Starting phenix.real_space_refine on Sun May 12 05:05:34 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8xxn_38754/05_2024/8xxn_38754.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8xxn_38754/05_2024/8xxn_38754.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.6 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8xxn_38754/05_2024/8xxn_38754.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8xxn_38754/05_2024/8xxn_38754.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8xxn_38754/05_2024/8xxn_38754.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8xxn_38754/05_2024/8xxn_38754.pdb" } resolution = 3.6 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= 0.000 sd= 0.007 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 7 Type Number sf(0) Gaussians Zn 3 6.06 5 P 1722 5.49 5 Mg 23 5.21 5 S 361 5.16 5 C 65373 2.51 5 N 20881 2.21 5 O 26202 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "SB PHE 138": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "ST PHE 92": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "SJ PHE 147": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "SW PHE 50": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "SW PHE 130": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "3H PHE 128": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "3H GLU 217": "OE1" <-> "OE2" Time to flip residues: 0.16s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5322/modules/chem_data/mon_lib" Total number of atoms: 114565 Number of models: 1 Model: "" Number of chains: 55 Chain: "Ln" Number of atoms: 230 Number of conformers: 1 Conformer: "" Number of residues, atoms: 24, 230 Classifications: {'peptide': 24} Link IDs: {'TRANS': 23} Chain: "S2" Number of atoms: 36535 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1723, 36535 Classifications: {'DNA': 15, 'RNA': 1708} Modifications used: {'5*END': 1, 'rna2p_pur': 146, 'rna2p_pyr': 131, 'rna3p_pur': 753, 'rna3p_pyr': 675} Link IDs: {'rna2p': 276, 'rna3p': 1446} Chain breaks: 3 Unresolved non-hydrogen bonds: 252 Unresolved non-hydrogen angles: 410 Unresolved non-hydrogen dihedrals: 196 Unresolved non-hydrogen chiralities: 57 Planarities with less than four sites: {' G:plan2': 3, ' A:plan': 1, ' C:plan': 11, ' U:plan': 3, ' G:plan': 3, ' C:plan2': 11, ' A:plan2': 1} Unresolved non-hydrogen planarities: 203 Chain: "SA" Number of atoms: 1741 Number of conformers: 1 Conformer: "" Number of residues, atoms: 221, 1741 Classifications: {'peptide': 221} Link IDs: {'PTRANS': 12, 'TRANS': 208} Chain: "SB" Number of atoms: 1738 Number of conformers: 1 Conformer: "" Number of residues, atoms: 214, 1738 Classifications: {'peptide': 214} Link IDs: {'PTRANS': 5, 'TRANS': 208} Chain: "SD" Number of atoms: 1765 Number of conformers: 1 Conformer: "" Number of residues, atoms: 227, 1765 Classifications: {'peptide': 227} Link IDs: {'PTRANS': 11, 'TRANS': 215} Chain: "SE" Number of atoms: 2076 Number of conformers: 1 Conformer: "" Number of residues, atoms: 262, 2076 Classifications: {'peptide': 262} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 14, 'TRANS': 247} Chain: "SF" Number of atoms: 1495 Number of conformers: 1 Conformer: "" Number of residues, atoms: 189, 1495 Classifications: {'peptide': 189} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 5, 'TRANS': 183} Chain: "SH" Number of atoms: 1497 Number of conformers: 1 Conformer: "" Number of residues, atoms: 186, 1497 Classifications: {'peptide': 186} Link IDs: {'PTRANS': 9, 'TRANS': 176} Chain breaks: 1 Chain: "SI" Number of atoms: 1686 Number of conformers: 1 Conformer: "" Number of residues, atoms: 206, 1686 Classifications: {'peptide': 206} Link IDs: {'PTRANS': 7, 'TRANS': 198} Chain: "SK" Number of atoms: 827 Number of conformers: 1 Conformer: "" Number of residues, atoms: 98, 827 Classifications: {'peptide': 98} Link IDs: {'PTRANS': 7, 'TRANS': 90} Chain: "SL" Number of atoms: 1247 Number of conformers: 1 Conformer: "" Number of residues, atoms: 153, 1247 Classifications: {'peptide': 153} Link IDs: {'CIS': 2, 'PTRANS': 6, 'TRANS': 144} Chain: "SP" Number of atoms: 985 Number of conformers: 1 Conformer: "" Number of residues, atoms: 121, 985 Classifications: {'peptide': 121} Link IDs: {'PTRANS': 7, 'TRANS': 113} Chain: "SQ" Number of atoms: 1142 Number of conformers: 1 Conformer: "" Number of residues, atoms: 144, 1142 Classifications: {'peptide': 144} Link IDs: {'PTRANS': 6, 'TRANS': 137} Chain: "SR" Number of atoms: 1090 Number of conformers: 1 Conformer: "" Number of residues, atoms: 135, 1090 Classifications: {'peptide': 135} Link IDs: {'PTRANS': 7, 'TRANS': 127} Chain: "SS" Number of atoms: 1198 Number of conformers: 1 Conformer: "" Number of residues, atoms: 145, 1198 Classifications: {'peptide': 145} Link IDs: {'PTRANS': 3, 'TRANS': 141} Chain: "ST" Number of atoms: 1112 Number of conformers: 1 Conformer: "" Number of residues, atoms: 143, 1112 Classifications: {'peptide': 143} Link IDs: {'CIS': 2, 'PTRANS': 4, 'TRANS': 136} Chain: "SU" Number of atoms: 817 Number of conformers: 1 Conformer: "" Number of residues, atoms: 103, 817 Classifications: {'peptide': 103} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 5, 'TRANS': 97} Chain: "SV" Number of atoms: 636 Number of conformers: 1 Conformer: "" Number of residues, atoms: 83, 636 Classifications: {'peptide': 83} Link IDs: {'PTRANS': 1, 'TRANS': 81} Chain: "SX" Number of atoms: 1098 Number of conformers: 1 Conformer: "" Number of residues, atoms: 141, 1098 Classifications: {'peptide': 141} Link IDs: {'PTRANS': 5, 'TRANS': 135} Chain: "Sa" Number of atoms: 821 Number of conformers: 1 Conformer: "" Number of residues, atoms: 102, 821 Classifications: {'peptide': 102} Link IDs: {'PTRANS': 7, 'TRANS': 94} Chain: "Sc" Number of atoms: 506 Number of conformers: 1 Conformer: "" Number of residues, atoms: 64, 506 Classifications: {'peptide': 64} Link IDs: {'PTRANS': 2, 'TRANS': 61} Chain: "Sd" Number of atoms: 459 Number of conformers: 1 Conformer: "" Number of residues, atoms: 55, 459 Classifications: {'peptide': 55} Modifications used: {'COO': 1} Link IDs: {'CIS': 1, 'PTRANS': 1, 'TRANS': 52} Chain: "Sg" Number of atoms: 2436 Number of conformers: 1 Conformer: "" Number of residues, atoms: 313, 2436 Classifications: {'peptide': 313} Link IDs: {'PTRANS': 10, 'TRANS': 302} Chain: "SC" Number of atoms: 1725 Number of conformers: 1 Conformer: "" Number of residues, atoms: 222, 1725 Classifications: {'peptide': 222} Link IDs: {'CIS': 1, 'PTRANS': 12, 'TRANS': 208} Chain: "SG" Number of atoms: 1923 Number of conformers: 1 Conformer: "" Number of residues, atoms: 237, 1923 Classifications: {'peptide': 237} Link IDs: {'PTRANS': 10, 'TRANS': 226} Chain: "SJ" Number of atoms: 1525 Number of conformers: 1 Conformer: "" Number of residues, atoms: 185, 1525 Classifications: {'peptide': 185} Link IDs: {'PTRANS': 6, 'TRANS': 178} Chain: "SM" Number of atoms: 940 Number of conformers: 1 Conformer: "" Number of residues, atoms: 122, 940 Classifications: {'peptide': 122} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 2, 'TRANS': 119} Unresolved non-hydrogen bonds: 10 Unresolved non-hydrogen angles: 11 Unresolved non-hydrogen dihedrals: 9 Planarities with less than four sites: {'ARG:plan': 1} Unresolved non-hydrogen planarities: 5 Chain: "SN" Number of atoms: 1208 Number of conformers: 1 Conformer: "" Number of residues, atoms: 150, 1208 Classifications: {'peptide': 150} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 8, 'TRANS': 141} Chain: "SO" Number of atoms: 1049 Number of conformers: 1 Conformer: "" Number of residues, atoms: 140, 1049 Classifications: {'peptide': 140} Modifications used: {'COO': 1} Link IDs: {'CIS': 2, 'PTRANS': 6, 'TRANS': 131} Chain: "SW" Number of atoms: 1034 Number of conformers: 1 Conformer: "" Number of residues, atoms: 129, 1034 Classifications: {'peptide': 129} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 3, 'TRANS': 125} Chain: "SY" Number of atoms: 1065 Number of conformers: 1 Conformer: "" Number of residues, atoms: 131, 1065 Classifications: {'peptide': 131} Link IDs: {'PTRANS': 5, 'TRANS': 125} Chain: "SZ" Number of atoms: 598 Number of conformers: 1 Conformer: "" Number of residues, atoms: 75, 598 Classifications: {'peptide': 75} Link IDs: {'PTRANS': 2, 'TRANS': 72} Chain: "Sb" Number of atoms: 651 Number of conformers: 1 Conformer: "" Number of residues, atoms: 83, 651 Classifications: {'peptide': 83} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 5, 'TRANS': 77} Chain: "Se" Number of atoms: 459 Number of conformers: 1 Conformer: "" Number of residues, atoms: 58, 459 Classifications: {'peptide': 58} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 3, 'TRANS': 54} Chain: "Sf" Number of atoms: 548 Number of conformers: 1 Conformer: "" Number of residues, atoms: 67, 548 Classifications: {'peptide': 67} Link IDs: {'PTRANS': 2, 'TRANS': 64} Chain: "C1" Number of atoms: 443 Number of conformers: 1 Conformer: "" Number of residues, atoms: 90, 443 Classifications: {'peptide': 90} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 76} Link IDs: {'PTRANS': 1, 'TRANS': 88} Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 292 Unresolved non-hydrogen angles: 369 Unresolved non-hydrogen dihedrals: 240 Unresolved non-hydrogen chiralities: 25 Planarities with less than four sites: {'GLN:plan1': 8, 'ASP:plan': 7, 'TYR:plan': 3, 'PHE%COO:plan': 1, 'ASN:plan1': 3, 'HIS:plan': 3, 'PHE:plan': 3, 'GLU:plan': 5, 'ARG:plan': 4} Unresolved non-hydrogen planarities: 162 Chain: "4A" Number of atoms: 1691 Number of conformers: 1 Conformer: "" Number of residues, atoms: 342, 1691 Classifications: {'peptide': 342} Incomplete info: {'truncation_to_alanine': 302} Link IDs: {'PTRANS': 9, 'TRANS': 332} Chain breaks: 3 Unresolved chain link angles: 9 Unresolved non-hydrogen bonds: 1086 Unresolved non-hydrogen angles: 1387 Unresolved non-hydrogen dihedrals: 879 Unresolved non-hydrogen chiralities: 113 Planarities with less than four sites: {'GLN:plan1': 17, 'HIS:plan': 5, 'TYR:plan': 10, 'ASN:plan1': 14, 'TRP:plan': 3, 'ASP:plan': 20, 'PHE:plan': 12, 'GLU:plan': 25, 'ARG:plan': 24} Unresolved non-hydrogen planarities: 584 Chain: "CD" Number of atoms: 1841 Number of conformers: 1 Conformer: "" Number of residues, atoms: 347, 1841 Classifications: {'peptide': 347} Incomplete info: {'truncation_to_alanine': 266} Link IDs: {'PTRANS': 13, 'TRANS': 333} Chain breaks: 1 Unresolved chain link angles: 10 Unresolved non-hydrogen bonds: 902 Unresolved non-hydrogen angles: 1151 Unresolved non-hydrogen dihedrals: 736 Unresolved non-hydrogen chiralities: 95 Planarities with less than four sites: {'GLN:plan1': 9, 'HIS:plan': 8, 'TYR:plan': 9, 'ASN:plan1': 7, 'TRP:plan': 2, 'ASP:plan': 20, 'PHE:plan': 8, 'GLU:plan': 28, 'ARG:plan': 11} Unresolved non-hydrogen planarities: 453 Chain: "3A" Number of atoms: 5379 Number of conformers: 1 Conformer: "" Number of residues, atoms: 692, 5379 Classifications: {'peptide': 692} Incomplete info: {'backbone_only': 1, 'truncation_to_alanine': 94} Link IDs: {'PTRANS': 25, 'TRANS': 666} Chain breaks: 4 Unresolved chain link angles: 2 Unresolved non-hydrogen bonds: 370 Unresolved non-hydrogen angles: 454 Unresolved non-hydrogen dihedrals: 304 Unresolved non-hydrogen chiralities: 24 Planarities with less than four sites: {'GLN:plan1': 9, 'HIS:plan': 1, 'TYR:plan': 1, 'TRP:plan': 1, 'ASP:plan': 7, 'PHE:plan': 2, 'GLU:plan': 20, 'ARG:plan': 8} Unresolved non-hydrogen planarities: 210 Chain: "3B" Number of atoms: 2966 Number of conformers: 1 Conformer: "" Number of residues, atoms: 536, 2966 Classifications: {'peptide': 536} Incomplete info: {'truncation_to_alanine': 388} Link IDs: {'CIS': 2, 'PCIS': 1, 'PTRANS': 23, 'TRANS': 509} Chain breaks: 3 Unresolved chain link angles: 18 Unresolved non-hydrogen bonds: 1526 Unresolved non-hydrogen angles: 1965 Unresolved non-hydrogen dihedrals: 1337 Unresolved non-hydrogen chiralities: 109 Planarities with less than four sites: {'GLN:plan1': 22, 'ASP:plan': 30, 'TYR:plan': 14, 'ASN:plan1': 16, 'TRP:plan': 16, 'HIS:plan': 13, 'PHE:plan': 26, 'GLU:plan': 23, 'ARG:plan': 21} Unresolved non-hydrogen planarities: 886 Chain: "3C" Number of atoms: 5070 Number of conformers: 1 Conformer: "" Number of residues, atoms: 625, 5070 Classifications: {'peptide': 625} Incomplete info: {'truncation_to_alanine': 8} Link IDs: {'PTRANS': 17, 'TRANS': 607} Chain breaks: 4 Unresolved non-hydrogen bonds: 27 Unresolved non-hydrogen angles: 31 Unresolved non-hydrogen dihedrals: 23 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'ASN:plan1': 3} Unresolved non-hydrogen planarities: 9 Chain: "3E" Number of atoms: 3437 Number of conformers: 1 Conformer: "" Number of residues, atoms: 416, 3437 Classifications: {'peptide': 416} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PCIS': 1, 'PTRANS': 10, 'TRANS': 404} Chain breaks: 4 Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 11 Unresolved non-hydrogen dihedrals: 8 Planarities with less than four sites: {'TYR:plan': 1} Unresolved non-hydrogen planarities: 7 Chain: "3F" Number of atoms: 2090 Number of conformers: 1 Conformer: "" Number of residues, atoms: 269, 2090 Classifications: {'peptide': 269} Link IDs: {'PTRANS': 10, 'TRANS': 258} Chain: "3G" Number of atoms: 667 Number of conformers: 1 Conformer: "" Number of residues, atoms: 84, 667 Classifications: {'peptide': 84} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 2, 'TRANS': 81} Chain: "3H" Number of atoms: 2413 Number of conformers: 1 Conformer: "" Number of residues, atoms: 295, 2413 Classifications: {'peptide': 295} Link IDs: {'PTRANS': 10, 'TRANS': 284} Chain breaks: 2 Chain: "3I" Number of atoms: 1497 Number of conformers: 1 Conformer: "" Number of residues, atoms: 305, 1497 Classifications: {'peptide': 305} Incomplete info: {'truncation_to_alanine': 261} Link IDs: {'CIS': 1, 'PTRANS': 11, 'TRANS': 292} Chain breaks: 1 Unresolved chain link angles: 11 Unresolved non-hydrogen bonds: 965 Unresolved non-hydrogen angles: 1241 Unresolved non-hydrogen dihedrals: 823 Unresolved non-hydrogen chiralities: 73 Planarities with less than four sites: {'GLN:plan1': 11, 'ASP:plan': 21, 'TYR:plan': 10, 'ASN:plan1': 16, 'TRP:plan': 5, 'HIS:plan': 11, 'PHE:plan': 18, 'GLU:plan': 18, 'ARG:plan': 13} Unresolved non-hydrogen planarities: 570 Chain: "3K" Number of