Starting phenix.real_space_refine on Sun Apr 14 07:42:36 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8f1k_28791/04_2024/8f1k_28791.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8f1k_28791/04_2024/8f1k_28791.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.8 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8f1k_28791/04_2024/8f1k_28791.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8f1k_28791/04_2024/8f1k_28791.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8f1k_28791/04_2024/8f1k_28791.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8f1k_28791/04_2024/8f1k_28791.pdb" } resolution = 2.8 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= 0.009 sd= 1.112 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 94 5.49 5 Mg 1 5.21 5 S 119 5.16 5 C 19057 2.51 5 N 5437 2.21 5 O 6144 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "G GLU 58": "OE1" <-> "OE2" Residue "G GLU 181": "OE1" <-> "OE2" Residue "G GLU 204": "OE1" <-> "OE2" Residue "G ASP 233": "OD1" <-> "OD2" Residue "H TYR 152": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H GLU 188": "OE1" <-> "OE2" Residue "H GLU 214": "OE1" <-> "OE2" Residue "H GLU 288": "OE1" <-> "OE2" Residue "H ASP 305": "OD1" <-> "OD2" Residue "I ASP 23": "OD1" <-> "OD2" Residue "I GLU 44": "OE1" <-> "OE2" Residue "I ASP 158": "OD1" <-> "OD2" Residue "I TYR 172": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I TYR 179": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I ASP 185": "OD1" <-> "OD2" Residue "I ASP 189": "OD1" <-> "OD2" Residue "I PHE 195": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I GLU 415": "OE1" <-> "OE2" Residue "I ASP 434": "OD1" <-> "OD2" Residue "I GLU 441": "OE1" <-> "OE2" Residue "I GLU 504": "OE1" <-> "OE2" Residue "I GLU 849": "OE1" <-> "OE2" Residue "I ASP 881": "OD1" <-> "OD2" Residue "I GLU 940": "OE1" <-> "OE2" Residue "I GLU 968": "OE1" <-> "OE2" Residue "I GLU 1137": "OE1" <-> "OE2" Residue "I GLU 1219": "OE1" <-> "OE2" Residue "I TYR 1285": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J GLU 16": "OE1" <-> "OE2" Residue "J GLU 42": "OE1" <-> "OE2" Residue "J ASP 129": "OD1" <-> "OD2" Residue "J GLU 204": "OE1" <-> "OE2" Residue "J GLU 225": "OE1" <-> "OE2" Residue "J ASP 284": "OD1" <-> "OD2" Residue "J GLU 301": "OE1" <-> "OE2" Residue "J GLU 402": "OE1" <-> "OE2" Residue "J GLU 414": "OE1" <-> "OE2" Residue "J GLU 532": "OE1" <-> "OE2" Residue "J GLU 556": "OE1" <-> "OE2" Residue "J GLU 562": "OE1" <-> "OE2" Residue "J ASP 684": "OD1" <-> "OD2" Residue "J GLU 704": "OE1" <-> "OE2" Residue "J ASP 1143": "OD1" <-> "OD2" Residue "J GLU 1158": "OE1" <-> "OE2" Residue "J ASP 1212": "OD1" <-> "OD2" Residue "J ASP 1239": "OD1" <-> "OD2" Residue "J ASP 1250": "OD1" <-> "OD2" Residue "J GLU 1278": "OE1" <-> "OE2" Residue "K GLU 11": "OE1" <-> "OE2" Residue "K ASP 36": "OD1" <-> "OD2" Residue "M GLU 150": "OE1" <-> "OE2" Residue "M GLU 169": "OE1" <-> "OE2" Residue "M PHE 206": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "M GLU 248": "OE1" <-> "OE2" Residue "M ASP 257": "OD1" <-> "OD2" Residue "M TYR 271": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "M GLU 288": "OE1" <-> "OE2" Residue "M ASP 338": "OD1" <-> "OD2" Residue "M TYR 361": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "M TYR 389": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "M GLU 398": "OE1" <-> "OE2" Residue "M PHE 403": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.08s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5288/modules/chem_data/mon_lib" Total number of atoms: 30854 Number of models: 1 Model: "" Number of chains: 14 Chain: "A" Number of atoms: 698 Number of conformers: 1 Conformer: "" Number of residues, atoms: 34, 698 Classifications: {'DNA': 34} Modifications used: {'5*END': 1} Link IDs: {'rna3p': 33} Chain: "C" Number of atoms: 249 Number of conformers: 1 Conformer: "" Number of residues, atoms: 12, 249 Classifications: {'DNA': 12} Link IDs: {'rna3p': 11} Chain: "G" Number of atoms: 1738 Number of conformers: 1 Conformer: "" Number of residues, atoms: 225, 1738 Classifications: {'peptide': 225} Link IDs: {'PCIS': 1, 'PTRANS': 8, 'TRANS': 215} Chain breaks: 1 Chain: "H" Number of atoms: 2336 Number of conformers: 1 Conformer: "" Number of residues, atoms: 302, 2336 Classifications: {'peptide': 302} Link IDs: {'PCIS': 1, 'PTRANS': 13, 'TRANS': 287} Chain breaks: 2 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: 3250 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 407, 3247 Classifications: {'peptide': 407} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 16, 'TRANS': 389} Chain breaks: 1 Conformer: "B" Number of residues, atoms: 407, 3247 Classifications: {'peptide': 407} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 16, 'TRANS': 389} Chain breaks: 1 bond proxies