Starting phenix.real_space_refine on Sat Mar 23 22:53:22 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6zbj_11156/03_2024/6zbj_11156.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6zbj_11156/03_2024/6zbj_11156.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.3 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6zbj_11156/03_2024/6zbj_11156.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6zbj_11156/03_2024/6zbj_11156.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6zbj_11156/03_2024/6zbj_11156.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6zbj_11156/03_2024/6zbj_11156.pdb" } resolution = 3.3 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.002 sd= 0.047 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 S 36 5.16 5 C 12430 2.51 5 N 3176 2.21 5 O 3706 1.98 5 H 19864 0.53 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A PHE 585": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "B PHE 1172": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "C PHE 585": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "D PHE 1172": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Time to flip residues: 0.06s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib" Total number of atoms: 39212 Number of models: 1 Model: "" Number of chains: 4 Chain: "A" Number of atoms: 11322 Number of conformers: 1 Conformer: "" Number of residues, atoms: 666, 11322 Classifications: {'peptide': 666} Link IDs: {'PTRANS': 17, 'TRANS': 648} Chain breaks: 5 Chain: "B" Number of atoms: 8284 Number of conformers: 1 Conformer: "" Number of residues, atoms: 501, 8284 Classifications: {'peptide': 501} Link IDs: {'PTRANS': 12, 'TRANS': 488} Chain breaks: 2 Chain: "C" Number of atoms: 11322 Number of conformers: 1 Conformer: "" Number of residues, atoms: 666, 11322 Classifications: {'peptide': 666} Link IDs: {'PTRANS': 17, 'TRANS': 648} Chain breaks: 5 Chain: "D" Number of atoms: 8284 Number of conformers: 1 Conformer: "" Number of residues, atoms: 501, 8284 Classifications: {'peptide': 501} Link IDs: {'PTRANS': 12, 'TRANS': 488} Chain breaks: 2 Time building chain proxies: 15.53, per 1000 atoms: 0.40 Number of scatterers: 39212 At special positions: 0 Unit cell: (190.629, 154.011, 132.471, 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 36 16.00 O 3706 8.00 N 3176 7.00 C 12430 6.00 H 19864 1.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=2, symmetry=0 Simple disulfide: pdb=" SG CYS A 813 " - pdb=" SG CYS A 845 " distance=2.03 Simple disulfide: pdb=" SG CYS C 813 " - pdb=" SG CYS C 845 " distance=2.03 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: 28.99 Conformation dependent library (CDL) restraints added in 3.9 seconds 4596 Ramachandran restraints generated. 2298 Oldfield, 0 Emsley, 2298 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 4564 Finding SS restraints... Secondary structure from input PDB file: 96 helices and 0 sheets defined 83.9% alpha, 0.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 2.65 Creating SS restraints... Processing helix chain 'A' and resid 21 through 46 Processing helix chain 'A' and resid 144 through 158 removed outlier: 3.894A pdb=" N LYS A 158 " --> pdb=" O ILE A 154 " (cutoff:3.500A) Processing helix chain 'A' and resid 159 through 174 removed outlier: 3.612A pdb=" N ASP A 164 " --> pdb=" O PRO A 160 " (cutoff:3.500A) removed outlier: 5.154A pdb=" N LEU A 165 " --> pdb=" O GLU A 161 " (cutoff:3.500A) Processing helix chain 'A' and resid 175 through 185 removed outlier: 3.600A pdb=" N TYR A 181 " --> pdb=" O HIS A 177 " (cutoff:3.500A) removed outlier: 3.763A pdb=" N LEU A 182 " --> pdb=" O GLY A 178 " (cutoff:3.500A) Processing helix chain 'A' and resid 185 through 211 removed outlier: 3.867A pdb=" N ILE A 189 " --> pdb=" O GLY A 185 " (cutoff:3.500A) removed outlier: 3.971A pdb=" N GLU A 191 " --> pdb=" O GLU A 187 " (cutoff:3.500A) removed outlier: 3.667A pdb=" N TYR A 194 " --> pdb=" O ASN A 190 " (cutoff:3.500A) Processing helix chain 'A' and resid 212 through 215 Processing helix chain 'A' and resid 219 through 223 removed outlier: 3.845A pdb=" N LYS A 223 " --> pdb=" O PHE A 220 " (cutoff:3.500A) Processing helix chain 'A' and resid 225 through 238 removed outlier: 3.529A pdb=" N LEU A 229 " --> pdb=" O ARG A 225 " (cutoff:3.500A) removed outlier: 3.774A pdb=" N ASP A 230 " --> pdb=" O ALA A 226 " (cutoff:3.500A) removed outlier: 3.706A pdb=" N VAL A 231 " --> pdb=" O ASN A 227 " (cutoff:3.500A) Processing helix chain 'A' and resid 241 through 247 Processing helix chain 'A' and resid 249 through 281 removed outlier: 4.119A pdb=" N ASP A 255 " --> pdb=" O GLY A 251 " (cutoff:3.500A) removed outlier: 3.611A pdb=" N LYS A 258 " --> pdb=" O GLU A 254 " (cutoff:3.500A) Processing helix chain 'A' and resid 286 through 321 removed outlier: 3.941A pdb=" N SER A 315 " --> pdb=" O HIS A 311 " (cutoff:3.500A) removed outlier: 3.611A pdb=" N VAL A 316 " --> pdb=" O ASN A 312 " (cutoff:3.500A) Processing helix chain 'A' and resid 322 through 324 No H-bonds generated for 'chain 'A' and resid 322 through 324' Processing helix chain 'A' and resid 326 through 338 Processing helix chain 'A' and resid 356 through 375 removed outlier: 3.921A pdb=" N THR A 375 " --> pdb=" O GLU A 371 " (cutoff:3.500A) Processing helix chain 'A' and resid 380 through 384 Processing helix chain 'A' and resid 386 through 400 removed outlier: 4.165A pdb=" N ASN A 398 " --> pdb=" O LEU A 394 " (cutoff:3.500A) Processing helix chain 'A' and resid 430 through 443 removed outlier: 3.500A pdb=" N ASN A 442 " --> pdb=" O LEU A 438 " (cutoff:3.500A) removed outlier: 3.578A pdb=" N ASP A 443 " --> pdb=" O ALA A 439 " (cutoff:3.500A) Processing helix chain 'A' and resid 460 through 465 removed outlier: 3.532A pdb=" N ILE A 463 " --> pdb=" O ASN A 460 " (cutoff:3.500A) Processing helix chain 'A' and resid 466 through 494 removed outlier: 3.754A pdb=" N ILE A 472 " --> pdb=" O LYS A 468 " (cutoff:3.500A) removed outlier: 3.819A pdb=" N LYS A 492 " --> pdb=" O ILE A 488 " (cutoff:3.500A) Processing helix chain 'A' and resid 495 through 522 removed outlier: 3.833A pdb=" N LEU A 512 " --> pdb=" O ASP A 508 " (cutoff:3.500A) removed outlier: 3.986A pdb=" N LYS A 515 " --> pdb=" O GLU A 511 " (cutoff:3.500A) removed outlier: 4.198A pdb=" N GLU A 518 " --> pdb=" O GLU A 514 " (cutoff:3.500A) Processing helix chain 'A' and resid 526 through 582 removed outlier: 3.641A pdb=" N LYS A 532 " --> pdb=" O ASP A 528 " (cutoff:3.500A) removed outlier: 3.629A pdb=" N GLU A 543 " --> pdb=" O THR A 539 " (cutoff:3.500A) removed outlier: 3.859A pdb=" N LYS A 550 " --> pdb=" O ARG A 546 " (cutoff:3.500A) removed outlier: 5.841A pdb=" N SER A 553 " --> pdb=" O ASN A 549 " (cutoff:3.500A) removed outlier: 4.477A pdb=" N SER A 554 " --> pdb=" O LYS A 550 " (cutoff:3.500A) removed outlier: 3.917A pdb=" N SER A 557 " --> pdb=" O SER A 553 " (cutoff:3.500A) removed outlier: 3.922A pdb=" N ASN A 560 " --> pdb=" O ASN A 556 " (cutoff:3.500A) removed outlier: 4.042A pdb=" N ASP A 573 " --> pdb=" O SER A 569 " (cutoff:3.500A) removed outlier: 4.097A pdb=" N LEU A 576 " --> pdb=" O GLU A 572 " (cutoff:3.500A) removed outlier: 4.995A pdb=" N GLY A 579 " --> pdb=" O SER A 575 " (cutoff:3.500A) removed outlier: 5.048A pdb=" N ILE A 580 " --> pdb=" O LEU A 576 " (cutoff:3.500A) Processing helix chain 'A' and resid 584 through 615 removed outlier: 3.801A pdb=" N THR A 590 " --> pdb=" O ASN A 586 " (cutoff:3.500A) removed outlier: 3.681A pdb=" N LEU A 595 " --> pdb=" O LEU A 591 " (cutoff:3.500A) removed outlier: 4.141A pdb=" N ASP A 598 " --> pdb=" O GLY A 594 " (cutoff:3.500A) removed outlier: 4.067A pdb=" N LYS A 601 " --> pdb=" O ALA A 597 " (cutoff:3.500A) removed outlier: 4.327A pdb=" N GLU A 604 " --> pdb=" O LYS A 600 " (cutoff:3.500A) removed outlier: 3.711A pdb=" N LYS A 607 " --> pdb=" O THR A 603 " (cutoff:3.500A) Processing helix chain 'A' and resid 631 through 666 removed outlier: 3.901A pdb=" N GLN A 638 " --> pdb=" O ILE A 634 " (cutoff:3.500A) removed outlier: 4.134A pdb=" N LYS A 641 " --> pdb=" O LEU A 637 " (cutoff:3.500A) removed