Starting phenix.real_space_refine (version: dev) on Tue Feb 21 03:36:09 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6qex_4539/02_2023/6qex_4539_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6qex_4539/02_2023/6qex_4539.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.6 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6qex_4539/02_2023/6qex_4539.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6qex_4539/02_2023/6qex_4539.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6qex_4539/02_2023/6qex_4539_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6qex_4539/02_2023/6qex_4539_updated.pdb" } resolution = 3.6 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= -0.000 sd= 0.002 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Anisotropic ADP refinement not supported. Converting 526 atoms to isotropic. 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 ARG 41": "NH1" <-> "NH2" Residue "A ASP 47": "OD1" <-> "OD2" Residue "A ARG 95": "NH1" <-> "NH2" Residue "A PHE 135": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 163": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 170": "OE1" <-> "OE2" Residue "A ASP 177": "OD1" <-> "OD2" Residue "A ASP 178": "OD1" <-> "OD2" Residue "A PHE 201": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 241": "OD1" <-> "OD2" Residue "A GLU 256": "OE1" <-> "OE2" Residue "A PHE 267": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 364": "OE1" <-> "OE2" Residue "A PHE 366": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 370": "OD1" <-> "OD2" Residue "A ASP 386": "OD1" <-> "OD2" Residue "A TYR 401": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 406": "OE1" <-> "OE2" Residue "A ASP 454": "OD1" <-> "OD2" Residue "A ARG 459": "NH1" <-> "NH2" Residue "A ARG 489": "NH1" <-> "NH2" Residue "A ARG 492": "NH1" <-> "NH2" Residue "A GLU 493": "OE1" <-> "OE2" Residue "A PHE 512": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 543": "NH1" <-> "NH2" Residue "A ASP 555": "OD1" <-> "OD2" Residue "A GLU 564": "OE1" <-> "OE2" Residue "A ASP 574": "OD1" <-> "OD2" Residue "A ARG 580": "NH1" <-> "NH2" Residue "A ARG 593": "NH1" <-> "NH2" Residue "A ASP 602": "OD1" <-> "OD2" Residue "A GLU 618": "OE1" <-> "OE2" Residue "A PHE 739": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 782": "OE1" <-> "OE2" Residue "A ASP 805": "OD1" <-> "OD2" Residue "A ASP 806": "OD1" <-> "OD2" Residue "A ARG 832": "NH1" <-> "NH2" Residue "A TYR 853": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 950": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 958": "NH1" <-> "NH2" Residue "A GLU 1013": "OE1" <-> "OE2" Residue "A ASP 1019": "OD1" <-> "OD2" Residue "A GLU 1024": "OE1" <-> "OE2" Residue "A ARG 1047": "NH1" <-> "NH2" Residue "A GLU 1059": "OE1" <-> "OE2" Residue "A ARG 1085": "NH1" <-> "NH2" Residue "A ARG 1103": "NH1" <-> "NH2" Residue "A PHE 1123": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 1124": "OD1" <-> "OD2" Residue "A ASP 1135": "OD1" <-> "OD2" Residue "A ARG 1138": "NH1" <-> "NH2" Residue "A GLU 1144": "OE1" <-> "OE2" Residue "A ASP 1171": "OD1" <-> "OD2" Residue "A GLU 1211": "OE1" <-> "OE2" Residue "A GLU 1216": "OE1" <-> "OE2" Residue "A ASP 1219": "OD1" <-> "OD2" Residue "A ARG 1222": "NH1" <-> "NH2" Residue "A GLU 1223": "OE1" <-> "OE2" Residue "A ARG 1233": "NH1" <-> "NH2" Residue "A GLU 1253": "OE1" <-> "OE2" Residue "A PHE 1268": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 41": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 66": "NH1" <-> "NH2" Residue "B PHE 76": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 82": "NH1" <-> "NH2" Residue "B TYR 91": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 104": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 161": "NH1" <-> "NH2" Residue "B ASP 173": "OD1" <-> "OD2" Residue "B ASP 176": "OD1" <-> "OD2" Residue "B TYR 179": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 219": "OE1" <-> "OE2" Residue "C TYR 32": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 50": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 60": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 64": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 94": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 103": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 111": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 155": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 175": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 220": "OE1" <-> "OE2" Residue "C ARG 222": "NH1" <-> "NH2" Time to flip residues: 0.05s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-4877/modules/chem_data/mon_lib" Total number of atoms: 13251 Number of models: 1 Model: "" Number of chains: 4 Chain: "A" Number of atoms: 9191 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1182, 9191 Classifications: {'peptide': 1182} Link IDs: {'PTRANS': 27, 'TRANS': 1154} Chain breaks: 1 Chain: "B" Number of atoms: 1713 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 220, 1710 Classifications: {'peptide': 220} Modifications used: {'COO': 1} Link IDs: {'CIS': 1, 'PCIS': 2, 'PTRANS': 10, 'TRANS': 206} Conformer: "B" Number of residues, atoms: 220, 1710 Classifications: {'peptide': 220} Modifications used: {'COO': 1} Link IDs: {'CIS': 1, 'PCIS': 2, 'PTRANS': 10, 'TRANS': 206} bond proxies already assigned to first conformer: 1747 Chain: "C" Number of atoms: 1717 Number of conformers: 1 Conformer: "" Number of residues, atoms: 225, 1717 Classifications: {'peptide': 225} Link IDs: {'PCIS': 3, 'PTRANS': 10, 'TRANS': 211} Chain: "A" Number of atoms: 630 Number of conformers: 1 Conformer: "" Number of residues, atoms: 22, 630 Unusual residues: {'3PE': 2, 'CLR': 16, 'NAG': 3, 'TA1': 1} Classifications: {'undetermined': 22} Link IDs: {None: 21} Unresolved non-hydrogen bonds: 27 Unresolved non-hydrogen angles: 30 Unresolved non-hydrogen dihedrals: 24 Unresolved non-hydrogen chiralities: 3 Time building chain proxies: 8.63, per 1000 atoms: 0.65 Number of scatterers: 13251 At special positions: 0 Unit cell: (89.04, 101.64, 210, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 53 16.00 P 2 15.00 O 2417 8.00 N 2131 7.00 C 8648 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=6, symmetry=0 Simple disulfide: pdb=" SG CYS B 23 " - pdb=" SG CYS B 93 " distance=2.04 Simple disulfide: pdb=" SG CYS B 140 " - pdb=" SG ACYS B 200 " distance=2.03 Simple disulfide: pdb=" SG CYS B 140 " - pdb=" SG BCYS B 200 " distance=2.05 Simple disulfide: pdb=" SG CYS B 220 " - pdb=" SG CYS C 137 " distance=2.03 Simple disulfide: pdb=" SG CYS C 22 " - pdb=" SG CYS C 96 " distance=2.03 Simple disulfide: pdb=" SG CYS C 149 " - pdb=" SG CYS C 204 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Links applied NAG-ASN " NAG A1301 " - " ASN A 91 " " NAG A1302 " - " ASN A 94 " " NAG A1303 " - " ASN A 99 " Time building additional restraints: 5.56 Conformation dependent library (CDL) restraints added in 2.1 seconds 3240 Ramachandran restraints generated. 