Starting phenix.real_space_refine on Sat Feb 17 13:24:03 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8fvu_29493/02_2024/8fvu_29493_neut_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8fvu_29493/02_2024/8fvu_29493.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.6 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8fvu_29493/02_2024/8fvu_29493.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8fvu_29493/02_2024/8fvu_29493.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8fvu_29493/02_2024/8fvu_29493_neut_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8fvu_29493/02_2024/8fvu_29493_neut_updated.pdb" } resolution = 3.6 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= 0.018 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: 6 Type Number sf(0) Gaussians Zn 3 6.06 5 P 3 5.49 5 S 112 5.16 5 C 11977 2.51 5 N 3158 2.21 5 O 3505 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A PHE 15": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 67": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 86": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 87": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 98": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 120": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 138": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 156": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 166": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 171": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 186": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 198": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 221": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 239": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 246": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 254": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 275": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 277": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 305": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 316": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 339": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 498": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 502": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 551": "OD1" <-> "OD2" Residue "A TYR 592": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 615": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 629": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 644": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 655": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 657": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 667": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 701": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 705": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 707": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 721": "OE1" <-> "OE2" Residue "A PHE 739": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 742": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 788": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 830": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 872": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 883": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 903": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 931": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 938": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 997": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 1095": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 1128": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 1192": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 1205": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 1229": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 1291": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 1310": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 1314": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 1386": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 109": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 118": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 134": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 197": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 201": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 202": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 213": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 271": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 290": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 363": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 366": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 402": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 406": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 439": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 441": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 473": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 487": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 493": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 575": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 611": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 616": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 659": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 679": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 715": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 931": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 961": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 972": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 996": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 1007": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "U TYR -7": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "U TYR 47": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.07s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5238/modules/chem_data/mon_lib" Total number of atoms: 18758 Number of models: 1 Model: "" Number of chains: 4 Chain: "A" Number of atoms: 10905 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1361, 10905 Classifications: {'peptide': 1361} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 56, 'TRANS': 1304} Chain breaks: 1 Chain: "B" Number of atoms: 7198 Number of conformers: 1 Conformer: "" Number of residues, atoms: 904, 7198 Classifications: {'peptide': 904} Modifications used: {'COO': 1} Link IDs: {'CIS': 3, 'PTRANS': 22, 'TRANS': 878} Chain breaks: 1 Chain: "U" Number of atoms: 621 Number of conformers: 1 Conformer: "" Number of residues, atoms: 79, 621 Classifications: {'peptide': 79} Link IDs: {'PTRANS': 2, 'TRANS': 76} Chain: "A" Number of atoms: 34 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 34 Unusual residues: {' ZN': 3, 'ATP': 1} Classifications: {'undetermined': 4} Link IDs: {None: 3} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 797 SG CYS A 100 75.533 37.632 96.426 1.00 47.62 S ATOM 989 SG CYS A 124 73.744 36.827 100.409 1.00 38.63 S ATOM 1576 SG CYS A 197 76.104 61.055 126.030 1.00 45.77 S ATOM 1795 SG CYS A 224 74.378 64.195 127.531 1.00 54.44 S ATOM 2528 SG CYS A 315 54.680 27.911 107.917 1.00 62.82 S ATOM 2551 SG CYS A 318 53.186 26.662 104.504 1.00 48.43 S ATOM 2740 SG CYS A 342 57.763 26.984 104.919 1.00 64.78 S Time building chain proxies: 9.55, per 1000 atoms: 0.51 Number of scatterers: 18758 At special positions: 0 Unit cell: (99.54, 156.42, 147.888, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) Zn 3 29.99 S 112 16.00 P 3 15.00 O 3505 8.00 N 3158 7.00 C 11977 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 6.24 Conformation dependent library (CDL) restraints added in 3.5 seconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN A1502 " pdb="ZN ZN A1502 " - pdb=" NE2 HIS A 117 " pdb="ZN ZN A1502 " - pdb=" SG CYS A 124 " pdb="ZN ZN A1502 " - pdb=" SG CYS A 100 " pdb=" ZN A1503 " pdb="ZN ZN A1503 " - pdb=" NE2 HIS A 217 " pdb="ZN ZN A1503 " - pdb=" SG CYS A 224 " pdb="ZN ZN A1503 " - pdb=" SG CYS A 197 " pdb=" ZN A1504 " pdb="ZN ZN A1504 " - pdb=" NE2 HIS A 335 " pdb="ZN ZN A1504 " - pdb=" SG CYS A 318 " pdb="ZN ZN A1504 " - pdb=" SG CYS A 342 " pdb="ZN ZN A1504 " - pdb=" SG CYS A 315 " Number of angles added : 3 4668 Ramachandran restraints generated. 2334 Oldfield, 0 Emsley, 2334 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 4464 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 114 helices and 11 sheets defined 42.0% alpha, 7.1% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 5.28 Creating SS restraints... Processing helix chain 'A' and resid 24 through 27 No H-bonds generated for 'chain 'A' and resid 24 through 27' Processing helix chain 'A' and resid 31 through 48 removed outlier: 3.784A pdb=" N ALA A 47 " --> pdb=" O GLN A 43 " (cutoff:3.500A) removed outlier: 3.802A pdb=" N LYS A 48 " --> pdb=" O LYS A 44 " (cutoff:3.500A) Processing helix chain 'A' and resid 55 through 57 No H-bonds generated for 'chain 'A' and resid 55 through 57' Processing helix chain 'A' and resid 60 through 69 removed outlier: 3.770A pdb=" N LYS A 65 " --> pdb=" O ALA A 61 " (cutoff:3.500A) removed outlier: 3.890A pdb=" N PHE A 67 " --> pdb=" O ARG A 63 " (cutoff:3.500A) removed outlier: 4.289A pdb=" N VAL A 68 " --> pdb=" O LEU A 64 " (cutoff:3.500A) removed outlier: 5.278A pdb=" N THR A 69 " --> pdb=" O LYS A 65 " (cutoff:3.500A) Processing helix chain 'A' and resid 78 through 84 removed outlier: 3.684A pdb=" N ALA A 84 " --> pdb=" O GLU A 80 " (cutoff:3.500A) Processing helix chain 'A' and resid 113 through 117 Processing helix chain 'A' and resid 152 through 155 No H-bonds generated for 'chain 'A' and resid 152 through 155' Processing helix chain 'A' and resid 159 through 165 removed outlier: 3.889A pdb=" N SER A 165 " --> pdb=" O ALA A 161 " (cutoff:3.500A) Processing helix chain 'A' and resid 171 through 173 No H-bonds generated for 'chain 'A' and resid 171 through 173' Processing helix chain 'A' and resid 178 through 183 Processing helix chain 'A' and resid 213 through 219 Processing helix chain 'A' and resid 225 through 230 Processing helix chain 'A' and resid 233 through 241 Processing helix chain 'A' and resid 251 through 253 No H-bonds generated for 'chain 'A' and resid 251 through 253' Processing helix chain 'A' and resid 274 through 276 No H-bonds generated for 'chain 'A' and resid 274 through 276' Processing helix chain 'A' and resid 278 through 282 Processing helix chain 'A' and resid 296 through 302 removed outlier: 3.738A pdb=" N LYS A 301 " --> pdb=" O ALA A 297 " (cutoff:3.500A) removed outlier: 3.586A pdb=" N ALA A 302 " --> pdb=" O ALA A 298 " (cutoff:3.500A) Processing helix chain 'A' and resid 331 through 338 Processing helix chain 'A' and resid 343 through 350 Processing helix chain 'A' and resid 395 through 412 Processing helix chain 