Starting phenix.real_space_refine on Thu Feb 22 23:35:15 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6xl5_22234/02_2024/6xl5_22234_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6xl5_22234/02_2024/6xl5_22234.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.5 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6xl5_22234/02_2024/6xl5_22234.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6xl5_22234/02_2024/6xl5_22234.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6xl5_22234/02_2024/6xl5_22234_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6xl5_22234/02_2024/6xl5_22234_updated.pdb" } resolution = 2.5 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= 0.002 sd= 0.092 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: 8 Type Number sf(0) Gaussians Sb 2 10.97 5 Zn 2 6.06 5 P 106 5.49 5 Mg 1 5.21 5 S 155 5.16 5 C 22215 2.51 5 N 6272 2.21 5 O 7075 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A GLU 163": "OE1" <-> "OE2" Residue "A ASP 164": "OD1" <-> "OD2" Residue "A GLU 181": "OE1" <-> "OE2" Residue "A GLU 226": "OE1" <-> "OE2" Residue "A ARG 235": "NH1" <-> "NH2" Residue "B GLU 67": "OE1" <-> "OE2" Residue "B GLU 80": "OE1" <-> "OE2" Residue "B GLU 181": "OE1" <-> "OE2" Residue "B TYR 185": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 62": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 73": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 84": "OE1" <-> "OE2" Residue "C ARG 180": "NH1" <-> "NH2" Residue "C ASP 222": "OD1" <-> "OD2" Residue "C ASP 254": "OD1" <-> "OD2" Residue "C ARG 268": "NH1" <-> "NH2" Residue "C ASP 303": "OD1" <-> "OD2" Residue "C GLU 304": "OE1" <-> "OE2" Residue "C ARG 332": "NH1" <-> "NH2" Residue "C ASP 342": "OD1" <-> "OD2" Residue "C TYR 367": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 413": "OE1" <-> "OE2" Residue "C ARG 465": "NH1" <-> "NH2" Residue "C GLU 477": "OE1" <-> "OE2" Residue "C ARG 540": "NH1" <-> "NH2" Residue "C ASP 648": "OD1" <-> "OD2" Residue "C GLU 705": "OE1" <-> "OE2" Residue "C GLU 738": "OE1" <-> "OE2" Residue "C PHE 804": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ASP 912": "OD1" <-> "OD2" Residue "C PHE 934": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 947": "OE1" <-> "OE2" Residue "C ASP 959": "OD1" <-> "OD2" Residue "C GLU 968": "OE1" <-> "OE2" Residue "C ASP 1004": "OD1" <-> "OD2" Residue "C GLU 1016": "OE1" <-> "OE2" Residue "C GLU 1083": "OE1" <-> "OE2" Residue "C GLU 1192": "OE1" <-> "OE2" Residue "C ASP 1240": "OD1" <-> "OD2" Residue "C TYR 1285": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 1305": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ASP 1310": "OD1" <-> "OD2" Residue "C ASP 1341": "OD1" <-> "OD2" Residue "D ARG 53": "NH1" <-> "NH2" Residue "D TYR 75": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D GLU 91": "OE1" <-> "OE2" Residue "D TYR 144": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D GLU 170": "OE1" <-> "OE2" Residue "D ASP 174": "OD1" <-> "OD2" Residue "D GLU 175": "OE1" <-> "OE2" Residue "D ASP 177": "OD1" <-> "OD2" Residue "D ASP 193": "OD1" <-> "OD2" Residue "D GLU 199": "OE1" <-> "OE2" Residue "D PHE 260": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 377": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ASP 413": "OD1" <-> "OD2" Residue "D GLU 414": "OE1" <-> "OE2" Residue "D ARG 425": "NH1" <-> "NH2" Residue "D ARG 431": "NH1" <-> "NH2" Residue "D GLU 443": "OE1" <-> "OE2" Residue "D GLU 532": "OE1" <-> "OE2" Residue "D GLU 660": "OE1" <-> "OE2" Residue "D PHE 719": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ARG 798": "NH1" <-> "NH2" Residue "D GLU 846": "OE1" <-> "OE2" Residue "D ASP 855": "OD1" <-> "OD2" Residue "D GLU 873": "OE1" <-> "OE2" Residue "D GLU 874": "OE1" <-> "OE2" Residue "D ASP 891": "OD1" <-> "OD2" Residue "D ARG 933": "NH1" <-> "NH2" Residue "D ASP 1051": "OD1" <-> "OD2" Residue "D PHE 1100": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D GLU 1110": "OE1" <-> "OE2" Residue "D ASP 1111": "OD1" <-> "OD2" Residue "D GLU 1168": "OE1" <-> "OE2" Residue "D ASP 1181": "OD1" <-> "OD2" Residue "D ASP 1208": "OD1" <-> "OD2" Residue "D ARG 1284": "NH1" <-> "NH2" Residue "D PHE 1319": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D GLU 1327": "OE1" <-> "OE2" Residue "D ASP 1368": "OD1" <-> "OD2" Residue "E GLU 42": "OE1" <-> "OE2" Residue "E GLU 56": "OE1" <-> "OE2" Residue "E GLU 76": "OE1" <-> "OE2" Residue "F GLU 90": "OE1" <-> "OE2" Residue "F ASP 125": "OD1" <-> "OD2" Residue "F ASP 149": "OD1" <-> "OD2" Residue "F ARG 157": "NH1" <-> "NH2" Residue "F ASP 267": "OD1" <-> "OD2" Residue "F ARG 279": "NH1" <-> "NH2" Residue "F ARG 339": "NH1" <-> "NH2" Residue "F TYR 394": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F ARG 397": "NH1" <-> "NH2" Residue "F ARG 465": "NH1" <-> "NH2" Residue "F ARG 476": "NH1" <-> "NH2" Residue "F GLU 491": "OE1" <-> "OE2" Residue "F ASP 492": "OD1" <-> "OD2" Residue "F GLU 524": "OE1" <-> "OE2" Residue "F GLU 529": "OE1" <-> "OE2" Residue "F GLU 605": "OE1" <-> "OE2" Residue "G PHE 40": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G PHE 60": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G GLU 79": "OE1" <-> "OE2" Residue "G ARG 80": "NH1" <-> "NH2" Residue "G GLU 84": "OE1" <-> "OE2" Residue "G ARG 90": "NH1" <-> "NH2" Residue "G ASP 94": "OD1" <-> "OD2" Residue "G TYR 127": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G ASP 171": "OD1" <-> "OD2" Residue "G GLU 185": "OE1" <-> "OE2" Residue "G PHE 190": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G ASP 217": "OD1" <-> "OD2" Residue "G GLU 257": "OE1" <-> "OE2" Residue "H ASP 35": "OD1" <-> "OD2" Residue "H ARG 56": "NH1" <-> "NH2" Residue "H PHE 60": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H ASP 71": "OD1" <-> "OD2" Residue "H ARG 80": "NH1" <-> "NH2" Residue "H ARG 81": "NH1" <-> "NH2" Residue "H ASP 94": "OD1" <-> "OD2" Residue "H ARG 110": "NH1" <-> "NH2" Residue "H GLU 120": "OE1" <-> "OE2" Residue "H GLU 149": "OE1" <-> "OE2" Residue "H ASP 189": "OD1" <-> "OD2" Residue "H GLU 194": "OE1" <-> "OE2" Residue "H ASP 217": "OD1" <-> "OD2" Residue "H ARG 220": "NH1" <-> "NH2" Residue "H TYR 223": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H ASP 254": "OD1" <-> "OD2" Time to flip residues: 0.17s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5238/modules/chem_data/mon_lib" Total number of atoms: 35828 Number of models: 1 Model: "" Number of chains: 20 Chain: "A" Number of atoms: 1793 Number of conformers: 1 Conformer: "" Number of residues, atoms: 231, 1793 Classifications: {'peptide': 231} Link IDs: {'PCIS': 1, 'PTRANS': 8, 'TRANS': 221} Chain: "B" Number of atoms: 1711 Number of conformers: 1 Conformer: "" Number of residues, atoms: 222, 1711 Classifications: {'peptide': 222} Link IDs: {'PCIS': 1, 'PTRANS': 7, 'TRANS': 213} Chain breaks: 1 Chain: "C" Number of atoms: 10570 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1340, 10570 Classifications: {'peptide': 1340} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 55, 'TRANS': 1283} Chain: "D" Number of atoms: 10394 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1336, 10394 Classifications: {'peptide': 1336} Link IDs: {'PCIS': 2, 'PTRANS': 53, 'TRANS': 1280} Chain breaks: 2 Chain: "E" Number of atoms: 627 Number of conformers: 1 Conformer: "" Number of residues, atoms: 79, 627 Classifications: {'peptide': 79} Link IDs: {'PTRANS': 2, 'TRANS': 76} Chain: "F" Number of atoms: 3878 Number of conformers: 1 Conformer: "" Number of residues, atoms: 476, 3878 Classifications: {'peptide': 476} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 14, 'TRANS': 461} Chain breaks: 2 Chain: "N" Number of atoms: 1109 Number of conformers: 1 Conformer: "" Number of residues, atoms: 54, 1109 Classifications: {'DNA': 54} Modifications used: {'5*END': 1} Link IDs: {'rna3p': 53} Chain: "T" Number of atoms: 1104 Number of conformers: 1 Conformer: "" Number of residues, atoms: 54, 1104 Classifications: {'DNA': 54} Modifications used: {'5*END': 1} Link IDs: {'rna3p': 53} Chain: "G" Number of atoms: 2208 Number of conformers: 1 Conformer: "" Number of residues, atoms: 268, 2208 Classifications: {'peptide': 268} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 11, 'TRANS': 255} Chain: "H" Number of atoms: 2208 Number of conformers: 1 Conformer: "" Number of residues, atoms: 268, 2208 Classifications: {'peptide': 268} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 11, 'TRANS': 255} Chain: "C" Number of atoms: 52 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 52 Unusual residues: {'1N7': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 34 Unresolved non-hydrogen angles: 50 Unresolved non-hydrogen dihedrals: 28 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'1N7:plan-1': 2} Unresolved non-hydrogen planarities: 8 Chain: "D" Number of atoms: 3 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 3 Unusual residues: {' MG': 1, ' ZN': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "T" Number of atoms: 26 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 26 Unusual residues: {'1N7': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 17 Unresolved non-hydrogen angles: 25 Unresolved non-hydrogen dihedrals: 14 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'1N7:plan-1': 1} Unresolved non-hydrogen planarities: 4 Chain: "G" Number of atoms: 51 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 51 Unusual residues: {'118': 1, '1N7': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 17 Unresolved non-hydrogen angles: 25 Unresolved non-hydrogen dihedrals: 14 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'1N7:plan-1': 1} Unresolved non-hydrogen planarities: 4 Chain: "H" Number of atoms: 52 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 52 Unusual residues: {'118': 1, '1N7': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 16 Unresolved non-hydrogen angles: 24 Unresolved non-hydrogen dihedrals: 13 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'1N7:plan-1': 1} Unresolved non-hydrogen planarities: 3 Chain: "A" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Classifications: {'water': 1} Chain: "C" Number of atoms: 22 Number of conformers: 1 Conformer: "" Number of residues, atoms: 22, 22 Classifications: {'water': 22} Link IDs: {None: 21} Chain: "D" Number of atoms: 15 Number of conformers: 1 Conformer: "" Number of residues, atoms: 15, 15 Classifications: {'water': 15} Link IDs: {None: 14} Chain: "F" Number of atoms: 3 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 3 Classifications: {'water': 3} Link IDs: {None: 2} Chain: "N" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Classifications: {'water': 1} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 14523 SG CYS D 70 81.657 84.624 57.453 1.00 60.18 S ATOM 14537 SG CYS D 72 78.764 83.895 56.623 1.00 62.43 S ATOM 14645 SG CYS D 85 79.503 84.961 53.727 1.00 61.19 S ATOM 14669 SG CYS D 88 78.979 87.091 56.479 1.00 58.84 S ATOM 20357 SG CYS D 814 115.203 142.345 64.775 1.00 51.71 S ATOM 20922 SG CYS D 888 112.902 140.407 66.658 1.00 48.63 S ATOM 20973 SG CYS D 895 116.415 139.842 66.983 1.00 45.92 S ATOM 20994 SG CYS D 898 115.033 142.648 68.430 1.00 45.52 S Time building chain proxies: 19.09, per 1000 atoms: 0.53 Number of scatterers: 35828 At special positions: 0 Unit cell: (181.288, 209.725, 161.737, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 8 Type Number sf(0) Sb 2 50.95 Zn 2 29.99 S 155 16.00 P 106 15.00 Mg 1 11.99 O 7075 8.00 N 6272 7.00 C 22215 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 13.99 Conformation dependent library (CDL) restraints added in 6.1 seconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN D1502 " pdb="ZN ZN D1502 " - pdb=" SG CYS D 72 " pdb="ZN ZN D1502 " - pdb=" SG CYS D 85 " pdb="ZN ZN D1502 " - pdb=" SG CYS D 70 " pdb="ZN ZN D1502 " - pdb=" SG CYS D 88 " pdb=" ZN D1503 " pdb="ZN ZN D1503 " - pdb=" SG CYS D 895 " pdb="ZN ZN D1503 " - pdb=" SG CYS D 814 " pdb="ZN ZN D1503 " - pdb=" SG CYS D 888 " pdb="ZN ZN D1503 " - pdb=" SG CYS D 898 " Number of angles added : 12 8388 Ramachandran restraints generated. 4194 Oldfield, 0 Emsley, 4194 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 7868 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 147 helices and 44 sheets defined 38.1% alpha, 13.5% beta 40 base pairs and 84 stacking pairs defined. Time for finding SS restraints: 17.61 Creating SS restraints... Processing helix chain 'A' and resid 35 through 47 Processing helix chain 'A' and resid 78 through 86 Processing helix chain 'A' and resid 112 through 114 No H-bonds generated for 'chain 'A' and resid 112 through 114' Processing helix chain 'A' and resid 155 through 157 No H-bonds generated for 'chain 'A' and resid 155 through 157' Processing helix chain 'A' and resid 213 through 227 Processing helix chain 'A' and resid 229 through 233 Processing helix chain 'B' and resid 35 through 49 Processing helix chain 'B' and resid 78 through 86 Processing helix chain 'B' and resid 112 through 114 No H-bonds generated for 'chain 'B' and resid 112 through 114' Processing helix chain 'B' and resid 213 through 230 removed outlier: 3.753A pdb=" N GLU B 229 " --> pdb=" O ALA B 225 " (cutoff:3.500A) removed outlier: 5.343A pdb=" N ALA B 230 " --> pdb=" O GLU B 226 " (cutoff:3.500A) Processing helix chain 'C' and resid 29 through 39 Processing helix chain 'C' and resid 48 through 56 removed outlier: 3.649A pdb=" N VAL C 56 " --> pdb=" O ALA C 52 " (cutoff:3.500A) Processing helix chain 'C' and resid 82 through 88 Processing helix chain 'C' and resid 206 through 212 removed outlier: 3.593A pdb=" N LEU C 210 " --> pdb=" O ALA C 206 " (cutoff:3.500A) Processing helix chain 'C' and resid 217 through 224 Processing helix chain 'C' and resid 243 through 246 Processing helix chain 'C' and resid 271 through 279 Processing helix chain 'C' and resid 289 through 292 No H-bonds generated for 'chain 'C' and resid 289 through 292' Processing helix chain 'C' and resid 319 through 328 removed outlier: 3.565A pdb=" N SER C 328 " --> pdb=" O LYS C 324 " (cutoff:3.500A) Processing helix chain 'C' and resid 346 through 351 Processing helix chain 'C' and resid 359 through 370 Processing helix chain 'C' and resid 378 through 388 removed outlier: 3.802A pdb=" N PHE C 385 " --> pdb=" O ALA C 381 " (cutoff:3.500A) Processing helix chain 'C' and resid 399 through 408 Processing helix chain 'C' and resid 422 through 436 Processing helix chain 'C' and resid 456 through 