Starting phenix.real_space_refine on Tue Mar 19 15:36:59 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8kd2_37122/03_2024/8kd2_37122.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8kd2_37122/03_2024/8kd2_37122.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.02 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8kd2_37122/03_2024/8kd2_37122.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8kd2_37122/03_2024/8kd2_37122.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8kd2_37122/03_2024/8kd2_37122.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8kd2_37122/03_2024/8kd2_37122.pdb" } resolution = 3.02 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.002 sd= 0.009 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians P 348 5.49 5 S 77 5.16 5 C 14551 2.51 5 N 4411 2.21 5 O 5307 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A GLU 289": "OE1" <-> "OE2" Residue "E GLU 305": "OE1" <-> "OE2" Residue "E GLU 432": "OE1" <-> "OE2" Residue "O GLU 50": "OE1" <-> "OE2" Residue "O GLU 59": "OE1" <-> "OE2" Residue "O GLU 94": "OE1" <-> "OE2" Residue "O GLU 97": "OE1" <-> "OE2" Residue "P GLU 63": "OE1" <-> "OE2" Residue "Q GLU 92": "OE1" <-> "OE2" Residue "S GLU 94": "OE1" <-> "OE2" Residue "S GLU 97": "OE1" <-> "OE2" Residue "S GLU 133": "OE1" <-> "OE2" Residue "T GLU 52": "OE1" <-> "OE2" Residue "U GLU 56": "OE1" <-> "OE2" Residue "U GLU 91": "OE1" <-> "OE2" Residue "V GLU 90": "OE1" <-> "OE2" Time to flip residues: 0.05s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib" Total number of atoms: 24694 Number of models: 1 Model: "" Number of chains: 16 Chain: "A" Number of atoms: 3097 Number of conformers: 1 Conformer: "" Number of residues, atoms: 391, 3097 Classifications: {'peptide': 391} Link IDs: {'PTRANS': 15, 'TRANS': 375} Chain breaks: 1 Chain: "B" Number of atoms: 4361 Number of conformers: 1 Conformer: "" Number of residues, atoms: 519, 4361 Classifications: {'peptide': 519} Link IDs: {'PTRANS': 12, 'TRANS': 506} Chain breaks: 4 Chain: "D" Number of atoms: 1474 Number of conformers: 1 Conformer: "" Number of residues, atoms: 182, 1474 Classifications: {'peptide': 182} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 7, 'TRANS': 174} Chain: "E" Number of atoms: 2399 Number of conformers: 1 Conformer: "" Number of residues, atoms: 290, 2399 Classifications: {'peptide': 290} Link IDs: {'PTRANS': 17, 'TRANS': 272} Chain breaks: 5 Chain: "F" Number of atoms: 146 Number of conformers: 1 Conformer: "" Number of residues, atoms: 19, 146 Classifications: {'peptide': 19} Link IDs: {'TRANS': 18} Chain breaks: 1 Chain: "G" Number of atoms: 160 Number of conformers: 1 Conformer: "" Number of residues, atoms: 18, 160 Classifications: {'peptide': 18} Link IDs: {'TRANS': 17} Chain breaks: 1 Chain: "O" Number of atoms: 791 Number of conformers: 1 Conformer: "" Number of residues, atoms: 96, 791 Classifications: {'peptide': 96} Link IDs: {'PTRANS': 3, 'TRANS': 92} Chain: "P" Number of atoms: 637 Number of conformers: 1 Conformer: "" Number of residues, atoms: 79, 637 Classifications: {'peptide': 79} Link IDs: {'PTRANS': 1, 'TRANS': 77} Chain: "Q" Number of atoms: 825 Number of conformers: 1 Conformer: "" Number of residues, atoms: 107, 825 Classifications: {'peptide': 107} Link IDs: {'PTRANS': 5, 'TRANS': 101} Chain: "R" Number of atoms: 715 Number of conformers: 1 Conformer: "" Number of residues, atoms: 91, 715 Classifications: {'peptide': 91} Link IDs: {'PTRANS': 2, 'TRANS': 88} Chain: "S" Number of atoms: 791 Number of conformers: 1 Conformer: "" Number of residues, atoms: 96, 791 Classifications: {'peptide': 96} Link IDs: {'PTRANS': 3, 'TRANS': 92} Chain: "T" Number of atoms: 618 Number of conformers: 1 Conformer: "" Number of residues, atoms: 77, 618 Classifications: {'peptide': 77} Link IDs: {'PTRANS': 1, 'TRANS': 75} Chain: "U" Number of atoms: 825 Number of conformers: 1 Conformer: "" Number of residues, atoms: 107, 825 Classifications: {'peptide': 107} Link IDs: {'PTRANS': 5, 'TRANS': 101} Chain: "V" Number of atoms: 721 Number of conformers: 1 Conformer: "" Number of residues, atoms: 92, 721 Classifications: {'peptide': 92} Link IDs: {'PTRANS': 2, 'TRANS': 89} Chain: "X" Number of atoms: 3590 Number of conformers: 1 Conformer: "" Number of residues, atoms: 174, 3590 Classifications: {'DNA': 174} Link IDs: {'rna3p': 173} Chain: "Y" Number of atoms: 3544 Number of conformers: 1 Conformer: "" Number of residues, atoms: 174, 3544 Classifications: {'DNA': 174} Link IDs: {'rna3p': 173} Time building chain proxies: 13.20, per 1000 atoms: 0.53 Number of scatterers: 24694 At special positions: 0 Unit cell: (134.9, 126.38, 189.57, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 77 16.00 P 348 15.00 O 5307 8.00 N 4411 7.00 C 14551 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=1, symmetry=0 Simple disulfide: pdb=" SG CYS E 303 " - pdb=" SG CYS E 306 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 11.73 Conformation dependent library (CDL) restraints added in 3.4 seconds 4224 Ramachandran restraints generated. 2112 Oldfield, 0 Emsley, 2112 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 4102 Finding SS restraints... Secondary structure from input PDB file: 92 helices and 16 sheets defined 58.2% alpha, 3.7% beta 137 base pairs and 269 stacking pairs defined. Time for finding SS restraints: 10.66 Creating SS restraints... Processing helix chain 'A' and resid 26 through 30 Processing helix chain 'A' and resid 42 through 55 removed outlier: 4.186A pdb=" N ARG A 46 " --> pdb=" O PRO A 42 " (cutoff:3.500A) Processing helix chain 'A' and resid 57 through 61 removed outlier: 3.536A pdb=" N LYS A 60 " --> pdb=" O LEU A 57 " (cutoff:3.500A) Processing helix chain 'A' and resid 70 through 75 Processing helix chain 'A' and resid 79 through 89 Processing helix chain 'A' and resid 97 through 104 removed outlier: 3.612A pdb=" N PHE A 104 " --> pdb=" O GLU A 100 " (cutoff:3.500A) Processing helix chain 'A' and resid 115 through 137 Processing helix chain 'A' and resid 164 through 173 removed outlier: 3.636A pdb=" N ILE A 171 " --> pdb=" O VAL A 167 " (cutoff:3.500A) removed outlier: 3.594A pdb=" N GLU A 172 " --> pdb=" O LEU A 168 " (cutoff:3.500A) Processing helix chain 'A' and resid 190 through 197 removed outlier: 3.550A pdb=" N PHE A 197 " --> pdb=" O VAL A 193 " (cutoff:3.500A) Processing helix chain 'A' and resid 226 through 230 Processing helix chain 'A' and resid 243 through 262 Proline residue: A 253 - end of helix Processing helix chain 'A' and resid 272 through 276 removed outlier: 4.038A pdb=" N SER A 275 " --> pdb=" O GLY A 272 " (cutoff:3.500A) Processing helix chain 'A' and resid 287 through 300 removed outlier: 4.060A pdb=" N CYS A 294 " --> pdb=" O GLY A 290 " (cutoff:3.500A) removed outlier: 4.112A pdb=" N VAL A 295 " --> pdb=" O HIS A 291 " (cutoff:3.500A) removed outlier: 3.626A pdb=" N VAL A 298 " --> pdb=" O CYS A 294 " (cutoff:3.500A) Processing helix chain 'A' and resid 314 through 330 removed outlier: 3.863A pdb=" N ASN A 330 " --> pdb=" O THR A 326 " (cutoff:3.500A) Processing helix chain 'A' and resid 365 through 381 Processing helix chain 'B' and resid 667 through 676 Processing helix chain 'B' and resid 678 through 694 removed outlier: 3.599A pdb=" N THR B 683 " --> pdb=" O LYS B 679 " (cutoff:3.500A) removed outlier: 4.494A pdb=" N GLU B 684 " --> pdb=" O HIS B 680 " (cutoff:3.500A) removed outlier: 3.835A pdb=" N TYR B 692 " --> pdb=" O ILE B 688 " (cutoff:3.500A) removed outlier: 3.764A pdb=" N SER B 693 " --> pdb=" O LEU B 689 " (cutoff:3.500A) Processing helix chain 'B' and resid 698 through 710 Processing helix chain 'B' and resid 714 through 723 removed outlier: 4.009A pdb=" N PHE B 723 " --> pdb=" O TRP B 719 " (cutoff:3.500A) Processing helix chain 'B' and resid 785 through 790 Processing helix chain 'B' and resid 801 through 840 Processing helix chain 'B' and resid 843 through 848 removed outlier: 4.090A pdb=" N ASN B 848 " --> pdb=" O ASN B 844 " (cutoff:3.500A) Processing helix chain 'B' and resid 861 through 871 Processing helix chain 'B' and resid 872 through 886 removed outlier: 4.072A pdb=" N PHE B 877 " --> pdb=" O LYS B 873 " (cutoff:3.500A) removed outlier: 3.917A pdb=" N GLU B 878 " --> pdb=" O GLU B 874 " (cutoff:3.500A) Processing helix chain 'B' and resid 890 through 929 removed outlier: 4.314A pdb=" N GLU B 911 " --> pdb=" O ARG B 907 " (cutoff:3.500A) removed outlier: 4.555A pdb=" N LYS B 914 " --> pdb=" O ARG B 910 " (cutoff:3.500A) removed outlier: 3.655A pdb=" N LYS B 922 " --> pdb=" O GLU B 918 " (cutoff:3.500A) removed outlier: 5.150A pdb=" N PHE B 925 " --> pdb=" O GLN B 921 " (cutoff:3.500A) removed outlier: 4.348A pdb=" N LYS B 926 " --> pdb=" O LYS B 922 " (cutoff:3.500A) Processing helix chain 'B' and resid 934 through 943 Processing helix chain 'B' and resid 944 through 957 Processing helix chain 'B' and resid 958 through 960 No H-bonds generated for 'chain 'B' and resid 958 through 960' Processing helix chain 'B' and resid 982 through 998 removed outlier: 4.267A pdb=" N TYR B 986 " --> pdb=" O LYS B 982 " (cutoff:3.500A) removed outlier: 3.865A pdb=" N ASP B 987 " --> pdb=" O ASN B 983 " (cutoff:3.500A) Processing helix chain 'B' and resid 1003 through 1022 Processing helix chain 'B' and resid 1142 through 1164 removed outlier: 3.523A pdb=" N ILE B1161 " --> pdb=" O ARG B1157 " (cutoff:3.500A) removed outlier: 3.995A pdb=" N MET B1164 " --> pdb=" O GLU B1160 " (cutoff:3.500A) Processing helix chain 'B' and resid 1164 through 1174 removed outlier: 3.717A pdb=" N VAL B1168 " --> pdb=" O MET B1164 " (cutoff:3.500A) Processing helix chain 'B' and resid 1179 through 1183 Processing helix chain 'B' and resid 1202 through 1217 Processing helix chain 'B' and resid 1220 through 1233 removed outlier: 3.588A pdb=" N TYR B1232 " --> pdb=" O LEU B1228 " (cutoff:3.500A) Processing helix chain 'B' and resid 1236 through 1240 removed outlier: 3.561A pdb=" N TYR B1240 " --> pdb=" O PHE B1237 " (cutoff:3.500A) Processing helix chain 'B' and resid 1241 through 1259 removed outlier: 3.753A pdb=" N THR B1255 " --> pdb=" O LYS B1251 " (cutoff:3.500A) removed outlier: 3.844A pdb=" N LEU B1256 " --> pdb=" O HIS B1252 " (cutoff:3.500A) removed outlier: 4.268A pdb=" N MET B1257 " --> pdb=" O ALA B1253 " (cutoff:3.500A) removed outlier: 3.675A pdb=" N ASP B1259 " --> pdb=" O THR B1255 " (cutoff:3.500A) Processing helix chain 'B' and resid 1260 through 1274 removed outlier: 3.901A pdb=" N ASN B1274 " --> pdb=" O VAL B1270 " (cutoff:3.500A) Processing helix chain 'B' and resid 1284 through 1292 removed outlier: 4.430A pdb=" N LEU B1288 " --> pdb=" O ILE B1284 " (cutoff:3.500A) Processing helix chain 'D' and resid 225 through 240 Processing helix chain 'D' and resid 253 through 265 Processing helix chain 'D' and resid 273 through 292 removed outlier: 4.292A pdb=" N GLN D 277 " --> pdb=" O GLY D 273 " (cutoff:3.500A) removed outlier: 3.747A pdb=" N ASP D 290 " --> pdb=" O LYS D 286 " (cutoff:3.500A) removed outlier: 4.005A pdb=" N LYS D 291 " --> pdb=" O LEU D 287 " (cutoff:3.500A) Processing helix chain 'D' and resid 292 through 297 removed outlier: 3.506A pdb=" N MET D 296 " --> pdb=" O CYS D 292 " (cutoff:3.500A) Processing helix chain 'D' and resid 302 through 316 removed outlier: 3.867A pdb=" N ASP D 316 " --> pdb=" O LYS D 312 " (cutoff:3.500A) Processing helix chain 'D' and resid 327 through 337 removed outlier: 3.595A pdb=" N LEU D 331 " --> pdb=" O GLY D 327 " (cutoff:3.500A) Processing helix chain 'D' and resid 337 through 343 removed outlier: 3.989A pdb=" N LEU D 341 " --> pdb=" O VAL D 337 " (cutoff:3.500A) removed outlier: 3.859A pdb=" N SER D 343 " --> pdb=" O PRO D 339 " (cutoff:3.500A) Processing helix chain 'D' and resid 348 through 369 removed outlier: 3.893A pdb=" N LEU D 354 " --> pdb=" O GLN D 350 " (cutoff:3.500A) removed outlier: 3.692A pdb=" N MET D 368 " --> pdb=" O VAL D 364 " (cutoff:3.500A) Processing helix chain 'D' and resid 369 through 374 Processing helix chain 'D' and resid 391 through 399 removed outlier: 3.550A pdb=" N LEU D 399 " --> pdb=" O GLU D 395 " (cutoff:3.500A) Processing helix chain 'E' and resid 306 through 311 removed outlier: 4.134A pdb=" N ILE E 310 " --> pdb=" O CYS E 306 " (cutoff:3.500A) removed outlier: 4.582A pdb=" N PHE E 311 " --> pdb=" O LYS E 307 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 306 through 311' Processing helix chain 'E' and resid 321 through 330 removed outlier: 4.212A pdb=" N ASN E 325 " --> pdb=" O LYS E 321 " (cutoff:3.500A) removed outlier: 3.742A pdb=" N LYS E 328 " --> pdb=" O SER E 324 " (cutoff:3.500A) removed outlier: 4.145A pdb=" N ASN E 330 " --> pdb=" O PHE E 326 " (cutoff:3.500A) Processing helix chain 'E' and resid 333 through 335 No H-bonds generated for 'chain 'E' and resid 333 through 335' Processing helix chain 'E' and resid 336 through 342 removed outlier: 3.558A pdb=" N ASN E 342 " --> pdb=" O LYS E 338 " (cutoff:3.500A) Processing helix chain 'E' and resid 357 through 361 Processing helix chain 'E' and resid 400 through 407 removed outlier: 3.529A pdb=" N ASP E 404 " --> pdb=" O SER E 400 " (cutoff:3.500A) Processing helix chain 'E' and resid 430 through 434 removed outlier: 4.001A pdb=" N ASN E 433 " --> pdb=" O HIS E 430 " (cutoff:3.500A) Processing helix chain 'E' and resid 544 through 561 Processing helix chain 'F' and resid 348 through 351 removed outlier: 3.758A pdb=" N SER F 351 " --> pdb=" O ASP F 348 " (cutoff:3.500A) No H-bonds generated for 'chain 'F' and resid 348 through 351' Processing helix chain 'F' and resid 352 through 360 removed outlier: 3.778A pdb=" N ILE F 356 " --> pdb=" O CYS