atoms: 1750 Number of conformers: 1 Conformer: "" Number of residues, atoms: 217, 1750 Classifications: {'peptide': 217} Link IDs: {'CIS': 1, 'PCIS': 2, 'PTRANS': 3, 'TRANS': 210} Chain: "3L" Number of atoms: 3111 Number of conformers: 1 Conformer: "" Number of residues, atoms: 372, 3111 Classifications: {'peptide': 372} Link IDs: {'CIS': 5, 'PTRANS': 11, 'TRANS': 355} Chain: "3M" Number of atoms: 2705 Number of conformers: 1 Conformer: "" Number of residues, atoms: 338, 2705 Classifications: {'peptide': 338} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 5, 'TRANS': 332} Chain breaks: 5 Unresolved non-hydrogen bonds: 12 Unresolved non-hydrogen angles: 14 Unresolved non-hydrogen dihedrals: 10 Planarities with less than four sites: {'ARG:plan': 2} Unresolved non-hydrogen planarities: 10 Chain: "3N" Number of atoms: 3617 Number of conformers: 1 Conformer: "" Number of residues, atoms: 447, 3617 Classifications: {'peptide': 447} Link IDs: {'PTRANS': 19, 'TRANS': 427} Chain breaks: 2 Chain: "S2" Number of atoms: 22 Number of conformers: 1 Conformer: "" Number of residues, atoms: 22, 22 Unusual residues: {' MG': 22} Classifications: {'undetermined': 22} Link IDs: {None: 21} Chain: "Sa" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} Chain: "Sd" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} Chain: "SG" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' MG': 1} Classifications: {'undetermined': 1} Chain: "Sf" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 59093 SG CYSSa 23 89.018 188.276 109.498 1.00 3.68 S ATOM 59114 SG CYSSa 26 88.636 187.312 106.032 1.00 3.21 S ATOM 59497 SG CYSSa 74 90.901 185.191 108.405 1.00 12.08 S ATOM 59516 SG CYSSa 77 91.962 188.427 106.766 1.00 10.95 S ATOM 60408 SG CYSSd 21 154.170 180.783 71.717 1.00 7.36 S ATOM 60432 SG CYSSd 24 151.271 178.280 72.728 1.00 11.69 S ATOM 60553 SG CYSSd 39 150.863 181.969 73.343 1.00 19.06 S ATOM 60579 SG CYSSd 42 153.365 180.041 75.201 1.00 35.58 S Time building chain proxies: 41.38, per 1000 atoms: 0.36 Number of scatterers: 114565 At special positions: 0 Unit cell: (238.368, 284.208, 309.42, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 7 Type Number sf(0) Zn 3 29.99 S 361 16.00 P 1722 15.00 Mg 23 11.99 O 26202 8.00 N 20881 7.00 C 65373 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: 36.77 Conformation dependent library (CDL) restraints added in 11.1 seconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZNSa 201 " pdb="ZN ZNSa 201 " - pdb=" SG CYSSa 26 " pdb="ZN ZNSa 201 " - pdb=" SG CYSSa 77 " pdb="ZN ZNSa 201 " - pdb=" SG CYSSa 74 " pdb="ZN ZNSa 201 " - pdb=" SG CYSSa 23 " pdb=" ZNSd 101 " pdb="ZN ZNSd 101 " - pdb=" SG CYSSd 42 " pdb="ZN ZNSd 101 " - pdb=" SG CYSSd 24 " pdb="ZN ZNSd 101 " - pdb=" SG CYSSd 39 " pdb="ZN ZNSd 101 " - pdb=" SG CYSSd 21 " Number of angles added : 12 20290 Ramachandran restraints generated. 10145 Oldfield, 0 Emsley, 10145 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 19392 Finding SS restraints... Secondary structure from input PDB file: 358 helices and 88 sheets defined 46.6% alpha, 13.6% beta 509 base pairs and 865 stacking pairs defined. Time for finding SS restraints: 31.24 Creating SS restraints... Processing helix chain 'Ln' and resid 2 through 24 Processing helix chain 'SA' and resid 11 through 22 Processing helix chain 'SA' and resid 34 through 38 removed outlier: 3.690A pdb=" N ILESA 38 " --> pdb=" O GLUSA 35 " (cutoff:3.500A) Processing helix chain 'SA' and resid 50 through 68 Processing helix chain 'SA' and resid 80 through 94 removed outlier: 6.557A pdb=" N ALASA 86 " --> pdb=" O THRSA 82 " (cutoff:3.500A) Processing helix chain 'SA' and resid 130 through 140 Processing helix chain 'SA' and resid 167 through 187 Processing helix chain 'SA' and resid 198 through 202 Processing helix chain 'SA' and resid 206 through 223 removed outlier: 4.340A pdb=" N LYSSA 212 " --> pdb=" O GLUSA 208 " (cutoff:3.500A) removed outlier: 5.202A pdb=" N GLNSA 215 " --> pdb=" O GLUSA 211 " (cutoff:3.500A) Processing helix chain 'SB' and resid 23 through 27 Processing helix chain 'SB' and resid 57 through 63 Processing helix chain 'SB' and resid 71 through 75 Processing helix chain 'SB' and resid 106 through 114 Processing helix chain 'SB' and resid 157 through 179 Processing helix chain 'SB' and resid 180 through 189 Processing helix chain 'SB' and resid 191 through 201 removed outlier: 3.985A pdb=" N LYSSB 195 " --> pdb=" O ASPSB 191 " (cutoff:3.500A) Processing helix chain 'SB' and resid 224 through 233 Processing helix chain 'SD' and resid 6 through 29 Processing helix chain 'SD' and resid 54 through 60 Processing helix chain 'SD' and resid 63 through 77 Processing helix chain 'SD' and resid 93 through 96 Processing helix chain 'SD' and resid 97 through 112 Processing helix chain 'SD' and resid 114 through 130 Processing helix chain 'SD' and resid 162 through 167 Processing helix chain 'SE' and resid 10 through 14 Processing helix chain 'SE' and resid 15 through 19 Processing helix chain 'SE' and resid 43 through 49 Processing helix chain 'SE' and resid 57 through 67 Processing helix chain 'SE' and resid 115 through 120 Processing helix chain 'SE' and resid 133 through 135 No H-bonds generated for 'chain 'SE' and resid 133 through 135' Processing helix chain 'SE' and resid 247 through 263 Processing helix chain 'SF' and resid 32 through 39 removed outlier: 3.985A pdb=" N TYRSF 38 " --> pdb=" O SERSF 34 " (cutoff:3.500A) Processing helix chain 'SF' and resid 42 through 46 Processing helix chain 'SF' and resid 67 through 77 Processing helix chain 'SF' and resid 85 through 104 Processing helix chain 'SF' and resid 107 through 120 Processing helix chain 'SF' and resid 142 through 162 Processing helix chain 'SF' and resid 168 through 183 Processing helix chain 'SF' and resid 187 through 203 Processing helix chain 'SH' and resid 20 through 31 Processing helix chain 'SH' and resid 35 through 40 Processing helix chain 'SH' and resid 68 through 75 Processing helix chain 'SH' and resid 76 through 87 Processing helix chain 'SH' and resid 117 through 120 Processing helix chain 'SH' and resid 121 through 134 Processing helix chain 'SH' and resid 169 through 181 removed outlier: 3.521A pdb=" N SERSH 174 " --> pdb=" O VALSH 170 " (cutoff:3.500A) removed outlier: 3.702A pdb=" N GLYSH 175 " --> pdb=" O GLUSH 171 " (cutoff:3.500A) Processing helix chain 'SI' and resid 87 through 94 removed outlier: 4.101A pdb=" N VALSI 91 " --> pdb=" O ASNSI 87 " (cutoff:3.500A) Processing helix chain 'SI' and resid 106 through 118 Processing helix chain 'SI' and resid 132 through 138 Processing helix chain 'SI' and resid 142 through 155 Processing helix chain 'SI' and resid 159 through 169 Processing helix chain 'SI' and resid 178 through 183 Processing helix chain 'SI' and resid 192 through 206 Processing helix chain 'SK' and resid 4 through 18 Processing helix chain 'SK' and resid 41 through 55 Processing helix chain 'SK' and resid 72 through 84 Processing helix chain 'SL' and resid 47 through 53 Processing helix chain 'SP' and resid 21 through 28 Processing helix chain 'SP' and resid 29 through 37 Processing helix chain 'SP' and resid 38 through 47 Processing helix chain 'SP' and resid 50 through 67 Processing helix chain 'SP' and resid 108 through 112 removed outlier: 4.079A pdb=" N ILESP 112 " --> pdb=" O PROSP 109 " (cutoff:3.500A) Processing helix chain 'SQ' and resid 47 through 52 removed outlier: 4.563A pdb=" N LEUSQ 51 " --> pdb=" O LEUSQ 47 " (cutoff:3.500A) Processing helix chain 'SQ' and resid 52 through 59 Processing helix chain 'SQ' and resid 77 through 99 Processing helix chain 'SQ' and resid 101 through 115 removed outlier: 3.718A pdb=" N LYSSQ 105 " --> pdb=" O ASPSQ 101 " (cutoff:3.500A) Processing helix chain 'SQ' and resid 116 through 120 Processing helix chain 'SR' and resid 6 through 20 Processing helix chain 'SR' and resid 27 through 38 Processing helix chain 'SR' and resid 43 through 63 Processing helix chain 'SR' and resid 70 through 82 Processing helix chain 'SR' and resid 99 through 109 Processing helix chain 'SS' and resid 25 through 31 Processing helix chain 'SS' and resid 37 through 49 Processing helix chain 'SS' and resid 60 through 73 Processing helix chain 'SS' and resid 74 through 78 removed outlier: 3.730A pdb=" N LYSSS 78 " --> pdb=" O ARGSS 75 " (cutoff:3.500A) Processing helix chain 'SS' and resid 80 through 84 removed outlier: 3.743A pdb=" N LEUSS 84 " --> pdb=" O ASPSS 81 " (cutoff:3.500A) Processing helix chain 'SS' and resid 100 through 118 Processing helix chain 'SS' and resid 119 through 127 Processing helix chain 'ST' and resid 10 through 25 Processing helix chain 'ST' and resid 51 through 67 Processing helix chain 'ST' and resid 71 through 79 Processing helix chain 'ST' and resid 96 through 110 Processing helix chain 'ST' and resid 124 through 144 Processing helix chain 'SU' and resid 28 through 47 Processing helix chain 'SU' and resid 94 through 104 removed outlier: 4.974A pdb=" N GLNSU 100 " --> pdb=" O GLUSU 96 " (cutoff:3.500A) Processing helix chain 'SV' and resid 56 through 63 Processing helix chain 'SV' and resid 64 through 77 Processing helix chain 'SX' and resid 9 through 22 Processing helix chain 'SX' and resid 24 through 33 removed outlier: 4.322A pdb=" N GLYSX 33 " --> pdb=" O LYSSX 29 " (cutoff:3.500A) Processing helix chain 'SX' and resid 33 through 39 Processing helix chain 'SX' and resid 89 through 94 Processing helix chain 'SX' and resid 129 through 135 Processing helix chain 'Sa' and resid 46 through 49 Processing helix chain 'Sa' and resid 50 through 57 Processing helix chain 'Sa' and resid 74 through 81 Processing helix chain 'Sa' and resid 88 through 94 Processing helix chain 'Sd' and resid 32 through 36 Processing helix chain 'Sd' and resid 40 through 46 Processing helix chain 'Sd' and resid 46 through 51 Processing helix chain 'SC' and resid 64 through 72 Processing helix chain 'SC' and resid 77 through 85 Processing helix chain 'SC' and resid 90 through 99 Processing helix chain 'SC' and resid 146 through 161 Processing helix chain 'SC' and resid 207 through 218 Processing helix chain 'SC' and resid 232 through 249 Processing helix chain 'SC' and resid 264 through 269 Processing helix chain 'SC' and resid 269 through 277 Processing helix chain 'SG' and resid 20 through 28 Processing helix chain 'SG' and resid 137 through 146 Processing helix chain 'SG' and resid 181 through 234 removed outlier: 3.940A pdb=" N ARGSG 191 " --> pdb=" O HISSG 187 " (cutoff:3.500A) removed outlier: 4.763A pdb=" N METSG 217 " --> pdb=" O LEUSG 213 " (cutoff:3.500A) removed outlier: 6.160A pdb=" N ALASG 220 " --> pdb=" O ARGSG 216 " (cutoff:3.500A) Processing helix chain 'SJ' and resid 21 through 36 Processing helix chain 'SJ' and resid 39 through 63 Processing helix chain 'SJ' and resid 67 through 85 Processing helix chain 'SJ' and resid 93 through 99 Processing helix chain 'SJ' and resid 101 through 108 Processing helix chain 'SJ' and resid 109 through 118 Processing helix chain 'SJ' and resid 122 through 132 Processing helix chain 'SJ' and resid 171 through 185 Processing helix chain 'SM' and resid 12 through 29 removed outlier: 4.554A pdb=" N ALASM 17 " --> pdb=" O ASPSM 13 " (cutoff:3.500A) Processing helix chain 'SM' and resid 34 through 44 Processing helix chain 'SM' and resid 58 through 72 Processing helix chain 'SM' and resid 81 through 90 Processing helix chain 'SM' and resid 116 through 132 removed outlier: 4.169A pdb=" N LYSSM 121 " --> pdb=" O GLUSM 117 " (cutoff:3.500A) removed outlier: 5.064A pdb=" N ASPSM 122 " --> pdb=" O SERSM 118 " (cutoff:3.500A) Processing helix chain 'SN' and resid 29 through 44 Processing helix chain 'SN' and resid 46 through 57 Processing helix chain 'SN' and resid 62 through 67 Processing helix chain 'SN' and resid 70 through 79 Processing helix chain 'SN' and resid 85 through 105 Processing helix chain 'SN' and resid 108 through 132 Processing helix chain 'SN' and resid 145 through 150 Processing helix chain 'SO' and resid 58 through 62 Processing helix chain 'SO' and resid 70 through 89 Processing helix chain 'SO' and resid 111 through 122 Processing helix chain 'SW' and resid 5 through 21 Processing helix chain 'SW' and resid 31 through 44 Processing helix chain 'SW' and resid 85 through 94 Processing helix chain 'SW' and resid 113 through 119 Processing helix chain 'SY' and resid 36 through 49 Processing helix chain 'SY' and resid 78 through 85 Processing helix chain 'SY' and resid 87 through 94 Processing helix chain 'SY' and resid 103 through 117 Processing helix chain 'SY' and resid 120 through 130 removed outlier: 4.679A pdb=" N GLYSY 128 " --> pdb=" O ASNSY 124 " (cutoff:3.500A) Processing helix chain 'SZ' and resid 51 through 62 Processing helix chain 'SZ' and resid 63 through 65 No H-bonds generated for 'chain 'SZ' and resid 63 through 65' Processing helix chain 'SZ' and resid 69 through 77 Processing helix chain 'SZ' and resid 81 through 95 Processing helix chain 'Sb' and resid 11 through 18 Processing helix chain 'Se' and resid 10 through 15 Processing helix chain 'Se' and resid 30 through 43 Processing helix chain 'Sf' and resid 123 through 127 removed outlier: 3.788A pdb=" N GLYSf 127 " --> pdb=" O ASPSf 124 " (cutoff:3.500A) Processing helix chain 'C1' and resid 59 through 68 Processing helix chain 'C1' and resid 89 through 100 Processing helix chain '4A' and resid 83 through 92 removed outlier: 4.291A pdb=" N ALA4A 87 " --> pdb=" O THR4A 83 " (cutoff:3.500A) Processing helix chain '4A' and resid 109 through 125 Processing helix chain '4A' and resid 139 through 150 Processing helix chain '4A' and resid 158 through 168 Processing helix chain '4A' and resid 183 through 191 Processing helix chain '4A' and resid 192 through 203 Processing helix chain '4A' and resid 217 through 228 Processing helix chain '4A' and resid 255 through 271 removed outlier: 3.763A pdb=" N ASP4A 261 " --> pdb=" O GLU4A 257 " (cutoff:3.500A) Processing helix chain '4A' and resid 281 through 295 Processing helix chain '4A' and resid 312 through 320 Processing helix chain '4A' and resid 330 through 336 Processing helix chain '4A' and resid 352 through 361 removed outlier: 3.773A pdb=" N ILE4A 357 " --> pdb=" O ARG4A 353 " (cutoff:3.500A) Processing helix