479 removed outlier: 3.716A pdb=" N GLU C 461 " --> pdb=" O GLY C 457 " (cutoff:3.500A) removed outlier: 4.072A pdb=" N ALA C 474 " --> pdb=" O ARG C 470 " (cutoff:3.500A) Processing helix chain 'C' and resid 489 through 491 No H-bonds generated for 'chain 'C' and resid 489 through 491' Processing helix chain 'C' and resid 495 through 508 Processing helix chain 'C' and resid 520 through 527 Processing helix chain 'C' and resid 552 through 554 No H-bonds generated for 'chain 'C' and resid 552 through 554' Processing helix chain 'C' and resid 608 through 613 removed outlier: 3.733A pdb=" N GLY C 612 " --> pdb=" O ALA C 608 " (cutoff:3.500A) removed outlier: 4.085A pdb=" N ASN C 613 " --> pdb=" O ILE C 609 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 608 through 613' Processing helix chain 'C' and resid 665 through 667 No H-bonds generated for 'chain 'C' and resid 665 through 667' Processing helix chain 'C' and resid 671 through 673 No H-bonds generated for 'chain 'C' and resid 671 through 673' Processing helix chain 'C' and resid 676 through 688 removed outlier: 4.207A pdb=" N ARG C 687 " --> pdb=" O ALA C 683 " (cutoff:3.500A) removed outlier: 4.095A pdb=" N GLN C 688 " --> pdb=" O ASN C 684 " (cutoff:3.500A) Processing helix chain 'C' and resid 705 through 711 Processing helix chain 'C' and resid 738 through 740 No H-bonds generated for 'chain 'C' and resid 738 through 740' Processing helix chain 'C' and resid 812 through 814 No H-bonds generated for 'chain 'C' and resid 812 through 814' Processing helix chain 'C' and resid 820 through 824 Processing helix chain 'C' and resid 897 through 906 Processing helix chain 'C' and resid 943 through 981 Processing helix chain 'C' and resid 988 through 991 No H-bonds generated for 'chain 'C' and resid 988 through 991' Processing helix chain 'C' and resid 995 through 999 Processing helix chain 'C' and resid 1007 through 1037 removed outlier: 3.663A pdb=" N LYS C1027 " --> pdb=" O HIS C1023 " (cutoff:3.500A) removed outlier: 3.734A pdb=" N GLU C1030 " --> pdb=" O GLU C1026 " (cutoff:3.500A) Processing helix chain 'C' and resid 1082 through 1084 No H-bonds generated for 'chain 'C' and resid 1082 through 1084' Processing helix chain 'C' and resid 1100 through 1104 Proline residue: C1104 - end of helix Processing helix chain 'C' and resid 1109 through 1133 removed outlier: 3.622A pdb=" N LEU C1113 " --> pdb=" O GLY C1110 " (cutoff:3.500A) removed outlier: 4.056A pdb=" N GLU C1114 " --> pdb=" O GLN C1111 " (cutoff:3.500A) removed outlier: 3.761A pdb=" N LEU C1117 " --> pdb=" O GLU C1114 " (cutoff:3.500A) removed outlier: 3.620A pdb=" N MET C1119 " --> pdb=" O HIS C1116 " (cutoff:3.500A) removed outlier: 3.780A pdb=" N ALA C1121 " --> pdb=" O GLY C1118 " (cutoff:3.500A) removed outlier: 3.785A pdb=" N LYS C1122 " --> pdb=" O MET C1119 " (cutoff:3.500A) removed outlier: 3.882A pdb=" N ASP C1126 " --> pdb=" O GLY C1123 " (cutoff:3.500A) removed outlier: 4.143A pdb=" N ASN C1129 " --> pdb=" O ASP C1126 " (cutoff:3.500A) Processing helix chain 'C' and resid 1138 through 1150 Processing helix chain 'C' and resid 1166 through 1175 Processing helix chain 'C' and resid 1192 through 1201 Processing helix chain 'C' and resid 1239 through 1242 No H-bonds generated for 'chain 'C' and resid 1239 through 1242' Processing helix chain 'C' and resid 1272 through 1280 Processing helix chain 'C' and resid 1284 through 1291 Processing helix chain 'C' and resid 1298 through 1309 removed outlier: 3.827A pdb=" N THR C1302 " --> pdb=" O VAL C1298 " (cutoff:3.500A) Processing helix chain 'C' and resid 1321 through 1332 Processing helix chain 'D' and resid 27 through 33 Processing helix chain 'D' and resid 59 through 62 No H-bonds generated for 'chain 'D' and resid 59 through 62' Processing helix chain 'D' and resid 95 through 99 Processing helix chain 'D' and resid 114 through 118 Processing helix chain 'D' and resid 123 through 128 Processing helix chain 'D' and resid 132 through 139 Processing helix chain 'D' and resid 162 through 171 removed outlier: 3.634A pdb=" N GLU D 170 " --> pdb=" O LEU D 166 " (cutoff:3.500A) Processing helix chain 'D' and resid 173 through 175 No H-bonds generated for 'chain 'D' and resid 173 through 175' Processing helix chain 'D' and resid 182 through 191 Processing helix chain 'D' and resid 194 through 207 Processing helix chain 'D' and resid 211 through 229 Processing helix chain 'D' and resid 234 through 237 Processing helix chain 'D' and resid 264 through 285 Processing helix chain 'D' and resid 289 through 307 Processing helix chain 'D' and resid 327 through 331 removed outlier: 3.869A pdb=" N ILE D 331 " --> pdb=" O LEU D 327 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 327 through 331' Processing helix chain 'D' and resid 337 through 341 Processing helix chain 'D' and resid 370 through 376 removed outlier: 3.664A pdb=" N GLU D 375 " --> pdb=" O LYS D 371 " (cutoff:3.500A) Processing helix chain 'D' and resid 378 through 387 Processing helix chain 'D' and resid 394 through 403 Processing helix chain 'D' and resid 406 through 415 removed outlier: 3.902A pdb=" N ASP D 410 " --> pdb=" O ALA D 406 " (cutoff:3.500A) Processing helix chain 'D' and resid 431 through 433 No H-bonds generated for 'chain 'D' and resid 431 through 433' Processing helix chain 'D' and resid 451 through 457 removed outlier: 4.615A pdb=" N ALA D 455 " --> pdb=" O LEU D 452 " (cutoff:3.500A) Processing helix chain 'D' and resid 474 through 482 Processing helix chain 'D' and resid 486 through 488 No H-bonds generated for 'chain 'D' and resid 486 through 488' Processing helix chain 'D' and resid 505 through 513 Processing helix chain 'D' and resid 530 through 538 Processing helix chain 'D' and resid 574 through 582 removed outlier: 3.811A pdb=" N MET D 581 " --> pdb=" O ALA D 577 " (cutoff:3.500A) removed outlier: 4.620A pdb=" N ILE D 582 " --> pdb=" O ILE D 578 " (cutoff:3.500A) Processing helix chain 'D' and resid 589 through 591 No H-bonds generated for 'chain 'D' and resid 589 through 591' Processing helix chain 'D' and resid 598 through 612 Processing helix chain 'D' and resid 614 through 635 removed outlier: 3.559A pdb=" N ILE D 619 " --> pdb=" O LYS D 615 " (cutoff:3.500A) Processing helix chain 'D' and resid 650 through 669 Processing helix chain 'D' and resid 675 through 702 Processing helix chain 'D' and resid 721 through 727 Processing helix chain 'D' and resid 734 through 741 removed outlier: 3.760A pdb=" N GLN D 739 " --> pdb=" O ALA D 735 " (cutoff:3.500A) Processing helix chain 'D' and resid 769 through 804 removed outlier: 4.302A pdb=" N GLY D 778 " --> pdb=" O ILE D 774 " (cutoff:3.500A) removed outlier: 3.596A pdb=" N LYS D 781 " --> pdb=" O HIS D 777 " (cutoff:3.500A) removed outlier: 3.903A pdb=" N THR D 790 " --> pdb=" O THR D 786 " (cutoff:3.500A) removed outlier: 5.161A pdb=" N ALA D 791 " --> pdb=" O ALA D 787 " (cutoff:3.500A) removed outlier: 4.163A pdb=" N ASN D 792 " --> pdb=" O LEU D 788 " (cutoff:3.500A) Processing helix chain 'D' and resid 835 through 839 Processing helix chain 'D' and resid 866 through 874 Processing helix chain 'D' and resid 896 through 899 No H-bonds generated for 'chain 'D' and resid 896 through 899' Processing helix chain 'D' and resid 915 through 929 Proline residue: D 926 - end of helix removed outlier: 5.314A pdb=" N GLN D 929 " --> pdb=" O GLU D 925 " (cutoff:3.500A) Processing helix chain 'D' and resid 1138 through 1145 Processing helix chain 'D' and resid 1217 through 1223 Processing helix chain 'D' and resid 1226 through 1244 removed outlier: 3.782A pdb=" N VAL D1240 " --> pdb=" O GLU D1236 " (cutoff:3.500A) removed outlier: 3.876A pdb=" N GLN D1244 " --> pdb=" O VAL D1240 " (cutoff:3.500A) Processing helix chain 'D' and resid 1251 through 1260 removed outlier: 3.535A pdb=" N ILE D1256 " --> pdb=" O HIS D1252 " (cutoff:3.500A) Processing helix chain 'D' and resid 1282 through 1294 Processing helix chain 'D' and resid 1309 through 1313 removed outlier: 3.525A pdb=" N SER D1313 " --> pdb=" O ILE D1309 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 1309 through 1313' Processing helix chain 'D' and resid 1319 through 1325 Processing helix chain 'D' and resid 1328 through 1338 Processing helix chain 'D' and resid 1347 through 1352 Processing helix chain 'D' and resid 1360 through 1371 removed outlier: 4.499A pdb=" N ALA D1364 " --> pdb=" O THR D1361 " (cutoff:3.500A) removed outlier: 3.652A pdb=" N TYR D1365 " --> pdb=" O GLY D1362 " (cutoff:3.500A) removed outlier: 4.069A pdb=" N ARG D1371 " --> pdb=" O ASP D1368 " (cutoff:3.500A) Processing helix chain 'E' and resid 7 through 12 removed outlier: 3.909A pdb=" N LYS E 12 " --> pdb=" O ASP E 8 " (cutoff:3.500A) Processing helix chain 'E' and resid 16 through 31 removed outlier: 3.695A pdb=" N LEU E 21 " --> pdb=" O PHE E 17 " (cutoff:3.500A) Processing helix chain 'E' and resid 46 through 56 removed outlier: 3.528A pdb=" N GLU E 56 " --> pdb=" O ARG E 52 " (cutoff:3.500A) Processing helix chain 'E' and resid 61 through 77 Processing helix chain 'F' and resid 97 through 105 Processing helix chain 'F' and resid 113 through 136 removed outlier: 3.672A pdb=" N ILE F 117 " --> pdb=" O ARG F 113 " (cutoff:3.500A) removed outlier: 4.375A pdb=" N GLU F 136 " --> pdb=" O CYS F 132 " (cutoff:3.500A) Processing helix chain 'F' and resid 138 through 152 Processing helix chain 'F' and resid 158 through 160 No H-bonds generated for 'chain 'F' and resid 158 through 160' Processing helix chain 'F' and resid 214 through 232 removed outlier: 3.833A pdb=" N ARG F 218 " --> pdb=" O PRO F 214 " (cutoff:3.500A) removed outlier: 3.705A pdb=" N GLU F 219 " --> pdb=" O GLU F 215 " (cutoff:3.500A) Processing helix chain 'F' and resid 243 through 256 removed outlier: 4.534A pdb=" N GLU F 248 " --> pdb=" O ALA F 245 " (cutoff:3.500A) removed outlier: 4.710A pdb=" N ILE F 249 " --> pdb=" O GLN F 246 " (cutoff:3.500A) Processing helix chain 'F' and resid 263 through 294 removed outlier: 3.935A pdb=" N MET F 288 " --> pdb=" O GLU F 284 " (cutoff:3.500A) removed outlier: 3.645A pdb=" N CYS F 291 " --> pdb=" O ILE F 287 " (cutoff:3.500A) Processing helix chain 'F' and resid 306 through 309 No H-bonds generated for 'chain 'F' and resid 306 through 309' Processing helix chain 'F' and resid 317 through 320 No H-bonds generated for 'chain 'F' and resid 317 through 320' Processing helix chain 'F' and resid 325 through 333 removed outlier: 3.789A pdb=" N LYS F 329 " --> pdb=" O PRO F 325 " (cutoff:3.500A) removed outlier: 4.240A pdb=" N LEU F 330 " --> pdb=" O TRP F 326 " (cutoff:3.500A) removed outlier: 4.522A pdb=" N HIS F 331 " --> pdb=" O SER F 327 " (cutoff:3.500A) removed outlier: 3.786A pdb=" N ASP F 332 " --> pdb=" O GLU F 328 " (cutoff:3.500A) removed outlier: 3.975A pdb=" N VAL F 333 " --> pdb=" O LYS F 329 " (cutoff:3.500A) No H-bonds generated for 'chain 'F' and resid 325 through 333' Processing helix chain 'F' and resid 338 through 341 No H-bonds generated for 'chain 'F' and resid 338 through 341' Processing helix chain 'F' and resid 344 through 351 removed outlier: 4.411A pdb=" N GLU F 349 " --> pdb=" O GLN F 345 " (cutoff:3.500A) Processing helix chain 'F' and resid 355 through 394 removed outlier: 3.585A pdb=" N ASN F 383 " --> pdb=" O MET F 379 " (cutoff:3.500A) removed outlier: 5.817A pdb=" N ARG F 385 " --> pdb=" O GLU F 381 " (cutoff:3.500A) removed outlier: 5.892A pdb=" N LEU F 386 " --> pdb=" O ALA F 382 " (cutoff:3.500A) removed outlier: 3.516A pdb=" N VAL F 387 " --> pdb=" O ASN F 383 " (cutoff:3.500A) removed outlier: 4.812A pdb=" N LYS F 393 " --> pdb=" O SER F 389 " (cutoff:3.500A) removed outlier: 4.487A pdb=" N TYR F 394 " --> pdb=" O ILE F 390 " (cutoff:3.500A) Processing helix chain 'F' and resid 401 through 418 Processing helix chain 'F' and resid 421 through 423 No H-bonds generated for 'chain 'F' and resid 421 through 423' Processing helix chain 'F' and resid 427 through 446 removed outlier: 4.380A pdb=" N TRP F 433 " --> pdb=" O THR F 429 " (cutoff:3.500A) removed outlier: 3.829A pdb=" N TRP F 434 " --> pdb=" O TYR F 430 " (cutoff:3.500A) Processing helix chain 'F' and resid 454 through 474 Processing helix chain 'F' and resid 480 through 486 Processing helix chain 'F' and resid 491 through 500 Processing helix chain 'F' and resid 511 through 513 No H-bonds generated for 'chain 'F' and resid 511 through 513' Processing helix chain 'F' and resid 519 through 522 Processing helix chain 'F' and resid 531 through 549 Processing helix chain 'F' and resid 553 through 562 Processing helix chain 'F' and resid 573 through 579 Processing helix chain 'F' and resid 584 through 599 Processing helix chain 'F' and resid 608 through 610 No H-bonds generated for 'chain 'F' and resid 608 through 610' Processing helix chain 'G' and resid 4 through 11 Processing helix chain 'G' and resid 15 through 24 Processing helix chain 'G' and resid 43 through 58 removed outlier: 3.900A pdb=" N LYS G 48 " --> pdb=" O ASP G 44 " (cutoff:3.500A) removed outlier: 3.738A pdb=" N GLN G 51 " --> pdb=" O MET G 47 " (cutoff:3.500A) removed outlier: 3.892A pdb=" N LEU G 58 " --> pdb=" O SER G 54 " (cutoff:3.500A) Processing helix chain 'G' and resid 62 through 70 Processing helix chain 'G' and resid 75 through 106 Processing helix chain 'G' and resid 136 through 153 removed outlier: 3.951A pdb=" N ILE G 140 " --> pdb=" O PHE G 136 " (cutoff:3.500A) removed outlier: 4.475A pdb=" N LYS G 141 " --> pdb=" O SER G 137 " (cutoff:3.500A) removed outlier: 4.002A pdb=" N LEU G 142 " --> pdb=" O SER G 138 " (cutoff:3.500A) removed outlier: 4.010A pdb=" N ILE G 143 " --> pdb=" O TYR G 139 " (cutoff:3.500A) Proline residue: G 144 - end of helix removed outlier: 3.633A pdb=" N MET G 151 " --> pdb=" O GLY G 147 " (cutoff:3.500A) Processing helix chain 'G' and resid 218 through 232 Processing helix chain 'H' and resid 4 through 11 Processing helix chain 'H' and resid 15 through 24 Processing helix chain 'H' and resid 43 through 58 removed outlier: 3.705A pdb=" N GLN H 51 " --> pdb=" O MET H 47 " (cutoff:3.500A) removed outlier: 3.536A pdb=" N LEU H 58 " --> pdb=" O SER H 54 " (cutoff:3.500A) Processing helix chain 'H' and resid 62 through 68 removed outlier: 3.708A pdb=" N THR H 67 " --> pdb=" O THR H 63 " (cutoff:3.500A) Processing helix chain 'H' and resid 76 through 108 Processing helix chain 'H' and resid 136 through 153 Proline residue: H 144 - end of helix Processing helix chain 'H' and resid 216 through 232 removed outlier: 5.124A pdb=" N ARG