'A' and resid 421 through 423 No H-bonds generated for 'chain 'A' and resid 421 through 423' Processing helix chain 'A' and resid 431 through 433 No H-bonds generated for 'chain 'A' and resid 431 through 433' Processing helix chain 'A' and resid 455 through 457 No H-bonds generated for 'chain 'A' and resid 455 through 457' Processing helix chain 'A' and resid 459 through 461 No H-bonds generated for 'chain 'A' and resid 459 through 461' Processing helix chain 'A' and resid 476 through 489 Processing helix chain 'A' and resid 515 through 522 removed outlier: 4.181A pdb=" N ASP A 521 " --> pdb=" O SER A 517 " (cutoff:3.500A) Processing helix chain 'A' and resid 532 through 545 removed outlier: 3.562A pdb=" N GLN A 541 " --> pdb=" O ASN A 537 " (cutoff:3.500A) removed outlier: 7.682A pdb=" N ASN A 544 " --> pdb=" O GLN A 540 " (cutoff:3.500A) removed outlier: 6.902A pdb=" N GLN A 545 " --> pdb=" O GLN A 541 " (cutoff:3.500A) Processing helix chain 'A' and resid 561 through 568 removed outlier: 4.241A pdb=" N LEU A 566 " --> pdb=" O VAL A 562 " (cutoff:3.500A) removed outlier: 3.531A pdb=" N ILE A 567 " --> pdb=" O ILE A 563 " (cutoff:3.500A) Processing helix chain 'A' and resid 590 through 592 No H-bonds generated for 'chain 'A' and resid 590 through 592' Processing helix chain 'A' and resid 604 through 614 Processing helix chain 'A' and resid 619 through 631 removed outlier: 3.854A pdb=" N LYS A 624 " --> pdb=" O THR A 620 " (cutoff:3.500A) Processing helix chain 'A' and resid 633 through 637 removed outlier: 3.646A pdb=" N GLN A 636 " --> pdb=" O GLN A 633 " (cutoff:3.500A) Processing helix chain 'A' and resid 642 through 652 Processing helix chain 'A' and resid 665 through 676 removed outlier: 4.328A pdb=" N SER A 675 " --> pdb=" O MET A 671 " (cutoff:3.500A) removed outlier: 4.134A pdb=" N LEU A 676 " --> pdb=" O GLU A 672 " (cutoff:3.500A) Processing helix chain 'A' and resid 685 through 701 removed outlier: 3.668A pdb=" N PHE A 701 " --> pdb=" O LEU A 697 " (cutoff:3.500A) Processing helix chain 'A' and resid 709 through 715 removed outlier: 3.776A pdb=" N ALA A 715 " --> pdb=" O ASP A 711 " (cutoff:3.500A) Processing helix chain 'A' and resid 745 through 761 Processing helix chain 'A' and resid 765 through 767 No H-bonds generated for 'chain 'A' and resid 765 through 767' Processing helix chain 'A' and resid 769 through 777 removed outlier: 3.781A pdb=" N GLN A 777 " --> pdb=" O TYR A 773 " (cutoff:3.500A) Processing helix chain 'A' and resid 789 through 795 Processing helix chain 'A' and resid 803 through 814 removed outlier: 3.893A pdb=" N HIS A 810 " --> pdb=" O LYS A 806 " (cutoff:3.500A) removed outlier: 3.861A pdb=" N HIS A 813 " --> pdb=" O SER A 809 " (cutoff:3.500A) Processing helix chain 'A' and resid 818 through 821 No H-bonds generated for 'chain 'A' and resid 818 through 821' Processing helix chain 'A' and resid 835 through 850 removed outlier: 3.743A pdb=" N LEU A 843 " --> pdb=" O LEU A 839 " (cutoff:3.500A) removed outlier: 3.750A pdb=" N GLY A 846 " --> pdb=" O GLN A 842 " (cutoff:3.500A) removed outlier: 3.584A pdb=" N GLN A 849 " --> pdb=" O ARG A 845 " (cutoff:3.500A) Processing helix chain 'A' and resid 852 through 873 Processing helix chain 'A' and resid 877 through 879 No H-bonds generated for 'chain 'A' and resid 877 through 879' Processing helix chain 'A' and resid 881 through 888 Processing helix chain 'A' and resid 895 through 899 Processing helix chain 'A' and resid 901 through 905 Processing helix chain 'A' and resid 907 through 912 Processing helix chain 'A' and resid 951 through 953 No H-bonds generated for 'chain 'A' and resid 951 through 953' Processing helix chain 'A' and resid 957 through 977 removed outlier: 4.249A pdb=" N TYR A 974 " --> pdb=" O ASN A 970 " (cutoff:3.500A) removed outlier: 4.353A pdb=" N MET A 977 " --> pdb=" O SER A 973 " (cutoff:3.500A) Processing helix chain 'A' and resid 1014 through 1026 removed outlier: 3.778A pdb=" N ALA A1026 " --> pdb=" O THR A1022 " (cutoff:3.500A) Processing helix chain 'A' and resid 1040 through 1043 No H-bonds generated for 'chain 'A' and resid 1040 through 1043' Processing helix chain 'A' and resid 1045 through 1048 No H-bonds generated for 'chain 'A' and resid 1045 through 1048' Processing helix chain 'A' and resid 1052 through 1054 No H-bonds generated for 'chain 'A' and resid 1052 through 1054' Processing helix chain 'A' and resid 1067 through 1075 removed outlier: 3.542A pdb=" N THR A1075 " --> pdb=" O GLU A1071 " (cutoff:3.500A) Processing helix chain 'A' and resid 1145 through 1152 Processing helix chain 'A' and resid 1170 through 1179 removed outlier: 3.817A pdb=" N VAL A1178 " --> pdb=" O MET A1174 " (cutoff:3.500A) removed outlier: 4.392A pdb=" N SER A1179 " --> pdb=" O THR A1175 " (cutoff:3.500A) Processing helix chain 'A' and resid 1196 through 1204 removed outlier: 3.757A pdb=" N SER A1201 " --> pdb=" O PRO A1197 " (cutoff:3.500A) Proline residue: A1203 - end of helix Processing helix chain 'A' and resid 1221 through 1232 removed outlier: 3.983A pdb=" N GLY A1232 " --> pdb=" O ALA A1228 " (cutoff:3.500A) Processing helix chain 'A' and resid 1246 through 1250 Processing helix chain 'A' and resid 1252 through 1260 removed outlier: 3.506A pdb=" N CYS A1259 " --> pdb=" O ILE A1255 " (cutoff:3.500A) removed outlier: 4.292A pdb=" N GLN A1260 " --> pdb=" O ILE A1256 " (cutoff:3.500A) Processing helix chain 'A' and resid 1279 through 1288 Processing helix chain 'A' and resid 1307 through 1316 removed outlier: 3.548A pdb=" N PHE A1313 " --> pdb=" O GLY A1309 " (cutoff:3.500A) Processing helix chain 'A' and resid 1332 through 1334 No H-bonds generated for 'chain 'A' and resid 1332 through 1334' Processing helix chain 'A' and resid 1340 through 1352 removed outlier: 3.768A pdb=" N LEU A1351 " --> pdb=" O SER A1347 " (cutoff:3.500A) removed outlier: 3.676A pdb=" N ARG A1352 " --> pdb=" O GLN A1348 " (cutoff:3.500A) Processing helix chain 'A' and resid 1371 through 1380 removed outlier: 3.762A pdb=" N VAL A1376 " --> pdb=" O ALA A1372 " (cutoff:3.500A) removed outlier: 4.590A pdb=" N GLU A1379 " --> pdb=" O ASN A1375 " (cutoff:3.500A) removed outlier: 3.814A pdb=" N ARG A1380 " --> pdb=" O VAL A1376 " (cutoff:3.500A) Processing helix chain 'B' and resid 95 through 110 removed outlier: 3.817A pdb=" N HIS B 110 " --> pdb=" O LYS B 106 " (cutoff:3.500A) Processing helix chain 'B' and resid 112 through 114 No H-bonds generated for 'chain 'B' and resid 112 through 114' Processing helix chain 'B' and resid 177 through 188 Processing helix chain 'B' and resid 192 through 194 No H-bonds generated for 'chain 'B' and resid 192 through 194' Processing helix chain 'B' and resid 205 through 207 No H-bonds generated for 'chain 'B' and resid 205 through 207' Processing helix chain 'B' and resid 212 through 219 Processing helix chain 'B' and resid 232 through 241 removed outlier: 5.643A pdb=" N LYS B 238 " --> pdb=" O ALA B 234 " (cutoff:3.500A) removed outlier: 5.874A pdb=" N LEU B 239 " --> pdb=" O MET B 235 " (cutoff:3.500A) removed outlier: 5.096A pdb=" N ARG B 240 " --> pdb=" O LEU B 236 " (cutoff:3.500A) removed outlier: 6.199A pdb=" N GLN B 241 " --> pdb=" O LEU B 237 " (cutoff:3.500A) Processing helix chain 'B' and resid 250 through 252 No H-bonds generated for 'chain 'B' and resid 250 through 252' Processing helix chain 'B' and resid 255 through 257 No H-bonds generated for 'chain 'B' and resid 255 through 257' Processing helix chain 'B' and resid 259 through 267 Processing helix chain 'B' and resid 281 through 289 removed outlier: 3.713A pdb=" N ARG B 285 " --> pdb=" O GLU B 282 " (cutoff:3.500A) removed outlier: 5.100A pdb=" N ALA B 288 " --> pdb=" O ARG B 285 " (cutoff:3.500A) Processing helix chain 'B' and resid 302 through 311 Processing helix chain 'B' and resid 315 through 327 removed outlier: 4.084A pdb=" N GLN B 326 " --> pdb=" O LEU B 322 " (cutoff:3.500A) Processing helix chain 'B' and resid 329 through 336 removed outlier: 4.141A pdb=" N LYS B 336 " --> pdb=" O ARG B 332 " (cutoff:3.500A) Processing helix chain 'B' and resid 338 through 340 No H-bonds generated for 'chain 'B' and resid 338 through 340' Processing helix chain 'B' and resid 346 through 348 No H-bonds generated for 'chain 'B' and resid 346 through 348' Processing helix chain 'B' and resid 361 through 370 Processing helix chain 'B' and resid 377 through 380 Processing helix chain 'B' and resid 383 through 402 Processing helix chain 'B' and resid 410 through 413 No H-bonds generated for 'chain 'B' and resid 410 through 413' Processing helix chain 'B' and resid 418 through 424 Processing helix chain 'B' and resid 444 through 459 Processing helix chain 'B' and resid 464 through 476 removed outlier: 3.768A pdb=" N LYS B 476 " --> pdb=" O GLY B 472 " (cutoff:3.500A) Processing helix chain 'B' and resid 480 through 483 No H-bonds generated for 'chain 'B' and resid 480 through 483' Processing helix chain 'B' and resid 488 through 496 Processing helix chain 'B' and resid 499 through 511 removed outlier: 3.854A pdb=" N ALA B 511 " --> pdb=" O LYS B 507 " (cutoff:3.500A) Processing helix chain 'B' and resid 530 through 533 No H-bonds generated for 'chain 'B' and resid 530 through 533' Processing helix chain 'B' and resid 542 through 565 removed outlier: 4.367A pdb=" N ALA B 548 " --> pdb=" O GLU B 544 " (cutoff:3.500A) removed outlier: 3.718A pdb=" N SER B 565 " --> pdb=" O LEU B 561 " (cutoff:3.500A) Processing helix chain 'B' and resid 574 through 577 No H-bonds generated for 'chain 'B' and resid 574 through 577' Processing helix chain 'B' and resid 593 through 601 Processing helix chain 'B' and resid 606 through 608 No H-bonds generated for 'chain 'B' and resid 606 through 608' Processing helix chain 'B' and resid 646 through 652 Processing helix chain 'B' and resid 674 through 685 removed outlier: 3.701A pdb=" N LYS B 682 " --> pdb=" O ARG B 678 " (cutoff:3.500A) removed outlier: 3.905A pdb=" N SER B 685 " --> pdb=" O GLY B 681 " (cutoff:3.500A) Processing helix chain 'B' and resid 704 through 706 No H-bonds generated for 'chain 'B' and resid 704 through 706' Processing helix chain 'B' and resid 708 through 710 No H-bonds generated for 'chain 'B' and resid 708 through 710' Processing helix chain 'B' and resid 726 through 734 Processing helix chain 'B' and resid 778 through 789 removed outlier: 3.531A pdb=" N LEU B 783 " --> pdb=" O ALA B 780 " (cutoff:3.500A) Processing helix chain 'B' and resid 808 through 814 Processing helix chain 'B' and resid 834 through 843 Processing helix chain 'B' and resid 864 through 872 Processing helix chain 'B' and resid 892 through 905 removed outlier: 5.208A pdb=" N SER B 897 " --> pdb=" O GLY B 894 " (cutoff:3.500A) removed outlier: 3.505A pdb=" N GLU B 904 " --> pdb=" O LYS B 901 " (cutoff:3.500A) Processing helix chain 'B' and resid 923 through 930 Processing helix chain 'B' and resid 960 through 