F 352 " (cutoff:3.500A) Processing helix chain 'G' and resid 322 through 330 removed outlier: 3.539A pdb=" N ASN G 330 " --> pdb=" O PHE G 326 " (cutoff:3.500A) Processing helix chain 'O' and resid 44 through 57 removed outlier: 3.543A pdb=" N LEU O 48 " --> pdb=" O GLY O 44 " (cutoff:3.500A) Processing helix chain 'O' and resid 63 through 76 Processing helix chain 'O' and resid 85 through 114 Processing helix chain 'O' and resid 120 through 131 Processing helix chain 'P' and resid 24 through 29 removed outlier: 4.065A pdb=" N GLN P 27 " --> pdb=" O ASP P 24 " (cutoff:3.500A) removed outlier: 3.766A pdb=" N ILE P 29 " --> pdb=" O ILE P 26 " (cutoff:3.500A) Processing helix chain 'P' and resid 30 through 41 Processing helix chain 'P' and resid 49 through 76 removed outlier: 4.114A pdb=" N GLU P 53 " --> pdb=" O LEU P 49 " (cutoff:3.500A) removed outlier: 3.655A pdb=" N ALA P 76 " --> pdb=" O TYR P 72 " (cutoff:3.500A) Processing helix chain 'P' and resid 82 through 93 removed outlier: 3.528A pdb=" N VAL P 86 " --> pdb=" O THR P 82 " (cutoff:3.500A) Processing helix chain 'Q' and resid 26 through 37 Processing helix chain 'Q' and resid 45 through 73 removed outlier: 4.139A pdb=" N VAL Q 49 " --> pdb=" O ALA Q 45 " (cutoff:3.500A) Processing helix chain 'Q' and resid 79 through 90 removed outlier: 3.542A pdb=" N ASP Q 90 " --> pdb=" O ALA Q 86 " (cutoff:3.500A) Processing helix chain 'Q' and resid 90 through 97 Processing helix chain 'R' and resid 34 through 46 Processing helix chain 'R' and resid 52 through 81 removed outlier: 3.802A pdb=" N ASN R 81 " --> pdb=" O LEU R 77 " (cutoff:3.500A) Processing helix chain 'R' and resid 87 through 99 Processing helix chain 'R' and resid 100 through 119 removed outlier: 3.626A pdb=" N ALA R 104 " --> pdb=" O PRO R 100 " (cutoff:3.500A) Processing helix chain 'S' and resid 44 through 57 removed outlier: 3.822A pdb=" N SER S 57 " --> pdb=" O ARG S 53 " (cutoff:3.500A) Processing helix chain 'S' and resid 63 through 79 removed outlier: 3.581A pdb=" N PHE S 67 " --> pdb=" O ARG S 63 " (cutoff:3.500A) removed outlier: 3.915A pdb=" N ASP S 77 " --> pdb=" O GLU S 73 " (cutoff:3.500A) removed outlier: 4.116A pdb=" N PHE S 78 " --> pdb=" O ILE S 74 " (cutoff:3.500A) Processing helix chain 'S' and resid 85 through 114 Processing helix chain 'S' and resid 120 through 132 Processing helix chain 'T' and resid 30 through 41 Processing helix chain 'T' and resid 49 through 76 removed outlier: 4.149A pdb=" N GLU T 53 " --> pdb=" O LEU T 49 " (cutoff:3.500A) removed outlier: 3.534A pdb=" N ALA T 76 " --> pdb=" O TYR T 72 " (cutoff:3.500A) Processing helix chain 'T' and resid 82 through 92 removed outlier: 3.800A pdb=" N VAL T 86 " --> pdb=" O THR T 82 " (cutoff:3.500A) Processing helix chain 'U' and resid 16 through 22 Processing helix chain 'U' and resid 26 through 37 Processing helix chain 'U' and resid 45 through 74 removed outlier: 4.251A pdb=" N VAL U 49 " --> pdb=" O ALA U 45 " (cutoff:3.500A) Processing helix chain 'U' and resid 79 through 90 removed outlier: 3.572A pdb=" N ASP U 90 " --> pdb=" O ALA U 86 " (cutoff:3.500A) Processing helix chain 'U' and resid 90 through 97 Processing helix chain 'V' and resid 34 through 46 Processing helix chain 'V' and resid 52 through 81 Processing helix chain 'V' and resid 87 through 98 Processing helix chain 'V' and resid 101 through 120 removed outlier: 3.947A pdb=" N LYS V 105 " --> pdb=" O GLY V 101 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 63 through 64 removed outlier: 8.838A pdb=" N TYR A 64 " --> pdb=" O VAL A 21 " (cutoff:3.500A) removed outlier: 7.026A pdb=" N TYR A 23 " --> pdb=" O TYR A 64 " (cutoff:3.500A) removed outlier: 6.337A pdb=" N ALA A 22 " --> pdb=" O VAL A 143 " (cutoff:3.500A) removed outlier: 6.016A pdb=" N ALA A 142 " --> pdb=" O VAL A 307 " (cutoff:3.500A) removed outlier: 6.453A pdb=" N VAL A 267 " --> pdb=" O MET A 306 " (cutoff:3.500A) removed outlier: 7.328A pdb=" N VAL A 308 " --> pdb=" O VAL A 267 " (cutoff:3.500A) removed outlier: 5.812A pdb=" N LEU A 269 " --> pdb=" O VAL A 308 " (cutoff:3.500A) removed outlier: 6.618A pdb=" N LEU A 181 " --> pdb=" O VAL A 268 " (cutoff:3.500A) removed outlier: 7.732A pdb=" N GLN A 270 " --> pdb=" O LEU A 181 " (cutoff:3.500A) removed outlier: 7.046A pdb=" N ILE A 183 " --> pdb=" O GLN A 270 " (cutoff:3.500A) removed outlier: 6.456A pdb=" N VAL A 180 " --> pdb=" O MET A 204 " (cutoff:3.500A) removed outlier: 7.526A pdb=" N CYS A 206 " --> pdb=" O VAL A 180 " (cutoff:3.500A) removed outlier: 5.912A pdb=" N TYR A 182 " --> pdb=" O CYS A 206 " (cutoff:3.500A) removed outlier: 7.739A pdb=" N PHE A 208 " --> pdb=" O TYR A 182 " (cutoff:3.500A) removed outlier: 6.363A pdb=" N ASP A 184 " --> pdb=" O PHE A 208 " (cutoff:3.500A) removed outlier: 8.823A pdb=" N LYS A 210 " --> pdb=" O ASP A 184 " (cutoff:3.500A) removed outlier: 7.648A pdb=" N VAL A 236 " --> pdb=" O THR A 205 " (cutoff:3.500A) removed outlier: 6.779A pdb=" N SER A 207 " --> pdb=" O VAL A 236 " (cutoff:3.500A) removed outlier: 7.301A pdb=" N LEU A 238 " --> pdb=" O SER A 207 " (cutoff:3.500A) removed outlier: 6.647A pdb=" N HIS A 209 " --> pdb=" O LEU A 238 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA1 Processing sheet with id=AA2, first strand: chain 'B' and resid 756 through 757 removed outlier: 3.567A pdb=" N LYS B 756 " --> pdb=" O VAL B 783 " (cutoff:3.500A) removed outlier: 3.633A pdb=" N VAL B 783 " --> pdb=" O LYS B 756 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA2 Processing sheet with id=AA3, first strand: chain 'B' and resid 1136 through 1141 removed outlier: 3.715A pdb=" N PHE B1136 " --> pdb=" O PHE B1305 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'D' and resid 244 through 246 Processing sheet with id=AA5, first strand: chain 'E' and resid 437 through 439 Processing sheet with id=AA6, first strand: chain 'E' and resid 475 through 476 removed outlier: 3.821A pdb=" N LYS E 476 " --> pdb=" O LYS E 490 " (cutoff:3.500A) removed outlier: 3.778A pdb=" N LYS E 490 " --> pdb=" O LYS E 476 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA6 Processing sheet with id=AA7, first strand: chain 'E' and resid 521 through 523 removed outlier: 3.696A pdb=" N ILE E 542 " --> pdb=" O GLN E 521 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'O' and resid 83 through 84 removed outlier: 6.976A pdb=" N ARG O 83 " --> pdb=" O VAL P 81 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA8 Processing sheet with id=AA9, first strand: chain 'O' and resid 118 through 119 Processing sheet with id=AB1, first strand: chain 'P' and resid 96 through 98 removed outlier: 6.175A pdb=" N THR P 96 " --> pdb=" O THR U 101 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB1 Processing sheet with id=AB2, first strand: chain 'Q' and resid 42 through 43 removed outlier: 7.091A pdb=" N ARG Q 42 " --> pdb=" O ILE R 86 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB2 Processing sheet with id=AB3, first strand: chain 'Q' and resid 77 through 78 Processing sheet with id=AB4, first strand: chain 'Q' and resid 100 through 102 Processing sheet with id=AB5, first strand: chain 'S' and resid 83 through 84 removed outlier: 6.957A pdb=" N ARG S 83 " --> pdb=" O VAL T 81 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB5 Processing sheet with id=AB6, first strand: chain 'U' and resid 42 through 43 removed outlier: 7.355A pdb=" N ARG U 42 " --> pdb=" O ILE V 86 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB6 Processing sheet with id=AB7, first strand: chain 'U' and resid 77 through 78 841 hydrogen bonds defined for protein. 2481 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 357 hydrogen bonds 714 hydrogen bond angles 0 basepair planarities 137 basepair parallelities 269 stacking parallelities Total time for adding SS restraints: 15.85 Time building geometry restraints manager: 12.58 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 6292 1.34 - 1.46: 7273 1.46 - 1.58: 11520 1.58 - 1.70: 694 1.70 - 1.82: 119 Bond restraints: 25898 Sorted by residual: bond pdb=" N ASN E 45 " pdb=" CA ASN E 45 " ideal model delta sigma weight residual 1.457 1.492 -0.035 1.29e-02 6.01e+03 7.25e+00 bond pdb=" N TYR E 46 " pdb=" CA TYR E 46 " ideal model delta sigma weight residual 1.457 1.489 -0.032 1.26e-02 6.30e+03 6.62e+00 bond pdb=" N LEU E 48 " pdb=" CA LEU E 48 " ideal model delta sigma weight residual 1.457 1.488 -0.030 1.29e-02 6.01e+03 5.55e+00 bond pdb=" N LYS E 49 " pdb=" CA LYS E 49 " ideal model delta sigma weight residual 1.454 1.484 -0.031 1.34e-02 5.57e+03 5.27e+00 bond pdb=" N LEU B 883 " pdb=" CA LEU B 883 " ideal model delta sigma weight residual 1.458 1.485 -0.027 1.23e-02 6.61e+03 4.72e+00 ... (remaining 25893 not shown) Histogram of bond angle deviations from ideal: 97.26 - 104.82: 1525 104.82 - 112.38: 13700 112.38 - 119.94: 9964 119.94 - 127.50: 10625 127.50 - 135.06: 629 Bond angle restraints: 36443 Sorted by residual: angle pdb=" CA LEU D 248 " pdb=" C LEU D 248 " pdb=" N PRO D 249 " ideal model delta sigma weight residual 120.58 117.53 3.05 7.40e-01 1.83e+00 1.70e+01 angle pdb=" C ASN E 516 " pdb=" N ASN E 517 " pdb=" CA ASN E 517 " ideal model delta sigma weight residual 121.54 129.15 -7.61 1.91e+00 2.74e-01 1.59e+01 angle pdb=" CB MET A 373 " pdb=" CG MET A 373 " pdb=" SD MET A 373 " ideal model delta sigma weight residual 112.70 124.58 -11.88 3.00e+00 1.11e-01 1.57e+01 angle pdb=" CB ILE E 523 " pdb=" CG1 ILE E 523 " pdb=" CD1 ILE E 523 " ideal model delta sigma weight residual 113.80 121.72 -7.92 2.10e+00 2.27e-01 1.42e+01 angle pdb=" CG ARG D 247 " pdb=" CD ARG D 247 " pdb=" NE ARG D 247 " ideal model delta sigma weight residual 112.00 120.24 -8.24 2.20e+00 2.07e-01 1.40e+01 ... (remaining 36438 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 27.36: 11714 27.36 - 54.71: 2548 54.71 - 82.07: 390 82.07 - 109.42: 12 109.42 - 136.78: 2 Dihedral angle restraints: 14666 sinusoidal: 8322 harmonic: 6344 Sorted by residual: dihedral pdb=" C4' DC X 11 " pdb=" C3' DC X 11 " pdb=" O3' DC X 11 " pdb=" P DG X 12 " ideal model delta sinusoidal sigma weight residual 220.00 83.22 136.78 1 3.50e+01 8.16e-04 1.35e+01 dihedral pdb=" C4' DC Y -73 " pdb=" C3' DC Y -73 " pdb=" O3' DC Y -73 " pdb=" P DT Y -72 " ideal model delta sinusoidal sigma weight residual 220.00 85.00 135.00 1 3.50e+01 8.16e-04 1.34e+01 dihedral pdb=" CA MET A 360 " pdb=" C MET A 360 " pdb=" N PHE A 361 " pdb=" CA PHE A 361 " ideal model delta harmonic sigma weight residual -180.00 -162.00 -18.00 0 5.00e+00 4.00e-02 1.30e+01 ... (remaining 14663 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.060: 3535 0.060 - 0.120: 467 0.120 - 0.181: 35 0.181 - 0.241: 3 0.241 - 0.301: 1 Chirality restraints: 4041 Sorted by residual: chirality pdb=" CG LEU D 363 " pdb=" CB LEU D 363 " pdb=" CD1 LEU D 363 " pdb=" CD2 LEU D 363 " both_signs ideal model delta sigma weight residual False -2.59 -2.29 -0.30 2.00e-01 2.50e+01 2.26e+00 chirality pdb=" CB THR B 833 " pdb=" CA THR B 833 " pdb=" OG1 THR B 833 " pdb=" CG2 THR B 833 " both_signs ideal model delta sigma weight residual False 2.55 2.33 0.22 2.00e-01 2.50e+01 1.27e+00 chirality pdb=" CA ASN E 517 " pdb=" N ASN E 517 " pdb=" C ASN E 517 " pdb=" CB ASN E 517 " both_signs ideal model delta sigma weight residual False 2.51 2.32 0.19 2.00e-01 2.50e+01 8.63e-01 ... (remaining 4038 not shown) Planarity restraints: 3424 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TRP B 916 " 0.030 2.00e-02 2.50e+03 2.41e-02 1.45e+01 pdb=" CG TRP B 916 " -0.064 2.00e-02 2.50e+03 pdb=" CD1 TRP B 916 " 0.026 2.00e-02 2.50e+03 pdb=" CD2 TRP B 916 " -0.001 2.00e-02 2.50e+03 pdb=" NE1 TRP B 916 " -0.001 2.00e-02 2.50e+03 pdb=" CE2 TRP B 916 " -0.000 2.00e-02 2.50e+03 pdb=" CE3 TRP B 916 " -0.000 2.00e-02 2.50e+03 pdb=" CZ2 TRP B 916 " 0.000 2.00e-02 2.50e+03 pdb=" CZ3 TRP B 916 " 0.002 2.00e-02 2.50e+03 pdb=" CH2 TRP B 916 " 0.008 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ASN A 105 " 0.013 2.00e-02 2.50e+03 2.54e-02 6.45e+00 pdb=" C ASN A 105 " -0.044 2.00e-02 2.50e+03 pdb=" O ASN A 105 " 0.017 2.00e-02 2.50e+03 pdb=" N VAL A 106 " 0.014 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TRP E 301 " 0.013 2.00e-02 2.50e+03 1.47e-02 5.43e+00 pdb=" CG TRP E 301 " -0.040 2.00e-02 2.50e+03 pdb=" CD1 TRP E 301 " 0.018 2.00e-02 2.50e+03 pdb=" CD2 TRP E 301 " 0.003 2.00e-02 2.50e+03 pdb=" NE1 TRP E 301 " -0.001 2.00e-02 2.50e+03 pdb=" CE2 TRP E 301 " 0.000 2.00e-02 2.50e+03 pdb=" CE3 TRP E 301 " 0.006 2.00e-02 2.50e+03 pdb=" CZ2 TRP E 301 " -0.000 2.00e-02 2.50e+03 pdb=" CZ3 TRP E 301 " -0.000 2.00e-02 2.50e+03 pdb=" CH2 TRP E 301 " 0.000 2.00e-02 2.50e+03 ... (remaining 3421 not shown) Histogram of nonbonded interaction distances: 1.46 - 2.15: 1 2.15 - 2.83: 7181 2.83 - 3.52: 35443 3.52 - 4.21: 64119 4.21 - 4.90: 100474 Nonbonded interactions: 207218 Sorted by model distance: nonbonded pdb=" CB GLU B 813 " pdb=" CD2 LEU E 48 " model vdw 1.457 3.860 nonbonded pdb=" N2 DG X 20 " pdb=" O6 DG Y -19 " model vdw 2.168 2.520 nonbonded pdb=" OH TYR A 343 " pdb=" OE2 GLU B 822 " model vdw 2.210 2.440 nonbonded pdb=" CA GLU B 813 " pdb=" CD2 LEU E 48 " model vdw 2.212 3.890 nonbonded pdb=" O SER A 275 " pdb=" OG SER A 275 " model vdw 2.238 2.440 ... (remaining 207213 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = chain 'O' selection = chain 'S' } ncs_group { reference = (chain 'P' and resid 24 through 100) selection = chain 'T' } ncs_group { reference = chain 'Q' selection = chain 'U' } ncs_group { reference = chain 'R' selection = (chain 'V' and resid 29 through 119) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=0.