H 220 " --> pdb=" O ASP H 217 " (cutoff:3.500A) removed outlier: 3.563A pdb=" N ASN H 221 " --> pdb=" O SER H 218 " (cutoff:3.500A) removed outlier: 3.610A pdb=" N ASP H 232 " --> pdb=" O TRP H 229 " (cutoff:3.500A) Processing helix chain 'H' and resid 255 through 257 No H-bonds generated for 'chain 'H' and resid 255 through 257' Processing sheet with id= A, first strand: chain 'A' and resid 12 through 18 removed outlier: 6.613A pdb=" N THR A 27 " --> pdb=" O VAL A 14 " (cutoff:3.500A) removed outlier: 4.173A pdb=" N ILE A 16 " --> pdb=" O LYS A 25 " (cutoff:3.500A) removed outlier: 6.220A pdb=" N LYS A 25 " --> pdb=" O ILE A 16 " (cutoff:3.500A) removed outlier: 5.077A pdb=" N GLN A 18 " --> pdb=" O HIS A 23 " (cutoff:3.500A) removed outlier: 7.107A pdb=" N HIS A 23 " --> pdb=" O GLN A 18 " (cutoff:3.500A) Processing sheet with id= B, first strand: chain 'A' and resid 170 through 172 removed outlier: 6.751A pdb=" N LYS A 145 " --> pdb=" O THR A 57 " (cutoff:3.500A) removed outlier: 4.339A pdb=" N VAL A 59 " --> pdb=" O ARG A 143 " (cutoff:3.500A) removed outlier: 6.426A pdb=" N ARG A 143 " --> pdb=" O VAL A 59 " (cutoff:3.500A) removed outlier: 4.751A pdb=" N ILE A 61 " --> pdb=" O SER A 141 " (cutoff:3.500A) removed outlier: 7.282A pdb=" N SER A 141 " --> pdb=" O ILE A 61 " (cutoff:3.500A) Processing sheet with id= C, first strand: chain 'A' and resid 90 through 92 Processing sheet with id= D, first strand: chain 'A' and resid 108 through 111 Processing sheet with id= E, first strand: chain 'B' and resid 17 through 20 removed outlier: 6.212A pdb=" N HIS B 23 " --> pdb=" O VAL B 19 " (cutoff:3.500A) Processing sheet with id= F, first strand: chain 'B' and resid 90 through 92 Processing sheet with id= G, first strand: chain 'B' and resid 97 through 105 removed outlier: 3.716A pdb=" N GLU B 58 " --> pdb=" O LYS B 145 " (cutoff:3.500A) removed outlier: 6.450A pdb=" N GLN B 147 " --> pdb=" O VAL B 56 " (cutoff:3.500A) removed outlier: 5.339A pdb=" N VAL B 56 " --> pdb=" O GLN B 147 " (cutoff:3.500A) removed outlier: 6.671A pdb=" N GLY B 149 " --> pdb=" O CYS B 54 " (cutoff:3.500A) removed outlier: 5.095A pdb=" N CYS B 54 " --> pdb=" O GLY B 149 " (cutoff:3.500A) Processing sheet with id= H, first strand: chain 'B' and resid 108 through 111 removed outlier: 3.557A pdb=" N CYS B 131 " --> pdb=" O VAL B 110 " (cutoff:3.500A) Processing sheet with id= I, first strand: chain 'C' and resid 93 through 95 Processing sheet with id= J, first strand: chain 'C' and resid 136 through 138 Processing sheet with id= K, first strand: chain 'C' and resid 148 through 151 Processing sheet with id= L, first strand: chain 'C' and resid 154 through 160 removed outlier: 4.944A pdb=" N TYR C 172 " --> pdb=" O PHE C 188 " (cutoff:3.500A) Processing sheet with id= M, first strand: chain 'C' and resid 227 through 231 Processing sheet with id= N, first strand: chain 'C' and resid 238 through 240 Processing sheet with id= O, first strand: chain 'C' and resid 529 through 531 Processing sheet with id= P, first strand: chain 'C' and resid 603 through 607 Processing sheet with id= Q, first strand: chain 'C' and resid 633 through 637 Processing sheet with id= R, first strand: chain 'C' and resid 748 through 752 removed outlier: 6.006A pdb=" N LYS C 735 " --> pdb=" O VAL C 724 " (cutoff:3.500A) removed outlier: 5.725A pdb=" N VAL C 724 " --> pdb=" O LYS C 735 " (cutoff:3.500A) Processing sheet with id= S, first strand: chain 'C' and resid 1226 through 1232 removed outlier: 4.376A pdb=" N THR C1226 " --> pdb=" O PHE C 804 " (cutoff:3.500A) removed outlier: 6.536A pdb=" N ILE C1096 " --> pdb=" O ALA C 803 " (cutoff:3.500A) Processing sheet with id= T, first strand: chain 'C' and resid 887 through 889 Processing sheet with id= U, first strand: chain 'C' and resid 1065 through 1067 removed outlier: 7.490A pdb=" N VAL C 818 " --> pdb=" O SER C1077 " (cutoff:3.500A) removed outlier: 4.244A pdb=" N ILE C1079 " --> pdb=" O VAL C 818 " (cutoff:3.500A) Processing sheet with id= V, first strand: chain 'C' and resid 66 through 75 removed outlier: 6.687A pdb=" N LYS C 99 " --> pdb=" O VAL C 71 " (cutoff:3.500A) removed outlier: 4.575A pdb=" N TYR C 73 " --> pdb=" O ARG C 97 " (cutoff:3.500A) removed outlier: 6.675A pdb=" N ARG C 97 " --> pdb=" O TYR C 73 " (cutoff:3.500A) removed outlier: 3.662A pdb=" N ASP C 116 " --> pdb=" O ILE C 104 " (cutoff:3.500A) Processing sheet with id= W, first strand: chain 'C' and resid 830 through 841 removed outlier: 3.702A pdb=" N ASP C 930 " --> pdb=" O TYR C1053 " (cutoff:3.500A) removed outlier: 6.498A pdb=" N ALA C1055 " --> pdb=" O VAL C 928 " (cutoff:3.500A) removed outlier: 5.809A pdb=" N VAL C 928 " --> pdb=" O ALA C1055 " (cutoff:3.500A) Processing sheet with id= X, first strand: chain 'D' and resid 103 through 106 Processing sheet with id= Y, first strand: chain 'D' and resid 252 through 254 Processing sheet with id= Z, first strand: chain 'D' and resid 350 through 354 Processing sheet with id= AA, first strand: chain 'D' and resid 355 through 358 removed outlier: 5.979A pdb=" N ILE D 447 " --> pdb=" O THR D 356 " (cutoff:3.500A) removed outlier: 6.183A pdb=" N GLY D 358 " --> pdb=" O ILE D 447 " (cutoff:3.500A) removed outlier: 5.684A pdb=" N LEU D 449 " --> pdb=" O GLY D 358 " (cutoff:3.500A) No H-bonds generated for sheet with id= AA Processing sheet with id= AB, first strand: chain 'D' and resid 547 through 557 Processing sheet with id= AC, first strand: chain 'D' and resid 705 through 709 removed outlier: 4.019A pdb=" N THR D 705 " --> pdb=" O GLN D 716 " (cutoff:3.500A) Processing sheet with id= AD, first strand: chain 'D' and resid 820 through 823 Processing sheet with id= AE, first strand: chain 'D' and resid 957 through 961 removed outlier: 3.644A pdb=" N GLU D 993 " --> pdb=" O LEU D 984 " (cutoff:3.500A) Processing sheet with id= AF, first strand: chain 'D' and resid 965 through 967 removed outlier: 3.515A pdb=" N LEU D 973 " --> pdb=" O LEU D1003 " (cutoff:3.500A) Processing sheet with id= AG, first strand: chain 'D' and resid 1024 through 1026 Processing sheet with id= AH, first strand: chain 'D' and resid 1034 through 1038 Processing sheet with id= AI, first strand: chain 'D' and resid 1047 through 1049 Processing sheet with id= AJ, first strand: chain 'D' and resid 1162 through 1165 removed outlier: 3.505A pdb=" N LEU D1175 " --> pdb=" O GLU D1188 " (cutoff:3.500A) Processing sheet with id= AK, first strand: chain 'D' and resid 1279 through 1281 removed outlier: 6.762A pdb=" N THR D1301 " --> pdb=" O VAL D1267 " (cutoff:3.500A) Processing sheet with id= AL, first strand: chain 'D' and resid 145 through 148 removed outlier: 7.033A pdb=" N ASP D 177 " --> pdb=" O ILE D 147 " (cutoff:3.500A) Processing sheet with id= AM, first strand: chain 'D' and resid 825 through 827 removed outlier: 7.157A pdb=" N GLU D 827 " --> pdb=" O VAL D 831 " (cutoff:3.500A) removed outlier: 5.716A pdb=" N VAL D 831 " --> pdb=" O GLU D 827 " (cutoff:3.500A) Processing sheet with id= AN, first strand: chain 'F' and resid 162 through 165 removed outlier: 7.735A pdb=" N ARG F 260 " --> pdb=" O THR F 163 " (cutoff:3.500A) Processing sheet with id= AO, first strand: chain 'G' and resid 117 through 121 removed outlier: 6.862A pdb=" N GLU G 261 " --> pdb=" O TYR G 245 " (cutoff:3.500A) removed outlier: 5.520A pdb=" N TYR G 245 " --> pdb=" O GLU G 261 " (cutoff:3.500A) removed outlier: 7.319A pdb=" N GLN G 263 " --> pdb=" O GLU G 243 " (cutoff:3.500A) removed outlier: 5.607A pdb=" N GLU G 243 " --> pdb=" O GLN G 263 " (cutoff:3.500A) removed outlier: 5.297A pdb=" N CYS G 165 " --> pdb=" O TYR G 245 " (cutoff:3.500A) removed outlier: 4.142A pdb=" N ILE G 125 " --> pdb=" O VAL G 187 " (cutoff:3.500A) Processing sheet with id= AP, first strand: chain 'G' and resid 235 through 237 Processing sheet with id= AQ, first strand: chain 'H' and resid 117 through 121 removed outlier: 4.187A pdb=" N ILE H 125 " --> pdb=" O VAL H 187 " (cutoff:3.500A) Processing sheet with id= AR, first strand: chain 'H' and resid 235 through 237 1298 hydrogen bonds defined for protein. 3588 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 107 hydrogen bonds 214 hydrogen bond angles 0 basepair planarities 40 basepair parallelities 84 stacking parallelities Total time for adding SS restraints: 19.69 Time building geometry restraints manager: 15.17 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.39: 14344 1.39 - 1.58: 21765 1.58 - 1.76: 218 1.76 - 1.95: 263 1.95 - 2.13: 8 Bond restraints: 36598 Sorted by residual: bond pdb=" C GLU D 765 " pdb=" N GLY D 766 " ideal model delta sigma weight residual 1.333 1.275 0.058 2.14e-02 2.18e+03 7.42e+00 bond pdb=" O3' DG N 58 " pdb=" P DG N 59 " ideal model delta sigma weight residual 1.607 1.645 -0.038 1.50e-02 4.44e+03 6.27e+00 bond pdb=" C PHE D 437 " pdb=" N GLU D 438 " ideal model delta sigma weight residual 1.327 1.270 0.057 2.31e-02 1.87e+03 5.99e+00 bond pdb=" CB VAL D 507 " pdb=" CG2 VAL D 507 " ideal model delta sigma weight residual 1.521 1.442 0.079 3.30e-02 9.18e+02 5.79e+00 bond pdb=" CB ARG B 45 " pdb=" CG ARG B 45 " ideal model delta sigma weight residual 1.520 1.449 0.071 3.00e-02 1.11e+03 5.60e+00 ... (remaining 36593 not shown) Histogram of bond angle deviations from ideal: 94.87 - 102.73: 364 102.73 - 110.59: 11439 110.59 - 118.45: 17639 118.45 - 126.31: 19845 126.31 - 134.17: 644 Bond angle restraints: 49931 Sorted by residual: angle pdb=" N ASP C1296 " pdb=" CA ASP C1296 " pdb=" C ASP C1296 " ideal model delta sigma weight residual 113.50 123.55 -10.05 1.23e+00 6.61e-01 6.67e+01 angle pdb=" N TYR G 114 " pdb=" CA TYR G 114 " pdb=" C TYR G 114 " ideal model delta sigma weight residual 107.70 120.74 -13.04 2.09e+00 2.29e-01 3.89e+01 angle pdb=" N ASP D 505 " pdb=" CA ASP D 505 " pdb=" C ASP D 505 " ideal model delta sigma weight residual 111.33 117.76 -6.43 1.21e+00 6.83e-01 2.82e+01 angle pdb=" N ALA F 501 " pdb=" CA ALA F 501 " pdb=" C ALA F 501 " ideal model delta sigma weight residual 108.24 116.78 -8.54 1.81e+00 3.05e-01 2.23e+01 angle pdb=" N ILE F 500 " pdb=" CA ILE F 500 " pdb=" C ILE F 500 " ideal model delta sigma weight residual 112.50 118.97 -6.47 1.39e+00 5.18e-01 2.17e+01 ... (remaining 49926 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.47: 21552 35.47 - 70.93: 844 70.93 - 106.40: 34 106.40 - 141.86: 2 141.86 - 177.33: 3 Dihedral angle restraints: 22435 sinusoidal: 10230 harmonic: 12205 Sorted by residual: dihedral pdb=" CA GLU F 154 " pdb=" C GLU F 154 " pdb=" N GLU F 155 " pdb=" CA GLU F 155 " ideal model delta harmonic sigma weight residual 180.00 150.96 29.04 0 5.00e+00 4.00e-02 3.37e+01 dihedral pdb=" CA HIS A 160 " pdb=" C HIS A 160 " pdb=" N SER A 161 " pdb=" CA SER A 161 " ideal model delta harmonic sigma weight residual 180.00 151.88 28.12 0 5.00e+00 4.00e-02 3.16e+01 dihedral pdb=" CA GLU F 328 " pdb=" C GLU F 328 " pdb=" N LYS F 329 " pdb=" CA LYS F 329 " ideal model delta harmonic sigma weight residual 180.00 -152.21 -27.79 0 5.00e+00 4.00e-02 3.09e+01 ... (remaining 22432 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.072: 4539 0.072 - 0.145: 1028 0.145 - 0.217: 98 0.217 - 0.290: 11 0.290 - 0.362: 5 Chirality restraints: 5681 Sorted by residual: chirality pdb=" CA ASP C1296 " pdb=" N ASP C1296 " pdb=" C ASP C1296 " pdb=" CB ASP C1296 " both_signs ideal model delta sigma weight residual False 2.51 2.15 0.36 2.00e-01 2.50e+01 3.28e+00 chirality pdb=" CB VAL D1353 " pdb=" CA VAL D1353 " pdb=" CG1 VAL D1353 " pdb=" CG2 VAL D1353 " both_signs ideal model delta sigma weight residual False -2.63 -2.31 -0.32 2.00e-01 2.50e+01 2.62e+00 chirality pdb=" CB VAL C1293 " pdb=" CA VAL C1293 " pdb=" CG1 VAL C1293 " pdb=" CG2 VAL C1293 " both_signs ideal model delta sigma weight residual False -2.63 -2.33 -0.30 2.00e-01 2.50e+01 2.27e+00 ... (remaining 5678 not shown) Planarity restraints: 6095 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA ILE H 77 " -0.025 2.00e-02 2.50e+03 4.94e-02 2.44e+01 pdb=" C ILE H 77 " 0.086 2.00e-02 2.50e+03 pdb=" O ILE H 77 " -0.031 2.00e-02 2.50e+03 pdb=" N ILE H 78 " -0.029 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CG GLU G 79 " 0.022 2.00e-02 2.50e+03 4.37e-02 1.91e+01 pdb=" CD GLU G 79 " -0.076 2.00e-02 2.50e+03 pdb=" OE1 GLU G 79 " 0.027 2.00e-02 2.50e+03 pdb=" OE2 GLU G 79 " 0.027 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ASN G 221 " -0.019 2.00e-02 2.50e+03 3.82e-02 1.46e+01 pdb=" C ASN G 221 " 0.066 2.00e-02 2.50e+03 pdb=" O ASN G 221 " -0.025 2.00e-02 2.50e+03 pdb=" N ALA G 222 " -0.022 2.00e-02 2.50e+03 ... (remaining 6092 not shown) Histogram of nonbonded interaction distances: 2.09 - 2.65: 685 2.65 - 3.22: 32154 3.22 - 3.78: 58521 3.78 - 4.34: 83321 4.34 - 4.90: 133498 Nonbonded interactions: 308179 Sorted by model distance: nonbonded pdb=" OD1 ASP D 460 " pdb="MG MG D1501 " model vdw 2.093 2.170 nonbonded pdb=" OD1 ASP D 464 " pdb="MG MG D1501 " model vdw 2.190 2.170 nonbonded pdb=" O GLY D 613 " pdb=" OG1 THR D 617 " model vdw 2.200 2.440 nonbonded pdb=" O THR D 816 " pdb=" NH2 ARG D 860 " model vdw 2.201 2.520 nonbonded pdb=" OE1 GLU D 993 " pdb=" OH TYR D 995 " model vdw 2.208 2.440 ... (remaining 308174 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = (chain 'A' and (resid 5 through 159 or resid 169 through 234)) selection = (chain 'B' and resid 5 through 234) } ncs_group { reference = chain 'G' selection = (chain 'H' and (resid 2 through 269 or (resid 301 and (name C1 or name C10 or na \ me C11 or name C12 or name C13 or name C14 or name C15 or name C16 or name C17 o \ r name C18 or name C19 or name C2 or name C20 or name C21 or name C22 or name C2 \ 3 or name C3 or name C4 or name C5 or name C6 or name C7 or name C8 or name C9 o \ r name O2 or name O3 or name O4 )) or resid 302)) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 2.390 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: 13.740 Check model and map are aligned: 0.500 Set scattering table: 0.320 Process input model: 113.670 Find NCS groups from input model: 1.570 Set up NCS constraints: 0.170 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.020 Load rotamer database and sin/cos tables:12.690 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 145.090 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8182 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.010 0.106 36598 Z= 0.675 Angle : 0.932 13.039 49931 Z= 0.528 Chirality : 0.060 0.362 5681 Planarity : 0.006 0.063 6095 Dihedral : 16.923 177.330 14567 Min Nonbonded Distance : 2.093 Molprobity Statistics. All-atom Clashscore : 7.