Starting phenix.real_space_refine (version: 1.21rc1) on Thu Oct 12 07:29:13 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8kd2_37122/10_2023/8kd2_37122.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8kd2_37122/10_2023/8kd2_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_37122/10_2023/8kd2_37122.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8kd2_37122/10_2023/8kd2_37122.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8kd2_37122/10_2023/8kd2_37122.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8kd2_37122/10_2023/8kd2_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: 0.06s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5097/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: 12.68, per 1000 atoms: 0.51 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: 12.58 Conformation dependent library (CDL) restraints added in 2.7 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: 9.95 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: 16.23 Time building geometry restraints manager: 13.30 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: 11539 27.36 - 54.71: 2433 54.71 - 82.07: 388 82.07 - 109.42: 12 109.42 - 136.78: 2 Dihedral angle restraints: 14374 sinusoidal: 8030 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 14371 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: 6.750 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 33.520 Check model and map are aligned: 0.390 Set scattering table: 0.250 Process input model: 79.640 Find NCS groups from input model: 0.790 Set up NCS constraints: 0.120 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.760 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 124.250 ------------------------------------------------------------------------------- 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 : 25.701 136.778 10269 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 *********************** 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 : 2.207 Fit side-chains outliers start: 13 outliers final: 4 residues processed: 258 average time/residue: 0.3358 time to fit residues: 141.3954 Evaluate side-chains 235 residues out of total 1917 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 231 time to evaluate : 2.663 Switching outliers to nearest non-outliers outliers start: 4 outliers final: 0 residues processed: 4 average time/residue: 0.2315 time to fit residues: 5.4609 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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: 2.9990 chunk 115 optimal weight: 8.9990 chunk 141 optimal weight: 2.9990 chunk 220 optimal weight: 3.9990 overall best weight: 2.5388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 177 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 364 ASN B 690 ASN ** B 815 HIS ** 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 60 ASN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7911 moved from start: 0.3848 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.009 0.142 25898 Z= 0.533 Angle : 0.807 21.795 36443 Z= 0.440 Chirality : 0.049 0.316 4041 Planarity : 0.006 0.084 3424 Dihedral : 28.230 139.850 5863 Min Nonbonded Distance : 1.971 Molprobity Statistics. All-atom Clashscore : 18.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.21 % Favored : 95.79 % Rotamer: Outliers : 8.45 % Allowed : 26.40 % Favored : 65.15 % 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: -0.82 (0.17), residues: 2112 helix: 0.20 (0.14), residues: 1159 sheet: 0.09 (0.57), residues: 82 loop : -1.60 (0.20), residues: 871 *********************** 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 468 residues out of total 1917 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 162 poor density : 306 time to evaluate : 2.544 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 162 outliers final: 69 residues processed: 425 average time/residue: 0.3778 time to fit residues: 247.2973 Evaluate side-chains 326 residues out of total 1917 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 69 poor density : 257 time to evaluate : 2.375 Switching outliers to nearest non-outliers outliers start: 69 outliers final: 0 residues processed: 69 average time/residue: 0.2455 time to fit residues: 33.3116 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 243 random chunks: chunk 122 optimal weight: 2.9990 chunk 68 optimal weight: 2.9990 chunk 183 optimal weight: 0.1980 chunk 150 optimal weight: 0.8980 chunk 60 optimal weight: 1.9990 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: 1.9990 chunk 177 optimal weight: 0.9990 overall best weight: 1.2186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 43 HIS ** 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 779 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B1254 HIS B1274 ASN ** B1293 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B1299 ASN D 295 ASN ** E 325 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** O 68 GLN ** S 108 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** U 73 ASN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7908 moved from start: 0.4136 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.091 25898 Z= 0.281 Angle : 0.600 9.641 36443 Z= 0.331 Chirality : 0.039 0.188 4041 Planarity : 0.004 0.047 3424 Dihedral : 28.206 140.135 5863 Min Nonbonded Distance : 2.052 Molprobity Statistics. All-atom Clashscore : 13.