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 9.430 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: 33.760 Check model and map are aligned: 0.370 Set scattering table: 0.230 Process input model: 80.850 Find NCS groups from input model: 0.740 Set up NCS constraints: 0.130 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:2.670 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 128.210 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7165 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 : 0.004 0.045 25898 Z= 0.213 Angle : 0.704 11.877 36443 Z= 0.384 Chirality : 0.041 0.301 4041 Planarity : 0.005 0.083 3424 Dihedral : 25.700 136.778 10561 Min Nonbonded Distance : 1.457 Molprobity Statistics. All-atom Clashscore : 8.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.31 % Favored : 95.69 % Rotamer: Outliers : 0.68 % Allowed : 37.92 % Favored : 61.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.56 (0.17), residues: 2112 helix: 0.58 (0.15), residues: 1142 sheet: 0.55 (0.64), residues: 75 loop : -1.73 (0.18), residues: 895 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.064 0.003 TRP B 916 HIS 0.016 0.001 HIS R 46 PHE 0.033 0.002 PHE A 160 TYR 0.029 0.002 TYR P 88 ARG 0.018 0.001 ARG O 129 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4224 Ramachandran restraints generated. 2112 Oldfield, 0 Emsley, 2112 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4224 Ramachandran restraints generated. 2112 Oldfield, 0 Emsley, 2112 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 266 residues out of total 1917 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 253 time to evaluate : 2.346 Fit side-chains REVERT: B 717 PHE cc_start: 0.2539 (OUTLIER) cc_final: 0.2129 (t80) outliers start: 13 outliers final: 4 residues processed: 258 average time/residue: 0.3253 time to fit residues: 136.3693 Evaluate side-chains 236 residues out of total 1917 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 231 time to evaluate : 2.198 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 717 PHE Chi-restraints excluded: chain B residue 1020 LEU Chi-restraints excluded: chain B residue 1144 ILE Chi-restraints excluded: chain D residue 248 LEU Chi-restraints excluded: chain O residue 120 MET Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 243 random chunks: chunk 205 optimal weight: 3.9990 chunk 184 optimal weight: 2.9990 chunk 102 optimal weight: 0.6980 chunk 62 optimal weight: 6.9990 chunk 124 optimal weight: 7.9990 chunk 98 optimal weight: 2.9990 chunk 190 optimal weight: 5.9990 chunk 73 optimal weight: 1.9990 chunk 115 optimal weight: 8.9990 chunk 141 optimal weight: 2.9990 chunk 220 optimal weight: 3.9990 overall best weight: 2.3388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 150 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 177 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 364 ASN B 690 ASN ** B 815 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 974 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B1254 HIS D 295 ASN E 259 ASN E 304 ASN ** E 448 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** O 68 GLN P 25 ASN P 75 HIS Q 82 HIS ** R 46 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** R 60 ASN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7877 moved from start: 0.3534 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.203 25898 Z= 0.492 Angle : 0.768 22.949 36443 Z= 0.417 Chirality : 0.047 0.254 4041 Planarity : 0.006 0.077 3424 Dihedral : 27.921 139.700 6166 Min Nonbonded Distance : 1.984 Molprobity Statistics. All-atom Clashscore : 17.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.21 % Favored : 95.79 % Rotamer: Outliers : 8.09 % Allowed : 27.13 % Favored : 64.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.69 (0.17), residues: 2112 helix: 0.35 (0.15), residues: 1161 sheet: 0.17 (0.59), residues: 81 loop : -1.60 (0.20), residues: 870 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.039 0.003 TRP B 916 HIS 0.015 0.003 HIS R 46 PHE 0.030 0.003 PHE B 668 TYR 0.036 0.003 TYR B 755 ARG 0.010 0.001 ARG T 45 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4224 Ramachandran restraints generated. 2112 Oldfield, 0 Emsley, 2112 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4224 Ramachandran restraints generated. 2112 Oldfield, 0 Emsley, 2112 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 450 residues out of total 1917 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 155 poor density : 295 time to evaluate : 2.657 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 174 LEU cc_start: 0.7485 (OUTLIER) cc_final: 0.7269 (mm) REVERT: A 289 GLU cc_start: 0.6895 (tm-30) cc_final: 0.6663 (tm-30) REVERT: A 306 MET cc_start: 0.8803 (OUTLIER) cc_final: 0.7530 (tmm) REVERT: A 346 TYR cc_start: 0.8488 (OUTLIER) cc_final: 0.7637 (t80) REVERT: B 709 TYR cc_start: 0.6827 (OUTLIER) cc_final: 0.4461 (t80) REVERT: B 805 GLU cc_start: 0.7152 (pp20) cc_final: 0.6835 (pp20) REVERT: B 817 TYR cc_start: 0.8662 (OUTLIER) cc_final: 0.8267 (t80) REVERT: B 860 MET cc_start: 0.6098 (mmp) cc_final: 0.5670 (mpp) REVERT: B 962 LYS cc_start: 0.5070 (OUTLIER) cc_final: 0.4156 (ptpp) REVERT: B 986 TYR cc_start: 0.6025 (OUTLIER) cc_final: 0.4588 (t80) REVERT: B 1164 MET cc_start: 0.7066 (OUTLIER) cc_final: 0.6109 (pp-130) REVERT: B 1167 ARG cc_start: 0.7551 (OUTLIER) cc_final: 0.6739 (pmt-80) REVERT: B 1248 SER cc_start: 0.8093 (t) cc_final: 0.7595 (m) REVERT: B 1284 ILE cc_start: 0.7074 (OUTLIER) cc_final: 0.6840 (pp) REVERT: D 220 ILE cc_start: 0.5832 (mt) cc_final: 0.5449 (mm) REVERT: D 222 LEU cc_start: 0.7422 (OUTLIER) cc_final: 0.7153 (pp) REVERT: D 354 LEU cc_start: 0.7371 (OUTLIER) cc_final: 0.6934 (pp) REVERT: E 35 ARG cc_start: 0.6699 (OUTLIER) cc_final: 0.6325 (mpp80) REVERT: E 365 LYS cc_start: 0.8825 (OUTLIER) cc_final: 0.8523 (ptpp) REVERT: E 376 ASN cc_start: 0.6776 (OUTLIER) cc_final: 0.6515 (t0) REVERT: E 472 THR cc_start: 0.6905 (OUTLIER) cc_final: 0.6615 (p) REVERT: E 514 TYR cc_start: 0.6579 (t80) cc_final: 0.6319 (t80) REVERT: E 560 MET cc_start: 0.6305 (mmm) cc_final: 0.6009 (mmm) REVERT: O 42 ARG cc_start: 0.8248 (OUTLIER) cc_final: 0.7928 (mmm-85) REVERT: P 85 ASP cc_start: 0.8478 (p0) cc_final: 0.8266 (p0) REVERT: P 88 TYR cc_start: 0.8997 (m-10) cc_final: 0.8726 (m-80) REVERT: P 92 ARG cc_start: 0.8621 (OUTLIER) cc_final: 0.7264 (ptp-170) REVERT: Q 36 LYS cc_start: 0.8075 (OUTLIER) cc_final: 0.7595 (pttp) REVERT: Q 56 GLU cc_start: 0.8747 (OUTLIER) cc_final: 0.8444 (tt0) REVERT: Q 74 LYS cc_start: 0.8669 (OUTLIER) cc_final: 0.8271 (mptp) REVERT: Q 91 GLU cc_start: 0.8422 (OUTLIER) cc_final: 0.8037 (tt0) REVERT: R 56 MET cc_start: 0.8975 (tpp) cc_final: 0.8746 (tpp) REVERT: R 113 LYS cc_start: 0.8324 (OUTLIER) cc_final: 0.8026 (ttpp) REVERT: S 109 LEU cc_start: 0.9434 (OUTLIER) cc_final: 0.9220 (mp) REVERT: T 79 LYS cc_start: 0.8995 (OUTLIER) cc_final: 0.8567 (tppt) REVERT: U 56 GLU cc_start: 0.8939 (OUTLIER) cc_final: 0.8313 (tm-30) outliers start: 155 outliers final: 67 residues processed: 412 average time/residue: 0.3758 time to fit residues: 238.4560 Evaluate side-chains 343 residues out of total 1917 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 93 poor density : 250 time to evaluate : 2.312 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 28 ASP Chi-restraints excluded: chain A residue 94 LEU Chi-restraints excluded: chain A residue 129 GLU Chi-restraints excluded: chain A residue 174 LEU Chi-restraints excluded: chain A residue 201 ASP Chi-restraints excluded: chain A residue 218 THR Chi-restraints excluded: chain A residue 242 ILE Chi-restraints excluded: chain A residue 250 VAL Chi-restraints excluded: chain A residue 265 SER Chi-restraints excluded: chain A residue 300 SER Chi-restraints excluded: chain A residue 306 MET Chi-restraints excluded: chain A residue 314 THR Chi-restraints excluded: chain A residue 331 ASN Chi-restraints excluded: chain A residue 345 GLU Chi-restraints excluded: chain A residue 346 TYR Chi-restraints excluded: chain B residue 668 PHE Chi-restraints excluded: chain B residue 698 ASP Chi-restraints excluded: chain B residue 703 VAL Chi-restraints excluded: chain B residue 709 TYR Chi-restraints excluded: chain B residue 718 THR Chi-restraints excluded: chain B residue 779 ASN Chi-restraints excluded: chain B residue 810 ILE Chi-restraints excluded: chain B residue 815 HIS Chi-restraints excluded: chain B residue 817 TYR Chi-restraints excluded: chain B residue 872 ASP Chi-restraints excluded: chain B residue 883 LEU Chi-restraints excluded: chain B residue 907 ARG Chi-restraints excluded: chain B residue 962 LYS Chi-restraints excluded: chain B residue 986 TYR Chi-restraints excluded: chain B residue 997 THR Chi-restraints excluded: chain B residue 1010 LEU Chi-restraints excluded: chain B residue 1020 LEU Chi-restraints excluded: chain B residue 1024 ILE Chi-restraints excluded: chain B residue 1144 ILE Chi-restraints excluded: chain B residue 1146 ILE Chi-restraints excluded: chain B residue 1164 MET Chi-restraints excluded: chain B residue 1167 ARG Chi-restraints excluded: chain B residue 1179 THR Chi-restraints excluded: chain B residue 1196 LEU Chi-restraints excluded: chain B residue 1207 VAL Chi-restraints excluded: chain B residue 1220 GLU Chi-restraints excluded: chain B residue 1228 LEU Chi-restraints excluded: chain B residue 1229 ARG Chi-restraints excluded: chain B residue 1266 MET Chi-restraints excluded: chain B residue 1284 ILE Chi-restraints excluded: chain B residue 1312 VAL Chi-restraints excluded: chain B residue 1322 LEU Chi-restraints excluded: chain D residue 222 LEU Chi-restraints excluded: chain D residue 230 SER Chi-restraints excluded: chain D residue 261 TYR Chi-restraints excluded: chain D residue 265 VAL Chi-restraints excluded: chain D residue 287 LEU Chi-restraints excluded: chain D residue 305 GLN Chi-restraints excluded: chain D residue 321 VAL Chi-restraints excluded: chain D residue 344 SER Chi-restraints excluded: chain D residue 354 LEU Chi-restraints excluded: chain D residue 360 GLU Chi-restraints excluded: chain D residue 401 MET Chi-restraints excluded: chain E residue 35 ARG Chi-restraints excluded: chain E residue 365 LYS Chi-restraints excluded: chain E residue 376 ASN Chi-restraints excluded: chain E residue 415 LEU Chi-restraints excluded: chain E residue 423 THR Chi-restraints excluded: chain E residue 452 VAL Chi-restraints excluded: chain E residue 472 THR Chi-restraints excluded: chain E residue 474 VAL Chi-restraints excluded: chain E residue 542 ILE Chi-restraints excluded: chain O residue 42 ARG Chi-restraints excluded: chain O residue 87 SER Chi-restraints excluded: chain P residue 92 ARG Chi-restraints excluded: chain P residue 96 THR Chi-restraints excluded: chain Q residue 36 LYS Chi-restraints excluded: chain Q residue 56 GLU Chi-restraints excluded: chain Q residue 74 LYS Chi-restraints excluded: chain Q residue 91 GLU Chi-restraints excluded: chain R residue 48 ASP Chi-restraints excluded: chain R residue 60 ASN Chi-restraints excluded: chain R residue 81 ASN Chi-restraints excluded: chain R residue 84 SER Chi-restraints excluded: chain R residue 113 LYS Chi-restraints excluded: chain S residue 59 GLU Chi-restraints excluded: chain S residue 80 THR Chi-restraints excluded: chain S residue 103 LEU Chi-restraints excluded: chain S residue 109 LEU Chi-restraints excluded: chain T residue 30 THR Chi-restraints excluded: chain T residue 44 LYS Chi-restraints excluded: chain T residue 49 LEU Chi-restraints excluded: chain T residue 79 LYS Chi-restraints excluded: chain T residue 93 GLN Chi-restraints excluded: chain T residue 96 THR Chi-restraints excluded: chain U residue 56 GLU Chi-restraints excluded: chain U residue 71 ARG Chi-restraints excluded: chain V residue 49 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 243 random chunks: chunk 122 optimal weight: 6.9990 chunk 68 optimal weight: 4.9990 chunk 183 optimal weight: 0.3980 chunk 150 optimal weight: 0.9980 chunk 60 optimal weight: 0.9990 chunk 221 optimal weight: 3.9990 chunk 238 optimal weight: 2.9990 chunk 196 optimal weight: 2.9990 chunk 219 optimal weight: 1.9990 chunk 75 optimal weight: 2.9990 chunk 177 optimal weight: 0.9990 overall best weight: 1.0786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 150 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 296 ASN ** A 330 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 341 ASN ** B 815 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 974 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B1254 HIS B1274 ASN ** B1293 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B1299 ASN E 304 ASN ** E 325 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 346 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** O 68 GLN ** R 46 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** R 60 ASN ** S 108 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7875 moved from start: 0.3777 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.071 25898 Z= 0.260 Angle : 0.577 9.803 36443 Z= 0.320 Chirality : 0.038 0.182 4041 Planarity : 0.004 0.047 3424 Dihedral : 27.862 139.987 6159 Min Nonbonded Distance : 2.039 Molprobity Statistics. All-atom Clashscore : 13.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.84 % Favored : 96.16 % Rotamer: Outliers : 5.63 % Allowed : 28.06 % Favored : 66.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.21 (0.18), residues: 2112 helix: 0.80 (0.15), residues: 1166 sheet: -0.01 (0.57), residues: 82 loop : -1.46 (0.20), residues: 864 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP E 301 HIS 0.007 0.001 HIS B 815 PHE 0.027 0.002 PHE A 160 TYR 0.019 0.002 TYR R 37 ARG 0.008 0.000 ARG A 316 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4224 Ramachandran restraints generated. 