Starting phenix.real_space_refine (version: dev) on Mon Feb 27 19:50:12 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6pb4_20286/02_2023/6pb4_20286_trim_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6pb4_20286/02_2023/6pb4_20286.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.35 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6pb4_20286/02_2023/6pb4_20286.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6pb4_20286/02_2023/6pb4_20286.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6pb4_20286/02_2023/6pb4_20286_trim_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6pb4_20286/02_2023/6pb4_20286_trim_updated.pdb" } resolution = 4.35 write_initial_geo_file = False refinement { macro_cycles = 10 } 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 ------------------------------------------------------------------------------- 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= -0.009 sd= 0.338 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 Process input model Symmetric amino acids flipped Residue "A TYR 185": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A PHE 231": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "B PHE 8": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "C PHE 57": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "C TYR 73": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "C PHE 253": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "C ARG 268": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "C ARG 332": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "C TYR 584": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "C PHE 804": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "C PHE 1270": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "D TYR 360": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "D TYR 555": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "D TYR 609": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "D PHE 719": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "D PHE 773": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "D PHE 1199": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "D ARG 1355": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "F PHE 221": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "F PHE 266": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Time to flip residues: 0.08s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-4877/modules/chem_data/mon_lib" Total number of atoms: 69922 Number of models: 1 Model: "" Number of chains: 14 Chain: "A" Number of atoms: 3599 Number of conformers: 1 Conformer: "" Number of residues, atoms: 230, 3599 Classifications: {'peptide': 230} Link IDs: {'PCIS': 1, 'PTRANS': 8, 'TRANS': 220} Chain: "B" Number of atoms: 3556 Number of conformers: 1 Conformer: "" Number of residues, atoms: 228, 3556 Classifications: {'peptide': 228} Link IDs: {'PCIS': 1, 'PTRANS': 8, 'TRANS': 218} Chain: "C" Number of atoms: 21151 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1340, 21151 Classifications: {'peptide': 1340} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 55, 'TRANS': 1283} Chain: "D" Number of atoms: 21012 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1337, 21012 Classifications: {'peptide': 1337} Link IDs: {'PCIS': 1, 'PTRANS': 54, 'TRANS': 1281} Chain breaks: 2 Chain: "E" Number of atoms: 1261 Number of conformers: 1 Conformer: "" Number of residues, atoms: 79, 1261 Classifications: {'peptide': 79} Link IDs: {'PTRANS': 2, 'TRANS': 76} Chain: "F" Number of atoms: 7918 Number of conformers: 1 Conformer: "" Number of residues, atoms: 483, 7918 Classifications: {'peptide': 483} Link IDs: {'PTRANS': 15, 'TRANS': 467} Chain breaks: 1 Chain: "G" Number of atoms: 3156 Number of conformers: 1 Conformer: "" Number of residues, atoms: 197, 3156 Classifications: {'peptide': 197} Link IDs: {'PTRANS': 4, 'TRANS': 192} Chain: "H" Number of atoms: 3156 Number of conformers: 1 Conformer: "" Number of residues, atoms: 197, 3156 Classifications: {'peptide': 197} Link IDs: {'PTRANS': 4, 'TRANS': 192} Chain: "1" Number of atoms: 2481 Number of conformers: 1 Conformer: "" Number of residues, atoms: 78, 2481 Classifications: {'DNA': 78} Modifications used: {'3*END': 1} Link IDs: {'rna3p': 77} Chain: "2" Number of atoms: 2485 Number of conformers: 1 Conformer: "" Number of residues, atoms: 78, 2485 Classifications: {'DNA': 78} Modifications used: {'3*END': 1} Link IDs: {'rna3p': 77} Chain: "3" Number of atoms: 100 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 100 Unusual residues: {'GTP': 1} Classifications: {'RNA': 2, 'undetermined': 1} Modifications used: {'3*END': 1, 'rna3p_pur': 2} Link IDs: {'rna3p': 1, None: 1} Not linked: pdbres="GTP 3 1 " pdbres=" A 3 2 " Chain: "D" Number of atoms: 3 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 3 Unusual residues: {' MG': 1, ' ZN': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "G" Number of atoms: 22 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 22 Classifications: {'RNA': 1} Modifications used: {'rna3p': 1} Chain: "H" Number of atoms: 22 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 22 Classifications: {'RNA': 1} Modifications used: {'rna3p': 1} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 29206 SG CYS D 70 108.252 108.311 126.147 1.00 20.00 S ATOM 29235 SG CYS D 72 104.923 110.858 128.106 1.00 20.00 S ATOM 41047 SG CYS D 814 107.674 46.822 91.527 1.00 20.00 S ATOM 42184 SG CYS D 888 105.694 49.603 91.940 1.00 20.00 S ATOM 42276 SG CYS D 895 108.730 49.042 89.185 1.00 20.00 S ATOM 42313 SG CYS D 898 105.720 47.290 87.924 1.00 20.00 S Time building chain proxies: 24.06, per 1000 atoms: 0.34 Number of scatterers: 69922 At special positions: 0 Unit cell: (202.5, 178.2, 192.6, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 8 Type Number sf(0) Zn 2 29.99 S 147 16.00 P 163 15.00 Mg 1 11.99 O 7142 8.00 N 6293 7.00 C 21765 6.00 H 34409 1.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=1, symmetry=0 Number of additional bonds: simple=1, symmetry=0 Coordination: Other bonds: Time building additional restraints: 48.19 Conformation dependent library (CDL) restraints added in 4.1 seconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN D1501 " pdb="ZN ZN D1501 " - pdb=" SG CYS D 72 " pdb="ZN ZN D1501 " - pdb=" SG CYS D 70 " pdb=" ZN D1502 " pdb="ZN ZN D1502 " - pdb=" SG CYS D 814 " pdb="ZN ZN D1502 " - pdb=" SG CYS D 898 " pdb="ZN ZN D1502 " - pdb=" SG CYS D 895 " pdb="ZN ZN D1502 " - pdb=" SG CYS D 888 " Number of angles added : 6 8138 Ramachandran restraints generated. 