chain '4A' and resid 377 through 392 removed outlier: 4.623A pdb=" N ARG4A 382 " --> pdb=" O GLU4A 378 " (cutoff:3.500A) removed outlier: 4.113A pdb=" N THR4A 383 " --> pdb=" O GLU4A 379 " (cutoff:3.500A) Processing helix chain 'CD' and resid 113 through 117 removed outlier: 3.565A pdb=" N GLYCD 116 " --> pdb=" O PROCD 113 " (cutoff:3.500A) Processing helix chain 'CD' and resid 163 through 178 Proline residue: CD 170 - end of helix Processing helix chain 'CD' and resid 180 through 192 Processing helix chain 'CD' and resid 193 through 197 removed outlier: 4.088A pdb=" N METCD 196 " --> pdb=" O LEUCD 193 " (cutoff:3.500A) Processing helix chain 'CD' and resid 198 through 211 removed outlier: 4.252A pdb=" N VALCD 202 " --> pdb=" O SERCD 198 " (cutoff:3.500A) Processing helix chain 'CD' and resid 212 through 230 removed outlier: 5.020A pdb=" N GLYCD 228 " --> pdb=" O SERCD 224 " (cutoff:3.500A) Processing helix chain 'CD' and resid 232 through 246 Processing helix chain 'CD' and resid 246 through 254 Processing helix chain 'CD' and resid 256 through 271 Processing helix chain 'CD' and resid 277 through 283 Processing helix chain 'CD' and resid 288 through 305 Processing helix chain 'CD' and resid 323 through 342 Processing helix chain 'CD' and resid 343 through 355 Processing helix chain 'CD' and resid 359 through 374 Processing helix chain 'CD' and resid 377 through 394 Processing helix chain 'CD' and resid 397 through 419 Proline residue: CD 413 - end of helix Processing helix chain 'CD' and resid 421 through 437 Processing helix chain 'CD' and resid 440 through 447 Processing helix chain '3A' and resid 7 through 22 Processing helix chain '3A' and resid 23 through 37 Processing helix chain '3A' and resid 38 through 41 removed outlier: 4.057A pdb=" N ARG3A 41 " --> pdb=" O LYS3A 38 " (cutoff:3.500A) No H-bonds generated for 'chain '3A' and resid 38 through 41' Processing helix chain '3A' and resid 46 through 62 removed outlier: 3.861A pdb=" N ILE3A 50 " --> pdb=" O ILE3A 46 " (cutoff:3.500A) Processing helix chain '3A' and resid 63 through 78 Processing helix chain '3A' and resid 83 through 116 Processing helix chain '3A' and resid 125 through 133 Processing helix chain '3A' and resid 136 through 145 Processing helix chain '3A' and resid 145 through 164 removed outlier: 4.648A pdb=" N TRP3A 149 " --> pdb=" O LEU3A 145 " (cutoff:3.500A) Processing helix chain '3A' and resid 170 through 189 Processing helix chain '3A' and resid 190 through 211 Processing helix chain '3A' and resid 222 through 243 Processing helix chain '3A' and resid 245 through 263 Processing helix chain '3A' and resid 268 through 287 Processing helix chain '3A' and resid 288 through 307 removed outlier: 3.881A pdb=" N GLU3A 305 " --> pdb=" O HIS3A 301 " (cutoff:3.500A) removed outlier: 4.365A pdb=" N ARG3A 307 " --> pdb=" O SER3A 303 " (cutoff:3.500A) Processing helix chain '3A' and resid 312 through 328 Processing helix chain '3A' and resid 336 through 343 Processing helix chain '3A' and resid 351 through 360 Processing helix chain '3A' and resid 367 through 378 removed outlier: 4.452A pdb=" N ASP3A 373 " --> pdb=" O GLY3A 369 " (cutoff:3.500A) removed outlier: 3.833A pdb=" N VAL3A 375 " --> pdb=" O ILE3A 371 " (cutoff:3.500A) Processing helix chain '3A' and resid 379 through 383 removed outlier: 3.695A pdb=" N VAL3A 383 " --> pdb=" O LEU3A 380 " (cutoff:3.500A) Processing helix chain '3A' and resid 384 through 389 removed outlier: 4.618A pdb=" N ASP3A 389 " --> pdb=" O PRO3A 385 " (cutoff:3.500A) Processing helix chain '3A' and resid 389 through 396 Processing helix chain '3A' and resid 402 through 417 Processing helix chain '3A' and resid 421 through 426 removed outlier: 3.572A pdb=" N GLN3A 426 " --> pdb=" O PRO3A 422 " (cutoff:3.500A) Processing helix chain '3A' and resid 427 through 447 Processing helix chain '3A' and resid 452 through 459 Processing helix chain '3A' and resid 463 through 477 Processing helix chain '3A' and resid 515 through 520 Processing helix chain '3A' and resid 521 through 538 Processing helix chain '3A' and resid 539 through 560 Processing helix chain '3A' and resid 563 through 600 Processing helix chain '3A' and resid 603 through 639 Processing helix chain '3A' and resid 643 through 685 Proline residue: 3A 666 - end of helix Processing helix chain '3A' and resid 708 through 725 Processing helix chain '3B' and resid 199 through 213 Processing helix chain '3B' and resid 239 through 251 Processing helix chain '3B' and resid 290 through 294 Processing helix chain '3B' and resid 713 through 722 Processing helix chain '3B' and resid 733 through 744 Processing helix chain '3C' and resid 51 through 73 Processing helix chain '3C' and resid 75 through 93 Processing helix chain '3C' and resid 96 through 100 Processing helix chain '3C' and resid 103 through 122 Processing helix chain '3C' and resid 131 through 149 removed outlier: 5.226A pdb=" N ALA3C 137 " --> pdb=" O ASN3C 133 " (cutoff:3.500A) Processing helix chain '3C' and resid 325 through 339 Processing helix chain '3C' and resid 346 through 362 Processing helix chain '3C' and resid 367 through 386 removed outlier: 4.555A pdb=" N ASN3C 386 " --> pdb=" O LEU3C 382 " (cutoff:3.500A) Processing helix chain '3C' and resid 394 through 415 Processing helix chain '3C' and resid 443 through 462 Processing helix chain '3C' and resid 466 through 474 removed outlier: 4.290A pdb=" N VAL3C 470 " --> pdb=" O SER3C 466 " (cutoff:3.500A) Processing helix chain '3C' and resid 475 through 490 Processing helix chain '3C' and resid 495 through 511 Processing helix chain '3C' and resid 545 through 558 Processing helix chain '3C' and resid 562 through 579 Processing helix chain '3C' and resid 581 through 593 Processing helix chain '3C' and resid 594 through 596 No H-bonds generated for 'chain '3C' and resid 594 through 596' Processing helix chain '3C' and resid 597 through 602 removed outlier: 4.510A pdb=" N ASP3C 602 " --> pdb=" O ILE3C 598 " (cutoff:3.500A) Processing helix chain '3C' and resid 602 through 624 Processing helix chain '3C' and resid 625 through 639 removed outlier: 4.007A pdb=" N ASP3C 635 " --> pdb=" O ASN3C 631 " (cutoff:3.500A) Processing helix chain '3C' and resid 641 through 646 Processing helix chain '3C' and resid 660 through 669 Processing helix chain '3C' and resid 678 through 702 Proline residue: 3C 696 - end of helix Processing helix chain '3C' and resid 711 through 724 Processing helix chain '3C' and resid 732 through 746 Processing helix chain '3C' and resid 748 through 757 Processing helix chain '3C' and resid 759 through 765 Processing helix chain '3C' and resid 766 through 769 Processing helix chain '3C' and resid 771 through 796 Processing helix chain '3C' and resid 804 through 812 Processing helix chain '3C' and resid 814 through 828 Processing helix chain '3C' and resid 850 through 878 Processing helix chain '3E' and resid 6 through 12 Processing helix chain '3E' and resid 18 through 30 removed outlier: 4.453A pdb=" N LEU3E 22 " --> pdb=" O LEU3E 18 " (cutoff:3.500A) Processing helix chain '3E' and resid 34 through 48 Processing helix chain '3E' and resid 50 through 62 Processing helix chain '3E' and resid 68 through 95 Proline residue: 3E 90 - end of helix Processing helix chain '3E' and resid 111 through 121 Processing helix chain '3E' and resid 125 through 142 Processing helix chain '3E' and resid 143 through 158 Processing helix chain '3E' and resid 164 through 180 Processing helix chain '3E' and resid 182 through 199 Processing helix chain '3E' and resid 203 through 225 Processing helix chain '3E' and resid 228 through 237 removed outlier: 3.564A pdb=" N LEU3E 237 " --> pdb=" O ILE3E 233 " (cutoff:3.500A) Processing helix chain '3E' and resid 239 through 249 removed outlier: 4.449A pdb=" N ALA3E 245 " --> pdb=" O GLN3E 241 " (cutoff:3.500A) Processing helix chain '3E' and resid 253 through 263 Processing helix chain '3E' and resid 266 through 284 removed outlier: 5.691A pdb=" N LYS3E 275 " --> pdb=" O ARG3E 271 " (cutoff:3.500A) removed outlier: 5.249A pdb=" N ASP3E 276 " --> pdb=" O GLN3E 272 " (cutoff:3.500A) Processing helix chain '3E' and resid 290 through 301 Processing helix chain '3E' and resid 305 through 320 Processing helix chain '3E' and resid 328 through 348 Processing helix chain '3E' and resid 353 through 360 Processing helix chain '3E' and resid 363 through 379 Processing helix chain '3E' and resid 399 through 426 removed outlier: 4.339A pdb=" N SER3E 410 " --> pdb=" O GLU3E 406 " (cutoff:3.500A) Processing helix chain '3F' and resid 95 through 108 Processing helix chain '3F' and resid 149 through 164 Processing helix chain '3F' and resid 182 through 194 Processing helix chain '3F' and resid 242 through 254 Processing helix chain '3F' and resid 267 through 295 Processing helix chain '3F' and resid 302 through 314 Processing helix chain '3F' and resid 319 through 357 Processing helix chain '3G' and resid 251 through 260 Processing helix chain '3G' and resid 289 through 301 removed outlier: 3.538A pdb=" N SER3G 301 " --> pdb=" O ILE3G 297 " (cutoff:3.500A) Processing helix chain '3H' and resid 43 through 56 Processing helix chain '3H' and resid 97 through 110 Processing helix chain '3H' and resid 130 through 144 Processing helix chain '3H' and resid 153 through 160 Processing helix chain '3H' and resid 170 through 180 Processing helix chain '3H' and resid 183 through 190 Processing helix chain '3H' and resid 194 through 196 No H-bonds generated for 'chain '3H' and resid 194 through 196' Processing helix chain '3H' and resid 208 through 222 Processing helix chain '3H' and resid 228 through 232 removed outlier: 3.706A pdb=" N LEU3H 231 " --> pdb=" O HIS3H 228 " (cutoff:3.500A) removed outlier: 3.927A pdb=" N SER3H 232 " --> pdb=" O GLU3H 229 " (cutoff:3.500A) No H-bonds generated for 'chain '3H' and resid 228 through 232' Processing helix chain '3H' and resid 236 through 289 Processing helix chain '3H' and resid 314 through 349 Processing helix chain '3I' and resid 156 through 158 No H-bonds generated for 'chain '3I' and resid 156 through 158' Processing helix chain '3K' and resid 3 through 15 removed outlier: 4.436A pdb=" N LYS3K 13 " --> pdb=" O ALA3K 9 " (cutoff:3.500A) Processing helix chain '3K' and resid 17 through 21 removed outlier: 3.994A pdb=" N ARG3K 20 " --> pdb=" O GLY3K 17 " (cutoff:3.500A) removed outlier: 3.887A pdb=" N TYR3K 21 " --> pdb=" O ILE3K 18 " (cutoff:3.500A) No H-bonds generated for 'chain '3K' and resid 17 through 21' Processing helix chain '3K' and resid 25 through 40 removed outlier: 4.370A pdb=" N ARG3K 31 " --> pdb=" O ALA3K 27 " (cutoff:3.500A) Processing helix chain '3K' and resid 43 through 57 Processing helix chain '3K' and resid 58 through 61 removed outlier: 3.517A pdb=" N PHE3K 61 " --> pdb=" O PRO3K 58 " (cutoff:3.500A) No H-bonds generated for 'chain '3K' and resid 58 through 61' Processing helix chain '3K' and resid 62 through 77 Processing helix chain '3K' and resid 80 through 89 Processing helix chain '3K' and resid 98 through 111 Processing helix chain '3K' and resid 113 through 119 Processing helix chain '3K' and resid 126 through 131 Processing helix chain '3K' and resid 133 through 150 Processing helix chain '3K' and resid 154 through 163 Processing helix chain '3K' and resid 166 through 176 removed outlier: 4.406A pdb=" N VAL3K 172 " --> pdb=" O SER3K 168 " (cutoff:3.500A) Processing helix chain '3K' and resid 192 through 196 removed outlier: 3.956A pdb=" N SER3K 195 " --> pdb=" O GLN3K 192 " (cutoff:3.500A) removed outlier: 3.612A pdb=" N ILE3K 196 " --> pdb=" O GLU3K 193 " (cutoff:3.500A) No H-bonds generated for 'chain '3K' and resid 192 through 196' Processing helix chain '3K' and resid 210 through 218 Processing helix chain '3L' and resid 183 through 204 Processing helix chain '3L' and resid 209 through 218 Processing helix chain '3L' and resid 223 through 247 removed outlier: 4.829A pdb=" N ASN3L 229 " --> pdb=" O HIS3L 225 " (cutoff:3.500A) Processing helix chain '3L' and resid 251 through 261 Processing helix chain '3L' and resid 274 through 290 Processing helix chain '3L' and resid 295 through 301 Processing helix chain '3L' and resid 308 through 326 Processing helix chain '3L' and resid 328 through 340 removed outlier: 4.609A pdb=" N ARG3L 334 " --> pdb=" O GLN3L 330 " (cutoff:3.500A) Processing helix chain '3L' and resid 357 through 375 Processing helix chain '3L' and resid 388 through 402 Processing helix chain '3L' and resid 406 through 417 Processing helix chain '3L' and resid 437 through 461 removed outlier: 4.655A pdb=" N LYS3L 445 " --> pdb=" O LEU3L 441 " (cutoff:3.500A) removed outlier: 5.286A pdb=" N VAL3L 446 " --> pdb=" O GLN3L 442 " (cutoff:3.500A) removed outlier: 4.319A pdb=" N GLN3L 453 " --> pdb=" O ASP3L 449 " (cutoff:3.500A) Processing helix chain '3L' and resid 471 through 483 Processing helix chain '3L' and resid 489 through 498 Processing helix chain '3L' and resid 524 through 552 Processing helix chain '3M' and resid 12 through 26 Processing helix chain '3M' and resid 39 through 53 removed outlier: 4.715A pdb=" N VAL3M 51 " --> pdb=" O GLU3M 47 " (cutoff:3.500A) Processing helix chain '3M' and resid 61 through 72 Processing helix chain '3M' and resid 79 through 95 Processing helix chain '3M' and resid 99 through 113 Processing helix chain '3M' and resid 117 through 134 removed outlier: 3.798A pdb=" N TYR3M 121 " --> pdb=" O THR3M 117 " (cutoff:3.500A) Processing helix chain '3M' and resid 143 through 155 Processing helix chain '3M' and resid 157 through 175 Processing helix chain '3M' and resid 177 through 192 Processing helix chain '3M' and resid 194 through 198 removed outlier: 4.174A pdb=" N SER3M 198 " --> pdb=" O ASP3M 195 " (cutoff:3.500A) Processing helix chain '3M' and resid 201 through 214 Processing helix chain '3M' and resid 226 through 232 Processing helix chain '3M' and resid 237 through 246 Processing helix chain '3M' and resid 248 through 259 Processing helix chain '3M' and resid 269 through 289 Processing helix chain '3M' and resid 294 through 302 Processing helix chain '3M' and resid 306 through 319 Processing helix chain '3M' and resid 343 through 372 Processing helix chain '3N' and resid 22 through 26 removed outlier: 3.955A pdb=" N PHE3N 25 " --> pdb=" O