2112 Oldfield, 0 Emsley, 2112 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4224 Ramachandran restraints generated. 2112 Oldfield, 0 Emsley, 2112 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 377 residues out of total 1917 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 108 poor density : 269 time to evaluate : 2.575 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 74 MET cc_start: 0.7423 (OUTLIER) cc_final: 0.7064 (ttp) REVERT: A 172 GLU cc_start: 0.7373 (OUTLIER) cc_final: 0.6659 (tm-30) REVERT: A 289 GLU cc_start: 0.6823 (tm-30) cc_final: 0.6604 (tm-30) REVERT: A 313 TYR cc_start: 0.6787 (m-80) cc_final: 0.6537 (m-80) REVERT: B 671 LYS cc_start: 0.8062 (mttm) cc_final: 0.7779 (mtmt) REVERT: B 709 TYR cc_start: 0.6895 (OUTLIER) cc_final: 0.4443 (t80) REVERT: B 817 TYR cc_start: 0.8682 (OUTLIER) cc_final: 0.8186 (t80) REVERT: B 860 MET cc_start: 0.6003 (mmp) cc_final: 0.5625 (mpp) REVERT: B 912 TRP cc_start: 0.7681 (OUTLIER) cc_final: 0.7117 (t-100) REVERT: B 917 ARG cc_start: 0.8373 (OUTLIER) cc_final: 0.7502 (ttm170) REVERT: B 962 LYS cc_start: 0.5074 (OUTLIER) cc_final: 0.4246 (ptpp) REVERT: B 986 TYR cc_start: 0.6011 (OUTLIER) cc_final: 0.4618 (t80) REVERT: B 1136 PHE cc_start: 0.4220 (OUTLIER) cc_final: 0.3430 (m-10) REVERT: B 1164 MET cc_start: 0.7299 (OUTLIER) cc_final: 0.6091 (pp-130) REVERT: B 1167 ARG cc_start: 0.7640 (OUTLIER) cc_final: 0.6886 (pmt-80) REVERT: B 1248 SER cc_start: 0.8109 (t) cc_final: 0.7809 (m) REVERT: B 1284 ILE cc_start: 0.6941 (OUTLIER) cc_final: 0.6697 (pp) REVERT: D 220 ILE cc_start: 0.5899 (mt) cc_final: 0.5502 (mm) REVERT: D 223 GLN cc_start: 0.7667 (mt0) cc_final: 0.7451 (pt0) REVERT: D 347 MET cc_start: 0.5694 (tmt) cc_final: 0.4884 (tpt) REVERT: D 354 LEU cc_start: 0.7335 (OUTLIER) cc_final: 0.6911 (pp) REVERT: D 386 LEU cc_start: 0.7625 (OUTLIER) cc_final: 0.7405 (pt) REVERT: E 35 ARG cc_start: 0.6721 (OUTLIER) cc_final: 0.6287 (mpp80) REVERT: E 465 LYS cc_start: 0.8727 (OUTLIER) cc_final: 0.8486 (ttmt) REVERT: E 560 MET cc_start: 0.6540 (mmm) cc_final: 0.6305 (mmm) REVERT: O 59 GLU cc_start: 0.8146 (OUTLIER) cc_final: 0.7727 (pp20) REVERT: Q 56 GLU cc_start: 0.8710 (OUTLIER) cc_final: 0.8314 (tt0) REVERT: Q 74 LYS cc_start: 0.8598 (OUTLIER) cc_final: 0.8167 (mptp) REVERT: R 68 GLU cc_start: 0.7969 (OUTLIER) cc_final: 0.7404 (mp0) REVERT: U 56 GLU cc_start: 0.8923 (OUTLIER) cc_final: 0.8308 (tm-30) outliers start: 108 outliers final: 47 residues processed: 347 average time/residue: 0.3748 time to fit residues: 201.4389 Evaluate side-chains 322 residues out of total 1917 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 68 poor density : 254 time to evaluate : 2.242 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 28 ASP Chi-restraints excluded: chain A residue 74 MET Chi-restraints excluded: chain A residue 83 ILE Chi-restraints excluded: chain A residue 172 GLU Chi-restraints excluded: chain A residue 181 LEU Chi-restraints excluded: chain A residue 265 SER Chi-restraints excluded: chain A residue 314 THR Chi-restraints excluded: chain B residue 698 ASP Chi-restraints excluded: chain B residue 699 LEU Chi-restraints excluded: chain B residue 709 TYR Chi-restraints excluded: chain B residue 817 TYR Chi-restraints excluded: chain B residue 883 LEU Chi-restraints excluded: chain B residue 912 TRP Chi-restraints excluded: chain B residue 914 LYS Chi-restraints excluded: chain B residue 917 ARG Chi-restraints excluded: chain B residue 934 THR Chi-restraints excluded: chain B residue 962 LYS Chi-restraints excluded: chain B residue 986 TYR Chi-restraints excluded: chain B residue 997 THR Chi-restraints excluded: chain B residue 1010 LEU Chi-restraints excluded: chain B residue 1020 LEU Chi-restraints excluded: chain B residue 1024 ILE Chi-restraints excluded: chain B residue 1136 PHE Chi-restraints excluded: chain B residue 1144 ILE Chi-restraints excluded: chain B residue 1164 MET Chi-restraints excluded: chain B residue 1167 ARG Chi-restraints excluded: chain B residue 1179 THR Chi-restraints excluded: chain B residue 1194 MET Chi-restraints excluded: chain B residue 1196 LEU Chi-restraints excluded: chain B residue 1207 VAL Chi-restraints excluded: chain B residue 1228 LEU Chi-restraints excluded: chain B residue 1250 VAL Chi-restraints excluded: chain B residue 1266 MET Chi-restraints excluded: chain B residue 1284 ILE Chi-restraints excluded: chain D residue 222 LEU Chi-restraints excluded: chain D residue 230 SER Chi-restraints excluded: chain D residue 265 VAL Chi-restraints excluded: chain D residue 298 LEU Chi-restraints excluded: chain D residue 321 VAL Chi-restraints excluded: chain D residue 323 ILE Chi-restraints excluded: chain D residue 354 LEU Chi-restraints excluded: chain D residue 359 THR Chi-restraints excluded: chain D residue 386 LEU Chi-restraints excluded: chain E residue 35 ARG Chi-restraints excluded: chain E residue 45 ASN Chi-restraints excluded: chain E residue 415 LEU Chi-restraints excluded: chain E residue 436 LEU Chi-restraints excluded: chain E residue 452 VAL Chi-restraints excluded: chain E residue 465 LYS Chi-restraints excluded: chain E residue 474 VAL Chi-restraints excluded: chain E residue 498 ILE Chi-restraints excluded: chain E residue 542 ILE Chi-restraints excluded: chain O residue 59 GLU Chi-restraints excluded: chain O residue 87 SER Chi-restraints excluded: chain P residue 96 THR Chi-restraints excluded: chain Q residue 56 GLU Chi-restraints excluded: chain Q residue 74 LYS Chi-restraints excluded: chain R residue 48 ASP Chi-restraints excluded: chain R residue 61 SER Chi-restraints excluded: chain R residue 68 GLU Chi-restraints excluded: chain R residue 84 SER Chi-restraints excluded: chain R residue 109 SER Chi-restraints excluded: chain S residue 45 THR Chi-restraints excluded: chain S residue 103 LEU Chi-restraints excluded: chain T residue 44 LYS Chi-restraints excluded: chain T residue 96 THR Chi-restraints excluded: chain U residue 56 GLU Chi-restraints excluded: chain V residue 49 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 243 random chunks: chunk 218 optimal weight: 1.9990 chunk 166 optimal weight: 0.9990 chunk 114 optimal weight: 0.8980 chunk 24 optimal weight: 0.8980 chunk 105 optimal weight: 4.9990 chunk 148 optimal weight: 1.9990 chunk 221 optimal weight: 3.9990 chunk 234 optimal weight: 1.9990 chunk 115 optimal weight: 4.9990 chunk 210 optimal weight: 10.0000 chunk 63 optimal weight: 0.8980 overall best weight: 1.1384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 38 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 150 HIS ** A 330 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 341 ASN ** B 815 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 983 ASN B1173 ASN B1254 HIS ** B1293 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 304 ASN ** E 325 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 346 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** O 68 GLN O 108 ASN P 25 ASN ** P 93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 46 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 108 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7953 moved from start: 0.4401 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.060 25898 Z= 0.278 Angle : 0.576 11.626 36443 Z= 0.318 Chirality : 0.038 0.162 4041 Planarity : 0.004 0.048 3424 Dihedral : 27.654 140.507 6159 Min Nonbonded Distance : 2.038 Molprobity Statistics. All-atom Clashscore : 14.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.50 % Favored : 95.50 % Rotamer: Outliers : 5.79 % Allowed : 27.23 % Favored : 66.98 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.02 (0.18), residues: 2112 helix: 0.99 (0.15), residues: 1168 sheet: -0.18 (0.56), residues: 81 loop : -1.41 (0.21), residues: 863 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP E 301 HIS 0.007 0.001 HIS B 815 PHE 0.024 0.001 PHE A 160 TYR 0.020 0.002 TYR A 198 ARG 0.011 0.000 ARG D 247 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4224 Ramachandran restraints generated. 2112 Oldfield, 0 Emsley, 2112 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4224 Ramachandran restraints generated. 2112 Oldfield, 0 Emsley, 2112 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 396 residues out of total 1917 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 111 poor density : 285 time to evaluate : 2.361 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 72 GLN cc_start: 0.6639 (OUTLIER) cc_final: 0.6320 (pt0) REVERT: A 74 MET cc_start: 0.7791 (OUTLIER) cc_final: 0.7462 (ttp) REVERT: A 120 CYS cc_start: 0.8609 (m) cc_final: 0.8301 (m) REVERT: A 174 LEU cc_start: 0.7829 (OUTLIER) cc_final: 0.7582 (mm) REVERT: A 289 GLU cc_start: 0.6872 (tm-30) cc_final: 0.6651 (tm-30) REVERT: A 305 MET cc_start: 0.8284 (ttt) cc_final: 0.7936 (ttt) REVERT: A 313 TYR cc_start: 0.6977 (m-80) cc_final: 0.6732 (m-80) REVERT: B 671 LYS cc_start: 0.8054 (mttm) cc_final: 0.7699 (mtmt) REVERT: B 709 TYR cc_start: 0.7010 (OUTLIER) cc_final: 0.4485 (t80) REVERT: B 791 GLU cc_start: 0.8373 (mt-10) cc_final: 0.8009 (mp0) REVERT: B 817 TYR cc_start: 0.8632 (OUTLIER) cc_final: 0.8090 (t80) REVERT: B 860 MET cc_start: 0.6012 (mmp) cc_final: 0.5699 (mpp) REVERT: B 911 GLU cc_start: 0.7430 (OUTLIER) cc_final: 0.6751 (pm20) REVERT: B 912 TRP cc_start: 0.7824 (OUTLIER) cc_final: 0.7271 (t-100) REVERT: B 914 LYS cc_start: 0.7974 (OUTLIER) cc_final: 0.7706 (ptpp) REVERT: B 917 ARG cc_start: 0.8384 (OUTLIER) cc_final: 0.7714 (ttm170) REVERT: B 962 LYS cc_start: 0.5027 (OUTLIER) cc_final: 0.4158 (ptpp) REVERT: B 978 ASP cc_start: 0.8069 (m-30) cc_final: 0.7867 (m-30) REVERT: B 986 TYR cc_start: 0.6120 (OUTLIER) cc_final: 0.4707 (t80) REVERT: B 1164 MET cc_start: 0.7427 (OUTLIER) cc_final: 0.6368 (pp-130) REVERT: B 1167 ARG cc_start: 0.7709 (OUTLIER) cc_final: 0.7069 (pmt-80) REVERT: B 1248 SER cc_start: 0.8221 (t) cc_final: 0.7907 (m) REVERT: B 1284 ILE cc_start: 0.7004 (OUTLIER) cc_final: 0.6761 (pp) REVERT: D 220 ILE cc_start: 0.6003 (mt) cc_final: 0.5424 (mm) REVERT: D 347 MET cc_start: 0.5862 (tmt) cc_final: 0.5012 (tpt) REVERT: E 376 ASN cc_start: 0.6968 (OUTLIER) cc_final: 0.6578 (t0) REVERT: E 465 LYS cc_start: 0.8743 (OUTLIER) cc_final: 0.8534 (ttmt) REVERT: E 472 THR cc_start: 0.7064 (OUTLIER) cc_final: 0.6687 (p) REVERT: O 59 GLU cc_start: 0.8261 (OUTLIER) cc_final: 0.7775 (pp20) REVERT: P 25 ASN cc_start: 0.8745 (m-40) cc_final: 0.8398 (m-40) REVERT: Q 74 LYS cc_start: 0.8562 (OUTLIER) cc_final: 0.8103 (mptp) REVERT: T 88 TYR cc_start: 0.8629 (m-10) cc_final: 0.8336 (m-10) REVERT: U 51 LEU cc_start: 0.9367 (OUTLIER) cc_final: 0.9091 (tp) REVERT: U 56 GLU cc_start: 0.8925 (OUTLIER) cc_final: 0.8322 (tm-30) outliers start: 111 outliers final: 58 residues processed: 370 average time/residue: 0.3678 time to fit residues: 210.8428 Evaluate side-chains 342 residues out of total 1917 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 79 poor density : 263 time to evaluate : 1.913 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 28 ASP Chi-restraints excluded: chain A residue 72 GLN Chi-restraints excluded: chain A residue 74 MET Chi-restraints excluded: chain A residue 174 LEU Chi-restraints excluded: chain A residue 181 LEU Chi-restraints excluded: chain A residue 218 THR Chi-restraints excluded: chain A residue 221 LEU Chi-restraints excluded: chain A residue 242 ILE Chi-restraints excluded: chain A residue 265 SER Chi-restraints excluded: chain A residue 314 THR Chi-restraints excluded: chain A residue 331 ASN Chi-restraints excluded: chain B residue 698 ASP Chi-restraints excluded: chain B residue 699 LEU Chi-restraints excluded: chain B residue 709 TYR Chi-restraints excluded: chain B residue 817 TYR Chi-restraints excluded: chain B residue 872 ASP Chi-restraints excluded: chain B residue 883 LEU Chi-restraints excluded: chain B residue 907 ARG Chi-restraints excluded: chain B residue 911 GLU Chi-restraints excluded: chain B residue 912 TRP Chi-restraints excluded: chain B residue 914 LYS Chi-restraints excluded: chain B residue 917 ARG Chi-restraints excluded: chain B residue 934 THR Chi-restraints excluded: chain B residue 962 LYS Chi-restraints excluded: chain B residue 986 TYR Chi-restraints excluded: chain B residue 997 THR Chi-restraints excluded: chain B residue 1010 LEU Chi-restraints excluded: chain B residue 1020 LEU Chi-restraints excluded: chain B residue 1024 ILE Chi-restraints excluded: chain B residue 1144 ILE Chi-restraints excluded: chain B residue 1164 MET Chi-restraints excluded: chain B residue 1167 ARG Chi-restraints excluded: chain B residue 1179 THR Chi-restraints excluded: chain B residue 1196 LEU Chi-restraints excluded: chain B residue 1207 VAL Chi-restraints excluded: chain B residue 1228 LEU Chi-restraints excluded: chain B residue 1250 VAL Chi-restraints excluded: chain B residue 1266 MET Chi-restraints excluded: chain B residue 1284 ILE Chi-restraints excluded: chain B residue 1312 VAL Chi-restraints excluded: chain B residue 1322 LEU Chi-restraints excluded: chain D residue 230 SER Chi-restraints excluded: chain D residue 235 ASP Chi-restraints excluded: chain D residue 256 MET Chi-restraints excluded: chain D residue 287 LEU Chi-restraints excluded: chain D residue 298 LEU Chi-restraints excluded: chain D residue 321 VAL Chi-restraints excluded: chain D residue 323 ILE Chi-restraints excluded: chain D residue 360 GLU Chi-restraints excluded: chain E residue 35 