4069 Oldfield, 0 Emsley, 4069 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 7596 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 139 helices and 38 sheets defined 35.8% alpha, 9.0% beta 45 base pairs and 112 stacking pairs defined. Time for finding SS restraints: 25.98 Creating SS restraints... Processing helix chain 'A' and resid 35 through 49 removed outlier: 3.523A pdb=" N ALA A 42 " --> pdb=" O THR A 38 " (cutoff:3.500A) removed outlier: 3.838A pdb=" N ILE A 46 " --> pdb=" O ALA A 42 " (cutoff:3.500A) Processing helix chain 'A' and resid 78 through 86 Processing helix chain 'A' and resid 112 through 114 No H-bonds generated for 'chain 'A' and resid 112 through 114' Processing helix chain 'A' and resid 156 through 161 Processing helix chain 'A' and resid 213 through 232 removed outlier: 4.249A pdb=" N ALA A 230 " --> pdb=" O GLU A 226 " (cutoff:3.500A) removed outlier: 3.819A pdb=" N PHE A 231 " --> pdb=" O GLN A 227 " (cutoff:3.500A) Processing helix chain 'B' and resid 36 through 49 Processing helix chain 'B' and resid 78 through 86 Processing helix chain 'B' and resid 155 through 161 Processing helix chain 'B' and resid 213 through 227 Processing helix chain 'C' and resid 5 through 9 Processing helix chain 'C' and resid 29 through 39 Processing helix chain 'C' and resid 48 through 56 Processing helix chain 'C' and resid 83 through 88 Processing helix chain 'C' and resid 206 through 212 Processing helix chain 'C' and resid 217 through 224 removed outlier: 4.258A pdb=" N LEU C 223 " --> pdb=" O GLN C 219 " (cutoff:3.500A) Processing helix chain 'C' and resid 271 through 280 Processing helix chain 'C' and resid 289 through 292 Processing helix chain 'C' and resid 319 through 328 Processing helix chain 'C' and resid 347 through 353 Processing helix chain 'C' and resid 359 through 370 Processing helix chain 'C' and resid 378 through 389 removed outlier: 3.663A pdb=" N PHE C 389 " --> pdb=" O PHE C 385 " (cutoff:3.500A) Processing helix chain 'C' and resid 399 through 408 Processing helix chain 'C' and resid 422 through 437 Processing helix chain 'C' and resid 448 through 450 No H-bonds generated for 'chain 'C' and resid 448 through 450' Processing helix chain 'C' and resid 456 through 481 removed outlier: 4.360A pdb=" N ALA C 474 " --> pdb=" O ARG C 470 " (cutoff:3.500A) removed outlier: 3.633A pdb=" N LEU C 481 " --> pdb=" O GLU C 477 " (cutoff:3.500A) Processing helix chain 'C' and resid 496 through 505 Processing helix chain 'C' and resid 520 through 527 Processing helix chain 'C' and resid 545 through 548 No H-bonds generated for 'chain 'C' and resid 545 through 548' Processing helix chain 'C' and resid 552 through 554 No H-bonds generated for 'chain 'C' and resid 552 through 554' Processing helix chain 'C' and resid 610 through 613 No H-bonds generated for 'chain 'C' and resid 610 through 613' Processing helix chain 'C' and resid 663 through 666 No H-bonds generated for 'chain 'C' and resid 663 through 666' Processing helix chain 'C' and resid 671 through 673 No H-bonds generated for 'chain 'C' and resid 671 through 673' Processing helix chain 'C' and resid 676 through 685 Processing helix chain 'C' and resid 705 through 708 No H-bonds generated for 'chain 'C' and resid 705 through 708' Processing helix chain 'C' and resid 821 through 825 Processing helix chain 'C' and resid 859 through 864 removed outlier: 4.758A pdb=" N LYS C 864 " --> pdb=" O ALA C 860 " (cutoff:3.500A) Processing helix chain 'C' and resid 897 through 906 removed outlier: 3.864A pdb=" N ILE C 905 " --> pdb=" O LEU C 901 " (cutoff:3.500A) removed outlier: 3.569A pdb=" N PHE C 906 " --> pdb=" O LEU C 902 " (cutoff:3.500A) Processing helix chain 'C' and resid 944 through 980 removed outlier: 4.495A pdb=" N ALA C 969 " --> pdb=" O GLN C 965 " (cutoff:3.500A) removed outlier: 4.170A pdb=" N SER C 973 " --> pdb=" O ALA C 969 " (cutoff:3.500A) removed outlier: 4.724A pdb=" N ARG C 974 " --> pdb=" O GLY C 970 " (cutoff:3.500A) removed outlier: 4.194A pdb=" N ILE C 975 " --> pdb=" O LEU C 971 " (cutoff:3.500A) removed outlier: 5.028A pdb=" N LEU C 979 " --> pdb=" O ILE C 975 " (cutoff:3.500A) removed outlier: 4.143A pdb=" N VAL C 980 " --> pdb=" O ARG C 976 " (cutoff:3.500A) Processing helix chain 'C' and resid 995 through 997 No H-bonds generated for 'chain 'C' and resid 995 through 997' Processing helix chain 'C' and resid 1009 through 1037 removed outlier: 3.741A pdb=" N PHE C1025 " --> pdb=" O LEU C1021 " (cutoff:3.500A) Processing helix chain 'C' and resid 1100 through 1106 Proline residue: C1104 - end of helix Processing helix chain 'C' and resid 1109 through 1133 removed outlier: 4.187A pdb=" N LYS C1122 " --> pdb=" O MET C1119 " (cutoff:3.500A) removed outlier: 4.108A pdb=" N LYS C1133 " --> pdb=" O ALA C1130 " (cutoff:3.500A) Processing helix chain 'C' and resid 1138 through 1149 Processing helix chain 'C' and resid 1167 through 1176 Processing helix chain 'C' and resid 1192 through 1202 Processing helix chain 'C' and resid 1239 through 1241 No H-bonds generated for 'chain 'C' and resid 1239 through 1241' Processing helix chain 'C' and resid 1262 through 1264 No H-bonds generated for 'chain 'C' and resid 1262 through 1264' Processing helix chain 'C' and resid 1272 through 1281 removed outlier: 3.824A pdb=" N LEU C1278 " --> pdb=" O GLU C1274 " (cutoff:3.500A) Processing helix chain 'C' and resid 1284 through 1292 Processing helix chain 'C' and resid 1298 through 1309 Processing helix chain 'C' and resid 1321 through 1333 Processing helix chain 'D' and resid 27 through 33 Processing helix chain 'D' and resid 59 through 62 No H-bonds generated for 'chain 'D' and resid 59 through 62' Processing helix chain 'D' and resid 125 through 128 No H-bonds generated for 'chain 'D' and resid 125 through 128' Processing helix chain 'D' and resid 132 through 139 Processing helix chain 'D' and resid 165 through 172 removed outlier: 3.517A pdb=" N PHE D 172 " --> pdb=" O ALA D 168 " (cutoff:3.500A) Processing helix chain 'D' and resid 182 through 191 removed outlier: 4.203A pdb=" N GLN D 186 " --> pdb=" O GLU D 183 " (cutoff:3.500A) removed outlier: 4.534A pdb=" N ALA D 187 " --> pdb=" O ALA D 184 " (cutoff:3.500A) Processing helix chain 'D' and resid 194 through 207 removed outlier: 3.758A pdb=" N ASN D 206 " --> pdb=" O ARG D 202 " (cutoff:3.500A) Processing helix chain 'D' and resid 211 through 230 Processing helix chain 'D' and resid 235 through 237 No H-bonds generated for 'chain 'D' and resid 235 through 237' Processing helix chain 'D' and resid 247 through 249 No H-bonds generated for 'chain 'D' and resid 247 through 249' Processing helix chain 'D' and resid 265 through 283 removed outlier: 4.172A pdb=" N TYR D 269 " --> pdb=" O ASN D 266 " (cutoff:3.500A) removed outlier: 4.089A pdb=" N ARG D 281 " --> pdb=" O ARG D 278 " (cutoff:3.500A) Processing helix chain 'D' and resid 289 through 307 Processing helix chain 'D' and resid 328 through 331 Processing helix chain 'D' and resid 337 through 340 No H-bonds generated for 'chain 'D' and resid 337 through 340' Processing helix chain 'D' and resid 370 through 388 removed outlier: 3.780A pdb=" N LYS D 378 " --> pdb=" O LEU D 374 " (cutoff:3.500A) Proline residue: D 379 - end of helix Processing helix chain 'D' and resid 394 through 403 Processing helix chain 'D' and resid 406 through 416 Processing helix chain 'D' and resid 431 through 433 No H-bonds generated for 'chain 'D' and resid 431 through 433' Processing helix chain 'D' and resid 451 through 457 Processing helix chain 'D' and resid 474 through 482 Processing helix chain 'D' and resid 486 through 488 No H-bonds generated for 'chain 'D' and resid 486 through 488' Processing helix chain 'D' and resid 506 through 513 Processing helix chain 'D' and resid 530 through 539 Processing helix chain 'D' and resid 574 through 582 removed outlier: 3.838A pdb=" N MET D 581 " --> pdb=" O ALA D 577 " (cutoff:3.500A) removed outlier: 4.356A pdb=" N ILE D 582 " --> pdb=" O ILE D 578 " (cutoff:3.500A) Processing helix chain 'D' and resid 590 through 592 No H-bonds generated for 'chain 'D' and resid 590 through 592' Processing helix chain 'D' and resid 598 through 611 Processing helix chain 'D' and