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.02 % Favored : 95.98 % Rotamer: Outliers : 3.39 % Allowed : 27.23 % Favored : 69.38 % 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: -0.36 (0.18), residues: 2112 helix: 0.69 (0.15), residues: 1164 sheet: -0.20 (0.56), residues: 82 loop : -1.52 (0.20), residues: 866 *********************** 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 339 residues out of total 1917 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 65 poor density : 274 time to evaluate : 2.571 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 65 outliers final: 22 residues processed: 324 average time/residue: 0.3820 time to fit residues: 190.8787 Evaluate side-chains 279 residues out of total 1917 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 257 time to evaluate : 2.233 Switching outliers to nearest non-outliers outliers start: 22 outliers final: 0 residues processed: 22 average time/residue: 0.2462 time to fit residues: 12.4249 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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: 9.9990 chunk 24 optimal weight: 0.8980 chunk 105 optimal weight: 3.9990 chunk 148 optimal weight: 0.0040 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: 0.7980 overall best weight: 0.9396 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 150 HIS ** A 330 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 341 ASN B 779 ASN ** B 815 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B1173 ASN B1254 HIS ** B1293 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 295 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 ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 46 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** R 60 ASN ** S 108 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 73 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7930 moved from start: 0.4492 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 25898 Z= 0.241 Angle : 0.566 9.305 36443 Z= 0.313 Chirality : 0.037 0.172 4041 Planarity : 0.004 0.047 3424 Dihedral : 27.965 140.726 5863 Min Nonbonded Distance : 2.103 Molprobity Statistics. All-atom Clashscore : 14.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.26 % Favored : 95.74 % Rotamer: Outliers : 2.97 % Allowed : 27.18 % Favored : 69.85 % 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: 0.99 (0.15), residues: 1171 sheet: -0.19 (0.56), residues: 81 loop : -1.44 (0.20), residues: 860 *********************** 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 349 residues out of total 1917 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 57 poor density : 292 time to evaluate : 2.335 Fit side-chains revert: symmetry clash outliers start: 57 outliers final: 17 residues processed: 336 average time/residue: 0.3879 time to fit residues: 204.2076 Evaluate side-chains 289 residues out of total 1917 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 272 time to evaluate : 2.280 Switching outliers to nearest non-outliers outliers start: 17 outliers final: 0 residues processed: 17 average time/residue: 0.2433 time to fit residues: 10.7624 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 243 random chunks: chunk 195 optimal weight: 0.6980 chunk 133 optimal weight: 0.0370 chunk 3 optimal weight: 0.7980 chunk 174 optimal weight: 0.0870 chunk 96 optimal weight: 4.9990 chunk 200 optimal weight: 2.9990 chunk 162 optimal weight: 0.9980 chunk 0 optimal weight: 5.9990 chunk 119 optimal weight: 1.9990 chunk 210 optimal weight: 10.0000 chunk 59 optimal weight: 8.9990 overall best weight: 0.5236 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 76 GLN A 296 ASN ** A 330 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 341 ASN B 779 ASN ** B 815 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B1254 HIS ** B1293 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 369 HIS D 389 ASN E 304 ASN ** E 325 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 346 HIS ** P 25 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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: 10 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7901 moved from start: 0.4606 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 25898 Z= 0.186 Angle : 0.538 9.303 36443 Z= 0.299 Chirality : 0.036 0.190 4041 Planarity : 0.004 0.048 3424 Dihedral : 27.874 140.877 5863 Min Nonbonded Distance : 2.136 Molprobity Statistics. All-atom Clashscore : 13.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.79 % Favored : 96.21 % Rotamer: Outliers : 1.67 % Allowed : 27.96 % Favored : 70.37 % 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: 1.23 (0.15), residues: 1172 sheet: -0.50 (0.55), residues: 92 loop : -1.37 (0.21), residues: 848 *********************** 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 305 residues out of total 1917 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 273 time to evaluate : 2.573 Fit side-chains revert: symmetry clash outliers start: 32 outliers final: 10 residues processed: 299 average time/residue: 0.3860 time to fit residues: 179.0380 Evaluate side-chains 273 residues out of total 1917 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 263 time to evaluate : 2.661 Switching outliers to nearest non-outliers outliers start: 10 outliers final: 0 residues processed: 10 average time/residue: 0.2237 time to fit residues: 7.4435 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 243 random chunks: chunk 79 optimal weight: 7.9990 chunk 211 optimal weight: 5.9990 chunk 46 optimal weight: 0.0020 chunk 137 optimal weight: 20.0000 chunk 57 optimal weight: 0.9990 chunk 235 optimal weight: 1.9990 chunk 195 optimal weight: 0.9990 chunk 108 optimal weight: 3.9990 chunk 19 optimal weight: 3.9990 chunk 77 optimal weight: 10.0000 chunk 123 optimal weight: 0.9980 overall best weight: 0.9994 ------------------------------------------------------------------------------- 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 ** B 815 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B1254 HIS ** B1293 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 295 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 325 ASN ** 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: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7978 moved from start: 0.5025 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 25898 Z= 0.253 Angle : 0.571 11.744 36443 Z= 0.313 Chirality : 0.038 0.187 4041 Planarity : 0.004 0.047 3424 Dihedral : 27.839 141.123 5863 Min Nonbonded Distance : 2.091 Molprobity Statistics. All-atom Clashscore : 14.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.45 % Favored : 95.55 % Rotamer: Outliers : 1.67 % Allowed : 28.27 % Favored : 70.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.17 (0.18), residues: 2112 helix: 1.18 (0.15), residues: 1164 sheet: -0.58 (0.54), residues: 92 loop : -1.32 (0.21), residues: 856 *********************** 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 323 residues out of total 1917 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 291 time to evaluate : 2.404 Fit side-chains outliers start: 32 outliers final: 11 residues processed: 316 average time/residue: 0.3964 time to fit residues: 195.5464 Evaluate side-chains 273 residues out of total 1917 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 262 time to evaluate : 2.314 Switching outliers to nearest non-outliers outliers start: 11 outliers final: 0 residues processed: 11 average time/residue: 0.2254 time to fit residues: 7.5738 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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: 4.9990 chunk 133 optimal weight: 4.9990 chunk 171 optimal weight: 0.6980 chunk 197 optimal weight: 0.5980 chunk 131 optimal weight: 0.8980 chunk 234 optimal weight: 1.9990 chunk 146 optimal weight: 0.9990 chunk 142 optimal weight: 0.9980 chunk 108 optimal weight: 2.9990 chunk 144 optimal weight: 0.5980 overall best weight: 0.7580 ------------------------------------------------------------------------------- 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 295 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 325 ASN ** 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: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7964 moved from start: 0.5191 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 25898 Z= 0.212 Angle : 0.556 9.161 36443 Z= 0.305 Chirality : 0.037 0.159 4041 Planarity : 0.004 0.065 3424 Dihedral : 27.842 141.370 5863 Min Nonbonded Distance : 2.138 Molprobity Statistics. All-atom Clashscore : 14.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.36 % Favored : 95.64 % Rotamer: Outliers : 0.99 % Allowed : 28.38 % Favored : 70.63 % 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: 0.18 (0.18), residues: 2112 helix: 1.19 (0.15), residues: 1172 sheet: -0.61 (0.55), residues: 93 loop : -1.31 (0.21), residues: 847 *********************** 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 301 residues out of total 1917 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 282 time to evaluate : 2.375 Fit side-chains outliers start: 19 outliers final: 9 residues processed: 295 average time/residue: 0.3816 time to fit residues: 177.7524 Evaluate side-chains 265 residues out of total 1917 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 256 time to evaluate : 2.569 Switching outliers to nearest non-outliers outliers start: 9 outliers final: 0 residues processed: 9 average time/residue: 0.2313 time to fit residues: 7.2152 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 243 random chunks: chunk 93 optimal weight: 0.9980 chunk 139 optimal weight: 0.9990 chunk 70 optimal weight: 5.9990 chunk 46 optimal weight: 0.0370 chunk 45 optimal weight: 6.9990 chunk 148 optimal weight: 0.9980 chunk 159 optimal weight: 1.9990 chunk 115 optimal weight: 0.0370 chunk 21 optimal weight: 0.7980 chunk 184 optimal weight: 0.5980 chunk 213 optimal weight: 3.9990 overall best weight: 0.4936 ------------------------------------------------------------------------------- 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 295 ASN ** E 325 ASN ** 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: 0.7941 moved from start: 0.5233 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.054 25898 Z= 0.184 Angle : 0.556 17.127 36443 Z= 0.301 Chirality : 0.036 0.184 4041 Planarity : 0.004 0.047 3424 Dihedral : 27.738 141.366 5863 Min Nonbonded Distance : 2.160 Molprobity Statistics. All-atom Clashscore : 14.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.12 % Favored : 95.88 % Rotamer: Outliers : 0.99 % Allowed : 28.33 % Favored : 70.68 % 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: 0.30 (0.18), residues: 2112 helix: 1.30 (0.15), residues: 1171 sheet: -0.62 (0.55), residues: 94 loop : -1.29 (0.21), residues: 847 *********************** 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 289 residues out of total 1917 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 270 time to evaluate : 2.549 Fit side-chains outliers start: 19 outliers final: 7 residues processed: 285 average time/residue: 0.3848 time to fit residues: 172.3999 Evaluate side-chains 270 residues out of total 1917 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 263 time to evaluate : 2.311 Switching outliers to nearest non-outliers outliers start: 7 outliers final: 0 residues processed: 7 average time/residue: 0.2276 time to fit residues: 6.1704 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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: 0.5980 chunk 218 optimal weight: 1.9990 chunk 131 optimal weight: 0.6980 chunk 95 optimal weight: 0.0670 chunk 171 optimal weight: 0.7980 chunk 66 optimal weight: 6.9990 chunk 197 optimal weight: 0.9980 chunk 206 optimal weight: 0.8980 chunk 217 optimal weight: 1.9990 chunk 143 optimal weight: 1.9990 overall best weight: 0.6118 ------------------------------------------------------------------------------- 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 ** B 815 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B1247 GLN ** B1293 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 263 HIS ** E 325 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 104 GLN ** 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: 0.7952 moved from start: 0.5365 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 25898 Z= 0.195 Angle : 0.549 9.300 36443 Z= 0.300 Chirality : 0.036 0.171 4041 Planarity : 0.004 0.048 3424 Dihedral : 27.700 141.240 5863 Min Nonbonded Distance : 2.131 Molprobity Statistics. All-atom Clashscore : 13.