ARG Chi-restraints excluded: chain E residue 45 ASN Chi-restraints excluded: chain E residue 46 TYR Chi-restraints excluded: chain E residue 376 ASN Chi-restraints excluded: chain E residue 408 ASP Chi-restraints excluded: chain E residue 415 LEU Chi-restraints excluded: chain E residue 416 ILE Chi-restraints excluded: chain E residue 423 THR Chi-restraints excluded: chain E residue 452 VAL Chi-restraints excluded: chain E residue 465 LYS Chi-restraints excluded: chain E residue 472 THR Chi-restraints excluded: chain E residue 474 VAL Chi-restraints excluded: chain E residue 498 ILE Chi-restraints excluded: chain E residue 542 ILE Chi-restraints excluded: chain O residue 59 GLU Chi-restraints excluded: chain O residue 87 SER Chi-restraints excluded: chain O residue 92 LEU Chi-restraints excluded: chain P residue 96 THR Chi-restraints excluded: chain Q residue 62 ILE Chi-restraints excluded: chain Q residue 74 LYS Chi-restraints excluded: chain R residue 48 ASP Chi-restraints excluded: chain R residue 84 SER Chi-restraints excluded: chain R residue 109 SER Chi-restraints excluded: chain S residue 103 LEU Chi-restraints excluded: chain T residue 44 LYS Chi-restraints excluded: chain T residue 96 THR Chi-restraints excluded: chain U residue 51 LEU Chi-restraints excluded: chain U residue 56 GLU Chi-restraints excluded: chain V residue 49 THR Chi-restraints excluded: chain V residue 76 ARG Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 243 random chunks: chunk 195 optimal weight: 1.9990 chunk 133 optimal weight: 4.9990 chunk 3 optimal weight: 0.5980 chunk 174 optimal weight: 1.9990 chunk 96 optimal weight: 3.9990 chunk 200 optimal weight: 2.9990 chunk 162 optimal weight: 0.5980 chunk 0 optimal weight: 5.9990 chunk 119 optimal weight: 5.9990 chunk 210 optimal weight: 10.0000 chunk 59 optimal weight: 3.9990 overall best weight: 1.6386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 43 HIS A 76 GLN A 296 ASN ** A 330 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 341 ASN ** B1293 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 325 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 346 HIS O 68 GLN ** P 93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 46 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** R 92 GLN ** S 108 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8071 moved from start: 0.5419 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.070 25898 Z= 0.360 Angle : 0.635 11.313 36443 Z= 0.348 Chirality : 0.040 0.161 4041 Planarity : 0.005 0.060 3424 Dihedral : 27.867 141.787 6159 Min Nonbonded Distance : 2.047 Molprobity Statistics. All-atom Clashscore : 15.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.73 % Favored : 95.27 % Rotamer: Outliers : 6.62 % Allowed : 26.55 % Favored : 66.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.23 (0.18), residues: 2112 helix: 0.76 (0.15), residues: 1178 sheet: -0.70 (0.56), residues: 83 loop : -1.38 (0.21), residues: 851 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.002 TRP E 301 HIS 0.010 0.002 HIS E 469 PHE 0.033 0.002 PHE A 160 TYR 0.022 0.002 TYR A 198 ARG 0.005 0.001 ARG A 248 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4224 Ramachandran restraints generated. 2112 Oldfield, 0 Emsley, 2112 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4224 Ramachandran restraints generated. 2112 Oldfield, 0 Emsley, 2112 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 404 residues out of total 1917 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 127 poor density : 277 time to evaluate : 2.393 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 72 GLN cc_start: 0.6854 (OUTLIER) cc_final: 0.6595 (pt0) REVERT: A 163 LEU cc_start: 0.6969 (OUTLIER) cc_final: 0.6733 (mp) REVERT: A 172 GLU cc_start: 0.7703 (OUTLIER) cc_final: 0.7115 (tp30) REVERT: A 174 LEU cc_start: 0.8034 (OUTLIER) cc_final: 0.7751 (mm) REVERT: A 189 HIS cc_start: 0.6724 (OUTLIER) cc_final: 0.6221 (p90) REVERT: A 289 GLU cc_start: 0.7011 (tm-30) cc_final: 0.6767 (tm-30) REVERT: A 305 MET cc_start: 0.8383 (ttt) cc_final: 0.8117 (ttt) REVERT: B 671 LYS cc_start: 0.8171 (mttm) cc_final: 0.7747 (mttm) REVERT: B 817 TYR cc_start: 0.8711 (OUTLIER) cc_final: 0.8184 (t80) REVERT: B 860 MET cc_start: 0.6169 (mmp) cc_final: 0.5892 (mpp) REVERT: B 906 ARG cc_start: 0.7651 (mtp-110) cc_final: 0.7426 (mtp-110) REVERT: B 912 TRP cc_start: 0.7904 (OUTLIER) cc_final: 0.7545 (t-100) REVERT: B 917 ARG cc_start: 0.8402 (OUTLIER) cc_final: 0.7814 (ttm170) REVERT: B 962 LYS cc_start: 0.5114 (OUTLIER) cc_final: 0.4165 (ptpp) REVERT: B 978 ASP cc_start: 0.8302 (OUTLIER) cc_final: 0.8090 (m-30) REVERT: B 986 TYR cc_start: 0.6254 (OUTLIER) cc_final: 0.5058 (t80) REVERT: B 989 LEU cc_start: 0.7962 (OUTLIER) cc_final: 0.7558 (mm) REVERT: B 1164 MET cc_start: 0.7757 (OUTLIER) cc_final: 0.6674 (pp-130) REVERT: B 1167 ARG cc_start: 0.7839 (OUTLIER) cc_final: 0.7286 (pmt-80) REVERT: B 1229 ARG cc_start: 0.7649 (OUTLIER) cc_final: 0.6668 (ptt180) REVERT: B 1248 SER cc_start: 0.8345 (t) cc_final: 0.8013 (m) REVERT: B 1284 ILE cc_start: 0.7144 (OUTLIER) cc_final: 0.6918 (pp) REVERT: B 1300 MET cc_start: 0.7606 (tpp) cc_final: 0.7355 (tpp) REVERT: D 220 ILE cc_start: 0.6050 (mt) cc_final: 0.5596 (mm) REVERT: D 263 HIS cc_start: 0.6290 (t-170) cc_final: 0.6015 (t-170) REVERT: D 347 MET cc_start: 0.6156 (tmt) cc_final: 0.5348 (tpt) REVERT: D 381 ARG cc_start: 0.6993 (OUTLIER) cc_final: 0.6774 (ptp90) REVERT: E 365 LYS cc_start: 0.8936 (OUTLIER) cc_final: 0.8529 (ptmm) REVERT: E 376 ASN cc_start: 0.7163 (OUTLIER) cc_final: 0.6677 (t0) REVERT: E 465 LYS cc_start: 0.8752 (OUTLIER) cc_final: 0.8502 (ttmt) REVERT: O 59 GLU cc_start: 0.8322 (OUTLIER) cc_final: 0.7788 (pp20) REVERT: P 25 ASN cc_start: 0.8897 (m-40) cc_final: 0.8602 (m-40) REVERT: Q 11 ARG cc_start: 0.2479 (OUTLIER) cc_final: -0.1883 (mtm-85) REVERT: Q 74 LYS cc_start: 0.8632 (OUTLIER) cc_final: 0.8159 (mptp) REVERT: Q 91 GLU cc_start: 0.8353 (OUTLIER) cc_final: 0.8056 (tt0) REVERT: U 56 GLU cc_start: 0.8940 (OUTLIER) cc_final: 0.8327 (tm-30) outliers start: 127 outliers final: 66 residues processed: 375 average time/residue: 0.3773 time to fit residues: 216.1661 Evaluate side-chains 346 residues out of total 1917 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 91 poor density : 255 time to evaluate : 2.494 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 28 ASP Chi-restraints excluded: chain A residue 72 GLN Chi-restraints excluded: chain A residue 83 ILE Chi-restraints excluded: chain A residue 163 LEU Chi-restraints excluded: chain A residue 165 ASP Chi-restraints excluded: chain A residue 172 GLU Chi-restraints excluded: chain A residue 174 LEU Chi-restraints excluded: chain A residue 181 LEU Chi-restraints excluded: chain A residue 189 HIS Chi-restraints excluded: chain A residue 232 TYR Chi-restraints excluded: chain A residue 236 VAL Chi-restraints excluded: chain A residue 242 ILE Chi-restraints excluded: chain A residue 265 SER Chi-restraints excluded: chain A residue 269 LEU Chi-restraints excluded: chain A residue 314 THR Chi-restraints excluded: chain A residue 331 ASN Chi-restraints excluded: chain B residue 698 ASP Chi-restraints excluded: chain B residue 699 LEU Chi-restraints excluded: chain B residue 703 VAL Chi-restraints excluded: chain B residue 817 TYR Chi-restraints excluded: chain B residue 857 HIS Chi-restraints excluded: chain B residue 883 LEU Chi-restraints excluded: chain B residue 898 LEU Chi-restraints excluded: chain B residue 907 ARG Chi-restraints excluded: chain B residue 912 TRP Chi-restraints excluded: chain B residue 914 LYS Chi-restraints excluded: chain B residue 917 ARG Chi-restraints excluded: chain B residue 934 THR Chi-restraints excluded: chain B residue 962 LYS Chi-restraints excluded: chain B residue 978 ASP Chi-restraints excluded: chain B residue 986 TYR Chi-restraints excluded: chain B residue 989 LEU Chi-restraints excluded: chain B residue 1020 LEU Chi-restraints excluded: chain B residue 1024 ILE Chi-restraints excluded: chain B residue 1144 ILE Chi-restraints excluded: chain B residue 1164 MET Chi-restraints excluded: chain B residue 1167 ARG Chi-restraints excluded: chain B residue 1169 THR Chi-restraints excluded: chain B residue 1179 THR Chi-restraints excluded: chain B residue 1207 VAL Chi-restraints excluded: chain B residue 1228 LEU Chi-restraints excluded: chain B residue 1229 ARG Chi-restraints excluded: chain B residue 1243 ASP Chi-restraints excluded: chain B residue 1250 VAL Chi-restraints excluded: chain B residue 1284 ILE Chi-restraints excluded: chain B residue 1322 LEU Chi-restraints excluded: chain D residue 222 LEU Chi-restraints excluded: chain D residue 230 SER Chi-restraints excluded: chain D residue 235 ASP Chi-restraints excluded: chain D residue 287 LEU Chi-restraints excluded: chain D residue 298 LEU Chi-restraints excluded: chain D residue 321 VAL Chi-restraints excluded: chain D residue 323 ILE Chi-restraints excluded: chain D residue 344 SER Chi-restraints excluded: chain D residue 360 GLU Chi-restraints excluded: chain D residue 381 ARG Chi-restraints excluded: chain D residue 392 SER Chi-restraints excluded: chain E residue 35 ARG Chi-restraints excluded: chain E residue 346 HIS Chi-restraints excluded: chain E residue 365 LYS Chi-restraints excluded: chain E residue 376 ASN Chi-restraints excluded: chain E residue 408 ASP Chi-restraints excluded: chain E residue 415 LEU Chi-restraints excluded: chain E residue 423 THR Chi-restraints excluded: chain E residue 452 VAL Chi-restraints excluded: chain E residue 465 LYS Chi-restraints excluded: chain E residue 474 VAL Chi-restraints excluded: chain E residue 498 ILE Chi-restraints excluded: chain E residue 542 ILE Chi-restraints excluded: chain O residue 59 GLU Chi-restraints excluded: chain O residue 87 SER Chi-restraints excluded: chain O residue 92 LEU Chi-restraints excluded: chain P residue 96 THR Chi-restraints excluded: chain Q residue 11 ARG Chi-restraints excluded: chain Q residue 62 ILE Chi-restraints excluded: chain Q residue 74 LYS Chi-restraints excluded: chain Q residue 91 GLU Chi-restraints excluded: chain R residue 48 ASP Chi-restraints excluded: chain R residue 84 SER Chi-restraints excluded: chain R residue 109 SER Chi-restraints excluded: chain S residue 87 SER Chi-restraints excluded: chain S residue 92 LEU Chi-restraints excluded: chain S residue 103 LEU Chi-restraints excluded: chain T residue 29 ILE Chi-restraints excluded: chain T residue 44 LYS Chi-restraints excluded: chain T residue 77 LYS Chi-restraints excluded: chain T residue 93 GLN Chi-restraints excluded: chain T residue 96 THR Chi-restraints excluded: chain U residue 56 GLU Chi-restraints excluded: chain U residue 114 VAL Chi-restraints excluded: chain V residue 49 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 243 random chunks: chunk 79 optimal weight: 1.9990 chunk 211 optimal weight: 5.9990 chunk 46 optimal weight: 0.1980 chunk 137 optimal weight: 20.0000 chunk 57 optimal weight: 4.9990 chunk 235 optimal weight: 1.9990 chunk 195 optimal weight: 0.9990 chunk 108 optimal weight: 0.7980 chunk 19 optimal weight: 4.9990 chunk 77 optimal weight: 0.5980 chunk 123 optimal weight: 2.9990 overall best weight: 0.9184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 330 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 341 ASN ** B1293 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 389 ASN E 304 ASN ** E 325 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 346 HIS O 68 GLN ** P 93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 46 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 108 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8041 moved from start: 0.5500 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 25898 Z= 0.242 Angle : 0.577 10.778 36443 Z= 0.317 Chirality : 0.037 0.164 4041 Planarity : 0.004 0.046 3424 Dihedral : 27.771 142.269 6159 Min Nonbonded Distance : 2.026 Molprobity Statistics. All-atom Clashscore : 14.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.59 % Favored : 95.41 % Rotamer: Outliers : 4.85 % Allowed : 26.97 % Favored : 68.18 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.01 (0.18), residues: 2112 helix: 0.99 (0.15), residues: 1179 sheet: -0.89 (0.56), residues: 84 loop : -1.34 (0.21), residues: 849 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP E 301 HIS 0.017 0.001 HIS E 346 PHE 0.044 0.001 PHE A 160 TYR 0.019 0.002 TYR A 198 ARG 0.004 0.000 ARG E 51 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4224 Ramachandran restraints generated. 2112 Oldfield, 0 Emsley, 2112 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4224 Ramachandran restraints generated. 