already assigned to first conformer: 3293 Chain: "B" Number of atoms: 693 Number of conformers: 1 Conformer: "" Number of residues, atoms: 34, 693 Classifications: {'DNA': 34} Link IDs: {'rna3p': 33} Chain: "D" Number of atoms: 302 Number of conformers: 1 Conformer: "" Number of residues, atoms: 15, 302 Classifications: {'DNA': 15} Link IDs: {'rna3p': 14} 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: 3 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 3 Classifications: {'water': 3} Link IDs: {None: 2} 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: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Classifications: {'water': 2} Link IDs: {None: 1} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 16027 SG CYS J 70 105.451 99.331 129.651 1.00 45.57 S ATOM 16041 SG CYS J 72 104.116 98.628 133.017 1.00 59.51 S ATOM 16149 SG CYS J 85 107.521 97.218 132.171 1.00 61.17 S ATOM 16173 SG CYS J 88 104.464 95.692 130.621 1.00 52.63 S ATOM 21861 SG CYS J 814 114.290 70.250 68.683 1.00 43.60 S ATOM 22426 SG CYS J 888 111.272 71.086 70.882 1.00 37.73 S ATOM 22477 SG CYS J 895 112.816 73.704 68.530 1.00 39.94 S ATOM 22498 SG CYS J 898 110.808 70.911 67.121 1.00 46.81 S Time building chain proxies: 18.63, per 1000 atoms: 0.60 Number of scatterers: 30854 At special positions: 0 Unit cell: (151.62, 167.865, 179.778, 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 94 15.00 Mg 1 11.99 O 6144 8.00 N 5437 7.00 C 19057 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: 12.78 Conformation dependent library (CDL) restraints added in 6.6 seconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN J1502 " pdb="ZN ZN J1502 " - pdb=" SG CYS J 72 " pdb="ZN ZN J1502 " - pdb=" SG CYS J 85 " pdb="ZN ZN J1502 " - pdb=" SG CYS J 88 " pdb="ZN ZN J1502 " - pdb=" SG CYS J 70 " 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 7328 Ramachandran restraints generated. 3664 Oldfield, 0 Emsley, 3664 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 6852 Finding SS restraints... Secondary structure from input PDB file: 142 helices and 50 sheets defined 42.6% alpha, 15.9% beta 43 base pairs and 78 stacking pairs defined. Time for finding SS restraints: 11.45 Creating SS restraints... Processing helix chain 'G' and resid 34 through 50 removed outlier: 3.648A pdb=" N THR G 38 " --> pdb=" O GLY G 34 " (cutoff:3.500A) removed outlier: 3.620A pdb=" N ALA G 42 " --> pdb=" O THR G 38 " (cutoff:3.500A) Processing helix chain 'G' and resid 77 through 87 removed outlier: 3.706A 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: 4.439A pdb=" N ALA G 230 " --> pdb=" O GLU G 226 " (cutoff:3.500A) removed outlier: 4.450A pdb=" N PHE G 231 " --> pdb=" O GLN G 227 " (cutoff:3.500A) removed outlier: 3.626A pdb=" N ASP G 233 " --> pdb=" O GLU G 229 " (cutoff:3.500A) Processing helix chain 'H' and resid 34 through 50 removed outlier: 3.525A 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 154 through 159 removed outlier: 3.555A pdb=" N ILE H 159 " --> pdb=" O SER H 156 " (cutoff:3.500A) Processing helix chain 'H' and resid 212 through 228 removed outlier: 3.587A pdb=" N LEU H 228 " --> pdb=" O LEU H 224 " (cutoff:3.500A) Processing helix chain 'H' and resid 250 through 255 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 283 Processing helix chain 'H' and resid 285 through 291 Processing helix chain 'H' and resid 296 through 309 removed outlier: 3.828A pdb=" N LEU H 300 " --> pdb=" O GLY H 296 " (cutoff:3.500A) Processing helix chain 'I' and resid 4 through 9 removed outlier: 3.592A pdb=" N LYS I 9 " --> pdb=" O TYR I 5 " (cutoff:3.500A) Processing helix chain 'I' and resid 28 through 40 removed outlier: 3.777A pdb=" N SER I 34 " --> pdb=" O ILE I 30 " (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: 4.154A 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 Processing helix chain 'I' and resid 270 through 281 Processing helix chain 'I' and resid 288 through 293 removed outlier: 3.667A pdb=" N ILE I 292 " --> pdb=" O VAL I 289 " (cutoff:3.500A) Processing helix chain 'I' and resid 318 through 328 Processing helix chain 'I' and resid 346 through 354 Processing helix chain 'I' and resid 359 through 371 removed outlier: 3.526A pdb=" N LEU I 363 " --> pdb=" O ARG I 359 " (cutoff:3.500A) Processing helix chain 'I' and resid 377 through 390 removed outlier: 3.928A 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 479 removed outlier: 3.686A pdb=" N ARG I 470 " --> pdb=" O VAL I 466 " (cutoff:3.500A) Processing helix chain 'I' and resid 488 through 493 Processing helix chain 'I' and resid 495 through 509 removed outlier: 3.738A pdb=" N SER I 509 " --> pdb=" O PHE I 505 " (cutoff:3.500A) Processing helix chain 'I' and resid 519 through 528 Processing helix chain 'I' and resid 545 through 549 Processing helix chain 'I' and resid 