PRO3N 22 " (cutoff:3.500A) Processing helix chain '3N' and resid 54 through 60 Processing helix chain '3N' and resid 176 through 182 Processing helix chain '3N' and resid 204 through 209 removed outlier: 3.879A pdb=" N ARG3N 208 " --> pdb=" O LYS3N 204 " (cutoff:3.500A) Processing helix chain '3N' and resid 232 through 239 Processing helix chain '3N' and resid 249 through 257 Processing helix chain '3N' and resid 258 through 261 Processing helix chain '3N' and resid 308 through 327 Processing helix chain '3N' and resid 408 through 413 Processing helix chain '3N' and resid 416 through 428 Processing helix chain '3N' and resid 428 through 443 removed outlier: 3.784A pdb=" N LEU3N 432 " --> pdb=" O ASN3N 428 " (cutoff:3.500A) Processing helix chain '3N' and resid 472 through 480 Processing helix chain '3N' and resid 483 through 501 Processing sheet with id=AA1, first strand: chain 'SA' and resid 40 through 41 Processing sheet with id=AA2, first strand: chain 'SA' and resid 97 through 100 removed outlier: 6.950A pdb=" N VALSA 74 " --> pdb=" O THRSA 97 " (cutoff:3.500A) removed outlier: 7.881A pdb=" N ILESA 99 " --> pdb=" O VALSA 74 " (cutoff:3.500A) removed outlier: 6.626A pdb=" N VALSA 76 " --> pdb=" O ILESA 99 " (cutoff:3.500A) removed outlier: 6.147A pdb=" N LEUSA 122 " --> pdb=" O ILESA 145 " (cutoff:3.500A) removed outlier: 7.990A pdb=" N LEUSA 147 " --> pdb=" O LEUSA 122 " (cutoff:3.500A) removed outlier: 7.465A pdb=" N VALSA 124 " --> pdb=" O LEUSA 147 " (cutoff:3.500A) removed outlier: 6.739A pdb=" N THRSA 144 " --> pdb=" O ILESA 159 " (cutoff:3.500A) removed outlier: 7.756A pdb=" N ILESA 161 " --> pdb=" O THRSA 144 " (cutoff:3.500A) removed outlier: 6.744A pdb=" N ALASA 146 " --> pdb=" O ILESA 161 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'SB' and resid 43 through 50 removed outlier: 4.206A pdb=" N ASPSB 90 " --> pdb=" O LEUSB 97 " (cutoff:3.500A) removed outlier: 6.345A pdb=" N ASNSB 99 " --> pdb=" O THRSB 88 " (cutoff:3.500A) removed outlier: 4.930A pdb=" N THRSB 88 " --> pdb=" O ASNSB 99 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'SB' and resid 69 through 70 removed outlier: 3.566A pdb=" N ASPSB 104 " --> pdb=" O LYSSB 83 " (cutoff:3.500A) removed outlier: 7.857A pdb=" N ARGSB 213 " --> pdb=" O LEUSB 105 " (cutoff:3.500A) removed outlier: 5.551A pdb=" N VALSB 212 " --> pdb=" O VALSB 140 " (cutoff:3.500A) removed outlier: 6.687A pdb=" N VALSB 140 " --> pdb=" O VALSB 212 " (cutoff:3.500A) removed outlier: 6.434A pdb=" N LEUSB 134 " --> pdb=" O LEUSB 218 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'SD' and resid 37 through 41 Processing sheet with id=AA6, first strand: chain 'SD' and resid 148 through 155 Processing sheet with id=AA7, first strand: chain 'SD' and resid 209 through 210 removed outlier: 3.635A pdb=" N SERSD 209 " --> pdb=" O ILESR 40 " (cutoff:3.500A) removed outlier: 3.724A pdb=" N ILESR 40 " --> pdb=" O SERSD 209 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA7 Processing sheet with id=AA8, first strand: chain 'SE' and resid 71 through 72 removed outlier: 3.663A pdb=" N HISSE 112 " --> pdb=" O ARGSE 100 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'SE' and resid 146 through 148 removed outlier: 6.083A pdb=" N ILESE 136 " --> pdb=" O VALSE 131 " (cutoff:3.500A) removed outlier: 4.489A pdb=" N VALSE 131 " --> pdb=" O ILESE 136 " (cutoff:3.500A) removed outlier: 6.756A pdb=" N HISSE 138 " --> pdb=" O ILESE 129 " (cutoff:3.500A) removed outlier: 4.395A pdb=" N ILESE 129 " --> pdb=" O HISSE 138 " (cutoff:3.500A) removed outlier: 6.487A pdb=" N VALSE 140 " --> pdb=" O ARGSE 127 " (cutoff:3.500A) removed outlier: 6.050A pdb=" N ASPSE 163 " --> pdb=" O ILESE 169 " (cutoff:3.500A) removed outlier: 6.541A pdb=" N ILESE 169 " --> pdb=" O ASPSE 163 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'SE' and resid 217 through 218 removed outlier: 6.578A pdb=" N VALSE 207 " --> pdb=" O ARGSE 198 " (cutoff:3.500A) removed outlier: 4.722A pdb=" N ARGSE 198 " --> pdb=" O VALSE 207 " (cutoff:3.500A) removed outlier: 6.378A pdb=" N HISSE 209 " --> pdb=" O THRSE 196 " (cutoff:3.500A) removed outlier: 6.714A pdb=" N LEUSE 180 " --> pdb=" O ILESE 228 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'SF' and resid 123 through 126 removed outlier: 8.216A pdb=" N ALASF 138 " --> pdb=" O ASNSc 45 " (cutoff:3.500A) removed outlier: 8.725A pdb=" N LYSSc 47 " --> pdb=" O ALASF 138 " (cutoff:3.500A) removed outlier: 6.531A pdb=" N ASPSF 140 " --> pdb=" O LYSSc 47 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'SH' and resid 47 through 52 removed outlier: 3.570A pdb=" N HISSH 91 " --> pdb=" O LYSSH 58 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'SH' and resid 185 through 188 removed outlier: 6.292A pdb=" N ILESH 154 " --> pdb=" O ASNSH 186 " (cutoff:3.500A) removed outlier: 7.572A pdb=" N GLUSH 188 " --> pdb=" O ILESH 154 " (cutoff:3.500A) removed outlier: 5.790A pdb=" N VALSH 156 " --> pdb=" O GLUSH 188 " (cutoff:3.500A) removed outlier: 3.657A pdb=" N PHESW 50 " --> pdb=" O VALSH 146 " (cutoff:3.500A) removed outlier: 5.225A pdb=" N ASNSW 64 " --> pdb=" O GLYSW 48 " (cutoff:3.500A) removed outlier: 4.374A pdb=" N PHESW 50 " --> pdb=" O VALSW 62 " (cutoff:3.500A) removed outlier: 6.437A pdb=" N VALSW 62 " --> pdb=" O PHESW 50 " (cutoff:3.500A) removed outlier: 4.434A pdb=" N ILESW 52 " --> pdb=" O LYSSW 60 " (cutoff:3.500A) removed outlier: 6.078A pdb=" N LYSSW 60 " --> pdb=" O ILESW 52 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'SI' and resid 3 through 4 removed outlier: 3.996A pdb=" N ILESI 3 " --> pdb=" O GLYSI 30 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'SI' and resid 37 through 38 removed outlier: 6.707A pdb=" N ARGSI 42 " --> pdb=" O LEUSI 58 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'SI' and resid 62 through 67 removed outlier: 3.790A pdb=" N PHESI 65 " --> pdb=" O ARGSI 74 " (cutoff:3.500A) removed outlier: 3.550A pdb=" N CYSSI 72 " --> pdb=" O TRPSI 67 " (cutoff:3.500A) removed outlier: 4.184A pdb=" N ASPSI 80 " --> pdb=" O LEUSI 103 " (cutoff:3.500A) removed outlier: 7.071A pdb=" N ILESI 101 " --> pdb=" O VALSI 82 " (cutoff:3.500A) removed outlier: 8.461A pdb=" N GLYSI 187 " --> pdb=" O VALSI 62 " (cutoff:3.500A) removed outlier: 6.358A pdb=" N ASNSI 64 " --> pdb=" O GLYSI 187 " (cutoff:3.500A) removed outlier: 7.739A pdb=" N VALSI 189 " --> pdb=" O ASNSI 64 " (cutoff:3.500A) removed outlier: 7.142A pdb=" N SERSI 66 " --> pdb=" O VALSI 189 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'SK' and resid 20 through 24 Processing sheet with id=AB9, first strand: chain 'SL' and resid 72 through 79 removed outlier: 17.963A pdb=" N ILESL 72 " --> pdb=" O LEUSL 93 " (cutoff:3.500A) removed outlier: 14.704A pdb=" N LEUSL 93 " --> pdb=" O ILESL 72 " (cutoff:3.500A) removed outlier: 9.316A pdb=" N SERSL 74 " --> pdb=" O ASPSL 91 " (cutoff:3.500A) removed outlier: 6.285A pdb=" N ASPSL 91 " --> pdb=" O SERSL 74 " (cutoff:3.500A) removed outlier: 3.868A pdb=" N VALSL 76 " --> pdb=" O ARGSL 89 " (cutoff:3.500A) removed outlier: 7.128A pdb=" N VALSL 87 " --> pdb=" O THRSL 78 " (cutoff:3.500A) removed outlier: 3.517A pdb=" N ARGSL 90 " --> pdb=" O LYSSL 107 " (cutoff:3.500A) removed outlier: 4.821A pdb=" N PHESL 140 " --> pdb=" O SERSL 110 " (cutoff:3.500A) removed outlier: 6.535A pdb=" N THRSL 127 " --> pdb=" O LEUSL 143 " (cutoff:3.500A) removed outlier: 4.556A pdb=" N VALSL 145 " --> pdb=" O ILESL 125 " (cutoff:3.500A) removed outlier: 6.905A pdb=" N ILESL 125 " --> pdb=" O VALSL 145 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'SP' and resid 76 through 78 removed outlier: 5.859A pdb=" N VALSP 76 " --> pdb=" O GLYSP 95 " (cutoff:3.500A) removed outlier: 7.737A pdb=" N TYRSP 97 " --> pdb=" O VALSP 76 " (cutoff:3.500A) removed outlier: 8.160A pdb=" N THRSP 78 " --> pdb=" O TYRSP 97 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'SQ' and resid 10 through 16 removed outlier: 3.516A pdb=" N HISSQ 24 " --> pdb=" O ARGSQ 69 " (cutoff:3.500A) removed outlier: 3.554A pdb=" N ARGSQ 69 " --> pdb=" O HISSQ 24 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'SR' and resid 97 through 98 Processing sheet with id=AC4, first strand: chain 'ST' and resid 81 through 84 Processing sheet with id=AC5, first strand: chain 'ST' and resid 113 through 115 Processing sheet with id=AC6, first strand: chain 'SU' and resid 54 through 55 Processing sheet with id=AC7, first strand: chain 'SU' and resid 54 through 55 Processing sheet with id=AC8, first strand: chain 'SV' and resid 15 through 17 Processing sheet with id=AC9, first strand: chain 'SV' and resid 32 through 37 Processing sheet with id=AD1, first strand: chain 'SX' and resid 46 through 58 removed outlier: 6.712A pdb=" N ARGSX 71 " --> pdb=" O LEUSX 52 " (cutoff:3.500A) removed outlier: 5.069A pdb=" N LYSSX 54 " --> pdb=" O CYSSX 69 " (cutoff:3.500A) removed outlier: 6.638A pdb=" N CYSSX 69 " --> pdb=" O LYSSX 54 " (cutoff:3.500A) removed outlier: 4.429A pdb=" N GLYSX 56 " --> pdb=" O ARGSX 67 " (cutoff:3.500A) removed outlier: 5.866A pdb=" N ARGSX 67 " --> pdb=" O GLYSX 56 " (cutoff:3.500A) removed outlier: 4.509A pdb=" N PHESX 120 " --> pdb=" O THRSX 82 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'Sa' and resid 20 through 22 Processing sheet with id=AD3, first strand: chain 'Sa' and resid 36 through 43 Processing sheet with id=AD4, first strand: chain 'Sc' and resid 10 through 13 Processing sheet with id=AD5, first strand: chain 'Sd' and resid 30 through 31 Processing sheet with id=AD6, first strand: chain 'Sg' and resid 4 through 11 removed outlier: 5.212A pdb=" N METSg 5 " --> pdb=" O THRSg 313 " (cutoff:3.500A) removed outlier: 6.814A pdb=" N THRSg 313 " --> pdb=" O METSg 5 " (cutoff:3.500A) removed outlier: 5.740A pdb=" N LEUSg 7 " --> pdb=" O GLNSg 311 " (cutoff:3.500A) removed outlier: 6.550A pdb=" N GLNSg 311 " --> pdb=" O LEUSg 7 " (cutoff:3.500A) removed outlier: 4.764A pdb=" N GLYSg 9 " --> pdb=" O VALSg 309 " (cutoff:3.500A) removed outlier: 3.840A pdb=" N VALSg 309 " --> pdb=" O GLYSg 9 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'Sg' and resid 18 through 23 removed outlier: 6.744A pdb=" N LYSSg 44 " --> pdb=" O PROSg 55 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'Sg' and resid 66 through 71 removed outlier: 6.521A pdb=" N GLYSg 81 " --> pdb=" O SERSg 67 " (cutoff:3.500A) removed outlier: 4.078A pdb=" N VALSg 69 " --> pdb=" O LEUSg 79 " (cutoff:3.500A) removed outlier: 6.548A pdb=" N LEUSg 79 " --> pdb=" O VALSg 69 " (cutoff:3.500A) removed outlier: 4.843A pdb=" N ILESg 71 " --> pdb=" O PHESg 77 " (cutoff:3.500A) removed outlier: 7.220A pdb=" N PHESg 77 " --> pdb=" O ILESg 71 " (cutoff:3.500A) removed outlier: 4.786A pdb=" N THRSg 86 " --> pdb=" O SERSg 82 " (cutoff:3.500A) removed outlier: 5.887A pdb=" N ASPSg 91 " --> pdb=" O THRSg 97 " (cutoff:3.500A) removed outlier: 5.643A pdb=" N THRSg 97 " --> pdb=" O ASPSg 91 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'Sg' and resid 108 through 113 Processing sheet with id=AE1, first strand: chain 'Sg' and resid 154 through 156 removed outlier: 7.319A pdb=" N ASNSg 178 " --> pdb=" O LEUSg 184 " (cutoff:3.500A) removed outlier: 7.390A pdb=" N LEUSg 184 " --> pdb=" O ASNSg 178 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'Sg' and resid 195 through 200 removed outlier: 4.835A pdb=" N GLYSg 211 " --> pdb=" O GLNSg 215 " (cutoff:3.500A) removed outlier: 5.419A pdb=" N GLNSg 215 " --> pdb=" O GLYSg 211 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'Sg' and resid 236 through 240 removed outlier: 6.283A pdb=" N ALASg 251 " --> pdb=" O ASNSg 237 " (cutoff:3.500A) removed outlier: 4.544A pdb=" N LEUSg 239 " --> pdb=" O CYSSg 249 " (cutoff:3.500A) removed outlier: 7.065A pdb=" N CYSSg 249 " --> pdb=" O LEUSg 239 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'SC' and resid 103 through 115 removed outlier: 5.088A pdb=" N ASPSC 104 " --> pdb=" O GLYSC 131 " (cutoff:3.500A) removed outlier: 7.384A pdb=" N GLYSC 131 " --> pdb=" O ASPSC 104 " (cutoff:3.500A) removed outlier: 5.413A pdb=" N VALSC 106 " --> pdb=" O ALASC 129 " (cutoff:3.500A) removed outlier: 6.525A pdb=" N ALASC 129 " --> pdb=" O VALSC 106 " (cutoff:3.500A) Processing sheet with id=AE5, first strand: chain 'SC' and resid 184 through 188 Processing sheet with id=AE6, first strand: chain 'SG' and resid 5 through 6 removed outlier: 3.832A pdb=" N ILESG 113 " --> pdb=" O SERSG 6 " (cutoff:3.500A) removed outlier: 6.861A pdb=" N VALSG 112 " --> pdb=" O ILESG 52 " (cutoff:3.500A) removed outlier: 5.634A pdb=" N ILESG 52 " --> pdb=" O VALSG 112 " (cutoff:3.500A) removed outlier: 6.360A pdb=" N VALSG 114 " --> pdb=" O VALSG 50 " (cutoff:3.500A) removed outlier: 7.668A pdb=" N VALSG 50 " --> pdb=" O VALSG 114 " (cutoff:3.500A) Processing sheet with id=AE7, first strand: chain 'SG' and resid 30 through 31 removed outlier: 4.004A pdb=" N LYSSG 30 " --> pdb=" O VALSG 102 " (cutoff:3.500A) removed outlier: 3.563A pdb=" N VALSG 102 " --> pdb=" O LYSSG 30 " (cutoff:3.500A) No H-bonds generated for sheet with id=AE7 Processing sheet with id=AE8, first strand: chain 'SG' and resid 72 through 77 removed outlier: 3.715A pdb=" N LYSSG 93 " --> pdb=" O LEUSG 77 " (cutoff:3.500A) Processing sheet with id=AE9, first strand: chain 'SG' and resid 160 through 162 Processing sheet with id=AF1, first strand: chain 'SJ' and resid 140 through 141 Processing sheet with id=AF2, first strand: chain 'SM' and resid 32 through 33 removed outlier: 3.947A pdb=" N ALASM 32 " --> pdb=" O VALSM 110 " (cutoff:3.500A) removed outlier: 3.636A pdb=" N VALSM 110 " --> pdb=" O ALASM 32 " (cutoff:3.500A) Processing sheet with id=AF3, first strand: chain 'SO' and resid 52 through 57 removed outlier: 3.501A pdb=" N VALSO 42 " --> pdb=" O VALSO 56 " (cutoff:3.500A) removed outlier: 6.446A pdb=" N LEUSO 93 " --> pdb=" O ILESO 126 " (cutoff:3.500A) removed outlier: 4.765A pdb=" N ARGSO 128 " --> pdb=" O LEUSO 93 " (cutoff:3.500A) Processing sheet with id=AF4, first strand: chain 'SW' and resid 80 through 81 removed outlier: 5.358A pdb=" N ILESW 125 " --> pdb=" O THRSW 105 " (cutoff:3.500A) removed outlier: 5.662A pdb=" N THRSW 105 " --> pdb=" O ILESW 125 " (cutoff:3.500A) Processing sheet with id=AF5, first strand: chain 'SY' and resid 6 through 15 removed outlier: 4.663A pdb=" N