1620 Oldfield, 0 Emsley, 1620 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3004 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 53 helices and 14 sheets defined 46.2% alpha, 12.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 2.21 Creating SS restraints... Processing helix chain 'A' and resid 36 through 39 No H-bonds generated for 'chain 'A' and resid 36 through 39' Processing helix chain 'A' and resid 45 through 64 removed outlier: 3.698A pdb=" N VAL A 52 " --> pdb=" O LYS A 48 " (cutoff:3.500A) removed outlier: 3.653A pdb=" N ALA A 58 " --> pdb=" O GLY A 54 " (cutoff:3.500A) removed outlier: 3.999A pdb=" N GLY A 64 " --> pdb=" O ILE A 60 " (cutoff:3.500A) Processing helix chain 'A' and resid 66 through 92 removed outlier: 3.756A pdb=" N VAL A 71 " --> pdb=" O LEU A 67 " (cutoff:3.500A) removed outlier: 3.859A pdb=" N ASP A 87 " --> pdb=" O GLY A 83 " (cutoff:3.500A) removed outlier: 4.572A pdb=" N LEU A 88 " --> pdb=" O ASN A 84 " (cutoff:3.500A) removed outlier: 3.966A pdb=" N MET A 89 " --> pdb=" O LEU A 85 " (cutoff:3.500A) removed outlier: 3.580A pdb=" N ASN A 91 " --> pdb=" O ASP A 87 " (cutoff:3.500A) removed outlier: 4.362A pdb=" N ILE A 92 " --> pdb=" O LEU A 88 " (cutoff:3.500A) Processing helix chain 'A' and resid 98 through 157 removed outlier: 3.972A pdb=" N LEU A 107 " --> pdb=" O PHE A 103 " (cutoff:3.500A) removed outlier: 4.144A pdb=" N THR A 112 " --> pdb=" O GLU A 108 " (cutoff:3.500A) removed outlier: 3.995A pdb=" N ARG A 113 " --> pdb=" O GLU A 109 " (cutoff:3.500A) removed outlier: 3.971A pdb=" N ARG A 157 " --> pdb=" O HIS A 153 " (cutoff:3.500A) Processing helix chain 'A' and resid 160 through 165 Processing helix chain 'A' and resid 169 through 185 Processing helix chain 'A' and resid 189 through 210 removed outlier: 3.528A pdb=" N PHE A 194 " --> pdb=" O ILE A 190 " (cutoff:3.500A) Processing helix chain 'A' and resid 212 through 237 removed outlier: 4.052A pdb=" N VAL A 217 " --> pdb=" O LYS A 213 " (cutoff:3.500A) Proline residue: A 223 - end of helix Processing helix chain 'A' and resid 241 through 247 Processing helix chain 'A' and resid 251 through 259 Processing helix chain 'A' and resid 261 through 267 Processing helix chain 'A' and resid 270 through 322 removed outlier: 4.077A pdb=" N GLU A 283 " --> pdb=" O LYS A 279 " (cutoff:3.500A) Processing helix chain 'A' and resid 328 through 370 removed outlier: 4.652A pdb=" N SER A 349 " --> pdb=" O VAL A 345 " (cutoff:3.500A) Proline residue: A 350 - end of helix removed outlier: 3.772A pdb=" N GLU A 353 " --> pdb=" O SER A 349 " (cutoff:3.500A) removed outlier: 4.796A pdb=" N GLU A 364 " --> pdb=" O GLY A 360 " (cutoff:3.500A) removed outlier: 4.303A pdb=" N ILE A 365 " --> pdb=" O ALA A 361 " (cutoff:3.500A) Processing helix chain 'A' and resid 433 through 440 Processing helix chain 'A' and resid 458 through 460 No H-bonds generated for 'chain 'A' and resid 458 through 460' Processing helix chain 'A' and resid 463 through 468 Processing helix chain 'A' and resid 484 through 491 removed outlier: 4.758A pdb=" N GLY A 491 " --> pdb=" O ASN A 487 " (cutoff:3.500A) Processing helix chain 'A' and resid 497 through 507 Processing helix chain 'A' and resid 511 through 515 Processing helix chain 'A' and resid 526 through 528 No H-bonds generated for 'chain 'A' and resid 526 through 528' Processing helix chain 'A' and resid 533 through 547 removed outlier: 4.706A pdb=" N ARG A 547 " --> pdb=" O ARG A 543 " (cutoff:3.500A) Processing helix chain 'A' and resid 563 through 575 Processing helix chain 'A' and resid 612 through 618 Processing helix chain 'A' and resid 621 through 629 Processing helix chain 'A' and resid 701 through 704 Processing helix chain 'A' and resid 708 through 722 Processing helix chain 'A' and resid 726 through 740 Processing helix chain 'A' and resid 745 through 797 removed outlier: 4.304A pdb=" N LEU A 760 " --> pdb=" O SER A 756 " (cutoff:3.500A) Processing helix chain 'A' and resid 801 through 804 No H-bonds generated for 'chain 'A' and resid 801 through 804' Processing helix chain 'A' and resid 811 through 819 Processing helix chain 'A' and resid 830 through 853 removed outlier: 4.913A pdb=" N THR A 845 " --> pdb=" O ALA A 841 " (cutoff:3.500A) removed outlier: 4.228A pdb=" N GLY A 846 " --> pdb=" O ASN A 842 " (cutoff:3.500A) Processing helix chain 'A' and resid 855 through 879 Proline residue: A 866 - end of helix removed outlier: 3.785A pdb=" N GLU A 875 " --> pdb=" O ALA A 871 " (cutoff:3.500A) Processing helix chain 'A' and resid 885 through 901 removed outlier: 6.061A pdb=" N ILE A 896 " --> pdb=" O GLY A 892 " (cutoff:3.500A) removed outlier: 6.050A pdb=" N ALA A 897 " --> pdb=" O ALA A 893 " (cutoff:3.500A) removed outlier: 3.998A pdb=" N THR A 898 " --> pdb=" O GLY A 894 " (cutoff:3.500A) Processing helix chain 'A' and resid 904 through 910 removed outlier: 4.138A pdb=" N SER A 909 " --> pdb=" O ARG A 905 " (cutoff:3.500A) Processing helix chain 'A' and resid 913 through 923 Processing helix chain 'A' and resid 925 through 965 removed outlier: 3.563A pdb=" N ARG A 929 " --> pdb=" O GLN A 925 " (cutoff:3.500A) removed outlier: 3.951A pdb=" N GLY A 939 " --> pdb=" O ALA A 935 " (cutoff:3.500A) removed outlier: 4.203A pdb=" N TYR A 950 " --> pdb=" O GLN A 946 " (cutoff:3.500A) Processing helix chain 'A' and resid 971 through 992 Processing helix chain 'A' and resid 999 through 1013 Processing helix chain 'A' and resid 1078 through 1083 Processing helix chain 'A' and resid 1106 through 1112 removed outlier: 3.632A pdb=" N ARG A1110 " --> pdb=" O VAL A1106 " (cutoff:3.500A) Processing helix chain 'A' and resid 1127 through 1134 removed outlier: 4.460A pdb=" N GLY A1134 " --> pdb=" O ASN A1130 " (cutoff:3.500A) Processing helix chain 'A' and resid 1142 through 1151 Processing helix chain 'A' and resid 1155 through 1160 Processing helix chain 'A' and resid 1171 through 1173 No H-bonds generated for 'chain 'A' and resid 1171 through 1173' Processing helix chain 'A' and resid 1178 through 1192 removed outlier: 4.398A pdb=" N ARG A1192 " --> pdb=" O ARG A1188 " (cutoff:3.500A) Processing helix chain 'A' and resid 1208 through 1221 removed outlier: 3.945A pdb=" N LYS A1212 " --> pdb=" O THR A1208 " (cutoff:3.500A) removed outlier: 3.613A pdb=" N VAL A1213 " --> pdb=" O GLU A1209 " (cutoff:3.500A) removed outlier: 4.234A pdb=" N ALA A1217 " --> pdb=" O VAL A1213 " (cutoff:3.500A) removed outlier: 3.530A pdb=" N LEU A1218 " --> pdb=" O VAL A1214 " (cutoff:3.500A) Processing helix chain 'A' and resid 1235 through 1238 No H-bonds generated for 'chain 'A' and resid 1235 through 1238' Processing helix chain 'A' and resid 1257 through 1262 Processing helix chain 'A' and resid 1266 through 1271 Processing helix chain 'B' and resid 128 through 132 Processing helix chain 'B' and resid 192 through 194 No H-bonds generated for 'chain 'B' and resid 192 through 194' Processing helix chain 'C' and resid 88 through 90 No H-bonds generated for 'chain 'C' and resid 88 through 90' Processing helix chain 'C' and resid 163 through 166 Processing sheet with id= A, first strand: chain 'A' and resid 415 through 417 removed outlier: 3.744A pdb=" N ARG A 395 " --> pdb=" O MET A 450 " (cutoff:3.500A) removed outlier: 3.585A pdb=" N MET A 450 " --> pdb=" O ARG A 395 " (cutoff:3.500A) Processing sheet with id= B, first strand: chain 'A' and resid 605 through 608 removed outlier: 6.515A pdb=" N GLY A 600 " --> pdb=" O VAL A 607 " (cutoff:3.500A) removed outlier: 6.925A pdb=" N THR A 582 " --> pdb=" O VAL A 423 " (cutoff:3.500A) removed outlier: 8.542A pdb=" N LEU A 425 " --> pdb=" O THR A 582 " (cutoff:3.500A) removed outlier: 7.552A pdb=" N VAL A 584 " --> pdb=" O LEU A 425 " (cutoff:3.500A) Processing sheet with id= C, first strand: chain 'A' and resid 1058 through 1060 Processing sheet with id= D, first strand: chain 'A' and resid 1066 through 1069 removed outlier: 6.629A pdb=" N LEU A1242 " --> pdb=" O ALA A1067 " (cutoff:3.500A) removed outlier: 7.881A pdb=" N VAL A1069 " --> pdb=" O LEU A1242 " (cutoff:3.500A) removed outlier: 6.209A pdb=" N VAL A1244 " --> pdb=" O VAL A1069 " (cutoff:3.500A) removed outlier: 3.967A pdb=" N GLU A1253 " --> pdb=" O VAL A1245 " (cutoff:3.500A) removed outlier: 6.565A pdb=" N GLN A1247 " --> pdb=" O VAL A1251 " (cutoff:3.500A) removed outlier: 5.343A pdb=" N VAL A1251 " --> pdb=" O GLN A1247 " (cutoff:3.500A) Processing sheet with id= E, first strand: chain 'A' and resid 1114 through 1116 removed outlier: 4.022A pdb=" N LEU A1198 " --> pdb=" O GLY A1114 " (cutoff:3.500A) removed outlier: 3.608A pdb=" N VAL A1116 " --> pdb=" O LEU A1198 " (cutoff:3.500A) removed outlier: 4.027A pdb=" N ASP A1200 " --> pdb=" O VAL A1116 " (cutoff:3.500A) removed outlier: 6.354A pdb=" N THR A1226 " --> pdb=" O LEU A1197 " (cutoff:3.500A) removed outlier: 7.979A pdb=" N LEU A1199 " --> pdb=" O THR A1226 " (cutoff:3.500A) removed outlier: 6.613A pdb=" N ILE A1228 " --> pdb=" O LEU A1199 " (cutoff:3.500A) Processing sheet with id= F, first strand: chain 'B' and resid 19 through 23 Processing sheet with id= G, first strand: chain 'B' and resid 90 through 94 removed outlier: 6.082A pdb=" N LEU B 42 " --> pdb=" O LEU B 51 " (cutoff:3.500A) removed outlier: 5.166A pdb=" N LEU B 51 " --> pdb=" O LEU B 42 " (cutoff:3.500A) Processing sheet with id= H, first strand: chain 'B' and resid 122 through 124 removed outlier: 6.014A pdb=" N TYR B 179 " --> pdb=" O ASN B 144 " (cutoff:3.500A) Processing sheet with id= I, first strand: chain 'B' and resid 159 through 161 removed outlier: 4.520A pdb=" N TRP B 154 " --> pdb=" O ARG B 161 " (cutoff:3.500A) removed outlier: 3.872A pdb=" N ASN B 151 " --> pdb=" O THR B 203 " (cutoff:3.500A) Processing sheet with id= J, first strand: chain 'C' and resid 3 through 6 Processing sheet with id= K, first strand: chain 'C' and resid 116 through 118 removed outlier: 3.613A pdb=" N LEU C 99 " --> pdb=" O TYR C 33 " (cutoff:3.500A) removed outlier: 6.390A pdb=" N LYS C 38 " --> pdb=" O TRP C 47 " (cutoff:3.500A) removed outlier: 5.286A pdb=" N TRP C 47 " --> pdb=" O LYS C 38 " (cutoff:3.500A) Processing sheet with id= L, first strand: chain 'C' and resid 129 through 133 removed outlier: 4.127A pdb=" N GLY C 148 " --> pdb=" O LEU C 133 " (cutoff:3.500A) Processing sheet with id= M, first strand: chain 'C' and resid 145 through 147 Processing sheet with id= N, first strand: chain 'C' and resid 203 through 208 630 hydrogen bonds defined for protein. 1805 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 5.07 Time building geometry restraints manager: 5.87 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.17 - 1.30: 2085 1.30 - 1.44: 3518 1.44 - 1.57: 7870 1.57 - 1.70: 5 1.70 - 1.83: 87 Bond restraints: 13565 Sorted by residual: bond pdb=" C7 NAG A1302 " pdb=" N2 NAG A1302 " ideal model delta sigma weight residual 1.337 1.492 -0.155 1.10e-02 8.26e+03 1.98e+02 bond pdb=" C7 NAG A1303 " pdb=" N2 NAG A1303 " ideal model delta sigma weight residual 1.337 1.492 -0.155 1.10e-02 8.26e+03 1.98e+02 bond pdb=" C7 NAG A1301 " pdb=" N2 NAG A1301 " ideal model delta sigma weight residual 1.337 1.482 -0.145 1.10e-02 8.26e+03 1.74e+02 bond pdb=" C2 NAG A1302 " pdb=" N2 NAG A1302 " ideal model delta sigma weight residual 1.454 1.517 -0.063 1.00e-02 1.00e+04 4.01e+01 bond pdb=" C2 NAG A1303 " pdb=" N2 NAG A1303 " ideal model delta sigma weight residual 1.454 1.517 -0.063 1.00e-02 1.00e+04 3.97e+01 ... (remaining 