resid 614 through 635 Processing helix chain 'D' and resid 651 through 670 removed outlier: 4.088A pdb=" N GLU D 663 " --> pdb=" O ALA D 659 " (cutoff:3.500A) Processing helix chain 'D' and resid 675 through 701 Processing helix chain 'D' and resid 723 through 727 Processing helix chain 'D' and resid 734 through 741 Processing helix chain 'D' and resid 769 through 787 removed outlier: 4.684A pdb=" N HIS D 777 " --> pdb=" O PHE D 773 " (cutoff:3.500A) removed outlier: 4.779A pdb=" N GLY D 778 " --> pdb=" O ILE D 774 " (cutoff:3.500A) removed outlier: 3.936A pdb=" N ALA D 779 " --> pdb=" O SER D 775 " (cutoff:3.500A) Processing helix chain 'D' and resid 790 through 804 Processing helix chain 'D' and resid 835 through 839 Processing helix chain 'D' and resid 866 through 874 Processing helix chain 'D' and resid 916 through 929 removed outlier: 3.547A pdb=" N GLU D 925 " --> pdb=" O GLN D 921 " (cutoff:3.500A) Proline residue: D 926 - end of helix removed outlier: 4.490A pdb=" N GLN D 929 " --> pdb=" O GLU D 925 " (cutoff:3.500A) Processing helix chain 'D' and resid 1138 through 1145 Processing helix chain 'D' and resid 1218 through 1221 No H-bonds generated for 'chain 'D' and resid 1218 through 1221' Processing helix chain 'D' and resid 1227 through 1244 removed outlier: 4.127A pdb=" N GLN D1244 " --> pdb=" O VAL D1240 " (cutoff:3.500A) Processing helix chain 'D' and resid 1251 through 1260 removed outlier: 4.161A pdb=" N ILE D1256 " --> pdb=" O ILE D1253 " (cutoff:3.500A) Processing helix chain 'D' and resid 1280 through 1287 Processing helix chain 'D' and resid 1309 through 1314 Processing helix chain 'D' and resid 1328 through 1337 Processing helix chain 'D' and resid 1347 through 1351 Processing helix chain 'D' and resid 1363 through 1374 Processing helix chain 'E' and resid 7 through 13 removed outlier: 3.567A pdb=" N ILE E 13 " --> pdb=" O ALA E 9 " (cutoff:3.500A) Processing helix chain 'E' and resid 16 through 26 Processing helix chain 'E' and resid 28 through 31 No H-bonds generated for 'chain 'E' and resid 28 through 31' Processing helix chain 'E' and resid 46 through 55 Processing helix chain 'E' and resid 61 through 79 Processing helix chain 'F' and resid 97 through 106 Processing helix chain 'F' and resid 115 through 135 Processing helix chain 'F' and resid 145 through 152 Processing helix chain 'F' and resid 160 through 164 Processing helix chain 'F' and resid 214 through 221 removed outlier: 3.526A pdb=" N PHE F 221 " --> pdb=" O ALA F 217 " (cutoff:3.500A) Processing helix chain 'F' and resid 223 through 232 Processing helix chain 'F' and resid 243 through 257 Processing helix chain 'F' and resid 264 through 292 removed outlier: 3.637A pdb=" N TYR F 268 " --> pdb=" O GLN F 265 " (cutoff:3.500A) removed outlier: 3.674A pdb=" N SER F 272 " --> pdb=" O LEU F 269 " (cutoff:3.500A) removed outlier: 4.204A pdb=" N VAL F 275 " --> pdb=" O SER F 272 " (cutoff:3.500A) removed outlier: 4.044A pdb=" N MET F 276 " --> pdb=" O MET F 273 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N MET F 277 " --> pdb=" O ARG F 274 " (cutoff:3.500A) removed outlier: 4.702A pdb=" N ARG F 281 " --> pdb=" O ASP F 278 " (cutoff:3.500A) removed outlier: 4.216A pdb=" N GLU F 284 " --> pdb=" O ARG F 281 " (cutoff:3.500A) removed outlier: 4.011A pdb=" N MET F 288 " --> pdb=" O ARG F 285 " (cutoff:3.500A) removed outlier: 4.408A pdb=" N VAL F 292 " --> pdb=" O LYS F 289 " (cutoff:3.500A) Processing helix chain 'F' and resid 300 through 305 Processing helix chain 'F' and resid 314 through 319 Processing helix chain 'F' and resid 334 through 343 removed outlier: 3.725A pdb=" N HIS F 338 " --> pdb=" O SER F 334 " (cutoff:3.500A) removed outlier: 3.757A pdb=" N LYS F 343 " --> pdb=" O ARG F 339 " (cutoff:3.500A) Processing helix chain 'F' and resid 345 through 351 Processing helix chain 'F' and resid 356 through 375 removed outlier: 3.599A pdb=" N ARG F 363 " --> pdb=" O LYS F 359 " (cutoff:3.500A) removed outlier: 4.168A pdb=" N ALA F 372 " --> pdb=" O GLY F 368 " (cutoff:3.500A) Processing helix chain 'F' and resid 377 through 382 Processing helix chain 'F' and resid 384 through 394 removed outlier: 3.831A pdb=" N LYS F 393 " --> pdb=" O SER F 389 " (cutoff:3.500A) removed outlier: 3.960A pdb=" N TYR F 394 " --> pdb=" O ILE F 390 " (cutoff:3.500A) Processing helix chain 'F' and resid 401 through 417 Processing helix chain 'F' and resid 427 through 445 removed outlier: 3.814A pdb=" N ALA F 444 " --> pdb=" O THR F 440 " (cutoff:3.500A) Processing helix chain 'F' and resid 454 through 474 removed outlier: 3.705A pdb=" N ARG F 468 " --> pdb=" O ASN F 464 " (cutoff:3.500A) Processing helix chain 'F' and resid 480 through 487 Processing helix chain 'F' and resid 491 through 498 Processing helix chain 'F' and resid 519 through 521 No H-bonds generated for 'chain 'F' and resid 519 through 521' Processing helix chain 'F' and resid 531 through 550 removed outlier: 3.769A pdb=" N GLY F 550 " --> pdb=" O ASP F 546 " (cutoff:3.500A) Processing helix chain 'F' and resid 553 through 561 Processing helix chain 'F' and resid 573 through 579 removed outlier: 3.861A pdb=" N GLY F 577 " --> pdb=" O LEU F 573 " (cutoff:3.500A) Processing helix chain 'F' and resid 585 through 599 Processing helix chain 'G' and resid 10 through 17 removed outlier: 3.944A pdb=" N HIS G 17 " --> pdb=" O TRP G 13 " (cutoff:3.500A) Processing helix chain 'G' and resid 72 through 74 No H-bonds generated for 'chain 'G' and resid 72 through 74' Processing helix chain 'G' and resid 101 through 108 Processing helix chain 'G' and resid 112 through 136 Processing helix chain 'G' and resid 139 through 151 removed outlier: 3.595A pdb=" N ALA G 151 " --> pdb=" O LEU G 147 " (cutoff:3.500A) Processing helix chain 'G' and resid 171 through 176 Processing helix chain 'G' and resid 180 through 190 Processing helix chain 'H' and resid 10 through 17 removed outlier: 4.419A pdb=" N HIS H 17 " --> pdb=" O TRP H 13 " (cutoff:3.500A) Processing helix chain 'H' and resid 99 through 108 removed outlier: 3.778A pdb=" N GLN H 104 " --> pdb=" O LYS H 100 " (cutoff:3.500A) Processing helix chain 'H' and resid 114 through 136 Processing helix chain 'H' and resid 139 through 150 Processing helix chain 'H' and resid 169 through 175 removed outlier: 3.829A pdb=" N GLN H 174 " --> pdb=" O GLN H 170 " (cutoff:3.500A) Processing helix chain 'H' and resid 180 through 191 Processing sheet with id= A, first strand: chain 'A' and resid 24 through 28 Processing sheet with id= B, first strand: chain 'A' and resid 90 through 92 Processing sheet with id= C, first strand: chain 'A' and resid 97 through 105 removed outlier: 5.719A pdb=" N GLN A 147 " --> pdb=" O VAL A 56 " (cutoff:3.500A) removed outlier: 5.616A pdb=" N VAL A 56 " --> pdb=" O GLN A 147 " (cutoff:3.500A) removed outlier: 7.391A pdb=" N GLY A 149 " --> pdb=" O CYS A 54 " (cutoff:3.500A) removed outlier: 5.208A pdb=" N CYS A 54 " --> pdb=" O GLY A 149 " (cutoff:3.500A) Processing sheet with id= D, first strand: chain 'A' and resid 108 through 110 Processing sheet with id= E, first strand: chain 'B' and resid 24 through 26 removed outlier: 4.371A pdb=" N LEU B 198 " --> pdb=" O ALA B 190 " (cutoff:3.500A) Processing sheet with id= F, first strand: chain 'B' and resid 52 through 56 Processing sheet with id= G, first strand: chain 'B' and resid 59 through 61 Processing sheet with id= H, first