551 through 555 Processing helix chain 'I' and resid 608 through 612 removed outlier: 3.569A 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 646 through 650 removed outlier: 4.036A pdb=" N VAL I 650 " --> pdb=" O ARG I 647 " (cutoff:3.500A) Processing helix chain 'I' and resid 664 through 668 removed outlier: 3.691A pdb=" N ILE I 668 " --> pdb=" O ALA I 665 " (cutoff:3.500A) Processing helix chain 'I' and resid 670 through 674 Processing helix chain 'I' and resid 675 through 687 removed outlier: 4.049A pdb=" N ARG I 687 " --> pdb=" O ALA I 683 " (cutoff:3.500A) Processing helix chain 'I' and resid 704 through 712 Processing helix chain 'I' and resid 738 through 741 removed outlier: 3.825A 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 Processing helix chain 'I' and resid 942 through 984 removed outlier: 3.837A pdb=" N GLN I 955 " --> pdb=" O MET I 951 " (cutoff:3.500A) removed outlier: 3.789A pdb=" N ALA I 956 " --> pdb=" O GLN I 952 " (cutoff:3.500A) removed outlier: 3.608A pdb=" N GLY I 983 " --> pdb=" O LEU I 979 " (cutoff:3.500A) removed outlier: 4.057A pdb=" N VAL I 984 " --> pdb=" O VAL I 980 " (cutoff:3.500A) Processing helix chain 'I' and resid 985 through 992 removed outlier: 3.536A pdb=" N LEU I 989 " --> pdb=" O GLU I 985 " (cutoff:3.500A) Processing helix chain 'I' and resid 1011 through 1037 Processing helix chain 'I' and resid 1081 through 1085 removed outlier: 3.571A pdb=" N MET I1085 " --> pdb=" O ILE I1082 " (cutoff:3.500A) Processing helix chain 'I' and resid 1101 through 1107 removed outlier: 4.453A pdb=" N SER I1105 " --> pdb=" O LEU I1101 " (cutoff:3.500A) removed outlier: 3.938A pdb=" N ARG I1106 " --> pdb=" O GLY I1102 " (cutoff:3.500A) Processing helix chain 'I' and resid 1109 through 1134 removed outlier: 3.508A pdb=" N GLN I1134 " --> pdb=" O ALA I1130 " (cutoff:3.500A) Processing helix chain 'I' and resid 1137 through 1151 removed outlier: 3.549A pdb=" N LEU I1141 " --> pdb=" O GLU I1137 " (cutoff:3.500A) Processing helix chain 'I' and resid 1160 through 1164 removed outlier: 3.828A 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 Processing helix chain 'I' and resid 1238 through 1243 Processing helix chain 'I' and resid 1271 through 1282 Processing helix chain 'I' and resid 1283 through 1292 Processing helix chain 'I' and resid 1297 through 1310 removed outlier: 3.574A pdb=" N THR I1302 " --> pdb=" O VAL I1298 " (cutoff:3.500A) Processing helix chain 'I' and resid 1320 through 1332 removed outlier: 3.875A pdb=" N ASN I1324 " --> pdb=" O PRO I1320 " (cutoff:3.500A) Processing helix chain 'J' and resid 4 through 11 removed outlier: 3.799A pdb=" N GLN J 11 " --> pdb=" O PHE J 7 " (cutoff:3.500A) Processing helix chain 'J' and resid 26 through 33 Processing helix chain 'J' and resid 58 through 63 Processing helix chain 'J' and resid 77 through 81 Processing helix chain 'J' and resid 94 through 100 removed outlier: 3.770A pdb=" N VAL J 97 " --> pdb=" O GLN J 94 " (cutoff:3.500A) removed outlier: 3.578A pdb=" N ARG J 98 " --> pdb=" O THR J 95 " (cutoff:3.500A) Processing helix chain 'J' and resid 114 through 119 removed outlier: 3.626A 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 173 Processing helix chain 'J' and resid 181 through 191 removed outlier: 3.509A pdb=" N ILE J 185 " --> pdb=" O GLY J 181 " (cutoff:3.500A) Processing helix chain 'J' and resid 193 through 208 removed outlier: 3.733A pdb=" N THR J 208 " --> pdb=" O GLU J 204 " (cutoff:3.500A) Processing helix chain 'J' and resid 211 through 230 removed outlier: 3.513A pdb=" N SER J 230 " --> pdb=" O ALA J 226 " (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 removed outlier: 3.799A pdb=" N ASN J 294 " --> pdb=" O ILE J 290 " (cutoff:3.500A) Processing helix chain 'J' and resid 326 through 332 Processing helix chain 'J' and resid 336 through 342 Processing helix chain 'J' and resid 370 through 377 removed outlier: 3.612A pdb=" N GLU J 375 " --> pdb=" O LYS J 371 " (cutoff:3.500A) Processing helix chain 'J' and resid 377 through 388 removed outlier: 3.519A 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 405 through 416 removed outlier: 4.088A pdb=" N TRP J 409 " --> pdb=" O GLU J 405 " (cutoff:3.500A) removed outlier: 4.156A pdb=" N ASP J 410 " --> pdb=" O ALA J 406 " (cutoff:3.500A) 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: 3.502A pdb=" N TYR J 457 " --> pdb=" O VAL J 453 " (cutoff:3.500A) Processing helix chain 'J' and resid 473 through 483 Processing helix chain 'J' and resid 485 through 489 Processing helix chain 'J' and resid 504 through 514 Processing helix chain 'J' and resid 529 through 539 Processing helix chain 'J' and resid 574 through 581 removed outlier: 3.816A 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 597 through 612 Processing helix chain 'J' and resid 614 through 636 