13560 not shown) Histogram of bond angle deviations from ideal: 82.38 - 93.33: 3 93.33 - 104.28: 228 104.28 - 115.23: 8699 115.23 - 126.18: 9354 126.18 - 137.14: 179 Bond angle restraints: 18463 Sorted by residual: angle pdb=" N SER A 90 " pdb=" CA SER A 90 " pdb=" C SER A 90 " ideal model delta sigma weight residual 111.28 121.42 -10.14 1.09e+00 8.42e-01 8.65e+01 angle pdb=" N GLU A 86 " pdb=" CA GLU A 86 " pdb=" C GLU A 86 " ideal model delta sigma weight residual 111.28 120.68 -9.40 1.09e+00 8.42e-01 7.43e+01 angle pdb=" O12 3PE A1322 " pdb=" P 3PE A1322 " pdb=" O14 3PE A1322 " ideal model delta sigma weight residual 123.79 100.24 23.55 3.00e+00 1.11e-01 6.16e+01 angle pdb=" O12 3PE A1321 " pdb=" P 3PE A1321 " pdb=" O14 3PE A1321 " ideal model delta sigma weight residual 123.79 100.99 22.80 3.00e+00 1.11e-01 5.77e+01 angle pdb=" N ASP A 100 " pdb=" CA ASP A 100 " pdb=" CB ASP A 100 " ideal model delta sigma weight residual 110.01 118.13 -8.12 1.45e+00 4.76e-01 3.14e+01 ... (remaining 18458 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.98: 6943 17.98 - 35.97: 761 35.97 - 53.95: 140 53.95 - 71.93: 39 71.93 - 89.92: 9 Dihedral angle restraints: 7892 sinusoidal: 3207 harmonic: 4685 Sorted by residual: dihedral pdb=" CB CYS B 220 " pdb=" SG CYS B 220 " pdb=" SG CYS C 137 " pdb=" CB CYS C 137 " ideal model delta sinusoidal sigma weight residual -86.00 -173.43 87.43 1 1.00e+01 1.00e-02 9.17e+01 dihedral pdb=" CA LYS B 55 " pdb=" C LYS B 55 " pdb=" N VAL B 56 " pdb=" CA VAL B 56 " ideal model delta harmonic sigma weight residual -180.00 -136.40 -43.60 0 5.00e+00 4.00e-02 7.61e+01 dihedral pdb=" CA PRO B 100 " pdb=" C PRO B 100 " pdb=" N PRO B 101 " pdb=" CA PRO B 101 " ideal model delta harmonic sigma weight residual 180.00 150.18 29.82 0 5.00e+00 4.00e-02 3.56e+01 ... (remaining 7889 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.329: 2121 0.329 - 0.657: 26 0.657 - 0.986: 1 0.986 - 1.315: 2 1.315 - 1.644: 2 Chirality restraints: 2152 Sorted by residual: chirality pdb=" C1 NAG A1301 " pdb=" ND2 ASN A 91 " pdb=" C2 NAG A1301 " pdb=" O5 NAG A1301 " both_signs ideal model delta sigma weight residual False -2.40 -0.76 -1.64 2.00e-01 2.50e+01 6.75e+01 chirality pdb=" C1 NAG A1302 " pdb=" ND2 ASN A 94 " pdb=" C2 NAG A1302 " pdb=" O5 NAG A1302 " both_signs ideal model delta sigma weight residual False -2.40 -0.92 -1.48 2.00e-01 2.50e+01 5.45e+01 chirality pdb=" C10 TA1 A1320 " pdb=" C02 TA1 A1320 " pdb=" C11 TA1 A1320 " pdb=" C18 TA1 A1320 " both_signs ideal model delta sigma weight residual False 2.54 1.25 1.29 2.00e-01 2.50e+01 4.16e+01 ... (remaining 2149 not shown) Planarity restraints: 2229 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C29 TA1 A1320 " 0.264 2.00e-02 2.50e+03 2.29e-01 6.57e+02 pdb=" C30 TA1 A1320 " -0.058 2.00e-02 2.50e+03 pdb=" C31 TA1 A1320 " -0.021 2.00e-02 2.50e+03 pdb=" N01 TA1 A1320 " -0.386 2.00e-02 2.50e+03 pdb=" O14 TA1 A1320 " 0.202 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB ASN A 94 " 0.017 2.00e-02 2.50e+03 1.04e-01 1.36e+02 pdb=" CG ASN A 94 " -0.026 2.00e-02 2.50e+03 pdb=" OD1 ASN A 94 " 0.077 2.00e-02 2.50e+03 pdb=" ND2 ASN A 94 " -0.184 2.00e-02 2.50e+03 pdb=" C1 NAG A1302 " 0.117 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB ASN A 99 " -0.037 2.00e-02 2.50e+03 6.22e-02 4.84e+01 pdb=" CG ASN A 99 " 0.016 2.00e-02 2.50e+03 pdb=" OD1 ASN A 99 " -0.014 2.00e-02 2.50e+03 pdb=" ND2 ASN A 99 " 0.110 2.00e-02 2.50e+03 pdb=" C1 NAG A1303 " -0.074 2.00e-02 2.50e+03 ... (remaining 2226 not shown) Histogram of nonbonded interaction distances: 1.41 - 2.10: 4 2.10 - 2.80: 3549 2.80 - 3.50: 17501 3.50 - 4.20: 29171 4.20 - 4.90: 51373 Nonbonded interactions: 101598 Sorted by model distance: nonbonded pdb=" CD1 ILE A 92 " pdb=" CD PRO B 100 " model vdw 1.406 3.860 nonbonded pdb=" ND2 ASN A 84 " pdb=" O THR A 740 " model vdw 1.623 2.520 nonbonded pdb=" NH1 ARG A 148 " pdb=" CG1 VAL A 179 " model vdw 1.898 3.540 nonbonded pdb=" CD1 ILE A 92 " pdb=" CG PRO B 100 " model vdw 1.999 3.860 nonbonded pdb=" O ILE A 700 " pdb=" CD1 ILE A 829 " model vdw 2.217 3.460 ... (remaining 101593 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians P 2 5.49 5 S 53 5.16 5 C 8648 2.51 5 N 2131 2.21 5 O 2417 1.98 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=0.47 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: 5.500 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.080 Construct map_model_manager: 0.010 Extract box with map and model: 14.840 Check model and map are aligned: 0.190 Process input model: 38.280 Find NCS groups from input model: 0.380 Set up NCS constraints: 0.060 Set refine NCS operators: 0.000 Set scattering table: 0.130 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:3.070 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 62.540 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7265 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 : 0.009 0.155 13565 Z= 0.612 Angle : 1.233 23.549 18463 Z= 0.611 Chirality : 0.103 1.644 2152 Planarity : 0.008 0.229 2226 Dihedral : 15.485 89.919 4870 Min Nonbonded Distance : 1.406 Molprobity Statistics. All-atom Clashscore : 8.33 Ramachandran Plot: Outliers : 0.06 % Allowed : 5.99 % Favored : 93.95 % Rotamer Outliers : 0.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 9.80 % Cis-general : 0.06 % Twisted Proline : 0.00 % Twisted General : 0.06 % 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: -3.39 (0.17), residues: 1620 helix: -1.96 (0.14), residues: 774 sheet: -1.77 (0.28), residues: 300 loop : -2.64 (0.22), residues: 546 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3240 Ramachandran restraints generated. 1620 Oldfield, 0 Emsley, 1620 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3240 Ramachandran restraints generated. 