strand: chain 'B' and resid 12 through 15 removed outlier: 3.592A pdb=" N GLU B 29 " --> pdb=" O ARG B 12 " (cutoff:3.500A) removed outlier: 3.572A pdb=" N VAL B 14 " --> pdb=" O THR B 27 " (cutoff:3.500A) removed outlier: 6.607A pdb=" N THR B 27 " --> pdb=" O VAL B 14 " (cutoff:3.500A) Processing sheet with id= I, first strand: chain 'B' and resid 109 through 111 removed outlier: 3.714A pdb=" N CYS B 131 " --> pdb=" O VAL B 110 " (cutoff:3.500A) Processing sheet with id= J, first strand: chain 'C' and resid 117 through 123 removed outlier: 3.606A pdb=" N LYS C 118 " --> pdb=" O LEU C 102 " (cutoff:3.500A) removed outlier: 3.781A pdb=" N SER C 72 " --> pdb=" O LYS C 99 " (cutoff:3.500A) removed outlier: 5.411A pdb=" N ARG C 101 " --> pdb=" O TYR C 70 " (cutoff:3.500A) removed outlier: 5.279A pdb=" N TYR C 70 " --> pdb=" O ARG C 101 " (cutoff:3.500A) Processing sheet with id= K, first strand: chain 'C' and resid 148 through 151 Processing sheet with id= L, first strand: chain 'C' and resid 154 through 161 removed outlier: 6.285A pdb=" N TYR C 172 " --> pdb=" O PHE C 188 " (cutoff:3.500A) Processing sheet with id= M, first strand: chain 'C' and resid 228 through 230 Processing sheet with id= N, first strand: chain 'C' and resid 231 through 233 Processing sheet with id= O, first strand: chain 'C' and resid 579 through 581 Processing sheet with id= P, first strand: chain 'C' and resid 634 through 638 Processing sheet with id= Q, first strand: chain 'C' and resid 750 through 752 removed outlier: 5.661A pdb=" N LYS C 735 " --> pdb=" O VAL C 724 " (cutoff:3.500A) removed outlier: 5.470A pdb=" N VAL C 724 " --> pdb=" O LYS C 735 " (cutoff:3.500A) Processing sheet with id= R, first strand: chain 'C' and resid 798 through 803 Processing sheet with id= S, first strand: chain 'C' and resid 816 through 818 Processing sheet with id= T, first strand: chain 'C' and resid 830 through 832 Processing sheet with id= U, first strand: chain 'C' and resid 876 through 878 removed outlier: 3.851A pdb=" N ILE C 929 " --> pdb=" O TYR C1053 " (cutoff:3.500A) removed outlier: 7.448A pdb=" N TYR C1053 " --> pdb=" O ILE C 929 " (cutoff:3.500A) removed outlier: 4.880A pdb=" N VAL C 931 " --> pdb=" O LYS C1051 " (cutoff:3.500A) removed outlier: 6.803A pdb=" N LYS C1051 " --> pdb=" O VAL C 931 " (cutoff:3.500A) removed outlier: 4.478A pdb=" N VAL C 933 " --> pdb=" O ILE C1049 " (cutoff:3.500A) removed outlier: 6.546A pdb=" N ILE C1049 " --> pdb=" O VAL C 933 " (cutoff:3.500A) removed outlier: 5.607A pdb=" N THR C 935 " --> pdb=" O LEU C1047 " (cutoff:3.500A) removed outlier: 8.564A pdb=" N LEU C1047 " --> pdb=" O THR C 935 " (cutoff:3.500A) removed outlier: 6.777A pdb=" N SER C 840 " --> pdb=" O LEU C1047 " (cutoff:3.500A) removed outlier: 4.866A pdb=" N ILE C1049 " --> pdb=" O CYS C 838 " (cutoff:3.500A) removed outlier: 6.922A pdb=" N CYS C 838 " --> pdb=" O ILE C1049 " (cutoff:3.500A) removed outlier: 4.718A pdb=" N LYS C1051 " --> pdb=" O LEU C 836 " (cutoff:3.500A) removed outlier: 6.911A pdb=" N LEU C 836 " --> pdb=" O LYS C1051 " (cutoff:3.500A) Processing sheet with id= V, first strand: chain 'C' and resid 887 through 889 Processing sheet with id= W, first strand: chain 'D' and resid 103 through 106 Processing sheet with id= X, first strand: chain 'D' and resid 143 through 145 Processing sheet with id= Y, first strand: chain 'D' and resid 252 through 254 Processing sheet with id= Z, first strand: chain 'D' and resid 350 through 354 Processing sheet with id= AA, first strand: chain 'D' and resid 548 through 552 Processing sheet with id= AB, first strand: chain 'D' and resid 820 through 822 Processing sheet with id= AC, first strand: chain 'D' and resid 965 through 967 Processing sheet with id= AD, first strand: chain 'D' and resid 1034 through 1036 removed outlier: 3.977A pdb=" N ARG D1036 " --> pdb=" O LYS D1079 " (cutoff:3.500A) removed outlier: 4.100A pdb=" N LYS D1079 " --> pdb=" O ARG D1036 " (cutoff:3.500A) Processing sheet with id= AE, first strand: chain 'D' and resid 1162 through 1165 Processing sheet with id= AF, first strand: chain 'D' and resid 950 through 952 removed outlier: 6.629A pdb=" N VAL D 952 " --> pdb=" O THR D1016 " (cutoff:3.500A) removed outlier: 5.773A pdb=" N THR D1016 " --> pdb=" O VAL D 952 " (cutoff:3.500A) Processing sheet with id= AG, first strand: chain 'D' and resid 981 through 985 Processing sheet with id= AH, first strand: chain 'G' and resid 19 through 23 removed outlier: 5.819A pdb=" N ALA G 95 " --> pdb=" O ILE G 42 " (cutoff:3.500A) removed outlier: 5.622A pdb=" N ILE G 42 " --> pdb=" O ALA G 95 " (cutoff:3.500A) removed outlier: 7.011A pdb=" N ILE G 97 " --> pdb=" O TYR G 40 " (cutoff:3.500A) removed outlier: 4.955A pdb=" N TYR G 40 " --> pdb=" O ILE G 97 " (cutoff:3.500A) Processing sheet with id= AI, first strand: chain 'G' and resid 48 through 50 Processing sheet with id= AJ, first strand: chain 'H' and resid 21 through 23 removed outlier: 6.420A pdb=" N ALA H 95 " --> pdb=" O ILE H 42 " (cutoff:3.500A) removed outlier: 5.787A pdb=" N ILE H 42 " --> pdb=" O ALA H 95 " (cutoff:3.500A) removed outlier: 6.547A pdb=" N ILE H 97 " --> pdb=" O TYR H 40 " (cutoff:3.500A) removed outlier: 4.941A pdb=" N TYR H 40 " --> pdb=" O ILE H 97 " (cutoff:3.500A) Processing sheet with id= AK, first strand: chain 'H' and resid 85 through 87 removed outlier: 6.599A pdb=" N ILE H 51 " --> pdb=" O ILE H 60 " (cutoff:3.500A) removed outlier: 5.154A pdb=" N ILE H 60 " --> pdb=" O ILE H 51 " (cutoff:3.500A) Processing sheet with id= AL, first strand: chain 'H' and resid 163 through 165 1070 hydrogen bonds defined for protein. 2868 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 106 hydrogen bonds 212 hydrogen bond angles 0 basepair planarities 45 basepair parallelities 112 stacking parallelities Total time for adding SS restraints: 26.34 Time building geometry restraints manager: 50.38 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.83 - 1.03: 34377 1.03 - 1.23: 302 1.23 - 1.43: 14734 1.43 - 1.63: 21123 1.63 - 1.83: 259 Bond restraints: 70795 Sorted by residual: bond pdb=" C ASP F 167 " pdb=" O ASP F 167 " ideal model delta sigma weight residual 1.233 1.254 -0.021 4.80e-03 4.34e+04 1.93e+01 bond pdb=" CB ILE C 833 " pdb=" HB ILE C 833 " ideal model delta sigma weight residual 0.970 0.901 0.069 2.00e-02 2.50e+03 1.18e+01 bond pdb=" C3' DT 1 47 " pdb=" O3' DT 1 47 " ideal model delta sigma weight residual 1.422 1.519 -0.097 3.00e-02 1.11e+03 1.04e+01 bond pdb=" C PRO C 375 " pdb=" N PRO C 376 " ideal model delta sigma weight residual 1.334 1.408 -0.074 2.34e-02 1.83e+03 9.98e+00 bond pdb=" C3' DG 2 42 " pdb=" O3' DG 2 42 " ideal model delta sigma weight residual 1.422 1.509 -0.087 3.00e-02 1.11e+03 8.38e+00 ... (remaining 70790 not shown) Histogram of bond angle deviations from ideal: 95.55 - 103.78: 878 103.78 - 112.00: 80975 112.00 - 120.23: 25603 120.23 - 128.46: 20557 128.46 - 136.69: 402 Bond angle restraints: 128415 Sorted by residual: angle pdb=" C3' DC 2 41 " pdb=" O3' DC 2 41 " pdb=" P DG 2 42 " ideal model delta sigma weight residual 120.20 127.47 -7.27 1.50e+00 4.44e-01 2.35e+01 angle pdb=" N GLY C 627 " pdb=" CA GLY C 627 " pdb=" C GLY C 627 " ideal model delta sigma weight residual 110.21 105.88 4.33 9.10e-01 1.21e+00 2.27e+01 angle pdb=" O3' DC 2 41 " pdb=" C3' DC 2 41 " pdb=" C2' DC 2 41 " ideal model delta sigma weight residual 111.50 118.41 -6.91 1.50e+00 4.44e-01 2.12e+01 angle pdb=" N VAL C 663 " pdb=" CA VAL C 663 " pdb=" C VAL C 663 " ideal model delta sigma weight residual 110.74 114.84 -4.10 9.10e-01 1.21e+00 2.03e+01 angle pdb=" C VAL D 407 " pdb=" N VAL D 408 " pdb=" CA VAL D 408 " ideal model delta sigma weight residual 120.60 126.25 -5.65 1.29e+00 6.01e-01 1.92e+01 ... (remaining 128410 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.99: 26606 35.99 - 71.98: 955 71.98 - 107.98: 33 107.98 - 143.97: 5 143.97 - 179.96: 10 Dihedral angle restraints: 27609 sinusoidal: 14516 harmonic: 13093 Sorted by residual: dihedral pdb=" CA LEU D 120 " pdb=" C LEU D 120 " pdb=" N PRO D 121 " pdb=" CA PRO D 121 " ideal model delta harmonic sigma weight residual -180.00 -116.23 -63.77 0 5.00e+00 4.00e-02 1.63e+02 dihedral pdb=" CA PHE F 165 " pdb=" C PHE F 165 " pdb=" N VAL F 166 " pdb=" CA VAL F 166 " ideal model delta harmonic sigma weight residual 180.00 -119.42 -60.58 0 5.00e+00 4.00e-02 1.47e+02 dihedral pdb=" CA GLN F 294 " pdb=" C GLN F 294 " pdb=" N CYS F 295 " pdb=" CA CYS F 295 " ideal model delta harmonic sigma weight residual -180.00 -130.50 -49.50 0 5.00e+00 4.00e-02 9.80e+01 ... (remaining 27606 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.086: 4899 0.086 - 0.172: 735 0.172 - 0.257: 33 0.257 - 0.343: 1 0.343 - 0.429: 1 Chirality restraints: 5669 Sorted by residual: chirality pdb=" CB ILE C 833 " pdb=" CA ILE C 833 " pdb=" CG1 ILE C 833 " pdb=" CG2 ILE C 833 " both_signs ideal model delta sigma weight residual False 2.64 2.22 0.43 2.00e-01 2.50e+01 4.60e+00 chirality pdb=" CB ILE F 452 " pdb=" CA ILE F 452 " pdb=" CG1 ILE F 452 " pdb=" CG2 ILE F 452 " both_signs ideal model delta sigma weight residual False 2.64 2.32 0.33 2.00e-01 2.50e+01 2.67e+00 chirality pdb=" CB VAL C 724 " pdb=" CA VAL C 724 " pdb=" CG1 VAL C 724 " pdb=" CG2 VAL C 724 " both_signs ideal model delta sigma weight residual False -2.63 -2.38 -0.25 2.00e-01 2.50e+01 1.54e+00 ... (remaining 5666 not shown) Planarity restraints: 9956 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C LEU D 120 " 0.060 5.00e-02 4.00e+02 9.12e-02 1.33e+01 pdb=" N PRO D 121 " -0.158 5.00e-02 4.00e+02 pdb=" CA PRO D 121 " 0.048 5.00e-02 4.00e+02 pdb=" CD PRO D 121 " 0.049 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C1' DC 1 80 " 0.045 2.00e-02 2.50e+03 2.07e-02 1.18e+01 pdb=" N1 DC 1 80 " -0.048 2.00e-02 2.50e+03 pdb=" C2 DC 1 80 " 0.002 2.00e-02 2.50e+03 pdb=" O2 DC 1 80 " -0.012 2.00e-02 2.50e+03 pdb=" N3 DC 1 80 " 0.005 2.00e-02 2.50e+03 pdb=" C4 DC 1 80 " 0.007 2.00e-02 2.50e+03 pdb=" N4 DC 1 80 " 0.009 2.00e-02 2.50e+03 pdb=" C5 DC 1 80 " 0.002 2.00e-02 2.50e+03 pdb=" C6 DC 1 80 " 0.001 2.00e-02 2.50e+03 pdb=" H5 DC 1 80 " -0.001 2.00e-02 2.50e+03 pdb=" H6 DC 1 80 " -0.011 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1' DT 1 47 " 0.046 2.00e-02 2.50e+03 1.96e-02 1.15e+01 pdb=" N1 DT 1 47 " -0.043 2.00e-02 2.50e+03 pdb=" C2 DT 1 47 " -0.001 2.00e-02 2.50e+03 pdb=" O2 DT 1 47 " -0.019 2.00e-02 2.50e+03 pdb=" N3 DT 1 47 " 0.006 2.00e-02 2.50e+03 pdb=" C4 DT 1 47 " 0.006 2.00e-02 2.50e+03 pdb=" O4 DT 1 47 " 0.007 2.00e-02 2.50e+03 pdb=" C5 DT 1 47 " 0.002 2.00e-02 2.50e+03 pdb=" C7 DT 1 47 " -0.003 2.00e-02 2.50e+03 pdb=" C6 DT 1 47 " -0.006 2.00e-02 2.50e+03 pdb=" H3 DT 1 47 " 0.010 2.00e-02 2.50e+03 pdb=" H6 DT 1 47 " -0.005 2.00e-02 2.50e+03 ... (remaining 9953 not shown) Histogram of nonbonded interaction distances: 1.10 - 1.80: 261 1.80 - 2.50: 56934 2.50 - 3.20: 221091 3.20 - 3.90: 274016 3.90 - 4.60: 430501 Nonbonded interactions: 982803 Sorted by model distance: nonbonded pdb=" OD1 ASP D 464 " pdb="HO2' G 3 3 " model vdw 1.096 1.850 nonbonded pdb=" O GLU D1334 " pdb=" HZ3 LYS D1340 " model vdw 1.561 1.850 nonbonded pdb="HH11 ARG D 905 " pdb=" O ILE D 908 " model vdw 1.565 1.850 nonbonded pdb=" O ASN D 274 " pdb=" H ARG D 278 " model vdw 1.578 1.850 nonbonded pdb=" O GLN D 186 " pdb=" H LYS D 190 " model vdw 1.588 1.850 ... (remaining 982798 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = (chain 'A' and resid 6 through 233) selection = chain 'B' } ncs_group { reference = chain 'G' selection = chain 'H' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Set scattering table Set to: electron Number of scattering types: 8 Type Number sf(0) Gaussians Zn 2 6.06 5 P 163 5.49 5 Mg 1 5.21 5 S 147 5.16 5 C 21765 2.51 5 N 6293 2.21 5 O 7142 1.98 5 H 34409 0.53 5 sf(0) = scattering factor at diffraction angle 0. Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 2.870 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: 0.770 Extract box with map and model: 15.470 Check model and map are aligned: 0.780 Process input model: 207.780 Find NCS groups from input model: 1.370 Set up NCS constraints: 0.190 Set refine NCS operators: 0.000 Set scattering table: 0.460 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: 232.370 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.3905 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 : 0.010 0.115 36386 Z= 0.647 Angle : 1.164 10.216 49818 Z= 0.658 Chirality : 0.058 0.429 5669 Planarity : 0.007 0.091 5925 Dihedral : 16.288 179.873 14202 Min Nonbonded Distance : 1.840 Molprobity Statistics. All-atom Clashscore : 11.04 Ramachandran Plot: Outliers : 0.42 % Allowed : 11.45 % Favored : 88.13 % Rotamer Outliers : 0.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.60 % Cis-general : 0.00 % Twisted Proline : 1.95 % Twisted General : 1.07 % 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: -4.77 (0.10), residues: 4069 helix: -3.14 (0.09), residues: 1468 sheet: -3.20 (0.22), residues: 406 loop : -3.23 (0.11), residues: 2195 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8138 Ramachandran restraints generated. 4069 Oldfield, 0 Emsley, 4069 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8138 Ramachandran restraints generated. 4069 Oldfield, 0 Emsley, 4069 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 516 residues out of total 3505 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 514 time to evaluate : 4.185 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 2 outliers final: 1 residues processed: 516 average time/residue: 1.0776 time to fit residues: 852.6748 Evaluate side-chains 357 residues out of total 3505 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 356 time to evaluate : 4.297 Switching outliers to nearest non-outliers revert: symmetry clash outliers start: 1 outliers final: 1 residues processed: 1 average time/residue: 0.6306 time to fit residues: 6.5509 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 419 random chunks: chunk 353 optimal weight: 10.0000 chunk 317 optimal weight: 5.9990 chunk 176 optimal weight: 10.0000 chunk 108 optimal weight: 0.9990 chunk 214 optimal weight: 0.9980 chunk 169 optimal weight: 6.9990 chunk 328 optimal weight: 10.0000 chunk 127 optimal weight: 3.9990 chunk 199 optimal weight: 3.9990 chunk 244 optimal weight: 9.9990 chunk 380 optimal weight: 8.9990 overall best weight: 3.1988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 165 HIS ** C 658 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 725 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C1257 GLN D1197 ASN D1279 GLN ** F 265 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 159 HIS H 65 ASN H 194 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.3838 moved from start: 0.1874 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.066 36386 Z= 0.245 Angle : 0.744 8.791 49818 Z= 0.414 Chirality : 0.043 0.237 5669 Planarity : 0.006 0.116 5925 Dihedral : 19.840 178.097 6091 Min Nonbonded Distance : 1.913 Molprobity Statistics. All-atom Clashscore : 16.11 Ramachandran Plot: Outliers : 0.32 % Allowed : 9.93 % Favored : 89.75 % Rotamer Outliers : 0.