removed outlier: 3.744A pdb=" N GLY J 636 " --> pdb=" O ALA J 632 " (cutoff:3.500A) Processing helix chain 'J' and resid 640 through 644 Processing helix chain 'J' and resid 649 through 670 Processing helix chain 'J' and resid 674 through 702 removed outlier: 3.632A pdb=" N ARG J 678 " --> pdb=" O THR J 674 " (cutoff:3.500A) Processing helix chain 'J' and resid 720 through 728 Processing helix chain 'J' and resid 733 through 742 Processing helix chain 'J' and resid 768 through 805 removed outlier: 3.882A pdb=" N HIS J 777 " --> pdb=" O PHE J 773 " (cutoff:3.500A) removed outlier: 4.355A pdb=" N GLY J 778 " --> pdb=" O ILE J 774 " (cutoff:3.500A) removed outlier: 4.202A pdb=" N THR J 790 " --> pdb=" O THR J 786 " (cutoff:3.500A) removed outlier: 5.345A pdb=" N ALA J 791 " --> pdb=" O ALA J 787 " (cutoff:3.500A) removed outlier: 4.524A pdb=" N ASN J 792 " --> pdb=" O LEU J 788 " (cutoff:3.500A) Processing helix chain 'J' and resid 835 through 840 Processing helix chain 'J' and resid 865 through 875 Processing helix chain 'J' and resid 896 through 900 Processing helix chain 'J' and resid 914 through 925 Processing helix chain 'J' and resid 926 through 930 removed outlier: 3.509A pdb=" N LEU J 930 " --> pdb=" O GLY J 927 " (cutoff:3.500A) Processing helix chain 'J' and resid 1069 through 1074 removed outlier: 3.728A pdb=" N ASP J1073 " --> pdb=" O GLY J1070 " (cutoff:3.500A) Processing helix chain 'J' and resid 1137 through 1147 Processing helix chain 'J' and resid 1216 through 1224 Processing helix chain 'J' and resid 1225 through 1244 removed outlier: 3.802A pdb=" N VAL J1229 " --> pdb=" O GLY J1225 " (cutoff:3.500A) removed outlier: 3.727A pdb=" N LEU J1243 " --> pdb=" O ASP J1239 " (cutoff:3.500A) removed outlier: 4.462A pdb=" N GLN J1244 " --> pdb=" O VAL J1240 " (cutoff:3.500A) Processing helix chain 'J' and resid 1249 through 1261 removed outlier: 4.411A pdb=" N ILE J1253 " --> pdb=" O ASN J1249 " (cutoff:3.500A) Processing helix chain 'J' and resid 1282 through 1294 Processing helix chain 'J' and resid 1308 through 1314 Processing helix chain 'J' and resid 1318 through 1326 Processing helix chain 'J' and resid 1327 through 1339 Processing helix chain 'J' and resid 1346 through 1353 removed outlier: 3.517A pdb=" N ASN J1350 " --> pdb=" O GLY J1346 " (cutoff:3.500A) Processing helix chain 'J' and resid 1359 through 1361 No H-bonds generated for 'chain 'J' and resid 1359 through 1361' 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: 3.572A pdb=" N LEU K 21 " --> pdb=" O PHE K 17 " (cutoff:3.500A) Processing helix chain 'K' and resid 45 through 56 Processing helix chain 'K' and resid 60 through 80 removed outlier: 4.474A pdb=" N LEU K 80 " --> pdb=" O GLU K 76 " (cutoff:3.500A) Processing helix chain 'M' and resid 16 through 25 removed outlier: 3.875A pdb=" N GLN M 21 " --> pdb=" O PRO M 17 " (cutoff:3.500A) Processing helix chain 'M' and resid 29 through 42 Processing helix chain 'M' and resid 119 through 130 removed outlier: 3.501A pdb=" N LEU M 130 " --> pdb=" O TRP M 126 " (cutoff:3.500A) Processing helix chain 'M' and resid 134 through 147 Processing helix chain 'M' and resid 157 through 166 removed outlier: 3.798A pdb=" N GLY M 166 " --> pdb=" O LEU M 162 " (cutoff:3.500A) Processing helix chain 'M' and resid 171 through 184 removed outlier: 3.929A pdb=" N VAL M 175 " --> pdb=" O ASP M 171 " (cutoff:3.500A) removed outlier: 3.685A pdb=" N ARG M 184 " --> pdb=" O LYS M 180 " (cutoff:3.500A) Processing helix chain 'M' and resid 194 through 204 Processing helix chain 'M' and resid 212 through 222 Processing helix chain 'M' and resid 224 through 229 Processing helix chain 'M' and resid 233 through 240 Processing helix chain 'M' and resid 242 through 255 removed outlier: 4.039A pdb=" N GLU M 248 " --> pdb=" O ASP M 244 " (cutoff:3.500A) Processing helix chain 'M' and resid 259 through 264 removed outlier: 3.510A pdb=" N GLN M 262 " --> pdb=" O ARG M 259 " (cutoff:3.500A) removed outlier: 3.660A pdb=" N SER M 263 " --> pdb=" O PRO M 260 " (cutoff:3.500A) removed outlier: 3.892A pdb=" N ILE M 264 " --> pdb=" O GLY M 261 " (cutoff:3.500A) No H-bonds generated for 'chain 'M' and resid 259 through 264' Processing helix chain 'M' and resid 300 through 306 removed outlier: 3.949A pdb=" N MET M 306 " --> pdb=" O HIS M 302 " (cutoff:3.500A) Processing helix chain 'M' and resid 312 through 351 removed outlier: 3.693A pdb=" N ILE M 319 " --> pdb=" O ASP M 315 " (cutoff:3.500A) removed outlier: 3.526A pdb=" N ARG M 320 " --> pdb=" O SER M 316 " (cutoff:3.500A) removed outlier: 3.644A pdb=" N SER M 321 " --> pdb=" O GLN M 317 " (cutoff:3.500A) removed outlier: 3.702A pdb=" N ASN M 322 " --> pdb=" O PHE M 318 " (cutoff:3.500A) Processing helix chain 'M' and resid 353 through 358 Processing helix chain 'M' and resid 359 through 362 removed