1620 Oldfield, 0 Emsley, 1620 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 185 residues out of total 1370 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 175 time to evaluate : 1.558 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 10 outliers final: 3 residues processed: 184 average time/residue: 0.2715 time to fit residues: 71.8128 Evaluate side-chains 119 residues out of total 1370 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 116 time to evaluate : 1.400 Switching outliers to nearest non-outliers outliers start: 3 outliers final: 0 residues processed: 3 average time/residue: 0.2849 time to fit residues: 3.1476 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 162 random chunks: chunk 136 optimal weight: 1.9990 chunk 122 optimal weight: 0.9980 chunk 68 optimal weight: 0.8980 chunk 41 optimal weight: 6.9990 chunk 82 optimal weight: 3.9990 chunk 65 optimal weight: 1.9990 chunk 126 optimal weight: 0.6980 chunk 49 optimal weight: 5.9990 chunk 77 optimal weight: 0.6980 chunk 94 optimal weight: 6.9990 chunk 147 optimal weight: 0.6980 overall best weight: 0.7980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 84 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 438 GLN ** A 537 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 725 GLN A 750 GLN A 773 GLN A 838 GLN A 839 ASN A1054 GLN A1105 ASN ** A1153 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1239 ASN A1248 ASN ** B 35 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 130 GLN B 144 ASN B 216 ASN C 31 ASN Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7252 moved from start: 0.1668 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.044 13565 Z= 0.197 Angle : 0.642 15.818 18463 Z= 0.323 Chirality : 0.042 0.260 2152 Planarity : 0.004 0.050 2226 Dihedral : 8.281 66.477 1964 Min Nonbonded Distance : 2.136 Molprobity Statistics. All-atom Clashscore : 10.08 Ramachandran Plot: Outliers : 0.06 % Allowed : 4.20 % Favored : 95.74 % Rotamer Outliers : 2.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 9.80 % Cis-general : 0.06 % Twisted Proline : 0.00 % Twisted General : 0.06 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.67 (0.20), residues: 1620 helix: -0.14 (0.18), residues: 773 sheet: -1.40 (0.29), residues: 297 loop : -2.20 (0.23), residues: 550 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3240 Ramachandran restraints generated. 1620 Oldfield, 0 Emsley, 1620 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3240 Ramachandran restraints generated. 1620 Oldfield, 0 Emsley, 1620 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 160 residues out of total 1370 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 34 poor density : 126 time to evaluate : 1.423 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 34 outliers final: 14 residues processed: 152 average time/residue: 0.2578 time to fit residues: 58.7992 Evaluate side-chains 126 residues out of total 1370 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 112 time to evaluate : 1.417 Switching outliers to nearest non-outliers outliers start: 14 outliers final: 0 residues processed: 14 average time/residue: 0.1287 time to fit residues: 5.4517 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 162 random chunks: chunk 81 optimal weight: 4.9990 chunk 45 optimal weight: 0.9980 chunk 122 optimal weight: 0.9990 chunk 100 optimal weight: 0.3980 chunk 40 optimal weight: 3.9990 chunk 147 optimal weight: 1.9990 chunk 159 optimal weight: 4.9990 chunk 131 optimal weight: 0.7980 chunk 146 optimal weight: 0.5980 chunk 50 optimal weight: 0.5980 chunk 118 optimal weight: 2.9990 overall best weight: 0.6780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 84 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 537 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 612 HIS ** A1153 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 35 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 130 GLN B 195 HIS C 62 GLN ** C 102 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7247 moved from start: 0.2185 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.039 13565 Z= 0.180 Angle : 0.601 16.228 18463 Z= 0.301 Chirality : 0.042 0.381 2152 Planarity : 0.004 0.049 2226 Dihedral : 7.738 66.098 1964 Min Nonbonded Distance : 2.158 Molprobity Statistics. All-atom Clashscore : 9.60 Ramachandran Plot: Outliers : 0.06 % Allowed : 4.39 % Favored : 95.55 % Rotamer Outliers : 2.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 9.80 % Cis-general : 0.06 % Twisted Proline : 0.00 % Twisted General : 0.06 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.89 (0.20), residues: 1620 helix: 0.61 (0.19), residues: 773 sheet: -1.06 (0.29), residues: 297 loop : -1.98 (0.24), residues: 550 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3240 Ramachandran restraints generated. 1620 Oldfield, 0 Emsley, 1620 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3240 Ramachandran restraints generated. 1620 Oldfield, 0 Emsley, 1620 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 152 residues out of total 1370 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 125 time to evaluate : 1.476 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 27 outliers final: 13 residues processed: 147 average time/residue: 0.2486 time to fit residues: 55.1067 Evaluate side-chains 124 residues out of total 1370 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 111 time to evaluate : 1.440 Switching outliers to nearest non-outliers outliers start: 13 outliers final: 0 residues processed: 13 average time/residue: 0.1233 time to fit residues: 5.0469 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 162 random chunks: chunk 145 optimal weight: 0.8980 chunk 110 optimal weight: 9.9990 chunk 76 optimal weight: 0.8980 chunk 16 optimal weight: 1.9990 chunk 70 optimal weight: 3.9990 chunk 98 optimal weight: 7.9990 chunk 147 optimal weight: 0.8980 chunk 156 optimal weight: 0.1980 chunk 77 optimal weight: 0.1980 chunk 140 optimal weight: 0.9980 chunk 42 optimal weight: 5.9990 overall best weight: 0.6180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 84 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 537 GLN ** A1130 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1153 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 35 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 102 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7235 moved from start: 0.2495 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.036 13565 Z= 0.167 Angle : 0.584 15.867 18463 Z= 0.288 Chirality : 0.041 0.287 2152 Planarity : 0.004 0.049 2226 Dihedral : 7.462 66.621 1964 Min Nonbonded Distance : 2.175 Molprobity Statistics. All-atom Clashscore : 9.