2112 Oldfield, 0 Emsley, 2112 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 363 residues out of total 1917 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 93 poor density : 270 time to evaluate : 2.034 Fit side-chains revert: symmetry clash REVERT: A 72 GLN cc_start: 0.6813 (OUTLIER) cc_final: 0.6549 (pt0) REVERT: A 120 CYS cc_start: 0.8630 (m) cc_final: 0.8355 (m) REVERT: A 172 GLU cc_start: 0.7646 (OUTLIER) cc_final: 0.7102 (tp30) REVERT: A 174 LEU cc_start: 0.7926 (OUTLIER) cc_final: 0.7492 (mm) REVERT: A 189 HIS cc_start: 0.6535 (OUTLIER) cc_final: 0.6078 (p90) REVERT: A 289 GLU cc_start: 0.7005 (tm-30) cc_final: 0.6771 (tm-30) REVERT: A 305 MET cc_start: 0.8328 (ttt) cc_final: 0.8087 (ttt) REVERT: A 306 MET cc_start: 0.8870 (OUTLIER) cc_final: 0.7490 (tmm) REVERT: B 671 LYS cc_start: 0.8178 (mttm) cc_final: 0.7757 (mttm) REVERT: B 756 LYS cc_start: 0.7815 (OUTLIER) cc_final: 0.7348 (pttm) REVERT: B 817 TYR cc_start: 0.8676 (OUTLIER) cc_final: 0.8122 (t80) REVERT: B 860 MET cc_start: 0.6155 (mmp) cc_final: 0.5892 (mpp) REVERT: B 912 TRP cc_start: 0.7914 (OUTLIER) cc_final: 0.7674 (t-100) REVERT: B 917 ARG cc_start: 0.8416 (OUTLIER) cc_final: 0.7798 (ttm170) REVERT: B 978 ASP cc_start: 0.8221 (OUTLIER) cc_final: 0.8020 (m-30) REVERT: B 986 TYR cc_start: 0.6266 (OUTLIER) cc_final: 0.5090 (t80) REVERT: B 989 LEU cc_start: 0.8003 (OUTLIER) cc_final: 0.7639 (mm) REVERT: B 1164 MET cc_start: 0.7699 (OUTLIER) cc_final: 0.6617 (pp-130) REVERT: B 1167 ARG cc_start: 0.7837 (OUTLIER) cc_final: 0.7306 (pmt-80) REVERT: B 1229 ARG cc_start: 0.7565 (OUTLIER) cc_final: 0.6560 (ptt180) REVERT: B 1248 SER cc_start: 0.8350 (t) cc_final: 0.8020 (m) REVERT: B 1284 ILE cc_start: 0.7172 (OUTLIER) cc_final: 0.6915 (pp) REVERT: D 220 ILE cc_start: 0.6033 (mt) cc_final: 0.5587 (mm) REVERT: D 263 HIS cc_start: 0.6288 (t-170) cc_final: 0.6014 (t-170) REVERT: D 347 MET cc_start: 0.6187 (tmt) cc_final: 0.5298 (tpp) REVERT: E 465 LYS cc_start: 0.8776 (OUTLIER) cc_final: 0.8571 (ttmt) REVERT: F 278 LEU cc_start: 0.3571 (OUTLIER) cc_final: 0.3325 (pt) REVERT: O 59 GLU cc_start: 0.8330 (OUTLIER) cc_final: 0.7759 (pp20) REVERT: P 25 ASN cc_start: 0.8883 (m-40) cc_final: 0.8572 (m-40) REVERT: Q 11 ARG cc_start: 0.2629 (OUTLIER) cc_final: -0.1680 (mtm-85) REVERT: Q 74 LYS cc_start: 0.8584 (OUTLIER) cc_final: 0.8109 (mptp) REVERT: Q 91 GLU cc_start: 0.8335 (OUTLIER) cc_final: 0.8057 (tt0) REVERT: R 90 GLU cc_start: 0.8409 (OUTLIER) cc_final: 0.7727 (mp0) REVERT: U 56 GLU cc_start: 0.8907 (OUTLIER) cc_final: 0.8297 (tm-30) outliers start: 93 outliers final: 54 residues processed: 345 average time/residue: 0.3689 time to fit residues: 195.6874 Evaluate side-chains 334 residues out of total 1917 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 78 poor density : 256 time to evaluate : 2.562 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 28 ASP Chi-restraints excluded: chain A residue 72 GLN Chi-restraints excluded: chain A residue 165 ASP Chi-restraints excluded: chain A residue 172 GLU Chi-restraints excluded: chain A residue 174 LEU Chi-restraints excluded: chain A residue 181 LEU Chi-restraints excluded: chain A residue 189 HIS Chi-restraints excluded: chain A residue 232 TYR Chi-restraints excluded: chain A residue 236 VAL Chi-restraints excluded: chain A residue 242 ILE Chi-restraints excluded: chain A residue 265 SER Chi-restraints excluded: chain A residue 269 LEU Chi-restraints excluded: chain A residue 306 MET Chi-restraints excluded: chain A residue 314 THR Chi-restraints excluded: chain A residue 331 ASN Chi-restraints excluded: chain B residue 698 ASP Chi-restraints excluded: chain B residue 699 LEU Chi-restraints excluded: chain B residue 756 LYS Chi-restraints excluded: chain B residue 817 TYR Chi-restraints excluded: chain B residue 872 ASP Chi-restraints excluded: chain B residue 883 LEU Chi-restraints excluded: chain B residue 907 ARG Chi-restraints excluded: chain B residue 912 TRP Chi-restraints excluded: chain B residue 917 ARG Chi-restraints excluded: chain B residue 934 THR Chi-restraints excluded: chain B residue 978 ASP Chi-restraints excluded: chain B residue 986 TYR Chi-restraints excluded: chain B residue 989 LEU Chi-restraints excluded: chain B residue 1020 LEU Chi-restraints excluded: chain B residue 1024 ILE Chi-restraints excluded: chain B residue 1144 ILE Chi-restraints excluded: chain B residue 1164 MET Chi-restraints excluded: chain B residue 1167 ARG Chi-restraints excluded: chain B residue 1169 THR Chi-restraints excluded: chain B residue 1179 THR Chi-restraints excluded: chain B residue 1207 VAL Chi-restraints excluded: chain B residue 1218 ASP Chi-restraints excluded: chain B residue 1219 LEU Chi-restraints excluded: chain B residue 1228 LEU Chi-restraints excluded: chain B residue 1229 ARG Chi-restraints excluded: chain B residue 1284 ILE Chi-restraints excluded: chain B residue 1322 LEU Chi-restraints excluded: chain D residue 230 SER Chi-restraints excluded: chain D residue 235 ASP Chi-restraints excluded: chain D residue 256 MET Chi-restraints excluded: chain D residue 287 LEU Chi-restraints excluded: chain D residue 298 LEU Chi-restraints excluded: chain D residue 344 SER Chi-restraints excluded: chain D residue 360 GLU Chi-restraints excluded: chain E residue 35 ARG Chi-restraints excluded: chain E residue 415 LEU Chi-restraints excluded: chain E residue 416 ILE Chi-restraints excluded: chain E residue 423 THR Chi-restraints excluded: chain E residue 436 LEU Chi-restraints excluded: chain E residue 452 VAL Chi-restraints excluded: chain E residue 465 LYS Chi-restraints excluded: chain E residue 474 VAL Chi-restraints excluded: chain E residue 498 ILE Chi-restraints excluded: chain E residue 544 GLU Chi-restraints excluded: chain F residue 278 LEU Chi-restraints excluded: chain O residue 59 GLU Chi-restraints excluded: chain O residue 87 SER Chi-restraints excluded: chain O residue 92 LEU Chi-restraints excluded: chain P residue 96 THR Chi-restraints excluded: chain Q residue 11 ARG Chi-restraints excluded: chain Q residue 62 ILE Chi-restraints excluded: chain Q residue 74 LYS Chi-restraints excluded: chain Q residue 91 GLU Chi-restraints excluded: chain R residue 84 SER Chi-restraints excluded: chain R residue 90 GLU Chi-restraints excluded: chain R residue 109 SER Chi-restraints excluded: chain S residue 103 LEU Chi-restraints excluded: chain T residue 29 ILE Chi-restraints excluded: chain T residue 44 LYS Chi-restraints excluded: chain T residue 96 THR Chi-restraints excluded: chain U residue 56 GLU Chi-restraints excluded: chain U residue 114 VAL Chi-restraints excluded: chain V residue 49 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 243 random chunks: chunk 226 optimal weight: 20.0000 chunk 26 optimal weight: 3.9990 chunk 133 optimal weight: 7.9990 chunk 171 optimal weight: 1.9990 chunk 197 optimal weight: 0.8980 chunk 131 optimal weight: 0.9990 chunk 234 optimal weight: 1.9990 chunk 146 optimal weight: 0.8980 chunk 142 optimal weight: 0.6980 chunk 108 optimal weight: 0.1980 chunk 144 optimal weight: 0.5980 overall best weight: 0.6580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 330 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 341 ASN D 389 ASN ** E 325 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 46 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 108 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8014 moved from start: 0.5541 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 25898 Z= 0.205 Angle : 0.556 10.066 36443 Z= 0.306 Chirality : 0.036 0.183 4041 Planarity : 0.004 0.046 3424 Dihedral : 27.614 142.108 6159 Min Nonbonded Distance : 2.136 Molprobity Statistics. All-atom Clashscore : 14.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.31 % Favored : 95.69 % Rotamer: Outliers : 4.69 % Allowed : 26.97 % Favored : 68.34 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.17 (0.18), residues: 2112 helix: 1.21 (0.15), residues: 1168 sheet: -0.99 (0.53), residues: 94 loop : -1.32 (0.21), residues: 850 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.028 0.001 TRP E 492 HIS 0.007 0.001 HIS B 815 PHE 0.025 0.001 PHE A 160 TYR 0.016 0.001 TYR R 37 ARG 0.007 0.000 ARG D 381 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4224 Ramachandran restraints generated. 2112 Oldfield, 0 Emsley, 2112 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4224 Ramachandran restraints generated. 2112 Oldfield, 0 Emsley, 2112 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 371 residues out of total 1917 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 90 poor density : 281 time to evaluate : 1.992 Fit side-chains revert: symmetry clash REVERT: A 72 GLN cc_start: 0.6838 (OUTLIER) cc_final: 0.6583 (pt0) REVERT: A 105 ASN cc_start: 0.8327 (t0) cc_final: 0.8124 (t0) REVERT: A 120 CYS cc_start: 0.8610 (m) cc_final: 0.8324 (m) REVERT: A 172 GLU cc_start: 0.7529 (OUTLIER) cc_final: 0.6988 (tm-30) REVERT: A 174 LEU cc_start: 0.7908 (OUTLIER) cc_final: 0.7532 (mm) REVERT: A 305 MET cc_start: 0.8265 (ttt) cc_final: 0.7925 (ttt) REVERT: B 671 LYS cc_start: 0.8141 (mttm) cc_final: 0.7684 (mttm) REVERT: B 805 GLU cc_start: 0.7326 (pp20) cc_final: 0.7001 (pp20) REVERT: B 817 TYR cc_start: 0.8648 (OUTLIER) cc_final: 0.8050 (t80) REVERT: B 860 MET cc_start: 0.6193 (mmp) cc_final: 0.5899 (mpp) REVERT: B 916 TRP cc_start: 0.8232 (m-10) cc_final: 0.7792 (m-10) REVERT: B 940 LYS cc_start: 0.8357 (mmtt) cc_final: 0.8003 (tttt) REVERT: B 962 LYS cc_start: 0.5070 (OUTLIER) cc_final: 0.4197 (ptpp) REVERT: B 986 TYR cc_start: 0.6193 (OUTLIER) cc_final: 0.5021 (t80) REVERT: B 1164 MET cc_start: 0.7610 (OUTLIER) cc_final: 0.6599 (pp-130) REVERT: B 1167 ARG cc_start: 0.7823 (OUTLIER) cc_final: 0.7307 (pmt-80) REVERT: B 1229 ARG cc_start: 0.7492 (OUTLIER) cc_final: 0.7171 (ptt180) REVERT: B 1248 SER cc_start: 0.8333 (t) cc_final: 0.8001 (m) REVERT: B 1284 ILE cc_start: 0.7157 (OUTLIER) cc_final: 0.6896 (pp) REVERT: D 220 ILE cc_start: 0.5996 (mt) cc_final: 0.5569 (mm) REVERT: D 263 HIS cc_start: 0.6362 (t-170) cc_final: 0.6095 (t-170) REVERT: D 347 MET cc_start: 0.6201 (tmt) cc_final: 0.5457 (tpt) REVERT: E 376 ASN cc_start: 0.6957 (OUTLIER) cc_final: 0.6556 (t0) REVERT: F 278 LEU cc_start: 0.3593 (OUTLIER) cc_final: 0.3313 (pt) REVERT: O 59 GLU cc_start: 0.8344 (OUTLIER) cc_final: 0.7771 (pp20) REVERT: P 25 ASN cc_start: 0.8849 (m-40) cc_final: 0.8507 (m-40) REVERT: Q 56 GLU cc_start: 0.8695 (OUTLIER) cc_final: 0.8323 (tt0) REVERT: Q 91 GLU cc_start: 0.8313 (OUTLIER) cc_final: 0.8071 (tt0) REVERT: R 90 GLU cc_start: 0.8417 (OUTLIER) cc_final: 0.7778 (mp0) REVERT: T 88 TYR cc_start: 0.8697 (m-10) cc_final: 0.8429 (m-10) REVERT: U 51 LEU cc_start: 0.9364 (OUTLIER) cc_final: 0.9094 (tp) REVERT: U 56 GLU cc_start: 0.8890 (OUTLIER) cc_final: 0.8281 (tt0) outliers start: 90 outliers final: 53 residues processed: 350 average time/residue: 0.3611 time to fit residues: 197.3267 Evaluate side-chains 331 residues out of total 1917 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 71 poor density : 260 time to evaluate : 2.353 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 72 GLN Chi-restraints excluded: chain A residue 172 GLU Chi-restraints excluded: chain A residue 174 LEU Chi-restraints excluded: chain A residue 181 LEU Chi-restraints excluded: chain A residue 226 VAL Chi-restraints excluded: chain A residue 236 VAL Chi-restraints excluded: chain A residue 242 ILE Chi-restraints excluded: chain A residue 265 SER Chi-restraints excluded: chain A residue 269 LEU Chi-restraints excluded: chain A residue 314 THR Chi-restraints excluded: chain A residue 331 ASN Chi-restraints excluded: chain B residue 698 ASP Chi-restraints excluded: chain B residue 699 LEU Chi-restraints excluded: chain B residue 817 TYR Chi-restraints excluded: chain B residue 872 ASP Chi-restraints excluded: chain B residue 883 LEU Chi-restraints excluded: chain B residue 962 LYS Chi-restraints excluded: chain B residue 986 TYR Chi-restraints excluded: chain B residue 1020 LEU Chi-restraints excluded: chain B residue 1024 ILE Chi-restraints excluded: chain B residue 1144 ILE Chi-restraints excluded: chain B residue 1164 MET Chi-restraints excluded: chain B residue 1167 ARG Chi-restraints excluded: chain B residue 1169 THR Chi-restraints excluded: chain B residue 1179 THR Chi-restraints excluded: chain B residue 1196 LEU Chi-restraints excluded: chain B residue 1207 VAL Chi-restraints excluded: chain B residue 1218 ASP Chi-restraints excluded: chain B residue 1219 LEU Chi-restraints excluded: chain B residue 1228 LEU Chi-restraints excluded: chain B residue 1229 ARG Chi-restraints excluded: chain B residue 1284 ILE Chi-restraints excluded: chain D residue 230 SER Chi-restraints excluded: chain D residue 235 ASP Chi-restraints excluded: chain D residue 256 MET Chi-restraints excluded: chain D residue 298 LEU Chi-restraints excluded: chain D residue 344 SER Chi-restraints excluded: chain D residue 360 GLU Chi-restraints excluded: chain E residue 35 ARG Chi-restraints excluded: chain E residue 360 THR Chi-restraints excluded: chain E residue 376 ASN Chi-restraints excluded: chain E residue 408 ASP Chi-restraints excluded: chain E residue 415 LEU Chi-restraints excluded: chain E residue 416 ILE Chi-restraints excluded: chain E residue 423 THR Chi-restraints excluded: chain E residue 452 VAL Chi-restraints excluded: chain E residue 474 VAL Chi-restraints excluded: chain E residue 498 ILE Chi-restraints excluded: chain E residue 544 GLU Chi-restraints excluded: chain F residue 278 LEU Chi-restraints excluded: chain O residue 59 GLU Chi-restraints excluded: chain O residue 87 SER Chi-restraints excluded: chain O residue 92 LEU Chi-restraints excluded: chain P residue 96 THR Chi-restraints excluded: chain Q residue 56 GLU Chi-restraints excluded: chain Q residue 62 ILE Chi-restraints excluded: chain Q residue 76 THR Chi-restraints excluded: chain Q residue 91 GLU Chi-restraints excluded: chain R residue 48 ASP Chi-restraints excluded: chain R residue 84 SER Chi-restraints excluded: chain R residue 90 GLU Chi-restraints excluded: chain R residue 109 SER Chi-restraints excluded: chain S residue 87 SER Chi-restraints excluded: chain S residue 103 LEU Chi-restraints excluded: chain T residue 29 ILE Chi-restraints excluded: chain T residue 44 LYS Chi-restraints excluded: chain T residue 96 THR Chi-restraints excluded: chain U residue 51 LEU Chi-restraints excluded: chain U residue 56 GLU Chi-restraints excluded: chain U residue 114 VAL Chi-restraints excluded: chain V residue 49 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 243 random chunks: chunk 93 optimal weight: 1.9990 chunk 139 optimal weight: 0.9990 chunk 70 optimal weight: 6.9990 chunk 46 optimal weight: 0.0770 chunk 45 optimal weight: 7.9990 chunk 148 optimal weight: 1.9990 chunk 159 optimal weight: 1.9990 chunk 115 optimal weight: 0.0370 chunk 21 optimal weight: 1.9990 chunk 184 optimal weight: 1.9990 chunk 213 optimal weight: 3.9990 overall best weight: 1.0222 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 330 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 341 ASN B1254 HIS D 389 ASN ** E 325 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 46 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 108 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8056 moved from start: 0.5826 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.053 25898 Z= 0.255 Angle : 0.577 9.678 36443 Z= 0.316 Chirality : 0.038 0.175 4041 Planarity : 0.004 0.046 3424 Dihedral : 27.613 142.109 6159 Min Nonbonded Distance : 2.076 Molprobity Statistics. All-atom Clashscore : 15.