outlier: 3.826A pdb=" N LEU A 644 " --> pdb=" O GLN A 640 " (cutoff:3.500A) removed outlier: 3.827A pdb=" N GLU A 649 " --> pdb=" O ILE A 645 " (cutoff:3.500A) removed outlier: 3.584A pdb=" N ARG A 652 " --> pdb=" O ILE A 648 " (cutoff:3.500A) removed outlier: 3.695A pdb=" N LEU A 656 " --> pdb=" O ARG A 652 " (cutoff:3.500A) removed outlier: 4.182A pdb=" N LEU A 663 " --> pdb=" O LYS A 659 " (cutoff:3.500A) removed outlier: 3.915A pdb=" N LYS A 664 " --> pdb=" O ASN A 660 " (cutoff:3.500A) removed outlier: 3.509A pdb=" N ASP A 665 " --> pdb=" O ALA A 661 " (cutoff:3.500A) Processing helix chain 'A' and resid 682 through 693 removed outlier: 4.471A pdb=" N LYS A 688 " --> pdb=" O LEU A 684 " (cutoff:3.500A) removed outlier: 3.924A pdb=" N VAL A 691 " --> pdb=" O LEU A 687 " (cutoff:3.500A) Processing helix chain 'A' and resid 696 through 710 removed outlier: 3.782A pdb=" N LYS A 700 " --> pdb=" O GLU A 696 " (cutoff:3.500A) Processing helix chain 'A' and resid 796 through 822 removed outlier: 3.893A pdb=" N LYS A 809 " --> pdb=" O GLU A 805 " (cutoff:3.500A) removed outlier: 3.603A pdb=" N ILE A 812 " --> pdb=" O THR A 808 " (cutoff:3.500A) Processing helix chain 'A' and resid 827 through 832 Processing helix chain 'A' and resid 835 through 840 Processing helix chain 'A' and resid 841 through 845 removed outlier: 3.800A pdb=" N CYS A 845 " --> pdb=" O LEU A 842 " (cutoff:3.500A) Processing helix chain 'A' and resid 851 through 856 removed outlier: 3.796A pdb=" N ASN A 856 " --> pdb=" O PHE A 852 " (cutoff:3.500A) Processing helix chain 'A' and resid 857 through 891 removed outlier: 4.244A pdb=" N ASP A 871 " --> pdb=" O SER A 867 " (cutoff:3.500A) removed outlier: 4.077A pdb=" N HIS A 874 " --> pdb=" O ASN A 870 " (cutoff:3.500A) removed outlier: 4.422A pdb=" N PHE A 877 " --> pdb=" O GLN A 873 " (cutoff:3.500A) removed outlier: 3.689A pdb=" N TYR A 880 " --> pdb=" O PHE A 876 " (cutoff:3.500A) removed outlier: 3.606A pdb=" N LYS A 882 " --> pdb=" O GLU A 878 " (cutoff:3.500A) removed outlier: 4.241A pdb=" N ILE A 885 " --> pdb=" O GLN A 881 " (cutoff:3.500A) Processing helix chain 'A' and resid 894 through 906 Processing helix chain 'B' and resid 964 through 968 Processing helix chain 'B' and resid 973 through 980 removed outlier: 3.761A pdb=" N VAL B 977 " --> pdb=" O LEU B 973 " (cutoff:3.500A) Processing helix chain 'B' and resid 995 through 1008 Processing helix chain 'B' and resid 1011 through 1014 removed outlier: 3.625A pdb=" N PHE B1014 " --> pdb=" O ASP B1011 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 1011 through 1014' Processing helix chain 'B' and resid 1015 through 1022 Processing helix chain 'B' and resid 1025 through 1032 Processing helix chain 'B' and resid 1033 through 1100 removed outlier: 4.269A pdb=" N ASP B1056 " --> pdb=" O GLN B1052 " (cutoff:3.500A) removed outlier: 3.523A pdb=" N LEU B1057 " --> pdb=" O LEU B1053 " (cutoff:3.500A) removed outlier: 3.712A pdb=" N LYS B1083 " --> pdb=" O LYS B1079 " (cutoff:3.500A) removed outlier: 3.580A pdb=" N GLU B1090 " --> pdb=" O THR B1086 " (cutoff:3.500A) removed outlier: 3.524A pdb=" N ASN B1100 " --> pdb=" O LEU B1096 " (cutoff:3.500A) Processing helix chain 'B' and resid 1109 through 1146 removed outlier: 3.752A pdb=" N PHE B1113 " --> pdb=" O PHE B1109 " (cutoff:3.500A) removed outlier: 3.658A pdb=" N ALA B1119 " --> pdb=" O LYS B1115 " (cutoff:3.500A) removed outlier: 3.928A pdb=" N ALA B1122 " --> pdb=" O GLU B1118 " (cutoff:3.500A) removed outlier: 3.567A pdb=" N ASN B1130 " --> pdb=" O ASN B1126 " (cutoff:3.500A) removed outlier: 3.827A pdb=" N TYR B1144 " --> pdb=" O GLY B1140 " (cutoff:3.500A) Processing helix chain 'B' and resid 1156 through 1178 removed outlier: 3.888A pdb=" N THR B1162 " --> pdb=" O VAL B1158 " (cutoff:3.500A) removed outlier: 4.616A pdb=" N TYR B1166 " --> pdb=" O THR B1162 " (cutoff:3.500A) removed outlier: 4.172A pdb=" N ALA B1167 " --> pdb=" O GLU B1163 " (cutoff:3.500A) Processing helix chain 'B' and resid 1178 through 1211 removed outlier: 3.529A pdb=" N LEU B1182 " --> pdb=" O ILE B1178 " (cutoff:3.500A) removed outlier: 4.513A pdb=" N ASP B1184 " --> pdb=" O GLY B1180 " (cutoff:3.500A) removed outlier: 3.600A pdb=" N LYS B1192 " --> pdb=" O LEU B1188 " (cutoff:3.500A) Processing helix chain 'B' and resid 1220 through 1234 removed outlier: 3.517A pdb=" N ASN B1224 " --> pdb=" O SER B1220 " (cutoff:3.500A) removed outlier: 4.146A pdb=" N LYS B1226 " --> pdb=" O SER B1222 " (cutoff:3.500A) Processing helix chain 'B' and resid 1347 through 1392 removed outlier: 3.653A pdb=" N LEU B1351 " --> pdb=" O TYR B1347 " (cutoff:3.500A) removed outlier: 3.585A pdb=" N SER B1357 " --> pdb=" O GLY B1353 " (cutoff:3.500A) removed outlier: 3.971A pdb=" N PHE B1367 " --> pdb=" O GLU B1363 " (cutoff:3.500A) removed outlier: 3.979A pdb=" N ARG B1384 " --> pdb=" O ARG B1380 " (cutoff:3.500A) removed outlier: 3.868A pdb=" N VAL B1390 " --> pdb=" O TYR B1386 " (cutoff:3.500A) removed outlier: 3.704A pdb=" N LEU B1391 " --> pdb=" O PHE B1387 " (cutoff:3.500A) Processing helix chain 'B' and resid 1393 through 1399 removed outlier: 3.969A pdb=" N MET B1396 " --> pdb=" O SER B1393 " (cutoff:3.500A) removed outlier: 4.021A pdb=" N GLN B1397 " --> pdb=" O ASP B1394 " (cutoff:3.500A) Processing helix chain 'B' and resid 1410 through 1415 removed outlier: 4.117A pdb=" N LYS B1413 " --> pdb=" O ASP B1410 " (cutoff:3.500A) Processing helix chain 'B' and resid 1416 through 1473 removed outlier: 3.957A pdb=" N PHE B1440 " --> pdb=" O ASN B1436 " (cutoff:3.500A) removed outlier: 4.158A pdb=" N GLU B1443 " --> pdb=" O LYS B1439 " (cutoff:3.500A) removed outlier: 3.833A pdb=" N LYS B1450 " --> pdb=" O SER B1446 " (cutoff:3.500A) removed outlier: 3.830A pdb=" N LYS B1464 " --> pdb=" O GLU B1460 " (cutoff:3.500A) removed outlier: 3.651A pdb=" N VAL B1465 " --> pdb=" O SER B1461 " (cutoff:3.500A) removed outlier: 3.882A pdb=" N PHE B1473 " --> pdb=" O GLU B1469 " (cutoff:3.500A) Processing helix chain 'B' and resid 1496 through 1555 removed outlier: 3.627A pdb=" N LEU B1500 " --> pdb=" O PHE B1496 " (cutoff:3.500A) removed outlier: 3.802A pdb=" N ILE B1519 " --> pdb=" O ASP B1515 " (cutoff:3.500A) removed outlier: 3.666A pdb=" N VAL B1530 " --> pdb=" O ASN B1526 " (cutoff:3.500A) removed outlier: 3.574A pdb=" N GLU B1531 " --> pdb=" O ASP B1527 " (cutoff:3.500A) removed outlier: 3.824A pdb=" N LYS B1538 " --> pdb=" O GLU B1534 " (cutoff:3.500A) removed outlier: 3.840A pdb=" N PHE B1555 " --> pdb=" O LYS B1551 " (cutoff:3.500A) Processing helix chain 'C' and resid 21 through 46 Processing helix chain 'C' and resid 144 through 158 removed outlier: 3.894A pdb=" N LYS C 158 " --> pdb=" O ILE C 154 " (cutoff:3.500A) Processing helix chain 'C' and resid 159 through 174 removed outlier: 3.612A pdb=" N ASP C 164 " --> pdb=" O PRO C 160 " (cutoff:3.500A) removed outlier: 5.154A pdb=" N LEU C 165 " --> pdb=" O GLU C 161 " (cutoff:3.500A) Processing helix chain 'C' and resid 175 through 185 removed outlier: 3.600A pdb=" N TYR C 181 " --> pdb=" O HIS C 177 " (cutoff:3.500A) removed outlier: 3.763A pdb=" N LEU C 182 " --> pdb=" O GLY C 178 " (cutoff:3.500A) Processing helix chain 'C' and resid 185 through 211 removed outlier: 3.867A pdb=" N ILE C 189 " --> pdb=" O GLY C 185 " (cutoff:3.500A) removed outlier: 3.971A pdb=" N GLU C 191 " --> pdb=" O GLU C 187 " (cutoff:3.500A) removed outlier: 3.667A pdb=" N TYR C 194 " --> pdb=" O ASN C 190 " (cutoff:3.500A) Processing helix chain 'C' and resid 212 through 215 Processing helix chain 'C' and resid 219 through 223 removed outlier: 3.845A pdb=" N LYS C 223 " --> pdb=" O PHE C 220 " (cutoff:3.500A) Processing helix chain 'C' and resid 225 through 238 removed outlier: 3.529A pdb=" N LEU C 229 " --> pdb=" O ARG C 225 " (cutoff:3.500A) removed outlier: 3.774A pdb=" N ASP C 230 " --> pdb=" O ALA C 226 " (cutoff:3.500A) removed outlier: 3.706A pdb=" N VAL C 231 " --> pdb=" O ASN C 227 " (cutoff:3.500A) Processing helix chain 'C' and resid 241 through 247 Processing helix chain 'C' and resid 249 through 281 removed outlier: 