Starting phenix.real_space_refine on Fri Jul 26 14:50:44 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8u3b_41856/07_2024/8u3b_41856_neut.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8u3b_41856/07_2024/8u3b_41856.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.23 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8u3b_41856/07_2024/8u3b_41856.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8u3b_41856/07_2024/8u3b_41856.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8u3b_41856/07_2024/8u3b_41856_neut.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8u3b_41856/07_2024/8u3b_41856_neut.cif" } resolution = 3.23 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= 0.001 sd= 0.020 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 142 5.49 5 Mg 1 5.21 5 S 136 5.16 5 C 20427 2.51 5 N 5918 2.21 5 O 6660 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A PHE 8": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 35": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 226": "OE1" <-> "OE2" Residue "A PHE 249": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 250": "OD1" <-> "OD2" Residue "B ASP 15": "OD1" <-> "OD2" Residue "B PHE 35": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 68": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 136": "OE1" <-> "OE2" Residue "B TYR 152": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 174": "OD1" <-> "OD2" Residue "B ASP 197": "OD1" <-> "OD2" Residue "B GLU 204": "OE1" <-> "OE2" Residue "B ASP 212": "OD1" <-> "OD2" Residue "C TYR 5": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 7": "OE1" <-> "OE2" Residue "C TYR 26": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 35": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 57": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 62": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 73": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 77": "OE1" <-> "OE2" Residue "C TYR 123": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 126": "OE1" <-> "OE2" Residue "C PHE 136": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 142": "OE1" <-> "OE2" Residue "C TYR 172": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ASP 185": "OD1" <-> "OD2" Residue "C PHE 186": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 195": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 215": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 218": "OE1" <-> "OE2" Residue "C PHE 225": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 226": "OE1" <-> "OE2" Residue "C ARG 268": "NH1" <-> "NH2" Residue "C ARG 332": "NH1" <-> "NH2" Residue "C PHE 390": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 395": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 413": "OE1" <-> "OE2" Residue "C ASP 443": "OD1" <-> "OD2" Residue "C GLU 458": "OE1" <-> "OE2" Residue "C PHE 514": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 545": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 546": "OE1" <-> "OE2" Residue "C TYR 578": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 629": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ASP 632": "OD1" <-> "OD2" Residue "C GLU 641": "OE1" <-> "OE2" Residue "C PHE 645": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ASP 696": "OD1" <-> "OD2" Residue "C GLU 740": "OE1" <-> "OE2" Residue "C GLU 745": "OE1" <-> "OE2" Residue "C TYR 756": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 810": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 825": "OE1" <-> "OE2" Residue "C PHE 828": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 849": "OE1" <-> "OE2" Residue "C GLU 859": "OE1" <-> "OE2" Residue "C PHE 906": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ASP 942": "OD1" <-> "OD2" Residue "C GLU 962": "OE1" <-> "OE2" Residue "C GLU 963": "OE1" <-> "OE2" Residue "C ASP 995": "OD1" <-> "OD2" Residue "C GLU 1012": "OE1" <-> "OE2" Residue "C PHE 1025": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ASP 1041": "OD1" <-> "OD2" Residue "C TYR 1053": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 1089": "OE1" <-> "OE2" Residue "C ASP 1150": "OD1" <-> "OD2" Residue "C PHE 1187": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 1194": "OE1" <-> "OE2" Residue "C TYR 1213": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 1222": "OE1" <-> "OE2" Residue "C TYR 1229": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 1279": "OE1" <-> "OE2" Residue "C TYR 1305": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 1323": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 1329": "OE1" <-> "OE2" Residue "D ASP 67": "OD1" <-> "OD2" Residue "D PHE 116": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D GLU 162": "OE1" <-> "OE2" Residue "D ASP 264": "OD1" <-> "OD2" Residue "D ASP 267": "OD1" <-> "OD2" Residue "D ASP 308": "OD1" <-> "OD2" Residue "D TYR 349": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 377": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 380": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D GLU 402": "OE1" <-> "OE2" Residue "D GLU 414": "OE1" <-> "OE2" Residue "D TYR 512": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D GLU 554": "OE1" <-> "OE2" Residue "D GLU 562": "OE1" <-> "OE2" Residue "D TYR 626": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 631": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D GLU 666": "OE1" <-> "OE2" Residue "D PHE 668": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 723": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ASP 751": "OD1" <-> "OD2" Residue "D PHE 773": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ASP 802": "OD1" <-> "OD2" Residue "D GLU 811": "OE1" <-> "OE2" Residue "D ASP 855": "OD1" <-> "OD2" Residue "D GLU 866": "OE1" <-> "OE2" Residue "D ASP 878": "OD1" <-> "OD2" Residue "D GLU 981": "OE1" <-> "OE2" Residue "D GLU 1015": "OE1" <-> "OE2" Residue "D TYR 1099": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 1145": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D GLU 1215": "OE1" <-> "OE2" Residue "D TYR 1241": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D GLU 1281": "OE1" <-> "OE2" Residue "D GLU 1291": "OE1" <-> "OE2" Residue "D TYR 1302": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D GLU 1327": "OE1" <-> "OE2" Residue "D ARG 1355": "NH1" <-> "NH2" Residue "D TYR 1365": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E ASP 8": "OD1" <-> "OD2" Residue "E GLU 42": "OE1" <-> "OE2" Residue "E GLU 56": "OE1" <-> "OE2" Residue "E ASP 65": "OD1" <-> "OD2" Residue "F PHE 221": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F TYR 394": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F PHE 401": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F ASP 417": "OD1" <-> "OD2" Residue "F PHE 427": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F GLU 473": "OE1" <-> "OE2" Residue "F ASP 492": "OD1" <-> "OD2" Residue "F GLU 508": "OE1" <-> "OE2" Residue "F GLU 515": "OE1" <-> "OE2" Residue "F ASP 521": "OD1" <-> "OD2" Residue "F ASP 533": "OD1" <-> "OD2" Residue "F GLU 538": "OE1" <-> "OE2" Residue "F ASP 566": "OD1" <-> "OD2" Residue "F TYR 571": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F PHE 580": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F GLU 591": "OE1" <-> "OE2" Residue "G GLU 213": "OE1" <-> "OE2" Time to flip residues: 0.09s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5388/modules/chem_data/mon_lib" Total number of atoms: 33286 Number of models: 1 Model: "" Number of chains: 12 Chain: "A" Number of atoms: 2381 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 305, 2373 Classifications: {'peptide': 305} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PCIS': 2, 'PTRANS': 12, 'TRANS': 290} Chain breaks: 1 Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 2 Planarities with less than four sites: {'ASP:plan': 1} Unresolved non-hydrogen planarities: 3 Conformer: "B" Number of residues, atoms: 305, 2373 Classifications: {'peptide': 305} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PCIS': 2, 'PTRANS': 12, 'TRANS': 290} Chain breaks: 1 Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 2 Planarities with less than four sites: {'ASP:plan': 1} Unresolved non-hydrogen planarities: 3 bond proxies already assigned to first conformer: 2395 Chain: "B" Number of atoms: 1767 Number of conformers: 1 Conformer: "" Number of residues, atoms: 228, 1767 Classifications: {'peptide': 228} Link IDs: {'PCIS': 1, 'PTRANS': 8, 'TRANS': 218} Chain: "C" Number of atoms: 10576 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1341, 10576 Classifications: {'peptide': 1341} Link IDs: {'PCIS': 1, 'PTRANS': 55, 'TRANS': 1284} Chain: "D" Number of atoms: 10443 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1344, 10443 Classifications: {'peptide': 1344} Link IDs: {'PCIS': 2, 'PTRANS': 53, 'TRANS': 1288} Chain breaks: 2 Chain: "E" Number of atoms: 610 Number of conformers: 1 Conformer: "" Number of residues, atoms: 77, 610 Classifications: {'peptide': 77} Link IDs: {'PTRANS': 2, 'TRANS': 74} Chain: "F" Number of atoms: 3516 Number of conformers: 1 Conformer: "" Number of residues, atoms: 431, 3516 Classifications: {'peptide': 431} Link IDs: {'PTRANS': 12, 'TRANS': 418} Chain breaks: 3 Chain: "G" Number of atoms: 547 Number of conformers: 1 Conformer: "" Number of residues, atoms: 66, 547 Classifications: {'peptide': 66} Link IDs: {'PTRANS': 2, 'TRANS': 63} Chain: "H" Number of atoms: 547 Number of conformers: 1 Conformer: "" Number of residues, atoms: 66, 547 Classifications: {'peptide': 66} Link IDs: {'PTRANS': 2, 'TRANS': 63} Chain: "1" Number of atoms: 1415 Number of conformers: 1 Conformer: "" Number of residues, atoms: 69, 1415 Classifications: {'DNA': 69} Modifications used: {'5*END': 1} Link IDs: {'rna3p': 68} Chain: "2" Number of atoms: 1405 Number of conformers: 1 Conformer: "" Number of residues, atoms: 69, 1405 Classifications: {'DNA': 69} Link IDs: {'rna3p': 68} Chain: "3" Number of atoms: 76 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 76 Unusual residues: {'GTP': 1} Classifications: {'RNA': 2, 'undetermined': 1} Modifications used: {'rna3p_pur': 2} Link IDs: {'rna3p': 1, None: 1} Not linked: pdbres="GTP 3 1 " pdbres=" A 3 2 " Chain: "D" Number of atoms: 3 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 3 Unusual residues: {' MG': 1, ' ZN': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 15182 SG CYS D 70 48.767 128.993 81.345 1.00166.50 S ATOM 15196 SG CYS D 72 50.044 131.107 78.392 1.00175.94 S ATOM 15304 SG CYS D 85 47.532 128.978 77.734 1.00175.67 S ATOM 15328 SG CYS D 88 50.566 127.098 78.460 1.00169.54 S ATOM 21016 SG CYS D 814 25.816 73.390 114.196 1.00 99.14 S ATOM 21581 SG CYS D 888 29.094 75.032 113.221 1.00 89.23 S ATOM 21632 SG CYS D 895 27.446 76.105 116.422 1.00 82.85 S ATOM 21653 SG CYS D 898 28.851 72.888 116.383 1.00 83.62 S Time building chain proxies: 18.59, per 1000 atoms: 0.56 Number of scatterers: 33286 At special positions: 0 Unit cell: (155.819, 214.251, 202.741, 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 136 16.00 P 142 15.00 Mg 1 11.99 O 6660 8.00 N 5918 7.00 C 20427 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=2, symmetry=0 Number of additional bonds: simple=2, symmetry=0 Coordination: Other bonds: Time building additional restraints: 13.37 Conformation dependent library (CDL) restraints added in 5.4 seconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN D1501 " pdb="ZN ZN D1501 " - pdb=" SG CYS D 85 " pdb="ZN ZN D1501 " - pdb=" SG CYS D 72 " pdb="ZN ZN D1501 " - pdb=" SG CYS D 70 " pdb="ZN ZN D1501 " - pdb=" SG CYS D 88 " pdb=" ZN D1502 " pdb="ZN ZN D1502 " - pdb=" SG CYS D 895 " pdb="ZN ZN D1502 " - pdb=" SG CYS D 898 " pdb="ZN ZN D1502 " - pdb=" SG CYS D 888 " pdb="ZN ZN D1502 " - pdb=" SG CYS D 814 " Number of angles added : 12 7662 Ramachandran restraints generated. 