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.83 % Favored : 99.17 % Rotamer: Outliers : 0.00 % Allowed : 6.20 % Favored : 93.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.17 % 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: -2.54 (0.11), residues: 4194 helix: -1.82 (0.10), residues: 1636 sheet: -1.54 (0.20), residues: 513 loop : -1.50 (0.12), residues: 2045 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.033 0.002 TRP H 250 HIS 0.025 0.002 HIS C 554 PHE 0.024 0.003 PHE G 131 TYR 0.027 0.003 TYR G 164 ARG 0.009 0.001 ARG C 678 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8388 Ramachandran restraints generated. 4194 Oldfield, 0 Emsley, 4194 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8388 Ramachandran restraints generated. 4194 Oldfield, 0 Emsley, 4194 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 494 residues out of total 3645 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 494 time to evaluate : 3.957 Fit side-chains revert: symmetry clash REVERT: B 104 LYS cc_start: 0.7691 (tptm) cc_final: 0.7415 (tptp) REVERT: C 118 LYS cc_start: 0.8483 (mttm) cc_final: 0.8001 (ttmt) REVERT: C 240 GLU cc_start: 0.6776 (mm-30) cc_final: 0.6446 (mm-30) REVERT: C 386 GLU cc_start: 0.7859 (tm-30) cc_final: 0.7550 (tm-30) REVERT: C 488 MET cc_start: 0.7761 (mmm) cc_final: 0.7149 (mmm) REVERT: C 496 LYS cc_start: 0.7848 (ttmm) cc_final: 0.7596 (tttp) REVERT: C 834 GLN cc_start: 0.8272 (mt0) cc_final: 0.8057 (tt0) REVERT: C 899 GLU cc_start: 0.7493 (pt0) cc_final: 0.7206 (pt0) REVERT: C 937 ASP cc_start: 0.6773 (m-30) cc_final: 0.6467 (m-30) REVERT: C 950 GLU cc_start: 0.7709 (tm-30) cc_final: 0.7384 (tm-30) REVERT: C 955 GLN cc_start: 0.8276 (tp40) cc_final: 0.8041 (tp-100) REVERT: C 1131 MET cc_start: 0.8390 (mtt) cc_final: 0.8156 (mtt) REVERT: C 1171 ARG cc_start: 0.7497 (ttp80) cc_final: 0.7245 (ttp-110) REVERT: D 312 ARG cc_start: 0.7230 (ttp-170) cc_final: 0.6904 (tmt90) REVERT: D 1025 MET cc_start: 0.7718 (ttp) cc_final: 0.7336 (ttm) REVERT: D 1095 MET cc_start: 0.5853 (tmm) cc_final: 0.5595 (tpt) REVERT: D 1231 ARG cc_start: 0.7180 (ttp-110) cc_final: 0.6935 (ttm170) REVERT: D 1297 LYS cc_start: 0.7505 (mtpt) cc_final: 0.7198 (mtmt) REVERT: D 1334 GLU cc_start: 0.7505 (pt0) cc_final: 0.6931 (pp20) REVERT: E 67 ARG cc_start: 0.7536 (mtt90) cc_final: 0.7297 (mtt90) REVERT: F 160 ASP cc_start: 0.7981 (t0) cc_final: 0.7388 (p0) REVERT: F 277 MET cc_start: 0.7622 (tmm) cc_final: 0.6726 (tpt) REVERT: G 12 ARG cc_start: 0.7370 (mtt90) cc_final: 0.7159 (mtt90) REVERT: G 56 ARG cc_start: 0.7258 (ttp-170) cc_final: 0.6946 (ttm-80) REVERT: G 95 MET cc_start: 0.7195 (mtp) cc_final: 0.6934 (ttm) REVERT: G 231 GLU cc_start: 0.7772 (mt-10) cc_final: 0.7519 (pp20) REVERT: H 60 PHE cc_start: 0.7739 (m-80) cc_final: 0.7458 (m-80) REVERT: H 112 MET cc_start: 0.4435 (tpt) cc_final: 0.3347 (mtm) REVERT: H 174 TYR cc_start: 0.5876 (t80) cc_final: 0.5494 (t80) outliers start: 0 outliers final: 1 residues processed: 494 average time/residue: 1.9524 time to fit residues: 1110.7914 Evaluate side-chains 354 residues out of total 3645 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 353 time to evaluate : 3.876 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain F residue 500 ILE Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 428 random chunks: chunk 361 optimal weight: 0.7980 chunk 324 optimal weight: 0.0030 chunk 180 optimal weight: 0.8980 chunk 110 optimal weight: 0.9990 chunk 218 optimal weight: 0.6980 chunk 173 optimal weight: 0.7980 chunk 335 optimal weight: 20.0000 chunk 129 optimal weight: 1.9990 chunk 203 optimal weight: 0.9980 chunk 249 optimal weight: 1.9990 chunk 388 optimal weight: 8.9990 overall best weight: 0.6390 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 93 GLN A 194 GLN B 66 HIS B 93 GLN ** B 186 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 31 GLN C 36 GLN C 69 GLN C 330 HIS C 518 ASN C 620 ASN C 649 GLN C 799 ASN C 856 ASN C 894 GLN C 955 GLN C1013 GLN C1136 GLN C1237 HIS C1268 GLN D 45 ASN D 157 GLN D 274 ASN ** D 294 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 340 GLN D 365 GLN D 424 ASN ** D 495 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 680 ASN D 951 GLN D 962 ASN D 979 ASN D1197 ASN D1244 GLN E 72 GLN F 131 GLN F 227 GLN F 309 ASN F 338 HIS F 346 GLN ** F 362 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 383 ASN ** F 406 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 518 HIS F 579 GLN ** F 589 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 22 ASN ** G 45 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 51 GLN G 115 GLN G 154 ASN ** G 228 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 3 GLN H 22 ASN ** H 50 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 104 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 105 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 221 ASN ** H 251 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 47 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8099 moved from start: 0.1405 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 36598 Z= 0.178 Angle : 0.542 9.332 49931 Z= 0.292 Chirality : 0.042 0.214 5681 Planarity : 0.004 0.051 6095 Dihedral : 15.531 177.446 6155 Min Nonbonded Distance : 1.980 Molprobity Statistics. All-atom Clashscore : 9.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.76 % Favored : 98.24 % Rotamer: Outliers : 1.78 % Allowed : 11.91 % Favored : 86.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.17 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.13 (0.12), residues: 4194 helix: -0.25 (0.12), residues: 1641 sheet: -1.12 (0.21), residues: 496 loop : -0.97 (0.13), residues: 2057 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP G 229 HIS 0.014 0.001 HIS H 101 PHE 0.018 0.001 PHE C 906 TYR 0.017 0.001 TYR G 127 ARG 0.007 0.000 ARG F 596 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8388 Ramachandran restraints generated. 4194 Oldfield, 0 Emsley, 4194 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8388 Ramachandran restraints generated. 4194 Oldfield, 0 Emsley, 4194 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 456 residues out of total 3645 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 65 poor density : 391 time to evaluate : 3.734 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 137 ASN cc_start: 0.8410 (m-40) cc_final: 0.8143 (m-40) REVERT: A 200 LYS cc_start: 0.8981 (OUTLIER) cc_final: 0.8274 (ptpp) REVERT: B 6 THR cc_start: 0.8365 (p) cc_final: 0.8066 (m) REVERT: B 58 GLU cc_start: 0.8205 (pt0) cc_final: 0.7919 (pt0) REVERT: B 104 LYS cc_start: 0.7578 (tptm) cc_final: 0.7307 (tptp) REVERT: B 188 GLU cc_start: 0.8246 (OUTLIER) cc_final: 0.7966 (mp0) REVERT: B 191 ARG cc_start: 0.7436 (ttp80) cc_final: 0.6904 (ptm-80) REVERT: C 118 LYS cc_start: 0.8415 (mttm) cc_final: 0.8004 (ttmt) REVERT: C 239 MET cc_start: 0.6573 (OUTLIER) cc_final: 0.5990 (tmm) REVERT: C 439 LYS cc_start: 0.7923 (mttm) cc_final: 0.7704 (mtmt) REVERT: C 488 MET cc_start: 0.7621 (mmm) cc_final: 0.7067 (mmm) REVERT: C 600 THR cc_start: 0.8548 (m) cc_final: 0.8339 (p) REVERT: C 779 ARG cc_start: 0.7834 (ttt90) cc_final: 0.7529 (ttt-90) REVERT: C 937 ASP cc_start: 0.6784 (m-30) cc_final: 0.6393 (m-30) REVERT: C 955 GLN cc_start: 0.8249 (tp-100) cc_final: 0.7928 (tp-100) REVERT: C 1131 MET cc_start: 0.8223 (mtt) cc_final: 0.7983 (mtt) REVERT: C 1171 ARG cc_start: 0.7564 (ttp80) cc_final: 0.7274 (ttp-110) REVERT: D 158 GLN cc_start: 0.8698 (OUTLIER) cc_final: 0.8280 (tt0) REVERT: D 214 ARG cc_start: 0.7598 (mtp85) cc_final: 0.7397 (ttm110) REVERT: D 312 ARG cc_start: 0.7186 (ttp-170) cc_final: 0.6807 (tmt90) REVERT: D 707 ILE cc_start: 0.8077 (OUTLIER) cc_final: 0.7665 (tp) REVERT: D 1095 MET cc_start: 0.5931 (tmm) cc_final: 0.5641 (tpt) REVERT: F 160 ASP cc_start: 0.7845 (t0) cc_final: 0.7556 (p0) REVERT: F 277 MET cc_start: 0.7525 (tmm) cc_final: 0.6688 (tpt) REVERT: F 346 GLN cc_start: 0.5572 (OUTLIER) cc_final: 0.5363 (tm-30) REVERT: F 363 ARG cc_start: 0.6929 (ttp-110) cc_final: 0.6565 (ttp-110) REVERT: F 507 MET cc_start: 0.8715 (mtp) cc_final: 0.8472 (mtp) REVERT: F 561 MET cc_start: 0.8203 (mtp) cc_final: 0.7999 (ttm) REVERT: G 56 ARG cc_start: 0.7201 (ttp-170) cc_final: 0.6887 (ttm-80) REVERT: G 95 MET cc_start: 0.7025 (mtp) cc_final: 0.6699 (ttm) REVERT: H 60 PHE cc_start: 0.7842 (m-80) cc_final: 0.7576 (m-80) outliers start: 65 outliers final: 17 residues processed: 424 average time/residue: 1.8146 time to fit residues: 897.3446 Evaluate side-chains 340 residues out of total 3645 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 317 time to evaluate : 3.802 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 9 LEU Chi-restraints excluded: chain A residue 200 LYS Chi-restraints excluded: chain B residue 188 GLU Chi-restraints excluded: chain C residue 21 VAL Chi-restraints excluded: chain C residue 239 MET Chi-restraints excluded: chain C residue 327 GLN Chi-restraints excluded: chain C residue 377 THR Chi-restraints excluded: chain C residue 598 VAL Chi-restraints excluded: chain C residue 632 ASP Chi-restraints excluded: chain C residue 739 ASP Chi-restraints excluded: chain C residue 896 THR Chi-restraints excluded: chain D residue 83 VAL Chi-restraints excluded: chain D residue 158 GLN Chi-restraints excluded: chain D residue 553 THR Chi-restraints excluded: chain D residue 691 ASP Chi-restraints excluded: chain D residue 707 ILE Chi-restraints excluded: chain D residue 839 VAL Chi-restraints excluded: chain D residue 1169 THR Chi-restraints excluded: chain F residue 134 VAL Chi-restraints excluded: chain F residue 346 GLN Chi-restraints excluded: chain F residue 488 LEU Chi-restraints excluded: chain H residue 151 MET Chi-restraints excluded: chain H residue 238 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 428 random chunks: chunk 216 optimal weight: 5.9990 chunk 120 optimal weight: 3.9990 chunk 323 optimal weight: 10.0000 chunk 264 optimal weight: 1.9990 chunk 107 optimal weight: 4.9990 chunk 389 optimal weight: 5.9990 chunk 420 optimal weight: 10.0000 chunk 346 optimal weight: 2.9990 chunk 386 optimal weight: 7.9990 chunk 132 optimal weight: 4.9990 chunk 312 optimal weight: 5.9990 overall best weight: 3.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 93 GLN B 132 HIS ** B 186 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 41 GLN ** C 120 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C1136 GLN C1244 HIS D 320 ASN D 364 HIS ** D 365 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 488 ASN ** D 495 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 680 ASN D 910 ASN D1197 ASN D1366 HIS F 128 ASN F 406 GLN ** F 589 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 36 ASN ** G 45 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 188 ASN ** G 200 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 228 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 50 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 104 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 221 ASN H 251 ASN Total number of N/Q/H flips: 18 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8195 moved from start: 0.1434 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.009 0.083 36598 Z= 0.555 Angle : 0.669 12.139 49931 Z= 0.355 Chirality : 0.049 0.250 5681 Planarity : 0.005 0.066 6095 Dihedral : 15.661 175.615 6153 Min Nonbonded Distance : 1.973 Molprobity Statistics. All-atom Clashscore : 10.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.74 % Favored : 97.26 % Rotamer: Outliers : 2.91 % Allowed : 14.05 % Favored : 83.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.17 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.00 (0.12), residues: 4194 helix: -0.18 (0.12), residues: 1651 sheet: -1.06 (0.20), residues: 540 loop : -0.86 (0.13), residues: 2003 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.002 TRP D 580 HIS 0.016 0.002 HIS H 101 PHE 0.032 0.002 PHE H 7 TYR 0.016 0.002 TYR D 723 ARG 0.011 0.001 ARG C 352 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8388 Ramachandran restraints generated. 4194 Oldfield, 0 Emsley, 4194 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8388 Ramachandran restraints generated. 4194 Oldfield, 0 Emsley, 4194 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 441 residues out of total 3645 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 106 poor density : 335 time to evaluate : 3.659 Fit side-chains revert: symmetry clash REVERT: A 200 LYS cc_start: 0.9028 (OUTLIER) cc_final: 0.8326 (ptpp) REVERT: B 58 GLU cc_start: 0.8354 (pt0) cc_final: 0.7994 (pt0) REVERT: B 104 LYS cc_start: 0.7645 (tptm) cc_final: 0.7362 (tptp) REVERT: B 191 ARG cc_start: 0.7644 (ttp80) cc_final: 0.7093 (ptm-80) REVERT: B 205 MET cc_start: 0.8615 (OUTLIER) cc_final: 0.7826 (ttt) REVERT: C 118 LYS cc_start: 0.8523 (mttm) cc_final: 0.8151 (ttmt) REVERT: C 200 ARG cc_start: 0.8352 (OUTLIER) cc_final: 0.7519 (mmp-170) REVERT: C 239 MET cc_start: 0.6568 (OUTLIER) cc_final: 0.5956 (tmm) REVERT: C 240 GLU cc_start: 0.6753 (mm-30) cc_final: 0.6258 (mm-30) REVERT: C 439 LYS cc_start: 0.7988 (mttm) cc_final: 0.7757 (mtmt) REVERT: C 441 GLU cc_start: 0.6981 (OUTLIER) cc_final: 0.6641 (pm20) REVERT: C 488 MET cc_start: 0.7854 (mmm) cc_final: 0.7237 (mmm) REVERT: C 515 MET cc_start: 0.8473 (OUTLIER) cc_final: 0.6879 (tmm) REVERT: C 937 ASP cc_start: 0.6897 (m-30) cc_final: 0.6553 (m-30) REVERT: C 942 ASP cc_start: 0.8099 (OUTLIER) cc_final: 0.7793 (p0) REVERT: C 954 LYS cc_start: 0.8091 (mtmm) cc_final: 0.7707 (tmtt) REVERT: C 1171 ARG cc_start: 0.7527 (ttp80) cc_final: 0.7228 (ttp-110) REVERT: C 1219 GLU cc_start: 0.7784 (OUTLIER) cc_final: 0.7389 (pt0) REVERT: D 158 GLN cc_start: 0.8714 (OUTLIER) cc_final: 0.8288 (tt0) REVERT: D 215 LYS cc_start: 0.8504 (tptp) cc_final: 0.8011 (mttm) REVERT: D 312 ARG cc_start: 0.7313 (ttp-170) cc_final: 0.6954 (tmt90) REVERT: D 388 ARG cc_start: 0.7950 (OUTLIER) cc_final: 0.7678 (mtm180) REVERT: D 413 ASP cc_start: 0.7640 (OUTLIER) cc_final: 0.7425 (m-30) REVERT: D 707 ILE cc_start: 0.8366 (OUTLIER) cc_final: 0.8019 (tp) REVERT: D 1095 MET cc_start: 0.5897 (tmm) cc_final: 0.5595 (tpt) REVERT: D 1247 LYS cc_start: 0.8020 (OUTLIER) cc_final: 0.7643 (tttm) REVERT: E 67 ARG cc_start: 0.7521 (mtt90) cc_final: 0.7278 (mtt90) REVERT: F 91 ILE cc_start: 0.8396 (OUTLIER) cc_final: 0.8180 (mp) REVERT: F 160 ASP cc_start: 0.7869 (t0) cc_final: 0.7570 (p0) REVERT: F 277 MET cc_start: 0.7566 (tmm) cc_final: 0.6741 (tpt) REVERT: F 278 ASP cc_start: 0.8124 (t0) cc_final: 0.7918 (t0) REVERT: F 367 ILE cc_start: 0.8100 (OUTLIER) cc_final: 0.7830 (mp) REVERT: F 507 MET cc_start: 0.8765 (mtp) cc_final: 0.8504 (mtp) REVERT: G 56 ARG cc_start: 0.7303 (ttp-170) cc_final: 0.7014 (ttm-80) REVERT: G 95 MET cc_start: 0.7003 (mtp) cc_final: 0.6728 (ttm) REVERT: H 60 PHE cc_start: 0.7840 (m-80) cc_final: 0.7545 (m-80) outliers start: 106 outliers final: 46 residues processed: 402 average time/residue: 1.7999 time to fit residues: 847.1168 Evaluate side-chains 377 residues out of total 3645 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 61 poor density : 316 time to evaluate : 4.150 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 9 LEU Chi-restraints excluded: chain A residue 64 VAL Chi-restraints excluded: chain A residue 186 ASN Chi-restraints excluded: chain A residue 200 LYS Chi-restraints excluded: chain B residue 205 MET Chi-restraints excluded: chain C residue 21 VAL Chi-restraints excluded: chain C residue 103 VAL Chi-restraints excluded: chain C residue 200 ARG Chi-restraints excluded: chain C residue 239 MET Chi-restraints excluded: chain C residue 361 SER Chi-restraints excluded: chain C residue 377 THR Chi-restraints excluded: chain C residue 410 LEU Chi-restraints excluded: chain C residue 423 ASP Chi-restraints excluded: chain C residue 441 GLU Chi-restraints excluded: chain C residue 471 VAL Chi-restraints excluded: chain C residue 476 LYS Chi-restraints excluded: chain C residue 502 VAL Chi-restraints excluded: chain C residue 515 MET Chi-restraints excluded: chain C residue 581 THR Chi-restraints excluded: chain C residue 598 VAL Chi-restraints excluded: chain C residue 634 VAL Chi-restraints excluded: chain C residue 641 GLU Chi-restraints excluded: chain C residue 644 LEU Chi-restraints excluded: chain C residue 655 VAL Chi-restraints excluded: chain C residue 739 ASP Chi-restraints excluded: chain C residue 845 LEU Chi-restraints excluded: chain C residue 940 GLU Chi-restraints excluded: chain C residue 942 ASP Chi-restraints excluded: chain C residue 1075 VAL Chi-restraints excluded: chain C residue 1219 GLU Chi-restraints excluded: chain D residue 83 VAL Chi-restraints excluded: chain D residue 158 GLN Chi-restraints excluded: chain D residue 388 ARG Chi-restraints excluded: chain D residue 413 ASP Chi-restraints excluded: chain D residue 505 ASP Chi-restraints excluded: chain D residue 525 MET Chi-restraints excluded: chain D residue 553 THR Chi-restraints excluded: chain D residue 661 VAL Chi-restraints excluded: chain D residue 691 ASP Chi-restraints excluded: chain D residue 707 ILE Chi-restraints excluded: chain D residue 751 ASP Chi-restraints excluded: chain D residue 839 VAL Chi-restraints excluded: chain D residue 1169 THR Chi-restraints excluded: chain D residue 1243 LEU Chi-restraints excluded: chain D residue 1247 LYS Chi-restraints excluded: chain D residue 1353 VAL Chi-restraints excluded: chain D residue 1368 ASP Chi-restraints excluded: chain E residue 69 ARG Chi-restraints excluded: chain F residue 91 ILE Chi-restraints excluded: chain F residue 134 VAL Chi-restraints excluded: chain F residue 234 THR Chi-restraints excluded: chain F residue 262 VAL Chi-restraints excluded: chain F residue 367 ILE Chi-restraints excluded: chain F residue 500 ILE Chi-restraints excluded: chain F residue 527 THR Chi-restraints excluded: chain F residue 567 MET Chi-restraints excluded: chain G residue 181 VAL Chi-restraints excluded: chain H residue 151 MET Chi-restraints excluded: chain H residue 198 ILE Chi-restraints excluded: chain H residue 206 THR Chi-restraints excluded: chain H residue 238 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 428 random chunks: chunk 384 optimal weight: 6.9990 chunk 292 optimal weight: 20.0000 chunk 202 optimal weight: 0.5980 chunk 43 optimal weight: 0.7980 chunk 185 optimal weight: 0.7980 chunk 261 optimal weight: 0.7980 chunk 390 optimal weight: 20.0000 chunk 413 optimal weight: 2.9990 chunk 204 optimal weight: 0.6980 chunk 370 optimal weight: 6.9990 chunk 111 optimal weight: 0.9990 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 66 HIS A 93 GLN C1136 GLN ** D 495 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 680 ASN D1197 ASN ** F 589 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 45 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 228 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 22 ASN ** H 50 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 104 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 193 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8111 moved from start: 0.1837 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 36598 Z= 0.175 Angle : 0.514 10.520 49931 Z= 0.276 Chirality : 0.041 0.183 5681 Planarity : 0.004 0.054 6095 Dihedral : 15.355 177.000 6153 Min Nonbonded Distance : 1.994 Molprobity Statistics. All-atom Clashscore : 9.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.22 % Favored : 97.78 % Rotamer: Outliers : 2.22 % Allowed : 15.88 % Favored : 81.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.17 % 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: -0.38 (0.12), residues: 4194 helix: 0.50 (0.13), residues: 1641 sheet: -0.79 (0.21), residues: 507 loop : -0.65 (0.13), residues: 2046 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP D1193 HIS 0.015 0.001 HIS H 101 PHE 0.046 0.001 PHE H 7 TYR 0.015 0.001 TYR D 631 ARG 0.006 0.000 ARG C 352 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8388 Ramachandran restraints generated. 4194 Oldfield, 0 Emsley, 4194 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8388 Ramachandran restraints generated. 4194 Oldfield, 0 Emsley, 4194 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 420 residues out of total 3645 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 81 poor density : 339 time to evaluate : 4.037 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 199 ASP cc_start: 0.7492 (m-30) cc_final: 0.7247 (m-30) REVERT: A 200 LYS cc_start: 0.8983 (OUTLIER) cc_final: 0.8215 (ptpp) REVERT: B 6 THR cc_start: 0.8375 (p) cc_final: 0.8037 (m) REVERT: B 58 GLU cc_start: 0.8208 (pt0) cc_final: 0.7860 (pt0) REVERT: B 104 LYS cc_start: 0.7563 (tptm) cc_final: 0.7276 (tptp) REVERT: B 191 ARG cc_start: 0.7433 (ttp80) cc_final: 0.6862 (ptm-80) REVERT: C 118 LYS cc_start: 0.8410 (mttm) cc_final: 0.8199 (tppt) REVERT: C 200 ARG cc_start: 0.8323 (OUTLIER) cc_final: 0.7554 (mmp-170) REVERT: C 239 MET cc_start: 0.6498 (OUTLIER) cc_final: 0.5469 (tmm) REVERT: C 240 GLU cc_start: 0.6587 (mm-30) cc_final: 0.6205 (mm-30) REVERT: C 315 MET cc_start: 0.6131 (OUTLIER) cc_final: 0.5833 (ptm) REVERT: C 439 LYS cc_start: 0.7906 (mttm) cc_final: 0.7681 (mtmt) REVERT: C 488 MET cc_start: 0.7712 (mmm) cc_final: 0.7282 (mmm) REVERT: C 515 MET cc_start: 0.8293 (OUTLIER) cc_final: 0.6645 (tmm) REVERT: C 600 THR cc_start: 0.8673 (m) cc_final: 0.8465 (p) REVERT: C 779 ARG cc_start: 0.7870 (ttt90) cc_final: 0.7599 (ttt-90) REVERT: C 937 ASP cc_start: 0.6840 (m-30) cc_final: 0.6438 (m-30) REVERT: C 949 GLU cc_start: 0.7869 (tt0) cc_final: 0.7666 (tt0) REVERT: C 1171 ARG cc_start: 0.7531 (ttp80) cc_final: 0.7196 (ttp-110) REVERT: C 1219 GLU cc_start: 0.7641 (OUTLIER) cc_final: 0.7234 (pt0) REVERT: D 158 GLN cc_start: 0.8743 (OUTLIER) cc_final: 0.8413 (tt0) REVERT: D 312 ARG cc_start: 0.7240 (ttp-170) cc_final: 0.6886 (tmt90) REVERT: D 707 ILE cc_start: 0.8113 (OUTLIER) cc_final: 0.7685 (tp) REVERT: D 1095 MET cc_start: 0.5983 (tmm) cc_final: 0.5647 (tpt) REVERT: E 67 ARG cc_start: 0.7444 (mtt90) cc_final: 0.7211 (mtt90) REVERT: F 160 ASP cc_start: 0.7790 (t0) cc_final: 0.7540 (p0) REVERT: F 277 MET cc_start: 0.7723 (tmm) cc_final: 0.6818 (tmm) REVERT: F 278 ASP cc_start: 0.8096 (t0) cc_final: 0.7603 (t0) REVERT: F 354 THR cc_start: 0.7888 (OUTLIER) cc_final: 0.7569 (p) REVERT: G 56 ARG cc_start: 0.7240 (ttp-170) cc_final: 0.7021 (ttm-80) REVERT: G 95 MET cc_start: 0.6960 (mtp) cc_final: 0.6624 (ttm) REVERT: H 60 PHE cc_start: 0.7802 (m-80) cc_final: 0.7468 (m-80) outliers start: 81 outliers final: 32 residues processed: 392 average time/residue: 1.7783 time to fit residues: 818.8155 Evaluate side-chains 358 residues out of total 3645 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 41 poor density : 317 time to evaluate : 3.629 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 9 LEU Chi-restraints excluded: chain A residue 64 VAL Chi-restraints excluded: chain A residue 200 LYS Chi-restraints excluded: chain B residue 15 ASP Chi-restraints excluded: chain C residue 21 VAL Chi-restraints excluded: chain C residue 103 VAL Chi-restraints excluded: chain C residue 200 ARG Chi-restraints excluded: chain C residue 239 MET Chi-restraints excluded: chain C residue 315 MET Chi-restraints excluded: chain C residue 377 THR Chi-restraints excluded: chain C residue 423 ASP Chi-restraints excluded: chain C residue 456 VAL Chi-restraints excluded: chain C residue 476 LYS Chi-restraints excluded: chain C residue 502 VAL Chi-restraints excluded: chain C residue 515 MET Chi-restraints excluded: chain C residue 598 VAL Chi-restraints excluded: chain C residue 632 ASP Chi-restraints excluded: chain C residue 739 ASP Chi-restraints excluded: chain C residue 1060 ILE Chi-restraints excluded: chain C residue 1075 VAL Chi-restraints excluded: chain C residue 1219 GLU Chi-restraints excluded: chain D residue 83 VAL Chi-restraints excluded: chain D residue 158 GLN Chi-restraints excluded: chain D residue 256 ASP Chi-restraints excluded: chain D residue 553 THR Chi-restraints excluded: chain D residue 707 ILE Chi-restraints excluded: chain D residue 839 VAL Chi-restraints excluded: chain D residue 1169 THR Chi-restraints excluded: chain D residue 1250 ASP Chi-restraints excluded: chain D residue 1298 VAL Chi-restraints excluded: chain E residue 69 ARG Chi-restraints excluded: chain F residue 95 THR Chi-restraints excluded: chain F residue 134 VAL Chi-restraints excluded: chain F residue 262 VAL Chi-restraints excluded: chain F residue 354 THR Chi-restraints excluded: chain F residue 500 ILE Chi-restraints excluded: chain G residue 13 VAL Chi-restraints excluded: chain G residue 181 VAL Chi-restraints excluded: chain H residue 151 MET Chi-restraints excluded: chain H residue 206 THR Chi-restraints excluded: chain H residue 224 ILE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 428 random chunks: chunk 344 optimal weight: 2.9990 chunk 234 optimal weight: 6.9990 chunk 6 optimal weight: 0.0000 chunk 308 optimal weight: 1.9990 chunk 170 optimal weight: 2.9990 chunk 353 optimal weight: 2.9990 chunk 285 optimal weight: 0.2980 chunk 0 optimal weight: 7.9990 chunk 211 optimal weight: 0.6980 chunk 371 optimal weight: 10.0000 chunk 104 optimal weight: 0.0060 overall best weight: 0.6002 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 93 GLN C1136 GLN D 320 ASN ** D 495 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 667 GLN D 680 ASN D 875 ASN D1197 ASN ** F 589 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 45 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 228 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 50 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 104 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 251 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8087 moved from start: 0.2151 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.043 36598 Z= 0.160 Angle : 0.489 9.846 49931 Z= 0.262 Chirality : 0.041 0.203 5681 Planarity : 0.004 0.055 6095 Dihedral : 15.052 177.451 6153 Min Nonbonded Distance : 2.012 Molprobity Statistics. All-atom Clashscore : 8.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.43 % Favored : 97.57 % Rotamer: Outliers : 2.30 % Allowed : 16.35 % Favored : 81.34 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.17 % 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: -0.01 (0.13), residues: 4194 helix: 0.86 (0.13), residues: 1648 sheet: -0.70 (0.20), residues: 545 loop : -0.45 (0.14), residues: 2001 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP D1193 HIS 0.015 0.001 HIS H 101 PHE 0.036 0.001 PHE H 7 TYR 0.014 0.001 TYR G 127 ARG 0.008 0.000 ARG B 170 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8388 Ramachandran restraints generated. 4194 Oldfield, 0 Emsley, 4194 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8388 Ramachandran restraints generated. 