963 removed outlier: 3.796A pdb=" N ASN B 963 " --> pdb=" O VAL B 960 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 960 through 963' Processing helix chain 'B' and resid 981 through 992 Processing helix chain 'B' and resid 1009 through 1014 removed outlier: 3.527A pdb=" N VAL B1014 " --> pdb=" O ASP B1010 " (cutoff:3.500A) Processing helix chain 'U' and resid 2 through 26 removed outlier: 3.546A pdb=" N GLY U 9 " --> pdb=" O ALA U 5 " (cutoff:3.500A) removed outlier: 3.871A pdb=" N ASP U 12 " --> pdb=" O THR U 8 " (cutoff:3.500A) Processing helix chain 'U' and resid 31 through 64 removed outlier: 3.855A pdb=" N ILE U 40 " --> pdb=" O ASN U 36 " (cutoff:3.500A) removed outlier: 4.074A pdb=" N SER U 53 " --> pdb=" O ASN U 49 " (cutoff:3.500A) removed outlier: 3.931A pdb=" N LYS U 56 " --> pdb=" O SER U 52 " (cutoff:3.500A) Processing sheet with id= A, first strand: chain 'A' and resid 86 through 88 Processing sheet with id= B, first strand: chain 'A' and resid 186 through 188 Processing sheet with id= C, first strand: chain 'A' and resid 304 through 306 Processing sheet with id= D, first strand: chain 'A' and resid 450 through 453 removed outlier: 4.442A pdb=" N ILE A 440 " --> pdb=" O LEU A 453 " (cutoff:3.500A) Processing sheet with id= E, first strand: chain 'A' and resid 465 through 470 removed outlier: 6.246A pdb=" N LEU A 577 " --> pdb=" O MET A 466 " (cutoff:3.500A) removed outlier: 7.705A pdb=" N VAL A 468 " --> pdb=" O LEU A 577 " (cutoff:3.500A) removed outlier: 6.628A pdb=" N ILE A 579 " --> pdb=" O VAL A 468 " (cutoff:3.500A) removed outlier: 8.116A pdb=" N GLY A 470 " --> pdb=" O ILE A 579 " (cutoff:3.500A) removed outlier: 6.661A pdb=" N VAL A 581 " --> pdb=" O GLY A 470 " (cutoff:3.500A) removed outlier: 6.478A pdb=" N LEU A 500 " --> pdb=" O LEU A 547 " (cutoff:3.500A) removed outlier: 7.654A pdb=" N LEU A 549 " --> pdb=" O LEU A 500 " (cutoff:3.500A) removed outlier: 6.363A pdb=" N PHE A 502 " --> pdb=" O LEU A 549 " (cutoff:3.500A) removed outlier: 7.167A pdb=" N ASP A 551 " --> pdb=" O PHE A 502 " (cutoff:3.500A) removed outlier: 6.937A pdb=" N LEU A 504 " --> pdb=" O ASP A 551 " (cutoff:3.500A) Processing sheet with id= F, first strand: chain 'A' and resid 728 through 731 Processing sheet with id= G, first strand: chain 'A' and resid 892 through 894 removed outlier: 6.529A pdb=" N SER A 915 " --> pdb=" O LEU A 893 " (cutoff:3.500A) removed outlier: 7.134A pdb=" N LEU A1032 " --> pdb=" O THR A1056 " (cutoff:3.500A) removed outlier: 4.124A pdb=" N CYS A1058 " --> pdb=" O LEU A1032 " (cutoff:3.500A) removed outlier: 6.970A pdb=" N LEU A1034 " --> pdb=" O CYS A1058 " (cutoff:3.500A) removed outlier: 4.694A pdb=" N ILE A1060 " --> pdb=" O LEU A1034 " (cutoff:3.500A) removed outlier: 6.773A pdb=" N SER A1081 " --> pdb=" O CYS A1058 " (cutoff:3.500A) removed outlier: 7.567A pdb=" N ILE A1060 " --> pdb=" O SER A1081 " (cutoff:3.500A) removed outlier: 6.282A pdb=" N GLU A1083 " --> pdb=" O ILE A1060 " (cutoff:3.500A) removed outlier: 6.465A pdb=" N GLU A1106 " --> pdb=" O LEU A1082 " (cutoff:3.500A) removed outlier: 7.948A pdb=" N VAL A1084 " --> pdb=" O GLU A1106 " (cutoff:3.500A) removed outlier: 6.618A pdb=" N SER A1108 " --> pdb=" O VAL A1084 " (cutoff:3.500A) removed outlier: 6.352A pdb=" N LYS A1133 " --> pdb=" O LEU A1107 " (cutoff:3.500A) removed outlier: 7.732A pdb=" N VAL A1109 " --> pdb=" O LYS A1133 " (cutoff:3.500A) removed outlier: 6.625A pdb=" N LEU A1135 " --> pdb=" O VAL A1109 " (cutoff:3.500A) removed outlier: 6.516A pdb=" N VAL A1159 " --> pdb=" O LEU A1134 " (cutoff:3.500A) removed outlier: 7.473A pdb=" N ILE A1136 " --> pdb=" O VAL A1159 " (cutoff:3.500A) removed outlier: 6.341A pdb=" N HIS A1161 " --> pdb=" O ILE A1136 " (cutoff:3.500A) removed outlier: 6.704A pdb=" N GLU A1185 " --> pdb=" O PHE A1160 " (cutoff:3.500A) removed outlier: 7.877A pdb=" N LEU A1162 " --> pdb=" O GLU A1185 " (cutoff:3.500A) removed outlier: 6.641A pdb=" N LYS A1187 " --> pdb=" O LEU A1162 " (cutoff:3.500A) removed outlier: 6.674A pdb=" N ILE A1210 " --> pdb=" O ILE A1186 " (cutoff:3.500A) removed outlier: 8.215A pdb=" N PHE A1188 " --> pdb=" O ILE A1210 " (cutoff:3.500A) removed outlier: 6.938A pdb=" N ASN A1212 " --> pdb=" O PHE A1188 " (cutoff:3.500A) removed outlier: 6.514A pdb=" N GLU A1239 " --> pdb=" O LEU A1211 " (cutoff:3.500A) removed outlier: 6.486A pdb=" N VAL A1267 " --> pdb=" O LEU A1240 " (cutoff:3.500A) removed outlier: 6.449A pdb=" N ASN A1296 " --> pdb=" O LEU A1268 " (cutoff:3.500A) removed outlier: 7.906A pdb=" N PHE A1270 " --> pdb=" O ASN A1296 " (cutoff:3.500A) removed outlier: 6.675A pdb=" N LYS A1298 " --> pdb=" O PHE A1270 " (cutoff:3.500A) removed outlier: 6.644A pdb=" N GLU A1325 " --> pdb=" O LEU A1297 " (cutoff:3.500A) removed outlier: 7.484A pdb=" N LEU A1299 " --> pdb=" O GLU A1325 " (cutoff:3.500A) removed outlier: 6.143A pdb=" N ASP A1327 " --> pdb=" O LEU A1299 " (cutoff:3.500A) removed outlier: 6.677A pdb=" N ARG A1358 " --> pdb=" O LEU A1326 " (cutoff:3.500A) removed outlier: 7.543A pdb=" N ILE A1328 " --> pdb=" O ARG A1358 " (cutoff:3.500A) removed outlier: 6.161A pdb=" N ASN A1360 " --> pdb=" O ILE A1328 " (cutoff:3.500A) removed outlier: 6.365A pdb=" N THR A1388 " --> pdb=" O LEU A1359 " (cutoff:3.500A) Processing sheet with id= H, first strand: chain 'B' and resid 139 through 142 removed outlier: 4.351A pdb=" N THR B 294 " --> pdb=" O LYS B 142 " (cutoff:3.500A) removed outlier: 6.617A pdb=" N ILE B 166 " --> pdb=" O ALA B 295 " (cutoff:3.500A) removed outlier: 7.781A pdb=" N VAL B 297 " --> pdb=" O ILE B 166 " (cutoff:3.500A) removed outlier: 7.249A pdb=" N GLU B 168 " --> pdb=" O VAL B 297 " (cutoff:3.500A) removed outlier: 6.685A pdb=" N PHE B 199 " --> pdb=" O LEU B 244 " (cutoff:3.500A) removed outlier: 7.943A pdb=" N LEU B 246 " --> pdb=" O PHE B 199 " (cutoff:3.500A) removed outlier: 6.488A pdb=" N PHE B 201 " --> pdb=" O LEU B 246 " (cutoff:3.500A) removed outlier: 7.570A pdb=" N ASP B 248 " --> pdb=" O PHE B 201 " (cutoff:3.500A) removed outlier: 7.026A pdb=" N LEU B 203 " --> pdb=" O ASP B 248 " (cutoff:3.500A) Processing sheet with id= I, first strand: chain 'B' and resid 427 through 430 Processing sheet with id= J, first strand: chain 'B' and resid 585 through 587 removed outlier: 5.895A pdb=" N LYS B 613 " --> pdb=" O ILE B 586 " (cutoff:3.500A) removed outlier: 6.751A pdb=" N GLU B 663 " --> pdb=" O LEU B 614 " (cutoff:3.500A) removed outlier: 7.617A pdb=" N PHE B 616 " --> pdb=" O GLU B 663 " (cutoff:3.500A) removed outlier: 6.716A pdb=" N THR B 665 " --> pdb=" O PHE B 616 " (cutoff:3.500A) removed outlier: 7.528A pdb=" N LEU B 692 " --> pdb=" O TYR B 715 " (cutoff:3.500A) removed outlier: 4.306A pdb=" N LEU B 717 " --> pdb=" O LEU B 692 " (cutoff:3.500A) removed outlier: 7.265A pdb=" N ILE B 694 " --> pdb=" O LEU B 717 " (cutoff:3.500A) removed outlier: 4.212A pdb=" N VAL B 719 " --> pdb=" O ILE B 694 " (cutoff:3.500A) removed outlier: 6.509A pdb=" N THR B 740 " --> pdb=" O LEU B 717 " (cutoff:3.500A) removed outlier: 7.930A pdb=" N VAL B 719 " --> pdb=" O THR B 740 " (cutoff:3.500A) removed outlier: 6.586A pdb=" N SER B 742 " --> pdb=" O VAL B 719 " (cutoff:3.500A) removed outlier: 6.406A pdb=" N LYS B 767 " --> pdb=" O LEU B 741 " (cutoff:3.500A) removed outlier: 7.632A pdb=" N ILE B 743 " --> pdb=" O LYS B 767 " (cutoff:3.500A) removed outlier: 6.149A pdb=" N ILE B 769 " --> pdb=" O ILE B 743 " (cutoff:3.500A) Processing sheet with id= K, first strand: chain 'B' and resid 911 through 913 removed outlier: 7.258A pdb=" N GLN B 941 " --> pdb=" O LEU B 912 " (cutoff:3.500A) No H-bonds generated for sheet with id= K 545 hydrogen bonds defined for protein. 1467 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: 7.00 Time building geometry restraints manager: 6.90 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: 3687 1.32 - 1.45: 4468 1.45 - 1.57: 10813 1.57 - 1.69: 7 1.69 - 1.82: 163 Bond restraints: 19138 Sorted by residual: bond pdb=" C4 ATP A1501 " pdb=" C5 ATP A1501 " ideal model delta sigma weight residual 1.388 1.484 -0.096 1.00e-02 1.00e+04 9.19e+01 bond pdb=" C5 ATP A1501 " pdb=" N7 ATP A1501 " ideal model delta sigma weight residual 1.387 1.301 0.086 1.00e-02 1.00e+04 7.46e+01 bond pdb=" C5 ATP A1501 " pdb=" C6 ATP A1501 " ideal model delta sigma weight residual 1.409 1.490 -0.081 1.00e-02 1.00e+04 6.53e+01 bond pdb=" C ALA B 295 " pdb=" O ALA B 295 " ideal model delta sigma weight residual 1.236 1.293 -0.058 1.21e-02 6.83e+03 2.29e+01 bond pdb=" C ALA B 295 " pdb=" N GLU B 296 " ideal model delta sigma weight residual 1.330 1.270 0.059 1.39e-02 5.18e+03 1.83e+01 ... (remaining 19133 not shown) Histogram of bond angle deviations from ideal: 99.51 - 107.06: 517 107.06 - 114.60: 11191 114.60 - 122.14: 10554 122.14 - 129.68: 3481 129.68 - 137.23: 111 Bond angle restraints: 25854 Sorted by residual: angle pdb=" PB ATP A1501 " pdb=" O3B ATP A1501 " pdb=" PG ATP A1501 " ideal model delta sigma weight residual 139.87 120.39 19.48 1.00e+00 1.00e+00 3.79e+02 angle pdb=" PA ATP A1501 " pdb=" O3A ATP A1501 " pdb=" PB ATP A1501 " ideal model delta sigma weight residual 136.83 121.45 15.38 1.00e+00 1.00e+00 2.36e+02 angle pdb=" N3 ATP A1501 " pdb=" C4 ATP A1501 " pdb=" N9 ATP A1501 " ideal model delta sigma weight residual 127.04 137.23 -10.19 1.15e+00 7.59e-01 7.87e+01 angle pdb=" C5 ATP A1501 " pdb=" C4 ATP A1501 " pdb=" N3 ATP A1501 " ideal model delta sigma weight residual 126.80 118.22 8.58 1.00e+00 1.00e+00 7.36e+01 angle pdb=" N THR B 360 " pdb=" CA THR B 360 " pdb=" C THR B 360 " ideal model delta sigma weight residual 114.62 104.91 9.71 1.14e+00 7.69e-01 7.26e+01 ... (remaining 25849 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.69: 11137 17.69 - 35.38: 351 35.38 - 53.06: 72 53.06 - 70.75: 39 70.75 - 88.44: 20 Dihedral angle restraints: 11619 sinusoidal: 4756 harmonic: 6863 Sorted by residual: dihedral pdb=" CA SER A 993 " pdb=" C SER A 993 " pdb=" N PRO A 994 " pdb=" CA PRO A 994 " ideal model delta harmonic sigma weight residual -180.00 -144.12 -35.88 0 5.00e+00 4.00e-02 5.15e+01 dihedral pdb=" CA SER A 926 " pdb=" C SER A 926 " pdb=" N PRO A 927 " pdb=" CA PRO A 927 " ideal model delta harmonic sigma weight residual 180.00 -159.71 -20.29 0 5.00e+00 4.00e-02 1.65e+01 dihedral pdb=" CA LEU A1353 " pdb=" C LEU A1353 " pdb=" N PRO A1354 " pdb=" CA PRO A1354 " ideal model delta harmonic sigma weight residual -180.00 -162.01 -17.99 0 5.00e+00 4.00e-02 1.30e+01 ... (remaining 11616 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.086: 2370 0.086 - 0.173: 511 0.173 - 0.259: 23 0.259 - 0.346: 1 0.346 - 0.432: 1 Chirality restraints: 2906 Sorted by residual: chirality pdb=" CA ALA B 295 " pdb=" N ALA B 295 " pdb=" C ALA B 295 " pdb=" CB ALA B 295 " both_signs ideal model delta sigma weight residual False 2.48 2.05 0.43 2.00e-01 2.50e+01 4.67e+00 chirality pdb=" C1' ATP A1501 " pdb=" C2' ATP