3831 Oldfield, 0 Emsley, 3831 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 7176 Finding SS restraints... Secondary structure from input PDB file: 149 helices and 48 sheets defined 46.5% alpha, 14.4% beta 16 base pairs and 58 stacking pairs defined. Time for finding SS restraints: 11.21 Creating SS restraints... Processing helix chain 'A' and resid 34 through 50 removed outlier: 3.567A pdb=" N THR A 38 " --> pdb=" O GLY A 34 " (cutoff:3.500A) removed outlier: 3.640A pdb=" N ALA A 42 " --> pdb=" O THR A 38 " (cutoff:3.500A) Processing helix chain 'A' and resid 77 through 86 Processing helix chain 'A' and resid 113 through 115 No H-bonds generated for 'chain 'A' and resid 113 through 115' Processing helix chain 'A' and resid 154 through 162 removed outlier: 3.591A pdb=" N ARG A 158 " --> pdb=" O PRO A 154 " (cutoff:3.500A) Processing helix chain 'A' and resid 212 through 234 removed outlier: 4.841A pdb=" N ALA A 230 " --> pdb=" O GLU A 226 " (cutoff:3.500A) removed outlier: 5.122A pdb=" N PHE A 231 " --> pdb=" O GLN A 227 " (cutoff:3.500A) removed outlier: 3.533A pdb=" N VAL A 232 " --> pdb=" O LEU A 228 " (cutoff:3.500A) Processing helix chain 'A' and resid 250 through 255 removed outlier: 3.993A pdb=" N LEU A 254 " --> pdb=" O ASP A 250 " (cutoff:3.500A) Processing helix chain 'A' and resid 256 through 261 Processing helix chain 'A' and resid 263 through 273 Processing helix chain 'A' and resid 277 through 284 removed outlier: 3.869A pdb=" N GLN A 283 " --> pdb=" O GLY A 279 " (cutoff:3.500A) Processing helix chain 'A' and resid 285 through 291 Processing helix chain 'A' and resid 296 through 310 Processing helix chain 'B' and resid 34 through 50 removed outlier: 3.752A pdb=" N THR B 38 " --> pdb=" O GLY B 34 " (cutoff:3.500A) Processing helix chain 'B' and resid 77 through 87 removed outlier: 3.700A pdb=" N GLY B 87 " --> pdb=" O LEU B 83 " (cutoff:3.500A) Processing helix chain 'B' and resid 113 through 115 No H-bonds generated for 'chain 'B' and resid 113 through 115' Processing helix chain 'B' and resid 154 through 161 removed outlier: 3.906A pdb=" N ARG B 158 " --> pdb=" O PRO B 154 " (cutoff:3.500A) removed outlier: 4.020A pdb=" N SER B 161 " --> pdb=" O THR B 157 " (cutoff:3.500A) Processing helix chain 'B' and resid 212 through 233 removed outlier: 4.827A pdb=" N ALA B 230 " --> pdb=" O GLU B 226 " (cutoff:3.500A) removed outlier: 5.336A pdb=" N PHE B 231 " --> pdb=" O GLN B 227 " (cutoff:3.500A) removed outlier: 4.514A pdb=" N ASP B 233 " --> pdb=" O GLU B 229 " (cutoff:3.500A) Processing helix chain 'C' and resid 4 through 9 Processing helix chain 'C' and resid 28 through 40 removed outlier: 3.856A pdb=" N SER C 34 " --> pdb=" O ILE C 30 " (cutoff:3.500A) removed outlier: 3.515A pdb=" N PHE C 38 " --> pdb=" O SER C 34 " (cutoff:3.500A) Processing helix chain 'C' and resid 48 through 57 Processing helix chain 'C' and resid 81 through 89 Processing helix chain 'C' and resid 206 through 213 removed outlier: 4.401A pdb=" N LEU C 210 " --> pdb=" O ALA C 206 " (cutoff:3.500A) Processing helix chain 'C' and resid 216 through 225 Processing helix chain 'C' and resid 242 through 247 Processing helix chain 'C' and resid 270 through 281 Processing helix chain 'C' and resid 318 through 328 Processing helix chain 'C' and resid 345 through 354 removed outlier: 3.503A pdb=" N GLU C 349 " --> pdb=" O PRO C 345 " (cutoff:3.500A) Processing helix chain 'C' and resid 358 through 371 Processing helix chain 'C' and resid 377 through 390 Processing helix chain 'C' and resid 398 through 409 Processing helix chain 'C' and resid 421 through 438 removed outlier: 3.598A pdb=" N ILE C 425 " --> pdb=" O SER C 421 " (cutoff:3.500A) Processing helix chain 'C' and resid 455 through 482 removed outlier: 3.670A pdb=" N ARG C 473 " --> pdb=" O VAL C 469 " (cutoff:3.500A) removed outlier: 4.323A pdb=" N ALA C 474 " --> pdb=" O ARG C 470 " (cutoff:3.500A) removed outlier: 3.609A pdb=" N SER C 480 " --> pdb=" O LYS C 476 " (cutoff:3.500A) removed outlier: 4.032A pdb=" N GLY C 482 " --> pdb=" O ARG C 478 " (cutoff:3.500A) Processing helix chain 'C' and resid 488 through 493 removed outlier: 3.819A pdb=" N MET C 492 " --> pdb=" O MET C 488 " (cutoff:3.500A) removed outlier: 3.605A pdb=" N ILE C 493 " --> pdb=" O PRO C 489 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 488 through 493' Processing helix chain 'C' and resid 495 through 509 Processing helix chain 'C' and resid 519 through 528 Processing helix chain 'C' and resid 551 through 555 removed outlier: 3.883A pdb=" N TYR C 555 " --> pdb=" O PRO C 552 " (cutoff:3.500A) Processing helix chain 'C' and resid 607 through 612 removed outlier: 4.031A pdb=" N GLY C 612 " --> pdb=" O ALA C 608 " (cutoff:3.500A) Processing helix chain 'C' and resid 648 through 650 No H-bonds generated for 'chain 'C' and resid 648 through 650' Processing helix chain 'C' and resid 656 through 661 removed outlier: 4.342A pdb=" N VAL C 660 " --> pdb=" O THR C 657 " (cutoff:3.500A) Processing helix chain 'C' and resid 662 through 667 Processing helix chain 'C' and resid 670 through 674 Processing helix chain 'C' and resid 675 through 687 removed outlier: 4.193A pdb=" N ARG C 687 " --> pdb=" O ALA C 683 " (cutoff:3.500A) Processing helix chain 'C' and resid 704 through 712 Processing helix chain 'C' and resid 820 through 825 Processing helix chain 'C' and resid 860 through 865 removed outlier: 3.854A pdb=" N LYS C 864 " --> pdb=" O ALA C 861 " (cutoff:3.500A) removed outlier: 3.502A pdb=" N LEU C 865 " --> pdb=" O LEU C 862 " (cutoff:3.500A) Processing helix chain 'C' and resid 896 through 907 removed outlier: 3.620A pdb=" N LYS C 900 " --> pdb=" O THR C 896 " (cutoff:3.500A) Processing helix chain 'C' and resid 942 through 980 removed outlier: 4.183A pdb=" N GLU C 962 " --> pdb=" O LYS C 958 " (cutoff:3.500A) removed outlier: 3.784A pdb=" N GLU C 963 " --> pdb=" O ASP C 959 " (cutoff:3.500A) removed outlier: 3.835A pdb=" N LEU C 967 " --> pdb=" O GLU C 963 " (cutoff:3.500A) removed outlier: 3.783A pdb=" N GLY C 970 " --> pdb=" O ILE C 966 " (cutoff:3.500A) removed outlier: 3.575A pdb=" N VAL C 980 " --> pdb=" O ARG C 976 " (cutoff:3.500A) Processing helix chain 'C' and resid 981 through 983 No H-bonds generated for 'chain 'C' and resid 981 through 983' Processing helix chain 'C' and resid 985 through 992 removed outlier: 3.696A pdb=" N LEU C 989 " --> pdb=" O GLU C 985 " (cutoff:3.500A) removed outlier: 4.262A pdb=" N ASP C 990 " --> pdb=" O ALA C 986 " (cutoff:3.500A) Processing helix chain 'C' and resid 994 through 998 removed outlier: 3.825A pdb=" N TRP C 997 " --> pdb=" O ARG C 994 " (cutoff:3.500A) removed outlier: 4.025A pdb=" N LEU C 998 " --> pdb=" O ASP C 995 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 994 through 998' Processing helix chain 'C' and resid 1005 through 1038 removed outlier: 3.810A pdb=" N ASN C1009 " --> pdb=" O GLU C1005 " (cutoff:3.500A) removed outlier: 3.660A pdb=" N GLN C1017 " --> pdb=" O GLN C1013 " (cutoff:3.500A) removed outlier: 3.615A pdb=" N TYR C1018 " --> pdb=" O LEU C1014 " (cutoff:3.500A) removed outlier: 3.836A pdb=" N ASP C1019 " --> pdb=" O ALA C1015 " (cutoff:3.500A) removed outlier: 4.741A pdb=" N GLU C1020 " --> pdb=" O GLU C1016 " (cutoff:3.500A) removed outlier: 3.511A pdb=" N HIS C1023 " --> pdb=" O ASP C1019 " (cutoff:3.500A) Processing helix chain 'C' and resid 1099 through 1103 removed outlier: 3.517A pdb=" N GLY C1102 " --> pdb=" O ASN C1099 " (cutoff:3.500A) Processing helix chain 'C' and resid 1109 through 1134 removed outlier: 3.514A pdb=" N GLN C1134 " --> pdb=" O ALA C1130 " (cutoff:3.500A) Processing helix chain 'C' and resid 1137 through 1150 Processing helix chain 'C' and resid 1165 through 1177 Processing helix chain 'C' and resid 1191 through 1202 Processing helix chain 'C' and resid 1238 through 1242 Processing helix chain 'C' and resid 1271 through 1281 Processing helix chain 'C' and resid 1283 through 1292 removed outlier: 3.725A pdb=" N LEU C1287 " --> pdb=" O ALA C1283 " (cutoff:3.500A) Processing helix chain 'C' and resid 1297 through 1310 removed outlier: 3.638A pdb=" N ASP C1310 " --> pdb=" O LYS C1306 " (cutoff:3.500A) Processing helix chain 'C' and resid 1320 through 1333 removed outlier: 3.652A pdb=" N ASN C1324 " --> pdb=" O PRO C1320 " (cutoff:3.500A) Processing helix chain 'D' and resid 26 through 33 Processing helix chain 'D' and resid 58 through 63 Processing helix chain 'D' and resid 95 through 100 Processing helix chain 'D' and resid 114 through 119 removed outlier: 3.518A pdb=" N SER D 119 " --> pdb=" O TRP D 115 " (cutoff:3.500A) Processing helix chain 'D' and resid 122 through 129 Processing helix chain 'D' and resid 131 through 140 removed outlier: 3.550A pdb=" N ILE D 135 " --> pdb=" O PRO D 131 " (cutoff:3.500A) Processing helix chain 'D' and resid 161 through 172 removed outlier: 3.514A pdb=" N LEU D 166 " --> pdb=" O GLU D 162 " (cutoff:3.500A) removed outlier: 3.655A pdb=" N GLU D 171 " --> pdb=" O ASP D 167 " (cutoff:3.500A) Processing helix chain 'D' and resid 181 through 192 Processing helix chain 'D' and resid 193 through 208 removed outlier: 3.931A pdb=" N GLU D 197 " --> pdb=" O ASP D 193 " (cutoff:3.500A) removed outlier: 3.747A pdb=" N ASN D 206 " --> pdb=" O ARG D 202 " (cutoff:3.500A) removed outlier: 3.738A pdb=" N GLU D 207 " --> pdb=" O GLU D 203 " (cutoff:3.500A) removed outlier: 3.900A pdb=" N THR D 208 " --> pdb=" O GLU D 204 " (cutoff:3.500A) Processing helix chain 'D' and resid 210 through 231 removed outlier: 3.843A pdb=" N GLY D 231 " --> pdb=" O PHE D 227 " (cutoff:3.500A) Processing helix chain 'D' and resid 233 through 236 Processing helix chain 'D' and resid 246 through 250 Processing helix chain 'D' and resid 263 through 285 removed outlier: 4.269A pdb=" N ASP D 267 " --> pdb=" O SER D 263 " (cutoff:3.500A) Processing helix chain 'D' and resid 288 through 308 removed outlier: 3.517A pdb=" N VAL D 292 " --> pdb=" O PRO D 288 " (cutoff:3.500A) Processing helix chain 'D' and resid 326 through 332 Processing helix chain 'D' and resid 336 through 341 Processing helix chain 'D' and resid 370 through 377 Processing helix chain 'D' and resid 377 through 388 Processing helix chain 'D' and resid 393 through 403 Processing helix chain 'D' and resid 405 through 417 removed outlier: 3.586A pdb=" N TRP D 409 " --> pdb=" O GLU D 405 " (cutoff:3.500A) removed outlier: 3.847A pdb=" N ARG D 417 " --> pdb=" O ASP D 413 " (cutoff:3.500A) Processing helix chain 'D' and resid 430 through 432 No H-bonds generated for 'chain 'D' and resid 430 through 432' Processing helix chain 'D' and resid 450 through 452 No H-bonds generated for 'chain 'D' and resid 450 through 452' Processing helix