4194 Oldfield, 0 Emsley, 4194 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 439 residues out of total 3645 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 84 poor density : 355 time to evaluate : 4.368 Fit side-chains REVERT: B 6 THR cc_start: 0.8329 (p) cc_final: 0.8001 (m) REVERT: B 51 MET cc_start: 0.8826 (mmm) cc_final: 0.8531 (tpt) REVERT: B 58 GLU cc_start: 0.8209 (pt0) cc_final: 0.7882 (pt0) REVERT: B 104 LYS cc_start: 0.7490 (tptm) cc_final: 0.7184 (tptp) REVERT: B 191 ARG cc_start: 0.7345 (ttp80) cc_final: 0.6801 (ptm-80) REVERT: C 118 LYS cc_start: 0.8253 (mttm) cc_final: 0.8047 (tppt) REVERT: C 200 ARG cc_start: 0.8301 (OUTLIER) cc_final: 0.7504 (mmp-170) REVERT: C 239 MET cc_start: 0.6503 (OUTLIER) cc_final: 0.5724 (tmm) REVERT: C 240 GLU cc_start: 0.6259 (mm-30) cc_final: 0.5868 (mm-30) REVERT: C 315 MET cc_start: 0.6065 (ptm) cc_final: 0.5770 (ptm) REVERT: C 439 LYS cc_start: 0.7936 (mttm) cc_final: 0.7725 (mtmt) REVERT: C 488 MET cc_start: 0.7682 (mmm) cc_final: 0.7285 (mmm) REVERT: C 515 MET cc_start: 0.8310 (OUTLIER) cc_final: 0.6590 (tmm) REVERT: C 731 ARG cc_start: 0.8445 (OUTLIER) cc_final: 0.8139 (ptm160) REVERT: C 739 ASP cc_start: 0.7781 (OUTLIER) cc_final: 0.7345 (m-30) REVERT: C 937 ASP cc_start: 0.6742 (m-30) cc_final: 0.6404 (m-30) REVERT: C 1171 ARG cc_start: 0.7524 (ttp80) cc_final: 0.7277 (ttp-110) REVERT: C 1219 GLU cc_start: 0.7552 (OUTLIER) cc_final: 0.7167 (pt0) REVERT: D 158 GLN cc_start: 0.8741 (tt0) cc_final: 0.8425 (tt0) REVERT: D 312 ARG cc_start: 0.7248 (ttp-170) cc_final: 0.6872 (tmt90) REVERT: D 1040 MET cc_start: 0.3102 (OUTLIER) cc_final: 0.2492 (pmm) REVERT: D 1095 MET cc_start: 0.5992 (tmm) cc_final: 0.5662 (tpp) REVERT: F 273 MET cc_start: 0.7108 (tpt) cc_final: 0.6340 (tpt) REVERT: F 277 MET cc_start: 0.7844 (tmm) cc_final: 0.7353 (tpt) REVERT: F 288 MET cc_start: 0.1481 (mmt) cc_final: 0.0938 (mmm) REVERT: F 354 THR cc_start: 0.7984 (OUTLIER) cc_final: 0.7757 (p) REVERT: G 56 ARG cc_start: 0.7243 (ttp-170) cc_final: 0.6988 (ttm-80) REVERT: G 95 MET cc_start: 0.6916 (mtp) cc_final: 0.6544 (ttm) REVERT: G 112 MET cc_start: 0.3242 (mmm) cc_final: 0.2942 (mmp) REVERT: G 178 ASN cc_start: 0.6532 (t0) cc_final: 0.5817 (m110) REVERT: H 44 ASP cc_start: 0.7952 (m-30) cc_final: 0.7306 (t70) REVERT: H 101 HIS cc_start: 0.7391 (t70) cc_final: 0.7120 (t-170) outliers start: 84 outliers final: 28 residues processed: 412 average time/residue: 1.7658 time to fit residues: 854.7127 Evaluate side-chains 353 residues out of total 3645 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 36 poor density : 317 time to evaluate : 3.662 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 9 LEU Chi-restraints excluded: chain A residue 64 VAL Chi-restraints excluded: chain C residue 21 VAL Chi-restraints excluded: chain C residue 103 VAL Chi-restraints excluded: chain C residue 200 ARG Chi-restraints excluded: chain C residue 239 MET Chi-restraints excluded: chain C residue 377 THR Chi-restraints excluded: chain C residue 423 ASP Chi-restraints excluded: chain C residue 476 LYS Chi-restraints excluded: chain C residue 515 MET Chi-restraints excluded: chain C residue 598 VAL Chi-restraints excluded: chain C residue 644 LEU Chi-restraints excluded: chain C residue 731 ARG Chi-restraints excluded: chain C residue 739 ASP Chi-restraints excluded: chain C residue 1060 ILE Chi-restraints excluded: chain C residue 1075 VAL Chi-restraints excluded: chain C residue 1219 GLU Chi-restraints excluded: chain D residue 83 VAL Chi-restraints excluded: chain D residue 256 ASP Chi-restraints excluded: chain D residue 553 THR Chi-restraints excluded: chain D residue 661 VAL Chi-restraints excluded: chain D residue 751 ASP Chi-restraints excluded: chain D residue 839 VAL Chi-restraints excluded: chain D residue 1040 MET Chi-restraints excluded: chain D residue 1169 THR Chi-restraints excluded: chain D residue 1250 ASP Chi-restraints excluded: chain D residue 1298 VAL Chi-restraints excluded: chain F residue 134 VAL Chi-restraints excluded: chain F residue 262 VAL Chi-restraints excluded: chain F residue 354 THR Chi-restraints excluded: chain F residue 500 ILE Chi-restraints excluded: chain G residue 13 VAL Chi-restraints excluded: chain G residue 181 VAL Chi-restraints excluded: chain H residue 198 ILE Chi-restraints excluded: chain H residue 206 THR Chi-restraints excluded: chain H residue 224 ILE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 428 random chunks: chunk 139 optimal weight: 5.9990 chunk 372 optimal weight: 8.9990 chunk 81 optimal weight: 0.8980 chunk 242 optimal weight: 2.9990 chunk 102 optimal weight: 2.9990 chunk 414 optimal weight: 0.0470 chunk 343 optimal weight: 1.9990 chunk 191 optimal weight: 1.9990 chunk 34 optimal weight: 10.0000 chunk 136 optimal weight: 4.9990 chunk 217 optimal weight: 3.9990 overall best weight: 1.5884 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 93 GLN C 582 ASN C1136 GLN ** D 495 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 680 ASN D1197 ASN ** F 589 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 45 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 178 ASN ** G 228 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 50 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 251 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8132 moved from start: 0.2096 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 36598 Z= 0.269 Angle : 0.536 12.168 49931 Z= 0.283 Chirality : 0.043 0.150 5681 Planarity : 0.004 0.056 6095 Dihedral : 15.130 176.764 6153 Min Nonbonded Distance : 1.991 Molprobity Statistics. All-atom Clashscore : 8.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.69 % Favored : 97.31 % Rotamer: Outliers : 2.47 % Allowed : 17.31 % Favored : 80.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.17 % 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: 0.02 (0.13), residues: 4194 helix: 0.76 (0.13), residues: 1655 sheet: -0.55 (0.21), residues: 516 loop : -0.35 (0.14), residues: 2023 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP D1193 HIS 0.013 0.001 HIS H 101 PHE 0.035 0.001 PHE H 7 TYR 0.021 0.001 TYR H 102 ARG 0.007 0.000 ARG B 170 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8388 Ramachandran restraints generated. 4194 Oldfield, 0 Emsley, 4194 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8388 Ramachandran restraints generated. 4194 Oldfield, 0 Emsley, 4194 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 408 residues out of total 3645 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 90 poor density : 318 time to evaluate : 3.860 Fit side-chains REVERT: B 6 THR cc_start: 0.8359 (p) cc_final: 0.8012 (m) REVERT: B 58 GLU cc_start: 0.8278 (pt0) cc_final: 0.7915 (pt0) REVERT: B 104 LYS cc_start: 0.7489 (tptm) cc_final: 0.7162 (tptp) REVERT: B 191 ARG cc_start: 0.7391 (ttp80) cc_final: 0.6837 (ptm-80) REVERT: B 231 PHE cc_start: 0.8393 (OUTLIER) cc_final: 0.8076 (m-80) REVERT: C 118 LYS cc_start: 0.8274 (mttm) cc_final: 0.8025 (tppt) REVERT: C 200 ARG cc_start: 0.8313 (OUTLIER) cc_final: 0.7497 (mmp-170) REVERT: C 239 MET cc_start: 0.6454 (OUTLIER) cc_final: 0.5777 (tmm) REVERT: C 240 GLU cc_start: 0.6188 (mm-30) cc_final: 0.5818 (mm-30) REVERT: C 315 MET cc_start: 0.6147 (ptm) cc_final: 0.5870 (ptm) REVERT: C 439 LYS cc_start: 0.7967 (mttm) cc_final: 0.7747 (mtmt) REVERT: C 488 MET cc_start: 0.7736 (mmm) cc_final: 0.7322 (mmm) REVERT: C 496 LYS cc_start: 0.7882 (OUTLIER) cc_final: 0.7506 (mmmt) REVERT: C 515 MET cc_start: 0.8384 (OUTLIER) cc_final: 0.6752 (tmm) REVERT: C 641 GLU cc_start: 0.7604 (OUTLIER) cc_final: 0.7259 (pt0) REVERT: C 731 ARG cc_start: 0.8459 (OUTLIER) cc_final: 0.8232 (ptm160) REVERT: C 937 ASP cc_start: 0.6741 (m-30) cc_final: 0.6390 (m-30) REVERT: C 1171 ARG cc_start: 0.7533 (ttp80) cc_final: 0.7195 (ttp-110) REVERT: D 81 ARG cc_start: 0.7691 (ttm-80) cc_final: 0.7414 (ttm-80) REVERT: D 158 GLN cc_start: 0.8733 (tt0) cc_final: 0.8419 (tt0) REVERT: D 312 ARG cc_start: 0.7260 (ttp-170) cc_final: 0.6897 (tmt90) REVERT: D 388 ARG cc_start: 0.7974 (OUTLIER) cc_final: 0.7654 (mtm180) REVERT: D 707 ILE cc_start: 0.8226 (OUTLIER) cc_final: 0.7918 (tt) REVERT: D 1040 MET cc_start: 0.3290 (OUTLIER) cc_final: 0.2720 (pmt) REVERT: D 1095 MET cc_start: 0.6074 (tmm) cc_final: 0.5699 (tpt) REVERT: E 67 ARG cc_start: 0.7437 (mtt90) cc_final: 0.7188 (mtt90) REVERT: F 277 MET cc_start: 0.7858 (tmm) cc_final: 0.7169 (mmm) REVERT: F 288 MET cc_start: 0.1407 (mmt) cc_final: 0.1088 (mmm) REVERT: F 354 THR cc_start: 0.8058 (OUTLIER) cc_final: 0.7830 (p) REVERT: G 95 MET cc_start: 0.7074 (mtp) cc_final: 0.6790 (ttm) REVERT: G 112 MET cc_start: 0.3230 (mmm) cc_final: 0.2950 (mmp) REVERT: G 178 ASN cc_start: 0.6539 (t0) cc_final: 0.5717 (m110) REVERT: G 251 ASN cc_start: 0.6891 (OUTLIER) cc_final: 0.6688 (p0) REVERT: H 44 ASP cc_start: 0.7971 (m-30) cc_final: 0.7302 (t70) REVERT: H 101 HIS cc_start: 0.7422 (t70) cc_final: 0.7129 (t-170) outliers start: 90 outliers final: 45 residues processed: 377 average time/residue: 1.7618 time to fit residues: 782.1034 Evaluate side-chains 367 residues out of total 3645 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 57 poor density : 310 time to evaluate : 3.589 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 9 LEU Chi-restraints excluded: chain A residue 64 VAL Chi-restraints excluded: chain A residue 186 ASN Chi-restraints excluded: chain B residue 15 ASP Chi-restraints excluded: chain B residue 231 PHE Chi-restraints excluded: chain C residue 21 VAL Chi-restraints excluded: chain C residue 82 VAL Chi-restraints excluded: chain C residue 103 VAL Chi-restraints excluded: chain C residue 200 ARG Chi-restraints excluded: chain C residue 239 MET Chi-restraints excluded: chain C residue 377 THR Chi-restraints excluded: chain C residue 410 LEU Chi-restraints excluded: chain C residue 423 ASP Chi-restraints excluded: chain C residue 456 VAL Chi-restraints excluded: chain C residue 476 LYS Chi-restraints excluded: chain C residue 496 LYS Chi-restraints excluded: chain C residue 515 MET Chi-restraints excluded: chain C residue 598 VAL Chi-restraints excluded: chain C residue 623 LEU Chi-restraints excluded: chain C residue 632 ASP Chi-restraints excluded: chain C residue 641 GLU Chi-restraints excluded: chain C residue 644 LEU Chi-restraints excluded: chain C residue 655 VAL Chi-restraints excluded: chain C residue 731 ARG Chi-restraints excluded: chain C residue 739 ASP Chi-restraints excluded: chain C residue 1075 VAL Chi-restraints excluded: chain D residue 83 VAL Chi-restraints excluded: chain D residue 191 SER Chi-restraints excluded: chain D residue 388 ARG Chi-restraints excluded: chain D residue 485 MET Chi-restraints excluded: chain D residue 553 THR Chi-restraints excluded: chain D residue 661 VAL Chi-restraints excluded: chain D residue 707 ILE Chi-restraints excluded: chain D residue 751 ASP Chi-restraints excluded: chain D residue 793 SER Chi-restraints excluded: chain D residue 839 VAL Chi-restraints excluded: chain D residue 1040 MET Chi-restraints excluded: chain D residue 1169 THR Chi-restraints excluded: chain D residue 1243 LEU Chi-restraints excluded: chain D residue 1250 ASP Chi-restraints excluded: chain D residue 1298 VAL Chi-restraints excluded: chain E residue 69 ARG Chi-restraints excluded: chain F residue 95 THR Chi-restraints excluded: chain F residue 134 VAL Chi-restraints excluded: chain F residue 262 VAL Chi-restraints excluded: chain F residue 337 VAL Chi-restraints excluded: chain F residue 354 THR Chi-restraints excluded: chain F residue 488 LEU Chi-restraints excluded: chain F residue 500 ILE Chi-restraints excluded: chain F residue 527 THR Chi-restraints excluded: chain G residue 13 VAL Chi-restraints excluded: chain G residue 181 VAL Chi-restraints excluded: chain G residue 251 ASN Chi-restraints excluded: chain G residue 262 ILE Chi-restraints excluded: chain H residue 151 MET Chi-restraints excluded: chain H residue 206 THR Chi-restraints excluded: chain H residue 224 ILE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 428 random chunks: chunk 399 optimal weight: 20.0000 chunk 46 optimal weight: 0.1980 chunk 235 optimal weight: 0.9990 chunk 302 optimal weight: 10.0000 chunk 234 optimal weight: 0.8980 chunk 348 optimal weight: 2.9990 chunk 231 optimal weight: 3.9990 chunk 412 optimal weight: 9.9990 chunk 258 optimal weight: 0.5980 chunk 251 optimal weight: 0.6980 chunk 190 optimal weight: 5.9990 overall best weight: 0.6782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 93 GLN C 628 HIS C1136 GLN C1157 GLN ** D 495 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 667 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 680 ASN ** E 75 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 147 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 265 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 589 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 45 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 228 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 50 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 251 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8089 moved from start: 0.2337 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 36598 Z= 0.164 Angle : 0.491 11.441 49931 Z= 0.261 Chirality : 0.041 0.147 5681 Planarity : 0.004 0.057 6095 Dihedral : 14.987 177.689 6153 Min Nonbonded Distance : 2.006 Molprobity Statistics. All-atom Clashscore : 8.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.27 % Favored : 97.73 % Rotamer: Outliers : 2.11 % Allowed : 17.75 % Favored : 80.14 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.17 % 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: 0.22 (0.13), residues: 4194 helix: 0.95 (0.13), residues: 1665 sheet: -0.43 (0.21), residues: 518 loop : -0.27 (0.14), residues: 2011 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP D1193 HIS 0.012 0.001 HIS H 101 PHE 0.030 0.001 PHE H 7 TYR 0.019 0.001 TYR H 102 ARG 0.007 0.000 ARG B 170 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8388 Ramachandran restraints generated. 4194 Oldfield, 0 Emsley, 4194 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8388 Ramachandran restraints generated. 4194 Oldfield, 0 Emsley, 4194 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 414 residues out of total 3645 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 77 poor density : 337 time to evaluate : 4.006 Fit side-chains REVERT: B 6 THR cc_start: 0.8341 (p) cc_final: 0.8004 (m) REVERT: B 51 MET cc_start: 0.8805 (mmm) cc_final: 0.8507 (tpt) REVERT: B 58 GLU cc_start: 0.8224 (pt0) cc_final: 0.7855 (pt0) REVERT: B 104 LYS cc_start: 0.7457 (tptm) cc_final: 0.7120 (tptp) REVERT: B 191 ARG cc_start: 0.7270 (ttp80) cc_final: 0.6749 (ptm-80) REVERT: C 118 LYS cc_start: 0.8291 (mttm) cc_final: 0.7945 (ttmm) REVERT: C 200 ARG cc_start: 0.8302 (OUTLIER) cc_final: 0.7534 (mmp-170) REVERT: C 239 MET cc_start: 0.6459 (OUTLIER) cc_final: 0.5639 (tmm) REVERT: C 240 GLU cc_start: 0.6072 (mm-30) cc_final: 0.5815 (mm-30) REVERT: C 315 MET cc_start: 0.6031 (ptm) cc_final: 0.5766 (ptm) REVERT: C 439 LYS cc_start: 0.7949 (mttm) cc_final: 0.7740 (mtmt) REVERT: C 496 LYS cc_start: 0.7825 (OUTLIER) cc_final: 0.7458 (mmmt) REVERT: C 515 MET cc_start: 0.8312 (OUTLIER) cc_final: 0.6674 (tmm) REVERT: C 542 ARG cc_start: 0.7482 (ptp-170) cc_final: 0.6941 (mtp180) REVERT: C 779 ARG cc_start: 0.7818 (ttp80) cc_final: 0.7559 (ttt-90) REVERT: C 867 GLU cc_start: 0.7559 (pm20) cc_final: 0.7162 (pm20) REVERT: C 937 ASP cc_start: 0.6663 (m-30) cc_final: 0.6377 (m-30) REVERT: C 943 LYS cc_start: 0.8465 (ptmm) cc_final: 0.8091 (ptmm) REVERT: C 1171 ARG cc_start: 0.7548 (ttp80) cc_final: 0.7182 (ttp-110) REVERT: C 1219 GLU cc_start: 0.7537 (OUTLIER) cc_final: 0.7152 (pt0) REVERT: D 81 ARG cc_start: 0.7587 (ttm-80) cc_final: 0.7312 (ttm-80) REVERT: D 158 GLN cc_start: 0.8727 (tt0) cc_final: 0.8411 (tt0) REVERT: D 312 ARG cc_start: 0.7251 (ttp-170) cc_final: 0.6872 (tmt90) REVERT: D 707 ILE cc_start: 0.8122 (OUTLIER) cc_final: 0.7796 (tt) REVERT: D 1040 MET cc_start: 0.3681 (OUTLIER) cc_final: 0.2957 (pmt) REVERT: D 1095 MET cc_start: 0.6003 (tmm) cc_final: 0.5612 (tpt) REVERT: F 277 MET cc_start: 0.7975 (tmm) cc_final: 0.7148 (mmm) REVERT: F 288 MET cc_start: 0.1357 (mmt) cc_final: 0.0798 (mmm) REVERT: F 354 THR cc_start: 0.8206 (OUTLIER) cc_final: 0.7993 (p) REVERT: G 95 MET cc_start: 0.7090 (mtp) cc_final: 0.6851 (ttm) REVERT: G 178 ASN cc_start: 0.6594 (t0) cc_final: 0.5842 (m110) REVERT: G 251 ASN cc_start: 0.6930 (OUTLIER) cc_final: 0.6714 (p0) REVERT: H 44 ASP cc_start: 0.7970 (m-30) cc_final: 0.7260 (t70) REVERT: H 101 HIS cc_start: 0.7449 (t70) cc_final: 0.6782 (t-170) REVERT: H 108 LYS cc_start: 0.5245 (OUTLIER) cc_final: 0.5006 (ttpp) REVERT: H 112 MET cc_start: 0.4729 (ttm) cc_final: 0.4110 (mtm) REVERT: H 187 VAL cc_start: 0.8313 (t) cc_final: 0.8012 (p) outliers start: 77 outliers final: 42 residues processed: 392 average time/residue: 1.7519 time to fit residues: 807.1028 Evaluate side-chains 364 residues out of total 3645 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 52 poor density : 312 time to evaluate : 3.889 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 9 LEU Chi-restraints excluded: chain A residue 64 VAL Chi-restraints excluded: chain B residue 15 ASP Chi-restraints excluded: chain B residue 204 GLU Chi-restraints excluded: chain C residue 21 VAL Chi-restraints excluded: chain C residue 103 VAL Chi-restraints excluded: chain C residue 200 ARG Chi-restraints excluded: chain C residue 239 MET Chi-restraints excluded: chain C residue 377 THR Chi-restraints excluded: chain C residue 410 LEU Chi-restraints excluded: chain C residue 423 ASP Chi-restraints excluded: chain C residue 456 VAL Chi-restraints excluded: chain C residue 496 LYS Chi-restraints excluded: chain C residue 515 MET Chi-restraints excluded: chain C residue 598 VAL Chi-restraints excluded: chain C residue 623 LEU Chi-restraints excluded: chain C residue 644 LEU Chi-restraints excluded: chain C residue 739 ASP Chi-restraints excluded: chain C residue 1060 ILE Chi-restraints excluded: chain C residue 1075 VAL Chi-restraints excluded: chain C residue 1219 GLU Chi-restraints excluded: chain D residue 83 VAL Chi-restraints excluded: chain D residue 191 SER Chi-restraints excluded: chain D residue 256 ASP Chi-restraints excluded: chain D residue 553 THR Chi-restraints excluded: chain D residue 707 ILE Chi-restraints excluded: chain D residue 751 ASP Chi-restraints excluded: chain D residue 812 ASP Chi-restraints excluded: chain D residue 839 VAL Chi-restraints excluded: chain D residue 1028 ILE Chi-restraints excluded: chain D residue 1040 MET Chi-restraints excluded: chain D residue 1169 THR Chi-restraints excluded: chain D residue 1209 VAL Chi-restraints excluded: chain D residue 1243 LEU Chi-restraints excluded: chain D residue 1250 ASP Chi-restraints excluded: chain D residue 1298 VAL Chi-restraints excluded: chain F residue 95 THR Chi-restraints excluded: chain F residue 134 VAL Chi-restraints excluded: chain F residue 262 VAL Chi-restraints excluded: chain F residue 337 VAL Chi-restraints excluded: chain F residue 354 THR Chi-restraints excluded: chain F residue 500 ILE Chi-restraints excluded: chain F residue 527 THR Chi-restraints excluded: chain G residue 13 VAL Chi-restraints excluded: chain G residue 181 VAL Chi-restraints excluded: chain G residue 251 ASN Chi-restraints excluded: chain G residue 262 ILE Chi-restraints excluded: chain H residue 108 LYS Chi-restraints excluded: chain H residue 151 MET Chi-restraints excluded: chain H residue 206 THR Chi-restraints excluded: chain H residue 219 LEU Chi-restraints excluded: chain H residue 224 ILE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 428 random chunks: chunk 255 optimal weight: 4.9990 chunk 164 optimal weight: 0.1980 chunk 246 optimal weight: 3.9990 chunk 124 optimal weight: 2.9990 chunk 81 optimal weight: 3.9990 chunk 79 optimal weight: 6.9990 chunk 262 optimal weight: 0.2980 chunk 281 optimal weight: 50.0000 chunk 203 optimal weight: 6.9990 chunk 38 optimal weight: 5.9990 chunk 324 optimal weight: 7.9990 overall best weight: 2.2986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 93 GLN ** C 120 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 582 ASN C 628 HIS C1136 GLN C1157 GLN ** D 495 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D1197 ASN ** F 362 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 589 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 45 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 70 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 115 GLN ** G 228 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 22 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 50 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 251 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8155 moved from start: 0.2154 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.055 36598 Z= 0.357 Angle : 0.579 14.315 49931 Z= 0.303 Chirality : 0.044 0.180 5681 Planarity : 0.004 0.056 6095 Dihedral : 15.155 176.080 6153 Min Nonbonded Distance : 1.980 Molprobity Statistics. All-atom Clashscore : 9.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.86 % Favored : 97.14 % Rotamer: Outliers : 2.30 % Allowed : 18.13 % Favored : 79.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.17 % 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: 0.05 (0.13), residues: 4194 helix: 0.76 (0.13), residues: 1647 sheet: -0.49 (0.21), residues: 517 loop : -0.32 (0.14), residues: 2030 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP D1193 HIS 0.014 0.001 HIS H 101 PHE 0.025 0.002 PHE H 7 TYR 0.025 0.002 TYR F 148 ARG 0.007 0.000 ARG G 12 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8388 Ramachandran restraints generated. 4194 Oldfield, 0 Emsley, 4194 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8388 Ramachandran restraints generated. 4194 Oldfield, 0 Emsley, 4194 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 394 residues out of total 3645 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 84 poor density : 310 time to evaluate : 3.900 Fit side-chains REVERT: B 58 GLU cc_start: 0.8317 (pt0) cc_final: 0.7947 (pt0) REVERT: B 104 LYS cc_start: 0.7510 (tptm) cc_final: 0.7146 (tptp) REVERT: B 191 ARG cc_start: 0.7429 (ttp80) cc_final: 0.6862 (ptm-80) REVERT: C 118 LYS cc_start: 0.8380 (mttm) cc_final: 0.7935 (ttmm) REVERT: C 200 ARG cc_start: 0.8380 (OUTLIER) cc_final: 0.7508 (mmp-170) REVERT: C 239 MET cc_start: 0.6441 (OUTLIER) cc_final: 0.5672 (tmm) REVERT: C 240 GLU cc_start: 0.6133 (mm-30) cc_final: 0.5839 (mm-30) REVERT: C 315 MET cc_start: 0.6100 (ptm) cc_final: 0.5807 (ptm) REVERT: C 439 LYS cc_start: 0.7946 (mttm) cc_final: 0.7717 (mtmt) REVERT: C 515 MET cc_start: 0.8409 (OUTLIER) cc_final: 0.6819 (tmm) REVERT: C 542 ARG cc_start: 0.7540 (ptp-170) cc_final: 0.7014 (mtp180) REVERT: C 867 GLU cc_start: 0.7619 (pm20) cc_final: 0.7180 (pm20) REVERT: C 937 ASP cc_start: 0.6753 (m-30) cc_final: 0.6457 (m-30) REVERT: C 943 LYS cc_start: 0.8499 (ptmm) cc_final: 0.8092 (ptmm) REVERT: C 1171 ARG cc_start: 0.7554 (ttp80) cc_final: 0.7235 (ttp-110) REVERT: D 81 ARG cc_start: 0.7676 (ttm-80) cc_final: 0.7398 (ttm-80) REVERT: D 158 GLN cc_start: 0.8721 (OUTLIER) cc_final: 0.8390 (tt0) REVERT: D 312 ARG cc_start: 0.7282 (ttp-170) cc_final: 0.6932 (tmt90) REVERT: D 707 ILE cc_start: 0.8296 (OUTLIER) cc_final: 0.8026 (tt) REVERT: D 1040 MET cc_start: 0.3481 (OUTLIER) cc_final: 0.2806 (pmt) REVERT: D 1095 MET cc_start: 0.5982 (tmm) cc_final: 0.5580 (tpt) REVERT: E 67 ARG cc_start: 0.7451 (mtt90) cc_final: 0.7209 (mtt90) REVERT: F 277 MET cc_start: 0.7821 (tmm) cc_final: 0.6867 (mmm) REVERT: F 288 MET cc_start: 0.1484 (mmt) cc_final: 0.1034 (mmm) REVERT: F 354 THR cc_start: 0.8174 (OUTLIER) cc_final: 0.7967 (p) REVERT: F 362 ASN cc_start: 0.7476 (t0) cc_final: 0.6917 (t0) REVERT: G 95 MET cc_start: 0.6996 (mtp) cc_final: 0.6713 (ttm) REVERT: G 251 ASN cc_start: 0.6951 (OUTLIER) cc_final: 0.6737 (p0) REVERT: H 44 ASP cc_start: 0.7947 (m-30) cc_final: 0.7258 (t70) REVERT: H 101 HIS cc_start: 0.7451 (t70) cc_final: 0.7089 (t-170) REVERT: H 112 MET cc_start: 0.4695 (ttm) cc_final: 0.4203 (mtm) REVERT: H 187 VAL cc_start: 0.8392 (t) cc_final: 0.8098 (p) outliers start: 84 outliers final: 48 residues processed: 365 average time/residue: 1.8055 time to fit residues: 773.8907 Evaluate side-chains 364 residues out of total 3645 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 56 poor density : 308 time to evaluate : 3.569 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 9 LEU Chi-restraints excluded: chain A residue 64 VAL Chi-restraints excluded: chain A residue 186 ASN Chi-restraints excluded: chain B residue 15 ASP Chi-restraints excluded: chain B residue 204 GLU Chi-restraints excluded: chain C residue 20 GLN Chi-restraints excluded: chain C residue 21 VAL Chi-restraints excluded: chain C residue 82 VAL Chi-restraints excluded: chain C residue 103 VAL Chi-restraints excluded: chain C residue 200 ARG Chi-restraints excluded: chain C residue 239 MET Chi-restraints excluded: chain C residue 377 THR Chi-restraints excluded: chain C residue 410 LEU Chi-restraints excluded: chain C residue 423 ASP Chi-restraints excluded: chain C residue 456 VAL Chi-restraints excluded: chain C residue 476 LYS Chi-restraints excluded: chain C residue 492 MET Chi-restraints excluded: chain C residue 515 MET Chi-restraints excluded: chain C residue 598 VAL Chi-restraints excluded: chain C residue 623 LEU Chi-restraints excluded: chain C residue 632 ASP Chi-restraints excluded: chain C residue 644 LEU Chi-restraints excluded: chain C residue 655 VAL Chi-restraints excluded: chain C residue 739 ASP Chi-restraints excluded: chain C residue 1075 VAL Chi-restraints excluded: chain C residue 1136 GLN Chi-restraints excluded: chain D residue 83 VAL Chi-restraints excluded: chain D residue 158 GLN Chi-restraints excluded: chain D residue 191 SER Chi-restraints excluded: chain D residue 553 THR Chi-restraints excluded: chain D residue 661 VAL Chi-restraints excluded: chain D residue 707 ILE Chi-restraints excluded: chain D residue 751 ASP Chi-restraints excluded: chain D residue 812 ASP Chi-restraints excluded: chain D residue 839 VAL Chi-restraints excluded: chain D residue 1040 MET Chi-restraints excluded: chain D residue 1169 THR Chi-restraints excluded: chain D residue 1209 VAL Chi-restraints excluded: chain D residue 1243 LEU Chi-restraints excluded: chain D residue 1250 ASP Chi-restraints excluded: chain E residue 69 ARG Chi-restraints excluded: chain F residue 95 THR Chi-restraints excluded: chain F residue 134 VAL Chi-restraints excluded: chain F residue 262 VAL Chi-restraints excluded: chain F residue 337 VAL Chi-restraints excluded: chain F residue 354 THR Chi-restraints excluded: chain F residue 527 THR Chi-restraints excluded: chain F residue 544 THR Chi-restraints excluded: chain G residue 13 VAL Chi-restraints excluded: chain G residue 112 MET Chi-restraints excluded: chain G residue 181 VAL Chi-restraints excluded: chain G residue 251 ASN Chi-restraints excluded: chain G residue 262 ILE Chi-restraints excluded: chain H residue 206 THR Chi-restraints excluded: chain H residue 219 LEU Chi-restraints excluded: chain H residue 224 ILE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 428 random chunks: chunk 375 optimal weight: 5.9990 chunk 395 optimal weight: 10.0000 chunk 360 optimal weight: 4.9990 chunk 384 optimal weight: 5.9990 chunk 231 optimal weight: 0.9990 chunk 167 optimal weight: 0.9990 chunk 301 optimal weight: 7.9990 chunk 117 optimal weight: 1.9990 chunk 347 optimal weight: 5.9990 chunk 363 optimal weight: 8.9990 chunk 383 optimal weight: 7.9990 overall best weight: 2.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 93 GLN ** C 120 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 628 HIS ** C 955 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C1136 GLN C1157 GLN ** D 495 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 667 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 589 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 45 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 70 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 228 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 22 ASN ** H 50 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 251 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8176 moved from start: 0.2109 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.068 36598 Z= 0.450 Angle : 0.625 15.792 49931 Z= 0.327 Chirality : 0.046 0.193 5681 Planarity : 0.005 0.056 6095 Dihedral : 15.287 175.632 6153 Min Nonbonded Distance : 1.986 Molprobity Statistics. All-atom Clashscore : 9.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.96 % Favored : 97.04 % Rotamer: Outliers : 2.22 % Allowed : 18.52 % Favored : 79.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.17 % 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: -0.18 (0.13), residues: 4194 helix: 0.50 (0.13), residues: 1649 sheet: -0.65 (0.21), residues: 535 loop : -0.37 (0.14), residues: 2010 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP D 580 HIS 0.014 0.001 HIS H 101 PHE 0.025 0.002 PHE H 7 TYR 0.036 0.002 TYR F 148 ARG 0.007 0.001 ARG G 12 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8388 Ramachandran restraints generated. 4194 Oldfield, 0 Emsley, 4194 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8388 Ramachandran restraints generated. 