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.88 % Favored : 96.12 % Rotamer: Outliers : 0.52 % Allowed : 28.85 % Favored : 70.63 % 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: 0.30 (0.18), residues: 2112 helix: 1.29 (0.15), residues: 1173 sheet: -0.59 (0.55), residues: 94 loop : -1.27 (0.21), residues: 845 *********************** 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 284 residues out of total 1917 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 274 time to evaluate : 2.297 Fit side-chains outliers start: 10 outliers final: 5 residues processed: 280 average time/residue: 0.3706 time to fit residues: 163.6345 Evaluate side-chains 265 residues out of total 1917 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 260 time to evaluate : 2.244 Switching outliers to nearest non-outliers outliers start: 5 outliers final: 0 residues processed: 5 average time/residue: 0.2464 time to fit residues: 5.3506 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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: 0.9980 chunk 160 optimal weight: 0.9980 chunk 242 optimal weight: 10.0000 chunk 222 optimal weight: 3.9990 chunk 192 optimal weight: 1.9990 chunk 20 optimal weight: 0.0170 chunk 148 optimal weight: 1.9990 chunk 118 optimal weight: 0.3980 chunk 153 optimal weight: 2.9990 overall best weight: 0.6818 ------------------------------------------------------------------------------- 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 ** B 815 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1293 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 263 HIS ** E 325 ASN ** 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: 0.7964 moved from start: 0.5484 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.057 25898 Z= 0.204 Angle : 0.573 17.749 36443 Z= 0.309 Chirality : 0.037 0.204 4041 Planarity : 0.004 0.048 3424 Dihedral : 27.687 141.325 5863 Min Nonbonded Distance : 2.143 Molprobity Statistics. All-atom Clashscore : 14.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.21 % Favored : 95.79 % Rotamer: Outliers : 0.42 % Allowed : 28.74 % Favored : 70.84 % 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: 0.36 (0.18), residues: 2112 helix: 1.33 (0.15), residues: 1171 sheet: -0.56 (0.55), residues: 94 loop : -1.23 (0.21), residues: 847 ********************** 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 274 residues out of total 1917 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 266 time to evaluate : 2.360 Fit side-chains outliers start: 8 outliers final: 3 residues processed: 270 average time/residue: 0.3846 time to fit residues: 162.9810 Evaluate side-chains 266 residues out of total 1917 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 263 time to evaluate : 2.595 Switching outliers to nearest non-outliers outliers start: 3 outliers final: 0 residues processed: 3 average time/residue: 0.2291 time to fit residues: 4.2911 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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: 0.9990 chunk 177 optimal weight: 0.5980 chunk 28 optimal weight: 0.8980 chunk 53 optimal weight: 0.9990 chunk 193 optimal weight: 0.5980 chunk 80 optimal weight: 0.9980 chunk 198 optimal weight: 0.7980 chunk 24 optimal weight: 0.9990 chunk 35 optimal weight: 1.9990 chunk 169 optimal weight: 0.8980 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 135 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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** B 983 ASN ** B1293 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 263 HIS ** E 325 ASN ** 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 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4146 r_free = 0.4146 target = 0.125521 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3662 r_free = 0.3662 target = 0.095751 restraints weight = 58005.475| |-----------------------------------------------------------------------------| r_work (start): 0.3592 rms_B_bonded: 1.80 r_work: 0.3378 rms_B_bonded: 3.24 restraints_weight: 0.5000 r_work (final): 0.3378 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8032 moved from start: 0.5649 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 25898 Z= 0.216 Angle : 0.570 12.365 36443 Z= 0.310 Chirality : 0.037 0.196 4041 Planarity : 0.004 0.048 3424 Dihedral : 27.688 141.395 5863 Min Nonbonded Distance : 2.111 Molprobity Statistics. All-atom Clashscore : 14.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.02 % Favored : 95.98 % Rotamer: Outliers : 0.57 % Allowed : 28.43 % Favored : 71.00 % 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: 0.35 (0.18), residues: 2112 helix: 1.30 (0.15), residues: 1170 sheet: -0.53 (0.56), residues: 94 loop : -1.20 (0.21), residues: 848 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5445.78 seconds wall clock time: 100 minutes 17.56 seconds (6017.56 seconds total)