PHESY 12 " --> pdb=" O GLNSY 22 " (cutoff:3.500A) removed outlier: 6.967A pdb=" N GLNSY 22 " --> pdb=" O PHESY 12 " (cutoff:3.500A) removed outlier: 5.087A pdb=" N THRSY 14 " --> pdb=" O ARGSY 20 " (cutoff:3.500A) removed outlier: 6.944A pdb=" N ARGSY 20 " --> pdb=" O THRSY 14 " (cutoff:3.500A) removed outlier: 7.264A pdb=" N LYSSY 68 " --> pdb=" O THRSY 62 " (cutoff:3.500A) removed outlier: 4.906A pdb=" N THRSY 62 " --> pdb=" O LYSSY 68 " (cutoff:3.500A) removed outlier: 6.223A pdb=" N THRSY 70 " --> pdb=" O PHESY 60 " (cutoff:3.500A) removed outlier: 3.790A pdb=" N PHESY 60 " --> pdb=" O THRSY 70 " (cutoff:3.500A) Processing sheet with id=AF6, first strand: chain 'SZ' and resid 97 through 99 Processing sheet with id=AF7, first strand: chain 'Sb' and resid 44 through 47 Processing sheet with id=AF8, first strand: chain 'Sb' and resid 64 through 65 Processing sheet with id=AF9, first strand: chain 'Sf' and resid 138 through 141 Processing sheet with id=AG1, first strand: chain 'C1' and resid 71 through 76 removed outlier: 7.332A pdb=" N HISC1 76 " --> pdb=" O GLYC1 80 " (cutoff:3.500A) removed outlier: 5.126A pdb=" N GLYC1 80 " --> pdb=" O HISC1 76 " (cutoff:3.500A) removed outlier: 6.222A pdb=" N ILEC1 31 " --> pdb=" O LYSC1 109 " (cutoff:3.500A) Processing sheet with id=AG2, first strand: chain '4A' and resid 22 through 25 removed outlier: 6.195A pdb=" N ILE4A 73 " --> pdb=" O ILE4A 234 " (cutoff:3.500A) removed outlier: 7.518A pdb=" N VAL4A 236 " --> pdb=" O ILE4A 73 " (cutoff:3.500A) removed outlier: 6.344A pdb=" N GLN4A 75 " --> pdb=" O VAL4A 236 " (cutoff:3.500A) removed outlier: 6.703A pdb=" N VAL4A 72 " --> pdb=" O LEU4A 211 " (cutoff:3.500A) removed outlier: 7.983A pdb=" N SER4A 213 " --> pdb=" O VAL4A 72 " (cutoff:3.500A) removed outlier: 6.255A pdb=" N ALA4A 74 " --> pdb=" O SER4A 213 " (cutoff:3.500A) removed outlier: 6.179A pdb=" N PHE4A 179 " --> pdb=" O VAL4A 210 " (cutoff:3.500A) removed outlier: 7.463A pdb=" N LEU4A 212 " --> pdb=" O PHE4A 179 " (cutoff:3.500A) removed outlier: 6.052A pdb=" N LEU4A 181 " --> pdb=" O LEU4A 212 " (cutoff:3.500A) removed outlier: 6.409A pdb=" N LEU4A 104 " --> pdb=" O VAL4A 180 " (cutoff:3.500A) removed outlier: 7.224A pdb=" N ASP4A 182 " --> pdb=" O LEU4A 104 " (cutoff:3.500A) removed outlier: 6.051A pdb=" N LEU4A 106 " --> pdb=" O ASP4A 182 " (cutoff:3.500A) removed outlier: 6.047A pdb=" N HIS4A 132 " --> pdb=" O VAL4A 156 " (cutoff:3.500A) Processing sheet with id=AG3, first strand: chain '4A' and resid 300 through 301 removed outlier: 7.008A pdb=" N SER4A 300 " --> pdb=" O ILE4A 327 " (cutoff:3.500A) removed outlier: 9.122A pdb=" N THR4A 329 " --> pdb=" O SER4A 300 " (cutoff:3.500A) removed outlier: 6.132A pdb=" N ALA4A 275 " --> pdb=" O LEU4A 326 " (cutoff:3.500A) removed outlier: 7.342A pdb=" N THR4A 328 " --> pdb=" O ALA4A 275 " (cutoff:3.500A) removed outlier: 5.749A pdb=" N ILE4A 277 " --> pdb=" O THR4A 328 " (cutoff:3.500A) removed outlier: 5.929A pdb=" N ARG4A 247 " --> pdb=" O ALA4A 372 " (cutoff:3.500A) removed outlier: 7.293A pdb=" N ASN4A 374 " --> pdb=" O ARG4A 247 " (cutoff:3.500A) removed outlier: 6.150A pdb=" N PHE4A 249 " --> pdb=" O ASN4A 374 " (cutoff:3.500A) removed outlier: 7.634A pdb=" N VAL4A 376 " --> pdb=" O PHE4A 249 " (cutoff:3.500A) removed outlier: 6.241A pdb=" N ILE4A 251 " --> pdb=" O VAL4A 376 " (cutoff:3.500A) Processing sheet with id=AG4, first strand: chain 'CD' and resid 150 through 153 removed outlier: 3.529A pdb=" N ALA3G 271 " --> pdb=" O PHE3G 282 " (cutoff:3.500A) removed outlier: 4.988A pdb=" N PHE3G 282 " --> pdb=" O ALA3G 271 " (cutoff:3.500A) removed outlier: 7.613A pdb=" N ASP3G 273 " --> pdb=" O LYS3G 280 " (cutoff:3.500A) removed outlier: 7.127A pdb=" N LYS3G 280 " --> pdb=" O ASP3G 273 " (cutoff:3.500A) Processing sheet with id=AG5, first strand: chain '3A' and resid 449 through 451 Processing sheet with id=AG6, first strand: chain '3B' and resid 188 through 190 Processing sheet with id=AG7, first strand: chain '3B' and resid 219 through 221 Processing sheet with id=AG8, first strand: chain '3B' and resid 224 through 225 Processing sheet with id=AG9, first strand: chain '3B' and resid 317 through 319 removed outlier: 3.946A pdb=" N GLN3B 701 " --> pdb=" O ILE3B 309 " (cutoff:3.500A) Processing sheet with id=AH1, first strand: chain '3B' and resid 340 through 342 removed outlier: 5.948A pdb=" N GLY3B 361 " --> pdb=" O GLN3B 367 " (cutoff:3.500A) removed outlier: 5.257A pdb=" N GLN3B 367 " --> pdb=" O GLY3B 361 " (cutoff:3.500A) Processing sheet with id=AH2, first strand: chain '3B' and resid 378 through 381 removed outlier: 6.071A pdb=" N ASP3B 408 " --> pdb=" O LYS3B 414 " (cutoff:3.500A) removed outlier: 6.165A pdb=" N LYS3B 414 " --> pdb=" O ASP3B 408 " (cutoff:3.500A) Processing sheet with id=AH3, first strand: chain '3B' and resid 430 through 431 Processing sheet with id=AH4, first strand: chain '3B' and resid 469 through 472 removed outlier: 4.281A pdb=" N ASP3B 469 " --> pdb=" O TRP3B 482 " (cutoff:3.500A) removed outlier: 4.378A pdb=" N ARG3B 505 " --> pdb=" O LEU3B 495 " (cutoff:3.500A) removed outlier: 7.357A pdb=" N GLN3B 497 " --> pdb=" O GLU3B 503 " (cutoff:3.500A) removed outlier: 6.421A pdb=" N GLU3B 503 " --> pdb=" O GLN3B 497 " (cutoff:3.500A) Processing sheet with id=AH5, first strand: chain '3B' and resid 516 through 519 Processing sheet with id=AH6, first strand: chain '3B' and resid 565 through 570 removed outlier: 6.392A pdb=" N ILE3B 587 " --> pdb=" O LYS3B 608 " (cutoff:3.500A) removed outlier: 4.799A pdb=" N LYS3B 608 " --> pdb=" O ILE3B 587 " (cutoff:3.500A) removed outlier: 6.267A pdb=" N HIS3B 593 " --> pdb=" O LEU3B 602 " (cutoff:3.500A) removed outlier: 5.822A pdb=" N LEU3B 602 " --> pdb=" O HIS3B 593 " (cutoff:3.500A) Processing sheet with id=AH7, first strand: chain '3B' and resid 613 through 616 Processing sheet with id=AH8, first strand: chain '3B' and resid 656 through 659 Processing sheet with id=AH9, first strand: chain '3C' and resid 419 through 421 removed outlier: 6.092A pdb=" N PHE3C 419 " --> pdb=" O VAL3C 440 " (cutoff:3.500A) No H-bonds generated for sheet with id=AH9 Processing sheet with id=AI1, first strand: chain '3C' and resid 801 through 803 Processing sheet with id=AI2, first strand: chain '3E' and resid 350 through 352 Processing sheet with id=AI3, first strand: chain '3F' and resid 233 through 234 removed outlier: 4.115A pdb=" N ILE3F 198 " --> pdb=" O LEU3F 170 " (cutoff:3.500A) removed outlier: 3.973A pdb=" N VAL3F 202 " --> pdb=" O ALA3F 174 " (cutoff:3.500A) removed outlier: 5.720A pdb=" N ILE3F 169 " --> pdb=" O GLY3F 122 " (cutoff:3.500A) removed outlier: 6.261A pdb=" N GLY3F 122 " --> pdb=" O ILE3F 169 " (cutoff:3.500A) removed outlier: 6.710A pdb=" N THR3F 123 " --> pdb=" O VAL3F 131 " (cutoff:3.500A) removed outlier: 4.819A pdb=" N VAL3F 131 " --> pdb=" O THR3F 123 " (cutoff:3.500A) removed outlier: 3.753A pdb=" N VAL3F 129 " --> pdb=" O VAL3F 91 " (cutoff:3.500A) removed outlier: 3.712A pdb=" N ARG3F 93 " --> pdb=" O VAL3F 129 " (cutoff:3.500A) removed outlier: 4.153A pdb=" N VAL3F 131 " --> pdb=" O ARG3F 93 " (cutoff:3.500A) Processing sheet with id=AI4, first strand: chain '3F' and resid 263 through 264 removed outlier: 6.512A pdb=" N VAL3H 39 " --> pdb=" O VAL3H 204 " (cutoff:3.500A) removed outlier: 7.284A pdb=" N LYS3H 206 " --> pdb=" O VAL3H 39 " (cutoff:3.500A) removed outlier: 6.420A pdb=" N ILE3H 41 " --> pdb=" O LYS3H 206 " (cutoff:3.500A) removed outlier: 4.477A pdb=" N ASP3H 42 " --> pdb=" O ILE3H 78 " (cutoff:3.500A) removed outlier: 7.805A pdb=" N ASN3H 80 " --> pdb=" O ASP3H 42 " (cutoff:3.500A) removed outlier: 4.221A pdb=" N LEU3H 76 " --> pdb=" O VAL3H 72 " (cutoff:3.500A) removed outlier: 6.654A pdb=" N VAL3H 72 " --> pdb=" O LEU3H 76 " (cutoff:3.500A) removed outlier: 4.755A pdb=" N ILE3H 78 " --> pdb=" O LEU3H 70 " (cutoff:3.500A) removed outlier: 6.518A pdb=" N LEU3H 70 " --> pdb=" O ILE3H 78 " (cutoff:3.500A) removed outlier: 3.952A pdb=" N GLY3H 65 " --> pdb=" O TYR3H 120 " (cutoff:3.500A) removed outlier: 6.857A pdb=" N GLY3H 69 " --> pdb=" O HIS3H 116 " (cutoff:3.500A) removed outlier: 6.232A pdb=" N HIS3H 116 " --> pdb=" O GLY3H 69 " (cutoff:3.500A) removed outlier: 9.019A pdb=" N LEU3H 150 " --> pdb=" O VAL3H 117 " (cutoff:3.500A) removed outlier: 7.311A pdb=" N TRP3H 119 " --> pdb=" O LEU3H 150 " (cutoff:3.500A) removed outlier: 8.238A pdb=" N TYR3H 152 " --> pdb=" O TRP3H 119 " (cutoff:3.500A) removed outlier: 6.550A pdb=" N GLN3H 121 " --> pdb=" O TYR3H 152 " (cutoff:3.500A) removed outlier: 3.523A pdb=" N GLU3H 199 " --> pdb=" O ARG3H 168 " (cutoff:3.500A) Processing sheet with id=AI5, first strand: chain '3G' and resid 304 through 305 Processing sheet with id=AI6, first strand: chain '3I' and resid 2 through 6 Processing sheet with id=AI7, first strand: chain '3I' and resid 13 through 18 removed outlier: 5.945A pdb=" N TYR3I 38 " --> pdb=" O ARG3I 44 " (cutoff:3.500A) removed outlier: 5.339A pdb=" N ARG3I 44 " --> pdb=" O TYR3I 38 " (cutoff:3.500A) Processing sheet with id=AI8, first strand: chain '3I' and resid 55 through 60 removed outlier: 4.162A pdb=" N SER3I 75 " --> pdb=" O SER3I 71 " (cutoff:3.500A) removed outlier: 6.028A pdb=" N ASP3I 80 " --> pdb=" O GLN3I 86 " (cutoff:3.500A) removed outlier: 6.099A pdb=" N GLN3I 86 " --> pdb=" O ASP3I 80 " (cutoff:3.500A) Processing sheet with id=AI9, first strand: chain '3I' and resid 96 through 101 removed outlier: 7.041A pdb=" N PHE3I 124 " --> pdb=" O TYR3I 139 " (cutoff:3.500A) Processing sheet with id=AJ1, first strand: chain '3I' and resid 149 through 154 removed outlier: 3.633A pdb=" N TYR3I 173 " --> pdb=" O ILE3I 161 " (cutoff:3.500A) removed outlier: 4.543A pdb=" N GLU3I 169 " --> pdb=" O HIS3I 165 " (cutoff:3.500A) removed outlier: 7.654A pdb=" N SER3I 174 " --> pdb=" O VAL3I 180 " (cutoff:3.500A) removed outlier: 6.492A pdb=" N VAL3I 180 " --> pdb=" O SER3I 174 " (cutoff:3.500A) Processing sheet with id=AJ2, first strand: chain '3I' and resid 191 through 196 removed outlier: 4.053A pdb=" N SER3I 207 " --> pdb=" O THR3I 211 " (cutoff:3.500A) removed outlier: 4.683A pdb=" N THR3I 211 " --> pdb=" O SER3I 207 " (cutoff:3.500A) removed outlier: 6.521A pdb=" N ASP3I 216 " --> pdb=" O HIS3I 222 " (cutoff:3.500A) removed outlier: 5.441A pdb=" N HIS3I 222 " --> pdb=" O ASP3I 216 " (cutoff:3.500A) Processing sheet with id=AJ3, first strand: chain '3I' and resid 232 through 238 removed outlier: 6.712A pdb=" N GLY3I 247 " --> pdb=" O ASN3I 233 " (cutoff:3.500A) removed outlier: 4.497A pdb=" N ALA3I 235 " --> pdb=" O VAL3I 245 " (cutoff:3.500A) removed outlier: 6.830A pdb=" N VAL3I 245 " --> pdb=" O ALA3I 235 " (cutoff:3.500A) removed outlier: 5.519A pdb=" N LEU3I 237 " --> pdb=" O HIS3I 243 " (cutoff:3.500A) removed outlier: 7.648A pdb=" N HIS3I 243 " --> pdb=" O LEU3I 237 " (cutoff:3.500A) removed outlier: 5.429A pdb=" N GLY3I 248 " --> pdb=" O GLU3I 266 " (cutoff:3.500A) removed outlier: 6.808A pdb=" N GLU3I 266 " --> pdb=" O GLY3I 248 " (cutoff:3.500A) removed outlier: 7.368A pdb=" N PHE3I 265 " --> pdb=" O GLY3I 283 " (cutoff:3.500A) removed outlier: 4.261A pdb=" N GLY3I 283 " --> pdb=" O PHE3I 265 " (cutoff:3.500A) removed outlier: 6.216A pdb=" N HIS3I 271 " --> pdb=" O GLU3I 277 " (cutoff:3.500A) removed outlier: 5.357A pdb=" N GLU3I 277 " --> pdb=" O HIS3I 271 " (cutoff:3.500A) Processing sheet with id=AJ4, first strand: chain '3K' and resid 180 through 181 Processing sheet with id=AJ5, first strand: chain '3M' and resid 291 through 293 removed outlier: 7.307A pdb=" N TYR3M 322 " --> pdb=" O SER3M 335 " (cutoff:3.500A) Processing sheet with id=AJ6, first strand: chain '3N' and resid 169 through 175 removed outlier: 7.011A pdb=" N VAL3N 519 " --> pdb=" O LYS3N 171 " (cutoff:3.500A) removed outlier: 5.193A pdb=" N GLU3N 173 " --> pdb=" O ILE3N 517 " (cutoff:3.500A) removed outlier: 7.351A pdb=" N ILE3N 517 " --> pdb=" O GLU3N 173 " (cutoff:3.500A) removed outlier: 4.036A pdb=" N LYS3N 505 " --> pdb=" O LEU3N 522 " (cutoff:3.500A) removed outlier: 3.650A pdb=" N VAL3N 272 " --> pdb=" O LYS3N 275 " (cutoff:3.500A) removed outlier: 7.528A pdb=" N PHE3N 246 " --> pdb=" O PHE3N 278 " (cutoff:3.500A) removed outlier: 4.029A pdb=" N VAL3N 373 " --> pdb=" O ARG3N 361 " (cutoff:3.500A) removed outlier: 3.584A pdb=" N ARG3N 361 " --> pdb=" O VAL3N 373 " (cutoff:3.500A) removed outlier: 5.951A pdb=" N ARG3N 362 " --> pdb=" O ASP3N 192 " (cutoff:3.500A) removed outlier: 5.809A pdb=" N ASP3N 192 " --> pdb=" O ARG3N 362 " (cutoff:3.500A) Processing sheet with id=AJ7, first strand: chain '3N' and resid 215 through 216 removed outlier: 3.669A pdb=" N LYS3N 215 " --> pdb=" O ILE3N 465 " (cutoff:3.500A) removed outlier: 6.606A pdb=" N TYR3N 451 " --> pdb=" O LEU3N 466 " (cutoff:3.500A) removed outlier: 4.168A pdb=" N THR3N 468 " --> pdb=" O LEU3N 449 " (cutoff:3.500A) removed outlier: 6.342A pdb=" N LEU3N 449 " --> pdb=" O THR3N 468 " (cutoff:3.500A) removed outlier: 4.380A pdb=" N GLN3N 470 " --> pdb=" O LEU3N 447 " (cutoff:3.500A) removed outlier: 6.615A pdb=" N LEU3N 447 " --> pdb=" O GLN3N 470 " (cutoff:3.500A) removed outlier: 8.780A pdb=" N TYR3N 446 " --> pdb=" O VAL3N 388 " (cutoff:3.500A) removed outlier: 6.417A pdb=" N PHE3N 390 " --> pdb=" O TYR3N 446 " (cutoff:3.500A) removed outlier: 7.717A pdb=" N LYS3N 448 " --> pdb=" O PHE3N 390 " (cutoff:3.500A) removed outlier: 6.444A pdb=" N ASN3N 392 " --> pdb=" O LYS3N 448 " (cutoff:3.500A) removed outlier: 7.711A pdb=" N GLY3N 450 " --> pdb=" O ASN3N 392 " (cutoff:3.500A) removed outlier: 7.117A pdb=" N LYS3N 394 " --> pdb=" O GLY3N 450 " (cutoff:3.500A) removed outlier: 7.800A pdb=" N VAL3N 452 " --> pdb=" O LYS3N 394 " (cutoff:3.500A) removed outlier: 6.231A pdb=" N LEU3N 396 " --> pdb=" O VAL3N 452 " (cutoff:3.500A) removed outlier: 8.041A pdb=" N ARG3N 454 " --> pdb=" O LEU3N 396 " (cutoff:3.500A) removed outlier: 7.153A pdb=" N GLU3N 398 " --> pdb=" O ARG3N 454 " (cutoff:3.500A) 4125 hydrogen bonds defined for protein. 