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.60 % Cis-general : 0.00 % Twisted Proline : 1.30 % Twisted General : 0.38 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.96 (0.11), residues: 4069 helix: -2.30 (0.11), residues: 1494 sheet: -2.82 (0.22), residues: 418 loop : -2.87 (0.12), residues: 2157 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8138 Ramachandran restraints generated. 4069 Oldfield, 0 Emsley, 4069 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8138 Ramachandran restraints generated. 4069 Oldfield, 0 Emsley, 4069 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 452 residues out of total 3505 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 451 time to evaluate : 4.099 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 1 outliers final: 1 residues processed: 452 average time/residue: 1.1093 time to fit residues: 763.2331 Evaluate side-chains 361 residues out of total 3505 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 360 time to evaluate : 4.124 Switching outliers to nearest non-outliers outliers start: 1 outliers final: 0 residues processed: 1 average time/residue: 0.6098 time to fit residues: 6.3047 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 419 random chunks: chunk 211 optimal weight: 8.9990 chunk 118 optimal weight: 1.9990 chunk 316 optimal weight: 20.0000 chunk 259 optimal weight: 0.9990 chunk 104 optimal weight: 0.7980 chunk 381 optimal weight: 9.9990 chunk 411 optimal weight: 10.0000 chunk 339 optimal weight: 9.9990 chunk 378 optimal weight: 20.0000 chunk 129 optimal weight: 0.3980 chunk 305 optimal weight: 9.9990 overall best weight: 2.6386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 194 GLN ** C 658 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 725 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 767 GLN D 266 ASN D1197 ASN ** F 265 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 31 HIS G 159 HIS ** G 174 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.3817 moved from start: 0.2568 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.065 36386 Z= 0.215 Angle : 0.675 9.072 49818 Z= 0.374 Chirality : 0.042 0.188 5669 Planarity : 0.005 0.075 5925 Dihedral : 19.593 177.360 6091 Min Nonbonded Distance : 1.860 Molprobity Statistics. All-atom Clashscore : 15.24 Ramachandran Plot: Outliers : 0.22 % Allowed : 9.46 % Favored : 90.32 % Rotamer Outliers : 0.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.60 % Cis-general : 0.00 % Twisted Proline : 1.30 % Twisted General : 0.23 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.45 (0.12), residues: 4069 helix: -1.72 (0.12), residues: 1506 sheet: -2.61 (0.22), residues: 442 loop : -2.68 (0.12), residues: 2121 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8138 Ramachandran restraints generated. 4069 Oldfield, 0 Emsley, 4069 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8138 Ramachandran restraints generated. 4069 Oldfield, 0 Emsley, 4069 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 438 residues out of total 3505 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 438 time to evaluate : 4.126 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 438 average time/residue: 1.0662 time to fit residues: 710.8939 Evaluate side-chains 360 residues out of total 3505 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 360 time to evaluate : 4.135 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 5.1558 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 419 random chunks: chunk 376 optimal weight: 5.9990 chunk 286 optimal weight: 20.0000 chunk 197 optimal weight: 8.9990 chunk 42 optimal weight: 20.0000 chunk 181 optimal weight: 6.9990 chunk 255 optimal weight: 10.0000 chunk 382 optimal weight: 0.7980 chunk 405 optimal weight: 20.0000 chunk 199 optimal weight: 5.9990 chunk 362 optimal weight: 10.0000 chunk 109 optimal weight: 8.9990 overall best weight: 5.7588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 84 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 276 GLN C 580 GLN ** C 658 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 686 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 725 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D1197 ASN E 31 GLN ** F 265 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 31 HIS G 159 HIS H 174 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.3964 moved from start: 0.3101 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.079 36386 Z= 0.297 Angle : 0.714 9.291 49818 Z= 0.397 Chirality : 0.043 0.173 5669 Planarity : 0.005 0.074 5925 Dihedral : 19.609 179.138 6091 Min Nonbonded Distance : 1.735 Molprobity Statistics. All-atom Clashscore : 20.88 Ramachandran Plot: Outliers : 0.22 % Allowed : 11.16 % Favored : 88.62 % Rotamer Outliers : 0.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.60 % Cis-general : 0.00 % Twisted Proline : 0.65 % Twisted General : 0.20 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.46 (0.11), residues: 4069 helix: -1.60 (0.12), residues: 1488 sheet: -2.71 (0.21), residues: 476 loop : -2.75 (0.12), residues: 2105 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8138 Ramachandran restraints generated. 4069 Oldfield, 0 Emsley, 4069 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8138 Ramachandran restraints generated. 4069 Oldfield, 0 Emsley, 4069 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 403 residues out of total 3505 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 402 time to evaluate : 4.260 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 1 outliers final: 1 residues processed: 403 average time/residue: 1.0463 time to fit residues: 640.8950 Evaluate side-chains 341 residues out of total 3505 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 340 time to evaluate : 4.555 Switching outliers to nearest non-outliers outliers start: 1 outliers final: 0 residues processed: 1 average time/residue: 0.5922 time to fit residues: 6.2904 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 419 random chunks: chunk 337 optimal weight: 0.9980 chunk 229 optimal weight: 3.9990 chunk 5 optimal weight: 9.9990 chunk 301 optimal weight: 10.0000 chunk 167 optimal weight: 8.9990 chunk 345 optimal weight: 9.9990 chunk 279 optimal weight: 30.0000 chunk 0 optimal weight: 10.0000 chunk 206 optimal weight: 8.9990 chunk 363 optimal weight: 5.9990 chunk 102 optimal weight: 10.0000 overall best weight: 5.7988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 37 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 84 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 658 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 686 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 725 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C1257 GLN D 954 ASN D1197 ASN ** F 265 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 31 HIS G 80 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.4001 moved from start: 0.3599 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.065 36386 Z= 0.280 Angle : 0.692 9.717 49818 Z= 0.386 Chirality : 0.042 0.174 5669 Planarity : 0.005 0.071 5925 Dihedral : 19.615 179.393 6091 Min Nonbonded Distance : 1.808 Molprobity Statistics. All-atom Clashscore : 20.88 Ramachandran Plot: Outliers : 0.22 % Allowed : 11.06 % Favored : 88.72 % Rotamer Outliers : 0.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.60 % Cis-general : 0.00 % Twisted Proline : 0.65 % Twisted General : 0.20 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.38 (0.12), residues: 4069 helix: -1.58 (0.12), residues: 1500 sheet: -2.64 (0.21), residues: 483 loop : -2.67 (0.12), residues: 2086 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8138 Ramachandran restraints generated. 4069 Oldfield, 0 Emsley, 4069 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8138 Ramachandran restraints generated. 4069 Oldfield, 0 Emsley, 4069 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 407 residues out of total 3505 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 406 time to evaluate : 4.121 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 1 outliers final: 0 residues processed: 407 average time/residue: 1.0529 time to fit residues: 653.8572 Evaluate side-chains 346 residues out of total 3505 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 346 time to evaluate : 4.146 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 5.1734 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 419 random chunks: chunk 136 optimal weight: 5.9990 chunk 364 optimal weight: 0.1980 chunk 80 optimal weight: 9.9990 chunk 237 optimal weight: 1.9990 chunk 99 optimal weight: 10.0000 chunk 405 optimal weight: 10.0000 chunk 336 optimal weight: 30.0000 chunk 187 optimal weight: 0.0980 chunk 33 optimal weight: 9.9990 chunk 134 optimal weight: 10.0000 chunk 212 optimal weight: 8.9990 overall best weight: 3.4586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 37 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 686 GLN ** C1257 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D1197 ASN D1218 HIS ** F 265 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 31 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.3951 moved from start: 0.3909 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.062 36386 Z= 0.215 Angle : 0.633 9.514 49818 Z= 0.353 Chirality : 0.041 0.171 5669 Planarity : 0.005 0.072 5925 Dihedral : 19.512 179.032 6091 Min Nonbonded Distance : 1.834 Molprobity Statistics. All-atom Clashscore : 17.37 Ramachandran Plot: Outliers : 0.17 % Allowed : 10.25 % Favored : 89.58 % Rotamer Outliers : 0.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.60 % Cis-general : 0.00 % Twisted Proline : 0.65 % Twisted General : 0.20 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.08 (0.12), residues: 4069 helix: -1.26 (0.12), residues: 1505 sheet: -2.55 (0.21), residues: 480 loop : -2.53 (0.12), residues: 2084 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8138 Ramachandran restraints generated. 4069 Oldfield, 0 Emsley, 4069 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8138 Ramachandran restraints generated. 4069 Oldfield, 0 Emsley, 4069 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 406 residues out of total 3505 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 406 time to evaluate : 4.192 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 406 average time/residue: 1.0777 time to fit residues: 667.1526 Evaluate side-chains 346 residues out of total 3505 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 346 time to evaluate : 4.152 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 5.1430 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 419 random chunks: chunk 390 optimal weight: 6.9990 chunk 45 optimal weight: 10.0000 chunk 230 optimal weight: 10.0000 chunk 296 optimal weight: 10.0000 chunk 229 optimal weight: 10.0000 chunk 341 optimal weight: 3.9990 chunk 226 optimal weight: 10.0000 chunk 403 optimal weight: 9.9990 chunk 252 optimal weight: 8.9990 chunk 246 optimal weight: 8.9990 chunk 186 optimal weight: 9.9990 overall best weight: 7.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 37 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 84 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 658 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 659 GLN ** C 725 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 760 ASN C1257 GLN ** D1197 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D1252 HIS ** F 265 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 31 HIS ** G 159 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.4134 moved from start: 0.4431 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.006 0.075 36386 Z= 0.374 Angle : 0.757 9.622 49818 Z= 0.423 Chirality : 0.044 0.248 5669 Planarity : 0.006 0.158 5925 Dihedral : 19.667 178.885 6091 Min Nonbonded Distance : 1.704 Molprobity Statistics. All-atom Clashscore : 29.75 Ramachandran Plot: Outliers : 0.22 % Allowed : 13.22 % Favored : 86.56 % Rotamer Outliers : 0.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.60 % Cis-general : 0.00 % Twisted Proline : 0.65 % Twisted General : 0.20 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.50 (0.12), residues: 4069 helix: -1.65 (0.12), residues: 1481 sheet: -2.69 (0.21), residues: 477 loop : -2.78 (0.12), residues: 2111 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8138 Ramachandran restraints generated. 4069 Oldfield, 0 Emsley, 4069 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8138 Ramachandran restraints generated. 4069 Oldfield, 0 Emsley, 4069 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 385 residues out of total 3505 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 385 time to evaluate : 4.135 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 385 average time/residue: 1.0701 time to fit residues: 627.8535 Evaluate side-chains 331 residues out of total 3505 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 331 time to evaluate : 4.121 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 5.1135 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 419 random chunks: chunk 249 optimal weight: 10.0000 chunk 161 optimal weight: 6.9990 chunk 241 optimal weight: 8.9990 chunk 121 optimal weight: 6.9990 chunk 79 optimal weight: 9.9990 chunk 78 optimal weight: 6.9990 chunk 256 optimal weight: 10.0000 chunk 275 optimal weight: 9.9990 chunk 199 optimal weight: 4.9990 chunk 37 optimal weight: 8.9990 chunk 317 optimal weight: 20.0000 overall best weight: 6.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 84 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 725 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 232 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 265 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.4121 moved from start: 0.4828 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.074 36386 Z= 0.312 Angle : 0.708 9.661 49818 Z= 0.396 Chirality : 0.043 0.183 5669 Planarity : 0.006 0.078 5925 Dihedral : 19.695 178.654 6091 Min Nonbonded Distance : 1.777 Molprobity Statistics. All-atom Clashscore : 25.92 Ramachandran Plot: Outliers : 0.20 % Allowed : 11.99 % Favored : 87.81 % Rotamer Outliers : 0.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.60 % Cis-general : 0.00 % Twisted Proline : 0.65 % Twisted General : 0.15 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.41 (0.12), residues: 4069 helix: -1.55 (0.12), residues: 1477 sheet: -2.62 (0.21), residues: 462 loop : -2.74 (0.12), residues: 2130 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8138 Ramachandran restraints generated. 