4.119A pdb=" N ASP C 255 " --> pdb=" O GLY C 251 " (cutoff:3.500A) removed outlier: 3.611A pdb=" N LYS C 258 " --> pdb=" O GLU C 254 " (cutoff:3.500A) Processing helix chain 'C' and resid 286 through 321 removed outlier: 3.941A pdb=" N SER C 315 " --> pdb=" O HIS C 311 " (cutoff:3.500A) removed outlier: 3.611A pdb=" N VAL C 316 " --> pdb=" O ASN C 312 " (cutoff:3.500A) Processing helix chain 'C' and resid 322 through 324 No H-bonds generated for 'chain 'C' and resid 322 through 324' Processing helix chain 'C' and resid 326 through 338 Processing helix chain 'C' and resid 356 through 375 removed outlier: 3.921A pdb=" N THR C 375 " --> pdb=" O GLU C 371 " (cutoff:3.500A) Processing helix chain 'C' and resid 380 through 384 Processing helix chain 'C' and resid 386 through 400 removed outlier: 4.165A pdb=" N ASN C 398 " --> pdb=" O LEU C 394 " (cutoff:3.500A) Processing helix chain 'C' and resid 430 through 443 removed outlier: 3.500A pdb=" N ASN C 442 " --> pdb=" O LEU C 438 " (cutoff:3.500A) removed outlier: 3.578A pdb=" N ASP C 443 " --> pdb=" O ALA C 439 " (cutoff:3.500A) Processing helix chain 'C' and resid 460 through 465 removed outlier: 3.532A pdb=" N ILE C 463 " --> pdb=" O ASN C 460 " (cutoff:3.500A) Processing helix chain 'C' and resid 466 through 494 removed outlier: 3.754A pdb=" N ILE C 472 " --> pdb=" O LYS C 468 " (cutoff:3.500A) removed outlier: 3.819A pdb=" N LYS C 492 " --> pdb=" O ILE C 488 " (cutoff:3.500A) Processing helix chain 'C' and resid 495 through 522 removed outlier: 3.833A pdb=" N LEU C 512 " --> pdb=" O ASP C 508 " (cutoff:3.500A) removed outlier: 3.986A pdb=" N LYS C 515 " --> pdb=" O GLU C 511 " (cutoff:3.500A) removed outlier: 4.198A pdb=" N GLU C 518 " --> pdb=" O GLU C 514 " (cutoff:3.500A) Processing helix chain 'C' and resid 526 through 582 removed outlier: 3.641A pdb=" N LYS C 532 " --> pdb=" O ASP C 528 " (cutoff:3.500A) removed outlier: 3.629A pdb=" N GLU C 543 " --> pdb=" O THR C 539 " (cutoff:3.500A) removed outlier: 3.859A pdb=" N LYS C 550 " --> pdb=" O ARG C 546 " (cutoff:3.500A) removed outlier: 5.841A pdb=" N SER C 553 " --> pdb=" O ASN C 549 " (cutoff:3.500A) removed outlier: 4.477A pdb=" N SER C 554 " --> pdb=" O LYS C 550 " (cutoff:3.500A) removed outlier: 3.917A pdb=" N SER C 557 " --> pdb=" O SER C 553 " (cutoff:3.500A) removed outlier: 3.922A pdb=" N ASN C 560 " --> pdb=" O ASN C 556 " (cutoff:3.500A) removed outlier: 4.042A pdb=" N ASP C 573 " --> pdb=" O SER C 569 " (cutoff:3.500A) removed outlier: 4.097A pdb=" N LEU C 576 " --> pdb=" O GLU C 572 " (cutoff:3.500A) removed outlier: 4.995A pdb=" N GLY C 579 " --> pdb=" O SER C 575 " (cutoff:3.500A) removed outlier: 5.048A pdb=" N ILE C 580 " --> pdb=" O LEU C 576 " (cutoff:3.500A) Processing helix chain 'C' and resid 584 through 615 removed outlier: 3.801A pdb=" N THR C 590 " --> pdb=" O ASN C 586 " (cutoff:3.500A) removed outlier: 3.681A pdb=" N LEU C 595 " --> pdb=" O LEU C 591 " (cutoff:3.500A) removed outlier: 4.141A pdb=" N ASP C 598 " --> pdb=" O GLY C 594 " (cutoff:3.500A) removed outlier: 4.067A pdb=" N LYS C 601 " --> pdb=" O ALA C 597 " (cutoff:3.500A) removed outlier: 4.327A pdb=" N GLU C 604 " --> pdb=" O LYS C 600 " (cutoff:3.500A) removed outlier: 3.711A pdb=" N LYS C 607 " --> pdb=" O THR C 603 " (cutoff:3.500A) Processing helix chain 'C' and resid 631 through 666 removed outlier: 3.901A pdb=" N GLN C 638 " --> pdb=" O ILE C 634 " (cutoff:3.500A) removed outlier: 4.134A pdb=" N LYS C 641 " --> pdb=" O LEU C 637 " (cutoff:3.500A) removed outlier: 3.826A pdb=" N LEU C 644 " --> pdb=" O GLN C 640 " (cutoff:3.500A) removed outlier: 3.827A pdb=" N GLU C 649 " --> pdb=" O ILE C 645 " (cutoff:3.500A) removed outlier: 3.584A pdb=" N ARG C 652 " --> pdb=" O ILE C 648 " (cutoff:3.500A) removed outlier: 3.695A pdb=" N LEU C 656 " --> pdb=" O ARG C 652 " (cutoff:3.500A) removed outlier: 4.182A pdb=" N LEU C 663 " --> pdb=" O LYS C 659 " (cutoff:3.500A) removed outlier: 3.915A pdb=" N LYS C 664 " --> pdb=" O ASN C 660 " (cutoff:3.500A) removed outlier: 3.509A pdb=" N ASP C 665 " --> pdb=" O ALA C 661 " (cutoff:3.500A) Processing helix chain 'C' and resid 682 through 693 removed outlier: 4.471A pdb=" N LYS C 688 " --> pdb=" O LEU C 684 " (cutoff:3.500A) removed outlier: 3.924A pdb=" N VAL C 691 " --> pdb=" O LEU C 687 " (cutoff:3.500A) Processing helix chain 'C' and resid 696 through 710 removed outlier: 3.782A pdb=" N LYS C 700 " --> pdb=" O GLU C 696 " (cutoff:3.500A) Processing helix chain 'C' and resid 796 through 822 removed outlier: 3.893A pdb=" N LYS C 809 " --> pdb=" O GLU C 805 " (cutoff:3.500A) removed outlier: 3.603A pdb=" N ILE C 812 " --> pdb=" O THR C 808 " (cutoff:3.500A) Processing helix chain 'C' and resid 827 through 832 Processing helix chain 'C' and resid 835 through 840 Processing helix chain 'C' and resid 841 through 845 removed outlier: 3.800A pdb=" N CYS C 845 " --> pdb=" O LEU C 842 " (cutoff:3.500A) Processing helix chain 'C' and resid 851 through 856 removed outlier: 3.796A pdb=" N ASN C 856 " --> pdb=" O PHE C 852 " (cutoff:3.500A) Processing helix chain 'C' and resid 857 through 891 removed outlier: 4.244A pdb=" N ASP C 871 " --> pdb=" O SER C 867 " (cutoff:3.500A) removed outlier: 4.077A pdb=" N HIS C 874 " --> pdb=" O ASN C 870 " (cutoff:3.500A) removed outlier: 4.422A pdb=" N PHE C 877 " --> pdb=" O GLN C 873 " (cutoff:3.500A) removed outlier: 3.689A pdb=" N TYR C 880 " --> pdb=" O PHE C 876 " (cutoff:3.500A) removed outlier: 3.606A pdb=" N LYS C 882 " --> pdb=" O GLU C 878 " (cutoff:3.500A) removed outlier: 4.241A pdb=" N ILE C 885 " --> pdb=" O GLN C 881 " (cutoff:3.500A) Processing helix chain 'C' and resid 894 through 906 Processing helix chain 'D' and resid 964 through 968 Processing helix chain 'D' and resid 973 through 980 removed outlier: 3.761A pdb=" N VAL D 977 " --> pdb=" O LEU D 973 " (cutoff:3.500A) Processing helix chain 'D' and resid 995 through 1008 Processing helix chain 'D' and resid 1011 through 1014 removed outlier: 3.625A pdb=" N PHE D1014 " --> pdb=" O ASP D1011 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 1011 through 1014' Processing helix chain 'D' and resid 1015 through 1022 Processing helix chain 'D' and resid 1025 through 1032 Processing helix chain 'D' and resid 1033 through 1100 removed outlier: 4.269A pdb=" N ASP D1056 " --> pdb=" O GLN D1052 " (cutoff:3.500A) removed outlier: 3.523A pdb=" N LEU D1057 " --> pdb=" O LEU D1053 " (cutoff:3.500A) removed outlier: 3.712A pdb=" N LYS D1083 " --> pdb=" O LYS D1079 " (cutoff:3.500A) removed outlier: 3.580A pdb=" N GLU D1090 " --> pdb=" O THR D1086 " (cutoff:3.500A) removed outlier: 3.524A pdb=" N ASN D1100 " --> pdb=" O LEU D1096 " (cutoff:3.500A) Processing helix chain 'D' and resid 1109 through 1146 removed outlier: 3.752A pdb=" N PHE D1113 " --> pdb=" O PHE D1109 " (cutoff:3.500A) removed outlier: 3.658A pdb=" N ALA D1119 " --> pdb=" O LYS D1115 " (cutoff:3.500A) removed outlier: 3.928A pdb=" N ALA D1122 " --> pdb=" O GLU D1118 " (cutoff:3.500A) removed outlier: 3.567A pdb=" N ASN D1130 " --> pdb=" O ASN D1126 " (cutoff:3.500A) removed outlier: 3.827A pdb=" N TYR D1144 " --> pdb=" O GLY D1140 " (cutoff:3.500A) Processing helix chain 'D' and resid 1156 through 1178 removed outlier: 3.888A pdb=" N THR D1162 " --> pdb=" O VAL D1158 " (cutoff:3.500A) removed outlier: 4.616A pdb=" N TYR D1166 " --> pdb=" O THR D1162 " (cutoff:3.500A) removed outlier: 4.172A pdb=" N ALA D1167 " --> pdb=" O GLU D1163 " (cutoff:3.500A) Processing helix chain 'D' and resid 1178 through 1211 removed outlier: 3.529A pdb=" N LEU D1182 " --> pdb=" O ILE D1178 " (cutoff:3.500A) removed outlier: 4.513A pdb=" N ASP D1184 " --> pdb=" O GLY D1180 " (cutoff:3.500A) removed outlier: 3.600A pdb=" N LYS D1192 " --> pdb=" O LEU D1188 " (cutoff:3.500A) Processing helix chain 'D' and resid 1220 through 1234 removed outlier: 3.517A pdb=" N ASN D1224 " --> pdb=" O SER D1220 " (cutoff:3.500A) removed outlier: 4.146A pdb=" N LYS D1226 " --> pdb=" O SER D1222 " (cutoff:3.500A) Processing helix chain 'D' and resid 1347 through 1392 removed outlier: 3.653A pdb=" N LEU