A1501 " pdb=" N9 ATP A1501 " pdb=" O4' ATP A1501 " both_signs ideal model delta sigma weight residual False 2.41 2.72 -0.31 2.00e-01 2.50e+01 2.39e+00 chirality pdb=" CA ILE A 559 " pdb=" N ILE A 559 " pdb=" C ILE A 559 " pdb=" CB ILE A 559 " both_signs ideal model delta sigma weight residual False 2.43 2.68 -0.25 2.00e-01 2.50e+01 1.54e+00 ... (remaining 2903 not shown) Planarity restraints: 3305 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA LYS A1403 " 0.017 2.00e-02 2.50e+03 3.33e-02 1.11e+01 pdb=" C LYS A1403 " -0.058 2.00e-02 2.50e+03 pdb=" O LYS A1403 " 0.021 2.00e-02 2.50e+03 pdb=" OXT LYS A1403 " 0.020 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TYR A1310 " -0.030 2.00e-02 2.50e+03 1.61e-02 5.20e+00 pdb=" CG TYR A1310 " 0.012 2.00e-02 2.50e+03 pdb=" CD1 TYR A1310 " 0.012 2.00e-02 2.50e+03 pdb=" CD2 TYR A1310 " 0.012 2.00e-02 2.50e+03 pdb=" CE1 TYR A1310 " 0.008 2.00e-02 2.50e+03 pdb=" CE2 TYR A1310 " 0.009 2.00e-02 2.50e+03 pdb=" CZ TYR A1310 " 0.002 2.00e-02 2.50e+03 pdb=" OH TYR A1310 " -0.025 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ALA B1024 " 0.011 2.00e-02 2.50e+03 2.16e-02 4.68e+00 pdb=" C ALA B1024 " -0.037 2.00e-02 2.50e+03 pdb=" O ALA B1024 " 0.013 2.00e-02 2.50e+03 pdb=" OXT ALA B1024 " 0.013 2.00e-02 2.50e+03 ... (remaining 3302 not shown) Histogram of nonbonded interaction distances: 2.34 - 2.85: 6479 2.85 - 3.36: 17711 3.36 - 3.88: 30238 3.88 - 4.39: 36379 4.39 - 4.90: 58752 Nonbonded interactions: 149559 Sorted by model distance: nonbonded pdb=" OG1 THR A 189 " pdb=" OG1 THR A 194 " model vdw 2.338 2.440 nonbonded pdb=" OD2 ASP A 828 " pdb=" NZ LYS A1385 " model vdw 2.342 2.520 nonbonded pdb=" OG SER A 796 " pdb=" OG1 THR A 870 " model vdw 2.343 2.440 nonbonded pdb=" OD1 ASP A 552 " pdb=" NZ LYS A 554 " model vdw 2.352 2.520 nonbonded pdb=" NZ LYS A 476 " pdb=" O1G ATP A1501 " model vdw 2.394 2.520 ... (remaining 149554 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model ========== 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: 0.010 Normalize map: mean=0, sd=1: 5.690 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.010 Extract box with map and model: 16.270 Check model and map are aligned: 0.310 Set scattering table: 0.200 Process input model: 52.880 Find NCS groups from input model: 0.480 Set up NCS constraints: 0.070 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:2.740 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 78.680 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8015 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 : 0.012 0.096 19138 Z= 0.775 Angle : 1.221 19.480 25854 Z= 0.848 Chirality : 0.065 0.432 2906 Planarity : 0.004 0.033 3305 Dihedral : 10.950 88.439 7155 Min Nonbonded Distance : 2.338 Molprobity Statistics. All-atom Clashscore : 2.29 Ramachandran Plot: Outliers : 1.41 % Allowed : 6.86 % Favored : 91.73 % Rotamer: Outliers : 0.00 % Allowed : 0.43 % Favored : 99.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.13 % Twisted Proline : 1.25 % 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: -1.70 (0.16), residues: 2334 helix: -1.03 (0.14), residues: 1070 sheet: -0.59 (0.31), residues: 264 loop : -1.22 (0.20), residues: 1000 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.004 TRP B 917 HIS 0.005 0.001 HIS B 731 PHE 0.018 0.003 PHE A 701 TYR 0.030 0.004 TYR A1310 ARG 0.003 0.000 ARG A 497 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4668 Ramachandran restraints generated. 2334 Oldfield, 0 Emsley, 2334 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4668 Ramachandran restraints generated. 2334 Oldfield, 0 Emsley, 2334 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 517 residues out of total 2096 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 517 time to evaluate : 2.172 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 1 MET cc_start: 0.4910 (ppp) cc_final: 0.4342 (ppp) REVERT: A 248 ASP cc_start: 0.7646 (t0) cc_final: 0.7439 (t0) REVERT: A 283 ASP cc_start: 0.8324 (t0) cc_final: 0.8092 (m-30) REVERT: A 398 GLN cc_start: 0.8792 (mm-40) cc_final: 0.8552 (tm-30) REVERT: A 583 THR cc_start: 0.8991 (p) cc_final: 0.8540 (t) REVERT: A 672 GLU cc_start: 0.8210 (tp30) cc_final: 0.7847 (tp30) REVERT: A 684 ILE cc_start: 0.8377 (mm) cc_final: 0.8176 (mt) REVERT: A 718 ASP cc_start: 0.8302 (t0) cc_final: 0.7867 (t70) REVERT: A 739 PHE cc_start: 0.8780 (p90) cc_final: 0.8339 (p90) REVERT: A 813 HIS cc_start: 0.8251 (t70) cc_final: 0.8035 (t-90) REVERT: A 946 ILE cc_start: 0.8587 (mp) cc_final: 0.8332 (pt) REVERT: A 1100 LYS cc_start: 0.9071 (mmtm) cc_final: 0.8514 (ttmm) REVERT: A 1154 SER cc_start: 0.7810 (m) cc_final: 0.7350 (p) REVERT: A 1190 ASP cc_start: 0.7696 (t0) cc_final: 0.7356 (t70) REVERT: B 125 ASP cc_start: 0.8267 (t0) cc_final: 0.8054 (t0) REVERT: B 367 TYR cc_start: 0.7756 (t80) cc_final: 0.7374 (t80) REVERT: B 423 THR cc_start: 0.7259 (m) cc_final: 0.6790 (p) REVERT: B 674 LYS cc_start: 0.7732 (tttt) cc_final: 0.7520 (tptt) REVERT: B 970 PHE cc_start: 0.7668 (p90) cc_final: 0.7086 (p90) REVERT: U 12 ASP cc_start: 0.8070 (t70) cc_final: 0.7703 (t0) outliers start: 0 outliers final: 0 residues processed: 517 average time/residue: 0.3461 time to fit residues: 262.9938 Evaluate side-chains 221 residues out of total 2096 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 221 time to evaluate : 2.114 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 233 random chunks: chunk 196 optimal weight: 0.9980 chunk 176 optimal weight: 0.7980 chunk 97 optimal weight: 0.8980 chunk 60 optimal weight: 0.5980 chunk 119 optimal weight: 2.9990 chunk 94 optimal weight: 0.8980 chunk 182 optimal weight: 0.9990 chunk 70 optimal weight: 0.9980 chunk 111 optimal weight: 2.9990 chunk 135 optimal weight: 2.9990 chunk 211 optimal weight: 5.9990 overall best weight: 0.8380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 4 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 463 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 545 GLN A 584 ASN A 639 GLN A 862 HIS A 875 ASN A1036 HIS A1381 HIS B 145 HIS B 180 GLN ** B 552 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** U 38 GLN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8156 moved from start: 0.3140 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.051 19138 Z= 0.239 Angle : 0.674 12.042 25854 Z= 0.354 Chirality : 0.044 0.191 2906 Planarity : 0.004 0.032 3305 Dihedral : 5.821 81.165 2530 Min Nonbonded Distance : 2.197 Molprobity Statistics. All-atom Clashscore : 6.58 Ramachandran Plot: Outliers : 0.26 % Allowed : 7.71 % Favored : 92.03 % Rotamer: Outliers : 2.24 % Allowed : 8.16 % Favored : 89.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.13 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.98 (0.17), residues: 2334 helix: 0.14 (0.16), residues: 1048 sheet: -0.81 (0.32), residues: 272 loop : -1.38 (0.20), residues: 1014 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.002 TRP B 186 HIS 0.006 0.001 HIS B 797 PHE 0.026 0.002 PHE A 246 TYR 0.017 0.002 TYR B 594 ARG 0.006 0.001 ARG A1330 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4668 Ramachandran restraints generated. 2334 Oldfield, 0 Emsley, 2334 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4668 Ramachandran restraints generated. 2334 Oldfield, 0 Emsley, 2334 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 304 residues out of total 2096 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 47 poor density : 257 time to evaluate : 2.221 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 398 GLN cc_start: 0.8726 (mm-40) cc_final: 0.8435 (tm-30) REVERT: A 672 GLU cc_start: 0.8434 (tp30) cc_final: 0.8019 (tp30) REVERT: A 783 MET cc_start: 0.8351 (mtp) cc_final: 0.8002 (mmm) REVERT: A 1176 MET cc_start: 0.8194 (tpp) cc_final: 0.7740 (tpp) REVERT: A 1190 ASP cc_start: 0.7627 (t0) cc_final: 0.7214 (t70) REVERT: A 1363 SER cc_start: 0.9288 (m) cc_final: 0.9073 (p) REVERT: A 1401 ILE cc_start: 0.8234 (mm) cc_final: 0.7879 (mm) REVERT: B 125 ASP cc_start: 0.8526 (t0) cc_final: 0.8216 (t0) REVERT: B 161 LEU cc_start: 0.8613 (mt) cc_final: 0.8406 (tp) REVERT: B 235 MET cc_start: 0.8087 (ptp) cc_final: 0.7082 (tmm) REVERT: B 256 GLN cc_start: 0.7662 (tm-30) cc_final: 0.7385 (mp10) REVERT: B 367 TYR cc_start: 0.7837 (t80) cc_final: 0.7616 (t80) REVERT: B 368 ASP cc_start: 0.8254 (t0) cc_final: 0.7993 (t0) REVERT: B 604 ASN cc_start: 0.7687 (t0) cc_final: 0.7471 (t0) REVERT: B 775 MET cc_start: 0.7494 (OUTLIER) cc_final: 0.7042 (ttt) REVERT: B 847 LEU cc_start: 0.7897 (tp) cc_final: 0.7264 (mp) REVERT: B 875 MET cc_start: 0.6912 (OUTLIER) cc_final: 0.6698 (ptp) REVERT: U 12 ASP cc_start: 0.8349 (t70) cc_final: 0.7977 (t0) REVERT: U 36 ASN cc_start: 0.8809 (m-40) cc_final: 0.8593 (m110) REVERT: U 40 ILE cc_start: 0.8492 (OUTLIER) cc_final: 0.8252 (mp) outliers start: 47 outliers final: 23 residues processed: 292 average time/residue: 0.3076 time to fit residues: 139.1455 Evaluate side-chains 218 residues out of total 2096 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 192 time to evaluate : 2.095 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 132 VAL Chi-restraints excluded: chain A residue 173 VAL Chi-restraints excluded: chain A residue 189 THR Chi-restraints excluded: chain A residue 419 MET Chi-restraints excluded: chain A residue 433 LEU Chi-restraints excluded: chain A residue 469 GLU Chi-restraints excluded: chain A residue 720 ASP Chi-restraints excluded: chain A residue 723 LEU Chi-restraints excluded: chain A residue 915 SER Chi-restraints excluded: chain A residue 936 THR Chi-restraints excluded: chain A residue 1019 ILE Chi-restraints excluded: chain A residue 1244 THR Chi-restraints excluded: chain A residue 1274 LEU Chi-restraints excluded: chain B residue 100 ASP Chi-restraints excluded: chain B residue 266 LYS Chi-restraints excluded: chain B residue 329 ARG Chi-restraints excluded: chain B residue 517 CYS Chi-restraints excluded: chain B residue 708 LEU Chi-restraints excluded: chain B residue 775 MET Chi-restraints excluded: chain B residue 875 MET Chi-restraints excluded: chain B residue 950 SER Chi-restraints excluded: chain B residue 969 PHE Chi-restraints excluded: chain B residue 1002 LEU Chi-restraints excluded: chain U residue 25 THR Chi-restraints excluded: chain U residue 32 THR Chi-restraints excluded: chain U residue 40 ILE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 233 random chunks: chunk 117 optimal weight: 3.9990 chunk 65 optimal weight: 2.9990 chunk 176 optimal weight: 4.9990 chunk 144 optimal weight: 5.9990 chunk 58 optimal weight: 1.9990 chunk 211 optimal weight: 20.0000 chunk 228 optimal weight: 0.7980 chunk 188 optimal weight: 1.9990 chunk 210 optimal weight: 5.9990 chunk 72 optimal weight: 0.9980 chunk 170 optimal weight: 4.9990 overall best weight: 1.7586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 633 GLN A 827 ASN A 875 ASN A1114 ASN B 306 GLN B 348 GLN ** B 552 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 800 HIS Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8305 moved from start: 0.3965 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.068 19138 Z= 0.380 Angle : 0.679 12.228 25854 Z= 0.355 Chirality : 0.046 0.204 2906 Planarity : 0.004 0.050 3305 Dihedral : 6.196 89.595 2530 Min Nonbonded Distance : 2.107 Molprobity Statistics. All-atom Clashscore : 7.65 Ramachandran Plot: Outliers : 0.17 % Allowed : 8.95 % Favored : 90.87 % Rotamer: Outliers : 2.67 % Allowed : 9.73 % Favored : 87.