outlier: 3.731A pdb=" N MET M 362 " --> pdb=" O GLU M 359 " (cutoff:3.500A) No H-bonds generated for 'chain 'M' and resid 359 through 362' Processing helix chain 'M' and resid 366 through 374 removed outlier: 3.607A pdb=" N ILE M 370 " --> pdb=" O VAL M 366 " (cutoff:3.500A) removed outlier: 3.507A pdb=" N GLN M 372 " --> pdb=" O ALA M 368 " (cutoff:3.500A) removed outlier: 3.645A pdb=" N ALA M 373 " --> pdb=" O ASP M 369 " (cutoff:3.500A) Processing helix chain 'M' and resid 377 through 385 Processing helix chain 'M' and resid 417 through 430 Processing helix chain 'M' and resid 438 through 447 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 18 removed outlier: 6.733A pdb=" N THR G 27 " --> pdb=" O VAL G 14 " (cutoff:3.500A) removed outlier: 4.276A pdb=" N ILE G 16 " --> pdb=" O LYS G 25 " (cutoff:3.500A) removed outlier: 6.483A 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: 7.069A pdb=" N HIS G 23 " --> pdb=" O GLN G 18 " (cutoff:3.500A) removed outlier: 5.614A pdb=" N HIS G 23 " --> pdb=" O THR G 207 " (cutoff:3.500A) removed outlier: 7.258A pdb=" N THR G 207 " --> pdb=" O HIS G 23 " (cutoff:3.500A) removed outlier: 5.515A pdb=" N LYS G 25 " --> pdb=" O MET G 205 " (cutoff:3.500A) removed outlier: 7.072A pdb=" N MET G 205 " --> pdb=" O LYS G 25 " (cutoff:3.500A) removed outlier: 5.624A pdb=" N THR G 27 " --> pdb=" O ILE G 203 " (cutoff:3.500A) removed outlier: 7.228A pdb=" N ILE G 203 " --> pdb=" O THR G 27 " (cutoff:3.500A) removed outlier: 5.516A pdb=" N GLU G 29 " --> pdb=" O LEU G 201 " (cutoff:3.500A) removed outlier: 7.715A 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: 3.710A pdb=" N GLU G 58 " --> pdb=" O LYS G 145 " (cutoff:3.500A) removed outlier: 6.428A pdb=" N GLN G 147 " --> pdb=" O VAL G 56 " (cutoff:3.500A) removed outlier: 5.433A pdb=" N VAL G 56 " --> pdb=" O GLN G 147 " (cutoff:3.500A) removed outlier: 6.810A pdb=" N GLY G 149 " --> pdb=" O CYS G 54 " (cutoff:3.500A) removed outlier: 5.229A 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 92 Processing sheet with id=AA4, first strand: chain 'G' and resid 108 through 111 removed outlier: 6.553A pdb=" N GLY G 108 " --> pdb=" O HIS G 132 " (cutoff:3.500A) removed outlier: 4.734A pdb=" N HIS G 132 " --> pdb=" O GLY G 108 " (cutoff:3.500A) removed outlier: 6.748A pdb=" N VAL G 110 " --> pdb=" O ILE G 130 " (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 15 through 18 removed outlier: 6.343A pdb=" N ASP H 199 " --> pdb=" O PRO H 30 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'H' and resid 97 through 105 removed outlier: 3.795A pdb=" N GLU H 58 " --> pdb=" O LYS H 145 " (cutoff:3.500A) removed outlier: 6.241A pdb=" N GLN H 147 " --> pdb=" O VAL H 56 " (cutoff:3.500A) removed outlier: 5.403A pdb=" N VAL H 56 " --> pdb=" O GLN H 147 " (cutoff:3.500A) removed outlier: 6.805A pdb=" N GLY H 149 " --> pdb=" O CYS H 54 " (cutoff:3.500A) removed outlier: 5.249A pdb=" N CYS H 54 " --> pdb=" O GLY H 149 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'H' and resid 90 through 91 Processing sheet with id=AA9, first strand: chain 'H' and resid 108 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: 6.541A 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: 6.767A pdb=" N LYS I 99 " --> pdb=" O VAL I 71 " (cutoff:3.500A) removed outlier: 4.574A pdb=" N TYR I 73 " --> pdb=" O ARG I 97 " (cutoff:3.500A) removed outlier: 6.731A pdb=" N ARG I 97 " --> pdb=" O TYR I 73 " (cutoff:3.500A) removed outlier: 4.327A pdb=" N LEU I 75 " --> pdb=" O PRO I 95 " (cutoff:3.500A) removed outlier: 6.437A pdb=" N ALA I 94 " --> pdb=" O GLY I 125 " (cutoff:3.500A) removed outlier: 6.652A pdb=" N GLY I 125 " --> pdb=" O ALA I 94 " (cutoff:3.500A) removed outlier: 7.043A pdb=" N LEU I 96 " --> pdb=" O TYR I 123 " (cutoff:3.500A) removed outlier: 4.580A pdb=" N TYR I 123 " --> pdb=" O LEU I 96 " (cutoff:3.500A) removed outlier: 6.068A pdb=" N VAL I 98 " --> pdb=" O GLU I 121 " (cutoff:3.500A) removed outlier: 4.454A pdb=" N GLU I 121 " --> pdb=" O VAL I 98 " (cutoff:3.500A) removed outlier: 6.822A pdb=" N LEU I 100 " --> pdb=" O GLU I 119 " (cutoff:3.500A) removed outlier: 4.562A pdb=" N GLU I 119 " --> pdb=" O LEU I 100 " (cutoff:3.500A) removed outlier: 6.621A pdb=" N LEU I 102 " --> pdb=" O ILE I 117 " (cutoff:3.500A) removed outlier: 4.414A pdb=" N ILE I 117 " --> pdb=" O LEU I 102 " (cutoff:3.500A) removed outlier: 6.665A pdb=" N ILE I 104 " --> pdb=" O LYS I 115 " (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 removed outlier: 3.556A pdb=" N SER I 147 " --> pdb=" O ARG I 529 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'I' and resid 154 through 160 removed outlier: 3.579A pdb=" N ASP I 160 " --> pdb=" O LEU I 171 " (cutoff:3.500A) removed outlier: 3.755A pdb=" N LEU I 171 " --> pdb=" O ASP I 160 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'I' and resid 227 through 231 Processing sheet with id=AB8, first strand: chain 'I' and resid 239 through 240 Processing sheet with id=AB9, first strand: chain 'I' and resid 249 through 250 removed outlier: 4.370A pdb=" N GLU I 249 " --> pdb=" O ILE I 269 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'I' and resid 255 through 257 removed outlier: 7.364A pdb=" N ILE I 255 " --> pdb=" O TYR I 262 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'I' and resid 580 through 581 removed outlier: 5.459A pdb=" N GLU I 602 " --> pdb=" O LYS I 593 " (cutoff:3.500A) removed outlier: 7.412A pdb=" N THR I 595 " --> pdb=" O THR I 600 " (cutoff:3.500A) removed outlier: 6.135A pdb=" N THR I 600 " --> pdb=" O THR I 595 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'I' and resid 580 through 581 Processing sheet with id=AC4, first strand: chain 'I' and resid 716 through 717 removed outlier: 6.473A 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: 6.790A pdb=" N ARG I 731 " --> pdb=" O VAL I 727 " (cutoff:3.500A) removed outlier: 4.709A pdb=" N VAL I 727 " --> pdb=" O ARG I 731 " (cutoff:3.500A) removed outlier: 6.545A 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: 7.051A pdb=" N ILE I 816 " --> pdb=" O LYS I1078 " (cutoff:3.500A) removed outlier: 7.854A pdb=" N ASN I1080 " --> pdb=" O ILE I 816 " (cutoff:3.500A) removed outlier: 6.607A pdb=" N VAL I 818 " --> pdb=" O ASN I1080 " (cutoff:3.500A) removed outlier: 3.628A pdb=" N LEU I 817 " --> pdb=" O VAL I1097 " (cutoff:3.500A) removed outlier: 8.632A pdb=" N ILE I1096 " --> pdb=" O ASN I 799 " (cutoff:3.500A) removed outlier: 6.435A pdb=" N ARG I 801 " --> pdb=" O ILE I1096 " (cutoff:3.500A) removed outlier: 7.743A pdb=" N LEU I1098 " --> pdb=" O ARG I 801 " (cutoff:3.500A) removed outlier: 6.244A pdb=" N ALA I 803 " --> pdb=" O LEU I1098 " (cutoff:3.500A) removed outlier: 4.558A pdb=" N THR I1226 " --> pdb=" O PHE I 804 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'I' and resid 846 through 847 removed outlier: 3.808A pdb=" N GLY I 846 " --> pdb=" O THR I 843 " (cutoff:3.500A) removed outlier: 6.420A pdb=" N ASP I 842 " --> pdb=" O VAL I1046 " (cutoff:3.500A) removed outlier: 6.595A pdb=" N VAL I1046 " --> pdb=" O ASP I 842 " (cutoff:3.500A) removed outlier: 3.809A pdb=" N ASP I 930 " --> pdb=" O TYR I1053 " (cutoff:3.500A) removed outlier: 6.797A pdb=" N ALA I1055 " --> pdb=" O VAL I 928 " (cutoff:3.500A) removed outlier: 5.973A pdb=" N VAL I 928 " --> pdb=" O ALA I1055 " (cutoff:3.500A) removed outlier: 8.635A pdb=" N LYS I1057 " --> pdb=" O GLY I 926 " (cutoff:3.500A) removed outlier: 8.847A 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: 6.705A pdb=" N LEU I 918 " --> pdb=" O LEU I 883 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'I' and resid 1244 through 1246 Processing sheet with id=AD4, first strand: chain 'I' and resid 1268 through 1270 removed outlier: 3.771A pdb=" N GLN I1268 " --> pdb=" O VAL J 347 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'I' and resid 1335 through 1340 removed outlier: 3.835A pdb=" N ALA J 19 " --> pdb=" O GLU I1340 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'J' and resid 34 through 37 removed outlier: 7.624A pdb=" N HIS J 104 " --> pdb=" O PHE J 35 " (cutoff:3.500A) removed outlier: 4.408A pdb=" N GLU J 37 " --> pdb=" O HIS J 104 " (cutoff:3.500A) removed outlier: 7.699A pdb=" N GLU J 106 " --> pdb=" O GLU J 37 " (cutoff:3.500A) removed outlier: 9.925A pdb=" N LEU J 107 " --> pdb=" O PRO J 243 " (cutoff:3.500A) removed outlier: 10.397A pdb=" N SER J 109 " --> pdb=" O VAL J 241 " (cutoff:3.500A) removed outlier: 7.126A pdb=" N VAL J 241 " --> pdb=" O SER J 109 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'J' and resid 159 through 160 removed outlier: 6.831A pdb=" N ASP J 177 " --> pdb=" O ILE J 147 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'J' and resid 253 through 254 Processing sheet with id=AD9, first strand: chain 'J' and resid 526 through 527 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 Processing sheet with id=AE4, first strand: chain 'J' and resid 825 through 827 removed outlier: 6.557A pdb=" N GLU J 827 " --> pdb=" O VAL J 831 " (cutoff:3.500A) removed outlier: 5.221A pdb=" N VAL J 831 " --> pdb=" O GLU J 827 " (cutoff:3.500A) Processing sheet with id=AE5, first strand: chain 'J' and resid 848 through 849 removed outlier: 6.451A pdb=" N VAL J 848 " --> pdb=" O LEU J 857 " (cutoff:3.500A) Processing sheet with id=AE6, first strand: chain 'J' and resid 949 through 951 removed outlier: 4.154A pdb=" N ALA J1018 " --> pdb=" O ILE J 950 " (cutoff:3.500A) removed outlier: 4.174A pdb=" N LEU J 973 " --> pdb=" O LEU J1003 " (cutoff:3.500A) Processing sheet with id=AE7, first strand: chain 'J' and resid 991 through 996 removed outlier: 3.982A pdb=" N GLU J 993 " --> pdb=" O LEU J 984 " (cutoff:3.500A) removed outlier: 3.510A pdb=" N GLY J 956 " --> pdb=" O VAL J1011 " (cutoff:3.500A) removed outlier: 3.659A pdb=" N VAL J1011 " --> pdb=" O GLY J 956 " (cutoff:3.500A) Processing sheet with id=AE8, first strand: chain 'J' and resid 1098 through 1100 Processing sheet with id=AE9, first strand: chain 'J' and resid 1046 through 1048 removed outlier: 4.712A pdb=" N LEU J1059 " --> pdb=" O VAL J1107 " (cutoff:3.500A) removed outlier: 3.532A pdb=" N VAL J1107 " --> pdb=" O LEU J1059 " (cutoff:3.500A) Processing sheet with id=AF1, first strand: chain 'J' and resid 1186 through 1188 Processing sheet with id=AF2, first strand: chain 'J' and resid 1279 through 1281 removed outlier: 4.406A pdb=" N LYS J1263 " --> pdb=" O ASP J1305 " (cutoff:3.500A) removed outlier: 7.231A pdb=" N THR J1301 " --> pdb=" O VAL J1267 " (cutoff:3.500A) Processing sheet with id=AF3, first strand: chain 'M' and resid 47 through 49 Processing sheet with id=AF4, first strand: chain 'M' and resid 284 through 289 removed outlier: 6.713A pdb=" N VAL M 276 " --> pdb=" O HIS M 391 " (cutoff:3.500A) Processing sheet with id=AF5, first strand: chain 'M' and resid 406 through 408 1270 hydrogen bonds defined for protein. 3540 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 102 hydrogen bonds 204 hydrogen bond angles 0 basepair planarities 43 basepair parallelities 78 stacking parallelities Total time for adding SS restraints: 18.30 Time building geometry restraints manager: 13.77 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: 9382 1.33 - 1.45: 4355 1.45 - 1.57: 17371 1.57 - 1.69: 185 1.69 - 1.81: 206 Bond restraints: 31499 Sorted by residual: bond pdb=" N TRP H 321 " pdb=" CA TRP H 321 " ideal model delta sigma weight residual 1.463 1.457 0.007 6.90e-03 2.10e+04 8.90e-01 bond pdb=" C3' DG A 4 " pdb=" C2' DG A 4 " ideal model delta sigma weight residual 1.525 1.543 -0.018 2.00e-02 2.50e+03 8.36e-01 bond pdb=" O4' DT A 20 " pdb=" C1' DT A 20 " ideal model delta sigma weight residual 1.414 1.396 0.018 2.00e-02 2.50e+03 7.96e-01 bond pdb=" C3' DA A 16 " pdb=" C2' DA A 16 " ideal model delta sigma weight residual 1.525 1.543 -0.018 2.00e-02 2.50e+03 7.87e-01 bond pdb=" CA SER I1295 " pdb=" CB SER I1295 " ideal model delta sigma weight residual 1.539 1.527 0.012 1.36e-02 5.41e+03 7.81e-01 ... (remaining 31494 not shown) Histogram of bond angle deviations from ideal: 99.91 - 106.73: 1375 106.73 - 113.55: 17451 113.55 - 120.37: 11460 120.37 - 127.18: 12280 127.18 - 134.00: 400 Bond angle restraints: 42966 Sorted by residual: angle pdb=" N ALA M 14 " pdb=" CA ALA M 14 " pdb=" C ALA M 14 " ideal model delta sigma weight residual 113.43 108.87 4.56 1.26e+00 6.30e-01 1.31e+01 angle pdb=" C LYS J1192 " pdb=" N TRP J1193 " pdb=" CA TRP J1193 " ideal model delta sigma weight residual 121.54 127.65 -6.11 1.91e+00 2.74e-01 1.02e+01 angle pdb=" N ILE J1210 " pdb=" CA ILE J1210 " pdb=" C ILE J1210 " ideal model delta sigma weight residual 111.48 108.51 2.97 9.40e-01 1.13e+00 9.97e+00 angle pdb=" C SER G 50 " pdb=" N MET G 51 " pdb=" CA MET G 51 " ideal model delta sigma weight residual 122.15 112.24 9.91 3.47e+00 8.31e-02 8.15e+00 angle pdb=" N VAL I1293 " pdb=" CA VAL I1293 " pdb=" C VAL I1293 " ideal model delta sigma weight residual 110.72 113.19 -2.47 1.01e+00 9.80e-01 5.98e+00 ... (remaining 42961 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.59: 17361 17.59 - 35.18: 1150 35.18 - 52.76: 499 52.76 - 70.35: 142 70.35 - 87.94: 25 Dihedral angle restraints: 19177 sinusoidal: 8552 harmonic: 10625 Sorted by residual: dihedral pdb=" CA ARG H 191 " pdb=" C ARG H 191 " pdb=" N VAL H 192 " pdb=" CA VAL H 192 " ideal model delta harmonic sigma weight residual 180.00 156.59 23.41 0 5.00e+00 4.00e-02 2.19e+01 dihedral pdb=" CA SER G 49 " pdb=" C SER G 49 " pdb=" N SER G 50 " pdb=" CA SER G 50 " ideal model delta harmonic sigma weight residual -180.00 -161.05 -18.95 0 5.00e+00 4.00e-02 1.44e+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 -163.19 -16.81 0 5.00e+00 4.00e-02 1.13e+01 ... (remaining 19174 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.032: 3267 0.032 - 0.064: 1154 0.064 - 0.097: 285 0.097 - 0.129: 194 0.129 - 0.161: 26 Chirality restraints: 4926 Sorted by residual: chirality pdb=" CB VAL J1255 " pdb=" CA VAL J1255 " pdb=" CG1 VAL J1255 " pdb=" CG2 VAL J1255 " both_signs ideal model delta sigma weight residual False -2.63 -2.47 -0.16 2.00e-01 2.50e+01 6.48e-01 chirality pdb=" CA VAL H 192 " pdb=" N VAL H 192 " pdb=" C VAL H 192 " pdb=" CB VAL H 192 " both_signs ideal model delta sigma weight residual False 2.44 2.58 -0.14 2.00e-01 2.50e+01 5.13e-01 chirality pdb=" CA ILE I 177 " pdb=" N ILE I 177 " pdb=" C ILE I 177 " pdb=" CB ILE I 177 " both_signs ideal model delta sigma weight residual False 2.43 2.57 -0.14 2.00e-01 2.50e+01 4.96e-01 ... (remaining 4923 not shown) Planarity restraints: 5288 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA ILE I 292 " 0.009 2.00e-02 2.50e+03 1.87e-02 3.51e+00 pdb=" C ILE I 292 " -0.032 2.00e-02 2.50e+03 pdb=" O ILE I 292 " 0.012 2.00e-02 2.50e+03 pdb=" N ALA I 293 " 0.011 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C THR I 589 " 0.027 5.00e-02 4.00e+02 4.09e-02 2.67e+00 pdb=" N PRO I 590 " -0.071 5.00e-02 4.00e+02 pdb=" CA PRO I 590 " 0.021 5.00e-02 4.00e+02 pdb=" CD PRO I 590 " 0.023 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C LEU J 245 " 0.025 5.00e-02 4.00e+02 3.86e-02 2.38e+00 pdb=" N PRO J 246 " -0.067 5.00e-02 4.00e+02 pdb=" CA PRO J 246 " 0.020 5.00e-02 4.00e+02 pdb=" CD PRO J 246 " 0.021 5.00e-02 4.00e+02 ... (remaining 5285 not shown) Histogram of nonbonded interaction distances: 2.13 - 2.68: 542 2.68 - 3.24: 27709 3.24 - 3.79: 46198 3.79 - 4.35: 65914 4.35 - 4.90: 107639 Nonbonded interactions: 248002 Sorted by model distance: nonbonded pdb=" OD1 ASN J1268 " pdb=" OG1 THR J1301 " model vdw 2.130 2.440 nonbonded pdb=" OD1 ASP J 462 " pdb="MG MG J1501 " model vdw 2.143 2.170 nonbonded pdb=" OE1 GLU I 562 " pdb=" OG SER I 662 " model vdw 2.165 2.440 nonbonded pdb=" O PRO J 121 " pdb=" NH1 ARG J 123 " model vdw 2.190 2.520 nonbonded pdb=" OD1 ASP M 149 " pdb=" OG1 THR M 151 " model vdw 2.218 2.440 ... (remaining 247997 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=0.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 2.100 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: 8.990 Check model and map are aligned: 0.420 Set scattering table: 0.230 Process input model: 105.340 Find NCS groups from input model: 1.130 Set up NCS constraints: 0.160 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: 0.020 Load rotamer database and sin/cos tables:13.790 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 132.200 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8072 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 : 0.002 0.043 31499 Z= 0.154 Angle : 0.471 9.909 42966 Z= 0.265 Chirality : 0.040 0.161 4926 Planarity : 0.004 0.041 5288 Dihedral : 15.011 87.940 12325 Min Nonbonded Distance : 2.130 Molprobity Statistics. All-atom Clashscore : 4.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.35 % Favored : 97.65 % Rotamer: Outliers : 1.30 % Allowed : 6.58 % Favored : 92.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.29 % 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: 0.58 (0.14), residues: 3664 helix: 1.52 (0.14), residues: 1391 sheet: 0.69 (0.25), residues: 463 loop : -0.59 (0.14), residues: 1810 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP J 409 HIS 0.005 0.001 HIS I 447 PHE 0.010 0.001 PHE I1164 TYR 0.013 0.001 TYR J 631 ARG 0.003 0.000 ARG M 342 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7328 Ramachandran restraints generated. 3664 Oldfield, 0 Emsley, 3664 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7328 Ramachandran restraints generated. 3664 Oldfield, 0 Emsley, 3664 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 238 residues out of total 3162 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 41 poor density : 197 time to evaluate : 3.885 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: J 161 THR cc_start: 0.9199 (OUTLIER) cc_final: 0.8923 (p) outliers start: 41 outliers final: 11 residues processed: 231 average time/residue: 1.8659 time to fit residues: 495.3884 Evaluate side-chains 157 residues out of total 3162 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 145 time to evaluate : 3.598 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 64 VAL Chi-restraints excluded: chain G residue 194 GLN Chi-restraints excluded: chain I residue 47 TYR Chi-restraints excluded: chain I residue 574 SER Chi-restraints excluded: chain I residue 630 VAL Chi-restraints excluded: chain I residue 913 VAL Chi-restraints excluded: chain I residue 1023 HIS Chi-restraints excluded: chain I residue 1295 SER Chi-restraints excluded: chain J residue 161 THR Chi-restraints excluded: chain J residue 253 VAL Chi-restraints excluded: chain J residue 1255 VAL Chi-restraints excluded: chain M residue 407 VAL Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 373 random chunks: chunk 314 optimal weight: 8.9990 chunk 282 optimal weight: 9.9990 chunk 156 optimal weight: 1.9990 chunk 96 optimal weight: 3.9990 chunk 190 optimal weight: 3.9990 chunk 151 optimal weight: 5.9990 chunk 292 optimal weight: 50.0000 chunk 113 optimal weight: 5.9990 chunk 177 optimal weight: 0.9990 chunk 217 optimal weight: 1.9990 chunk 338 optimal weight: 8.9990 overall best weight: 2.5990 ------------------------------------------------------------------------------- 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: