Starting phenix.real_space_refine on Fri Dec 15 06:54:08 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8f1i_28797/12_2023/8f1i_28797.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8f1i_28797/12_2023/8f1i_28797.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.0 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8f1i_28797/12_2023/8f1i_28797.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8f1i_28797/12_2023/8f1i_28797.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8f1i_28797/12_2023/8f1i_28797.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8f1i_28797/12_2023/8f1i_28797.pdb" } resolution = 3.0 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.006 sd= 1.056 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 7 Type Number sf(0) Gaussians Zn 2 6.06 5 P 91 5.49 5 Mg 1 5.21 5 S 119 5.16 5 C 18953 2.51 5 N 5402 2.21 5 O 6102 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "G GLU 72": "OE1" <-> "OE2" Residue "G GLU 226": "OE1" <-> "OE2" Residue "H GLU 67": "OE1" <-> "OE2" Residue "I ASP 158": "OD1" <-> "OD2" Residue "I TYR 172": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I ASP 189": "OD1" <-> "OD2" Residue "I ASP 434": "OD1" <-> "OD2" Residue "I ASP 596": "OD1" <-> "OD2" Residue "I ASP 648": "OD1" <-> "OD2" Residue "I TYR 652": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I ASP 696": "OD1" <-> "OD2" Residue "I PHE 804": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I ASP 814": "OD1" <-> "OD2" Residue "I GLU 867": "OE1" <-> "OE2" Residue "I GLU 908": "OE1" <-> "OE2" Residue "I GLU 962": "OE1" <-> "OE2" Residue "I GLU 1020": "OE1" <-> "OE2" Residue "I GLU 1024": "OE1" <-> "OE2" Residue "I ASP 1041": "OD1" <-> "OD2" Residue "I TYR 1053": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I ASP 1310": "OD1" <-> "OD2" Residue "J GLU 15": "OE1" <-> "OE2" Residue "J ASP 18": "OD1" <-> "OD2" Residue "J GLU 52": "OE1" <-> "OE2" Residue "J GLU 199": "OE1" <-> "OE2" Residue "J GLU 203": "OE1" <-> "OE2" Residue "J GLU 225": "OE1" <-> "OE2" Residue "J GLU 375": "OE1" <-> "OE2" Residue "J PHE 377": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J PHE 437": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J ASP 505": "OD1" <-> "OD2" Residue "J GLU 534": "OE1" <-> "OE2" Residue "J TYR 609": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J ASP 802": "OD1" <-> "OD2" Residue "J PHE 892": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J TYR 1302": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J GLU 1334": "OE1" <-> "OE2" Residue "M ASP 149": "OD1" <-> "OD2" Residue "M GLU 150": "OE1" <-> "OE2" Residue "M GLU 168": "OE1" <-> "OE2" Residue "M GLU 169": "OE1" <-> "OE2" Residue "M ASP 194": "OD1" <-> "OD2" Residue "M PHE 206": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "M GLU 214": "OE1" <-> "OE2" Residue "M TYR 271": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "M PHE 318": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "M GLU 398": "OE1" <-> "OE2" Residue "M GLU 448": "OE1" <-> "OE2" Time to flip residues: 0.10s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/modules/chem_data/mon_lib" Total number of atoms: 30670 Number of models: 1 Model: "" Number of chains: 14 Chain: "A" Number of atoms: 679 Number of conformers: 1 Conformer: "" Number of residues, atoms: 33, 679 Classifications: {'DNA': 33} Link IDs: {'rna3p': 32} Chain: "C" Number of atoms: 250 Number of conformers: 1 Conformer: "" Number of residues, atoms: 12, 250 Classifications: {'DNA': 12} Link IDs: {'rna3p': 11} Chain: "G" Number of atoms: 1718 Number of conformers: 1 Conformer: "" Number of residues, atoms: 223, 1718 Classifications: {'peptide': 223} Link IDs: {'PCIS': 1, 'PTRANS': 8, 'TRANS': 213} Chain breaks: 1 Chain: "H" Number of atoms: 2282 Number of conformers: 1 Conformer: "" Number of residues, atoms: 295, 2282 Classifications: {'peptide': 295} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PCIS': 1, 'PTRANS': 12, 'TRANS': 281} Chain breaks: 2 Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 3 Unresolved non-hydrogen dihedrals: 1 Unresolved non-hydrogen chiralities: 1 Chain: "I" Number of atoms: 10450 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1327, 10450 Classifications: {'peptide': 1327} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PCIS': 1, 'PTRANS': 55, 'TRANS': 1270} Chain breaks: 1 Unresolved non-hydrogen bonds: 7 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 1 Chain: "J" Number of atoms: 10498 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1349, 10498 Classifications: {'peptide': 1349} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PCIS': 1, 'PTRANS': 54, 'TRANS': 1293} Chain breaks: 2 Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 5 Unresolved non-hydrogen dihedrals: 3 Planarities with less than four sites: {'GLU:plan': 1} Unresolved non-hydrogen planarities: 4 Chain: "K" Number of atoms: 627 Number of conformers: 1 Conformer: "" Number of residues, atoms: 79, 627 Classifications: {'peptide': 79} Link IDs: {'PTRANS': 2, 'TRANS': 76} Chain: "M" Number of atoms: 3222 Number of conformers: 1 Conformer: "" Number of residues, atoms: 405, 3222 Classifications: {'peptide': 405} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PCIS': 1, 'PTRANS': 16, 'TRANS': 387} Chain breaks: 1 Unresolved non-hydrogen bonds: 9 Unresolved non-hydrogen angles: 11 Unresolved non-hydrogen dihedrals: 7 Planarities with less than four sites: {'ARG:plan': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 8 Chain: "B" Number of atoms: 671 Number of conformers: 1 Conformer: "" Number of residues, atoms: 33, 671 Classifications: {'DNA': 33} Link IDs: {'rna3p': 32} Chain: "D" Number of atoms: 262 Number of conformers: 1 Conformer: "" Number of residues, atoms: 13, 262 Classifications: {'DNA': 13} Link IDs: {'rna3p': 12} Chain: "J" 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: "A" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Classifications: {'water': 2} Link IDs: {None: 1} Chain: "M" Number of atoms: 5 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 5 Classifications: {'water': 5} Link IDs: {None: 4} Chain: "B" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Classifications: {'water': 1} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 15935 SG CYS J 70 46.409 121.167 79.332 1.00 53.39 S ATOM 15949 SG CYS J 72 47.500 124.806 78.997 1.00 64.74 S ATOM 16057 SG CYS J 85 44.299 123.580 77.275 1.00 77.40 S ATOM 16081 SG CYS J 88 47.810 122.223 76.210 1.00 64.45 S ATOM 21769 SG CYS J 814 36.188 53.884 76.523 1.00 75.93 S ATOM 22334 SG CYS J 888 39.144 56.335 76.304 1.00 50.81 S ATOM 22385 SG CYS J 895 37.583 55.458 79.676 1.00 54.52 S ATOM 22406 SG CYS J 898 39.609 52.900 77.892 1.00 71.63 S Time building chain proxies: 16.68, per 1000 atoms: 0.54 Number of scatterers: 30670 At special positions: 0 Unit cell: (151.62, 174.363, 165.699, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 7 Type Number sf(0) Zn 2 29.99 S 119 16.00 P 91 15.00 Mg 1 11.99 O 6102 8.00 N 5402 7.00 C 18953 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 12.18 Conformation dependent library (CDL) restraints added in 5.8 seconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN J1502 " pdb="ZN ZN J1502 " - pdb=" SG CYS J 70 " pdb="ZN ZN J1502 " - pdb=" SG CYS J 88 " pdb="ZN ZN J1502 " - pdb=" SG CYS J 72 " pdb="ZN ZN J1502 " - pdb=" SG CYS J 85 " pdb=" ZN J1503 " pdb="ZN ZN J1503 " - pdb=" SG CYS J 895 " pdb="ZN ZN J1503 " - pdb=" SG CYS J 898 " pdb="ZN ZN J1503 " - pdb=" SG CYS J 888 " pdb="ZN ZN J1503 " - pdb=" SG CYS J 814 " Number of angles added : 12 7304 Ramachandran restraints generated. 3652 Oldfield, 0 Emsley, 3652 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 6830 Finding SS restraints... Secondary structure from input PDB file: 132 helices and 49 sheets defined 40.0% alpha, 14.8% beta 42 base pairs and 75 stacking pairs defined. Time for finding SS restraints: 10.39 Creating SS restraints... Processing helix chain 'G' and resid 34 through 50 removed outlier: 3.610A pdb=" N ASN G 41 " --> pdb=" O HIS G 37 " (cutoff:3.500A) removed outlier: 3.893A pdb=" N ALA G 42 " --> pdb=" O THR G 38 " (cutoff:3.500A) Processing helix chain 'G' and resid 77 through 87 removed outlier: 3.998A pdb=" N GLY G 87 " --> pdb=" O LEU G 83 " (cutoff:3.500A) Processing helix chain 'G' and resid 113 through 115 No H-bonds generated for 'chain 'G' and resid 113 through 115' Processing helix chain 'G' and resid 212 through 234 removed outlier: 4.651A pdb=" N ALA G 230 " --> pdb=" O GLU G 226 " (cutoff:3.500A) removed outlier: 4.999A pdb=" N PHE G 231 " --> pdb=" O GLN G 227 " (cutoff:3.500A) removed outlier: 3.772A pdb=" N VAL G 232 " --> pdb=" O LEU G 228 " (cutoff:3.500A) removed outlier: 4.140A pdb=" N ASP G 233 " --> pdb=" O GLU G 229 " (cutoff:3.500A) removed outlier: 3.925A pdb=" N LEU G 234 " --> pdb=" O ALA G 230 " (cutoff:3.500A) Processing helix chain 'H' and resid 34 through 50 removed outlier: 3.586A pdb=" N THR H 38 " --> pdb=" O GLY H 34 " (cutoff:3.500A) Processing helix chain 'H' and resid 77 through 87 Processing helix chain 'H' and resid 113 through 115 No H-bonds generated for 'chain 'H' and resid 113 through 115' Processing helix chain 'H' and resid 212 through 227 Processing helix chain 'H' and resid 250 through 255 removed outlier: 3.630A pdb=" N LEU H 254 " --> pdb=" O ASP H 250 " (cutoff:3.500A) Processing helix chain 'H' and resid 256 through 260 Processing helix chain 'H' and resid 263 through 273 Processing helix chain 'H' and resid 277 through 284 removed outlier: 3.694A pdb=" N GLN H 283 " --> pdb=" O GLY H 279 " (cutoff:3.500A) removed outlier: 3.808A pdb=" N ARG H 284 " --> pdb=" O ASP H 280 " (cutoff:3.500A) Processing helix chain 'H' and resid 285 through 291 Processing helix chain 'H' and resid 296 through 309 Processing helix chain 'I' and resid 6 through 10 Processing helix chain 'I' and resid 28 through 40 removed outlier: 3.740A pdb=" N LEU I 32 " --> pdb=" O LEU I 28 " (cutoff:3.500A) removed outlier: 3.566A pdb=" N LYS I 37 " --> pdb=" O ASP I 33 " (cutoff:3.500A) removed outlier: 3.582A pdb=" N PHE I 38 " --> pdb=" O SER I 34 " (cutoff:3.500A) Processing helix chain 'I' and resid 48 through 55 Processing helix chain 'I' and resid 81 through 89 Processing helix chain 'I' and resid 206 through 213 removed outlier: 4.055A pdb=" N LEU I 210 " --> pdb=" O ALA I 206 " (cutoff:3.500A) Processing helix chain 'I' and resid 216 through 225 Processing helix chain 'I' and resid 242 through 247 removed outlier: 3.536A pdb=" N LEU I 246 " --> pdb=" O PRO I 243 " (cutoff:3.500A) Processing helix chain 'I' and resid 270 through 281 Processing helix chain 'I' and resid 288 through 294 removed outlier: 4.453A pdb=" N GLY I 294 " --> pdb=" O TYR I 291 " (cutoff:3.500A) Processing helix chain 'I' and resid 318 through 328 removed outlier: 3.834A pdb=" N SER I 328 " --> pdb=" O LYS I 324 " (cutoff:3.500A) Processing helix chain 'I' and resid 346 through 354 removed outlier: 3.568A pdb=" N ARG I 352 " --> pdb=" O SER I 348 " (cutoff:3.500A) removed outlier: 3.686A pdb=" N VAL I 353 " --> pdb=" O GLU I 349 " (cutoff:3.500A) Processing helix chain 'I' and resid 360 through 371 removed outlier: 3.540A pdb=" N VAL I 364 " --> pdb=" O LEU I 360 " (cutoff:3.500A) Processing helix chain 'I' and resid 377 through 390 removed outlier: 4.017A pdb=" N PHE I 389 " --> pdb=" O PHE I 385 " (cutoff:3.500A) Processing helix chain 'I' and resid 398 through 409 Processing helix chain 'I' and resid 421 through 438 Processing helix chain 'I' and resid 455 through 480 removed outlier: 3.735A pdb=" N ARG I 470 " --> pdb=" O VAL I 466 " (cutoff:3.500A) removed outlier: 3.746A pdb=" N SER I 480 " --> pdb=" O LYS I 476 " (cutoff:3.500A) Processing helix chain 'I' and resid 488 through 493 removed outlier: 3.817A pdb=" N MET I 492 " --> pdb=" O MET I 488 " (cutoff:3.500A) removed outlier: 3.894A pdb=" N ILE I 493 " --> pdb=" O PRO I 489 " (cutoff:3.500A) No H-bonds generated for 'chain 'I' and resid 488 through 493' Processing helix chain 'I' and resid 495 through 508 Processing helix chain 'I' and resid 519 through 527 removed outlier: 3.662A pdb=" N GLU I 523 " --> pdb=" O ASN I 519 " (cutoff:3.500A) Processing helix chain 'I' and resid 551 through 555 removed outlier: 3.878A pdb=" N TYR I 555 " --> pdb=" O PRO I 552 " (cutoff:3.500A) Processing helix chain 'I' and resid 608 through 612 removed outlier: 3.761A pdb=" N GLY I 612 " --> pdb=" O ALA I 608 " (cutoff:3.500A) No H-bonds generated for 'chain 'I' and resid 608 through 612' Processing helix chain 'I' and resid 663 through 667 removed outlier: 3.690A pdb=" N LEU I 667 " --> pdb=" O GLY I 664 " (cutoff:3.500A) Processing helix chain 'I' and resid 670 through 674 Processing helix chain 'I' and resid 675 through 686 removed outlier: 3.614A pdb=" N LEU I 680 " --> pdb=" O ALA I 676 " (cutoff:3.500A) removed outlier: 3.671A pdb=" N MET I 681 " --> pdb=" O ASN I 677 " (cutoff:3.500A) Processing helix chain 'I' and resid 704 through 712 Processing helix chain 'I' and resid 738 through 741 removed outlier: 3.900A pdb=" N MET I 741 " --> pdb=" O GLU I 738 " (cutoff:3.500A) No H-bonds generated for 'chain 'I' and resid 738 through 741' Processing helix chain 'I' and resid 820 through 825 Processing helix chain 'I' and resid 896 through 907 removed outlier: 3.608A pdb=" N PHE I 906 " --> pdb=" O LEU I 902 " (cutoff:3.500A) Processing helix chain 'I' and resid 942 through 982 removed outlier: 3.532A pdb=" N GLU I 949 " --> pdb=" O ALA I 945 " (cutoff:3.500A) removed outlier: 4.048A pdb=" N GLN I 955 " --> pdb=" O MET I 951 " (cutoff:3.500A) removed outlier: 4.040A pdb=" N ALA I 956 " --> pdb=" O GLN I 952 " (cutoff:3.500A) removed outlier: 3.526A pdb=" N LYS I 957 " --> pdb=" O LEU I 953 " (cutoff:3.500A) removed outlier: 3.709A pdb=" N LYS I 958 " --> pdb=" O LYS I 954 " (cutoff:3.500A) Processing helix chain 'I' and resid 987 through 992 removed outlier: 3.692A pdb=" N LYS I 991 " --> pdb=" O GLU I 987 " (cutoff:3.500A) Processing helix chain 'I' and resid 1011 through 1037 removed outlier: 3.646A pdb=" N TYR I1018 " --> pdb=" O LEU I1014 " (cutoff:3.500A) removed outlier: 3.526A pdb=" N ASP I1019 " --> pdb=" O ALA I1015 " (cutoff:3.500A) removed outlier: 3.772A pdb=" N LEU I1029 " --> pdb=" O PHE I1025 " (cutoff:3.500A) removed outlier: 3.610A pdb=" N LYS I1035 " --> pdb=" O ALA I1031 " (cutoff:3.500A) Processing helix chain 'I' and resid 1081 through 1085 Processing helix chain 'I' and resid 1099 through 1101 No H-bonds generated for 'chain 'I' and resid 1099 through 1101' Processing helix chain 'I' and resid 1102 through 1107 removed outlier: 3.539A pdb=" N ARG I1106 " --> pdb=" O GLY I1102 " (cutoff:3.500A) Processing helix chain 'I' and resid 1109 through 1134 removed outlier: 3.532A pdb=" N ILE I1124 " --> pdb=" O ALA I1120 " (cutoff:3.500A) removed outlier: 3.577A pdb=" N LYS I1127 " --> pdb=" O GLY I1123 " (cutoff:3.500A) removed outlier: 3.727A pdb=" N GLN I1134 " --> pdb=" O ALA I1130 " (cutoff:3.500A) Processing helix chain 'I' and resid 1137 through 1151 removed outlier: 3.515A pdb=" N LEU I1151 " --> pdb=" O ARG I1147 " (cutoff:3.500A) Processing helix chain 'I' and resid 1160 through 1164 removed outlier: 3.928A pdb=" N THR I1163 " --> pdb=" O ASP I1160 " (cutoff:3.500A) Processing helix chain 'I' and resid 1165 through 1176 Processing helix chain 'I' and resid 1191 through 1202 removed outlier: 3.578A pdb=" N LYS I1196 " --> pdb=" O GLU I1192 " (cutoff:3.500A) removed outlier: 3.770A pdb=" N GLU I1197 " --> pdb=" O ALA I1193 " (cutoff:3.500A) Processing helix chain 'I' and resid 1271 through 1282 Processing helix chain 'I' and resid 1283 through 1290 removed outlier: 3.537A pdb=" N LEU I1287 " --> pdb=" O ALA I1283 " (cutoff:3.500A) removed outlier: 3.569A pdb=" N MET I1290 " --> pdb=" O THR I1286 " (cutoff:3.500A) Processing helix chain 'I' and resid 1297 through 1310 removed outlier: 4.133A pdb=" N THR I1302 " --> pdb=" O VAL I1298 " (cutoff:3.500A) removed outlier: 3.830A pdb=" N LYS I1303 " --> pdb=" O ASN I1299 " (cutoff:3.500A) Processing helix chain 'I' and resid 1320 through 1331 removed outlier: 4.238A pdb=" N ASN I1324 " --> pdb=" O PRO I1320 " (cutoff:3.500A) removed outlier: 3.766A pdb=" N VAL I1325 " --> pdb=" O GLU I1321 " (cutoff:3.500A) removed outlier: 3.530A pdb=" N LEU I1326 " --> pdb=" O SER I1322 " (cutoff:3.500A) Processing helix chain 'J' and resid 4 through 10 Processing helix chain 'J' and resid 26 through 33 Processing helix chain 'J' and resid 58 through 63 removed outlier: 3.808A pdb=" N PHE J 62 " --> pdb=" O CYS J 58 " (cutoff:3.500A) Processing helix chain 'J' and resid 77 through 81 Processing helix chain 'J' and resid 94 through 100 removed outlier: 3.682A pdb=" N VAL J 97 " --> pdb=" O GLN J 94 " (cutoff:3.500A) removed outlier: 3.598A pdb=" N ARG J 98 " --> pdb=" O THR J 95 " (cutoff:3.500A) Processing helix chain 'J' and resid 114 through 119 removed outlier: 3.677A pdb=" N SER J 119 " --> pdb=" O TRP J 115 " (cutoff:3.500A) Processing helix chain 'J' and resid 122 through 129 Processing helix chain 'J' and resid 131 through 140 Processing helix chain 'J' and resid 161 through 172 Processing helix chain 'J' and resid 181 through 191 removed outlier: 3.606A pdb=" N ILE J 185 " --> pdb=" O GLY J 181 " (cutoff:3.500A) Processing helix chain 'J' and resid 193 through 208 removed outlier: 3.607A pdb=" N GLU J 197 " --> pdb=" O ASP J 193 " (cutoff:3.500A) removed outlier: 3.533A pdb=" N THR J 208 " --> pdb=" O GLU J 204 " (cutoff:3.500A) Processing helix chain 'J' and resid 211 through 230 removed outlier: 3.523A pdb=" N ARG J 220 " --> pdb=" O LYS J 216 " (cutoff:3.500A) removed outlier: 3.999A pdb=" N LEU J 223 " --> pdb=" O LYS J 219 " (cutoff:3.500A) Processing helix chain 'J' and resid 233 through 236 Processing helix chain 'J' and resid 246 through 250 Processing helix chain 'J' and resid 263 through 286 Processing helix chain 'J' and resid 288 through 308 Processing helix chain 'J' and resid 326 through 332 Processing helix chain 'J' and resid 336 through 342 removed outlier: 3.691A pdb=" N LEU J 342 " --> pdb=" O PHE J 338 " (cutoff:3.500A) Processing helix chain 'J' and resid 372 through 377 Processing helix chain 'J' and resid 377 through 388 removed outlier: 3.565A pdb=" N ARG J 388 " --> pdb=" O LYS J 384 " (cutoff:3.500A) Processing helix chain 'J' and resid 393 through 404 Processing helix chain 'J' and resid 407 through 416 Processing helix chain 'J' and resid 430 through 432 No H-bonds generated for 'chain 'J' and resid 430 through 432' Processing helix chain 'J' and resid 450 through 452 No H-bonds generated for 'chain 'J' and resid 450 through 452' Processing helix chain 'J' and resid 453 through 458 removed outlier: 3.546A pdb=" N TYR J 457 " --> pdb=" O VAL J 453 " (cutoff:3.500A) Processing helix chain 'J' and resid 475 through 483 removed outlier: 3.515A pdb=" N ARG J 481 " --> pdb=" O GLN J 477 " (cutoff:3.500A) Processing helix chain 'J' and resid 504 through 514 removed outlier: 3.757A pdb=" N GLY J 509 " --> pdb=" O ASP J 505 " (cutoff:3.500A) removed outlier: 3.606A pdb=" N LEU J 510 " --> pdb=" O VAL J 506 " (cutoff:3.500A) Processing helix chain 'J' and resid 529 through 539 Processing helix chain 'J' and resid 574 through 581 removed outlier: 3.772A pdb=" N MET J 581 " --> pdb=" O ALA J 577 " (cutoff:3.500A) Processing helix chain 'J' and resid 588 through 592 Processing helix chain 'J' and resid 598 through 612 removed outlier: 3.519A pdb=" N SER J 602 " --> pdb=" O LYS J 598 " (cutoff:3.500A) removed outlier: 3.926A pdb=" N MET J 604 " --> pdb=" O ALA J 600 " (cutoff:3.500A) Processing helix chain 'J' and resid 614 through 636 removed outlier: 3.884A pdb=" N GLY J 636 " --> pdb=" O ALA J 632 " (cutoff:3.500A) Processing helix chain 'J' and resid 649 through 670 Processing helix chain 'J' and resid 674 through 702 Processing helix chain 'J' and resid 720 through 728 Processing helix chain 'J' and resid 733 through 742 removed outlier: 3.579A pdb=" N ILE J 737 " --> pdb=" O SER J 733 " (cutoff:3.500A) Processing helix chain 'J' and resid 774 through 804 removed outlier: 5.351A pdb=" N ALA J 791 " --> pdb=" O ALA J 787 " (cutoff:3.500A) removed outlier: 4.445A pdb=" N ASN J 792 " --> pdb=" O LEU J 788 " (cutoff:3.500A) removed outlier: 3.643A pdb=" N SER J 793 " --> pdb=" O LYS J 789 " (cutoff:3.500A) removed outlier: 3.780A pdb=" N GLY J 794 " --> pdb=" O THR J 790 " (cutoff:3.500A) Processing helix chain 'J' and resid 865 through 875 Processing helix chain 'J' and resid 896 through 900 removed outlier: 3.868A pdb=" N GLY J 900 " --> pdb=" O ALA J 896 " (cutoff:3.500A) No H-bonds generated for 'chain 'J' and resid 896 through 900' Processing helix chain 'J' and resid 914 through 925 removed outlier: 3.814A pdb=" N ILE J 918 " --> pdb=" O ALA J 914 " (cutoff:3.500A) Processing helix chain 'J' and resid 926 through 930 removed outlier: 3.761A pdb=" N LEU J 930 " --> pdb=" O GLY J 927 " (cutoff:3.500A) Processing helix chain 'J' and resid 1137 through 1145 removed outlier: 3.610A pdb=" N VAL J1141 " --> pdb=" O GLY J1137 " (cutoff:3.500A) Processing helix chain 'J' and resid 1216 through 1225 Processing helix chain 'J' and resid 1228 through 1243 removed outlier: 4.090A pdb=" N VAL J1234 " --> pdb=" O THR J1230 " (cutoff:3.500A) removed outlier: 3.568A pdb=" N GLN J1238 " --> pdb=" O VAL J1234 " (cutoff:3.500A) removed outlier: 3.742A pdb=" N VAL J1240 " --> pdb=" O GLU J1236 " (cutoff:3.500A) removed outlier: 3.603A pdb=" N LEU J1243 " --> pdb=" O ASP J1239 " (cutoff:3.500A) Processing helix chain 'J' and resid 1250 through 1261 removed outlier: 3.787A pdb=" N ILE J1256 " --> pdb=" O HIS J1252 " (cutoff:3.500A) Processing helix chain 'J' and resid 1282 through 1294 removed outlier: 3.559A pdb=" N LEU J1292 " --> pdb=" O ALA J1288 " (cutoff:3.500A) Processing helix chain 'J' and resid 1319 through 1324 removed outlier: 3.594A pdb=" N SER J1324 " --> pdb=" O ILE J1320 " (cutoff:3.500A) Processing helix chain 'J' and resid 1327 through 1337 removed outlier: 3.775A pdb=" N GLU J1334 " --> pdb=" O ARG J1330 " (cutoff:3.500A) Processing helix chain 'J' and resid 1348 through 1354 Processing helix chain 'J' and resid 1362 through 1373 Processing helix chain 'K' and resid 6 through 14 Processing helix chain 'K' and resid 15 through 32 removed outlier: 4.085A pdb=" N VAL K 20 " --> pdb=" O ARG K 16 " (cutoff:3.500A) removed outlier: 3.843A pdb=" N LEU K 21 " --> pdb=" O PHE K 17 " (cutoff:3.500A) Processing helix chain 'K' and resid 45 through 56 removed outlier: 3.625A pdb=" N GLU K 56 " --> pdb=" O ARG K 52 " (cutoff:3.500A) Processing helix chain 'K' and resid 60 through 80 Processing helix chain 'M' and resid 18 through 25 removed outlier: 3.638A pdb=" N ALA M 22 " --> pdb=" O GLN M 18 " (cutoff:3.500A) Processing helix chain 'M' and resid 29 through 43 removed outlier: 3.910A pdb=" N GLN M 39 " --> pdb=" O GLN M 35 " (cutoff:3.500A) removed outlier: 3.526A pdb=" N ALA M 40 " --> pdb=" O GLU M 36 " (cutoff:3.500A) Processing helix chain 'M' and resid 119 through 129 Processing helix chain 'M' and resid 134 through 147 Processing helix chain 'M' and resid 157 through 166 removed outlier: 4.008A pdb=" N GLY M 166 " --> pdb=" O LEU M 162 " (cutoff:3.500A) Processing helix chain 'M' and resid 171 through 183 removed outlier: 3.667A pdb=" N VAL M 175 " --> pdb=" O ASP M 171 " (cutoff:3.500A) Processing helix chain 'M' and resid 194 through 206 removed outlier: 3.521A pdb=" N GLN M 205 " --> pdb=" O ILE M 201 " (cutoff:3.500A) removed outlier: 3.731A pdb=" N PHE M 206 " --> pdb=" O GLN M 202 " (cutoff:3.500A) Processing helix chain 'M' and resid 212 through 222 removed outlier: 3.561A pdb=" N ILE M 219 " --> pdb=" O GLU M 215 " (cutoff:3.500A) Processing helix chain 'M' and resid 224 through 229 Processing helix chain 'M' and resid 231 through 240 Processing helix chain 'M' and resid 242 through 255 removed outlier: 3.887A pdb=" N VAL M 250 " --> pdb=" O LEU M 246 " (cutoff:3.500A) Processing helix chain 'M' and resid 259 through 263 removed outlier: 3.604A pdb=" N GLN M 262 " --> pdb=" O ARG M 259 " (cutoff:3.500A) removed outlier: 3.863A pdb=" N SER M 263 " --> pdb=" O PRO M 260 " (cutoff:3.500A) No H-bonds generated for 'chain 'M' and resid 259 through 263' Processing helix chain 'M' and resid 300 through 305 Processing helix chain 'M' and resid 313 through 351 removed outlier: 4.366A pdb=" N ILE M 319 " --> pdb=" O ASP M 315 " (cutoff:3.500A) removed outlier: 3.800A pdb=" N ASP M 325 " --> pdb=" O SER M 321 " (cutoff:3.500A) removed outlier: 3.648A pdb=" N THR M 339 " --> pdb=" O SER M 335 " (cutoff:3.500A) Processing helix chain 'M' and resid 351 through 357 removed outlier: 3.813A pdb=" N PHE M 355 " --> pdb=" O GLN M 351 " (cutoff:3.500A) Processing helix chain 'M' and resid 366 through 371 Processing helix chain 'M' and resid 377 through 385 Processing helix chain 'M' and resid 417 through 429 removed outlier: 3.779A pdb=" N ALA M 422 " --> pdb=" O THR M 418 " (cutoff:3.500A) Processing helix chain 'M' and resid 438 through 447 removed outlier: 3.502A pdb=" N LEU M 445 " --> pdb=" O LYS M 441 " (cutoff:3.500A) Processing helix chain 'M' and resid 454 through 465 Processing helix chain 'M' and resid 469 through 473 Processing sheet with id=AA1, first strand: chain 'G' and resid 12 through 20 removed outlier: 3.517A pdb=" N GLU G 29 " --> pdb=" O ARG G 12 " (cutoff:3.500A) removed outlier: 6.611A pdb=" N THR G 27 " --> pdb=" O VAL G 14 " (cutoff:3.500A) removed outlier: 4.346A pdb=" N ILE G 16 " --> pdb=" O LYS G 25 " (cutoff:3.500A) removed outlier: 6.582A pdb=" N LYS G 25 " --> pdb=" O ILE G 16 " (cutoff:3.500A) removed outlier: 4.951A pdb=" N GLN G 18 " --> pdb=" O HIS G 23 " (cutoff:3.500A) removed outlier: 7.237A pdb=" N HIS G 23 " --> pdb=" O GLN G 18 " (cutoff:3.500A) removed outlier: 5.462A pdb=" N LYS G 25 " --> pdb=" O MET G 205 " (cutoff:3.500A) removed outlier: 7.320A pdb=" N MET G 205 " --> pdb=" O LYS G 25 " (cutoff:3.500A) removed outlier: 5.553A pdb=" N THR G 27 " --> pdb=" O ILE G 203 " (cutoff:3.500A) removed outlier: 7.092A pdb=" N ILE G 203 " --> pdb=" O THR G 27 " (cutoff:3.500A) removed outlier: 5.391A pdb=" N GLU G 29 " --> pdb=" O LEU G 201 " (cutoff:3.500A) removed outlier: 7.601A pdb=" N LEU G 201 " --> pdb=" O GLU G 29 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'G' and resid 97 through 105 removed outlier: 3.775A pdb=" N GLU G 58 " --> pdb=" O LYS G 145 " (cutoff:3.500A) removed outlier: 6.440A pdb=" N GLN G 147 " --> pdb=" O VAL G 56 " (cutoff:3.500A) removed outlier: 5.359A pdb=" N VAL G 56 " --> pdb=" O GLN G 147 " (cutoff:3.500A) removed outlier: 6.795A pdb=" N GLY G 149 " --> pdb=" O CYS G 54 " (cutoff:3.500A) removed outlier: 5.195A pdb=" N CYS G 54 " --> pdb=" O GLY G 149 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'G' and resid 90 through 91 Processing sheet with id=AA4, first strand: chain 'G' and resid 108 through 111 removed outlier: 3.689A pdb=" N CYS G 131 " --> pdb=" O VAL G 110 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'G' and resid 152 through 153 Processing sheet with id=AA6, first strand: chain 'H' and resid 17 through 18 removed outlier: 6.004A pdb=" N ASP H 199 " --> pdb=" O PRO H 30 " (cutoff:3.500A) removed outlier: 3.555A pdb=" N ALA H 190 " --> pdb=" O LEU H 198 " (cutoff:3.500A) removed outlier: 3.591A pdb=" N ARG H 182 " --> pdb=" O GLU H 206 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'H' and resid 97 through 101 removed outlier: 6.719A pdb=" N ARG H 143 " --> pdb=" O VAL H 59 " (cutoff:3.500A) removed outlier: 4.631A pdb=" N VAL H 59 " --> pdb=" O ARG H 143 " (cutoff:3.500A) removed outlier: 7.244A pdb=" N LYS H 145 " --> pdb=" O THR H 57 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'H' and resid 104 through 105 Processing sheet with id=AA9, first strand: chain 'H' and resid 109 through 111 Processing sheet with id=AB1, first strand: chain 'H' and resid 152 through 153 Processing sheet with id=AB2, first strand: chain 'I' and resid 13 through 14 removed outlier: 6.513A pdb=" N LYS I 13 " --> pdb=" O ALA I1183 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB2 Processing sheet with id=AB3, first strand: chain 'I' and resid 59 through 60 removed outlier: 3.668A pdb=" N GLU I 67 " --> pdb=" O VAL I 103 " (cutoff:3.500A) removed outlier: 3.690A pdb=" N ARG I 101 " --> pdb=" O GLN I 69 " (cutoff:3.500A) removed outlier: 6.873A pdb=" N LYS I 99 " --> pdb=" O VAL I 71 " (cutoff:3.500A) removed outlier: 4.640A pdb=" N TYR I 73 " --> pdb=" O ARG I 97 " (cutoff:3.500A) removed outlier: 6.786A pdb=" N ARG I 97 " --> pdb=" O TYR I 73 " (cutoff:3.500A) removed outlier: 4.555A pdb=" N LEU I 75 " --> pdb=" O PRO I 95 " (cutoff:3.500A) removed outlier: 5.949A pdb=" N ALA I 94 " --> pdb=" O GLU I 126 " (cutoff:3.500A) removed outlier: 4.467A pdb=" N GLU I 126 " --> pdb=" O ALA I 94 " (cutoff:3.500A) removed outlier: 5.623A pdb=" N LEU I 96 " --> pdb=" O MET I 124 " (cutoff:3.500A) removed outlier: 3.510A pdb=" N ASP I 116 " --> pdb=" O ILE I 104 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'I' and resid 136 through 137 Processing sheet with id=AB5, first strand: chain 'I' and resid 451 through 454 Processing sheet with id=AB6, first strand: chain 'I' and resid 154 through 155 removed outlier: 3.543A pdb=" N LEU I 184 " --> pdb=" O ILE I 176 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'I' and resid 284 through 286 removed outlier: 3.719A pdb=" N GLU I 240 " --> pdb=" O ILE I 229 " (cutoff:3.500A) removed outlier: 5.550A pdb=" N ILE I 229 " --> pdb=" O GLU I 240 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'I' and resid 255 through 257 removed outlier: 7.348A pdb=" N ILE I 255 " --> pdb=" O TYR I 262 " (cutoff:3.500A) removed outlier: 3.512A pdb=" N TYR I 262 " --> pdb=" O ILE I 255 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'I' and resid 301 through 302 removed outlier: 7.301A pdb=" N TYR I 301 " --> pdb=" O ILE I 310 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'I' and resid 580 through 581 removed outlier: 4.948A pdb=" N GLU I 602 " --> pdb=" O LYS I 593 " (cutoff:3.500A) removed outlier: 7.765A pdb=" N THR I 595 " --> pdb=" O THR I 600 " (cutoff:3.500A) removed outlier: 6.228A pdb=" N THR I 600 " --> pdb=" O THR I 595 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'I' and resid 580 through 581 Processing sheet with id=AC3, first strand: chain 'I' and resid 616 through 617 Processing sheet with id=AC4, first strand: chain 'I' and resid 716 through 717 removed outlier: 6.405A pdb=" N ALA I 716 " --> pdb=" O LEU I 783 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'I' and resid 748 through 752 removed outlier: 6.814A pdb=" N ARG I 731 " --> pdb=" O VAL I 727 " (cutoff:3.500A) removed outlier: 4.743A pdb=" N VAL I 727 " --> pdb=" O ARG I 731 " (cutoff:3.500A) removed outlier: 6.415A pdb=" N VAL I 733 " --> pdb=" O GLN I 725 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'I' and resid 757 through 758 Processing sheet with id=AC7, first strand: chain 'I' and resid 789 through 790 Processing sheet with id=AC8, first strand: chain 'I' and resid 1209 through 1210 removed outlier: 7.393A pdb=" N ILE I 816 " --> pdb=" O SER I1077 " (cutoff:3.500A) removed outlier: 6.521A pdb=" N ILE I1079 " --> pdb=" O ILE I 816 " (cutoff:3.500A) removed outlier: 6.861A pdb=" N VAL I 818 " --> pdb=" O ILE I1079 " (cutoff:3.500A) removed outlier: 3.627A pdb=" N LEU I 817 " --> pdb=" O VAL I1097 " (cutoff:3.500A) removed outlier: 8.494A pdb=" N ILE I1096 " --> pdb=" O ASN I 799 " (cutoff:3.500A) removed outlier: 6.267A pdb=" N ARG I 801 " --> pdb=" O ILE I1096 " (cutoff:3.500A) removed outlier: 7.674A pdb=" N LEU I1098 " --> pdb=" O ARG I 801 " (cutoff:3.500A) removed outlier: 6.157A pdb=" N ALA I 803 " --> pdb=" O LEU I1098 " (cutoff:3.500A) removed outlier: 4.414A pdb=" N THR I1226 " --> pdb=" O PHE I 804 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'I' and resid 830 through 841 removed outlier: 3.870A pdb=" N ASP I 930 " --> pdb=" O TYR I1053 " (cutoff:3.500A) removed outlier: 6.733A pdb=" N ALA I1055 " --> pdb=" O VAL I 928 " (cutoff:3.500A) removed outlier: 5.956A pdb=" N VAL I 928 " --> pdb=" O ALA I1055 " (cutoff:3.500A) removed outlier: 8.423A pdb=" N LYS I1057 " --> pdb=" O GLY I 926 " (cutoff:3.500A) removed outlier: 8.901A pdb=" N GLY I 926 " --> pdb=" O LYS I1057 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'I' and resid 849 through 850 Processing sheet with id=AD2, first strand: chain 'I' and resid 882 through 884 removed outlier: 6.748A pdb=" N LEU I 918 " --> pdb=" O LEU I 883 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'I' and resid 1268 through 1270 removed outlier: 3.748A pdb=" N GLN I1268 " --> pdb=" O VAL J 347 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'I' and resid 1335 through 1340 removed outlier: 3.873A pdb=" N ALA J 19 " --> pdb=" O GLU I1340 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'J' and resid 34 through 37 removed outlier: 7.695A pdb=" N HIS J 104 " --> pdb=" O PHE J 35 " (cutoff:3.500A) removed outlier: 4.403A pdb=" N GLU J 37 " --> pdb=" O HIS J 104 " (cutoff:3.500A) removed outlier: 7.827A pdb=" N GLU J 106 " --> pdb=" O GLU J 37 " (cutoff:3.500A) removed outlier: 10.013A pdb=" N LEU J 107 " --> pdb=" O PRO J 243 " (cutoff:3.500A) removed outlier: 10.455A pdb=" N SER J 109 " --> pdb=" O VAL J 241 " (cutoff:3.500A) removed outlier: 7.053A pdb=" N VAL J 241 " --> pdb=" O SER J 109 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'J' and resid 159 through 160 Processing sheet with id=AD7, first strand: chain 'J' and resid 253 through 255 removed outlier: 3.768A pdb=" N VAL J 253 " --> pdb=" O ALA J 261 " (cutoff:3.500A) removed outlier: 3.572A pdb=" N ALA J 261 " --> pdb=" O VAL J 253 " (cutoff:3.500A) removed outlier: 3.673A pdb=" N ARG J 259 " --> pdb=" O LEU J 255 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'J' and resid 350 through 357 removed outlier: 6.563A pdb=" N CYS J 366 " --> pdb=" O VAL J 440 " (cutoff:3.500A) removed outlier: 6.998A pdb=" N ILE J 442 " --> pdb=" O CYS J 366 " (cutoff:3.500A) removed outlier: 6.231A pdb=" N LEU J 368 " --> pdb=" O ILE J 442 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'J' and resid 547 through 557 Processing sheet with id=AE1, first strand: chain 'J' and resid 703 through 707 Processing sheet with id=AE2, first strand: chain 'J' and resid 809 through 811 Processing sheet with id=AE3, first strand: chain 'J' and resid 820 through 822 removed outlier: 3.676A pdb=" N VAL J 880 " --> pdb=" O MET J 822 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'J' and resid 825 through 826 removed outlier: 7.155A pdb=" N VAL J 825 " --> pdb=" O LYS J 832 " (cutoff:3.500A) Processing sheet with id=AE5, first strand: chain 'J' and resid 949 through 951 removed outlier: 3.921A pdb=" N ALA J1018 " --> pdb=" O ILE J 950 " (cutoff:3.500A) removed outlier: 3.584A pdb=" N LEU J 973 " --> pdb=" O LEU J1003 " (cutoff:3.500A) Processing sheet with id=AE6, first strand: chain 'J' and resid 957 through 961 removed outlier: 3.539A pdb=" N LEU J 984 " --> pdb=" O GLU J 993 " (cutoff:3.500A) removed outlier: 4.086A pdb=" N GLU J 993 " --> pdb=" O LEU J 984 " (cutoff:3.500A) Processing sheet with id=AE7, first strand: chain 'J' and resid 1035 through 1038 removed outlier: 3.530A pdb=" N LYS J1079 " --> pdb=" O ARG J1036 " (cutoff:3.500A) removed outlier: 3.693A pdb=" N THR J1038 " --> pdb=" O ALA J1077 " (cutoff:3.500A) removed outlier: 3.596A pdb=" N ALA J1077 " --> pdb=" O THR J1038 " (cutoff:3.500A) Processing sheet with id=AE8, first strand: chain 'J' and resid 1046 through 1048 removed outlier: 5.118A pdb=" N LEU J1059 " --> pdb=" O VAL J1107 " (cutoff:3.500A) removed outlier: 3.760A pdb=" N VAL J1107 " --> pdb=" O LEU J1059 " (cutoff:3.500A) Processing sheet with id=AE9, first strand: chain 'J' and resid 1187 through 1190 removed outlier: 3.627A pdb=" N GLU J1188 " --> pdb=" O LEU J1175 " (cutoff:3.500A) Processing sheet with id=AF1, first strand: chain 'J' and resid 1279 through 1281 removed outlier: 3.729A pdb=" N VAL J1267 " --> pdb=" O THR J1301 " (cutoff:3.500A) removed outlier: 7.809A pdb=" N THR J1301 " --> pdb=" O VAL J1267 " (cutoff:3.500A) Processing sheet with id=AF2, first strand: chain 'M' and resid 47 through 48 Processing sheet with id=AF3, first strand: chain 'M' and resid 284 through 289 removed outlier: 6.879A pdb=" N VAL M 276 " --> pdb=" O HIS M 391 " (cutoff:3.500A) Processing sheet with id=AF4, first strand: chain 'M' and resid 406 through 408 1131 hydrogen bonds defined for protein. 3180 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 100 hydrogen bonds 200 hydrogen bond angles 0 basepair planarities 42 basepair parallelities 75 stacking parallelities Total time for adding SS restraints: 14.17 Time building geometry restraints manager: 13.18 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.33: 9285 1.33 - 1.45: 4371 1.45 - 1.57: 17264 1.57 - 1.69: 178 1.69 - 1.81: 206 Bond restraints: 31304 Sorted by residual: bond pdb=" C LEU I1201 " pdb=" N GLY I1202 " ideal model delta sigma weight residual 1.332 1.348 -0.016 6.60e-03 2.30e+04 5.81e+00 bond pdb=" C GLU J 925 " pdb=" N PRO J 926 " ideal model delta sigma weight residual 1.334 1.351 -0.017 8.40e-03 1.42e+04 4.33e+00 bond pdb=" N PRO I 345 " pdb=" CA PRO I 345 " ideal model delta sigma weight residual 1.469 1.484 -0.016 1.28e-02 6.10e+03 1.48e+00 bond pdb=" C ASP J1184 " pdb=" N PRO J1185 " ideal model delta sigma weight residual 1.334 1.361 -0.028 2.34e-02 1.83e+03 1.39e+00 bond pdb=" C3' DC A 24 " pdb=" O3' DC A 24 " ideal model delta sigma weight residual 1.422 1.457 -0.035 3.00e-02 1.11e+03 1.36e+00 ... (remaining 31299 not shown) Histogram of bond angle deviations from ideal: 99.62 - 106.50: 1334 106.50 - 113.39: 17227 113.39 - 120.27: 11322 120.27 - 127.15: 12402 127.15 - 134.03: 397 Bond angle restraints: 42682 Sorted by residual: angle pdb=" N VAL I 21 " pdb=" CA VAL I 21 " pdb=" C VAL I 21 " ideal model delta sigma weight residual 113.53 109.48 4.05 9.80e-01 1.04e+00 1.71e+01 angle pdb=" N VAL J1226 " pdb=" CA VAL J1226 " pdb=" C VAL J1226 " ideal model delta sigma weight residual 111.90 108.95 2.95 8.10e-01 1.52e+00 1.33e+01 angle pdb=" C ASP J 902 " pdb=" N LEU J 903 " pdb=" CA LEU J 903 " ideal model delta sigma weight residual 121.54 128.49 -6.95 1.91e+00 2.74e-01 1.33e+01 angle pdb=" N ASN I 235 " pdb=" CA ASN I 