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.01 % Favored : 95.99 % Rotamer Outliers : 1.90 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 9.80 % Cis-general : 0.06 % Twisted Proline : 0.00 % Twisted General : 0.06 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.46 (0.21), residues: 1620 helix: 1.01 (0.19), residues: 768 sheet: -0.89 (0.30), residues: 298 loop : -1.80 (0.25), residues: 554 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3240 Ramachandran restraints generated. 1620 Oldfield, 0 Emsley, 1620 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3240 Ramachandran restraints generated. 1620 Oldfield, 0 Emsley, 1620 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 149 residues out of total 1370 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 125 time to evaluate : 1.485 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 24 outliers final: 11 residues processed: 141 average time/residue: 0.2591 time to fit residues: 54.8672 Evaluate side-chains 120 residues out of total 1370 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 109 time to evaluate : 1.327 Switching outliers to nearest non-outliers outliers start: 11 outliers final: 0 residues processed: 11 average time/residue: 0.1439 time to fit residues: 5.0001 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 162 random chunks: chunk 130 optimal weight: 0.9980 chunk 88 optimal weight: 0.6980 chunk 2 optimal weight: 0.8980 chunk 116 optimal weight: 30.0000 chunk 64 optimal weight: 1.9990 chunk 133 optimal weight: 0.5980 chunk 108 optimal weight: 7.9990 chunk 0 optimal weight: 5.9990 chunk 79 optimal weight: 6.9990 chunk 140 optimal weight: 0.9980 chunk 39 optimal weight: 20.0000 overall best weight: 0.8380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 84 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 270 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 518 HIS ** A1130 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1153 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1239 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7265 moved from start: 0.2747 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.034 13565 Z= 0.195 Angle : 0.594 16.087 18463 Z= 0.295 Chirality : 0.041 0.199 2152 Planarity : 0.004 0.042 2226 Dihedral : 7.397 66.276 1964 Min Nonbonded Distance : 2.158 Molprobity Statistics. All-atom Clashscore : 9.08 Ramachandran Plot: Outliers : 0.12 % Allowed : 4.45 % Favored : 95.43 % Rotamer Outliers : 1.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 9.80 % Cis-general : 0.06 % Twisted Proline : 0.00 % Twisted General : 0.06 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.28 (0.21), residues: 1620 helix: 1.15 (0.19), residues: 769 sheet: -0.81 (0.30), residues: 298 loop : -1.71 (0.25), residues: 553 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3240 Ramachandran restraints generated. 1620 Oldfield, 0 Emsley, 1620 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3240 Ramachandran restraints generated. 1620 Oldfield, 0 Emsley, 1620 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 125 residues out of total 1370 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 105 time to evaluate : 1.523 Fit side-chains revert: symmetry clash outliers start: 20 outliers final: 7 residues processed: 122 average time/residue: 0.2504 time to fit residues: 46.5250 Evaluate side-chains 109 residues out of total 1370 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 102 time to evaluate : 1.409 Switching outliers to nearest non-outliers outliers start: 7 outliers final: 0 residues processed: 7 average time/residue: 0.1234 time to fit residues: 3.7462 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 162 random chunks: chunk 52 optimal weight: 4.9990 chunk 141 optimal weight: 4.9990 chunk 30 optimal weight: 0.6980 chunk 91 optimal weight: 6.9990 chunk 38 optimal weight: 9.9990 chunk 156 optimal weight: 3.9990 chunk 130 optimal weight: 0.5980 chunk 72 optimal weight: 0.8980 chunk 13 optimal weight: 0.6980 chunk 51 optimal weight: 0.6980 chunk 82 optimal weight: 4.9990 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 84 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 270 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1130 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1153 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7251 moved from start: 0.2966 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.042 13565 Z= 0.181 Angle : 0.592 15.650 18463 Z= 0.294 Chirality : 0.041 0.220 2152 Planarity : 0.003 0.041 2226 Dihedral : 7.290 66.355 1964 Min Nonbonded Distance : 2.159 Molprobity Statistics. All-atom Clashscore : 9.04 Ramachandran Plot: Outliers : 0.06 % Allowed : 4.08 % Favored : 95.86 % Rotamer Outliers : 1.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 9.80 % Cis-general : 0.06 % Twisted Proline : 0.00 % Twisted General : 0.06 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.10 (0.21), residues: 1620 helix: 1.28 (0.19), residues: 769 sheet: -0.75 (0.30), residues: 303 loop : -1.56 (0.26), residues: 548 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3240 Ramachandran restraints generated. 1620 Oldfield, 0 Emsley, 1620 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3240 Ramachandran restraints generated. 