chain 'D' and resid 453 through 458 Processing helix chain 'D' and resid 473 through 483 Processing helix chain 'D' and resid 485 through 489 Processing helix chain 'D' and resid 503 through 515 Processing helix chain 'D' and resid 529 through 539 removed outlier: 3.588A pdb=" N ALA D 533 " --> pdb=" O GLY D 529 " (cutoff:3.500A) removed outlier: 3.542A pdb=" N SER D 539 " --> pdb=" O ARG D 535 " (cutoff:3.500A) Processing helix chain 'D' and resid 574 through 581 removed outlier: 3.898A pdb=" N MET D 581 " --> pdb=" O ALA D 577 " (cutoff:3.500A) Processing helix chain 'D' and resid 588 through 592 removed outlier: 3.592A pdb=" N ILE D 591 " --> pdb=" O PRO D 588 " (cutoff:3.500A) Processing helix chain 'D' and resid 597 through 613 removed outlier: 3.715A pdb=" N ILE D 601 " --> pdb=" O GLY D 597 " (cutoff:3.500A) Processing helix chain 'D' and resid 614 through 636 removed outlier: 3.582A pdb=" N GLY D 636 " --> pdb=" O ALA D 632 " (cutoff:3.500A) Processing helix chain 'D' and resid 640 through 644 Processing helix chain 'D' and resid 649 through 669 removed outlier: 3.692A pdb=" N GLN D 669 " --> pdb=" O GLN D 665 " (cutoff:3.500A) Processing helix chain 'D' and resid 674 through 703 removed outlier: 4.187A pdb=" N THR D 703 " --> pdb=" O ASP D 699 " (cutoff:3.500A) Processing helix chain 'D' and resid 720 through 728 Processing helix chain 'D' and resid 733 through 742 Processing helix chain 'D' and resid 768 through 804 removed outlier: 3.997A pdb=" N HIS D 777 " --> pdb=" O PHE D 773 " (cutoff:3.500A) removed outlier: 4.449A pdb=" N GLY D 778 " --> pdb=" O ILE D 774 " (cutoff:3.500A) removed outlier: 4.955A pdb=" N ALA D 791 " --> pdb=" O ALA D 787 " (cutoff:3.500A) removed outlier: 4.589A pdb=" N ASN D 792 " --> pdb=" O LEU D 788 " (cutoff:3.500A) Processing helix chain 'D' and resid 835 through 840 removed outlier: 3.575A pdb=" N LEU D 840 " --> pdb=" O ARG D 836 " (cutoff:3.500A) Processing helix chain 'D' and resid 865 through 876 Processing helix chain 'D' and resid 884 through 888 Processing helix chain 'D' and resid 896 through 900 Processing helix chain 'D' and resid 914 through 925 removed outlier: 3.792A pdb=" N ILE D 918 " --> pdb=" O ALA D 914 " (cutoff:3.500A) Processing helix chain 'D' and resid 926 through 930 Processing helix chain 'D' and resid 1137 through 1147 Processing helix chain 'D' and resid 1216 through 1224 Processing helix chain 'D' and resid 1225 through 1243 removed outlier: 4.210A pdb=" N VAL D1240 " --> pdb=" O GLU D1236 " (cutoff:3.500A) removed outlier: 3.543A pdb=" N TYR D1241 " --> pdb=" O VAL D1237 " (cutoff:3.500A) Processing helix chain 'D' and resid 1249 through 1261 removed outlier: 4.431A pdb=" N ILE D1253 " --> pdb=" O ASN D1249 " (cutoff:3.500A) Processing helix chain 'D' and resid 1282 through 1294 Processing helix chain 'D' and resid 1308 through 1315 Processing helix chain 'D' and resid 1318 through 1326 Processing helix chain 'D' and resid 1327 through 1339 Processing helix chain 'D' and resid 1346 through 1354 removed outlier: 4.027A pdb=" N ASN D1350 " --> pdb=" O GLY D1346 " (cutoff:3.500A) Processing helix chain 'D' and resid 1359 through 1361 No H-bonds generated for 'chain 'D' and resid 1359 through 1361' Processing helix chain 'D' and resid 1362 through 1373 Processing helix chain 'E' and resid 6 through 14 Processing helix chain 'E' and resid 15 through 33 Processing helix chain 'E' and resid 45 through 56 removed outlier: 3.510A pdb=" N GLU E 56 " --> pdb=" O ARG E 52 " (cutoff:3.500A) Processing helix chain 'E' and resid 60 through 78 Processing helix chain 'F' and resid 96 through 107 removed outlier: 4.169A pdb=" N THR F 107 " --> pdb=" O ARG F 103 " (cutoff:3.500A) Processing helix chain 'F' and resid 114 through 137 removed outlier: 3.508A pdb=" N TYR F 137 " --> pdb=" O SER F 133 " (cutoff:3.500A) Processing helix chain 'F' and resid 137 through 152 removed outlier: 3.741A pdb=" N ILE F 141 " --> pdb=" O TYR F 137 " (cutoff:3.500A) Processing helix chain 'F' and resid 216 through 237 removed outlier: 4.299A pdb=" N GLU F 223 " --> pdb=" O GLU F 219 " (cutoff:3.500A) removed outlier: 4.108A pdb=" N LEU F 224 " --> pdb=" O LYS F 220 " (cutoff:3.500A) removed outlier: 3.555A pdb=" N THR F 234 " --> pdb=" O VAL F 230 " (cutoff:3.500A) Processing helix chain 'F' and resid 242 through 258 removed outlier: 3.666A pdb=" N GLN F 258 " --> pdb=" O GLU F 254 " (cutoff:3.500A) Processing helix chain 'F' and resid 262 through 294 removed outlier: 3.962A pdb=" N MET F 276 " --> pdb=" O SER F 272 " (cutoff:3.500A) removed outlier: 4.470A pdb=" N LEU F 286 " --> pdb=" O THR F 282 " (cutoff:3.500A) removed outlier: 5.011A pdb=" N ILE F 287 " --> pdb=" O GLN F 283 " (cutoff:3.500A) Processing helix chain 'F' and resid 337 through 352 removed outlier: 4.465A pdb=" N LYS F 343 " --> pdb=" O ARG F 339 " (cutoff:3.500A) Processing helix chain 'F' and resid 354 through 383 removed outlier: 4.019A pdb=" N GLU F 378 " --> pdb=" O ARG F 374 " (cutoff:3.500A) removed outlier: 3.864A pdb=" N MET F 379 " --> pdb=" O ALA F 375 " (cutoff:3.500A) Processing helix chain 'F' and resid 383 through 393 Processing helix chain 'F' and resid 400 through 419 Processing helix chain 'F' and resid 420 through 424 removed outlier: 3.551A pdb=" N ARG F 423 " --> pdb=" O GLU F 420 " (cutoff:3.500A) Processing helix chain 'F' and resid 426 through 446 removed outlier: 3.875A pdb=" N TYR F 430 " --> pdb=" O LYS F 426 " (cutoff:3.500A) removed outlier: 4.341A pdb=" N TRP F 433 " --> pdb=" O THR F 429 " (cutoff:3.500A) removed outlier: 3.955A pdb=" N TRP F 434 " --> pdb=" O TYR F 430 " (cutoff:3.500A) Processing helix chain 'F' and resid 453 through 475 removed outlier: 3.697A pdb=" N GLN F 469 " --> pdb=" O ARG F 465 " (cutoff:3.500A) Processing helix chain 'F' and resid 479 through 488 Processing helix chain 'F' and resid 490 through 501 Processing helix chain 'F' and resid 518 through 523 removed outlier: 3.560A pdb=" N ILE F 523 " --> pdb=" O GLY F 520 " (cutoff:3.500A) Processing helix chain 'F' and resid 530 through 551 removed outlier: 3.643A pdb=" N LEU F 551 " --> pdb=" O VAL F 547 " (cutoff:3.500A) Processing helix chain 'F' and resid 552 through 564 Processing helix chain 'F' and resid 572 through 580 Processing helix chain 'F' and resid 583 through 600 removed outlier: 3.914A pdb=" N ILE F 587 " --> pdb=" O THR F 583 " (cutoff:3.500A) Processing helix chain 'F' and resid 606 through 611 Processing helix chain 'G' and resid 152 through 156 Processing helix chain 'G' and resid 157 through 169 Processing helix chain 'G' and resid 172 through 181 Processing helix chain 'G' and resid 183 through 199 removed outlier: 3.701A pdb=" N VAL G 187 " --> pdb=" O THR G 183 " (cutoff:3.500A) Processing helix chain 'G' and resid 202 through 213 removed outlier: 3.977A pdb=" N ALA G 206 " --> pdb=" O SER G 202 " (cutoff:3.500A) removed outlier: 4.153A pdb=" N GLU G 213 " --> pdb=" O TRP G 209 " (cutoff:3.500A) Processing helix chain 'H' and resid 152 through 156 removed outlier: 3.796A pdb=" N GLN H 155 " --> pdb=" O ASP H 152 " (cutoff:3.500A) Processing helix chain 'H' and resid 157 through 169 Processing helix chain 'H' and resid 172 through 181 Processing helix chain 'H' and resid 183 through 198 Processing helix chain 'H' and resid 202 through 214 removed outlier: 3.999A pdb=" N ALA H 206 " --> pdb=" O SER H 202 " (cutoff:3.500A) removed outlier: 3.654A pdb=" N GLU H 213 " --> pdb=" O TRP H 209 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 12 through 17 removed outlier: 4.868A pdb=" N LEU A 13 " --> pdb=" O GLU A 29 " (cutoff:3.500A) removed outlier: 6.647A pdb=" N GLU A 29 " --> pdb=" O LEU A 13 " (cutoff:3.500A) removed outlier: 3.716A pdb=" N ASP A 15 " --> pdb=" O THR A 27 " (cutoff:3.500A) removed outlier: 6.557A pdb=" N ASP A 199 " --> pdb=" O PRO A 30 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 97 through 105 removed outlier: 7.656A pdb=" N SER A 141 " --> pdb=" O ILE A 61 " (cutoff:3.500A) removed outlier: 4.893A pdb=" N ILE A 61 " --> pdb=" O SER A 141 " (cutoff:3.500A) removed outlier: 6.754A pdb=" N ARG A 143 " --> pdb=" O VAL A 59 " (cutoff:3.500A) removed outlier: 4.540A pdb=" N VAL A 59 " --> pdb=" O ARG A 143 " (cutoff:3.500A) removed outlier: 6.728A pdb=" N LYS A 145 " --> pdb=" O THR A 57 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 90 through 92 Processing sheet with id=AA4, first strand: chain 'A' and resid 108 through 111 Processing sheet with id=AA5, first strand: chain 'A' and resid 152 through 153 Processing sheet with id=AA6, first strand: chain 'B' and resid 12 through 15 removed outlier: 5.481A pdb=" N LEU B 13 " --> pdb=" O GLU B 29 " (cutoff:3.500A) removed outlier: 7.044A pdb=" N GLU B 29 " --> pdb=" O LEU B 13 " (cutoff:3.500A) removed outlier: 6.570A pdb=" N ASP B 199 " --> pdb=" O PRO B 30 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 97 through 105 removed outlier: 3.893A pdb=" N GLU B 58 " --> pdb=" O LYS B 145 " (cutoff:3.500A) removed outlier: 6.301A pdb=" N GLN B 147 " --> pdb=" O VAL B 56 " (cutoff:3.500A) removed outlier: 5.425A pdb=" N VAL B 56 " --> pdb=" O GLN B 147 " (cutoff:3.500A) removed outlier: 6.891A pdb=" N GLY B 149 " --> pdb=" O CYS B 54 " (cutoff:3.500A) removed outlier: 5.167A pdb=" N CYS B 54 " --> pdb=" O GLY B 149 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 90 through 92 Processing sheet with id=AA9, first strand: chain 'B' and resid 108 through 111 removed outlier: 3.707A pdb=" N CYS B 131 " --> pdb=" O VAL B 110 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'B' and resid 152 through 153 Processing sheet with id=AB2, first strand: chain 'C' and resid 13 through 14 removed outlier: 6.656A pdb=" N LYS C 13 " --> pdb=" O ALA C1183 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'C' and resid 59 through 60 removed outlier: 6.751A pdb=" N LYS C 99 " --> pdb=" O VAL C 71 " (cutoff:3.500A) removed outlier: 4.500A pdb=" N TYR C 73 " --> pdb=" O ARG C 97 " (cutoff:3.500A) removed outlier: 6.601A pdb=" N ARG C 97 " --> pdb=" O TYR C 73 " (cutoff:3.500A) removed outlier: 4.479A pdb=" N LEU C 75 " --> pdb=" O PRO C 95 " (cutoff:3.500A) removed outlier: 6.340A pdb=" N ALA C 94 " --> pdb=" O GLU C 126 " (cutoff:3.500A) removed outlier: 4.795A pdb=" N GLU C 126 " --> pdb=" O ALA C 94 " (cutoff:3.500A) removed outlier: 5.596A pdb=" N LEU C 96 " --> pdb=" O MET C 124 " (cutoff:3.500A) removed outlier: 3.644A pdb=" N ASP C 116 " --> pdb=" O ILE C 104 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'C' and resid 136 through 138 Processing sheet with id=AB5, first strand: chain 'C' and resid 451 through 454 Processing sheet with id=AB6, first strand: chain 'C' and resid 154 through 160 removed outlier: 3.660A pdb=" N LEU C 171 " --> pdb=" O ASP C 160 " (cutoff:3.500A) removed outlier: 5.305A pdb=" N TYR C 172 " --> pdb=" O PHE C 188 " (cutoff:3.500A) removed outlier: 3.550A pdb=" N LEU C 184 " --> pdb=" O ILE C 176 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'C' and resid 284 through 286 removed outlier: 5.172A pdb=" N ILE C 229 " --> pdb=" O GLU C 240 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'C' and resid 255 through 256 removed outlier: 3.558A pdb=" N VAL C 263 " --> pdb=" O ILE C 255 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'C' and resid 301 through 302 Processing sheet with id=AC1, first strand: chain 'C' and resid 580 through 581 removed outlier: 7.270A pdb=" N LEU C 587 " --> pdb=" O LEU C 606 " (cutoff:3.500A) removed outlier: 7.025A pdb=" N LEU C 606 " --> pdb=" O LEU C 587 " (cutoff:3.500A) removed outlier: 6.272A pdb=" N THR C 589 " --> pdb=" O HIS C 604 " (cutoff:3.500A) removed outlier: 6.419A pdb=" N HIS C 604 " --> pdb=" O THR C 589 " (cutoff:3.500A) removed outlier: 6.092A pdb=" N TYR C 591 " --> pdb=" O GLU C 602 " (cutoff:3.500A) removed outlier: 6.172A pdb=" N GLU C 602 " --> pdb=" O TYR C 591 " (cutoff:3.500A) removed outlier: 5.176A pdb=" N LYS C 593 " --> pdb=" O THR C 600 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'C' and resid 580 through 581 Processing sheet with id=AC3, first strand: chain 'C' and resid 616 through 617 Processing sheet with id=AC4, first strand: chain 'C' and resid 716 through 717 removed outlier: 6.438A pdb=" N ALA C 716 " --> pdb=" O LEU C 783 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'C' and resid 748 through 752 removed outlier: 6.739A pdb=" N ARG C 731 " --> pdb=" O VAL C 727 " (cutoff:3.500A) removed outlier: 4.797A pdb=" N VAL C 727 " --> pdb=" O ARG C 731 " (cutoff:3.500A) removed outlier: 6.855A pdb=" N VAL C 733 " --> pdb=" O GLN C 725 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'C' and resid 755 through 758 Processing sheet with id=AC7, first strand: chain 'C' and resid 1209 through 1210 removed outlier: 7.434A pdb=" N ILE C 816 " --> pdb=" O SER C1077 " (cutoff:3.500A) removed outlier: 6.667A pdb=" N ILE C1079 " --> pdb=" O ILE C 816 " (cutoff:3.500A) removed outlier: 7.032A pdb=" N VAL C 818 " --> pdb=" O ILE C1079 " (cutoff:3.500A) removed outlier: 8.997A pdb=" N ILE C1096 " --> pdb=" O ASN C 799 " (cutoff:3.500A) removed outlier: 6.284A pdb=" N ARG C 801 " --> pdb=" O ILE C1096 " (cutoff:3.500A) removed outlier: 7.479A pdb=" N LEU C1098 " --> pdb=" O ARG C 801 " (cutoff:3.500A) removed outlier: 6.358A pdb=" N ALA C 803 " --> pdb=" O LEU C1098 " (cutoff:3.500A) removed outlier: 4.438A pdb=" N THR C1226 " --> pdb=" O PHE C 804 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'C' and resid 846 through 847 removed outlier: 6.613A pdb=" N ASP C 842 " --> pdb=" O VAL C1046 " (cutoff:3.500A) removed outlier: 6.857A pdb=" N VAL C1046 " --> pdb=" O ASP C 842 " (cutoff:3.500A) removed outlier: 8.348A pdb=" N LEU C1047 " --> pdb=" O THR C 935 " (cutoff:3.500A) removed outlier: 5.348A pdb=" N THR C 935 " --> pdb=" O LEU C1047 " (cutoff:3.500A) removed outlier: 6.721A pdb=" N ILE C1049 " --> pdb=" O VAL C 933 " (cutoff:3.500A) removed outlier: 4.551A pdb=" N VAL C 933 " --> pdb=" O ILE C1049 " (cutoff:3.500A) removed outlier: 6.628A pdb=" N LYS C1051 " --> pdb=" O VAL C 931 " (cutoff:3.500A) removed outlier: 4.411A pdb=" N VAL C 931 " --> pdb=" O LYS C1051 " (cutoff:3.500A) removed outlier: 6.899A pdb=" N TYR C1053 " --> pdb=" O ILE C 929 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'C' and resid 849 through 850 Processing sheet with id=AD1, first strand: chain 'C' and resid 882 through 884 removed outlier: 6.752A pdb=" N LEU C 918 " --> pdb=" O LEU C 883 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'C' and resid 1244 through 1246 removed outlier: 7.790A pdb=" N ILE D 447 " --> pdb=" O ARG D 352 " (cutoff:3.500A) removed outlier: 6.461A pdb=" N VAL D 354 " --> pdb=" O ILE D 447 " (cutoff:3.500A) removed outlier: 7.466A pdb=" N LEU D 449 " --> pdb=" O VAL D 354 " (cutoff:3.500A) removed outlier: 6.283A pdb=" N THR D 356 " --> pdb=" O LEU D 449 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'C' and resid 1269 through 1270 Processing sheet with id=AD4, first strand: chain 'C' and resid 1335 through 1341 removed outlier: 3.525A pdb=" N ALA D 19 " --> pdb=" O GLU C1340 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'D' and resid 34 through 37 removed outlier: 7.691A pdb=" N HIS D 104 " --> pdb=" O PHE D 35 " (cutoff:3.500A) removed outlier: 4.452A pdb=" N GLU D 37 " --> pdb=" O HIS D 104 " (cutoff:3.500A) removed outlier: 7.935A pdb=" N GLU D 106 " --> pdb=" O GLU D 37 " (cutoff:3.500A) removed outlier: 10.128A pdb=" N LEU D 107 " --> pdb=" O PRO D 243 " (cutoff:3.500A) removed outlier: 10.410A pdb=" N SER D 109 " --> pdb=" O VAL D 241 " (cutoff:3.500A) removed outlier: 7.465A pdb=" N VAL D 241 " --> pdb=" O SER D 109 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'D' and resid 159 through 160 removed outlier: 7.100A pdb=" N ASP D 177 " --> pdb=" O ILE D 147 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'D' and resid 252 through 254 removed outlier: 6.399A pdb=" N PHE D 260 " --> pdb=" O ILE F 505 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'D' and resid 526 through 527 Processing sheet with id=AD9, first strand: chain 'D' and resid 706 through 708 Processing sheet with id=AE1, first strand: chain 'D' and resid 809 through 811 Processing sheet with id=AE2, first strand: chain 'D' and resid 820 through 822 Processing sheet with id=AE3, first strand: chain 'D' and resid 949 through 951 removed outlier: 6.818A pdb=" N ILE D 950 " --> pdb=" O VAL D1017 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'D' and resid 956 through 957 removed outlier: 3.696A pdb=" N GLY D 956 " --> pdb=" O VAL D1011 " (cutoff:3.500A) Processing sheet with id=AE5, first strand: chain 'D' and resid 965 through 967 Processing sheet with id=AE6, first strand: chain 'D' and resid 980 through 985 removed outlier: 4.268A pdb=" N THR D 980 " --> pdb=" O VAL D 997 " (cutoff:3.500A) removed outlier: 4.303A pdb=" N GLU D 993 " --> pdb=" O LEU D 984 " (cutoff:3.500A) Processing sheet with id=AE7, first strand: chain 'D' and resid 1025 through 1028 removed outlier: 6.217A pdb=" N MET D1025 " --> pdb=" O ARG D1123 " (cutoff:3.500A) removed outlier: 4.822A pdb=" N ARG D1123 " --> pdb=" O MET D1025 " (cutoff:3.500A) removed outlier: 6.480A pdb=" N VAL D1027 " --> pdb=" O LEU D1121 " (cutoff:3.500A) Processing sheet with id=AE8, first strand: chain 'D' and resid 1034 through 1038 Processing sheet with id=AE9, first strand: chain 'D' and resid 1046 through 1047 removed outlier: 3.617A pdb=" N THR D1047 " --> pdb=" O VAL D1060 " (cutoff:3.500A) removed outlier: 4.623A pdb=" N VAL D1060 " --> pdb=" O THR D1047 " (cutoff:3.500A) No H-bonds generated for sheet with id=AE9 Processing sheet with id=AF1, first strand: chain 'D' and resid 1156 through 1157 Processing sheet with id=AF2, first strand: chain 'D' and resid 1162 through 1165 Processing sheet with id=AF3, first strand: chain 'D' and resid 1279 through 1281 1412 hydrogen bonds defined for protein. 3989 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 38 hydrogen bonds 72 hydrogen bond angles 0 basepair planarities 16 basepair parallelities 58 stacking parallelities Total time for adding SS restraints: 16.50 Time building geometry restraints manager: 14.54 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 8127 1.33 - 1.45: 6509 1.45 - 1.57: 18909 1.57 - 1.69: 281 1.69 - 1.81: 240 Bond restraints: 34066 Sorted by residual: bond pdb=" C5 GTP 3 1 " pdb=" C6 GTP 3 1 " ideal model delta sigma weight residual 1.390 1.474 -0.084 2.00e-02 2.50e+03 1.77e+01 bond pdb=" C4 GTP 3 1 " pdb=" C5 GTP 3 1 " ideal model delta sigma weight residual 1.390 1.459 -0.069 2.00e-02 2.50e+03 1.20e+01 bond pdb=" CA ASP D 54 " pdb=" C ASP D 54 " ideal model delta sigma weight residual 1.524 1.490 0.034 1.29e-02 6.01e+03 6.97e+00 bond pdb=" C MET C1180 " pdb=" N PRO C1181 " ideal model delta sigma weight residual 1.334 1.306 0.028 1.11e-02 8.12e+03 6.33e+00 bond pdb=" CA ALA C 795 " pdb=" CB ALA C 795 " ideal model delta sigma weight residual 1.524 1.484 0.040 1.62e-02 3.81e+03 6.10e+00 ... (remaining 34061 not shown) Histogram of bond angle deviations from ideal: 95.20 - 103.44: 668 103.44 - 111.68: 16813 111.68 - 119.92: 14389 119.92 - 128.16: 14387 128.16 - 136.40: 326 Bond angle restraints: 46583 Sorted by residual: angle pdb=" O3' DG 2 34 " pdb=" C3' DG 2 34 " pdb=" C2' DG 2 34 " ideal model delta sigma weight residual 111.50 96.03 15.47 1.50e+00 4.44e-01 1.06e+02 angle pdb=" N ILE C1109 " pdb=" CA ILE C1109 " pdb=" C ILE C1109 " ideal model delta sigma weight residual 112.83 107.31 5.52 9.90e-01 1.02e+00 3.11e+01 angle pdb=" N GLN C1135 " pdb=" CA GLN C1135 " pdb=" CB GLN C1135 " ideal model delta sigma weight residual 114.17 108.15 6.02 1.14e+00 7.69e-01 2.79e+01 angle pdb=" N SER D 353 " pdb=" CA SER D 353 " pdb=" C SER D 353 " ideal model delta sigma weight residual 107.88 115.19 -7.31 1.41e+00 5.03e-01 2.69e+01 angle pdb=" C LYS D 39 " pdb=" N LYS D 40 " pdb=" CA LYS D 40 " ideal model delta sigma weight residual 122.38 107.93 14.45 2.90e+00 1.19e-01 2.48e+01 ... (remaining 46578 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.63: 19898 35.63 - 71.25: 721 71.25 - 106.88: 37 106.88 - 142.51: 1 142.51 - 178.14: 4 Dihedral angle restraints: 20661 sinusoidal: 9542 harmonic: 11119 Sorted by residual: dihedral pdb=" CA ASP C 340 " pdb=" C ASP C 340 " pdb=" N LEU C 341 " pdb=" CA LEU C 341 " ideal model delta harmonic sigma weight residual -180.00 -136.61 -43.39 0 5.00e+00 4.00e-02 7.53e+01 dihedral pdb=" CA GLN C1135 " pdb=" C GLN C1135 " pdb=" N GLN C1136 " pdb=" CA GLN C1136 " ideal model delta harmonic sigma weight residual 180.00 136.84 43.16 0 5.00e+00 4.00e-02 7.45e+01 dihedral pdb=" C5' GTP 3 1 " pdb=" O5' GTP 3 1 " pdb=" PA GTP 3 1 " pdb=" O3A GTP 3 1 " ideal model delta sinusoidal sigma weight residual 69.27 -108.87 178.14 1 2.00e+01 2.50e-03 4.80e+01 ... (remaining 20658 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.067: 4289 0.067 - 0.133: 936 0.133 - 0.200: 75 0.200 - 0.267: 12 0.267 - 0.333: 2 Chirality restraints: 5314 Sorted by residual: chirality pdb=" C3' DG 2 34 " pdb=" C4' DG 2 34 " pdb=" O3' DG 2 34 " pdb=" C2' DG 2 34 " both_signs ideal model delta sigma weight residual False -2.66 -2.99 0.33 2.00e-01 2.50e+01 2.78e+00 chirality pdb=" C3' DT 1 41 " pdb=" C4' DT 1 41 " pdb=" O3' DT 1 41 " pdb=" C2' DT 1 41 " both_signs ideal model delta sigma weight residual False -2.66 -2.37 -0.29 2.00e-01 2.50e+01 2.08e+00 chirality pdb=" CB THR C1184 " pdb=" CA THR C1184 " pdb=" OG1 THR C1184 " pdb=" CG2 THR C1184 " both_signs ideal model delta sigma weight residual False 2.55 2.29 0.27 2.00e-01 2.50e+01 1.77e+00 ... (remaining 5311 not shown) Planarity restraints: 5582 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C SER B 178 " 0.049 5.00e-02 4.00e+02 7.25e-02 8.40e+00 pdb=" N PRO B 179 " -0.125 5.00e-02 4.00e+02 pdb=" CA PRO B 179 " 0.037 5.00e-02 4.00e+02 pdb=" CD PRO B 179 " 0.039 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ARG B 166 " -0.044 5.00e-02 4.00e+02 6.55e-02 6.87e+00 pdb=" N PRO B 167 " 0.113 5.00e-02 4.00e+02 pdb=" CA PRO B 167 " -0.033 5.00e-02 4.00e+02 pdb=" CD PRO B 167 " -0.036 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA GLN C1135 " 0.013 2.00e-02 2.50e+03 2.61e-02 6.79e+00 pdb=" C GLN C1135 " -0.045 2.00e-02 2.50e+03 pdb=" O GLN C1135 " 0.016 2.00e-02 2.50e+03 pdb=" N GLN C1136 " 0.016 2.00e-02 2.50e+03 ... (remaining 5579 not shown) Histogram of nonbonded interaction distances: 1.99 - 2.57: 252 2.57 - 3.16: 27791 3.16 - 3.74: 48876 3.74 - 4.32: 67304 4.32 - 4.90: 112183 Nonbonded interactions: 256406 Sorted by model distance: nonbonded pdb=" OD1 ASP D 460 " pdb="MG MG D1503 " model vdw 1.992 2.170 nonbonded pdb=" O3' A 3 3 " pdb="MG MG D1503 " model vdw 2.046 2.170 nonbonded pdb=" NH2 ARG A 265 " pdb=" O ASN A 294 " model vdw 2.122 2.520 nonbonded pdb=" O GLU C 44 " pdb=" NE2 GLN C 46 " model vdw 2.123 2.520 nonbonded pdb=" NH1 ARG H 203 " pdb=" OP2 DA 1 19 " model vdw 2.127 2.520 ... (remaining 256401 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = chain 'G' selection = chain 'H' } 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=0.25 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: 3.180 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: 1.420 Check model and map are aligned: 0.250 Set scattering table: 0.320 Process input model: 102.040 Find NCS groups from input model: 0.770 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: 0.010 Load rotamer database and sin/cos tables:3.190 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 111.360 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8600 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 : 0.011 0.090 34066 Z= 0.749 Angle : 0.963 15.465 46583 Z= 0.552 Chirality : 0.053 0.333 5314 Planarity : 0.005 0.072 5582 Dihedral : 16.987 178.135 13485 Min Nonbonded Distance : 1.992 Molprobity Statistics. All-atom Clashscore : 10.95 Ramachandran Plot: Outliers : 0.13 % Allowed : 5.33 % Favored : 94.54 % Rotamer: Outliers : 0.00 % Allowed : 0.51 % Favored : 99.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.95 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.08 % 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: -0.98 (0.13), residues: 3831 helix: 0.42 (0.13), residues: 1568 sheet: -0.79 (0.22), residues: 463 loop : -1.58 (0.13), residues: 1800 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.002 TRP F 433 HIS 0.012 0.002 HIS D 469 PHE 0.038 0.003 PHE B 8 TYR 0.029 0.003 TYR C1285 ARG 0.014 0.001 ARG D 744 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7662 Ramachandran restraints generated. 3831 Oldfield, 0 Emsley, 3831 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7662 Ramachandran restraints generated. 3831 Oldfield, 0 Emsley, 3831 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 263 residues out of total 3310 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 263 time to evaluate : 3.516 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: C 160 ASP cc_start: 0.7893 (t70) cc_final: 0.7536 (p0) REVERT: C 337 PHE cc_start: 0.8203 (t80) cc_final: 0.7651 (t80) REVERT: C 339 ASN cc_start: 0.7266 (m110) cc_final: 0.7001 (t0) REVERT: C 1135 GLN cc_start: 0.8298 (tp-100) cc_final: 0.7926 (tp-100) REVERT: D 709 ARG cc_start: 0.6863 (pmt-80) cc_final: 0.5814 (pmt-80) REVERT: E 68 GLU cc_start: 0.8772 (tm-30) cc_final: 0.8341 (tm-30) REVERT: E 69 ARG cc_start: 0.8631 (ttm-80) cc_final: 0.8333 (tpp80) REVERT: F 242 HIS cc_start: 0.7600 (t-90) cc_final: 0.7224 (t-90) REVERT: F 561 MET cc_start: 0.8613 (tpp) cc_final: 0.8395 (tpp) REVERT: H 188 LYS cc_start: 0.8265 (ttpt) cc_final: 0.7653 (pptt) REVERT: H 194 MET cc_start: 0.9311 (mmt) cc_final: 0.8799 (mmm) REVERT: H 196 LYS cc_start: 0.8761 (mppt) cc_final: 0.8451 (mptt) outliers start: 0 outliers final: 0 residues processed: 263 average time/residue: 0.4537 time to fit residues: 194.2531 Evaluate side-chains 222 residues out of total 3310 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 222 time to evaluate : 3.280 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 394 random chunks: chunk 332 optimal weight: 20.0000 chunk 298 optimal weight: 9.9990 chunk 165 optimal weight: 0.8980 chunk 102 optimal weight: 1.9990 chunk 201 optimal weight: 0.0170 chunk 159 optimal weight: 2.9990 chunk 308 optimal weight: 0.9980 chunk 119 optimal weight: 0.8980 chunk 187 optimal weight: 0.9980 chunk 229 optimal weight: 0.8980 chunk 357 optimal weight: 1.9990 overall best weight: 0.7418 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 41 ASN ** B 66 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 84 ASN C 65 ASN D 232 ASN D 739 GLN D1126 GLN D1350 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8481 moved from start: 0.1320 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 34066 Z= 0.186 Angle : 0.608 11.707 46583 Z= 0.326 Chirality : 0.042 0.177 5314 Planarity : 0.004 0.054 5582 Dihedral : 17.190 170.165 5789 Min Nonbonded Distance : 2.042 Molprobity Statistics. All-atom Clashscore : 8.45 Ramachandran Plot: Outliers : 0.05 % Allowed : 4.36 % Favored : 95.59 % Rotamer: Outliers : 0.42 % Allowed : 5.19 % Favored : 94.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.95 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.08 % 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: -0.24 (0.13), residues: 3831 helix: 1.09 (0.13), residues: 1593 sheet: -0.37 (0.24), residues: 460 loop : -1.26 (0.14), residues: 1778 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP D1193 HIS 0.008 0.001 HIS G 193 PHE 0.022 0.001 PHE D 172 TYR 0.021 0.001 TYR C1018 ARG 0.011 0.001 ARG D 214 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7662 Ramachandran restraints generated. 3831 Oldfield, 0 Emsley, 3831 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7662 Ramachandran restraints generated. 3831 Oldfield, 0 Emsley, 3831 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 267 residues out of total 3310 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 253 time to evaluate : 3.538 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 316 MET cc_start: 0.3754 (mtt) cc_final: 0.3009 (mpp) REVERT: C 160 ASP cc_start: 0.7709 (t70) cc_final: 0.7320 (p0) REVERT: C 239 MET cc_start: 0.6726 (tmm) cc_final: 0.6513 (tmm) REVERT: C 479 LEU cc_start: 0.9215 (tp) cc_final: 0.8994 (tp) REVERT: C 1304 MET cc_start: 0.8842 (tpp) cc_final: 0.8462 (tpp) REVERT: C 1315 MET cc_start: 0.8904 (tpp) cc_final: 0.8541 (ttt) REVERT: D 715 LYS cc_start: 0.8864 (OUTLIER) cc_final: 0.8575 (mmmt) REVERT: D 1189 MET cc_start: 0.8687 (tmm) cc_final: 0.8438 (tmm) REVERT: E 68 GLU cc_start: 0.8710 (tm-30) cc_final: 0.8204 (tm-30) REVERT: E 69 ARG cc_start: 0.8603 (ttm-80) cc_final: 0.8355 (tpp80) REVERT: E 71 GLU cc_start: 0.8253 (tp30) cc_final: 0.8038 (tp30) REVERT: F 242 HIS cc_start: 0.7472 (t-90) cc_final: 0.7189 (t70) REVERT: F 561 MET cc_start: 0.8709 (tpp) cc_final: 0.8442 (tpp) REVERT: H 188 LYS cc_start: 0.8009 (ttpt) cc_final: 0.7462 (pptt) REVERT: H 194 MET cc_start: 0.9166 (mmt) cc_final: 0.8852 (mmt) outliers start: 14 outliers final: 5 residues processed: 262 average time/residue: 0.4368 time to fit residues: 189.2591 Evaluate side-chains 232 residues out of total 3310 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 226 time to evaluate : 3.587 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 628 HIS Chi-restraints excluded: chain C residue 895 LEU Chi-restraints excluded: chain D residue 703 THR Chi-restraints excluded: chain D residue 705 THR Chi-restraints excluded: chain D residue 715 LYS Chi-restraints excluded: chain D residue 743 MET Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 394 random chunks: chunk 198 optimal weight: 0.2980 chunk 111 optimal weight: 5.9990 chunk 297 optimal weight: 5.9990 chunk 243 optimal weight: 0.0670 chunk 98 optimal weight: 4.9990 chunk 358 optimal weight: 0.2980 chunk 387 optimal weight: 10.0000 chunk 319 optimal weight: 6.9990 chunk 355 optimal weight: 5.9990 chunk 122 optimal weight: 4.9990 chunk 287 optimal weight: 50.0000 overall best weight: 2.1322 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 66 HIS C 273 HIS D 669 GLN D 865 HIS E 31 GLN E 62 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8531 moved from start: 0.1457 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.057 34066 Z= 0.302 Angle : 0.592 10.628 46583 Z= 0.316 Chirality : 0.042 0.169 5314 Planarity : 0.004 0.047 5582 Dihedral : 17.077 166.130 5789 Min Nonbonded Distance : 2.001 Molprobity Statistics. All-atom Clashscore : 8.18 Ramachandran Plot: Outliers : 0.03 % Allowed : 4.78 % Favored : 95.20 % Rotamer: Outliers : 0.88 % Allowed : 7.61 % Favored : 91.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.95 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.05 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.08 (0.13), residues: 3831 helix: 1.27 (0.13), residues: 1601 sheet: -0.23 (0.24), residues: 455 loop : -1.25 (0.14), residues: 1775 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP D1193 HIS 0.006 0.001 HIS D 430 PHE 0.023 0.001 PHE D 172 TYR 0.016 0.001 TYR C1087 ARG 0.004 0.000 ARG F 285 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7662 Ramachandran restraints generated. 3831 Oldfield, 0 Emsley, 3831 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7662 Ramachandran restraints generated. 3831 Oldfield, 0 Emsley, 3831 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 272 residues out of total 3310 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 243 time to evaluate : 3.553 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 316 MET cc_start: 0.3688 (mtt) cc_final: 0.2764 (mpp) REVERT: C 239 MET cc_start: 0.6781 (tmm) cc_final: 0.6544 (tmm) REVERT: C 1315 MET cc_start: 0.8937 (tpp) cc_final: 0.8667 (ttt) REVERT: D 153 ASN cc_start: 0.7768 (m110) cc_final: 0.7353 (t160) REVERT: D 330 MET cc_start: 0.8622 (mtm) cc_final: 0.8417 (mtm) REVERT: E 68 GLU cc_start: 0.8735 (tm-30) cc_final: 0.8131 (tm-30) REVERT: F 242 HIS cc_start: 0.7376 (t-90) cc_final: 0.7059 (t70) REVERT: F 397 ARG cc_start: 0.7473 (mtt180) cc_final: 0.6922 (mpp80) REVERT: H 188 LYS cc_start: 0.7855 (ttpt) cc_final: 0.7199 (pptt) REVERT: H 194 MET cc_start: 0.9179 (mmt) cc_final: 0.8790 (mmt) outliers start: 29 outliers final: 15 residues processed: 261 average time/residue: 0.4557 time to fit residues: 195.2726 Evaluate side-chains 242 residues out of total 3310 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 227 time to evaluate : 3.619 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 131 CYS Chi-restraints excluded: chain B residue 203 ILE Chi-restraints excluded: chain B residue 205 MET Chi-restraints excluded: chain C residue 339 ASN Chi-restraints excluded: chain C residue 341 LEU Chi-restraints excluded: chain C residue 360 LEU Chi-restraints excluded: chain C residue 628 HIS Chi-restraints excluded: chain C residue 884 VAL Chi-restraints excluded: chain C residue 895 LEU Chi-restraints excluded: chain C residue 947 GLU Chi-restraints excluded: chain C residue 951 MET Chi-restraints excluded: chain D residue 499 ILE Chi-restraints excluded: chain D residue 703 THR Chi-restraints excluded: chain D residue 825 VAL Chi-restraints excluded: chain D residue 872 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 394 random chunks: chunk 354 optimal weight: 3.9990 chunk 269 optimal weight: 20.0000 chunk 186 optimal weight: 0.6980 chunk 39 optimal weight: 10.0000 chunk 171 optimal weight: 2.9990 chunk 240 optimal weight: 0.9990 chunk 359 optimal weight: 1.9990 chunk 380 optimal weight: 0.7980 chunk 187 optimal weight: 0.9980 chunk 340 optimal weight: 9.9990 chunk 102 optimal weight: 4.9990 overall best weight: 1.0984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C1080 ASN D 669 GLN D1252 HIS E 62 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8487 moved from start: 0.1869 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 34066 Z= 0.186 Angle : 0.533 10.917 46583 Z= 0.285 Chirality : 0.040 0.205 5314 Planarity : 0.004 0.046 5582 Dihedral : 16.998 160.645 5789 Min Nonbonded Distance : 2.036 Molprobity Statistics. All-atom Clashscore : 7.60 Ramachandran Plot: Outliers : 0.03 % Allowed : 4.07 % Favored : 95.90 % Rotamer: Outliers : 1.00 % Allowed : 9.30 % Favored : 89.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.95 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.05 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.20 (0.14), residues: 3831 helix: 1.50 (0.13), residues: 1600 sheet: 0.07 (0.24), residues: 439 loop : -1.14 (0.14), residues: 1792 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.001 TRP D1193 HIS 0.005 0.001 HIS G 193 PHE 0.018 0.001 PHE C 405 TYR 0.016 0.001 TYR B 68 ARG 0.006 0.000 ARG E 69 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7662 Ramachandran restraints generated. 3831 Oldfield, 0 Emsley, 3831 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7662 Ramachandran restraints generated. 3831 Oldfield, 0 Emsley, 3831 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 279 residues out of total 3310 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 33 poor density : 246 time to evaluate : 3.496 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 239 MET cc_start: 0.6667 (tmm) cc_final: 0.6408 (tmm) REVERT: C 1016 GLU cc_start: 0.8616 (OUTLIER) cc_final: 0.8372 (mp0) REVERT: D 29 MET cc_start: 0.8345 (tpp) cc_final: 0.7955 (ttp) REVERT: D 172 PHE cc_start: 0.8244 (m-10) cc_final: 0.8043 (m-80) REVERT: D 715 LYS cc_start: 0.8781 (OUTLIER) cc_final: 0.8539 (mmmt) REVERT: E 3 ARG cc_start: 0.8413 (mpt-90) cc_final: 0.8211 (mpt-90) REVERT: E 68 GLU cc_start: 0.8654 (tm-30) cc_final: 0.8132 (tm-30) REVERT: E 69 ARG cc_start: 0.8602 (tpp80) cc_final: 0.8337 (tpp80) REVERT: F 242 HIS cc_start: 0.7367 (t-90) cc_final: 0.7028 (t70) REVERT: F 561 MET cc_start: 0.8689 (tpp) cc_final: 0.8387 (tpp) REVERT: H 188 LYS cc_start: 0.7687 (ttpt) cc_final: 0.7024 (pptt) REVERT: H 194 MET cc_start: 0.9114 (mmt) cc_final: 0.8797 (mmt) outliers start: 33 outliers final: 20 residues processed: 268 average time/residue: 0.4295 time to fit residues: 190.5845 Evaluate side-chains 244 residues out of total 3310 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 222 time to evaluate : 3.680 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 131 CYS Chi-restraints excluded: chain C residue 164 THR Chi-restraints excluded: chain C residue 341 LEU Chi-restraints excluded: chain C residue 360 LEU Chi-restraints excluded: chain C residue 573 ASN Chi-restraints excluded: chain C residue 628 HIS Chi-restraints excluded: chain C residue 895 LEU Chi-restraints excluded: chain C residue 951 MET Chi-restraints excluded: chain C residue 1016 GLU Chi-restraints excluded: chain C residue 1080 ASN Chi-restraints excluded: chain C residue 1137 GLU Chi-restraints excluded: chain C residue 1184 THR Chi-restraints excluded: chain C residue 1255 THR Chi-restraints excluded: chain D residue 78 LEU Chi-restraints excluded: chain D residue 192 MET Chi-restraints excluded: chain D residue 554 GLU Chi-restraints excluded: chain D residue 703 THR Chi-restraints excluded: chain D residue 705 THR Chi-restraints excluded: chain D residue 715 LYS Chi-restraints excluded: chain D residue 825 VAL Chi-restraints excluded: chain D residue 872 LEU Chi-restraints excluded: chain E residue 56 GLU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 394 random chunks: chunk 317 optimal weight: 4.9990 chunk 216 optimal weight: 0.9990 chunk 5 optimal weight: 2.9990 chunk 283 optimal weight: 30.0000 chunk 157 optimal weight: 0.6980 chunk 324 optimal weight: 0.2980 chunk 263 optimal weight: 10.0000 chunk 0 optimal weight: 5.9990 chunk 194 optimal weight: 4.9990 chunk 341 optimal weight: 8.9990 chunk 96 optimal weight: 4.9990 overall best weight: 1.9986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 66 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C1111 GLN D 153 ASN ** D 294 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 669 GLN E 62 GLN ** F 406 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 600 HIS H 173 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8524 moved from start: 0.1920 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.051 34066 Z= 0.275 Angle : 0.560 10.686 46583 Z= 0.297 Chirality : 0.041 0.243 5314 Planarity : 0.004 0.046 5582 Dihedral : 16.983 160.065 5789 Min Nonbonded Distance : 2.020 Molprobity Statistics. All-atom Clashscore : 7.41 Ramachandran Plot: Outliers : 0.03 % Allowed : 4.73 % Favored : 95.25 % Rotamer: Outliers : 1.48 % Allowed : 9.82 % Favored : 88.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.95 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % 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: 0.23 (0.14), residues: 3831 helix: 1.52 (0.13), residues: 1606 sheet: -0.05 (0.24), residues: 459 loop : -1.09 (0.14), residues: 1766 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.001 TRP D1193 HIS 0.008 0.001 HIS H 193 PHE 0.019 0.001 PHE C 405 TYR 0.015 0.001 TYR C1087 ARG 0.005 0.000 ARG A 44 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7662 Ramachandran restraints generated. 3831 Oldfield, 0 Emsley, 3831 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7662 Ramachandran restraints generated. 3831 Oldfield, 0 Emsley, 3831 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 275 residues out of total 3310 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 49 poor density : 226 time to evaluate : 3.826 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 239 MET cc_start: 0.6750 (tmm) cc_final: 0.6496 (tmm) REVERT: C 1016 GLU cc_start: 0.8637 (OUTLIER) cc_final: 0.8405 (mp0) REVERT: C 1212 LEU cc_start: 0.9121 (OUTLIER) cc_final: 0.8858 (mp) REVERT: D 715 LYS cc_start: 0.8753 (OUTLIER) cc_final: 0.8408 (mmmt) REVERT: D 865 HIS cc_start: 0.7242 (OUTLIER) cc_final: 0.6955 (m90) REVERT: D 960 LEU cc_start: 0.8179 (mm) cc_final: 0.7892 (mt) REVERT: E 68 GLU cc_start: 0.8742 (tm-30) cc_final: 0.8218 (tm-30) REVERT: F 242 HIS cc_start: 0.7349 (t-90) cc_final: 0.6988 (t70) REVERT: H 188 LYS cc_start: 0.7713 (ttpt) cc_final: 0.6996 (pptt) REVERT: H 194 MET cc_start: 0.9138 (mmt) cc_final: 0.8832 (mmt) outliers start: 49 outliers final: 27 residues processed: 260 average time/residue: 0.4402 time to fit residues: 190.5518 Evaluate side-chains 250 residues out of total 3310 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 219 time to evaluate : 3.398 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 131 CYS Chi-restraints excluded: chain B residue 203 ILE Chi-restraints excluded: chain C residue 164 THR Chi-restraints excluded: chain C residue 360 LEU Chi-restraints excluded: chain C residue 398 SER Chi-restraints excluded: chain C residue 481 LEU Chi-restraints excluded: chain C residue 573 ASN Chi-restraints excluded: chain C residue 628 HIS Chi-restraints excluded: chain C residue 884 VAL Chi-restraints excluded: chain C residue 895 LEU Chi-restraints excluded: chain C residue 947 GLU Chi-restraints excluded: chain C residue 1016 GLU Chi-restraints excluded: chain C residue 1137 GLU Chi-restraints excluded: chain C residue 1184 THR Chi-restraints excluded: chain C residue 1212 LEU Chi-restraints excluded: chain C residue 1255 THR Chi-restraints excluded: chain D residue 78 LEU Chi-restraints excluded: chain D residue 192 MET Chi-restraints excluded: chain D residue 198 CYS Chi-restraints excluded: chain D residue 499 ILE Chi-restraints excluded: chain D residue 703 THR Chi-restraints excluded: chain D residue 705 THR Chi-restraints excluded: chain D residue 715 LYS Chi-restraints excluded: chain D residue 825 VAL Chi-restraints excluded: chain D residue 865 HIS Chi-restraints excluded: chain D residue 872 LEU Chi-restraints excluded: chain D residue 1178 THR Chi-restraints excluded: chain D residue 1209 VAL Chi-restraints excluded: chain D residue 1313 SER Chi-restraints excluded: chain E residue 56 GLU Chi-restraints excluded: chain F residue 600 HIS Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 394 random chunks: chunk 128 optimal weight: 3.9990 chunk 342 optimal weight: 7.9990 chunk 75 optimal weight: 0.5980 chunk 223 optimal weight: 1.9990 chunk 94 optimal weight: 0.9990 chunk 381 optimal weight: 6.9990 chunk 316 optimal weight: 2.9990 chunk 176 optimal weight: 7.9990 chunk 31 optimal weight: 2.9990 chunk 126 optimal weight: 4.9990 chunk 200 optimal weight: 9.9990 overall best weight: 1.9188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 66 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 294 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 62 GLN ** F 406 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 600 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8525 moved from start: 0.2022 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.055 34066 Z= 0.263 Angle : 0.554 11.503 46583 Z= 0.294 Chirality : 0.041 0.227 5314 Planarity : 0.004 0.046 5582 Dihedral : 16.931 160.104 5789 Min Nonbonded Distance : 2.017 Molprobity Statistics. All-atom Clashscore : 7.54 Ramachandran Plot: Outliers : 0.03 % Allowed : 4.62 % Favored : 95.35 % Rotamer: Outliers : 1.39 % Allowed : 10.72 % Favored : 87.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.95 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % 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: 0.31 (0.14), residues: 3831 helix: 1.57 (0.13), residues: 1605 sheet: 0.02 (0.24), residues: 459 loop : -1.04 (0.14), residues: 1767 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.001 TRP D1193 HIS 0.007 0.001 HIS G 193 PHE 0.018 0.001 PHE C 405 TYR 0.017 0.001 TYR C1018 ARG 0.007 0.000 ARG D 214 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7662 Ramachandran restraints generated. 3831 Oldfield, 0 Emsley, 3831 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7662 Ramachandran restraints generated. 3831 Oldfield, 0 Emsley, 3831 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 270 residues out of total 3310 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 46 poor density : 224 time to evaluate : 3.541 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 239 MET cc_start: 0.6866 (tmm) cc_final: 0.6576 (tmm) REVERT: C 959 ASP cc_start: 0.8450 (m-30) cc_final: 0.8048 (m-30) REVERT: C 1212 LEU cc_start: 0.9145 (OUTLIER) cc_final: 0.8885 (mp) REVERT: D 140 TYR cc_start: 0.8344 (m-10) cc_final: 0.8106 (m-10) REVERT: D 715 LYS cc_start: 0.8741 (OUTLIER) cc_final: 0.8520 (mmmt) REVERT: D 827 GLU cc_start: 0.8217 (tm-30) cc_final: 0.7858 (tm-30) REVERT: D 865 HIS cc_start: 0.7230 (OUTLIER) cc_final: 0.6937 (m90) REVERT: E 68 GLU cc_start: 0.8752 (tm-30) cc_final: 0.8436 (tm-30) REVERT: F 242 HIS cc_start: 0.7404 (t-90) cc_final: 0.7040 (t70) REVERT: F 397 ARG cc_start: 0.7503 (mtt180) cc_final: 0.7057 (mpp80) REVERT: F 561 MET cc_start: 0.8690 (tpp) cc_final: 0.8416 (tpp) REVERT: H 188 LYS cc_start: 0.7695 (ttpt) cc_final: 0.6955 (pptt) REVERT: H 194 MET cc_start: 0.9120 (mmt) cc_final: 0.8844 (mmt) outliers start: 46 outliers final: 32 residues processed: 258 average time/residue: 0.4242 time to fit residues: 181.9771 Evaluate side-chains 255 residues out of total 3310 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 35 poor density : 220 time to evaluate : 3.597 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 131 CYS Chi-restraints excluded: chain B residue 203 ILE Chi-restraints excluded: chain C residue 39 ILE Chi-restraints excluded: chain C residue 164 THR Chi-restraints excluded: chain C residue 341 LEU Chi-restraints excluded: chain C residue 360 LEU Chi-restraints excluded: chain C residue 398 SER Chi-restraints excluded: chain C residue 481 LEU Chi-restraints excluded: chain C residue 573 ASN Chi-restraints excluded: chain C residue 628 HIS Chi-restraints excluded: chain C residue 884 VAL Chi-restraints excluded: chain C residue 895 LEU Chi-restraints excluded: chain C residue 947 GLU Chi-restraints excluded: chain C residue 1137 GLU Chi-restraints excluded: chain C residue 1184 THR Chi-restraints excluded: chain C residue 1212 LEU Chi-restraints excluded: chain C residue 1255 THR Chi-restraints excluded: chain D residue 78 LEU Chi-restraints excluded: chain D residue 192 MET Chi-restraints excluded: chain D residue 198 CYS Chi-restraints excluded: chain D residue 554 GLU Chi-restraints excluded: chain D residue 703 THR Chi-restraints excluded: chain D residue 705 THR Chi-restraints excluded: chain D residue 715 LYS Chi-restraints excluded: chain D residue 803 VAL Chi-restraints excluded: chain D residue 807 LEU Chi-restraints excluded: chain D residue 825 VAL Chi-restraints excluded: chain D residue 865 HIS Chi-restraints excluded: chain D residue 872 LEU Chi-restraints excluded: chain D residue 1178 THR Chi-restraints excluded: chain D residue 1209 VAL Chi-restraints excluded: chain D residue 1313 SER Chi-restraints excluded: chain E residue 56 GLU Chi-restraints excluded: chain F residue 470 MET Chi-restraints excluded: chain G residue 189 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 394 random chunks: chunk 367 optimal weight: 5.9990 chunk 42 optimal weight: 10.0000 chunk 217 optimal weight: 0.9980 chunk 278 optimal weight: 8.9990 chunk 215 optimal weight: 2.9990 chunk 320 optimal weight: 3.9990 chunk 212 optimal weight: 4.9990 chunk 379 optimal weight: 8.9990 chunk 237 optimal weight: 0.9990 chunk 231 optimal weight: 2.9990 chunk 175 optimal weight: 1.9990 overall best weight: 1.9988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 66 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 294 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 62 GLN F 258 GLN ** F 406 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 600 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8531 moved from start: 0.2105 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.053 34066 Z= 0.273 Angle : 0.560 12.145 46583 Z= 0.297 Chirality : 0.041 0.240 5314 Planarity : 0.004 0.045 5582 Dihedral : 16.898 159.678 5789 Min Nonbonded Distance : 2.013 Molprobity Statistics. All-atom Clashscore : 7.53 Ramachandran Plot: Outliers : 0.03 % Allowed : 4.86 % Favored : 95.12 % Rotamer: Outliers : 1.57 % Allowed : 11.24 % Favored : 87.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.95 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % 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: 3831 helix: 1.58 (0.13), residues: 1605 sheet: 0.15 (0.24), residues: 445 loop : -0.99 (0.14), residues: 1781 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.001 TRP D1193 HIS 0.011 0.001 HIS H 193 PHE 0.018 0.001 PHE C 405 TYR 0.013 0.001 TYR C1018 ARG 0.006 0.000 ARG A 44 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7662 Ramachandran restraints generated. 3831 Oldfield, 0 Emsley, 3831 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7662 Ramachandran restraints generated. 3831 Oldfield, 0 Emsley, 3831 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 279 residues out of total 3310 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 52 poor density : 227 time to evaluate : 3.981 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: C 239 MET cc_start: 0.6901 (tmm) cc_final: 0.6601 (tmm) REVERT: C 241 LEU cc_start: 0.8533 (tp) cc_final: 0.8221 (tt) REVERT: C 959 ASP cc_start: 0.8462 (m-30) cc_final: 0.8057 (m-30) REVERT: C 1016 GLU cc_start: 0.8615 (OUTLIER) cc_final: 0.8238 (mp0) REVERT: C 1212 LEU cc_start: 0.9110 (OUTLIER) cc_final: 0.8835 (mp) REVERT: D 140 TYR cc_start: 0.8255 (m-10) cc_final: 0.7984 (m-10) REVERT: D 827 GLU cc_start: 0.8194 (tm-30) cc_final: 0.7827 (tm-30) REVERT: D 865 HIS cc_start: 0.7235 (OUTLIER) cc_final: 0.6937 (m90) REVERT: D 930 LEU cc_start: 0.9002 (OUTLIER) cc_final: 0.8616 (mp) REVERT: E 68 GLU cc_start: 0.8756 (tm-30) cc_final: 0.8403 (tm-30) REVERT: F 242 HIS cc_start: 0.7443 (t-90) cc_final: 0.7084 (t70) REVERT: F 397 ARG cc_start: 0.7581 (mtt180) cc_final: 0.7081 (mpp80) REVERT: F 561 MET cc_start: 0.8715 (tpp) cc_final: 0.8389 (tpp) REVERT: H 188 LYS cc_start: 0.7695 (ttpt) cc_final: 0.6928 (pptt) REVERT: H 194 MET cc_start: 0.9106 (mmt) cc_final: 0.8785 (mmt) outliers start: 52 outliers final: 36 residues processed: 264 average time/residue: 0.4280 time to fit residues: 189.1300 Evaluate side-chains 262 residues out of total 3310 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 40 poor density : 222 time to evaluate : 4.146 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 131 CYS Chi-restraints excluded: chain B residue 203 ILE Chi-restraints excluded: chain C residue 39 ILE Chi-restraints excluded: chain C residue 164 THR Chi-restraints excluded: chain C residue 273 HIS Chi-restraints excluded: chain C residue 321 LEU Chi-restraints excluded: chain C residue 341 LEU Chi-restraints excluded: chain C residue 360 LEU Chi-restraints excluded: chain C residue 398 SER Chi-restraints excluded: chain C residue 481 LEU Chi-restraints excluded: chain C residue 573 ASN Chi-restraints excluded: chain C residue 628 HIS Chi-restraints excluded: chain C residue 884 VAL Chi-restraints excluded: chain C residue 895 LEU Chi-restraints excluded: chain C residue 947 GLU Chi-restraints excluded: chain C residue 1016 GLU Chi-restraints excluded: chain C residue 1137 GLU Chi-restraints excluded: chain C residue 1184 THR Chi-restraints excluded: chain C residue 1212 LEU Chi-restraints excluded: chain C residue 1255 THR Chi-restraints excluded: chain D residue 78 LEU Chi-restraints excluded: chain D residue 198 CYS Chi-restraints excluded: chain D residue 499 ILE Chi-restraints excluded: chain D residue 554 GLU Chi-restraints excluded: chain D residue 703 THR Chi-restraints excluded: chain D residue 705 THR Chi-restraints excluded: chain D residue 743 MET Chi-restraints excluded: chain D residue 803 VAL Chi-restraints excluded: chain D residue 807 LEU Chi-restraints excluded: chain D residue 825 VAL Chi-restraints excluded: chain D residue 865 HIS Chi-restraints excluded: chain D residue 872 LEU Chi-restraints excluded: chain D residue 930 LEU Chi-restraints excluded: chain D residue 979 ASN Chi-restraints excluded: chain D residue 1178 THR Chi-restraints excluded: chain D residue 1209 VAL Chi-restraints excluded: chain D residue 1313 SER Chi-restraints excluded: chain E residue 13 ILE Chi-restraints excluded: chain E residue 56 GLU Chi-restraints excluded: chain F residue 600 HIS Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 394 random chunks: chunk 234 optimal weight: 2.9990 chunk 151 optimal weight: 0.0010 chunk 226 optimal weight: 0.7980 chunk 114 optimal weight: 0.0010 chunk 74 optimal weight: 6.9990 chunk 73 optimal weight: 0.7980 chunk 241 optimal weight: 0.2980 chunk 258 optimal weight: 4.9990 chunk 187 optimal weight: 1.9990 chunk 35 optimal weight: 5.9990 chunk 298 optimal weight: 0.9990 overall best weight: 0.3792 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 66 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 75 GLN ** D 294 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D1326 GLN E 62 GLN ** F 406 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8461 moved from start: 0.2419 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.041 34066 Z= 0.140 Angle : 0.517 12.992 46583 Z= 0.275 Chirality : 0.039 0.230 5314 Planarity : 0.004 0.049 5582 Dihedral : 16.798 157.933 5789 Min Nonbonded Distance : 2.048 Molprobity Statistics. All-atom Clashscore : 7.51 Ramachandran Plot: Outliers : 0.03 % Allowed : 3.99 % Favored : 95.98 % Rotamer: Outliers : 0.97 % Allowed : 11.93 % Favored : 87.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.95 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % 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: 3831 helix: 1.76 (0.13), residues: 1618 sheet: 0.46 (0.25), residues: 428 loop : -0.89 (0.14), residues: 1785 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.001 TRP D1193 HIS 0.030 0.001 HIS F 600 PHE 0.016 0.001 PHE C 405 TYR 0.014 0.001 TYR C1018 ARG 0.014 0.000 ARG F 603 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7662 Ramachandran restraints generated. 3831 Oldfield, 0 Emsley, 3831 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7662 Ramachandran restraints generated. 3831 Oldfield, 0 Emsley, 3831 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 277 residues out of total 3310 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 245 time to evaluate : 3.540 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: C 239 MET cc_start: 0.6853 (tmm) cc_final: 0.6549 (tmm) REVERT: C 241 LEU cc_start: 0.8508 (tp) cc_final: 0.8177 (tt) REVERT: C 959 ASP cc_start: 0.8448 (m-30) cc_final: 0.8137 (m-30) REVERT: D 29 MET cc_start: 0.8295 (tpp) cc_final: 0.7946 (ttp) REVERT: D 140 TYR cc_start: 0.8129 (m-10) cc_final: 0.7796 (m-10) REVERT: D 827 GLU cc_start: 0.8162 (tm-30) cc_final: 0.7781 (tm-30) REVERT: E 68 GLU cc_start: 0.8719 (tm-30) cc_final: 0.8390 (tm-30) REVERT: E 73 GLN cc_start: 0.8913 (tt0) cc_final: 0.8449 (pp30) REVERT: F 242 HIS cc_start: 0.7377 (t-90) cc_final: 0.7017 (t70) REVERT: F 397 ARG cc_start: 0.7453 (mtt180) cc_final: 0.7007 (mpp80) REVERT: F 561 MET cc_start: 0.8721 (tpp) cc_final: 0.8383 (tpp) REVERT: H 188 LYS cc_start: 0.7687 (ttpt) cc_final: 0.6969 (pptt) outliers start: 32 outliers final: 23 residues processed: 269 average time/residue: 0.4330 time to fit residues: 195.7415 Evaluate side-chains 250 residues out of total 3310 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 227 time to evaluate : 4.285 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 203 ILE Chi-restraints excluded: chain C residue 164 THR Chi-restraints excluded: chain C residue 321 LEU Chi-restraints excluded: chain C residue 360 LEU Chi-restraints excluded: chain C residue 573 ASN Chi-restraints excluded: chain C residue 628 HIS Chi-restraints excluded: chain C residue 884 VAL Chi-restraints excluded: chain C residue 895 LEU Chi-restraints excluded: chain D residue 78 LEU Chi-restraints excluded: chain D residue 192 MET Chi-restraints excluded: chain D residue 198 CYS Chi-restraints excluded: chain D residue 554 GLU Chi-restraints excluded: chain D residue 703 THR Chi-restraints excluded: chain D residue 705 THR Chi-restraints excluded: chain D residue 807 LEU Chi-restraints excluded: chain D residue 825 VAL Chi-restraints excluded: chain D residue 858 VAL Chi-restraints excluded: chain D residue 872 LEU Chi-restraints excluded: chain D residue 979 ASN Chi-restraints excluded: chain E residue 13 ILE Chi-restraints excluded: chain E residue 56 GLU Chi-restraints excluded: chain F residue 600 HIS Chi-restraints excluded: chain G residue 189 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 394 random chunks: chunk 345 optimal weight: 20.0000 chunk 363 optimal weight: 9.9990 chunk 331 optimal weight: 5.9990 chunk 353 optimal weight: 1.9990 chunk 212 optimal weight: 4.9990 chunk 154 optimal weight: 0.9990 chunk 277 optimal weight: 4.9990 chunk 108 optimal weight: 0.9980 chunk 319 optimal weight: 4.9990 chunk 334 optimal weight: 0.0670 chunk 352 optimal weight: 4.9990 overall best weight: 1.8124 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 66 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 294 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 62 GLN ** F 406 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 600 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8518 moved from start: 0.2347 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.047 34066 Z= 0.252 Angle : 0.559 14.499 46583 Z= 0.292 Chirality : 0.041 0.214 5314 Planarity : 0.004 0.047 5582 Dihedral : 16.774 157.496 5789 Min Nonbonded Distance : 2.024 Molprobity Statistics. All-atom Clashscore : 7.22 Ramachandran Plot: Outliers : 0.03 % Allowed : 4.44 % Favored : 95.54 % Rotamer: Outliers : 0.88 % Allowed : 12.47 % Favored : 86.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.95 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % 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: 3831 helix: 1.71 (0.13), residues: 1611 sheet: 0.46 (0.25), residues: 436 loop : -0.89 (0.14), residues: 1784 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.001 TRP D1193 HIS 0.014 0.001 HIS H 193 PHE 0.017 0.001 PHE C 405 TYR 0.013 0.001 TYR C1087 ARG 0.008 0.000 ARG D 709 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7662 Ramachandran restraints generated. 3831 Oldfield, 0 Emsley, 3831 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7662 Ramachandran restraints generated. 3831 Oldfield, 0 Emsley, 3831 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 253 residues out of total 3310 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 224 time to evaluate : 3.854 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 239 MET cc_start: 0.6886 (tmm) cc_final: 0.6581 (tmm) REVERT: C 241 LEU cc_start: 0.8527 (tp) cc_final: 0.8202 (tt) REVERT: C 315 MET cc_start: 0.7024 (pmm) cc_final: 0.6612 (pmm) REVERT: C 959 ASP cc_start: 0.8444 (m-30) cc_final: 0.8149 (m-30) REVERT: D 140 TYR cc_start: 0.8194 (m-10) cc_final: 0.7843 (m-10) REVERT: D 827 GLU cc_start: 0.8205 (tm-30) cc_final: 0.7811 (tm-30) REVERT: E 68 GLU cc_start: 0.8722 (tm-30) cc_final: 0.8391 (tm-30) REVERT: E 73 GLN cc_start: 0.8951 (tt0) cc_final: 0.8453 (pp30) REVERT: F 242 HIS cc_start: 0.7475 (t-90) cc_final: 0.7098 (t70) REVERT: F 561 MET cc_start: 0.8697 (tpp) cc_final: 0.8334 (tpp) REVERT: H 188 LYS cc_start: 0.7770 (ttpt) cc_final: 0.7061 (pptt) REVERT: H 194 MET cc_start: 0.9197 (mmt) cc_final: 0.8973 (mmt) outliers start: 29 outliers final: 26 residues processed: 242 average time/residue: 0.4540 time to fit residues: 184.6734 Evaluate side-chains 247 residues out of total 3310 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 221 time to evaluate : 3.595 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 203 ILE Chi-restraints excluded: chain C residue 164 THR Chi-restraints excluded: chain C residue 273 HIS Chi-restraints excluded: chain C residue 321 LEU Chi-restraints excluded: chain C residue 341 LEU Chi-restraints excluded: chain C residue 360 LEU Chi-restraints excluded: chain C residue 573 ASN Chi-restraints excluded: chain C residue 628 HIS Chi-restraints excluded: chain C residue 799 ASN Chi-restraints excluded: chain C residue 884 VAL Chi-restraints excluded: chain C residue 895 LEU Chi-restraints excluded: chain D residue 78 LEU Chi-restraints excluded: chain D residue 198 CYS Chi-restraints excluded: chain D residue 554 GLU Chi-restraints excluded: chain D residue 703 THR Chi-restraints excluded: chain D residue 705 THR Chi-restraints excluded: chain D residue 807 LEU Chi-restraints excluded: chain D residue 825 VAL Chi-restraints excluded: chain D residue 872 LEU Chi-restraints excluded: chain D residue 979 ASN Chi-restraints excluded: chain E residue 13 ILE Chi-restraints excluded: chain E residue 56 GLU Chi-restraints excluded: chain F residue 470 MET Chi-restraints excluded: chain F residue 600 HIS Chi-restraints excluded: chain G residue 189 VAL Chi-restraints excluded: chain H residue 195 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 394 random chunks: chunk 232 optimal weight: 2.9990 chunk 374 optimal weight: 1.9990 chunk 228 optimal weight: 1.9990 chunk 177 optimal weight: 0.5980 chunk 260 optimal weight: 5.9990 chunk 392 optimal weight: 10.0000 chunk 361 optimal weight: 1.9990 chunk 312 optimal weight: 1.9990 chunk 32 optimal weight: 0.4980 chunk 241 optimal weight: 4.9990 chunk 191 optimal weight: 0.9980 overall best weight: 1.2184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 66 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 294 ASN E 62 GLN F 406 GLN F 600 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8499 moved from start: 0.2445 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 34066 Z= 0.194 Angle : 0.547 14.224 46583 Z= 0.285 Chirality : 0.040 0.210 5314 Planarity : 0.004 0.046 5582 Dihedral : 16.740 156.838 5789 Min Nonbonded Distance : 2.029 Molprobity Statistics. All-atom Clashscore : 7.34 Ramachandran Plot: Outliers : 0.03 % Allowed : 4.39 % Favored : 95.59 % Rotamer: Outliers : 0.91 % Allowed : 12.56 % Favored : 86.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.95 % 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: 0.63 (0.14), residues: 3831 helix: 1.74 (0.13), residues: 1611 sheet: 0.59 (0.25), residues: 423 loop : -0.87 (0.14), residues: 1797 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.001 TRP D1193 HIS 0.010 0.001 HIS H 193 PHE 0.016 0.001 PHE C 405 TYR 0.014 0.001 TYR C1018 ARG 0.007 0.000 ARG D 709 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7662 Ramachandran restraints generated. 3831 Oldfield, 0 Emsley, 3831 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7662 Ramachandran restraints generated. 3831 Oldfield, 0 Emsley, 3831 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 255 residues out of total 3310 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 225 time to evaluate : 3.587 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 239 MET cc_start: 0.6885 (tmm) cc_final: 0.6580 (tmm) REVERT: C 241 LEU cc_start: 0.8502 (tp) cc_final: 0.8171 (tt) REVERT: C 315 MET cc_start: 0.6996 (pmm) cc_final: 0.6591 (pmm) REVERT: C 959 ASP cc_start: 0.8443 (m-30) cc_final: 0.8146 (m-30) REVERT: D 29 MET cc_start: 0.8358 (tpp) cc_final: 0.7918 (ttp) REVERT: D 140 TYR cc_start: 0.8133 (m-10) cc_final: 0.7774 (m-10) REVERT: D 827 GLU cc_start: 0.8180 (tm-30) cc_final: 0.7785 (tm-30) REVERT: E 68 GLU cc_start: 0.8712 (tm-30) cc_final: 0.8404 (tm-30) REVERT: E 73 GLN cc_start: 0.8963 (tt0) cc_final: 0.8465 (pp30) REVERT: F 242 HIS cc_start: 0.7370 (t-90) cc_final: 0.7005 (t70) REVERT: H 188 LYS cc_start: 0.7747 (ttpt) cc_final: 0.7019 (pptt) outliers start: 30 outliers final: 25 residues processed: 245 average time/residue: 0.4309 time to fit residues: 176.5927 Evaluate side-chains 248 residues out of total 3310 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 223 time to evaluate : 3.303 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 203 ILE Chi-restraints excluded: chain C residue 82 VAL Chi-restraints excluded: chain C residue 164 THR Chi-restraints excluded: chain C residue 273 HIS Chi-restraints excluded: chain C residue 341 LEU Chi-restraints excluded: chain C residue 360 LEU Chi-restraints excluded: chain C residue 573 ASN Chi-restraints excluded: chain C residue 628 HIS Chi-restraints excluded: chain C residue 799 ASN Chi-restraints excluded: chain C residue 884 VAL Chi-restraints excluded: chain C residue 895 LEU Chi-restraints excluded: chain D residue 198 CYS Chi-restraints excluded: chain D residue 554 GLU Chi-restraints excluded: chain D residue 703 THR Chi-restraints excluded: chain D residue 705 THR Chi-restraints excluded: chain D residue 743 MET Chi-restraints excluded: chain D residue 807 LEU Chi-restraints excluded: chain D residue 825 VAL Chi-restraints excluded: chain D residue 872 LEU Chi-restraints excluded: chain D residue 979 ASN Chi-restraints excluded: chain E residue 13 ILE Chi-restraints excluded: chain E residue 56 GLU Chi-restraints excluded: chain F residue 470 MET Chi-restraints excluded: chain G residue 189 VAL Chi-restraints excluded: chain H residue 195 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 394 random chunks: chunk 248 optimal weight: 2.9990 chunk 332 optimal weight: 40.0000 chunk 95 optimal weight: 9.9990 chunk 288 optimal weight: 7.9990 chunk 46 optimal weight: 8.9990 chunk 86 optimal weight: 4.9990 chunk 313 optimal weight: 5.9990 chunk 131 optimal weight: 3.9990 chunk 321 optimal weight: 3.9990 chunk 39 optimal weight: 9.9990 chunk 57 optimal weight: 0.9990 overall best weight: 3.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 66 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 294 ASN D 669 GLN E 62 GLN F 406 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3831 r_free = 0.3831 target = 0.117679 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.2844 r_free = 0.2844 target = 0.062431 restraints weight = 97681.752| |-----------------------------------------------------------------------------| r_work (start): 0.2813 rms_B_bonded: 3.44 r_work: 0.2616 rms_B_bonded: 3.74 restraints_weight: 0.5000 r_work (final): 0.2616 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2620 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2620 r_free = 0.2620 target_work(ls_wunit_k1) = 0.052 | | occupancies: max = 1.00 min = 0.25 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2620 r_free = 0.2620 target_work(ls_wunit_k1) = 0.052 | | occupancies: max = 1.00 min = 0.36 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2620 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8674 moved from start: 0.2265 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.075 34066 Z= 0.420 Angle : 0.634 15.585 46583 Z= 0.331 Chirality : 0.043 0.204 5314 Planarity : 0.004 0.054 5582 Dihedral : 16.857 157.165 5789 Min Nonbonded Distance : 1.993 Molprobity Statistics. All-atom Clashscore : 7.98 Ramachandran Plot: Outliers : 0.03 % Allowed : 5.04 % Favored : 94.93 % Rotamer: Outliers : 0.97 % Allowed : 12.62 % Favored : 86.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.95 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % 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: 3831 helix: 1.49 (0.13), residues: 1616 sheet: 0.38 (0.25), residues: 423 loop : -0.96 (0.14), residues: 1792 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP D1193 HIS 0.010 0.001 HIS H 193 PHE 0.019 0.001 PHE C 405 TYR 0.019 0.001 TYR C1087 ARG 0.007 0.001 ARG A 44 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 7229.69 seconds wall clock time: 129 minutes 39.90 seconds (7779.90 seconds total)