235 " pdb=" C ASN I 235 " ideal model delta sigma weight residual 108.46 113.75 -5.29 1.51e+00 4.39e-01 1.23e+01 angle pdb=" N VAL J 253 " pdb=" CA VAL J 253 " pdb=" C VAL J 253 " ideal model delta sigma weight residual 107.56 110.69 -3.13 9.10e-01 1.21e+00 1.19e+01 ... (remaining 42677 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.04: 18465 35.04 - 70.08: 576 70.08 - 105.12: 14 105.12 - 140.16: 0 140.16 - 175.21: 1 Dihedral angle restraints: 19056 sinusoidal: 8466 harmonic: 10590 Sorted by residual: dihedral pdb=" CA ASP J1184 " pdb=" C ASP J1184 " pdb=" N PRO J1185 " pdb=" CA PRO J1185 " ideal model delta harmonic sigma weight residual -180.00 -152.89 -27.11 0 5.00e+00 4.00e-02 2.94e+01 dihedral pdb=" CA LYS I 236 " pdb=" C LYS I 236 " pdb=" N LEU I 237 " pdb=" CA LEU I 237 " ideal model delta harmonic sigma weight residual 180.00 154.89 25.11 0 5.00e+00 4.00e-02 2.52e+01 dihedral pdb=" CA SER I1295 " pdb=" C SER I1295 " pdb=" N ASP I1296 " pdb=" CA ASP I1296 " ideal model delta harmonic sigma weight residual 180.00 -156.41 -23.59 0 5.00e+00 4.00e-02 2.23e+01 ... (remaining 19053 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.031: 3031 0.031 - 0.062: 1286 0.062 - 0.092: 343 0.092 - 0.123: 210 0.123 - 0.154: 24 Chirality restraints: 4894 Sorted by residual: chirality pdb=" CA GLN J 504 " pdb=" N GLN J 504 " pdb=" C GLN J 504 " pdb=" CB GLN J 504 " both_signs ideal model delta sigma weight residual False 2.51 2.36 0.15 2.00e-01 2.50e+01 5.94e-01 chirality pdb=" CA ILE J1090 " pdb=" N ILE J1090 " pdb=" C ILE J1090 " pdb=" CB ILE J1090 " both_signs ideal model delta sigma weight residual False 2.43 2.58 -0.14 2.00e-01 2.50e+01 5.17e-01 chirality pdb=" CA ILE J 434 " pdb=" N ILE J 434 " pdb=" C ILE J 434 " pdb=" CB ILE J 434 " both_signs ideal model delta sigma weight residual False 2.43 2.57 -0.14 2.00e-01 2.50e+01 5.00e-01 ... (remaining 4891 not shown) Planarity restraints: 5264 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C LYS J 850 " 0.030 5.00e-02 4.00e+02 4.59e-02 3.37e+00 pdb=" N PRO J 851 " -0.079 5.00e-02 4.00e+02 pdb=" CA PRO J 851 " 0.023 5.00e-02 4.00e+02 pdb=" CD PRO J 851 " 0.026 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C THR I 896 " 0.029 5.00e-02 4.00e+02 4.41e-02 3.12e+00 pdb=" N PRO I 897 " -0.076 5.00e-02 4.00e+02 pdb=" CA PRO I 897 " 0.023 5.00e-02 4.00e+02 pdb=" CD PRO I 897 " 0.025 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C GLU H 29 " -0.027 5.00e-02 4.00e+02 4.08e-02 2.66e+00 pdb=" N PRO H 30 " 0.071 5.00e-02 4.00e+02 pdb=" CA PRO H 30 " -0.023 5.00e-02 4.00e+02 pdb=" CD PRO H 30 " -0.021 5.00e-02 4.00e+02 ... (remaining 5261 not shown) Histogram of nonbonded interaction distances: 2.17 - 2.72: 1074 2.72 - 3.26: 28799 3.26 - 3.81: 46423 3.81 - 4.35: 60634 4.35 - 4.90: 104191 Nonbonded interactions: 241121 Sorted by model distance: nonbonded pdb=" OD1 ASP J 462 " pdb="MG MG J1501 " model vdw 2.170 2.170 nonbonded pdb=" OG1 THR I 851 " pdb=" OD1 ASP I 853 " model vdw 2.187 2.440 nonbonded pdb=" OD1 ASN J1268 " pdb=" OG1 THR J1301 " model vdw 2.188 2.440 nonbonded pdb=" O GLY G 34 " pdb=" OG1 THR G 38 " model vdw 2.206 2.440 nonbonded pdb=" OH TYR I 179 " pdb=" OE2 GLU I 458 " model vdw 2.219 2.440 ... (remaining 241116 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.780 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 5.200 Check model and map are aligned: 0.480 Set scattering table: 0.280 Process input model: 94.930 Find NCS groups from input model: 1.000 Set up NCS constraints: 0.110 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:10.580 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 113.380 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8233 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 : 0.003 0.035 31304 Z= 0.163 Angle : 0.526 7.032 42682 Z= 0.306 Chirality : 0.041 0.154 4894 Planarity : 0.004 0.046 5264 Dihedral : 14.605 175.205 12226 Min Nonbonded Distance : 2.170 Molprobity Statistics. All-atom Clashscore : 5.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.37 % Favored : 96.63 % Rotamer: Outliers : 0.89 % Allowed : 5.97 % Favored : 93.14 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.31 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.10 (0.14), residues: 3652 helix: 0.02 (0.15), residues: 1353 sheet: -0.32 (0.25), residues: 449 loop : -1.39 (0.13), residues: 1850 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP J 409 HIS 0.004 0.001 HIS J 104 PHE 0.011 0.001 PHE I1164 TYR 0.011 0.001 TYR I 123 ARG 0.004 0.000 ARG J 860 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7304 Ramachandran restraints generated. 3652 Oldfield, 0 Emsley, 3652 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7304 Ramachandran restraints generated. 3652 Oldfield, 0 Emsley, 3652 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 190 residues out of total 3153 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 162 time to evaluate : 3.282 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 28 outliers final: 3 residues processed: 189 average time/residue: 1.7617 time to fit residues: 385.9379 Evaluate side-chains 128 residues out of total 3153 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 125 time to evaluate : 3.498 Switching outliers to nearest non-outliers outliers start: 3 outliers final: 3 residues processed: 0 time to fit residues: 4.9303 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 372 random chunks: chunk 314 optimal weight: 20.0000 chunk 281 optimal weight: 6.9990 chunk 156 optimal weight: 9.9990 chunk 96 optimal weight: 0.5980 chunk 190 optimal weight: 7.9990 chunk 150 optimal weight: 7.9990 chunk 291 optimal weight: 9.9990 chunk 112 optimal weight: 8.9990 chunk 177 optimal weight: 7.9990 chunk 217 optimal weight: 10.0000 chunk 337 optimal weight: 0.8980 overall best weight: 4.8986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** H 137 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 147 GLN ** H 268 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 266 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 72 GLN M 20 GLN M 262 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8335 moved from start: 0.1282 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.050 31304 Z= 0.384 Angle : 0.573 8.662 42682 Z= 0.308 Chirality : 0.043 0.156 4894 Planarity : 0.004 0.044 5264 Dihedral : 15.485 173.393 5020 Min Nonbonded Distance : 2.130 Molprobity Statistics. All-atom Clashscore : 6.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.16 % Favored : 95.84 % Rotamer: Outliers : 1.56 % Allowed : 9.79 % Favored : 88.66 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.31 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.61 (0.14), residues: 3652 helix: 0.63 (0.15), residues: 1370 sheet: -0.18 (0.25), residues: 440 loop : -1.26 (0.14), residues: 1842 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP M 328 HIS 0.005 0.001 HIS I 447 PHE 0.010 0.001 PHE I 405 TYR 0.012 0.001 TYR J 679 ARG 0.010 0.000 ARG I 272 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7304 Ramachandran restraints generated. 3652 Oldfield, 0 Emsley, 3652 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7304 Ramachandran restraints generated. 