1620 Oldfield, 0 Emsley, 1620 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 135 residues out of total 1370 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 113 time to evaluate : 1.446 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 22 outliers final: 11 residues processed: 130 average time/residue: 0.2473 time to fit residues: 49.2691 Evaluate side-chains 113 residues out of total 1370 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 102 time to evaluate : 1.265 Switching outliers to nearest non-outliers revert: symmetry clash outliers start: 11 outliers final: 1 residues processed: 11 average time/residue: 0.1267 time to fit residues: 4.5375 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 162 random chunks: chunk 151 optimal weight: 0.5980 chunk 17 optimal weight: 1.9990 chunk 89 optimal weight: 5.9990 chunk 114 optimal weight: 20.0000 chunk 88 optimal weight: 0.6980 chunk 131 optimal weight: 1.9990 chunk 87 optimal weight: 2.9990 chunk 156 optimal weight: 2.9990 chunk 97 optimal weight: 0.7980 chunk 95 optimal weight: 8.9990 chunk 72 optimal weight: 0.8980 overall best weight: 0.9982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 84 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 270 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1130 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1153 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 102 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7282 moved from start: 0.3061 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.038 13565 Z= 0.218 Angle : 0.608 15.636 18463 Z= 0.304 Chirality : 0.042 0.260 2152 Planarity : 0.004 0.043 2226 Dihedral : 7.331 65.422 1964 Min Nonbonded Distance : 2.144 Molprobity Statistics. All-atom Clashscore : 9.56 Ramachandran Plot: Outliers : 0.12 % Allowed : 4.57 % Favored : 95.31 % Rotamer Outliers : 1.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 9.80 % Cis-general : 0.06 % Twisted Proline : 0.00 % Twisted General : 0.06 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.08 (0.21), residues: 1620 helix: 1.26 (0.19), residues: 767 sheet: -0.61 (0.31), residues: 295 loop : -1.58 (0.26), residues: 558 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3240 Ramachandran restraints generated. 1620 Oldfield, 0 Emsley, 1620 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3240 Ramachandran restraints generated. 1620 Oldfield, 0 Emsley, 1620 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 129 residues out of total 1370 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 111 time to evaluate : 1.548 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 18 outliers final: 9 residues processed: 125 average time/residue: 0.2578 time to fit residues: 49.0894 Evaluate side-chains 115 residues out of total 1370 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 106 time to evaluate : 1.757 Switching outliers to nearest non-outliers revert: symmetry clash outliers start: 9 outliers final: 1 residues processed: 9 average time/residue: 0.1427 time to fit residues: 4.2882 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 162 random chunks: chunk 96 optimal weight: 10.0000 chunk 62 optimal weight: 0.6980 chunk 93 optimal weight: 5.9990 chunk 47 optimal weight: 0.9980 chunk 30 optimal weight: 0.9980 chunk 99 optimal weight: 0.7980 chunk 106 optimal weight: 0.6980 chunk 77 optimal weight: 1.9990 chunk 14 optimal weight: 1.9990 chunk 122 optimal weight: 2.9990 chunk 142 optimal weight: 0.5980 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 84 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 183 ASN ** A 270 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1130 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1153 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 102 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7257 moved from start: 0.3237 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.036 13565 Z= 0.185 Angle : 0.603 15.409 18463 Z= 0.297 Chirality : 0.041 0.277 2152 Planarity : 0.003 0.040 2226 Dihedral : 7.171 65.897 1964 Min Nonbonded Distance : 2.150 Molprobity Statistics. All-atom Clashscore : 9.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.14 % Favored : 95.86 % Rotamer Outliers : 0.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 9.80 % Cis-general : 0.06 % Twisted Proline : 0.00 % Twisted General : 0.06 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.07 (0.21), residues: 1620 helix: 1.38 (0.19), residues: 766 sheet: -0.50 (0.31), residues: 295 loop : -1.50 (0.25), residues: 559 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3240 Ramachandran restraints generated. 1620 Oldfield, 0 Emsley, 1620 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3240 Ramachandran restraints generated. 1620 Oldfield, 0 Emsley, 1620 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 119 residues out of total 1370 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 110 time to evaluate : 1.460 Fit side-chains revert: symmetry clash outliers start: 9 outliers final: 5 residues processed: 117 average time/residue: 0.2625 time to fit residues: 46.5189 Evaluate side-chains 111 residues out of total 1370 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 106 time to evaluate : 1.452 Switching outliers to nearest non-outliers revert: symmetry clash outliers start: 5 outliers final: 1 residues processed: 5 average time/residue: 0.1283 time to fit residues: 3.4557 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 162 random chunks: chunk 149 optimal weight: 0.6980 chunk 136 optimal weight: 2.9990 chunk 145 optimal weight: 0.7980 chunk 87 optimal weight: 0.9980 chunk 63 optimal weight: 4.9990 chunk 114 optimal weight: 20.0000 chunk 44 optimal weight: 3.9990 chunk 131 optimal weight: 0.8980 chunk 137 optimal weight: 0.7980 chunk 144 optimal weight: 0.4980 chunk 95 optimal weight: 9.9990 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 84 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 270 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1130 ASN ** A1153 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 6 GLN ** C 102 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7254 moved from start: 0.3364 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.036 13565 Z= 0.185 Angle : 0.606 15.573 18463 Z= 0.297 Chirality : 0.041 0.295 2152 Planarity : 0.003 0.040 2226 Dihedral : 7.083 66.382 1964 Min Nonbonded Distance : 2.154 Molprobity Statistics. All-atom Clashscore : 9.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.51 % Favored : 95.49 % Rotamer Outliers : 0.