D1351 " --> pdb=" O TYR D1347 " (cutoff:3.500A) removed outlier: 3.585A pdb=" N SER D1357 " --> pdb=" O GLY D1353 " (cutoff:3.500A) removed outlier: 3.971A pdb=" N PHE D1367 " --> pdb=" O GLU D1363 " (cutoff:3.500A) removed outlier: 3.979A pdb=" N ARG D1384 " --> pdb=" O ARG D1380 " (cutoff:3.500A) removed outlier: 3.868A pdb=" N VAL D1390 " --> pdb=" O TYR D1386 " (cutoff:3.500A) removed outlier: 3.704A pdb=" N LEU D1391 " --> pdb=" O PHE D1387 " (cutoff:3.500A) Processing helix chain 'D' and resid 1393 through 1399 removed outlier: 3.969A pdb=" N MET D1396 " --> pdb=" O SER D1393 " (cutoff:3.500A) removed outlier: 4.021A pdb=" N GLN D1397 " --> pdb=" O ASP D1394 " (cutoff:3.500A) Processing helix chain 'D' and resid 1410 through 1415 removed outlier: 4.117A pdb=" N LYS D1413 " --> pdb=" O ASP D1410 " (cutoff:3.500A) Processing helix chain 'D' and resid 1416 through 1473 removed outlier: 3.957A pdb=" N PHE D1440 " --> pdb=" O ASN D1436 " (cutoff:3.500A) removed outlier: 4.158A pdb=" N GLU D1443 " --> pdb=" O LYS D1439 " (cutoff:3.500A) removed outlier: 3.833A pdb=" N LYS D1450 " --> pdb=" O SER D1446 " (cutoff:3.500A) removed outlier: 3.830A pdb=" N LYS D1464 " --> pdb=" O GLU D1460 " (cutoff:3.500A) removed outlier: 3.651A pdb=" N VAL D1465 " --> pdb=" O SER D1461 " (cutoff:3.500A) removed outlier: 3.882A pdb=" N PHE D1473 " --> pdb=" O GLU D1469 " (cutoff:3.500A) Processing helix chain 'D' and resid 1496 through 1555 removed outlier: 3.627A pdb=" N LEU D1500 " --> pdb=" O PHE D1496 " (cutoff:3.500A) removed outlier: 3.802A pdb=" N ILE D1519 " --> pdb=" O ASP D1515 " (cutoff:3.500A) removed outlier: 3.666A pdb=" N VAL D1530 " --> pdb=" O ASN D1526 " (cutoff:3.500A) removed outlier: 3.574A pdb=" N GLU D1531 " --> pdb=" O ASP D1527 " (cutoff:3.500A) removed outlier: 3.824A pdb=" N LYS D1538 " --> pdb=" O GLU D1534 " (cutoff:3.500A) removed outlier: 3.840A pdb=" N PHE D1555 " --> pdb=" O LYS D1551 " (cutoff:3.500A) 1382 hydrogen bonds defined for protein. 4068 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: 13.23 Time building geometry restraints manager: 30.18 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.84 - 1.03: 19856 1.03 - 1.23: 122 1.23 - 1.42: 7750 1.42 - 1.62: 11728 1.62 - 1.81: 60 Bond restraints: 39516 Sorted by residual: bond pdb=" N VAL C 29 " pdb=" CA VAL C 29 " ideal model delta sigma weight residual 1.459 1.499 -0.040 1.28e-02 6.10e+03 9.95e+00 bond pdb=" N VAL A 29 " pdb=" CA VAL A 29 " ideal model delta sigma weight residual 1.459 1.499 -0.040 1.28e-02 6.10e+03 9.95e+00 bond pdb=" N LYS A 223 " pdb=" CA LYS A 223 " ideal model delta sigma weight residual 1.454 1.494 -0.039 1.27e-02 6.20e+03 9.63e+00 bond pdb=" N LYS C 223 " pdb=" CA LYS C 223 " ideal model delta sigma weight residual 1.454 1.494 -0.039 1.27e-02 6.20e+03 9.63e+00 bond pdb=" N ILE A 224 " pdb=" CA ILE A 224 " ideal model delta sigma weight residual 1.459 1.497 -0.038 1.27e-02 6.20e+03 9.18e+00 ... (remaining 39511 not shown) Histogram of bond angle deviations from ideal: 97.99 - 104.84: 296 104.84 - 111.68: 45740 111.68 - 118.53: 10040 118.53 - 125.37: 15446 125.37 - 132.21: 468 Bond angle restraints: 71990 Sorted by residual: angle pdb=" CA LEU C 644 " pdb=" C LEU C 644 " pdb=" O LEU C 644 " ideal model delta sigma weight residual 120.42 114.29 6.13 1.06e+00 8.90e-01 3.35e+01 angle pdb=" CA LEU A 644 " pdb=" C LEU A 644 " pdb=" O LEU A 644 " ideal model delta sigma weight residual 120.42 114.29 6.13 1.06e+00 8.90e-01 3.35e+01 angle pdb=" N ILE C 321 " pdb=" CA ILE C 321 " pdb=" C ILE C 321 " ideal model delta sigma weight residual 113.00 105.76 7.24 1.30e+00 5.92e-01 3.10e+01 angle pdb=" N ILE A 321 " pdb=" CA ILE A 321 " pdb=" C ILE A 321 " ideal model delta sigma weight residual 113.00 105.76 7.24 1.30e+00 5.92e-01 3.10e+01 angle pdb=" C LYS D1470 " pdb=" CA LYS D1470 " pdb=" CB LYS D1470 " ideal model delta sigma weight residual 110.85 102.72 8.13 1.70e+00 3.46e-01 2.29e+01 ... (remaining 71985 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.93: 16798 17.93 - 35.86: 1111 35.86 - 53.80: 279 53.80 - 71.73: 54 71.73 - 89.66: 38 Dihedral angle restraints: 18280 sinusoidal: 10170 harmonic: 8110 Sorted by residual: dihedral pdb=" CB CYS C 813 " pdb=" SG CYS C 813 " pdb=" SG CYS C 845 " pdb=" CB CYS C 845 " ideal model delta sinusoidal sigma weight residual 93.00 144.91 -51.91 1 1.00e+01 1.00e-02 3.68e+01 dihedral pdb=" CB CYS A 813 " pdb=" SG CYS A 813 " pdb=" SG CYS A 845 " pdb=" CB CYS A 845 " ideal model delta sinusoidal sigma weight residual 93.00 144.91 -51.91 1 1.00e+01 1.00e-02 3.68e+01 dihedral pdb=" CA GLN C 855 " pdb=" C GLN C 855 " pdb=" N ASN C 856 " pdb=" CA ASN C 856 " ideal model delta harmonic sigma weight residual -180.00 -152.43 -27.57 0 5.00e+00 4.00e-02 3.04e+01 ... (remaining 18277 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.048: 1872 0.048 - 0.095: 726 0.095 - 0.143: 288 0.143 - 0.190: 60 0.190 - 0.238: 16 Chirality restraints: 2962 Sorted by residual: chirality pdb=" CB VAL A 669 " pdb=" CA VAL A 669 " pdb=" CG1 VAL A 669 " pdb=" CG2 VAL A 669 " both_signs ideal model delta sigma weight residual False -2.63 -2.39 -0.24 2.00e-01 2.50e+01 1.41e+00 chirality pdb=" CB VAL C 669 " pdb=" CA VAL C 669 " pdb=" CG1 VAL C 669 " pdb=" CG2 VAL C 669 " both_signs ideal model delta sigma weight residual False -2.63 -2.39 -0.24 2.00e-01 2.50e+01 1.41e+00 chirality pdb=" CA ILE A 380 " pdb=" N ILE A 380 " pdb=" C ILE A 380 " pdb=" CB ILE A 380 " both_signs ideal model delta sigma weight residual False 2.43 2.65 -0.22 2.00e-01 2.50e+01 1.20e+00 ... (remaining 2959 not shown) Planarity restraints: 5584 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TYR C 574 " -0.019 2.00e-02 2.50e+03 1.56e-02 7.28e+00 pdb=" CG TYR C 574 " -0.015 2.00e-02 2.50e+03 pdb=" CD1 TYR C 574 " 0.005 2.00e-02 2.50e+03 pdb=" CD2 TYR C 574 " 0.006 2.00e-02 2.50e+03 pdb=" CE1 TYR C 574 " -0.003 2.00e-02 2.50e+03 pdb=" CE2 TYR C 574 " -0.004 2.00e-02 2.50e+03 pdb=" CZ TYR C 574 " 0.011 2.00e-02 2.50e+03 pdb=" OH TYR C 574 " 0.009 2.00e-02 2.50e+03 pdb=" HD1 TYR C 574 " 0.024 2.00e-02 2.50e+03 pdb=" HD2 TYR C 574 " 0.026 2.00e-02 2.50e+03 pdb=" HE1 TYR C 574 " -0.018 2.00e-02 2.50e+03 pdb=" HE2 TYR C 574 " -0.021 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TYR A 574 " -0.019 2.00e-02 2.50e+03 1.56e-02 7.28e+00 pdb=" CG TYR A 574 " -0.015 2.00e-02 2.50e+03 pdb=" CD1 TYR A 574 " 0.005 2.00e-02 2.50e+03 pdb=" CD2 TYR A 574 " 0.006 2.00e-02 2.50e+03 pdb=" CE1 TYR A 574 " -0.003 2.00e-02 2.50e+03 pdb=" CE2 TYR A 574 " -0.004 2.00e-02 2.50e+03 pdb=" CZ TYR A 574 " 0.011 2.00e-02 2.50e+03 pdb=" OH TYR A 574 " 0.009 2.00e-02 2.50e+03 pdb=" HD1 TYR A 574 " 0.024 2.00e-02 2.50e+03 pdb=" HD2 TYR A 574 " 0.026 2.00e-02 2.50e+03 pdb=" HE1 TYR A 574 " -0.018 2.00e-02 2.50e+03 pdb=" HE2 TYR A 574 " -0.021 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA LEU A 394 " -0.013 2.00e-02 2.50e+03 2.65e-02 7.01e+00 pdb=" C LEU A 394 " 0.046 2.00e-02 2.50e+03 pdb=" O LEU A 394 " -0.017 2.00e-02 2.50e+03 pdb=" N ARG A 395 " -0.016 2.00e-02 2.50e+03 ... (remaining 5581 not shown) Histogram of nonbonded interaction distances: 1.61 - 2.21: 1953 2.21 - 2.81: 83961 2.81 - 3.40: 102754 3.40 - 4.00: 126453 4.00 - 4.60: 204542 Nonbonded interactions: 519663 Sorted by model distance: nonbonded pdb=" HG SER B1197 " pdb=" OH TYR B1455 " model vdw 1.612 1.850 nonbonded pdb=" HZ2 LYS B1192 " pdb=" OD1 ASN B1365 " model vdw 1.617 1.850 nonbonded pdb=" HZ2 LYS D1192 " pdb=" OD1 ASN D1365 " model vdw 1.619 1.850 nonbonded pdb=" OD1 ASN D 971 " pdb=" HZ2 LYS D 974 " model vdw 1.649 1.850 nonbonded pdb=" OD1 ASN B 971 " pdb=" HZ2 LYS B 974 " model vdw 1.658 1.850 ... (remaining 519658 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' selection = chain 'C' } ncs_group { reference = chain 'B' selection = chain 'D' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.970 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: 0.510 Extract box with map and model: 7.140 Check model and map are aligned: 0.530 Set scattering table: 0.340 Process input model: 109.620 Find NCS groups from input model: 1.300 Set up NCS constraints: 0.150 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:2.640 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 124.210 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8083 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.011 0.089 19652 Z= 0.685 Angle : 1.038 8.477 26372 Z= 0.658 Chirality : 0.059 0.238 2962 Planarity : 0.005 0.035 3326 Dihedral : 14.139 89.660 7726 Min Nonbonded Distance : 2.351 Molprobity Statistics. All-atom Clashscore : 1.