11988 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 1261 hydrogen bonds 1974 hydrogen bond angles 0 basepair planarities 509 basepair parallelities 865 stacking parallelities Total time for adding SS restraints: 76.71 Time building geometry restraints manager: 40.40 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.33: 20958 1.33 - 1.46: 41486 1.46 - 1.59: 53799 1.59 - 1.71: 3262 1.71 - 1.84: 576 Bond restraints: 120081 Sorted by residual: bond pdb=" C VALSH 66 " pdb=" N PROSH 67 " ideal model delta sigma weight residual 1.335 1.392 -0.057 1.19e-02 7.06e+03 2.29e+01 bond pdb=" CA SERCD 106 " pdb=" CB SERCD 106 " ideal model delta sigma weight residual 1.525 1.470 0.054 1.25e-02 6.40e+03 1.88e+01 bond pdb=" CA ARG3B 548 " pdb=" CB ARG3B 548 " ideal model delta sigma weight residual 1.526 1.598 -0.072 1.76e-02 3.23e+03 1.68e+01 bond pdb=" C VAL3A 428 " pdb=" N PRO3A 429 " ideal model delta sigma weight residual 1.336 1.384 -0.048 1.23e-02 6.61e+03 1.54e+01 bond pdb=" C ILECD 412 " pdb=" N PROCD 413 " ideal model delta sigma weight residual 1.335 1.388 -0.053 1.36e-02 5.41e+03 1.50e+01 ... (remaining 120076 not shown) Histogram of bond angle deviations from ideal: 93.33 - 102.16: 2111 102.16 - 111.00: 52638 111.00 - 119.84: 63680 119.84 - 128.68: 49788 128.68 - 137.52: 2362 Bond angle restraints: 170579 Sorted by residual: angle pdb=" N GLYSF 54 " pdb=" CA GLYSF 54 " pdb=" C GLYSF 54 " ideal model delta sigma weight residual 112.50 121.44 -8.94 1.16e+00 7.43e-01 5.93e+01 angle pdb=" C PRO3L 379 " pdb=" N MET3L 380 " pdb=" CA MET3L 380 " ideal model delta sigma weight residual 121.70 135.09 -13.39 1.80e+00 3.09e-01 5.53e+01 angle pdb=" C ARG3L 400 " pdb=" N MET3L 401 " pdb=" CA MET3L 401 " ideal model delta sigma weight residual 122.11 110.17 11.94 1.64e+00 3.72e-01 5.30e+01 angle pdb=" C SERSg 124 " pdb=" N ARGSg 125 " pdb=" CA ARGSg 125 " ideal model delta sigma weight residual 120.60 132.05 -11.45 1.60e+00 3.91e-01 5.12e+01 angle pdb=" CA ASP3M 114 " pdb=" C ASP3M 114 " pdb=" O ASP3M 114 " ideal model delta sigma weight residual 120.51 110.49 10.02 1.43e+00 4.89e-01 4.91e+01 ... (remaining 170574 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.66: 69839 35.66 - 71.33: 4844 71.33 - 106.99: 584 106.99 - 142.66: 11 142.66 - 178.32: 17 Dihedral angle restraints: 75295 sinusoidal: 45393 harmonic: 29902 Sorted by residual: dihedral pdb=" CA ALASX 126 " pdb=" C ALASX 126 " pdb=" N ASNSX 127 " pdb=" CA ASNSX 127 " ideal model delta harmonic sigma weight residual -180.00 -120.25 -59.75 0 5.00e+00 4.00e-02 1.43e+02 dihedral pdb=" CA HIS3L 432 " pdb=" C HIS3L 432 " pdb=" N PRO3L 433 " pdb=" CA PRO3L 433 " ideal model delta harmonic sigma weight residual 180.00 125.45 54.55 0 5.00e+00 4.00e-02 1.19e+02 dihedral pdb=" CA ASNSZ 46 " pdb=" C ASNSZ 46 " pdb=" N LEUSZ 47 " pdb=" CA LEUSZ 47 " ideal model delta harmonic sigma weight residual 180.00 130.05 49.95 0 5.00e+00 4.00e-02 9.98e+01 ... (remaining 75292 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.093: 18783 0.093 - 0.186: 1756 0.186 - 0.279: 132 0.279 - 0.371: 15 0.371 - 0.464: 2 Chirality restraints: 20688 Sorted by residual: chirality pdb=" CB ILESQ 32 " pdb=" CA ILESQ 32 " pdb=" CG1 ILESQ 32 " pdb=" CG2 ILESQ 32 " both_signs ideal model delta sigma weight residual False 2.64 2.18 0.46 2.00e-01 2.50e+01 5.39e+00 chirality pdb=" CB ILE3C 424 " pdb=" CA ILE3C 424 " pdb=" CG1 ILE3C 424 " pdb=" CG2 ILE3C 424 " both_signs ideal model delta sigma weight residual False 2.64 2.22 0.43 2.00e-01 2.50e+01 4.58e+00 chirality pdb=" CB THRSC 64 " pdb=" CA THRSC 64 " pdb=" OG1 THRSC 64 " pdb=" CG2 THRSC 64 " both_signs ideal model delta sigma weight residual False 2.55 2.20 0.35 2.00e-01 2.50e+01 3.12e+00 ... (remaining 20685 not shown) Planarity restraints: 15553 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TRP3N 435 " 0.043 2.00e-02 2.50e+03 4.51e-02 5.09e+01 pdb=" CG TRP3N 435 " -0.117 2.00e-02 2.50e+03 pdb=" CD1 TRP3N 435 " 0.064 2.00e-02 2.50e+03 pdb=" CD2 TRP3N 435 " 0.003 2.00e-02 2.50e+03 pdb=" NE1 TRP3N 435 " -0.014 2.00e-02 2.50e+03 pdb=" CE2 TRP3N 435 " 0.009 2.00e-02 2.50e+03 pdb=" CE3 TRP3N 435 " 0.005 2.00e-02 2.50e+03 pdb=" CZ2 TRP3N 435 " -0.012 2.00e-02 2.50e+03 pdb=" CZ3 TRP3N 435 " 0.003 2.00e-02 2.50e+03 pdb=" CH2 TRP3N 435 " 0.016 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C HIS3L 432 " -0.089 5.00e-02 4.00e+02 1.36e-01 2.94e+01 pdb=" N PRO3L 433 " 0.234 5.00e-02 4.00e+02 pdb=" CA PRO3L 433 " -0.074 5.00e-02 4.00e+02 pdb=" CD PRO3L 433 " -0.071 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ARGSP 130 " 0.087 5.00e-02 4.00e+02 1.29e-01 2.66e+01 pdb=" N PROSP 131 " -0.223 5.00e-02 4.00e+02 pdb=" CA PROSP 131 " 0.070 5.00e-02 4.00e+02 pdb=" CD PROSP 131 " 0.067 5.00e-02 4.00e+02 ... (remaining 15550 not shown) Histogram of nonbonded interaction distances: 2.06 - 2.63: 2207 2.63 - 3.20: 94964 3.20 - 3.77: 204995 3.77 - 4.33: 267205 4.33 - 4.90: 396885 Nonbonded interactions: 966256 Sorted by model distance: nonbonded pdb=" O2' CS21331 " pdb=" OP2 AS21332 " model vdw 2.065 2.440 nonbonded pdb=" OP2 GS21167 " pdb="MG MGS21914 " model vdw 2.076 2.170 nonbonded pdb=" OP1 US21072 " pdb="MG MGS21920 " model vdw 2.085 2.170 nonbonded pdb=" OP1 GS21837 " pdb="MG MGS21917 " model vdw 2.095 2.170 nonbonded pdb=" OP2 AS2 653 " pdb="MG MGS21910 " model vdw 2.099 2.170 ... (remaining 966251 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=0.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.010 Normalize map: mean=0, sd=1: 3.170 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: 0.100 Extract box with map and model: 17.960 Check model and map are aligned: 0.670 Set scattering table: 0.750 Process input model: 286.100 Find NCS groups from input model: 2.990 Set up NCS constraints: 0.290 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:2.440 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 314.500 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7155 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 : 0.006 0.093 120081 Z= 0.358 Angle : 1.034 15.226 170579 Z= 0.554 Chirality : 0.055 0.464 20688 Planarity : 0.008 0.140 15553 Dihedral : 20.664 178.323 55903 Min Nonbonded Distance : 2.065 Molprobity Statistics. All-atom Clashscore : 7.29 Ramachandran Plot: Outliers : 0.14 % Allowed : 7.17 % Favored : 92.70 % Rotamer: Outliers : 0.17 % Allowed : 0.55 % Favored : 99.28 % Cbeta Deviations : 0.01 % Peptide Plane: Cis-proline : 1.08 % Cis-general : 0.17 % Twisted Proline : 0.54 % Twisted General : 0.15 % 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: -1.97 (0.08), residues: 10145 helix: -0.44 (0.07), residues: 4515 sheet: -1.09 (0.13), residues: 1499 loop : -2.34 (0.09), residues: 4131 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.117 0.003 TRP3N 435 HIS 0.036 0.002 HIS3L 432 PHE 0.063 0.003 PHESd 14 TYR 0.043 0.002 TYRSX 134 ARG 0.023 0.001 ARG3B 505 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 20290 Ramachandran restraints generated. 10145 Oldfield, 0 Emsley, 10145 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 20290 Ramachandran restraints generated. 10145 Oldfield, 0 Emsley, 10145 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1526 residues out of total 9059 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 1513 time to evaluate : 7.468 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: Ln 9 ARG cc_start: 0.6678 (mtp85) cc_final: 0.5846 (ttp-170) REVERT: SH 39 GLN cc_start: 0.7156 (tm-30) cc_final: 0.6923 (tm-30) REVERT: SK 14 LEU cc_start: 0.7843 (tp) cc_final: 0.7535 (tp) REVERT: SK 38 LYS cc_start: 0.8068 (mtpt) cc_final: 0.7835 (mtpp) REVERT: SK 89 ILE cc_start: 0.8561 (tp) cc_final: 0.8296 (tp) REVERT: SL 42 LEU cc_start: 0.8748 (mt) cc_final: 0.8482 (mt) REVERT: SP 93 MET cc_start: 0.7977 (tpp) cc_final: 0.7720 (mmm) REVERT: SP 124 LYS cc_start: 0.8231 (mmtt) cc_final: 0.7988 (tttp) REVERT: SQ 87 SER cc_start: 0.8007 (t) cc_final: 0.7306 (p) REVERT: SS 40 TYR cc_start: 0.7995 (t80) cc_final: 0.7657 (t80) REVERT: SS 44 VAL cc_start: 0.8633 (p) cc_final: 0.8271 (p) REVERT: SU 46 LYS cc_start: 0.7864 (mmmm) cc_final: 0.7585 (ptpp) REVERT: SV 1 MET cc_start: 0.7648 (ppp) cc_final: 0.7079 (ptt) REVERT: SV 11 LEU cc_start: 0.7826 (mp) cc_final: 0.7550 (mt) REVERT: SX 95 GLU cc_start: 0.4711 (pm20) cc_final: 0.3878 (mp0) REVERT: Sd 7 TYR cc_start: 0.8528 (t80) cc_final: 0.8210 (t80) REVERT: SG 32 MET cc_start: 0.7632 (ppp) cc_final: 0.7317 (ppp) REVERT: SG 101 ILE cc_start: 0.7638 (mm) cc_final: 0.7393 (mm) REVERT: SG 126 ASP cc_start: 0.7678 (p0) cc_final: 0.7150 (p0) REVERT: SJ 144 ILE cc_start: 0.8317 (mm) cc_final: 0.7962 (mm) REVERT: Sf 137 ASP cc_start: 0.6376 (p0) cc_final: 0.6109 (p0) REVERT: 3A 12 LEU cc_start: 0.8625 (tp) cc_final: 0.8220 (tp) REVERT: 3B 511 ASN cc_start: 0.4576 (t0) cc_final: 0.4007 (p0) REVERT: 3B 544 PHE cc_start: 0.3258 (m-80) cc_final: 0.2106 (m-80) REVERT: 3K 174 MET cc_start: -0.0635 (tpp) cc_final: -0.0975 (tpt) REVERT: 3L 268 MET cc_start: -0.2131 (ptt) cc_final: -0.3173 (ptt) REVERT: 3L 304 MET cc_start: -0.1270 (ptt) cc_final: -0.2202 (ptt) REVERT: 3L 367 MET cc_start: 0.1967 (ptm) cc_final: 0.1587 (ptt) REVERT: 3N 413 LEU cc_start: 0.7668 (pp) cc_final: 0.7458 (tp) outliers start: 13 outliers final: 6 residues processed: 1522 average time/residue: 1.0005 time to fit residues: 2615.7047 Evaluate side-chains 1244 residues out of total 9059 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 1238 time to evaluate : 7.427 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain SI residue 7 ASN Chi-restraints excluded: chain SL residue 18 GLN Chi-restraints excluded: chain SR residue 26 ASN Chi-restraints excluded: chain SO residue 68 GLU Chi-restraints excluded: chain SO residue 105 THR Chi-restraints excluded: chain 3B residue 497 GLN Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1181 random chunks: chunk 997 optimal weight: 20.0000 chunk 895 optimal weight: 3.9990 chunk 496 optimal weight: 5.9990 chunk 305 optimal weight: 0.8980 chunk 603 optimal weight: 0.6980 chunk 478 optimal weight: 5.9990 chunk 925 optimal weight: 30.0000 chunk 358 optimal weight: 0.5980 chunk 562 optimal weight: 0.9990 chunk 688 optimal weight: 50.0000 chunk 1072 optimal weight: 30.0000 overall best weight: 1.4384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: SB 75 GLN SB 95 ASN SD 101 GLN SE 157 ASN ** SF 36 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** SF 110 GLN ** SF 203 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** SH 44 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** SK 7 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** SK 66 HIS SQ 80 GLN SQ 114 GLN SR 93 GLN SR 127 ASN ** SS 72 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** SS 85 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** SS 97 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** SU 47 ASN ** SV 35 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Sg 20 GLN ** Sg 104 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** SC 267 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** SG 65 GLN ** SG 155 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** SJ 154 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** SM 73 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** SN 36 GLN SW 64 ASN SY 94 HIS SZ 89 GLN ** Sb 83 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Se 3 HIS 3A 25 GLN ** 3A 175 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 3A 229 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 3A 270 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 3A 512 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 3A 588 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 3B 477 ASN 3B 518 HIS 3C 62 ASN 3C 69 ASN 3C 365 ASN ** 3C 637 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 3C 670 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 3C 869 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 3F 332 ASN 3G 307 HIS 3G 311 ASN 3H 238 HIS ** 3H 261 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 3K 62 GLN 3K 119 GLN ** 3L 364 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 3L 432 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 3L 436 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** 3L 495 HIS ** 3M 199 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 3M 205 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 3M 366 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 3N 31 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 3N 322 ASN ** 3N 469 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 3N 479 GLN Total number of N/Q/H flips: 33 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7149 moved from start: 0.1016 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.052 120081 Z= 0.209 Angle : 0.676 15.361 170579 Z= 0.348 Chirality : 0.042 0.326 20688 Planarity : 0.005 0.122 15553 Dihedral : 21.582 179.725 37957 Min Nonbonded Distance : 1.961 Molprobity Statistics. All-atom Clashscore : 12.00 Ramachandran Plot: Outliers : 0.13 % Allowed : 6.12 % Favored : 93.75 % Rotamer: Outliers : 1.54 % Allowed : 10.37 % Favored : 88.09 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.08 % Cis-general : 0.17 % Twisted Proline : 0.54 % Twisted General : 0.06 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.31 (0.08), residues: 10145 helix: 0.28 (0.08), residues: 4549 sheet: -0.81 (0.13), residues: 1505 loop : -2.22 (0.09), residues: 4091 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.037 0.002 TRP3N 435 HIS 0.018 0.001 HIS3L 432 PHE 0.031 0.002 PHE3L 493 TYR 0.027 0.001 TYR3N 451 ARG 0.010 0.000 ARGSQ 71 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 20290 Ramachandran restraints generated. 10145 Oldfield, 0 Emsley, 10145 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 20290 Ramachandran restraints generated. 