4194 Oldfield, 0 Emsley, 4194 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 397 residues out of total 3645 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 81 poor density : 316 time to evaluate : 3.862 Fit side-chains REVERT: B 58 GLU cc_start: 0.8339 (pt0) cc_final: 0.7975 (pt0) REVERT: B 104 LYS cc_start: 0.7520 (tptm) cc_final: 0.7154 (tptp) REVERT: B 191 ARG cc_start: 0.7533 (ttp80) cc_final: 0.7010 (ptm-80) REVERT: C 118 LYS cc_start: 0.8482 (mttm) cc_final: 0.8212 (ttmm) REVERT: C 200 ARG cc_start: 0.8398 (OUTLIER) cc_final: 0.7501 (mmp-170) REVERT: C 239 MET cc_start: 0.6458 (OUTLIER) cc_final: 0.5760 (tmm) REVERT: C 240 GLU cc_start: 0.6154 (mm-30) cc_final: 0.5884 (mm-30) REVERT: C 315 MET cc_start: 0.6250 (ptm) cc_final: 0.5947 (ptm) REVERT: C 439 LYS cc_start: 0.7973 (mttm) cc_final: 0.7749 (mtmt) REVERT: C 515 MET cc_start: 0.8437 (OUTLIER) cc_final: 0.6871 (tmm) REVERT: C 542 ARG cc_start: 0.7548 (ptp-170) cc_final: 0.7052 (mtp180) REVERT: C 779 ARG cc_start: 0.7953 (ttp80) cc_final: 0.7637 (ttt-90) REVERT: C 937 ASP cc_start: 0.6751 (m-30) cc_final: 0.6526 (m-30) REVERT: C 1171 ARG cc_start: 0.7560 (ttp80) cc_final: 0.7243 (ttp-110) REVERT: C 1219 GLU cc_start: 0.7721 (OUTLIER) cc_final: 0.7307 (pt0) REVERT: D 81 ARG cc_start: 0.7720 (ttm-80) cc_final: 0.7445 (ttm-80) REVERT: D 158 GLN cc_start: 0.8761 (OUTLIER) cc_final: 0.8409 (tt0) REVERT: D 215 LYS cc_start: 0.8515 (tptp) cc_final: 0.7972 (mttm) REVERT: D 312 ARG cc_start: 0.7301 (ttp-170) cc_final: 0.6957 (tmt90) REVERT: D 388 ARG cc_start: 0.7991 (OUTLIER) cc_final: 0.7723 (mtm180) REVERT: D 707 ILE cc_start: 0.8394 (OUTLIER) cc_final: 0.8152 (tt) REVERT: D 1040 MET cc_start: 0.3567 (OUTLIER) cc_final: 0.2885 (pmt) REVERT: D 1095 MET cc_start: 0.5825 (tmm) cc_final: 0.5472 (tpp) REVERT: D 1247 LYS cc_start: 0.8029 (OUTLIER) cc_final: 0.7644 (tttm) REVERT: E 56 GLU cc_start: 0.7958 (OUTLIER) cc_final: 0.7453 (mt-10) REVERT: F 273 MET cc_start: 0.7126 (tpt) cc_final: 0.6478 (tpt) REVERT: F 277 MET cc_start: 0.7828 (tmm) cc_final: 0.7252 (mmm) REVERT: F 354 THR cc_start: 0.8193 (OUTLIER) cc_final: 0.7982 (p) REVERT: G 95 MET cc_start: 0.7049 (mtp) cc_final: 0.6774 (ttm) REVERT: G 178 ASN cc_start: 0.6632 (t0) cc_final: 0.5964 (m110) REVERT: G 251 ASN cc_start: 0.6907 (OUTLIER) cc_final: 0.6688 (p0) REVERT: H 44 ASP cc_start: 0.7951 (m-30) cc_final: 0.7256 (t70) REVERT: H 101 HIS cc_start: 0.7465 (t70) cc_final: 0.7123 (t-170) REVERT: H 112 MET cc_start: 0.4786 (ttm) cc_final: 0.4296 (mtm) outliers start: 81 outliers final: 50 residues processed: 370 average time/residue: 1.8310 time to fit residues: 795.7268 Evaluate side-chains 367 residues out of total 3645 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 62 poor density : 305 time to evaluate : 3.759 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 9 LEU Chi-restraints excluded: chain A residue 64 VAL Chi-restraints excluded: chain A residue 186 ASN Chi-restraints excluded: chain B residue 15 ASP Chi-restraints excluded: chain B residue 204 GLU Chi-restraints excluded: chain C residue 20 GLN Chi-restraints excluded: chain C residue 21 VAL Chi-restraints excluded: chain C residue 82 VAL Chi-restraints excluded: chain C residue 103 VAL Chi-restraints excluded: chain C residue 200 ARG Chi-restraints excluded: chain C residue 239 MET Chi-restraints excluded: chain C residue 377 THR Chi-restraints excluded: chain C residue 410 LEU Chi-restraints excluded: chain C residue 423 ASP Chi-restraints excluded: chain C residue 456 VAL Chi-restraints excluded: chain C residue 476 LYS Chi-restraints excluded: chain C residue 496 LYS Chi-restraints excluded: chain C residue 515 MET Chi-restraints excluded: chain C residue 581 THR Chi-restraints excluded: chain C residue 598 VAL Chi-restraints excluded: chain C residue 632 ASP Chi-restraints excluded: chain C residue 644 LEU Chi-restraints excluded: chain C residue 655 VAL Chi-restraints excluded: chain C residue 728 ASP Chi-restraints excluded: chain C residue 739 ASP Chi-restraints excluded: chain C residue 1075 VAL Chi-restraints excluded: chain C residue 1219 GLU Chi-restraints excluded: chain D residue 83 VAL Chi-restraints excluded: chain D residue 158 GLN Chi-restraints excluded: chain D residue 191 SER Chi-restraints excluded: chain D residue 388 ARG Chi-restraints excluded: chain D residue 553 THR Chi-restraints excluded: chain D residue 661 VAL Chi-restraints excluded: chain D residue 707 ILE Chi-restraints excluded: chain D residue 751 ASP Chi-restraints excluded: chain D residue 812 ASP Chi-restraints excluded: chain D residue 839 VAL Chi-restraints excluded: chain D residue 1040 MET Chi-restraints excluded: chain D residue 1169 THR Chi-restraints excluded: chain D residue 1209 VAL Chi-restraints excluded: chain D residue 1243 LEU Chi-restraints excluded: chain D residue 1247 LYS Chi-restraints excluded: chain D residue 1250 ASP Chi-restraints excluded: chain E residue 56 GLU Chi-restraints excluded: chain E residue 69 ARG Chi-restraints excluded: chain F residue 95 THR Chi-restraints excluded: chain F residue 134 VAL Chi-restraints excluded: chain F residue 262 VAL Chi-restraints excluded: chain F residue 337 VAL Chi-restraints excluded: chain F residue 354 THR Chi-restraints excluded: chain F residue 527 THR Chi-restraints excluded: chain F residue 544 THR Chi-restraints excluded: chain G residue 13 VAL Chi-restraints excluded: chain G residue 112 MET Chi-restraints excluded: chain G residue 181 VAL Chi-restraints excluded: chain G residue 251 ASN Chi-restraints excluded: chain G residue 262 ILE Chi-restraints excluded: chain H residue 46 LEU Chi-restraints excluded: chain H residue 198 ILE Chi-restraints excluded: chain H residue 206 THR Chi-restraints excluded: chain H residue 219 LEU Chi-restraints excluded: chain H residue 224 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 428 random chunks: chunk 252 optimal weight: 3.9990 chunk 406 optimal weight: 2.9990 chunk 248 optimal weight: 1.9990 chunk 192 optimal weight: 0.5980 chunk 282 optimal weight: 10.0000 chunk 426 optimal weight: 4.9990 chunk 392 optimal weight: 30.0000 chunk 339 optimal weight: 10.0000 chunk 35 optimal weight: 0.8980 chunk 262 optimal weight: 2.9990 chunk 208 optimal weight: 2.9990 overall best weight: 1.8986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 93 GLN ** C 120 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 628 HIS C1136 GLN C1157 GLN ** D 495 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 667 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D1197 ASN ** F 589 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 45 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 70 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 178 ASN ** G 228 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 50 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 251 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8150 moved from start: 0.2230 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.052 36598 Z= 0.309 Angle : 0.570 14.838 49931 Z= 0.299 Chirality : 0.043 0.198 5681 Planarity : 0.004 0.056 6095 Dihedral : 15.207 176.192 6153 Min Nonbonded Distance : 1.984 Molprobity Statistics. All-atom Clashscore : 9.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.89 % Favored : 97.11 % Rotamer: Outliers : 1.87 % Allowed : 19.12 % Favored : 79.01 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.17 % 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: -0.05 (0.13), residues: 4194 helix: 0.65 (0.13), residues: 1647 sheet: -0.62 (0.21), residues: 512 loop : -0.34 (0.14), residues: 2035 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP D1193 HIS 0.014 0.001 HIS H 101 PHE 0.025 0.002 PHE H 7 TYR 0.036 0.001 TYR F 148 ARG 0.011 0.000 ARG D 77 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8388 Ramachandran restraints generated. 4194 Oldfield, 0 Emsley, 4194 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8388 Ramachandran restraints generated. 4194 Oldfield, 0 Emsley, 4194 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 381 residues out of total 3645 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 68 poor density : 313 time to evaluate : 3.869 Fit side-chains REVERT: B 58 GLU cc_start: 0.8278 (pt0) cc_final: 0.7905 (pt0) REVERT: B 104 LYS cc_start: 0.7498 (tptm) cc_final: 0.7149 (tptp) REVERT: B 191 ARG cc_start: 0.7455 (ttp80) cc_final: 0.6879 (ptm-80) REVERT: C 200 ARG cc_start: 0.8369 (OUTLIER) cc_final: 0.7493 (mmp-170) REVERT: C 239 MET cc_start: 0.6449 (OUTLIER) cc_final: 0.5789 (tmm) REVERT: C 240 GLU cc_start: 0.6138 (mm-30) cc_final: 0.5884 (mm-30) REVERT: C 315 MET cc_start: 0.6154 (ptm) cc_final: 0.5873 (ptm) REVERT: C 439 LYS cc_start: 0.8003 (mttm) cc_final: 0.7794 (mtmt) REVERT: C 515 MET cc_start: 0.8402 (OUTLIER) cc_final: 0.6824 (tmm) REVERT: C 542 ARG cc_start: 0.7484 (ptp-170) cc_final: 0.6985 (mtp180) REVERT: C 779 ARG cc_start: 0.7930 (ttp80) cc_final: 0.7617 (ttt-90) REVERT: C 937 ASP cc_start: 0.6750 (m-30) cc_final: 0.6450 (m-30) REVERT: C 1171 ARG cc_start: 0.7553 (ttp80) cc_final: 0.7224 (ttp-110) REVERT: C 1219 GLU cc_start: 0.7662 (OUTLIER) cc_final: 0.7251 (pt0) REVERT: D 81 ARG cc_start: 0.7695 (ttm-80) cc_final: 0.7422 (ttm-80) REVERT: D 158 GLN cc_start: 0.8768 (tt0) cc_final: 0.8418 (tt0) REVERT: D 312 ARG cc_start: 0.7281 (ttp-170) cc_final: 0.6917 (tmt90) REVERT: D 388 ARG cc_start: 0.7984 (OUTLIER) cc_final: 0.7644 (mtm180) REVERT: D 707 ILE cc_start: 0.8300 (OUTLIER) cc_final: 0.8040 (tt) REVERT: D 1040 MET cc_start: 0.3804 (OUTLIER) cc_final: 0.3030 (pmt) REVERT: D 1095 MET cc_start: 0.5793 (tmm) cc_final: 0.5472 (tpp) REVERT: D 1247 LYS cc_start: 0.8084 (OUTLIER) cc_final: 0.7710 (tttm) REVERT: E 56 GLU cc_start: 0.7914 (OUTLIER) cc_final: 0.7481 (mt-10) REVERT: F 273 MET cc_start: 0.7210 (tpt) cc_final: 0.6551 (tpt) REVERT: F 277 MET cc_start: 0.7843 (tmm) cc_final: 0.7239 (mmm) REVERT: G 95 MET cc_start: 0.7133 (mtp) cc_final: 0.6853 (ttm) REVERT: G 141 LYS cc_start: 0.6688 (mmtt) cc_final: 0.6351 (mppt) REVERT: G 178 ASN cc_start: 0.6747 (t0) cc_final: 0.5984 (m110) REVERT: G 251 ASN cc_start: 0.6874 (OUTLIER) cc_final: 0.6662 (p0) REVERT: H 44 ASP cc_start: 0.7882 (m-30) cc_final: 0.7247 (t70) REVERT: H 101 HIS cc_start: 0.7505 (t70) cc_final: 0.7061 (t-170) REVERT: H 112 MET cc_start: 0.4846 (ttm) cc_final: 0.4333 (mtm) REVERT: H 187 VAL cc_start: 0.8446 (t) cc_final: 0.8141 (p) outliers start: 68 outliers final: 44 residues processed: 359 average time/residue: 1.8191 time to fit residues: 769.4449 Evaluate side-chains 361 residues out of total 3645 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 54 poor density : 307 time to evaluate : 4.315 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 9 LEU Chi-restraints excluded: chain A residue 64 VAL Chi-restraints excluded: chain B residue 15 ASP Chi-restraints excluded: chain B residue 204 GLU Chi-restraints excluded: chain C residue 20 GLN Chi-restraints excluded: chain C residue 21 VAL Chi-restraints excluded: chain C residue 82 VAL Chi-restraints excluded: chain C residue 103 VAL Chi-restraints excluded: chain C residue 200 ARG Chi-restraints excluded: chain C residue 239 MET Chi-restraints excluded: chain C residue 377 THR Chi-restraints excluded: chain C residue 410 LEU Chi-restraints excluded: chain C residue 423 ASP Chi-restraints excluded: chain C residue 456 VAL Chi-restraints excluded: chain C residue 476 LYS Chi-restraints excluded: chain C residue 496 LYS Chi-restraints excluded: chain C residue 515 MET Chi-restraints excluded: chain C residue 598 VAL Chi-restraints excluded: chain C residue 632 ASP Chi-restraints excluded: chain C residue 644 LEU Chi-restraints excluded: chain C residue 655 VAL Chi-restraints excluded: chain C residue 739 ASP Chi-restraints excluded: chain C residue 1075 VAL Chi-restraints excluded: chain C residue 1136 GLN Chi-restraints excluded: chain C residue 1219 GLU Chi-restraints excluded: chain D residue 83 VAL Chi-restraints excluded: chain D residue 191 SER Chi-restraints excluded: chain D residue 388 ARG Chi-restraints excluded: chain D residue 553 THR Chi-restraints excluded: chain D residue 661 VAL Chi-restraints excluded: chain D residue 707 ILE Chi-restraints excluded: chain D residue 751 ASP Chi-restraints excluded: chain D residue 839 VAL Chi-restraints excluded: chain D residue 1040 MET Chi-restraints excluded: chain D residue 1169 THR Chi-restraints excluded: chain D residue 1209 VAL Chi-restraints excluded: chain D residue 1247 LYS Chi-restraints excluded: chain D residue 1250 ASP Chi-restraints excluded: chain E residue 56 GLU Chi-restraints excluded: chain E residue 69 ARG Chi-restraints excluded: chain F residue 95 THR Chi-restraints excluded: chain F residue 134 VAL Chi-restraints excluded: chain F residue 262 VAL Chi-restraints excluded: chain F residue 337 VAL Chi-restraints excluded: chain F residue 527 THR Chi-restraints excluded: chain G residue 13 VAL Chi-restraints excluded: chain G residue 181 VAL Chi-restraints excluded: chain G residue 251 ASN Chi-restraints excluded: chain G residue 262 ILE Chi-restraints excluded: chain H residue 13 VAL Chi-restraints excluded: chain H residue 46 LEU Chi-restraints excluded: chain H residue 206 THR Chi-restraints excluded: chain H residue 219 LEU Chi-restraints excluded: chain H residue 224 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 428 random chunks: chunk 269 optimal weight: 0.9990 chunk 361 optimal weight: 3.9990 chunk 104 optimal weight: 0.1980 chunk 313 optimal weight: 1.9990 chunk 50 optimal weight: 2.9990 chunk 94 optimal weight: 0.7980 chunk 340 optimal weight: 5.9990 chunk 142 optimal weight: 9.9990 chunk 349 optimal weight: 0.7980 chunk 43 optimal weight: 1.9990 chunk 62 optimal weight: 0.9980 overall best weight: 0.7582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 93 GLN ** C 120 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 628 HIS C1136 GLN ** D 495 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 667 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 589 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 45 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 70 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 228 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 50 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 251 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4123 r_free = 0.4123 target = 0.173121 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.3349 r_free = 0.3349 target = 0.103521 restraints weight = 38429.639| |-----------------------------------------------------------------------------| r_work (start): 0.3304 rms_B_bonded: 1.85 r_work: 0.3160 rms_B_bonded: 2.40 restraints_weight: 0.5000 r_work: 0.3018 rms_B_bonded: 3.78 restraints_weight: 0.2500 r_work (final): 0.3018 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7951 moved from start: 0.2462 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.052 36598 Z= 0.177 Angle : 0.518 12.688 49931 Z= 0.273 Chirality : 0.041 0.181 5681 Planarity : 0.004 0.057 6095 Dihedral : 15.013 177.130 6153 Min Nonbonded Distance : 1.997 Molprobity Statistics. All-atom Clashscore : 9.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.34 % Favored : 97.66 % Rotamer: Outliers : 1.48 % Allowed : 19.73 % Favored : 78.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.17 % 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: 0.23 (0.13), residues: 4194 helix: 0.92 (0.13), residues: 1653 sheet: -0.39 (0.22), residues: 495 loop : -0.25 (0.14), residues: 2046 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP D1193 HIS 0.015 0.001 HIS H 101 PHE 0.026 0.001 PHE H 183 TYR 0.034 0.001 TYR F 148 ARG 0.011 0.000 ARG D 77 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 14202.16 seconds wall clock time: 252 minutes 50.79 seconds (15170.79 seconds total)