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 9.80 % Cis-general : 0.06 % Twisted Proline : 0.00 % Twisted General : 0.06 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.15 (0.21), residues: 1620 helix: 1.44 (0.19), residues: 765 sheet: -0.46 (0.31), residues: 295 loop : -1.43 (0.26), residues: 560 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3240 Ramachandran restraints generated. 1620 Oldfield, 0 Emsley, 1620 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3240 Ramachandran restraints generated. 1620 Oldfield, 0 Emsley, 1620 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 120 residues out of total 1370 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 112 time to evaluate : 1.382 Fit side-chains revert: symmetry clash outliers start: 8 outliers final: 5 residues processed: 118 average time/residue: 0.2503 time to fit residues: 45.5052 Evaluate side-chains 108 residues out of total 1370 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 103 time to evaluate : 1.558 Switching outliers to nearest non-outliers revert: symmetry clash outliers start: 5 outliers final: 1 residues processed: 5 average time/residue: 0.1271 time to fit residues: 3.0462 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 162 random chunks: chunk 153 optimal weight: 0.0170 chunk 93 optimal weight: 0.6980 chunk 72 optimal weight: 6.9990 chunk 106 optimal weight: 3.9990 chunk 161 optimal weight: 2.9990 chunk 148 optimal weight: 0.5980 chunk 128 optimal weight: 0.8980 chunk 13 optimal weight: 0.3980 chunk 99 optimal weight: 0.7980 chunk 78 optimal weight: 3.9990 chunk 102 optimal weight: 0.0060 overall best weight: 0.3434 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 84 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 270 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 347 GLN A 391 ASN ** A 441 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1153 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 102 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7190 moved from start: 0.3547 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.041 13565 Z= 0.145 Angle : 0.596 18.689 18463 Z= 0.288 Chirality : 0.040 0.301 2152 Planarity : 0.003 0.040 2226 Dihedral : 6.856 66.713 1964 Min Nonbonded Distance : 2.174 Molprobity Statistics. All-atom Clashscore : 8.78 Ramachandran Plot: Outliers : 0.06 % Allowed : 3.52 % Favored : 96.42 % Rotamer Outliers : 0.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 9.80 % Cis-general : 0.06 % Twisted Proline : 0.00 % Twisted General : 0.06 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.34 (0.22), residues: 1620 helix: 1.56 (0.19), residues: 767 sheet: -0.44 (0.32), residues: 298 loop : -1.27 (0.26), residues: 555 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3240 Ramachandran restraints generated. 1620 Oldfield, 0 Emsley, 1620 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3240 Ramachandran restraints generated. 1620 Oldfield, 0 Emsley, 1620 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 111 residues out of total 1370 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 109 time to evaluate : 1.415 Fit side-chains revert: symmetry clash outliers start: 2 outliers final: 1 residues processed: 111 average time/residue: 0.2640 time to fit residues: 44.3813 Evaluate side-chains 103 residues out of total 1370 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 102 time to evaluate : 1.293 Switching outliers to nearest non-outliers revert: symmetry clash outliers start: 1 outliers final: 1 residues processed: 1 average time/residue: 0.1160 time to fit residues: 2.0701 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 162 random chunks: chunk 136 optimal weight: 0.9990 chunk 39 optimal weight: 4.9990 chunk 118 optimal weight: 0.0070 chunk 18 optimal weight: 0.7980 chunk 35 optimal weight: 0.0170 chunk 128 optimal weight: 0.7980 chunk 53 optimal weight: 0.0050 chunk 132 optimal weight: 0.8980 chunk 16 optimal weight: 0.9990 chunk 23 optimal weight: 7.9990 chunk 113 optimal weight: 3.9990 overall best weight: 0.3250 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 84 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 270 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1153 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 102 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4586 r_free = 0.4586 target = 0.218300 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 24)----------------| | r_work = 0.4350 r_free = 0.4350 target = 0.193228 restraints weight = 27848.435| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.4301 r_free = 0.4301 target = 0.192267 restraints weight = 46262.183| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.4268 r_free = 0.4268 target = 0.189106 restraints weight = 19237.767| |-----------------------------------------------------------------------------| r_work (final): 0.4285 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.4586 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.4586 r_free = 0.4586 target_work(ls_wunit_k1) = 0.218 | | occupancies: max = 1.00 min = 0.47 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.4586 r_free = 0.4586 target_work(ls_wunit_k1) = 0.218 | | occupancies: max = 1.00 min = 0.47 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.4586 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7206 moved from start: 0.3679 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.041 13565 Z= 0.138 Angle : 0.573 18.645 18463 Z= 0.279 Chirality : 0.040 0.310 2152 Planarity : 0.003 0.040 2226 Dihedral : 6.690 67.907 1964 Min Nonbonded Distance : 2.191 Molprobity Statistics. All-atom Clashscore : 8.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.58 % Favored : 96.42 % Rotamer Outliers : 0.66 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 9.80 % Cis-general : 0.06 % Twisted Proline : 0.00 % Twisted General : 0.06 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.52 (0.22), residues: 1620 helix: 1.71 (0.19), residues: 768 sheet: -0.34 (0.32), residues: 298 loop : -1.19 (0.26), residues: 554 =============================================================================== Job complete usr+sys time: 2330.24 seconds wall clock time: 50 minutes 20.97 seconds (3020.97 seconds total)