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.70 % Favored : 99.30 % Rotamer: Outliers : 0.00 % Allowed : 1.89 % Favored : 98.11 % 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: -1.34 (0.16), residues: 2298 helix: -0.80 (0.11), residues: 1818 sheet: None (None), residues: 0 loop : -0.46 (0.27), residues: 480 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.015 0.002 HIS A 814 PHE 0.026 0.003 PHE C 657 TYR 0.026 0.003 TYR C 683 ARG 0.009 0.002 ARG A 225 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4596 Ramachandran restraints generated. 2298 Oldfield, 0 Emsley, 2298 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4596 Ramachandran restraints generated. 2298 Oldfield, 0 Emsley, 2298 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 212 residues out of total 2218 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 212 time to evaluate : 3.334 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 27 GLU cc_start: 0.8903 (tt0) cc_final: 0.8671 (tm-30) REVERT: A 449 ASP cc_start: 0.7823 (t0) cc_final: 0.7151 (t0) REVERT: A 451 MET cc_start: 0.8227 (tpt) cc_final: 0.7986 (tpp) REVERT: A 853 ASN cc_start: 0.8494 (t0) cc_final: 0.8269 (t0) REVERT: C 27 GLU cc_start: 0.8902 (tt0) cc_final: 0.8670 (tm-30) REVERT: C 449 ASP cc_start: 0.7823 (t0) cc_final: 0.7153 (t0) REVERT: C 451 MET cc_start: 0.8226 (tpt) cc_final: 0.7986 (tpp) REVERT: C 853 ASN cc_start: 0.8494 (t0) cc_final: 0.8271 (t0) outliers start: 0 outliers final: 0 residues processed: 212 average time/residue: 0.8963 time to fit residues: 270.0707 Evaluate side-chains 104 residues out of total 2218 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 104 time to evaluate : 3.539 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 232 random chunks: chunk 195 optimal weight: 0.7980 chunk 175 optimal weight: 0.7980 chunk 97 optimal weight: 0.8980 chunk 60 optimal weight: 0.7980 chunk 118 optimal weight: 0.8980 chunk 93 optimal weight: 10.0000 chunk 181 optimal weight: 0.9990 chunk 70 optimal weight: 2.9990 chunk 110 optimal weight: 1.9990 chunk 135 optimal weight: 7.9990 chunk 210 optimal weight: 0.8980 overall best weight: 0.8380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 611 ASN ** A 821 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 611 ASN ** C 821 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8089 moved from start: 0.1733 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.024 19652 Z= 0.179 Angle : 0.571 6.121 26372 Z= 0.314 Chirality : 0.034 0.149 2962 Planarity : 0.003 0.028 3326 Dihedral : 4.952 21.076 2478 Min Nonbonded Distance : 2.095 Molprobity Statistics. All-atom Clashscore : 3.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.78 % Favored : 99.22 % Rotamer: Outliers : 0.90 % Allowed : 4.96 % Favored : 94.14 % 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: 0.38 (0.17), residues: 2298 helix: 0.47 (0.12), residues: 1836 sheet: None (None), residues: 0 loop : -0.14 (0.27), residues: 462 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.006 0.001 HIS A 814 PHE 0.010 0.001 PHE C 521 TYR 0.017 0.001 TYR C 559 ARG 0.003 0.000 ARG B1173 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4596 Ramachandran restraints generated. 2298 Oldfield, 0 Emsley, 2298 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4596 Ramachandran restraints generated. 2298 Oldfield, 0 Emsley, 2298 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 124 residues out of total 2218 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 104 time to evaluate : 3.180 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 36 GLU cc_start: 0.8472 (tm-30) cc_final: 0.8097 (tm-30) REVERT: A 485 GLU cc_start: 0.7989 (mm-30) cc_final: 0.7677 (tm-30) REVERT: A 853 ASN cc_start: 0.8503 (t0) cc_final: 0.8251 (t0) REVERT: B 1080 MET cc_start: 0.8498 (tpp) cc_final: 0.8062 (mmp) REVERT: C 36 GLU cc_start: 0.8474 (tm-30) cc_final: 0.8099 (tm-30) REVERT: C 485 GLU cc_start: 0.7987 (mm-30) cc_final: 0.7674 (tm-30) REVERT: C 853 ASN cc_start: 0.8501 (t0) cc_final: 0.8251 (t0) REVERT: D 1080 MET cc_start: 0.8496 (tpp) cc_final: 0.8066 (mmp) outliers start: 20 outliers final: 16 residues processed: 118 average time/residue: 0.9368 time to fit residues: 157.5619 Evaluate side-chains 100 residues out of total 2218 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 84 time to evaluate : 3.083 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 207 LEU Chi-restraints excluded: chain A residue 241 LYS Chi-restraints excluded: chain A residue 298 TYR Chi-restraints excluded: chain A residue 496 LYS Chi-restraints excluded: chain A residue 507 LYS Chi-restraints excluded: chain A residue 573 ASP Chi-restraints excluded: chain B residue 1392 GLU Chi-restraints excluded: chain B residue 1552 ILE Chi-restraints excluded: chain C residue 207 LEU Chi-restraints excluded: chain C residue 241 LYS Chi-restraints excluded: chain C residue 298 TYR Chi-restraints excluded: chain C residue 496 LYS Chi-restraints excluded: chain C residue 507 LYS Chi-restraints excluded: chain C residue 573 ASP Chi-restraints excluded: chain D residue 1392 GLU Chi-restraints excluded: chain D residue 1552 ILE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 232 random chunks: chunk 117 optimal weight: 0.7980 chunk 65 optimal weight: 3.9990 chunk 175 optimal weight: 2.9990 chunk 143 optimal weight: 0.0770 chunk 58 optimal weight: 3.9990 chunk 211 optimal weight: 4.9990 chunk 228 optimal weight: 2.9990 chunk 187 optimal weight: 2.9990 chunk 209 optimal weight: 9.9990 chunk 71 optimal weight: 3.9990 chunk 169 optimal weight: 2.9990 overall best weight: 1.9744 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8138 moved from start: 0.2432 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 19652 Z= 0.246 Angle : 0.524 6.631 26372 Z= 0.291 Chirality : 0.034 0.154 2962 Planarity : 0.003 0.032 3326 Dihedral : 4.436 20.106 2478 Min Nonbonded Distance : 2.129 Molprobity Statistics. All-atom Clashscore : 2.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.78 % Favored : 99.22 % Rotamer: Outliers : 1.08 % Allowed : 5.86 % Favored : 93.06 % 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: 1.37 (0.17), residues: 2298 helix: 1.16 (0.12), residues: 1852 sheet: None (None), residues: 0 loop : 0.18 (0.28), residues: 446 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.005 0.001 HIS A 814 PHE 0.009 0.001 PHE C 521 TYR 0.014 0.001 TYR C 559 ARG 0.003 0.000 ARG A 577 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4596 Ramachandran restraints generated. 2298 Oldfield, 0 Emsley, 2298 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4596 Ramachandran restraints generated. 