10145 Oldfield, 0 Emsley, 10145 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1434 residues out of total 9059 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 118 poor density : 1316 time to evaluate : 7.507 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: Ln 9 ARG cc_start: 0.6621 (mtp85) cc_final: 0.5828 (ttp-170) REVERT: SB 177 GLN cc_start: 0.7751 (tp40) cc_final: 0.7510 (mm-40) REVERT: SD 128 GLU cc_start: 0.6956 (OUTLIER) cc_final: 0.6465 (pm20) REVERT: SH 72 PHE cc_start: 0.6854 (m-80) cc_final: 0.6587 (m-80) REVERT: SK 89 ILE cc_start: 0.8492 (tp) cc_final: 0.8204 (tp) REVERT: SQ 87 SER cc_start: 0.7995 (t) cc_final: 0.7282 (p) REVERT: SQ 114 GLN cc_start: 0.7509 (OUTLIER) cc_final: 0.7273 (pt0) REVERT: SR 58 MET cc_start: 0.7499 (mtp) cc_final: 0.7282 (mmm) REVERT: SS 54 LYS cc_start: 0.7336 (ptmt) cc_final: 0.7080 (ptmt) REVERT: SS 116 LYS cc_start: 0.8263 (tttt) cc_final: 0.7974 (tppt) REVERT: ST 79 TYR cc_start: 0.7631 (m-80) cc_final: 0.7234 (m-80) REVERT: SU 34 LYS cc_start: 0.7884 (pptt) cc_final: 0.7576 (pttt) REVERT: SU 47 ASN cc_start: 0.6283 (p0) cc_final: 0.6016 (p0) REVERT: SV 1 MET cc_start: 0.7722 (ppp) cc_final: 0.7206 (ptt) REVERT: SX 61 GLN cc_start: 0.7042 (tp40) cc_final: 0.6721 (tt0) REVERT: Sd 7 TYR cc_start: 0.8563 (t80) cc_final: 0.8264 (t80) REVERT: SC 254 ASP cc_start: 0.8052 (p0) cc_final: 0.7850 (p0) REVERT: SG 32 MET cc_start: 0.7609 (ppp) cc_final: 0.6922 (ppp) REVERT: SG 126 ASP cc_start: 0.7805 (p0) cc_final: 0.7159 (p0) REVERT: SJ 154 GLN cc_start: 0.8413 (tm-30) cc_final: 0.8212 (tt0) REVERT: SM 19 GLN cc_start: 0.6945 (tp40) cc_final: 0.5967 (mm110) REVERT: SW 106 THR cc_start: 0.9240 (OUTLIER) cc_final: 0.8982 (p) REVERT: Sf 137 ASP cc_start: 0.6460 (p0) cc_final: 0.6039 (p0) REVERT: 3A 12 LEU cc_start: 0.8597 (tp) cc_final: 0.8294 (tp) REVERT: 3B 482 TRP cc_start: 0.6002 (p-90) cc_final: 0.5734 (p-90) REVERT: 3B 505 ARG cc_start: 0.4682 (mtm-85) cc_final: 0.4216 (mtm110) REVERT: 3B 511 ASN cc_start: 0.4862 (t0) cc_final: 0.4074 (p0) REVERT: 3B 526 LEU cc_start: 0.2758 (tp) cc_final: 0.2284 (tp) REVERT: 3B 551 GLU cc_start: 0.1348 (mp0) cc_final: 0.1008 (mp0) REVERT: 3E 94 MET cc_start: 0.6163 (tpp) cc_final: 0.5673 (tpt) REVERT: 3G 292 ASP cc_start: 0.3241 (t0) cc_final: 0.0960 (t0) REVERT: 3K 3 MET cc_start: 0.1559 (tmm) cc_final: 0.1207 (tmm) REVERT: 3K 174 MET cc_start: -0.0709 (tpp) cc_final: -0.1032 (tpt) REVERT: 3L 268 MET cc_start: -0.2162 (ptt) cc_final: -0.3275 (ptt) REVERT: 3L 304 MET cc_start: -0.1025 (ptt) cc_final: -0.2055 (ptt) outliers start: 118 outliers final: 81 residues processed: 1370 average time/residue: 1.0317 time to fit residues: 2439.0213 Evaluate side-chains 1307 residues out of total 9059 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 84 poor density : 1223 time to evaluate : 7.405 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain SB residue 66 VAL Chi-restraints excluded: chain SB residue 228 LEU Chi-restraints excluded: chain SD residue 91 VAL Chi-restraints excluded: chain SD residue 128 GLU Chi-restraints excluded: chain SD residue 170 THR Chi-restraints excluded: chain SF residue 110 GLN Chi-restraints excluded: chain SF residue 165 ASN Chi-restraints excluded: chain SF residue 182 LYS Chi-restraints excluded: chain SH residue 105 THR Chi-restraints excluded: chain SI residue 69 SER Chi-restraints excluded: chain SI residue 144 LYS Chi-restraints excluded: chain SK residue 52 LEU Chi-restraints excluded: chain SK residue 79 LEU Chi-restraints excluded: chain SL residue 146 THR Chi-restraints excluded: chain SP residue 29 SER Chi-restraints excluded: chain SQ residue 10 VAL Chi-restraints excluded: chain SQ residue 20 THR Chi-restraints excluded: chain SQ residue 22 VAL Chi-restraints excluded: chain SQ residue 114 GLN Chi-restraints excluded: chain SR residue 26 ASN Chi-restraints excluded: chain SR residue 71 ILE Chi-restraints excluded: chain SR residue 93 GLN Chi-restraints excluded: chain SR residue 123 THR Chi-restraints excluded: chain SS residue 53 THR Chi-restraints excluded: chain SS residue 67 VAL Chi-restraints excluded: chain SS residue 81 ASP Chi-restraints excluded: chain SS residue 103 LEU Chi-restraints excluded: chain SS residue 131 VAL Chi-restraints excluded: chain ST residue 9 VAL Chi-restraints excluded: chain ST residue 55 THR Chi-restraints excluded: chain ST residue 74 SER Chi-restraints excluded: chain ST residue 76 THR Chi-restraints excluded: chain SU residue 23 THR Chi-restraints excluded: chain SU residue 25 THR Chi-restraints excluded: chain SV residue 13 VAL Chi-restraints excluded: chain SX residue 131 LEU Chi-restraints excluded: chain Sa residue 63 VAL Chi-restraints excluded: chain Sc residue 28 THR Chi-restraints excluded: chain Sc residue 34 PHE Chi-restraints excluded: chain Sc residue 46 VAL Chi-restraints excluded: chain Sg residue 197 THR Chi-restraints excluded: chain SC residue 91 SER Chi-restraints excluded: chain SG residue 5 ILE Chi-restraints excluded: chain SG residue 110 ASN Chi-restraints excluded: chain SG residue 176 ILE Chi-restraints excluded: chain SG residue 217 MET Chi-restraints excluded: chain SJ residue 61 LEU Chi-restraints excluded: chain SJ residue 62 THR Chi-restraints excluded: chain SJ residue 114 VAL Chi-restraints excluded: chain SJ residue 153 SER Chi-restraints excluded: chain SM residue 42 LEU Chi-restraints excluded: chain SM residue 76 LEU Chi-restraints excluded: chain SN residue 22 VAL Chi-restraints excluded: chain SN residue 31 ASP Chi-restraints excluded: chain SN residue 46 THR Chi-restraints excluded: chain SN residue 131 THR Chi-restraints excluded: chain SO residue 65 ASP Chi-restraints excluded: chain SO residue 105 THR Chi-restraints excluded: chain SW residue 85 ASP Chi-restraints excluded: chain SW residue 106 THR Chi-restraints excluded: chain SY residue 34 THR Chi-restraints excluded: chain SY residue 40 ILE Chi-restraints excluded: chain SY residue 97 TYR Chi-restraints excluded: chain SZ residue 69 THR Chi-restraints excluded: chain SZ residue 89 GLN Chi-restraints excluded: chain 3A residue 197 LEU Chi-restraints excluded: chain 3A residue 230 LEU Chi-restraints excluded: chain 3A residue 498 ASN Chi-restraints excluded: chain 3B residue 497 GLN Chi-restraints excluded: chain 3B residue 517 LEU Chi-restraints excluded: chain 3B residue 541 VAL Chi-restraints excluded: chain 3C residue 77 THR Chi-restraints excluded: chain 3C residue 468 GLU Chi-restraints excluded: chain 3C residue 596 ASP Chi-restraints excluded: chain 3C residue 597 ASN Chi-restraints excluded: chain 3C residue 689 SER Chi-restraints excluded: chain 3C residue 788 LEU Chi-restraints excluded: chain 3C residue 799 TYR Chi-restraints excluded: chain 3E residue 50 MET Chi-restraints excluded: chain 3E residue 201 VAL Chi-restraints excluded: chain 3G residue 272 LYS Chi-restraints excluded: chain 3G residue 297 ILE Chi-restraints excluded: chain 3M residue 282 PHE Chi-restraints excluded: chain 3N residue 451 TYR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1181 random chunks: chunk 596 optimal weight: 10.0000 chunk 332 optimal weight: 0.0070 chunk 892 optimal weight: 7.9990 chunk 730 optimal weight: 1.9990 chunk 295 optimal weight: 3.9990 chunk 1074 optimal weight: 40.0000 chunk 1160 optimal weight: 20.0000 chunk 956 optimal weight: 50.0000 chunk 1065 optimal weight: 0.8980 chunk 366 optimal weight: 4.9990 chunk 861 optimal weight: 4.9990 overall best weight: 2.3804 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** SD 57 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** SE 157 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** SF 36 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** SF 110 GLN ** SF 203 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** SH 33 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** SH 44 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** SH 68 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** SI 7 ASN ** SK 7 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** SP 46 ASN SQ 80 GLN SR 93 GLN SR 127 ASN ** SS 72 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** SS 85 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** SS 97 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ST 91 HIS ** ST 126 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** SV 35 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** SX 16 HIS SX 87 ASN ** Sg 104 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** SC 267 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** SG 155 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** SJ 154 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** SM 72 HIS ** SM 73 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** SN 36 GLN ** SN 49 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** SO 83 GLN SW 56 HIS SY 94 HIS Sb 49 HIS Sb 65 GLN ** Sb 83 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Se 3 HIS ** 3A 270 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 3B 477 ASN 3B 518 HIS 3B 520 GLN ** 3C 630 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 3C 637 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 3C 670 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 3C 845 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 3C 869 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 3H 261 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 3L 225 HIS 3L 241 ASN 3L 296 ASN ** 3L 364 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 3L 436 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 3M 199 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 3M 205 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 3N 242 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 3N 322 ASN 3N 469 GLN Total number of N/Q/H flips: 25 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7193 moved from start: 0.1340 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.054 120081 Z= 0.275 Angle : 0.691 17.061 170579 Z= 0.353 Chirality : 0.043 0.334 20688 Planarity : 0.005 0.115 15553 Dihedral : 21.482 179.864 37949 Min Nonbonded Distance : 1.922 Molprobity Statistics. All-atom Clashscore : 11.93 Ramachandran Plot: Outliers : 0.13 % Allowed : 6.55 % Favored : 93.32 % Rotamer: Outliers : 2.49 % Allowed : 14.42 % Favored : 83.09 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.08 % Cis-general : 0.17 % Twisted Proline : 0.54 % Twisted General : 0.04 % 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: -1.05 (0.08), residues: 10145 helix: 0.58 (0.08), residues: 4540 sheet: -0.82 (0.13), residues: 1513 loop : -2.12 (0.09), residues: 4092 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.056 0.002 TRP3A 393 HIS 0.012 0.001 HIS3L 432 PHE 0.024 0.002 PHESJ 147 TYR 0.026 0.002 TYRSC 248 ARG 0.010 0.001 ARG3G 260 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 20290 Ramachandran restraints generated. 10145 Oldfield, 0 Emsley, 10145 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 20290 Ramachandran restraints generated. 10145 Oldfield, 0 Emsley, 10145 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1492 residues out of total 9059 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 191 poor density : 1301 time to evaluate : 7.664 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: Ln 9 ARG cc_start: 0.6554 (mtp85) cc_final: 0.5641 (ttp-170) REVERT: SA 158 ASP cc_start: 0.6630 (m-30) cc_final: 0.6402 (m-30) REVERT: SB 172 MET cc_start: 0.8562 (mtm) cc_final: 0.8361 (mtm) REVERT: SD 103 GLU cc_start: 0.6915 (OUTLIER) cc_final: 0.6317 (mt-10) REVERT: SD 128 GLU cc_start: 0.7073 (OUTLIER) cc_final: 0.6736 (pm20) REVERT: SQ 87 SER cc_start: 0.7967 (t) cc_final: 0.7226 (p) REVERT: SR 26 ASN cc_start: 0.8261 (OUTLIER) cc_final: 0.8030 (t0) REVERT: SR 38 ILE cc_start: 0.7101 (pt) cc_final: 0.6884 (pt) REVERT: SR 69 ILE cc_start: 0.6986 (tp) cc_final: 0.6607 (tp) REVERT: SS 116 LYS cc_start: 0.8380 (tttt) cc_final: 0.8167 (tppt) REVERT: ST 79 TYR cc_start: 0.7681 (m-80) cc_final: 0.7327 (m-80) REVERT: SU 34 LYS cc_start: 0.7861 (pptt) cc_final: 0.7532 (pttt) REVERT: SV 1 MET cc_start: 0.7753 (ppp) cc_final: 0.7222 (ptt) REVERT: Sa 46 GLU cc_start: 0.8274 (OUTLIER) cc_final: 0.7919 (pt0) REVERT: Sa 52 ASP cc_start: 0.7938 (p0) cc_final: 0.7661 (p0) REVERT: Sc 13 ARG cc_start: 0.7359 (ttm-80) cc_final: 0.6909 (ttm-80) REVERT: Sc 44 ARG cc_start: 0.7715 (mmm-85) cc_final: 0.7262 (mmm160) REVERT: Sd 7 TYR cc_start: 0.8566 (t80) cc_final: 0.8345 (t80) REVERT: SC 254 ASP cc_start: 0.8092 (p0) cc_final: 0.7651 (p0) REVERT: SG 126 ASP cc_start: 0.7952 (p0) cc_final: 0.7265 (p0) REVERT: SJ 154 GLN cc_start: 0.8551 (tm-30) cc_final: 0.8283 (tt0) REVERT: SY 39 GLU cc_start: 0.7940 (pm20) cc_final: 0.7728 (pm20) REVERT: Sf 137 ASP cc_start: 0.6540 (p0) cc_final: 0.6076 (p0) REVERT: CD 142 ASN cc_start: 0.7950 (OUTLIER) cc_final: 0.7050 (m110) REVERT: CD 143 TYR cc_start: 0.7634 (t80) cc_final: 0.7372 (t80) REVERT: 3A 12 LEU cc_start: 0.8647 (tp) cc_final: 0.8423 (tp) REVERT: 3B 482 TRP cc_start: 0.6354 (p-90) cc_final: 0.5759 (p-90) REVERT: 3B 501 ARG cc_start: -0.0962 (mmt180) cc_final: -0.1393 (mpt180) REVERT: 3B 526 LEU cc_start: 0.3239 (tp) cc_final: 0.2760 (tp) REVERT: 3B 544 PHE cc_start: 0.3578 (OUTLIER) cc_final: 0.2536 (m-10) REVERT: 3B 551 GLU cc_start: 0.1358 (mp0) cc_final: 0.1075 (mp0) REVERT: 3C 551 LEU cc_start: 0.8045 (OUTLIER) cc_final: 0.7839 (mt) REVERT: 3C 778 MET cc_start: 0.6156 (mmm) cc_final: 0.5259 (mmm) REVERT: 3K 7 MET cc_start: -0.3994 (ptp) cc_final: -0.4601 (mmt) REVERT: 3K 174 MET cc_start: -0.0814 (tpp) cc_final: -0.1032 (tpt) REVERT: 3L 268 MET cc_start: -0.2164 (ptt) cc_final: -0.3221 (ptt) REVERT: 3L 304 MET cc_start: -0.1003 (ptt) cc_final: -0.2089 (ptt) REVERT: 3L 326 MET cc_start: 0.0830 (ppp) cc_final: 0.0529 (ppp) REVERT: 3N 212 ARG cc_start: 0.4175 (mtm180) cc_final: 0.3970 (mtm180) outliers start: 191 outliers final: 118 residues processed: 1399 average time/residue: 0.9608 time to fit residues: 2324.2239 Evaluate side-chains 1335 residues out of total 9059 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 125 poor density : 1210 time to evaluate : 7.442 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain SA residue 43 SER Chi-restraints excluded: chain SB residue 66 VAL Chi-restraints excluded: chain SB residue 88 THR Chi-restraints excluded: chain SB residue 228 LEU Chi-restraints excluded: chain SD residue 91 VAL Chi-restraints excluded: chain SD residue 103 GLU Chi-restraints excluded: chain SD residue 128 GLU Chi-restraints excluded: chain SD residue 170 THR Chi-restraints excluded: chain SE residue 89 VAL Chi-restraints excluded: chain SE residue 169 ILE Chi-restraints excluded: chain SF residue 69 VAL Chi-restraints excluded: chain SF residue 113 VAL Chi-restraints excluded: chain SF residue 165 ASN Chi-restraints excluded: chain SF residue 182 LYS Chi-restraints excluded: chain SH residue 25 GLN Chi-restraints excluded: chain SH residue 46 THR Chi-restraints excluded: chain SH residue 95 ILE Chi-restraints