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.73 % Favored : 95.27 % Rotamer: Outliers : 4.54 % Allowed : 27.18 % Favored : 68.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.12 (0.18), residues: 2112 helix: 1.15 (0.15), residues: 1171 sheet: -0.99 (0.53), residues: 94 loop : -1.33 (0.21), residues: 847 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.001 TRP E 301 HIS 0.007 0.001 HIS B 815 PHE 0.022 0.001 PHE A 160 TYR 0.021 0.002 TYR R 37 ARG 0.005 0.000 ARG D 381 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4224 Ramachandran restraints generated. 2112 Oldfield, 0 Emsley, 2112 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4224 Ramachandran restraints generated. 2112 Oldfield, 0 Emsley, 2112 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 349 residues out of total 1917 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 87 poor density : 262 time to evaluate : 2.431 Fit side-chains revert: symmetry clash REVERT: A 72 GLN cc_start: 0.6871 (OUTLIER) cc_final: 0.6649 (pt0) REVERT: A 105 ASN cc_start: 0.8394 (t0) cc_final: 0.8164 (t0) REVERT: A 120 CYS cc_start: 0.8648 (m) cc_final: 0.8377 (m) REVERT: A 172 GLU cc_start: 0.7452 (OUTLIER) cc_final: 0.7040 (tm-30) REVERT: A 174 LEU cc_start: 0.7977 (OUTLIER) cc_final: 0.7712 (mm) REVERT: A 189 HIS cc_start: 0.6547 (OUTLIER) cc_final: 0.6172 (p90) REVERT: B 671 LYS cc_start: 0.8101 (mttm) cc_final: 0.7667 (mttm) REVERT: B 756 LYS cc_start: 0.7708 (OUTLIER) cc_final: 0.7397 (pttm) REVERT: B 805 GLU cc_start: 0.7396 (pp20) cc_final: 0.7099 (pp20) REVERT: B 817 TYR cc_start: 0.8670 (OUTLIER) cc_final: 0.8139 (t80) REVERT: B 860 MET cc_start: 0.6214 (mmp) cc_final: 0.5926 (mpp) REVERT: B 916 TRP cc_start: 0.8181 (m-10) cc_final: 0.7833 (m-90) REVERT: B 940 LYS cc_start: 0.8388 (mmtt) cc_final: 0.8046 (tttt) REVERT: B 962 LYS cc_start: 0.5141 (OUTLIER) cc_final: 0.4220 (ptpp) REVERT: B 986 TYR cc_start: 0.6320 (OUTLIER) cc_final: 0.5171 (t80) REVERT: B 1164 MET cc_start: 0.7655 (OUTLIER) cc_final: 0.6700 (pp-130) REVERT: B 1167 ARG cc_start: 0.7830 (OUTLIER) cc_final: 0.7371 (pmt-80) REVERT: B 1225 GLU cc_start: 0.7526 (mm-30) cc_final: 0.7230 (mm-30) REVERT: B 1229 ARG cc_start: 0.7518 (OUTLIER) cc_final: 0.6427 (ptt180) REVERT: B 1248 SER cc_start: 0.8338 (t) cc_final: 0.8029 (m) REVERT: B 1284 ILE cc_start: 0.7182 (OUTLIER) cc_final: 0.6930 (pp) REVERT: D 220 ILE cc_start: 0.6016 (mt) cc_final: 0.5551 (mm) REVERT: D 263 HIS cc_start: 0.6376 (t-170) cc_final: 0.6103 (t-170) REVERT: D 347 MET cc_start: 0.6244 (tmt) cc_final: 0.5542 (tpt) REVERT: E 35 ARG cc_start: 0.6841 (OUTLIER) cc_final: 0.6449 (mtm180) REVERT: E 365 LYS cc_start: 0.8898 (OUTLIER) cc_final: 0.8507 (ptmm) REVERT: E 376 ASN cc_start: 0.6999 (OUTLIER) cc_final: 0.6568 (t0) REVERT: F 278 LEU cc_start: 0.3697 (OUTLIER) cc_final: 0.3371 (pt) REVERT: O 59 GLU cc_start: 0.8336 (OUTLIER) cc_final: 0.7795 (pp20) REVERT: P 25 ASN cc_start: 0.8880 (m-40) cc_final: 0.8546 (m-40) REVERT: Q 11 ARG cc_start: 0.2936 (OUTLIER) cc_final: -0.1390 (mtm-85) REVERT: Q 91 GLU cc_start: 0.8301 (OUTLIER) cc_final: 0.8057 (tt0) REVERT: T 88 TYR cc_start: 0.8751 (m-10) cc_final: 0.8467 (m-10) REVERT: U 51 LEU cc_start: 0.9370 (OUTLIER) cc_final: 0.9101 (tp) REVERT: U 56 GLU cc_start: 0.8898 (OUTLIER) cc_final: 0.8286 (tt0) outliers start: 87 outliers final: 56 residues processed: 330 average time/residue: 0.3653 time to fit residues: 187.7171 Evaluate side-chains 332 residues out of total 1917 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 77 poor density : 255 time to evaluate : 2.616 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 72 GLN Chi-restraints excluded: chain A residue 165 ASP Chi-restraints excluded: chain A residue 172 GLU Chi-restraints excluded: chain A residue 174 LEU Chi-restraints excluded: chain A residue 181 LEU Chi-restraints excluded: chain A residue 189 HIS Chi-restraints excluded: chain A residue 236 VAL Chi-restraints excluded: chain A residue 242 ILE Chi-restraints excluded: chain A residue 265 SER Chi-restraints excluded: chain A residue 269 LEU Chi-restraints excluded: chain A residue 314 THR Chi-restraints excluded: chain A residue 331 ASN Chi-restraints excluded: chain B residue 698 ASP Chi-restraints excluded: chain B residue 699 LEU Chi-restraints excluded: chain B residue 703 VAL Chi-restraints excluded: chain B residue 756 LYS Chi-restraints excluded: chain B residue 817 TYR Chi-restraints excluded: chain B residue 872 ASP Chi-restraints excluded: chain B residue 883 LEU Chi-restraints excluded: chain B residue 962 LYS Chi-restraints excluded: chain B residue 986 TYR Chi-restraints excluded: chain B residue 1020 LEU Chi-restraints excluded: chain B residue 1024 ILE Chi-restraints excluded: chain B residue 1144 ILE Chi-restraints excluded: chain B residue 1164 MET Chi-restraints excluded: chain B residue 1167 ARG Chi-restraints excluded: chain B residue 1169 THR Chi-restraints excluded: chain B residue 1177 THR Chi-restraints excluded: chain B residue 1179 THR Chi-restraints excluded: chain B residue 1196 LEU Chi-restraints excluded: chain B residue 1207 VAL Chi-restraints excluded: chain B residue 1219 LEU Chi-restraints excluded: chain B residue 1228 LEU Chi-restraints excluded: chain B residue 1229 ARG Chi-restraints excluded: chain B residue 1250 VAL Chi-restraints excluded: chain B residue 1284 ILE Chi-restraints excluded: chain B residue 1312 VAL Chi-restraints excluded: chain D residue 230 SER Chi-restraints excluded: chain D residue 235 ASP Chi-restraints excluded: chain D residue 256 MET Chi-restraints excluded: chain D residue 287 LEU Chi-restraints excluded: chain D residue 298 LEU Chi-restraints excluded: chain D residue 344 SER Chi-restraints excluded: chain D residue 360 GLU Chi-restraints excluded: chain E residue 35 ARG Chi-restraints excluded: chain E residue 365 LYS Chi-restraints excluded: chain E residue 376 ASN Chi-restraints excluded: chain E residue 408 ASP Chi-restraints excluded: chain E residue 415 LEU Chi-restraints excluded: chain E residue 416 ILE Chi-restraints excluded: chain E residue 423 THR Chi-restraints excluded: chain E residue 452 VAL Chi-restraints excluded: chain E residue 474 VAL Chi-restraints excluded: chain E residue 498 ILE Chi-restraints excluded: chain E residue 544 GLU Chi-restraints excluded: chain F residue 278 LEU Chi-restraints excluded: chain O residue 59 GLU Chi-restraints excluded: chain O residue 87 SER Chi-restraints excluded: chain O residue 92 LEU Chi-restraints excluded: chain P residue 80 THR Chi-restraints excluded: chain P residue 96 THR Chi-restraints excluded: chain Q residue 11 ARG Chi-restraints excluded: chain Q residue 62 ILE Chi-restraints excluded: chain Q residue 76 THR Chi-restraints excluded: chain Q residue 91 GLU Chi-restraints excluded: chain R residue 48 ASP Chi-restraints excluded: chain R residue 84 SER Chi-restraints excluded: chain R residue 109 SER Chi-restraints excluded: chain S residue 87 SER Chi-restraints excluded: chain S residue 103 LEU Chi-restraints excluded: chain T residue 29 ILE Chi-restraints excluded: chain T residue 44 LYS Chi-restraints excluded: chain T residue 96 THR Chi-restraints excluded: chain U residue 51 LEU Chi-restraints excluded: chain U residue 56 GLU Chi-restraints excluded: chain U residue 114 VAL Chi-restraints excluded: chain V residue 49 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 243 random chunks: chunk 224 optimal weight: 4.9990 chunk 204 optimal weight: 0.9990 chunk 218 optimal weight: 1.9990 chunk 131 optimal weight: 0.6980 chunk 95 optimal weight: 0.2980 chunk 171 optimal weight: 0.6980 chunk 66 optimal weight: 6.9990 chunk 197 optimal weight: 0.7980 chunk 206 optimal weight: 0.6980 chunk 217 optimal weight: 1.9990 chunk 143 optimal weight: 1.9990 overall best weight: 0.6380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 330 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 341 ASN B1254 HIS ** E 325 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 46 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 108 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8029 moved from start: 0.5851 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.060 25898 Z= 0.207 Angle : 0.567 10.943 36443 Z= 0.309 Chirality : 0.037 0.174 4041 Planarity : 0.004 0.046 3424 Dihedral : 27.578 142.560 6159 Min Nonbonded Distance : 2.131 Molprobity Statistics. All-atom Clashscore : 14.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.31 % Favored : 95.69 % Rotamer: Outliers : 4.12 % Allowed : 27.80 % Favored : 68.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.20 (0.18), residues: 2112 helix: 1.24 (0.15), residues: 1167 sheet: -0.99 (0.53), residues: 94 loop : -1.30 (0.21), residues: 851 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.001 TRP E 301 HIS 0.007 0.001 HIS B 815 PHE 0.020 0.001 PHE E 552 TYR 0.020 0.001 TYR R 37 ARG 0.009 0.000 ARG U 71 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4224 Ramachandran restraints generated. 2112 Oldfield, 0 Emsley, 2112 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4224 Ramachandran restraints generated. 2112 Oldfield, 0 Emsley, 2112 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 346 residues out of total 1917 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 79 poor density : 267 time to evaluate : 2.365 Fit side-chains revert: symmetry clash REVERT: A 72 GLN cc_start: 0.6851 (OUTLIER) cc_final: 0.6601 (pt0) REVERT: A 105 ASN cc_start: 0.8360 (t0) cc_final: 0.8125 (t0) REVERT: A 120 CYS cc_start: 0.8598 (m) cc_final: 0.8314 (m) REVERT: A 172 GLU cc_start: 0.7404 (OUTLIER) cc_final: 0.7013 (tm-30) REVERT: A 174 LEU cc_start: 0.7915 (OUTLIER) cc_final: 0.7582 (mm) REVERT: A 189 HIS cc_start: 0.6365 (OUTLIER) cc_final: 0.5970 (p90) REVERT: B 671 LYS cc_start: 0.8085 (mttm) cc_final: 0.7691 (mttm) REVERT: B 756 LYS cc_start: 0.7636 (OUTLIER) cc_final: 0.7336 (pttm) REVERT: B 805 GLU cc_start: 0.7380 (pp20) cc_final: 0.7074 (pp20) REVERT: B 817 TYR cc_start: 0.8655 (OUTLIER) cc_final: 0.8029 (t80) REVERT: B 860 MET cc_start: 0.6205 (mmp) cc_final: 0.5920 (mpp) REVERT: B 916 TRP cc_start: 0.8206 (m-10) cc_final: 0.7836 (m-10) REVERT: B 940 LYS cc_start: 0.8386 (mmtt) cc_final: 0.8046 (tttt) REVERT: B 962 LYS cc_start: 0.5141 (OUTLIER) cc_final: 0.4233 (ptpp) REVERT: B 986 TYR cc_start: 0.6245 (OUTLIER) cc_final: 0.5096 (t80) REVERT: B 1164 MET cc_start: 0.7613 (OUTLIER) cc_final: 0.6660 (pp-130) REVERT: B 1167 ARG cc_start: 0.7819 (OUTLIER) cc_final: 0.7350 (pmt-80) REVERT: B 1229 ARG cc_start: 0.7492 (OUTLIER) cc_final: 0.7202 (ptt180) REVERT: B 1248 SER cc_start: 0.8345 (t) cc_final: 0.8037 (m) REVERT: B 1284 ILE cc_start: 0.7174 (OUTLIER) cc_final: 0.6922 (pp) REVERT: D 220 ILE cc_start: 0.6059 (mt) cc_final: 0.5647 (mm) REVERT: D 263 HIS cc_start: 0.6370 (t-170) cc_final: 0.6110 (t-170) REVERT: D 347 MET cc_start: 0.6262 (tmt) cc_final: 0.5685 (tpt) REVERT: E 35 ARG cc_start: 0.6801 (OUTLIER) cc_final: 0.6419 (mtm180) REVERT: E 61 ARG cc_start: 0.6080 (mmp80) cc_final: 0.5563 (mmm160) REVERT: E 376 ASN cc_start: 0.6950 (OUTLIER) cc_final: 0.6560 (t0) REVERT: F 278 LEU cc_start: 0.3682 (OUTLIER) cc_final: 0.3335 (pt) REVERT: O 59 GLU cc_start: 0.8343 (OUTLIER) cc_final: 0.7802 (pp20) REVERT: P 25 ASN cc_start: 0.8859 (m-40) cc_final: 0.8519 (m-40) REVERT: Q 11 ARG cc_start: 0.2868 (OUTLIER) cc_final: -0.1009 (mtm-85) REVERT: Q 91 GLU cc_start: 0.8289 (OUTLIER) cc_final: 0.8054 (tt0) REVERT: R 90 GLU cc_start: 0.8415 (OUTLIER) cc_final: 0.7772 (mp0) REVERT: U 51 LEU cc_start: 0.9362 (OUTLIER) cc_final: 0.9101 (tp) REVERT: U 56 GLU cc_start: 0.8876 (OUTLIER) cc_final: 0.8278 (tt0) outliers start: 79 outliers final: 51 residues processed: 329 average time/residue: 0.3789 time to fit residues: 195.4270 Evaluate side-chains 331 residues out of total 1917 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 72 poor density : 259 time to evaluate : 2.579 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 72 GLN Chi-restraints excluded: chain A residue 165 ASP Chi-restraints excluded: chain A residue 172 GLU Chi-restraints excluded: chain A residue 174 LEU Chi-restraints excluded: chain A residue 181 LEU Chi-restraints excluded: chain A residue 189 HIS Chi-restraints excluded: chain A residue 236 VAL Chi-restraints excluded: chain A residue 242 ILE Chi-restraints excluded: chain A residue 265 SER Chi-restraints excluded: chain A residue 269 LEU Chi-restraints excluded: chain A residue 314 THR Chi-restraints excluded: chain A residue 331 ASN Chi-restraints excluded: chain B residue 698 ASP Chi-restraints excluded: chain B residue 699 LEU Chi-restraints excluded: chain B residue 756 LYS Chi-restraints excluded: chain B residue 810 ILE Chi-restraints excluded: chain B residue 817 TYR Chi-restraints excluded: chain B residue 872 ASP Chi-restraints excluded: chain B residue 883 LEU Chi-restraints excluded: chain B residue 962 LYS Chi-restraints excluded: chain B residue 986 TYR Chi-restraints excluded: chain B residue 1020 LEU Chi-restraints excluded: chain B residue 1024 ILE Chi-restraints excluded: chain B residue 1144 ILE Chi-restraints excluded: chain B residue 1164 MET Chi-restraints excluded: chain B residue 1167 ARG Chi-restraints excluded: chain B residue 1169 THR Chi-restraints excluded: chain B residue 1179 THR Chi-restraints excluded: chain B residue 1196 LEU Chi-restraints excluded: chain B residue 1207 VAL Chi-restraints excluded: chain B residue 1219 LEU Chi-restraints excluded: chain B residue 1228 LEU Chi-restraints excluded: chain B residue 1229 ARG Chi-restraints excluded: chain B residue 1284 ILE Chi-restraints excluded: chain B residue 1312 VAL Chi-restraints excluded: chain D residue 235 ASP Chi-restraints excluded: chain D residue 256 MET Chi-restraints excluded: chain D residue 298 LEU Chi-restraints excluded: chain D residue 360 GLU Chi-restraints excluded: chain E residue 35 ARG Chi-restraints excluded: chain E residue 360 THR Chi-restraints excluded: chain E residue 376 ASN Chi-restraints excluded: chain E residue 408 ASP Chi-restraints excluded: chain E residue 415 LEU Chi-restraints excluded: chain E residue 416 ILE Chi-restraints excluded: chain E residue 423 THR Chi-restraints excluded: chain E residue 452 VAL Chi-restraints excluded: chain E residue 474 VAL Chi-restraints excluded: chain E residue 498 ILE Chi-restraints excluded: chain E residue 544 GLU Chi-restraints excluded: chain F residue 278 LEU Chi-restraints excluded: chain O residue 59 GLU Chi-restraints excluded: chain O residue 87 SER Chi-restraints excluded: chain O residue 92 LEU Chi-restraints excluded: chain P residue 80 THR Chi-restraints excluded: chain P residue 96 THR Chi-restraints excluded: chain Q residue 11 ARG Chi-restraints excluded: chain Q residue 62 ILE Chi-restraints excluded: chain Q residue 76 THR Chi-restraints excluded: chain Q residue 91 GLU Chi-restraints excluded: chain R residue 48 ASP Chi-restraints excluded: chain R residue 84 SER Chi-restraints excluded: chain R residue 90 GLU Chi-restraints excluded: chain R residue 109 SER Chi-restraints excluded: chain S residue 87 SER Chi-restraints excluded: chain S residue 103 LEU Chi-restraints excluded: chain T residue 44 LYS Chi-restraints excluded: chain T residue 96 THR Chi-restraints excluded: chain U residue 51 LEU Chi-restraints excluded: chain U residue 56 GLU Chi-restraints excluded: chain U residue 114 VAL Chi-restraints excluded: chain V residue 49 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 243 random chunks: chunk 230 optimal weight: 4.9990 chunk 140 optimal weight: 0.9980 chunk 109 optimal weight: 6.9990 chunk 160 optimal weight: 2.9990 chunk 242 optimal weight: 9.9990 chunk 222 optimal weight: 3.9990 chunk 192 optimal weight: 1.9990 chunk 20 optimal weight: 0.7980 chunk 148 optimal weight: 2.9990 chunk 118 optimal weight: 0.7980 chunk 153 optimal weight: 1.9990 overall best weight: 1.3184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 330 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 341 ASN B1150 HIS B1254 HIS D 358 GLN ** E 325 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 46 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 108 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8095 moved from start: 0.6211 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.055 25898 Z= 0.300 Angle : 0.610 11.913 36443 Z= 0.330 Chirality : 0.039 0.170 4041 Planarity : 0.004 0.046 3424 Dihedral : 27.672 142.742 6159 Min Nonbonded Distance : 2.085 Molprobity Statistics. All-atom Clashscore : 15.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.16 % Favored : 94.84 % Rotamer: Outliers : 4.28 % Allowed : 27.49 % Favored : 68.23 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.04 (0.18), residues: 2112 helix: 1.07 (0.15), residues: 1169 sheet: -1.15 (0.53), residues: 92 loop : -1.31 (0.21), residues: 851 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.002 TRP E 301 HIS 0.008 0.001 HIS B 815 PHE 0.028 0.002 PHE A 160 TYR 0.041 0.002 TYR T 88 ARG 0.007 0.000 ARG U 71 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4224 Ramachandran restraints generated. 2112 Oldfield, 0 Emsley, 2112 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4224 Ramachandran restraints generated. 2112 Oldfield, 0 Emsley, 2112 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 346 residues out of total 1917 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 82 poor density : 264 time to evaluate : 2.507 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 72 GLN cc_start: 0.6911 (OUTLIER) cc_final: 0.6702 (pt0) REVERT: A 105 ASN cc_start: 0.8470 (t0) cc_final: 0.8198 (t0) REVERT: A 120 CYS cc_start: 0.8663 (m) cc_final: 0.8424 (m) REVERT: A 172 GLU cc_start: 0.7557 (OUTLIER) cc_final: 0.7123 (tm-30) REVERT: A 174 LEU cc_start: 0.8010 (OUTLIER) cc_final: 0.7672 (mm) REVERT: A 189 HIS cc_start: 0.6599 (OUTLIER) cc_final: 0.6135 (p90) REVERT: B 671 LYS cc_start: 0.8078 (mttm) cc_final: 0.7672 (mttm) REVERT: B 756 LYS cc_start: 0.7707 (OUTLIER) cc_final: 0.7467 (pttm) REVERT: B 805 GLU cc_start: 0.7404 (pp20) cc_final: 0.7077 (pp20) REVERT: B 817 TYR cc_start: 0.8684 (OUTLIER) cc_final: 0.8149 (t80) REVERT: B 860 MET cc_start: 0.6291 (mmp) cc_final: 0.5995 (mpp) REVERT: B 916 TRP cc_start: 0.8281 (m-10) cc_final: 0.7879 (m-10) REVERT: B 940 LYS cc_start: 0.8477 (mmtt) cc_final: 0.8142 (tttt) REVERT: B 955 ILE cc_start: 0.9014 (mm) cc_final: 0.8797 (mt) REVERT: B 962 LYS cc_start: 0.5158 (OUTLIER) cc_final: 0.4248 (ptpp) REVERT: B 986 TYR cc_start: 0.6367 (OUTLIER) cc_final: 0.5209 (t80) REVERT: B 1164 MET cc_start: 0.7729 (OUTLIER) cc_final: 0.6702 (pp-130) REVERT: B 1167 ARG cc_start: 0.7859 (OUTLIER) cc_final: 0.7377 (pmt-80) REVERT: B 1229 ARG cc_start: 0.7571 (OUTLIER) cc_final: 0.6550 (ptt180) REVERT: B 1248 SER cc_start: 0.8385 (t) cc_final: 0.8055 (m) REVERT: B 1284 ILE cc_start: 0.7269 (OUTLIER) cc_final: 0.6995 (pp) REVERT: D 220 ILE cc_start: 0.6039 (mt) cc_final: 0.5601 (mm) REVERT: D 263 HIS cc_start: 0.6457 (t-170) cc_final: 0.6186 (t-170) REVERT: D 347 MET cc_start: 0.6281 (tmt) cc_final: 0.5633 (tpt) REVERT: E 35 ARG cc_start: 0.6893 (OUTLIER) cc_final: 0.6529 (mtm180) REVERT: E 61 ARG cc_start: 0.6127 (mmp80) cc_final: 0.5600 (mmm160) REVERT: E 376 ASN cc_start: 0.7160 (OUTLIER) cc_final: 0.6649 (t0) REVERT: F 278 LEU cc_start: 0.3750 (OUTLIER) cc_final: 0.3360 (pt) REVERT: O 59 GLU cc_start: 0.8350 (OUTLIER) cc_final: 0.7834 (pp20) REVERT: P 25 ASN cc_start: 0.8908 (m-40) cc_final: 0.8580 (m-40) REVERT: Q 11 ARG cc_start: 0.3210 (OUTLIER) cc_final: -0.0904 (mtm-85) REVERT: Q 91 GLU cc_start: 0.8313 (OUTLIER) cc_final: 0.8062 (tt0) REVERT: T 31 LYS cc_start: 0.9129 (OUTLIER) cc_final: 0.8879 (tttm) REVERT: U 51 LEU cc_start: 0.9374 (OUTLIER) cc_final: 0.9109 (tp) REVERT: U 56 GLU cc_start: 0.8908 (OUTLIER) cc_final: 0.8296 (tm-30) outliers start: 82 outliers final: 54 residues processed: 329 average time/residue: 0.3744 time to fit residues: 192.1800 Evaluate side-chains 334 residues out of total 1917 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 75 poor density : 259 time to evaluate : 1.879 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 72 GLN Chi-restraints excluded: chain A residue 165 ASP Chi-restraints excluded: chain A residue 172 GLU Chi-restraints excluded: chain A residue 174 LEU Chi-restraints excluded: chain A residue 181 LEU Chi-restraints excluded: chain A residue 189 HIS Chi-restraints excluded: chain A residue 232 TYR Chi-restraints excluded: chain A residue 236 VAL Chi-restraints excluded: chain A residue 242 ILE Chi-restraints excluded: chain A residue 265 SER Chi-restraints excluded: chain A residue 269 LEU Chi-restraints excluded: chain A residue 314 THR Chi-restraints excluded: chain A residue 331 ASN Chi-restraints excluded: chain A residue 341 ASN Chi-restraints excluded: chain B residue 698 ASP Chi-restraints excluded: chain B residue 699 LEU Chi-restraints excluded: chain B residue 756 LYS Chi-restraints excluded: chain B residue 810 ILE Chi-restraints excluded: chain B residue 817 TYR Chi-restraints excluded: chain B residue 872 ASP Chi-restraints excluded: chain B residue 883 LEU Chi-restraints excluded: chain B residue 934 THR Chi-restraints excluded: chain B residue 962 LYS Chi-restraints excluded: chain B residue 986 TYR Chi-restraints excluded: chain B residue 1020 LEU Chi-restraints excluded: chain B residue 1024 ILE Chi-restraints excluded: chain B residue 1144 ILE Chi-restraints excluded: chain B residue 1164 MET Chi-restraints excluded: chain B residue 1167 ARG Chi-restraints excluded: chain B residue 1169 THR Chi-restraints excluded: chain B residue 1179 THR Chi-restraints excluded: chain B residue 1196 LEU Chi-restraints excluded: chain B residue 1207 VAL Chi-restraints excluded: chain B residue 1210 LEU Chi-restraints excluded: chain B residue 1219 LEU Chi-restraints excluded: chain B residue 1228 LEU Chi-restraints excluded: chain B residue 1229 ARG Chi-restraints excluded: chain B residue 1284 ILE Chi-restraints excluded: chain B residue 1312 VAL Chi-restraints excluded: chain D residue 230 SER Chi-restraints excluded: chain D residue 235 ASP Chi-restraints excluded: chain D residue 298 LEU Chi-restraints excluded: chain D residue 344 SER Chi-restraints excluded: chain D residue 358 GLN Chi-restraints excluded: chain D residue 360 GLU Chi-restraints excluded: chain E residue 35 ARG Chi-restraints excluded: chain E residue 376 ASN Chi-restraints excluded: chain E residue 408 ASP Chi-restraints excluded: chain E residue 415 LEU Chi-restraints excluded: chain E residue 416 ILE Chi-restraints excluded: chain E residue 423 THR Chi-restraints excluded: chain E residue 452 VAL Chi-restraints excluded: chain E residue 474 VAL Chi-restraints excluded: chain E residue 498 ILE Chi-restraints excluded: chain E residue 544 GLU Chi-restraints excluded: chain F residue 278 LEU Chi-restraints excluded: chain O residue 59 GLU Chi-restraints excluded: chain O residue 87 SER Chi-restraints excluded: chain O residue 92 LEU Chi-restraints excluded: chain P residue 96 THR Chi-restraints excluded: chain Q residue 11 ARG Chi-restraints excluded: chain Q residue 62 ILE Chi-restraints excluded: chain Q residue 91 GLU Chi-restraints excluded: chain R residue 48 ASP Chi-restraints excluded: chain R residue 84 SER Chi-restraints excluded: chain R residue 109 SER Chi-restraints excluded: chain S residue 87 SER Chi-restraints excluded: chain S residue 103 LEU Chi-restraints excluded: chain T residue 31 LYS Chi-restraints excluded: chain T residue 44 LYS Chi-restraints excluded: chain T residue 96 THR Chi-restraints excluded: chain U residue 51 LEU Chi-restraints excluded: chain U residue 56 GLU Chi-restraints excluded: chain U residue 114 VAL Chi-restraints excluded: chain V residue 49 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 243 random chunks: chunk 205 optimal weight: 0.9990 chunk 59 optimal weight: 5.9990 chunk 177 optimal weight: 0.8980 chunk 28 optimal weight: 0.7980 chunk 53 optimal weight: 2.9990 chunk 193 optimal weight: 0.7980 chunk 80 optimal weight: 2.9990 chunk 198 optimal weight: 0.2980 chunk 24 optimal weight: 0.9990 chunk 35 optimal weight: 2.9990 chunk 169 optimal weight: 1.9990 overall best weight: 0.7582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 38 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 135 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 330 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B1254 HIS ** E 325 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 46 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 108 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4080 r_free = 0.4080 target = 0.121278 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3592 r_free = 0.3592 target = 0.091590 restraints weight = 57745.085| |-----------------------------------------------------------------------------| r_work (start): 0.3507 rms_B_bonded: 1.86 r_work: 0.3266 rms_B_bonded: 3.32 restraints_weight: 0.5000 r_work (final): 0.3266 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8161 moved from start: 0.6228 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.416 25898 Z= 0.353 Angle : 0.764 59.196 36443 Z= 0.452 Chirality : 0.040 0.672 4041 Planarity : 0.005 0.145 3424 Dihedral : 27.679 142.759 6159 Min Nonbonded Distance : 1.993 Molprobity Statistics. All-atom Clashscore : 16.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.21 % Favored : 94.79 % Rotamer: Outliers : 3.96 % Allowed : 27.65 % Favored : 68.39 % Cbeta Deviations : 0.05 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.05 % 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: 0.04 (0.18), residues: 2112 helix: 1.07 (0.15), residues: 1169 sheet: -1.16 (0.53), residues: 92 loop : -1.31 (0.21), residues: 851 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.001 TRP E 301 HIS 0.014 0.001 HIS A 38 PHE 0.057 0.002 PHE A 160 TYR 0.053 0.002 TYR T 88 ARG 0.006 0.000 ARG U 71 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5692.93 seconds wall clock time: 103 minutes 38.13 seconds (6218.13 seconds total)