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.13 % 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: -1.15 (0.18), residues: 2334 helix: 0.16 (0.17), residues: 1042 sheet: -1.06 (0.32), residues: 268 loop : -1.62 (0.19), residues: 1024 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.042 0.002 TRP B 186 HIS 0.009 0.001 HIS A 121 PHE 0.027 0.002 PHE U 69 TYR 0.024 0.002 TYR U 37 ARG 0.008 0.001 ARG A1330 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4668 Ramachandran restraints generated. 2334 Oldfield, 0 Emsley, 2334 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4668 Ramachandran restraints generated. 2334 Oldfield, 0 Emsley, 2334 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 264 residues out of total 2096 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 56 poor density : 208 time to evaluate : 1.995 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 1 MET cc_start: 0.4968 (ppp) cc_final: 0.4386 (ppp) REVERT: A 398 GLN cc_start: 0.8797 (mm-40) cc_final: 0.8284 (tm-30) REVERT: A 1131 MET cc_start: 0.8731 (tpp) cc_final: 0.8441 (mpp) REVERT: A 1174 MET cc_start: 0.8372 (mmm) cc_final: 0.8133 (mpp) REVERT: A 1190 ASP cc_start: 0.7678 (t0) cc_final: 0.7230 (t70) REVERT: B 161 LEU cc_start: 0.8666 (mt) cc_final: 0.8447 (tp) REVERT: B 235 MET cc_start: 0.7950 (ptp) cc_final: 0.7249 (tmm) REVERT: B 368 ASP cc_start: 0.8287 (t0) cc_final: 0.8043 (t0) REVERT: B 727 GLU cc_start: 0.7721 (mp0) cc_final: 0.7424 (tm-30) REVERT: B 852 ILE cc_start: 0.8227 (mm) cc_final: 0.7965 (mt) REVERT: B 875 MET cc_start: 0.6767 (OUTLIER) cc_final: 0.6562 (ptp) REVERT: U 12 ASP cc_start: 0.8521 (t70) cc_final: 0.8188 (t0) REVERT: U 15 GLN cc_start: 0.8572 (mm-40) cc_final: 0.8269 (tp-100) REVERT: U 40 ILE cc_start: 0.8582 (OUTLIER) cc_final: 0.8326 (mp) outliers start: 56 outliers final: 37 residues processed: 250 average time/residue: 0.2838 time to fit residues: 113.3615 Evaluate side-chains 210 residues out of total 2096 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 39 poor density : 171 time to evaluate : 2.149 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 140 ILE Chi-restraints excluded: chain A residue 182 SER Chi-restraints excluded: chain A residue 189 THR Chi-restraints excluded: chain A residue 203 CYS Chi-restraints excluded: chain A residue 249 ILE Chi-restraints excluded: chain A residue 256 ASN Chi-restraints excluded: chain A residue 332 LEU Chi-restraints excluded: chain A residue 419 MET Chi-restraints excluded: chain A residue 469 GLU Chi-restraints excluded: chain A residue 477 THR Chi-restraints excluded: chain A residue 557 CYS Chi-restraints excluded: chain A residue 572 LEU Chi-restraints excluded: chain A residue 704 CYS Chi-restraints excluded: chain A residue 723 LEU Chi-restraints excluded: chain A residue 726 CYS Chi-restraints excluded: chain A residue 915 SER Chi-restraints excluded: chain A residue 936 THR Chi-restraints excluded: chain A residue 973 SER Chi-restraints excluded: chain A residue 1020 LEU Chi-restraints excluded: chain A residue 1154 SER Chi-restraints excluded: chain A residue 1244 THR Chi-restraints excluded: chain B residue 100 ASP Chi-restraints excluded: chain B residue 135 THR Chi-restraints excluded: chain B residue 243 VAL Chi-restraints excluded: chain B residue 266 LYS Chi-restraints excluded: chain B residue 271 PHE Chi-restraints excluded: chain B residue 369 LEU Chi-restraints excluded: chain B residue 445 SER Chi-restraints excluded: chain B residue 517 CYS Chi-restraints excluded: chain B residue 708 LEU Chi-restraints excluded: chain B residue 811 ILE Chi-restraints excluded: chain B residue 875 MET Chi-restraints excluded: chain B residue 970 PHE Chi-restraints excluded: chain B residue 1012 LEU Chi-restraints excluded: chain U residue 21 GLN Chi-restraints excluded: chain U residue 25 THR Chi-restraints excluded: chain U residue 40 ILE Chi-restraints excluded: chain U residue 61 ILE Chi-restraints excluded: chain U residue 63 SER Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 233 random chunks: chunk 209 optimal weight: 5.9990 chunk 159 optimal weight: 3.9990 chunk 110 optimal weight: 0.4980 chunk 23 optimal weight: 4.9990 chunk 101 optimal weight: 0.7980 chunk 142 optimal weight: 2.9990 chunk 212 optimal weight: 2.9990 chunk 225 optimal weight: 5.9990 chunk 111 optimal weight: 2.9990 chunk 201 optimal weight: 5.9990 chunk 60 optimal weight: 0.7980 overall best weight: 1.6184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 121 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 253 HIS A 734 GLN A1260 GLN B 348 GLN B 357 HIS ** B 552 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8327 moved from start: 0.4410 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.065 19138 Z= 0.342 Angle : 0.638 12.622 25854 Z= 0.332 Chirality : 0.045 0.217 2906 Planarity : 0.004 0.052 3305 Dihedral : 6.254 87.038 2530 Min Nonbonded Distance : 2.126 Molprobity Statistics. All-atom Clashscore : 8.39 Ramachandran Plot: Outliers : 0.17 % Allowed : 9.34 % Favored : 90.49 % Rotamer: Outliers : 2.67 % Allowed : 11.07 % Favored : 86.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.13 % 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 (0.17), residues: 2334 helix: 0.17 (0.17), residues: 1045 sheet: -1.23 (0.32), residues: 261 loop : -1.90 (0.19), residues: 1028 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.051 0.002 TRP B 186 HIS 0.006 0.001 HIS A1129 PHE 0.019 0.002 PHE U 69 TYR 0.017 0.002 TYR U 37 ARG 0.007 0.000 ARG A1330 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4668 Ramachandran restraints generated. 2334 Oldfield, 0 Emsley, 2334 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4668 Ramachandran restraints generated. 2334 Oldfield, 0 Emsley, 2334 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 244 residues out of total 2096 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 56 poor density : 188 time to evaluate : 2.267 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 1 MET cc_start: 0.4819 (ppp) cc_final: 0.4532 (ppp) REVERT: A 655 TYR cc_start: 0.8673 (m-80) cc_final: 0.8419 (m-10) REVERT: A 985 LEU cc_start: 0.8672 (OUTLIER) cc_final: 0.8343 (pp) REVERT: A 1131 MET cc_start: 0.8742 (tpp) cc_final: 0.8443 (mpp) REVERT: A 1174 MET cc_start: 0.8412 (mmm) cc_final: 0.8171 (mpp) REVERT: A 1176 MET cc_start: 0.8330 (tpp) cc_final: 0.7766 (tpp) REVERT: A 1190 ASP cc_start: 0.7667 (t0) cc_final: 0.7261 (t0) REVERT: B 235 MET cc_start: 0.7875 (ptp) cc_final: 0.7238 (mtp) REVERT: B 368 ASP cc_start: 0.8339 (t0) cc_final: 0.8073 (t0) REVERT: B 727 GLU cc_start: 0.7765 (mp0) cc_final: 0.7435 (tm-30) REVERT: B 875 MET cc_start: 0.6746 (OUTLIER) cc_final: 0.6490 (ptp) REVERT: U 12 ASP cc_start: 0.8545 (t70) cc_final: 0.8249 (t0) REVERT: U 15 GLN cc_start: 0.8556 (mm-40) cc_final: 0.8272 (tp-100) REVERT: U 40 ILE cc_start: 0.8617 (OUTLIER) cc_final: 0.8296 (mp) REVERT: U 44 TYR cc_start: 0.9047 (t80) cc_final: 0.8760 (t80) outliers start: 56 outliers final: 39 residues processed: 231 average time/residue: 0.2880 time to fit residues: 105.4300 Evaluate side-chains 209 residues out of total 2096 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 42 poor density : 167 time to evaluate : 2.027 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 132 VAL Chi-restraints excluded: chain A residue 140 ILE Chi-restraints excluded: chain A residue 189 THR Chi-restraints excluded: chain A residue 240 ILE Chi-restraints excluded: chain A residue 256 ASN Chi-restraints excluded: chain A residue 332 LEU Chi-restraints excluded: chain A residue 419 MET Chi-restraints excluded: chain A residue 447 LYS Chi-restraints excluded: chain A residue 469 GLU Chi-restraints excluded: chain A residue 557 CYS Chi-restraints excluded: chain A residue 559 ILE Chi-restraints excluded: chain A residue 572 LEU Chi-restraints excluded: chain A residue 666 VAL Chi-restraints excluded: chain A residue 723 LEU Chi-restraints excluded: chain A residue 726 CYS Chi-restraints excluded: chain A residue 915 SER Chi-restraints excluded: chain A residue 936 THR Chi-restraints excluded: chain A residue 985 LEU Chi-restraints excluded: chain A residue 1020 LEU Chi-restraints excluded: chain A residue 1084 VAL Chi-restraints excluded: chain A residue 1154 SER Chi-restraints excluded: chain A residue 1244 THR Chi-restraints excluded: chain B residue 100 ASP Chi-restraints excluded: chain B residue 135 THR Chi-restraints excluded: chain B residue 167 ILE Chi-restraints excluded: chain B residue 243 VAL Chi-restraints excluded: chain B residue 271 PHE Chi-restraints excluded: chain B residue 331 LEU Chi-restraints excluded: chain B residue 369 LEU Chi-restraints excluded: chain B residue 517 CYS Chi-restraints excluded: chain B residue 708 LEU Chi-restraints excluded: chain B residue 778 GLU Chi-restraints excluded: chain B residue 811 ILE Chi-restraints excluded: chain B residue 837 VAL Chi-restraints excluded: chain B residue 875 MET Chi-restraints excluded: chain B residue 950 SER Chi-restraints excluded: chain B residue 969 PHE Chi-restraints excluded: chain B residue 970 PHE Chi-restraints excluded: chain B residue 1012 LEU Chi-restraints excluded: chain U residue 25 THR Chi-restraints excluded: chain U residue 40 ILE Chi-restraints excluded: chain U residue 61 ILE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 233 random chunks: chunk 187 optimal weight: 1.9990 chunk 127 optimal weight: 0.9990 chunk 3 optimal weight: 0.9980 chunk 167 optimal weight: 0.0470 chunk 92 optimal weight: 2.9990 chunk 192 optimal weight: 0.6980 chunk 155 optimal weight: 3.9990 chunk 0 optimal weight: 10.0000 chunk 115 optimal weight: 0.9980 chunk 202 optimal weight: 5.9990 chunk 56 optimal weight: 0.5980 overall best weight: 0.6678 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 552 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 604 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8274 moved from start: 0.4601 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 19138 Z= 0.182 Angle : 0.562 11.383 25854 Z= 0.295 Chirality : 0.042 0.243 2906 Planarity : 0.003 0.046 3305 Dihedral : 5.999 88.725 2530 Min Nonbonded Distance : 2.136 Molprobity Statistics. All-atom Clashscore : 7.09 Ramachandran Plot: Outliers : 0.13 % Allowed : 8.53 % Favored : 91.35 % Rotamer: Outliers : 2.72 % Allowed : 12.07 % Favored : 85.