4069 Oldfield, 0 Emsley, 4069 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8138 Ramachandran restraints generated. 4069 Oldfield, 0 Emsley, 4069 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 378 residues out of total 3505 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 378 time to evaluate : 4.181 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 378 average time/residue: 1.0724 time to fit residues: 614.9724 Evaluate side-chains 318 residues out of total 3505 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 318 time to evaluate : 4.193 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 5.1650 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 419 random chunks: chunk 367 optimal weight: 20.0000 chunk 386 optimal weight: 10.0000 chunk 352 optimal weight: 2.9990 chunk 376 optimal weight: 2.9990 chunk 226 optimal weight: 5.9990 chunk 163 optimal weight: 8.9990 chunk 295 optimal weight: 20.0000 chunk 115 optimal weight: 1.9990 chunk 340 optimal weight: 9.9990 chunk 355 optimal weight: 0.9990 chunk 375 optimal weight: 4.9990 overall best weight: 2.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 37 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 618 GLN ** D 232 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 265 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 31 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.4005 moved from start: 0.5005 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.080 36386 Z= 0.200 Angle : 0.629 9.533 49818 Z= 0.347 Chirality : 0.042 0.181 5669 Planarity : 0.005 0.140 5925 Dihedral : 19.482 178.359 6091 Min Nonbonded Distance : 1.878 Molprobity Statistics. All-atom Clashscore : 18.34 Ramachandran Plot: Outliers : 0.22 % Allowed : 9.88 % Favored : 89.90 % Rotamer Outliers : 0.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.60 % Cis-general : 0.00 % Twisted Proline : 0.65 % Twisted General : 0.15 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.94 (0.12), residues: 4069 helix: -1.07 (0.12), residues: 1488 sheet: -2.52 (0.22), residues: 446 loop : -2.51 (0.12), residues: 2135 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8138 Ramachandran restraints generated. 4069 Oldfield, 0 Emsley, 4069 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8138 Ramachandran restraints generated. 4069 Oldfield, 0 Emsley, 4069 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 401 residues out of total 3505 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 401 time to evaluate : 4.172 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 401 average time/residue: 1.0641 time to fit residues: 655.7130 Evaluate side-chains 332 residues out of total 3505 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 332 time to evaluate : 4.169 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 5.3002 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 419 random chunks: chunk 247 optimal weight: 6.9990 chunk 397 optimal weight: 20.0000 chunk 242 optimal weight: 6.9990 chunk 188 optimal weight: 0.7980 chunk 276 optimal weight: 20.0000 chunk 417 optimal weight: 10.0000 chunk 384 optimal weight: 10.0000 chunk 332 optimal weight: 8.9990 chunk 34 optimal weight: 5.9990 chunk 256 optimal weight: 9.9990 chunk 203 optimal weight: 7.9990 overall best weight: 5.7588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 84 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 725 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 232 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 702 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.4098 moved from start: 0.5278 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.068 36386 Z= 0.284 Angle : 0.671 9.492 49818 Z= 0.374 Chirality : 0.042 0.367 5669 Planarity : 0.005 0.068 5925 Dihedral : 19.472 179.951 6091 Min Nonbonded Distance : 1.766 Molprobity Statistics. All-atom Clashscore : 23.83 Ramachandran Plot: Outliers : 0.17 % Allowed : 11.65 % Favored : 88.18 % Rotamer Outliers : 0.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.60 % Cis-general : 0.00 % Twisted Proline : 0.65 % Twisted General : 0.15 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.09 (0.12), residues: 4069 helix: -1.20 (0.12), residues: 1488 sheet: -2.54 (0.21), residues: 467 loop : -2.61 (0.12), residues: 2114 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8138 Ramachandran restraints generated. 4069 Oldfield, 0 Emsley, 4069 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8138 Ramachandran restraints generated. 4069 Oldfield, 0 Emsley, 4069 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 371 residues out of total 3505 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 371 time to evaluate : 4.171 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 371 average time/residue: 1.0694 time to fit residues: 608.6995 Evaluate side-chains 320 residues out of total 3505 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 320 time to evaluate : 4.139 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 5.1751 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 419 random chunks: chunk 264 optimal weight: 7.9990 chunk 354 optimal weight: 0.8980 chunk 101 optimal weight: 2.9990 chunk 306 optimal weight: 1.9990 chunk 49 optimal weight: 0.9990 chunk 92 optimal weight: 10.0000 chunk 332 optimal weight: 2.9990 chunk 139 optimal weight: 5.9990 chunk 341 optimal weight: 4.9990 chunk 42 optimal weight: 10.0000 chunk 61 optimal weight: 7.9990 overall best weight: 1.9788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 232 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 31 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4039 r_free = 0.4039 target = 0.091354 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3637 r_free = 0.3637 target = 0.069260 restraints weight = 895003.621| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 47)----------------| | r_work = 0.3673 r_free = 0.3673 target = 0.071179 restraints weight = 587925.358| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 48)----------------| | r_work = 0.3697 r_free = 0.3697 target = 0.072488 restraints weight = 438019.570| |-----------------------------------------------------------------------------| r_work (final): 0.3613 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7333 moved from start: 0.5377 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.065 36386 Z= 0.187 Angle : 0.614 9.515 49818 Z= 0.338 Chirality : 0.041 0.210 5669 Planarity : 0.005 0.068 5925 Dihedral : 19.320 177.976 6091 Min Nonbonded Distance : 1.902 Molprobity Statistics. All-atom Clashscore : 17.65 Ramachandran Plot: Outliers : 0.17 % Allowed : 8.77 % Favored : 91.05 % Rotamer Outliers : 0.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.60 % Cis-general : 0.00 % Twisted Proline : 0.65 % Twisted General : 0.13 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.71 (0.12), residues: 4069 helix: -0.88 (0.13), residues: 1502 sheet: -2.35 (0.23), residues: 447 loop : -2.39 (0.13), residues: 2120 =============================================================================== Job complete usr+sys time: 12793.08 seconds wall clock time: 222 minutes 58.47 seconds (13378.47 seconds total)