2298 Oldfield, 0 Emsley, 2298 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 114 residues out of total 2218 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 90 time to evaluate : 3.365 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 253 MET cc_start: 0.8554 (ttt) cc_final: 0.8272 (tpp) REVERT: A 485 GLU cc_start: 0.8089 (mm-30) cc_final: 0.7714 (tm-30) REVERT: A 853 ASN cc_start: 0.8596 (t0) cc_final: 0.8270 (t0) REVERT: B 1080 MET cc_start: 0.8469 (tpp) cc_final: 0.8160 (mmp) REVERT: C 253 MET cc_start: 0.8554 (ttt) cc_final: 0.8272 (tpp) REVERT: C 485 GLU cc_start: 0.8085 (mm-30) cc_final: 0.7710 (tm-30) REVERT: C 853 ASN cc_start: 0.8594 (t0) cc_final: 0.8269 (t0) REVERT: D 1080 MET cc_start: 0.8469 (tpp) cc_final: 0.8160 (mmp) outliers start: 24 outliers final: 18 residues processed: 108 average time/residue: 0.8518 time to fit residues: 135.2140 Evaluate side-chains 96 residues out of total 2218 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 78 time to evaluate : 2.936 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 207 LEU Chi-restraints excluded: chain A residue 298 TYR Chi-restraints excluded: chain A residue 332 LYS Chi-restraints excluded: chain A residue 496 LYS Chi-restraints excluded: chain A residue 507 LYS Chi-restraints excluded: chain A residue 573 ASP Chi-restraints excluded: chain B residue 1376 ILE Chi-restraints excluded: chain B residue 1392 GLU Chi-restraints excluded: chain B residue 1552 ILE Chi-restraints excluded: chain C residue 207 LEU Chi-restraints excluded: chain C residue 298 TYR Chi-restraints excluded: chain C residue 332 LYS Chi-restraints excluded: chain C residue 496 LYS Chi-restraints excluded: chain C residue 507 LYS Chi-restraints excluded: chain C residue 573 ASP Chi-restraints excluded: chain D residue 1376 ILE Chi-restraints excluded: chain D residue 1392 GLU Chi-restraints excluded: chain D residue 1552 ILE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 232 random chunks: chunk 208 optimal weight: 3.9990 chunk 158 optimal weight: 2.9990 chunk 109 optimal weight: 5.9990 chunk 23 optimal weight: 8.9990 chunk 100 optimal weight: 0.5980 chunk 141 optimal weight: 2.9990 chunk 211 optimal weight: 3.9990 chunk 224 optimal weight: 0.8980 chunk 110 optimal weight: 3.9990 chunk 200 optimal weight: 2.9990 chunk 60 optimal weight: 4.9990 overall best weight: 2.0986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 489 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8156 moved from start: 0.3012 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.051 19652 Z= 0.213 Angle : 0.487 4.727 26372 Z= 0.270 Chirality : 0.033 0.156 2962 Planarity : 0.002 0.032 3326 Dihedral : 4.065 21.011 2478 Min Nonbonded Distance : 2.102 Molprobity Statistics. All-atom Clashscore : 3.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.87 % Favored : 99.13 % Rotamer: Outliers : 0.63 % Allowed : 7.21 % Favored : 92.16 % 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: 2.10 (0.18), residues: 2298 helix: 1.69 (0.12), residues: 1850 sheet: None (None), residues: 0 loop : 0.32 (0.28), residues: 448 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.004 0.001 HIS C 814 PHE 0.008 0.001 PHE A 179 TYR 0.015 0.001 TYR A 181 ARG 0.003 0.000 ARG C 577 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4596 Ramachandran restraints generated. 2298 Oldfield, 0 Emsley, 2298 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4596 Ramachandran restraints generated. 2298 Oldfield, 0 Emsley, 2298 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 102 residues out of total 2218 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 88 time to evaluate : 3.244 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 853 ASN cc_start: 0.8512 (t0) cc_final: 0.8183 (t0) REVERT: C 853 ASN cc_start: 0.8512 (t0) cc_final: 0.8184 (t0) outliers start: 14 outliers final: 10 residues processed: 94 average time/residue: 0.8081 time to fit residues: 115.2094 Evaluate side-chains 88 residues out of total 2218 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 78 time to evaluate : 3.229 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 207 LEU Chi-restraints excluded: chain A residue 298 TYR Chi-restraints excluded: chain B residue 1376 ILE Chi-restraints excluded: chain B residue 1392 GLU Chi-restraints excluded: chain B residue 1552 ILE Chi-restraints excluded: chain C residue 207 LEU Chi-restraints excluded: chain C residue 298 TYR Chi-restraints excluded: chain D residue 1376 ILE Chi-restraints excluded: chain D residue 1392 GLU Chi-restraints excluded: chain D residue 1552 ILE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 232 random chunks: chunk 186 optimal weight: 0.9980 chunk 127 optimal weight: 6.9990 chunk 3 optimal weight: 7.9990 chunk 166 optimal weight: 2.9990 chunk 92 optimal weight: 2.9990 chunk 191 optimal weight: 3.9990 chunk 155 optimal weight: 7.9990 chunk 0 optimal weight: 6.9990 chunk 114 optimal weight: 0.9990 chunk 201 optimal weight: 2.9990 chunk 56 optimal weight: 5.9990 overall best weight: 2.1988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 489 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8172 moved from start: 0.3246 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.034 19652 Z= 0.237 Angle : 0.482 5.170 26372 Z= 0.266 Chirality : 0.033 0.154 2962 Planarity : 0.002 0.032 3326 Dihedral : 3.917 18.498 2478 Min Nonbonded Distance : 2.091 Molprobity Statistics. All-atom Clashscore : 3.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.96 % Favored : 99.04 % Rotamer: Outliers : 0.90 % Allowed : 7.12 % Favored : 91.97 % 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: 2.41 (0.18), residues: 2298 helix: 1.94 (0.12), residues: 1844 sheet: None (None), residues: 0 loop : 0.32 (0.28), residues: 454 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.003 0.001 HIS C 814 PHE 0.008 0.001 PHE A 521 TYR 0.010 0.001 TYR D1343 ARG 0.003 0.000 ARG A 577 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4596 Ramachandran restraints generated. 2298 Oldfield, 0 Emsley, 2298 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4596 Ramachandran restraints generated. 2298 Oldfield, 0 Emsley, 2298 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 96 residues out of total 2218 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 76 time to evaluate : 3.203 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 853 ASN cc_start: 0.8436 (t0) cc_final: 0.8031 (t0) REVERT: C 853 ASN cc_start: 0.8434 (t0) cc_final: 0.8032 (t0) outliers start: 20 outliers final: 14 residues processed: 88 average time/residue: 0.7893 time to fit residues: 104.6147 Evaluate side-chains 90 residues out of total 2218 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 76 time to evaluate : 3.403 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 207 LEU Chi-restraints excluded: chain A residue 298 TYR Chi-restraints excluded: chain A residue 332 LYS Chi-restraints excluded: chain B residue 1075 LEU Chi-restraints excluded: chain B residue 1376 ILE Chi-restraints excluded: chain B residue 1392 GLU Chi-restraints excluded: chain B residue 1552 ILE Chi-restraints excluded: chain C residue 207 LEU Chi-restraints excluded: chain C residue 298 TYR Chi-restraints excluded: chain C residue 332 LYS Chi-restraints excluded: chain D residue 1075 LEU Chi-restraints excluded: chain D residue 1376 ILE Chi-restraints excluded: chain D residue 1392 GLU Chi-restraints excluded: chain D residue 1552 ILE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 232 random chunks: chunk 75 optimal weight: 2.9990 chunk 201 optimal weight: 2.9990 chunk 44 optimal weight: 1.9990 chunk 131 optimal weight: 10.0000 chunk 55 optimal weight: 8.9990 chunk 224 optimal weight: 0.8980 chunk 186 optimal weight: 0.4980 chunk 103 optimal weight: 0.9990 chunk 18 optimal weight: 5.9990 chunk 74 optimal weight: 1.9990 chunk 117 optimal weight: 1.9990 overall best weight: 1.2786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 853 ASN ** C 489 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 853 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8152 moved from start: 0.3426 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.030 19652 Z= 0.151 Angle : 0.442 4.566 26372 Z= 0.241 Chirality : 0.032 0.150 2962 Planarity : 0.002 0.032 3326 Dihedral : 3.764 17.074 2478 Min Nonbonded Distance : 2.082 Molprobity Statistics. All-atom Clashscore : 3.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.70 % Favored : 99.30 % Rotamer: Outliers : 0.63 % Allowed : 7.39 % Favored : 91.97 % 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: 2.87 (0.17), residues: 2298 helix: 2.24 (0.12), residues: 1854 sheet: None (None), residues: 0 loop : 0.54 (0.28), residues: 444 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.003 0.001 HIS A 587 PHE 0.007 0.001 PHE A 521 TYR 0.010 0.001 TYR C 559 ARG 0.001 0.000 ARG C 577 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4596 Ramachandran restraints generated. 2298 Oldfield, 0 Emsley, 2298 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4596 Ramachandran restraints generated. 2298 Oldfield, 0 Emsley, 2298 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 100 residues out of total 2218 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 86 time to evaluate : 3.541 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 851 LEU cc_start: 0.8845 (mt) cc_final: 0.8461 (mt) REVERT: A 853 ASN cc_start: 0.8401 (t160) cc_final: 0.8101 (t0) REVERT: C 851 LEU cc_start: 0.8846 (mt) cc_final: 0.8460 (mt) REVERT: C 853 ASN cc_start: 0.8402 (t160) cc_final: 0.8100 (t0) outliers start: 14 outliers final: 14 residues processed: 94 average time/residue: 0.8520 time to fit residues: 119.7740 Evaluate side-chains 90 residues out of total 2218 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 76 time to evaluate : 3.002 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 207 LEU Chi-restraints excluded: chain A residue 298 TYR Chi-restraints excluded: chain A residue 332 LYS Chi-restraints excluded: chain B residue 1075 LEU Chi-restraints excluded: chain B residue 1376 ILE Chi-restraints excluded: chain B residue 1392 GLU Chi-restraints excluded: chain B residue 1552 ILE Chi-restraints excluded: chain C residue 207 LEU Chi-restraints excluded: chain C residue 298 TYR Chi-restraints excluded: chain C residue 332 LYS Chi-restraints excluded: chain D residue 1075 LEU Chi-restraints excluded: chain D residue 1376 ILE Chi-restraints excluded: chain D residue 1392 GLU Chi-restraints excluded: chain D residue 1552 ILE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 232 random chunks: chunk 216 optimal weight: 1.9990 chunk 25 optimal weight: 7.9990 chunk 127 optimal weight: 3.9990 chunk 163 optimal weight: 6.9990 chunk 188 optimal weight: 0.6980 chunk 125 optimal weight: 0.3980 chunk 223 optimal weight: 0.5980 chunk 139 optimal weight: 5.9990 chunk 136 optimal weight: 10.0000 chunk 103 optimal weight: 0.9990 chunk 138 optimal weight: 20.0000 overall best weight: 0.9384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 489 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8146 moved from start: 0.3583 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.034 19652 Z= 0.142 Angle : 0.434 6.706 26372 Z= 0.236 Chirality : 0.031 0.149 2962 Planarity : 0.002 0.033 3326 Dihedral : 3.631 15.709 2478 Min Nonbonded Distance : 2.066 Molprobity Statistics. All-atom Clashscore : 3.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.78 % Favored : 99.22 % Rotamer: Outliers : 0.72 % Allowed : 7.62 % Favored : 91.66 % 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: 3.23 (0.18), residues: 2298 helix: 2.48 (0.12), residues: 1856 sheet: None (None), residues: 0 loop : 0.67 (0.29), residues: 442 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.003 0.001 HIS A 889 PHE 0.006 0.001 PHE A 521 TYR 0.011 0.001 TYR D1343 ARG 0.001 0.000 ARG A 148 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4596 Ramachandran restraints generated. 2298 Oldfield, 0 Emsley, 2298 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4596 Ramachandran restraints generated. 2298 Oldfield, 0 Emsley, 2298 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 96 residues out of total 2218 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 80 time to evaluate : 3.248 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 253 MET cc_start: 0.8606 (ttt) cc_final: 0.8282 (tpp) REVERT: A 851 LEU cc_start: 0.8832 (mt) cc_final: 0.8473 (mt) REVERT: A 853 ASN cc_start: 0.8309 (t160) cc_final: 0.8027 (t0) REVERT: A 884 MET cc_start: 0.8714 (mmm) cc_final: 0.8404 (mmm) REVERT: C 253 MET cc_start: 0.8604 (ttt) cc_final: 0.8280 (tpp) REVERT: C 851 LEU cc_start: 0.8834 (mt) cc_final: 0.8474 (mt) REVERT: C 853 ASN cc_start: 0.8311 (t160) cc_final: 0.8026 (t0) REVERT: C 884 MET cc_start: 0.8715 (mmm) cc_final: 0.8406 (mmm) outliers start: 16 outliers final: 16 residues processed: 90 average time/residue: 0.7989 time to fit residues: 108.4122 Evaluate side-chains 92 residues out of total 2218 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 76 time to evaluate : 3.285 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 207 LEU Chi-restraints excluded: chain A residue 298 TYR Chi-restraints excluded: chain A residue 332 LYS Chi-restraints excluded: chain A residue 481 ILE Chi-restraints excluded: chain B residue 1075 LEU Chi-restraints excluded: chain B residue 1376 ILE Chi-restraints excluded: chain B residue 1392 GLU Chi-restraints excluded: chain B residue 1552 ILE Chi-restraints excluded: chain C residue 207 LEU Chi-restraints excluded: chain C residue 298 TYR Chi-restraints excluded: chain C residue 332 LYS Chi-restraints excluded: chain C residue 481 ILE Chi-restraints excluded: chain D residue 1075 LEU Chi-restraints excluded: chain D residue 1376 ILE Chi-restraints excluded: chain D residue 1392 GLU Chi-restraints excluded: chain D residue 1552 ILE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 232 random chunks: chunk 89 optimal weight: 3.9990 chunk 133 optimal weight: 9.9990 chunk 67 optimal weight: 4.9990 chunk 43 optimal weight: 1.9990 chunk 142 optimal weight: 5.9990 chunk 152 optimal weight: 6.9990 chunk 110 optimal weight: 4.9990 chunk 20 optimal weight: 9.9990 chunk 175 optimal weight: 0.0770 chunk 203 optimal weight: 3.9990 chunk 214 optimal weight: 2.9990 overall best weight: 2.6146 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 489 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8191 moved from start: 0.3787 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.032 19652 Z= 0.276 Angle : 0.490 6.146 26372 Z= 0.271 Chirality : 0.033 0.155 2962 Planarity : 0.002 0.032 3326 Dihedral : 3.594 17.305 2478 Min Nonbonded Distance : 2.060 Molprobity Statistics. All-atom Clashscore : 4.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.04 % Favored : 98.96 % Rotamer: Outliers : 0.81 % Allowed : 7.84 % Favored : 91.34 % 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: 3.26 (0.17), residues: 2298 helix: 2.53 (0.12), residues: 1862 sheet: None (None), residues: 0 loop : 0.54 (0.28), residues: 436 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.003 0.001 HIS A 814 PHE 0.009 0.001 PHE A 877 TYR 0.009 0.001 TYR C 865 ARG 0.005 0.001 ARG C 577 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4596 Ramachandran restraints generated. 2298 Oldfield, 0 Emsley, 2298 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4596 Ramachandran restraints generated. 2298 Oldfield, 0 Emsley, 2298 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 90 residues out of total 2218 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 72 time to evaluate : 3.271 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 851 LEU cc_start: 0.8904 (mt) cc_final: 0.8534 (mt) REVERT: A 853 ASN cc_start: 0.8261 (t160) cc_final: 0.7975 (t0) REVERT: C 851 LEU cc_start: 0.8903 (mt) cc_final: 0.8533 (mt) REVERT: C 853 ASN cc_start: 0.8261 (t160) cc_final: 0.7977 (t0) outliers start: 18 outliers final: 14 residues processed: 84 average time/residue: 0.8405 time to fit residues: 105.2067 Evaluate side-chains 86 residues out of total 2218 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 72 time to evaluate : 3.502 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 207 LEU Chi-restraints excluded: chain A residue 298 TYR Chi-restraints excluded: chain A residue 332 LYS Chi-restraints excluded: chain B residue 1075 LEU Chi-restraints excluded: chain B residue 1376 ILE Chi-restraints excluded: chain B residue 1392 GLU Chi-restraints excluded: chain B residue 1552 ILE Chi-restraints excluded: chain C residue 207 LEU Chi-restraints excluded: chain C residue 298 TYR Chi-restraints excluded: chain C residue 332 LYS Chi-restraints excluded: chain D residue 1075 LEU Chi-restraints excluded: chain D residue 1376 ILE Chi-restraints excluded: chain D residue 1392 GLU Chi-restraints excluded: chain D residue 1552 ILE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 232 random chunks: chunk 195 optimal weight: 0.9990 chunk 208 optimal weight: 0.4980 chunk 214 optimal weight: 3.9990 chunk 125 optimal weight: 3.9990 chunk 90 optimal weight: 0.8980 chunk 163 optimal weight: 2.9990 chunk 63 optimal weight: 1.9990 chunk 188 optimal weight: 0.7980 chunk 197 optimal weight: 3.9990 chunk 207 optimal weight: 1.9990 chunk 136 optimal weight: 10.0000 overall best weight: 1.0384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8161 moved from start: 0.3862 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.031 19652 Z= 0.139 Angle : 0.433 6.205 26372 Z= 0.235 Chirality : 0.031 0.151 2962 Planarity : 0.002 0.029 3326 Dihedral : 3.566 15.883 2478 Min Nonbonded Distance : 2.066 Molprobity Statistics. All-atom Clashscore : 3.