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.13 % 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: -1.14 (0.18), residues: 2334 helix: 0.41 (0.17), residues: 1029 sheet: -1.20 (0.33), residues: 260 loop : -1.83 (0.19), residues: 1045 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.060 0.002 TRP B 186 HIS 0.011 0.001 HIS A 121 PHE 0.015 0.001 PHE B 201 TYR 0.014 0.001 TYR B 594 ARG 0.005 0.000 ARG B 985 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4668 Ramachandran restraints generated. 2334 Oldfield, 0 Emsley, 2334 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4668 Ramachandran restraints generated. 2334 Oldfield, 0 Emsley, 2334 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 249 residues out of total 2096 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 57 poor density : 192 time to evaluate : 2.036 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 1 MET cc_start: 0.4920 (ppp) cc_final: 0.4655 (ppp) REVERT: A 655 TYR cc_start: 0.8628 (m-80) cc_final: 0.8376 (m-10) REVERT: A 684 ILE cc_start: 0.8232 (mm) cc_final: 0.8024 (mt) REVERT: A 985 LEU cc_start: 0.8681 (OUTLIER) cc_final: 0.8375 (pp) REVERT: A 1131 MET cc_start: 0.8702 (tpp) cc_final: 0.8406 (mpp) REVERT: A 1176 MET cc_start: 0.8301 (tpp) cc_final: 0.7754 (tpp) REVERT: B 235 MET cc_start: 0.7765 (ptp) cc_final: 0.7089 (tmm) REVERT: B 368 ASP cc_start: 0.8320 (t0) cc_final: 0.8087 (t0) REVERT: B 727 GLU cc_start: 0.7739 (mp0) cc_final: 0.7393 (tm-30) REVERT: B 875 MET cc_start: 0.6675 (OUTLIER) cc_final: 0.6037 (mpp) REVERT: B 958 MET cc_start: 0.6859 (OUTLIER) cc_final: 0.6481 (mmm) REVERT: U 12 ASP cc_start: 0.8476 (t70) cc_final: 0.8177 (t0) REVERT: U 15 GLN cc_start: 0.8511 (mm-40) cc_final: 0.8269 (tp-100) REVERT: U 40 ILE cc_start: 0.8540 (OUTLIER) cc_final: 0.8214 (mp) outliers start: 57 outliers final: 36 residues processed: 229 average time/residue: 0.2620 time to fit residues: 97.8958 Evaluate side-chains 204 residues out of total 2096 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 40 poor density : 164 time to evaluate : 2.136 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 132 VAL Chi-restraints excluded: chain A residue 140 ILE Chi-restraints excluded: chain A residue 189 THR Chi-restraints excluded: chain A residue 332 LEU Chi-restraints excluded: chain A residue 419 MET Chi-restraints excluded: chain A residue 469 GLU Chi-restraints excluded: chain A residue 559 ILE Chi-restraints excluded: chain A residue 572 LEU Chi-restraints excluded: chain A residue 704 CYS Chi-restraints excluded: chain A residue 723 LEU Chi-restraints excluded: chain A residue 726 CYS Chi-restraints excluded: chain A residue 813 HIS Chi-restraints excluded: chain A residue 936 THR Chi-restraints excluded: chain A residue 943 VAL Chi-restraints excluded: chain A residue 985 LEU Chi-restraints excluded: chain A residue 1019 ILE Chi-restraints excluded: chain A residue 1020 LEU Chi-restraints excluded: chain A residue 1084 VAL Chi-restraints excluded: chain A residue 1244 THR Chi-restraints excluded: chain B residue 100 ASP Chi-restraints excluded: chain B residue 135 THR Chi-restraints excluded: chain B residue 167 ILE Chi-restraints excluded: chain B residue 243 VAL Chi-restraints excluded: chain B residue 262 GLU Chi-restraints excluded: chain B residue 266 LYS Chi-restraints excluded: chain B residue 271 PHE Chi-restraints excluded: chain B residue 445 SER Chi-restraints excluded: chain B residue 517 CYS Chi-restraints excluded: chain B residue 778 GLU Chi-restraints excluded: chain B residue 875 MET Chi-restraints excluded: chain B residue 958 MET Chi-restraints excluded: chain B residue 969 PHE Chi-restraints excluded: chain B residue 970 PHE Chi-restraints excluded: chain B residue 1012 LEU Chi-restraints excluded: chain U residue -8 ASP Chi-restraints excluded: chain U residue 21 GLN Chi-restraints excluded: chain U residue 25 THR Chi-restraints excluded: chain U residue 40 ILE Chi-restraints excluded: chain U residue 61 ILE Chi-restraints excluded: chain U residue 63 SER Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 233 random chunks: chunk 75 optimal weight: 1.9990 chunk 202 optimal weight: 0.9990 chunk 44 optimal weight: 2.9990 chunk 132 optimal weight: 0.9980 chunk 55 optimal weight: 0.8980 chunk 225 optimal weight: 0.0040 chunk 187 optimal weight: 0.0270 chunk 104 optimal weight: 0.6980 chunk 18 optimal weight: 4.9990 chunk 74 optimal weight: 1.9990 chunk 118 optimal weight: 0.9980 overall best weight: 0.5250 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 584 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8261 moved from start: 0.4756 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 19138 Z= 0.169 Angle : 0.542 11.092 25854 Z= 0.284 Chirality : 0.042 0.218 2906 Planarity : 0.003 0.044 3305 Dihedral : 5.841 86.912 2530 Min Nonbonded Distance : 2.194 Molprobity Statistics. All-atom Clashscore : 7.09 Ramachandran Plot: Outliers : 0.13 % Allowed : 8.53 % Favored : 91.35 % Rotamer: Outliers : 2.39 % Allowed : 12.98 % Favored : 84.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.13 % 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: -1.08 (0.18), residues: 2334 helix: 0.53 (0.17), residues: 1025 sheet: -1.28 (0.33), residues: 265 loop : -1.85 (0.19), residues: 1044 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.060 0.002 TRP B 186 HIS 0.013 0.001 HIS A 121 PHE 0.030 0.001 PHE A1170 TYR 0.014 0.001 TYR B 594 ARG 0.005 0.000 ARG B 985 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4668 Ramachandran restraints generated. 2334 Oldfield, 0 Emsley, 2334 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4668 Ramachandran restraints generated. 2334 Oldfield, 0 Emsley, 2334 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 227 residues out of total 2096 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 50 poor density : 177 time to evaluate : 2.385 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 1 MET cc_start: 0.4874 (ppp) cc_final: 0.4629 (ppp) REVERT: A 655 TYR cc_start: 0.8608 (m-80) cc_final: 0.8380 (m-10) REVERT: A 985 LEU cc_start: 0.8712 (OUTLIER) cc_final: 0.8434 (pp) REVERT: A 1131 MET cc_start: 0.8679 (tpp) cc_final: 0.8414 (mpp) REVERT: A 1176 MET cc_start: 0.8313 (tpp) cc_final: 0.7679 (tpp) REVERT: A 1190 ASP cc_start: 0.7371 (t0) cc_final: 0.6976 (t0) REVERT: B 235 MET cc_start: 0.7774 (ptp) cc_final: 0.6793 (tmm) REVERT: B 368 ASP cc_start: 0.8329 (t0) cc_final: 0.8086 (t0) REVERT: B 727 GLU cc_start: 0.7729 (mp0) cc_final: 0.7393 (tm-30) REVERT: U 12 ASP cc_start: 0.8472 (t70) cc_final: 0.8163 (t0) REVERT: U 15 GLN cc_start: 0.8547 (mm-40) cc_final: 0.8279 (tp-100) outliers start: 50 outliers final: 35 residues processed: 211 average time/residue: 0.2630 time to fit residues: 91.1819 Evaluate side-chains 203 residues out of total 2096 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 36 poor density : 167 time to evaluate : 2.114 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 132 VAL Chi-restraints excluded: chain A residue 140 ILE Chi-restraints excluded: chain A residue 189 THR Chi-restraints excluded: chain A residue 332 LEU Chi-restraints excluded: chain A residue 419 MET Chi-restraints excluded: chain A residue 457 GLU Chi-restraints excluded: chain A residue 469 GLU Chi-restraints excluded: chain A residue 557 CYS Chi-restraints excluded: chain A residue 559 ILE Chi-restraints excluded: chain A residue 572 LEU Chi-restraints excluded: chain A residue 583 THR Chi-restraints excluded: chain A residue 666 VAL Chi-restraints excluded: chain A residue 704 CYS Chi-restraints excluded: chain A residue 723 LEU Chi-restraints excluded: chain A residue 813 HIS Chi-restraints excluded: chain A residue 936 THR Chi-restraints excluded: chain A residue 985 LEU Chi-restraints excluded: chain A residue 1019 ILE Chi-restraints excluded: chain A residue 1020 LEU Chi-restraints excluded: chain A residue 1084 VAL Chi-restraints excluded: chain A residue 1244 THR Chi-restraints excluded: chain B residue 100 ASP Chi-restraints excluded: chain B residue 135 THR Chi-restraints excluded: chain B residue 167 ILE Chi-restraints excluded: chain B residue 262 GLU Chi-restraints excluded: chain B residue 271 PHE Chi-restraints excluded: chain B residue 445 SER Chi-restraints excluded: chain B residue 517 CYS Chi-restraints excluded: chain B residue 778 GLU Chi-restraints excluded: chain B residue 969 PHE Chi-restraints excluded: chain B residue 970 PHE Chi-restraints excluded: chain B residue 1002 LEU Chi-restraints excluded: chain B residue 1012 LEU Chi-restraints excluded: chain U residue -8 ASP Chi-restraints excluded: chain U residue 25 THR Chi-restraints excluded: chain U residue 61 ILE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 233 random chunks: chunk 217 optimal weight: 0.0980 chunk 25 optimal weight: 2.9990 chunk 128 optimal weight: 1.9990 chunk 164 optimal weight: 10.0000 chunk 127 optimal weight: 1.9990 chunk 189 optimal weight: 2.9990 chunk 125 optimal weight: 0.8980 chunk 224 optimal weight: 6.9990 chunk 140 optimal weight: 1.9990 chunk 136 optimal weight: 9.9990 chunk 103 optimal weight: 3.9990 overall best weight: 1.3986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 121 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 651 HIS U 27 ASN U 38 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8327 moved from start: 0.4955 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.058 19138 Z= 0.302 Angle : 0.599 10.779 25854 Z= 0.310 Chirality : 0.044 0.207 2906 Planarity : 0.004 0.048 3305 Dihedral : 6.003 88.453 2530 Min Nonbonded Distance : 2.140 Molprobity Statistics. All-atom Clashscore : 8.10 Ramachandran Plot: Outliers : 0.21 % Allowed : 9.64 % Favored : 90.15 % Rotamer: Outliers : 2.34 % Allowed : 12.93 % Favored : 84.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.13 % 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 (0.18), residues: 2334 helix: 0.36 (0.17), residues: 1043 sheet: -1.40 (0.32), residues: 265 loop : -2.02 (0.19), residues: 1026 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.054 0.002 TRP B 186 HIS 0.012 0.001 HIS A 121 PHE 0.017 0.002 PHE A 602 TYR 0.020 0.002 TYR U 37 ARG 0.005 0.000 ARG A1330 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4668 Ramachandran restraints generated. 2334 Oldfield, 0 Emsley, 2334 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4668 Ramachandran restraints generated. 2334 Oldfield, 0 Emsley, 2334 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 221 residues out of total 2096 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 49 poor density : 172 time to evaluate : 2.086 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 1 MET cc_start: 0.4945 (ppp) cc_final: 0.4638 (ppp) REVERT: A 191 LYS cc_start: 0.8479 (mmtp) cc_final: 0.8234 (mmtp) REVERT: A 655 TYR cc_start: 0.8641 (m-80) cc_final: 0.8390 (m-10) REVERT: A 985 LEU cc_start: 0.8728 (OUTLIER) cc_final: 0.8433 (pp) REVERT: A 1131 MET cc_start: 0.8727 (tpp) cc_final: 0.8406 (mpp) REVERT: A 1176 MET cc_start: 0.8369 (tpp) cc_final: 0.7688 (tpp) REVERT: A 1190 ASP cc_start: 0.7363 (t0) cc_final: 0.7025 (t0) REVERT: B 235 MET cc_start: 0.7767 (ptp) cc_final: 0.7077 (tmm) REVERT: B 368 ASP cc_start: 0.8339 (t0) cc_final: 0.8090 (t0) REVERT: B 727 GLU cc_start: 0.7678 (mp0) cc_final: 0.7410 (tm-30) REVERT: B 875 MET cc_start: 0.6794 (ptp) cc_final: 0.6543 (ptp) REVERT: U 12 ASP cc_start: 0.8556 (t70) cc_final: 0.8274 (t0) REVERT: U 15 GLN cc_start: 0.8589 (mm-40) cc_final: 0.8325 (tp-100) REVERT: U 40 ILE cc_start: 0.8637 (OUTLIER) cc_final: 0.8288 (mp) REVERT: U 44 TYR cc_start: 0.9048 (t80) cc_final: 0.8744 (t80) outliers start: 49 outliers final: 39 residues processed: 210 average time/residue: 0.2704 time to fit residues: 91.9292 Evaluate side-chains 203 residues out of total 2096 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 41 poor density : 162 time to evaluate : 2.093 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 132 VAL Chi-restraints excluded: chain A residue 140 ILE Chi-restraints excluded: chain A residue 189 THR Chi-restraints excluded: chain A residue 332 LEU Chi-restraints excluded: chain A residue 419 MET Chi-restraints excluded: chain A residue 469 GLU Chi-restraints excluded: chain A residue 477 THR Chi-restraints excluded: chain A residue 557 CYS Chi-restraints excluded: chain A residue 559 ILE Chi-restraints excluded: chain A residue 572 LEU Chi-restraints excluded: chain A residue 666 VAL Chi-restraints excluded: chain A residue 704 CYS Chi-restraints excluded: chain A residue 723 LEU Chi-restraints excluded: chain A residue 726 CYS Chi-restraints excluded: chain A residue 813 HIS Chi-restraints excluded: chain A residue 936 THR Chi-restraints excluded: chain A residue 985 LEU Chi-restraints excluded: chain A residue 1020 LEU Chi-restraints excluded: chain A residue 1084 VAL Chi-restraints excluded: chain A residue 1154 SER Chi-restraints excluded: chain A residue 1244 THR Chi-restraints excluded: chain B residue 100 ASP Chi-restraints excluded: chain B residue 135 THR Chi-restraints excluded: chain B residue 167 ILE Chi-restraints excluded: chain B residue 243 VAL Chi-restraints excluded: chain B residue 262 GLU Chi-restraints excluded: chain B residue 331 LEU Chi-restraints excluded: chain B residue 517 CYS Chi-restraints excluded: chain B residue 778 GLU Chi-restraints excluded: chain B residue 837 VAL Chi-restraints excluded: chain B residue 895 SER Chi-restraints excluded: chain B residue 969 PHE Chi-restraints excluded: chain B residue 970 PHE Chi-restraints excluded: chain B residue 985 ARG Chi-restraints excluded: chain B residue 1002 LEU Chi-restraints excluded: chain B residue 1012 LEU Chi-restraints excluded: chain U residue -8 ASP Chi-restraints excluded: chain U residue 25 THR Chi-restraints excluded: chain U residue 40 ILE Chi-restraints excluded: chain U residue 61 ILE Chi-restraints excluded: chain U residue 63 SER Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 233 random chunks: chunk 138 optimal weight: 0.8980 chunk 89 optimal weight: 0.8980 chunk 134 optimal weight: 1.9990 chunk 67 optimal weight: 1.9990 chunk 44 optimal weight: 1.9990 chunk 43 optimal weight: 0.9980 chunk 142 optimal weight: 0.2980 chunk 153 optimal weight: 9.9990 chunk 111 optimal weight: 3.9990 chunk 20 optimal weight: 2.9990 chunk 176 optimal weight: 0.9980 overall best weight: 0.8180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 121 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 584 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1137 GLN B 159 GLN U 38 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8296 moved from start: 0.5052 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 19138 Z= 0.204 Angle : 0.558 10.450 25854 Z= 0.290 Chirality : 0.042 0.196 2906 Planarity : 0.003 0.047 3305 Dihedral : 5.908 89.693 2530 Min Nonbonded Distance : 2.179 Molprobity Statistics. All-atom Clashscore : 7.62 Ramachandran Plot: Outliers : 0.13 % Allowed : 9.13 % Favored : 90.75 % Rotamer: Outliers : 2.19 % Allowed : 13.12 % Favored : 84.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.13 % 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 (0.18), residues: 2334 helix: 0.54 (0.17), residues: 1030 sheet: -1.35 (0.33), residues: 265 loop : -1.98 (0.19), residues: 1039 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.046 0.001 TRP B 186 HIS 0.018 0.001 HIS A 121 PHE 0.019 0.001 PHE B 201 TYR 0.016 0.001 TYR U 37 ARG 0.003 0.000 ARG A1330 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4668 Ramachandran restraints generated. 2334 Oldfield, 0 Emsley, 2334 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4668 Ramachandran restraints generated. 2334 Oldfield, 0 Emsley, 2334 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 216 residues out of total 2096 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 46 poor density : 170 time to evaluate : 2.210 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 1 MET cc_start: 0.4915 (ppp) cc_final: 0.4601 (ppp) REVERT: A 584 ASN cc_start: 0.8817 (m-40) cc_final: 0.8584 (m110) REVERT: A 655 TYR cc_start: 0.8606 (m-80) cc_final: 0.8373 (m-10) REVERT: A 985 LEU cc_start: 0.8723 (OUTLIER) cc_final: 0.8442 (pp) REVERT: A 1131 MET cc_start: 0.8719 (tpp) cc_final: 0.8422 (mpp) REVERT: A 1176 MET cc_start: 0.8392 (tpp) cc_final: 0.7766 (tpp) REVERT: A 1190 ASP cc_start: 0.7287 (t0) cc_final: 0.7002 (t0) REVERT: B 235 MET cc_start: 0.7770 (ptp) cc_final: 0.7037 (tmm) REVERT: B 368 ASP cc_start: 0.8291 (t0) cc_final: 0.8070 (t0) REVERT: B 727 GLU cc_start: 0.7683 (mp0) cc_final: 0.7385 (tm-30) REVERT: B 875 MET cc_start: 0.6827 (ptp) cc_final: 0.6558 (ptp) REVERT: U 12 ASP cc_start: 0.8541 (t70) cc_final: 0.8251 (t0) REVERT: U 15 GLN cc_start: 0.8554 (mm-40) cc_final: 0.8322 (tp-100) REVERT: U 44 TYR cc_start: 0.8974 (t80) cc_final: 0.8689 (t80) outliers start: 46 outliers final: 38 residues processed: 205 average time/residue: 0.2965 time to fit residues: 98.7289 Evaluate side-chains 201 residues out of total 2096 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 39 poor density : 162 time to evaluate : 2.172 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 132 VAL Chi-restraints excluded: chain A residue 140 ILE Chi-restraints excluded: chain A residue 189 THR Chi-restraints excluded: chain A residue 332 LEU Chi-restraints excluded: chain A residue 419 MET Chi-restraints excluded: chain A residue 469 GLU Chi-restraints excluded: chain A residue 557 CYS Chi-restraints excluded: chain A residue 559 ILE Chi-restraints excluded: chain A residue 572 LEU Chi-restraints excluded: chain A residue 666 VAL Chi-restraints excluded: chain A residue 704 CYS Chi-restraints excluded: chain A residue 723 LEU Chi-restraints excluded: chain A residue 726 CYS Chi-restraints excluded: chain A residue 813 HIS Chi-restraints excluded: chain A residue 874 SER Chi-restraints excluded: chain A residue 936 THR Chi-restraints excluded: chain A residue 985 LEU Chi-restraints excluded: chain A residue 1019 ILE Chi-restraints excluded: chain A residue 1020 LEU Chi-restraints excluded: chain A residue 1084 VAL Chi-restraints excluded: chain A residue 1154 SER Chi-restraints excluded: chain A residue 1244 THR Chi-restraints excluded: chain B residue 100 ASP Chi-restraints excluded: chain B residue 135 THR Chi-restraints excluded: chain B residue 167 ILE Chi-restraints excluded: chain B residue 192 LYS Chi-restraints excluded: chain B residue 243 VAL Chi-restraints excluded: chain B residue 262 GLU Chi-restraints excluded: chain B residue 517 CYS Chi-restraints excluded: chain B residue 778 GLU Chi-restraints excluded: chain B residue 969 PHE Chi-restraints excluded: chain B residue 970 PHE Chi-restraints excluded: chain B residue 985 ARG Chi-restraints excluded: chain B residue 1002 LEU Chi-restraints excluded: chain B residue 1012 LEU Chi-restraints excluded: chain U residue -8 ASP Chi-restraints excluded: chain U residue 25 THR Chi-restraints excluded: chain U residue 61 ILE Chi-restraints excluded: chain U residue 63 SER Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 233 random chunks: chunk 204 optimal weight: 5.9990 chunk 215 optimal weight: 3.9990 chunk 196 optimal weight: 5.9990 chunk 209 optimal weight: 1.9990 chunk 125 optimal weight: 0.9990 chunk 91 optimal weight: 2.9990 chunk 164 optimal weight: 0.9990 chunk 64 optimal weight: 0.7980 chunk 189 optimal weight: 1.9990 chunk 197 optimal weight: 0.9980 chunk 208 optimal weight: 0.5980 overall best weight: 0.8784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 121 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 584 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 633 GLN ** A 930 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8296 moved from start: 0.5155 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.057 19138 Z= 0.214 Angle : 0.558 10.414 25854 Z= 0.291 Chirality : 0.042 0.190 2906 Planarity : 0.003 0.047 3305 Dihedral : 5.853 89.249 2530 Min Nonbonded Distance : 2.172 Molprobity Statistics. All-atom Clashscore : 7.70 Ramachandran Plot: Outliers : 0.13 % Allowed : 9.51 % Favored : 90.36 % Rotamer: Outliers : 2.15 % Allowed : 13.45 % Favored : 84.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.13 % 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: -1.13 (0.18), residues: 2334 helix: 0.59 (0.17), residues: 1025 sheet: -1.34 (0.33), residues: 265 loop : -1.99 (0.19), residues: 1044 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.070 0.002 TRP B 186 HIS 0.012 0.001 HIS A 121 PHE 0.017 0.001 PHE B 201 TYR 0.016 0.001 TYR U 37 ARG 0.003 0.000 ARG A 167 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4668 Ramachandran restraints generated. 2334 Oldfield, 0 Emsley, 2334 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4668 Ramachandran restraints generated. 2334 Oldfield, 0 Emsley, 2334 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 217 residues out of total 2096 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 45 poor density : 172 time to evaluate : 2.204 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 1 MET cc_start: 0.4960 (ppp) cc_final: 0.4647 (ppp) REVERT: A 191 LYS cc_start: 0.8531 (mmtp) cc_final: 0.8312 (mmtp) REVERT: A 584 ASN cc_start: 0.8859 (m-40) cc_final: 0.8651 (m110) REVERT: A 655 TYR cc_start: 0.8592 (m-80) cc_final: 0.8360 (m-10) REVERT: A 782 MET cc_start: 0.9311 (ttm) cc_final: 0.8941 (ttm) REVERT: A 985 LEU cc_start: 0.8716 (OUTLIER) cc_final: 0.8452 (pp) REVERT: A 1131 MET cc_start: 0.8723 (tpp) cc_final: 0.8421 (mpp) REVERT: A 1176 MET cc_start: 0.8405 (tpp) cc_final: 0.7780 (tpp) REVERT: A 1190 ASP cc_start: 0.7331 (t0) cc_final: 0.7050 (t0) REVERT: B 235 MET cc_start: 0.7799 (ptp) cc_final: 0.7034 (tmm) REVERT: B 368 ASP cc_start: 0.8302 (t0) cc_final: 0.8067 (t0) REVERT: B 388 ARG cc_start: 0.9059 (mtp180) cc_final: 0.8606 (ttm110) REVERT: B 727 GLU cc_start: 0.7652 (mp0) cc_final: 0.7386 (tm-30) REVERT: B 875 MET cc_start: 0.6801 (ptp) cc_final: 0.6595 (ptp) REVERT: U 12 ASP cc_start: 0.8563 (t70) cc_final: 0.8296 (t0) REVERT: U 15 GLN cc_start: 0.8565 (mm-40) cc_final: 0.8335 (tp-100) REVERT: U 40 ILE cc_start: 0.8616 (OUTLIER) cc_final: 0.8259 (mp) REVERT: U 44 TYR cc_start: 0.8986 (t80) cc_final: 0.8703 (t80) outliers start: 45 outliers final: 40 residues processed: 206 average time/residue: 0.2805 time to fit residues: 93.9503 Evaluate side-chains 208 residues out of total 2096 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 42 poor density : 166 time to evaluate : 2.087 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 132 VAL Chi-restraints excluded: chain A residue 140 ILE Chi-restraints excluded: chain A residue 189 THR Chi-restraints excluded: chain A residue 256 ASN Chi-restraints excluded: chain A residue 332 LEU Chi-restraints excluded: chain A residue 419 MET Chi-restraints excluded: chain A residue 469 GLU Chi-restraints excluded: chain A residue 477 THR Chi-restraints excluded: chain A residue 557 CYS Chi-restraints excluded: chain A residue 559 ILE Chi-restraints excluded: chain A residue 572 LEU Chi-restraints excluded: chain A residue 666 VAL Chi-restraints excluded: chain A residue 704 CYS Chi-restraints excluded: chain A residue 723 LEU Chi-restraints excluded: chain A residue 726 CYS Chi-restraints excluded: chain A residue 813 HIS Chi-restraints excluded: chain A residue 874 SER Chi-restraints excluded: chain A residue 936 THR Chi-restraints excluded: chain A residue 985 LEU Chi-restraints excluded: chain A residue 1019 ILE Chi-restraints excluded: chain A residue 1020 LEU Chi-restraints excluded: chain A residue 1084 VAL Chi-restraints excluded: chain A residue 1154 SER Chi-restraints excluded: chain A residue 1244 THR Chi-restraints excluded: chain B residue 100 ASP Chi-restraints excluded: chain B residue 135 THR Chi-restraints excluded: chain B residue 167 ILE Chi-restraints excluded: chain B residue 262 GLU Chi-restraints excluded: chain B residue 517 CYS Chi-restraints excluded: chain B residue 775 MET Chi-restraints excluded: chain B residue 778 GLU Chi-restraints excluded: chain B residue 895 SER Chi-restraints excluded: chain B residue 969 PHE Chi-restraints excluded: chain B residue 970 PHE Chi-restraints excluded: chain B residue 985 ARG Chi-restraints excluded: chain B residue 1002 LEU Chi-restraints excluded: chain B residue 1012 LEU Chi-restraints excluded: chain U residue -8 ASP Chi-restraints excluded: chain U residue 25 THR Chi-restraints excluded: chain U residue 40 ILE Chi-restraints excluded: chain U residue 61 ILE Chi-restraints excluded: chain U residue 63 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 233 random chunks: chunk 137 optimal weight: 3.9990 chunk 221 optimal weight: 2.9990 chunk 135 optimal weight: 0.8980 chunk 104 optimal weight: 5.9990 chunk 153 optimal weight: 9.9990 chunk 232 optimal weight: 2.9990 chunk 213 optimal weight: 9.9990 chunk 184 optimal weight: 1.9990 chunk 19 optimal weight: 0.8980 chunk 142 optimal weight: 0.9980 chunk 113 optimal weight: 0.3980 overall best weight: 1.0382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 121 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 584 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 930 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8307 moved from start: 0.5260 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 19138 Z= 0.239 Angle : 0.573 10.255 25854 Z= 0.297 Chirality : 0.043 0.189 2906 Planarity : 0.004 0.047 3305 Dihedral : 5.844 89.564 2530 Min Nonbonded Distance : 2.165 Molprobity Statistics. All-atom Clashscore : 7.83 Ramachandran Plot: Outliers : 0.09 % Allowed : 9.34 % Favored : 90.57 % Rotamer: Outliers : 2.24 % Allowed : 13.50 % Favored : 84.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.13 % 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: -1.18 (0.18), residues: 2334 helix: 0.55 (0.17), residues: 1036 sheet: -1.30 (0.34), residues: 260 loop : -2.06 (0.19), residues: 1038 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.060 0.002 TRP B 186 HIS 0.007 0.001 HIS B 269 PHE 0.019 0.001 PHE B 201 TYR 0.017 0.001 TYR U 37 ARG 0.003 0.000 ARG A 167 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4668 Ramachandran restraints generated. 2334 Oldfield, 0 Emsley, 2334 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4668 Ramachandran restraints generated. 2334 Oldfield, 0 Emsley, 2334 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 221 residues out of total 2096 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 47 poor density : 174 time to evaluate : 2.176 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 1 MET cc_start: 0.4952 (ppp) cc_final: 0.4640 (ppp) REVERT: A 191 LYS cc_start: 0.8552 (mmtp) cc_final: 0.8351 (mmtp) REVERT: A 584 ASN cc_start: 0.8867 (m-40) cc_final: 0.8642 (m110) REVERT: A 655 TYR cc_start: 0.8609 (m-80) cc_final: 0.8371 (m-10) REVERT: A 782 MET cc_start: 0.9312 (ttm) cc_final: 0.8951 (ttm) REVERT: A 985 LEU cc_start: 0.8756 (OUTLIER) cc_final: 0.8436 (pp) REVERT: A 1131 MET cc_start: 0.8743 (tpp) cc_final: 0.8427 (mpp) REVERT: A 1176 MET cc_start: 0.8423 (tpp) cc_final: 0.7806 (tpp) REVERT: A 1190 ASP cc_start: 0.7347 (t0) cc_final: 0.7058 (t0) REVERT: B 235 MET cc_start: 0.7732 (ptp) cc_final: 0.7029 (tmm) REVERT: B 368 ASP cc_start: 0.8322 (t0) cc_final: 0.8087 (t0) REVERT: B 388 ARG cc_start: 0.9056 (mtp180) cc_final: 0.8594 (ttm110) REVERT: B 727 GLU cc_start: 0.7643 (mp0) cc_final: 0.7379 (tm-30) REVERT: B 875 MET cc_start: 0.6790 (ptp) cc_final: 0.6476 (ptp) REVERT: U 12 ASP cc_start: 0.8590 (t70) cc_final: 0.8319 (t0) REVERT: U 15 GLN cc_start: 0.8567 (mm-40) cc_final: 0.8354 (tp-100) REVERT: U 40 ILE cc_start: 0.8630 (OUTLIER) cc_final: 0.8261 (mp) REVERT: U 44 TYR cc_start: 0.9013 (t80) cc_final: 0.8723 (t80) outliers start: 47 outliers final: 42 residues processed: 211 average time/residue: 0.2735 time to fit residues: 93.4422 Evaluate side-chains 208 residues out of total 2096 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 44 poor density : 164 time to evaluate : 2.130 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 132 VAL Chi-restraints excluded: chain A residue 140 ILE Chi-restraints excluded: chain A residue 189 THR Chi-restraints excluded: chain A residue 256 ASN Chi-restraints excluded: chain A residue 332 LEU Chi-restraints excluded: chain A residue 419 MET Chi-restraints excluded: chain A residue 469 GLU Chi-restraints excluded: chain A residue 477 THR Chi-restraints excluded: chain A residue 557 CYS Chi-restraints excluded: chain A residue 559 ILE Chi-restraints excluded: chain A residue 666 VAL Chi-restraints excluded: chain A residue 704 CYS Chi-restraints excluded: chain A residue 723 LEU Chi-restraints excluded: chain A residue 726 CYS Chi-restraints excluded: chain A residue 813 HIS Chi-restraints excluded: chain A residue 874 SER Chi-restraints excluded: chain A residue 936 THR Chi-restraints excluded: chain A residue 943 VAL Chi-restraints excluded: chain A residue 985 LEU Chi-restraints excluded: chain A residue 1019 ILE Chi-restraints excluded: chain A residue 1020 LEU Chi-restraints excluded: chain A residue 1084 VAL Chi-restraints excluded: chain A residue 1154 SER Chi-restraints excluded: chain A residue 1244 THR Chi-restraints excluded: chain B residue 100 ASP Chi-restraints excluded: chain B residue 135 THR Chi-restraints excluded: chain B residue 167 ILE Chi-restraints excluded: chain B residue 192 LYS Chi-restraints excluded: chain B residue 262 GLU Chi-restraints excluded: chain B residue 369 LEU Chi-restraints excluded: chain B residue 517 CYS Chi-restraints excluded: chain B residue 775 MET Chi-restraints excluded: chain B residue 778 GLU Chi-restraints excluded: chain B residue 895 SER Chi-restraints excluded: chain B residue 969 PHE Chi-restraints excluded: chain B residue 970 PHE Chi-restraints excluded: chain B residue 985 ARG Chi-restraints excluded: chain B residue 1002 LEU Chi-restraints excluded: chain B residue 1012 LEU Chi-restraints excluded: chain U residue -8 ASP Chi-restraints excluded: chain U residue 25 THR Chi-restraints excluded: chain U residue 40 ILE Chi-restraints excluded: chain U residue 61 ILE Chi-restraints excluded: chain U residue 63 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 233 random chunks: chunk 146 optimal weight: 0.9990 chunk 196 optimal weight: 4.9990 chunk 56 optimal weight: 0.0370 chunk 170 optimal weight: 0.8980 chunk 27 optimal weight: 3.9990 chunk 51 optimal weight: 2.9990 chunk 185 optimal weight: 0.0770 chunk 77 optimal weight: 1.9990 chunk 190 optimal weight: 0.7980 chunk 23 optimal weight: 4.9990 chunk 34 optimal weight: 4.9990 overall best weight: 0.5618 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 121 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 584 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 930 HIS ** 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 = 0.3836 r_free = 0.3836 target = 0.142911 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3225 r_free = 0.3225 target = 0.098266 restraints weight = 30506.216| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3266 r_free = 0.3266 target = 0.101575 restraints weight = 19071.001| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3292 r_free = 0.3292 target = 0.103628 restraints weight = 12875.551| |-----------------------------------------------------------------------------| r_work (final): 0.3285 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7937 moved from start: 0.5323 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 19138 Z= 0.168 Angle : 0.548 10.224 25854 Z= 0.284 Chirality : 0.042 0.191 2906 Planarity : 0.003 0.045 3305 Dihedral : 5.746 89.959 2530 Min Nonbonded Distance : 2.179 Molprobity Statistics. All-atom Clashscore : 7.30 Ramachandran Plot: Outliers : 0.09 % Allowed : 8.83 % Favored : 91.09 % Rotamer: Outliers : 1.81 % Allowed : 13.98 % Favored : 84.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.13 % 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: -1.04 (0.18), residues: 2334 helix: 0.71 (0.17), residues: 1027 sheet: -1.23 (0.34), residues: 255 loop : -2.01 (0.19), residues: 1052 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.052 0.002 TRP B 186 HIS 0.007 0.001 HIS A 121 PHE 0.023 0.001 PHE U 69 TYR 0.015 0.001 TYR U 37 ARG 0.004 0.000 ARG A 167 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3529.76 seconds wall clock time: 65 minutes 19.62 seconds (3919.62 seconds total)