3652 Oldfield, 0 Emsley, 3652 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 185 residues out of total 3153 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 49 poor density : 136 time to evaluate : 3.654 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 49 outliers final: 11 residues processed: 171 average time/residue: 1.5832 time to fit residues: 318.6066 Evaluate side-chains 137 residues out of total 3153 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 126 time to evaluate : 3.561 Switching outliers to nearest non-outliers outliers start: 11 outliers final: 9 residues processed: 2 average time/residue: 1.2968 time to fit residues: 7.9448 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 372 random chunks: chunk 187 optimal weight: 2.9990 chunk 104 optimal weight: 10.0000 chunk 281 optimal weight: 8.9990 chunk 230 optimal weight: 4.9990 chunk 93 optimal weight: 5.9990 chunk 338 optimal weight: 5.9990 chunk 365 optimal weight: 0.9990 chunk 301 optimal weight: 20.0000 chunk 335 optimal weight: 2.9990 chunk 115 optimal weight: 9.9990 chunk 271 optimal weight: 9.9990 overall best weight: 3.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 103 ASN H 147 GLN ** H 268 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 266 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** M 20 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8328 moved from start: 0.1571 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 31304 Z= 0.283 Angle : 0.525 7.598 42682 Z= 0.281 Chirality : 0.041 0.215 4894 Planarity : 0.004 0.057 5264 Dihedral : 15.450 173.948 5020 Min Nonbonded Distance : 2.135 Molprobity Statistics. All-atom Clashscore : 6.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.50 % Favored : 96.50 % Rotamer: Outliers : 1.72 % Allowed : 10.74 % Favored : 87.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.31 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.32 (0.14), residues: 3652 helix: 0.98 (0.15), residues: 1384 sheet: -0.10 (0.25), residues: 446 loop : -1.20 (0.14), residues: 1822 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP M 328 HIS 0.004 0.001 HIS I 447 PHE 0.021 0.001 PHE J1100 TYR 0.013 0.001 TYR M 112 ARG 0.005 0.000 ARG M 233 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7304 Ramachandran restraints generated. 3652 Oldfield, 0 Emsley, 3652 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7304 Ramachandran restraints generated. 3652 Oldfield, 0 Emsley, 3652 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 192 residues out of total 3153 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 54 poor density : 138 time to evaluate : 3.536 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 54 outliers final: 16 residues processed: 177 average time/residue: 1.5694 time to fit residues: 330.1508 Evaluate side-chains 147 residues out of total 3153 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 131 time to evaluate : 3.342 Switching outliers to nearest non-outliers outliers start: 16 outliers final: 14 residues processed: 2 average time/residue: 0.8447 time to fit residues: 6.7874 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 372 random chunks: chunk 334 optimal weight: 1.9990 chunk 254 optimal weight: 8.9990 chunk 175 optimal weight: 5.9990 chunk 37 optimal weight: 20.0000 chunk 161 optimal weight: 1.9990 chunk 227 optimal weight: 0.0770 chunk 339 optimal weight: 7.9990 chunk 359 optimal weight: 1.9990 chunk 177 optimal weight: 7.9990 chunk 321 optimal weight: 0.4980 chunk 96 optimal weight: 9.9990 overall best weight: 1.3144 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: G 132 HIS H 147 GLN ** H 268 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 266 ASN J 489 ASN M 262 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8283 moved from start: 0.1804 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.034 31304 Z= 0.147 Angle : 0.478 8.047 42682 Z= 0.254 Chirality : 0.040 0.199 4894 Planarity : 0.003 0.044 5264 Dihedral : 15.259 174.080 5020 Min Nonbonded Distance : 2.164 Molprobity Statistics. All-atom Clashscore : 6.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.48 % Favored : 96.52 % Rotamer: Outliers : 1.56 % Allowed : 11.50 % Favored : 86.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.31 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.04 (0.14), residues: 3652 helix: 1.30 (0.15), residues: 1393 sheet: -0.07 (0.25), residues: 461 loop : -1.09 (0.14), residues: 1798 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP J1193 HIS 0.002 0.000 HIS J 865 PHE 0.010 0.001 PHE I 136 TYR 0.012 0.001 TYR J 679 ARG 0.009 0.000 ARG I 272 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7304 Ramachandran restraints generated. 3652 Oldfield, 0 Emsley, 3652 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7304 Ramachandran restraints generated. 3652 Oldfield, 0 Emsley, 3652 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 186 residues out of total 3153 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 49 poor density : 137 time to evaluate : 3.743 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 49 outliers final: 15 residues processed: 176 average time/residue: 1.4717 time to fit residues: 308.6913 Evaluate side-chains 147 residues out of total 3153 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 132 time to evaluate : 3.417 Switching outliers to nearest non-outliers outliers start: 15 outliers final: 13 residues processed: 2 average time/residue: 0.9234 time to fit residues: 7.0137 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 372 random chunks: chunk 299 optimal weight: 0.0070 chunk 204 optimal weight: 3.9990 chunk 5 optimal weight: 0.7980 chunk 267 optimal weight: 0.0370 chunk 148 optimal weight: 9.9990 chunk 306 optimal weight: 6.9990 chunk 248 optimal weight: 6.9990 chunk 0 optimal weight: 8.9990 chunk 183 optimal weight: 9.9990 chunk 322 optimal weight: 9.9990 chunk 90 optimal weight: 0.7980 overall best weight: 1.1278 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 103 ASN H 147 GLN ** H 268 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I1010 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 489 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8272 moved from start: 0.1974 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.035 31304 Z= 0.140 Angle : 0.480 11.679 42682 Z= 0.251 Chirality : 0.040 0.179 4894 Planarity : 0.003 0.048 5264 Dihedral : 15.202 173.994 5020 Min Nonbonded Distance : 2.162 Molprobity Statistics. All-atom Clashscore : 6.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.34 % Favored : 96.66 % Rotamer: Outliers : 1.56 % Allowed : 12.04 % Favored : 86.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.31 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.15 (0.14), residues: 3652 helix: 1.47 (0.15), residues: 1402 sheet: 0.02 (0.25), residues: 458 loop : -1.00 (0.14), residues: 1792 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP J1193 HIS 0.010 0.001 HIS H 66 PHE 0.011 0.001 PHE I 136 TYR 0.022 0.001 TYR I 291 ARG 0.009 0.000 ARG I 272 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7304 Ramachandran restraints generated. 3652 Oldfield, 0 Emsley, 3652 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7304 Ramachandran restraints generated. 3652 Oldfield, 0 Emsley, 3652 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 182 residues out of total 3153 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 49 poor density : 133 time to evaluate : 3.446 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 49 outliers final: 20 residues processed: 173 average time/residue: 1.4831 time to fit residues: 305.2507 Evaluate side-chains 149 residues out of total 3153 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 129 time to evaluate : 3.308 Switching outliers to nearest non-outliers outliers start: 20 outliers final: 18 residues processed: 2 average time/residue: 0.8914 time to fit residues: 6.7361 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 372 random chunks: chunk 120 optimal weight: 0.6980 chunk 323 optimal weight: 5.9990 chunk 71 optimal weight: 20.0000 chunk 211 optimal weight: 1.9990 chunk 88 optimal weight: 9.9990 chunk 359 optimal weight: 5.9990 chunk 298 optimal weight: 0.8980 chunk 166 optimal weight: 6.9990 chunk 29 optimal weight: 0.9980 chunk 119 optimal weight: 9.9990 chunk 188 optimal weight: 3.9990 overall best weight: 1.7184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: G 127 GLN H 147 GLN ** H 268 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 294 ASN I1010 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8284 moved from start: 0.2112 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 31304 Z= 0.168 Angle : 0.488 10.276 42682 Z= 0.256 Chirality : 0.040 0.203 4894 Planarity : 0.003 0.048 5264 Dihedral : 15.215 173.947 5020 Min Nonbonded Distance : 2.173 Molprobity Statistics. All-atom Clashscore : 6.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.53 % Favored : 96.47 % Rotamer: Outliers : 1.68 % Allowed : 12.65 % Favored : 85.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.31 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.26 (0.14), residues: 3652 helix: 1.57 (0.15), residues: 1404 sheet: 0.07 (0.25), residues: 461 loop : -0.95 (0.14), residues: 1787 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP J1193 HIS 0.009 0.001 HIS H 66 PHE 0.008 0.001 PHE I 136 TYR 0.027 0.001 TYR M 112 ARG 0.009 0.000 ARG J1123 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7304 Ramachandran restraints generated. 3652 Oldfield, 0 Emsley, 3652 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7304 Ramachandran restraints generated. 3652 Oldfield, 0 Emsley, 3652 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 184 residues out of total 3153 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 53 poor density : 131 time to evaluate : 3.551 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 53 outliers final: 25 residues processed: 175 average time/residue: 1.4303 time to fit residues: 298.1705 Evaluate side-chains 152 residues out of total 3153 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 127 time to evaluate : 3.472 Switching outliers to nearest non-outliers outliers start: 25 outliers final: 23 residues processed: 2 average time/residue: 0.8377 time to fit residues: 6.3562 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 372 random chunks: chunk 347 optimal weight: 0.7980 chunk 40 optimal weight: 10.0000 chunk 205 optimal weight: 0.9980 chunk 262 optimal weight: 10.0000 chunk 203 optimal weight: 8.9990 chunk 302 optimal weight: 0.7980 chunk 200 optimal weight: 0.7980 chunk 358 optimal weight: 7.9990 chunk 224 optimal weight: 0.8980 chunk 218 optimal weight: 6.9990 chunk 165 optimal weight: 7.9990 overall best weight: 0.8580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 147 GLN ** H 268 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 490 GLN I1023 HIS J 489 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8255 moved from start: 0.2282 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.046 31304 Z= 0.130 Angle : 0.490 10.314 42682 Z= 0.253 Chirality : 0.039 0.223 4894 Planarity : 0.003 0.043 5264 Dihedral : 15.158 174.175 5020 Min Nonbonded Distance : 2.152 Molprobity Statistics. All-atom Clashscore : 6.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.18 % Favored : 96.82 % Rotamer: Outliers : 1.24 % Allowed : 13.41 % Favored : 85.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.31 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.37 (0.14), residues: 3652 helix: 1.67 (0.15), residues: 1404 sheet: 0.11 (0.25), residues: 458 loop : -0.88 (0.14), residues: 1790 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP J1193 HIS 0.009 0.001 HIS H 66 PHE 0.014 0.001 PHE I 136 TYR 0.028 0.001 TYR M 112 ARG 0.008 0.000 ARG I 272 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7304 Ramachandran restraints generated. 3652 Oldfield, 0 Emsley, 3652 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7304 Ramachandran restraints generated. 3652 Oldfield, 0 Emsley, 3652 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 170 residues out of total 3153 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 39 poor density : 131 time to evaluate : 3.596 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 39 outliers final: 21 residues processed: 165 average time/residue: 1.4378 time to fit residues: 282.5104 Evaluate side-chains 148 residues out of total 3153 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 127 time to evaluate : 2.650 Switching outliers to nearest non-outliers outliers start: 21 outliers final: 21 residues processed: 1 average time/residue: 1.4244 time to fit residues: 5.1767 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 372 random chunks: chunk 221 optimal weight: 4.9990 chunk 143 optimal weight: 3.9990 chunk 214 optimal weight: 6.9990 chunk 108 optimal weight: 1.9990 chunk 70 optimal weight: 10.0000 chunk 69 optimal weight: 0.0040 chunk 227 optimal weight: 0.9990 chunk 244 optimal weight: 8.9990 chunk 177 optimal weight: 0.8980 chunk 33 optimal weight: 0.5980 chunk 281 optimal weight: 9.9990 overall best weight: 0.8996 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 147 GLN ** H 268 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I1023 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** I1220 GLN J 489 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8252 moved from start: 0.2375 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.045 31304 Z= 0.135 Angle : 0.494 10.677 42682 Z= 0.254 Chirality : 0.039 0.241 4894 Planarity : 0.003 0.044 5264 Dihedral : 15.159 174.190 5020 Min Nonbonded Distance : 2.155 Molprobity Statistics. All-atom Clashscore : 6.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.34 % Favored : 96.66 % Rotamer: Outliers : 0.99 % Allowed : 14.01 % Favored : 85.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.31 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.46 (0.14), residues: 3652 helix: 1.78 (0.15), residues: 1395 sheet: 0.13 (0.25), residues: 459 loop : -0.84 (0.14), residues: 1798 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP J1193 HIS 0.008 0.000 HIS H 66 PHE 0.009 0.001 PHE I 230 TYR 0.032 0.001 TYR M 112 ARG 0.010 0.000 ARG M 233 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7304 Ramachandran restraints generated. 3652 Oldfield, 0 Emsley, 3652 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7304 Ramachandran restraints generated. 3652 Oldfield, 0 Emsley, 3652 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 159 residues out of total 3153 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 128 time to evaluate : 2.909 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 31 outliers final: 22 residues processed: 153 average time/residue: 1.5497 time to fit residues: 279.2393 Evaluate side-chains 146 residues out of total 3153 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 124 time to evaluate : 2.695 Switching outliers to nearest non-outliers outliers start: 22 outliers final: 21 residues processed: 1 average time/residue: 0.4594 time to fit residues: 4.3132 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 372 random chunks: chunk 326 optimal weight: 0.7980 chunk 343 optimal weight: 10.0000 chunk 313 optimal weight: 7.9990 chunk 334 optimal weight: 0.0870 chunk 201 optimal weight: 4.9990 chunk 145 optimal weight: 7.9990 chunk 262 optimal weight: 7.9990 chunk 102 optimal weight: 0.5980 chunk 301 optimal weight: 0.6980 chunk 316 optimal weight: 6.9990 chunk 332 optimal weight: 8.9990 overall best weight: 1.4360 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Sorry: Reduce crashed with command 'molprobity.reduce -quiet -trim -'. Dumping stdin to file 'reduce_failure.pdb'. Return code: -15 Dumping stderr: