0.8518 (OUTLIER) cc_final: 0.6959 (p90) REVERT: F 1610 ILE cc_start: 0.8523 (mm) cc_final: 0.8209 (mt) REVERT: F 1729 GLU cc_start: 0.7503 (pp20) cc_final: 0.6908 (tm-30) outliers start: 23 outliers final: 18 residues processed: 147 average time/residue: 0.2686 time to fit residues: 55.9769 Evaluate side-chains 153 residues out of total 1320 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 132 time to evaluate : 1.158 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain F residue 230 LEU Chi-restraints excluded: chain F residue 412 THR Chi-restraints excluded: chain F residue 430 VAL Chi-restraints excluded: chain F residue 432 ASP Chi-restraints excluded: chain F residue 776 LEU Chi-restraints excluded: chain F residue 845 LEU Chi-restraints excluded: chain F residue 846 THR Chi-restraints excluded: chain F residue 936 THR Chi-restraints excluded: chain F residue 957 PHE Chi-restraints excluded: chain F residue 1144 THR Chi-restraints excluded: chain F residue 1148 VAL Chi-restraints excluded: chain F residue 1341 VAL Chi-restraints excluded: chain F residue 1346 TYR Chi-restraints excluded: chain F residue 1371 VAL Chi-restraints excluded: chain F residue 1374 VAL Chi-restraints excluded: chain F residue 1691 THR Chi-restraints excluded: chain F residue 1750 ILE Chi-restraints excluded: chain F residue 1773 TRP Chi-restraints excluded: chain F residue 1806 LEU Chi-restraints excluded: chain F residue 1815 ILE Chi-restraints excluded: chain F residue 1855 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 150 random chunks: chunk 109 optimal weight: 0.8980 chunk 17 optimal weight: 6.9990 chunk 33 optimal weight: 0.9980 chunk 119 optimal weight: 1.9990 chunk 49 optimal weight: 0.6980 chunk 122 optimal weight: 0.8980 chunk 15 optimal weight: 0.9980 chunk 21 optimal weight: 2.9990 chunk 104 optimal weight: 0.8980 chunk 6 optimal weight: 4.9990 chunk 86 optimal weight: 2.9990 overall best weight: 0.8780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: F1107 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3831 r_free = 0.3831 target = 0.157584 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 72)----------------| | r_work = 0.3073 r_free = 0.3073 target = 0.099062 restraints weight = 17925.739| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 42)----------------| | r_work = 0.3110 r_free = 0.3110 target = 0.101663 restraints weight = 11969.275| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 44)----------------| | r_work = 0.3129 r_free = 0.3129 target = 0.103063 restraints weight = 9954.189| |-----------------------------------------------------------------------------| r_work (final): 0.3119 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8273 moved from start: 0.2371 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.036 12682 Z= 0.159 Angle : 0.565 12.084 17116 Z= 0.279 Chirality : 0.041 0.173 1894 Planarity : 0.003 0.039 2122 Dihedral : 6.355 100.256 1954 Min Nonbonded Distance : 2.555 Molprobity Statistics. All-atom Clashscore : 3.95 Ramachandran Plot: Outliers : 0.20 % Allowed : 7.90 % Favored : 91.90 % Rotamer: Outliers : 1.73 % Allowed : 18.91 % Favored : 79.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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 (0.23), residues: 1481 helix: 1.20 (0.19), residues: 856 sheet: 0.03 (1.00), residues: 38 loop : -2.71 (0.25), residues: 587 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.026 0.001 TRP F 445 HIS 0.006 0.001 HIS F 384 PHE 0.017 0.001 PHE F1766 TYR 0.027 0.001 TYR F1093 ARG 0.009 0.000 ARG F1154 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2304.25 seconds wall clock time: 42 minutes 2.28 seconds (2522.28 seconds total)