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.61 % Favored : 99.39 % Rotamer: Outliers : 0.63 % Allowed : 7.94 % Favored : 91.43 % 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: 3.48 (0.18), residues: 2298 helix: 2.68 (0.12), residues: 1854 sheet: None (None), residues: 0 loop : 0.67 (0.29), residues: 444 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.003 0.001 HIS C 889 PHE 0.006 0.001 PHE C 521 TYR 0.008 0.001 TYR C 862 ARG 0.001 0.000 ARG A 148 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4596 Ramachandran restraints generated. 2298 Oldfield, 0 Emsley, 2298 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4596 Ramachandran restraints generated. 2298 Oldfield, 0 Emsley, 2298 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 90 residues out of total 2218 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 76 time to evaluate : 3.241 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 253 MET cc_start: 0.8615 (ttt) cc_final: 0.8261 (tpp) REVERT: A 851 LEU cc_start: 0.8872 (mt) cc_final: 0.8503 (mt) REVERT: A 853 ASN cc_start: 0.8214 (t160) cc_final: 0.7928 (t0) REVERT: C 253 MET cc_start: 0.8616 (ttt) cc_final: 0.8260 (tpp) REVERT: C 851 LEU cc_start: 0.8873 (mt) cc_final: 0.8504 (mt) REVERT: C 853 ASN cc_start: 0.8214 (t160) cc_final: 0.7929 (t0) outliers start: 14 outliers final: 14 residues processed: 84 average time/residue: 0.8317 time to fit residues: 104.1385 Evaluate side-chains 88 residues out of total 2218 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 74 time to evaluate : 3.275 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 207 LEU Chi-restraints excluded: chain A residue 298 TYR Chi-restraints excluded: chain A residue 332 LYS Chi-restraints excluded: chain B residue 1075 LEU Chi-restraints excluded: chain B residue 1376 ILE Chi-restraints excluded: chain B residue 1392 GLU Chi-restraints excluded: chain B residue 1552 ILE Chi-restraints excluded: chain C residue 207 LEU Chi-restraints excluded: chain C residue 298 TYR Chi-restraints excluded: chain C residue 332 LYS Chi-restraints excluded: chain D residue 1075 LEU Chi-restraints excluded: chain D residue 1376 ILE Chi-restraints excluded: chain D residue 1392 GLU Chi-restraints excluded: chain D residue 1552 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 232 random chunks: chunk 220 optimal weight: 1.9990 chunk 134 optimal weight: 20.0000 chunk 104 optimal weight: 0.6980 chunk 153 optimal weight: 3.9990 chunk 231 optimal weight: 0.0040 chunk 212 optimal weight: 1.9990 chunk 184 optimal weight: 1.9990 chunk 19 optimal weight: 9.9990 chunk 142 optimal weight: 4.9990 chunk 112 optimal weight: 1.9990 chunk 146 optimal weight: 6.9990 overall best weight: 1.3398 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D1219 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8166 moved from start: 0.3953 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 19652 Z= 0.165 Angle : 0.432 6.017 26372 Z= 0.236 Chirality : 0.031 0.150 2962 Planarity : 0.002 0.029 3326 Dihedral : 3.492 15.048 2478 Min Nonbonded Distance : 2.055 Molprobity Statistics. All-atom Clashscore : 3.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.78 % Favored : 99.22 % Rotamer: Outliers : 0.63 % Allowed : 7.94 % Favored : 91.43 % 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: 3.63 (0.18), residues: 2298 helix: 2.79 (0.12), residues: 1856 sheet: None (None), residues: 0 loop : 0.72 (0.29), residues: 442 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.003 0.001 HIS A 889 PHE 0.006 0.001 PHE C 521 TYR 0.007 0.001 TYR C 517 ARG 0.002 0.000 ARG A 577 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4596 Ramachandran restraints generated. 2298 Oldfield, 0 Emsley, 2298 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4596 Ramachandran restraints generated. 2298 Oldfield, 0 Emsley, 2298 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 88 residues out of total 2218 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 74 time to evaluate : 2.813 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 253 MET cc_start: 0.8608 (ttt) cc_final: 0.8248 (tpp) REVERT: A 851 LEU cc_start: 0.8869 (mt) cc_final: 0.8500 (mt) REVERT: A 853 ASN cc_start: 0.8222 (t160) cc_final: 0.7945 (t0) REVERT: C 253 MET cc_start: 0.8606 (ttt) cc_final: 0.8246 (tpp) REVERT: C 851 LEU cc_start: 0.8868 (mt) cc_final: 0.8500 (mt) REVERT: C 853 ASN cc_start: 0.8223 (t160) cc_final: 0.7946 (t0) outliers start: 14 outliers final: 14 residues processed: 82 average time/residue: 0.8685 time to fit residues: 106.0487 Evaluate side-chains 88 residues out of total 2218 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 74 time to evaluate : 3.418 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 207 LEU Chi-restraints excluded: chain A residue 298 TYR Chi-restraints excluded: chain A residue 332 LYS Chi-restraints excluded: chain B residue 1075 LEU Chi-restraints excluded: chain B residue 1376 ILE Chi-restraints excluded: chain B residue 1392 GLU Chi-restraints excluded: chain B residue 1552 ILE Chi-restraints excluded: chain C residue 207 LEU Chi-restraints excluded: chain C residue 298 TYR Chi-restraints excluded: chain C residue 332 LYS Chi-restraints excluded: chain D residue 1075 LEU Chi-restraints excluded: chain D residue 1376 ILE Chi-restraints excluded: chain D residue 1392 GLU Chi-restraints excluded: chain D residue 1552 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 232 random chunks: chunk 196 optimal weight: 2.9990 chunk 56 optimal weight: 1.9990 chunk 169 optimal weight: 3.9990 chunk 27 optimal weight: 0.5980 chunk 51 optimal weight: 2.9990 chunk 184 optimal weight: 0.8980 chunk 77 optimal weight: 2.9990 chunk 189 optimal weight: 2.9990 chunk 23 optimal weight: 8.9990 chunk 33 optimal weight: 3.9990 chunk 161 optimal weight: 0.6980 overall best weight: 1.4384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B1219 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1219 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3727 r_free = 0.3727 target = 0.075267 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.3134 r_free = 0.3134 target = 0.050356 restraints weight = 216437.175| |-----------------------------------------------------------------------------| r_work (start): 0.3087 rms_B_bonded: 3.70 r_work: 0.2943 rms_B_bonded: 3.97 restraints_weight: 0.5000 r_work (final): 0.2943 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8307 moved from start: 0.4072 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 19652 Z= 0.166 Angle : 0.439 8.102 26372 Z= 0.238 Chirality : 0.031 0.149 2962 Planarity : 0.002 0.029 3326 Dihedral : 3.449 14.465 2478 Min Nonbonded Distance : 2.047 Molprobity Statistics. All-atom Clashscore : 3.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.70 % Favored : 99.30 % Rotamer: Outliers : 0.63 % Allowed : 7.94 % Favored : 91.43 % 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: 3.78 (0.17), residues: 2298 helix: 2.90 (0.12), residues: 1858 sheet: None (None), residues: 0 loop : 0.73 (0.28), residues: 440 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.003 0.001 HIS C 889 PHE 0.006 0.001 PHE C 521 TYR 0.007 0.001 TYR C 559 ARG 0.002 0.000 ARG A 537 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 6159.35 seconds wall clock time: 110 minutes 42.58 seconds (6642.58 seconds total)