excluded: chain SH residue 105 THR Chi-restraints excluded: chain SI residue 91 VAL Chi-restraints excluded: chain SI residue 144 LYS Chi-restraints excluded: chain SK residue 52 LEU Chi-restraints excluded: chain SK residue 97 SER Chi-restraints excluded: chain SL residue 72 ILE Chi-restraints excluded: chain SL residue 146 THR Chi-restraints excluded: chain SP residue 46 ASN Chi-restraints excluded: chain SP residue 101 THR Chi-restraints excluded: chain SP residue 111 MET Chi-restraints excluded: chain SP residue 126 VAL Chi-restraints excluded: chain SQ residue 10 VAL Chi-restraints excluded: chain SQ residue 20 THR Chi-restraints excluded: chain SQ residue 22 VAL Chi-restraints excluded: chain SQ residue 32 ILE Chi-restraints excluded: chain SQ residue 56 LEU Chi-restraints excluded: chain SR residue 26 ASN Chi-restraints excluded: chain SR residue 71 ILE Chi-restraints excluded: chain SR residue 123 THR Chi-restraints excluded: chain SS residue 15 VAL Chi-restraints excluded: chain SS residue 44 VAL Chi-restraints excluded: chain SS residue 53 THR Chi-restraints excluded: chain SS residue 67 VAL Chi-restraints excluded: chain SS residue 68 ILE Chi-restraints excluded: chain SS residue 81 ASP Chi-restraints excluded: chain SS residue 89 ASP Chi-restraints excluded: chain SS residue 103 LEU Chi-restraints excluded: chain SS residue 117 ILE Chi-restraints excluded: chain SS residue 131 VAL Chi-restraints excluded: chain ST residue 9 VAL Chi-restraints excluded: chain ST residue 55 THR Chi-restraints excluded: chain ST residue 74 SER Chi-restraints excluded: chain ST residue 76 THR Chi-restraints excluded: chain SU residue 25 THR Chi-restraints excluded: chain SU residue 30 LYS Chi-restraints excluded: chain SU residue 40 ILE Chi-restraints excluded: chain SV residue 13 VAL Chi-restraints excluded: chain SX residue 53 GLU Chi-restraints excluded: chain SX residue 85 VAL Chi-restraints excluded: chain SX residue 131 LEU Chi-restraints excluded: chain Sa residue 46 GLU Chi-restraints excluded: chain Sa residue 63 VAL Chi-restraints excluded: chain Sc residue 11 LEU Chi-restraints excluded: chain Sc residue 28 THR Chi-restraints excluded: chain Sc residue 34 PHE Chi-restraints excluded: chain Sc residue 46 VAL Chi-restraints excluded: chain Sg residue 21 ILE Chi-restraints excluded: chain Sg residue 71 ILE Chi-restraints excluded: chain Sg residue 131 LEU Chi-restraints excluded: chain SC residue 91 SER Chi-restraints excluded: chain SC residue 104 ASP Chi-restraints excluded: chain SC residue 137 VAL Chi-restraints excluded: chain SG residue 110 ASN Chi-restraints excluded: chain SG residue 113 ILE Chi-restraints excluded: chain SG residue 163 ASN Chi-restraints excluded: chain SG residue 176 ILE Chi-restraints excluded: chain SJ residue 62 THR Chi-restraints excluded: chain SJ residue 112 THR Chi-restraints excluded: chain SJ residue 114 VAL Chi-restraints excluded: chain SJ residue 122 SER Chi-restraints excluded: chain SJ residue 153 SER Chi-restraints excluded: chain SM residue 42 LEU Chi-restraints excluded: chain SN residue 22 VAL Chi-restraints excluded: chain SN residue 46 THR Chi-restraints excluded: chain SN residue 131 THR Chi-restraints excluded: chain SO residue 36 SER Chi-restraints excluded: chain SO residue 66 ARG Chi-restraints excluded: chain SO residue 67 ASP Chi-restraints excluded: chain SO residue 68 GLU Chi-restraints excluded: chain SO residue 105 THR Chi-restraints excluded: chain SO residue 114 SER Chi-restraints excluded: chain SW residue 85 ASP Chi-restraints excluded: chain SY residue 34 THR Chi-restraints excluded: chain SY residue 40 ILE Chi-restraints excluded: chain SY residue 97 TYR Chi-restraints excluded: chain SZ residue 69 THR Chi-restraints excluded: chain SZ residue 76 ARG Chi-restraints excluded: chain CD residue 142 ASN Chi-restraints excluded: chain 3A residue 197 LEU Chi-restraints excluded: chain 3A residue 228 MET Chi-restraints excluded: chain 3A residue 230 LEU Chi-restraints excluded: chain 3A residue 278 LYS Chi-restraints excluded: chain 3A residue 498 ASN Chi-restraints excluded: chain 3B residue 517 LEU Chi-restraints excluded: chain 3B residue 541 VAL Chi-restraints excluded: chain 3B residue 544 PHE Chi-restraints excluded: chain 3C residue 76 VAL Chi-restraints excluded: chain 3C residue 77 THR Chi-restraints excluded: chain 3C residue 333 LEU Chi-restraints excluded: chain 3C residue 452 ASP Chi-restraints excluded: chain 3C residue 468 GLU Chi-restraints excluded: chain 3C residue 519 HIS Chi-restraints excluded: chain 3C residue 551 LEU Chi-restraints excluded: chain 3C residue 596 ASP Chi-restraints excluded: chain 3C residue 597 ASN Chi-restraints excluded: chain 3C residue 788 LEU Chi-restraints excluded: chain 3C residue 799 TYR Chi-restraints excluded: chain 3E residue 19 VAL Chi-restraints excluded: chain 3E residue 50 MET Chi-restraints excluded: chain 3E residue 187 GLU Chi-restraints excluded: chain 3E residue 201 VAL Chi-restraints excluded: chain 3G residue 244 THR Chi-restraints excluded: chain 3G residue 272 LYS Chi-restraints excluded: chain 3G residue 287 PHE Chi-restraints excluded: chain 3L residue 431 VAL Chi-restraints excluded: chain 3M residue 282 PHE Chi-restraints excluded: chain 3N residue 269 VAL Chi-restraints excluded: chain 3N residue 517 ILE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1181 random chunks: chunk 1061 optimal weight: 8.9990 chunk 807 optimal weight: 50.0000 chunk 557 optimal weight: 6.9990 chunk 118 optimal weight: 20.0000 chunk 512 optimal weight: 2.9990 chunk 721 optimal weight: 6.9990 chunk 1078 optimal weight: 50.0000 chunk 1141 optimal weight: 9.9990 chunk 563 optimal weight: 7.9990 chunk 1021 optimal weight: 5.9990 chunk 307 optimal weight: 5.9990 overall best weight: 5.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** SD 57 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** SE 157 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** SF 51 HIS SF 110 GLN ** SF 203 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** SH 114 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** SK 7 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** SP 53 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** SP 98 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** SQ 48 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** SQ 114 GLN SR 116 ASN SR 127 ASN ** SS 72 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** SS 85 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** SS 97 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Sg 104 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** SG 65 GLN ** SG 155 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** SJ 27 GLN ** SJ 154 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** SM 73 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** SN 36 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** SN 49 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Sb 83 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Se 3 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 3A 209 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 3A 270 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 3B 477 ASN ** 3B 518 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 3C 433 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 3C 465 HIS 3C 472 HIS ** 3C 600 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 3C 637 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 3C 670 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 3C 869 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 3E 373 ASN ** 3E 390 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 3H 261 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 3H 337 ASN ** 3L 364 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 3L 436 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 3M 199 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 3M 205 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 3N 242 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7297 moved from start: 0.1908 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.009 0.109 120081 Z= 0.584 Angle : 0.902 17.041 170579 Z= 0.451 Chirality : 0.053 0.342 20688 Planarity : 0.006 0.108 15553 Dihedral : 21.631 178.906 37946 Min Nonbonded Distance : 1.843 Molprobity Statistics. All-atom Clashscore : 15.02 Ramachandran Plot: Outliers : 0.15 % Allowed : 7.33 % Favored : 92.52 % Rotamer: Outliers : 3.92 % Allowed : 16.61 % Favored : 79.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.08 % Cis-general : 0.17 % Twisted Proline : 0.54 % Twisted General : 0.05 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.21 (0.08), residues: 10145 helix: 0.50 (0.08), residues: 4550 sheet: -1.00 (0.13), residues: 1548 loop : -2.25 (0.09), residues: 4047 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.070 0.003 TRP3A 393 HIS 0.015 0.002 HISSW 44 PHE 0.037 0.002 PHESJ 147 TYR 0.030 0.002 TYRSC 248 ARG 0.014 0.001 ARGSC 187 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 20290 Ramachandran restraints generated. 10145 Oldfield, 0 Emsley, 10145 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 20290 Ramachandran restraints generated. 10145 Oldfield, 0 Emsley, 10145 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1518 residues out of total 9059 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 300 poor density : 1218 time to evaluate : 7.606 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: Ln 9 ARG cc_start: 0.6638 (mtp85) cc_final: 0.5659 (ttp-170) REVERT: SA 158 ASP cc_start: 0.6745 (m-30) cc_final: 0.6429 (m-30) REVERT: SA 205 ARG cc_start: 0.6802 (OUTLIER) cc_final: 0.6199 (mtp-110) REVERT: SB 151 ARG cc_start: 0.8678 (OUTLIER) cc_final: 0.8251 (ptp-170) REVERT: SB 172 MET cc_start: 0.8668 (mtm) cc_final: 0.8235 (mtm) REVERT: SD 103 GLU cc_start: 0.7124 (OUTLIER) cc_final: 0.6640 (mt-10) REVERT: SD 128 GLU cc_start: 0.7201 (OUTLIER) cc_final: 0.6993 (pm20) REVERT: SK 5 LYS cc_start: 0.7732 (mptt) cc_final: 0.7475 (mptt) REVERT: SL 76 VAL cc_start: 0.9099 (OUTLIER) cc_final: 0.8689 (m) REVERT: SR 38 ILE cc_start: 0.7347 (pt) cc_final: 0.7105 (pt) REVERT: SS 40 TYR cc_start: 0.8449 (t80) cc_final: 0.8167 (t80) REVERT: ST 79 TYR cc_start: 0.7677 (m-80) cc_final: 0.7347 (m-80) REVERT: ST 126 GLN cc_start: 0.6802 (tp40) cc_final: 0.6514 (tp40) REVERT: SV 1 MET cc_start: 0.7831 (ppp) cc_final: 0.7364 (ptt) REVERT: SV 11 LEU cc_start: 0.7684 (OUTLIER) cc_final: 0.7418 (mp) REVERT: Sa 46 GLU cc_start: 0.8536 (OUTLIER) cc_final: 0.8014 (pt0) REVERT: Sa 52 ASP cc_start: 0.8182 (p0) cc_final: 0.7951 (p0) REVERT: Sc 13 ARG cc_start: 0.7579 (ttm-80) cc_final: 0.7033 (ttm-80) REVERT: Sc 44 ARG cc_start: 0.7899 (mmm-85) cc_final: 0.7384 (mmm160) REVERT: Sd 7 TYR cc_start: 0.8633 (t80) cc_final: 0.8383 (t80) REVERT: SC 254 ASP cc_start: 0.8242 (p0) cc_final: 0.7800 (p0) REVERT: SG 28 TYR cc_start: 0.8832 (m-10) cc_final: 0.8520 (m-10) REVERT: SG 65 GLN cc_start: 0.8775 (tp-100) cc_final: 0.8514 (tp40) REVERT: SG 126 ASP cc_start: 0.8081 (p0) cc_final: 0.7369 (p0) REVERT: SJ 154 GLN cc_start: 0.8836 (tm-30) cc_final: 0.8164 (tt0) REVERT: SY 38 THR cc_start: 0.9104 (OUTLIER) cc_final: 0.8862 (p) REVERT: Sb 33 MET cc_start: 0.8830 (OUTLIER) cc_final: 0.7711 (mmt) REVERT: Sf 119 ARG cc_start: 0.6455 (ttp80) cc_final: 0.6248 (ttp-110) REVERT: Sf 137 ASP cc_start: 0.6672 (p0) cc_final: 0.6212 (p0) REVERT: CD 142 ASN cc_start: 0.8050 (OUTLIER) cc_final: 0.7182 (m110) REVERT: 3A 12 LEU cc_start: 0.8758 (tp) cc_final: 0.8490 (tp) REVERT: 3B 501 ARG cc_start: -0.0387 (mmt180) cc_final: -0.1476 (tpt170) REVERT: 3B 503 GLU cc_start: 0.2928 (tt0) cc_final: 0.2404 (tt0) REVERT: 3B 529 LYS cc_start: 0.6259 (mmmt) cc_final: 0.5345 (mmtt) REVERT: 3B 544 PHE cc_start: 0.3828 (OUTLIER) cc_final: 0.2959 (m-80) REVERT: 3B 551 GLU cc_start: 0.1520 (mp0) cc_final: 0.1250 (mp0) REVERT: 3C 773 ASP cc_start: 0.6213 (p0) cc_final: 0.5940 (p0) REVERT: 3E 104 MET cc_start: 0.4600 (OUTLIER) cc_final: 0.4178 (pmm) REVERT: 3K 174 MET cc_start: -0.0764 (tpp) cc_final: -0.0976 (tpt) REVERT: 3L 268 MET cc_start: -0.2169 (ptt) cc_final: -0.3302 (ptt) REVERT: 3L 304 MET cc_start: -0.1141 (ptt) cc_final: -0.2043 (ptt) REVERT: 3N 410 ARG cc_start: 0.7142 (OUTLIER) cc_final: 0.6212 (mtm180) REVERT: 3N 413 LEU cc_start: 0.7714 (OUTLIER) cc_final: 0.7376 (pp) REVERT: 3N 466 LEU cc_start: 0.6524 (mm) cc_final: 0.6291 (mm) outliers start: 300 outliers final: 194 residues processed: 1392 average time/residue: 0.9568 time to fit residues: 2303.0708 Evaluate side-chains 1359 residues out of total 9059 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 208 poor density : 1151 time to evaluate : 7.471 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain SA residue 81 ASN Chi-restraints excluded: chain SA residue 205 ARG Chi-restraints excluded: chain SB residue 66 VAL Chi-restraints excluded: chain SB residue 88 THR Chi-restraints excluded: chain SB residue 151 ARG Chi-restraints excluded: chain SD residue 91 VAL Chi-restraints excluded: chain SD residue 103 GLU Chi-restraints excluded: chain SD residue 128 GLU Chi-restraints excluded: chain SD residue 168 VAL Chi-restraints excluded: chain SD residue 170 THR Chi-restraints excluded: chain SD residue 177 LEU Chi-restraints excluded: chain SD residue 181 VAL Chi-restraints excluded: chain SE residue 48 LEU Chi-restraints excluded: chain SE residue 81 THR Chi-restraints excluded: chain SE residue 89 VAL Chi-restraints excluded: chain SE residue 111 VAL Chi-restraints excluded: chain SE residue 126 VAL Chi-restraints excluded: chain SE residue 164 LEU Chi-restraints excluded: chain SE residue 169 ILE Chi-restraints excluded: chain SE residue 208 VAL Chi-restraints excluded: chain SF residue 69 VAL Chi-restraints excluded: chain SF residue 79 HIS Chi-restraints excluded: chain SF residue 83 ASN Chi-restraints excluded: chain SF residue 110 GLN Chi-restraints excluded: chain SF residue 133 THR Chi-restraints excluded: chain SF residue 139 VAL Chi-restraints excluded: chain SF residue 147 VAL Chi-restraints excluded: chain SF residue 165 ASN Chi-restraints excluded: chain SF residue 182 LYS Chi-restraints excluded: chain SH residue 33 ASN Chi-restraints excluded: chain SH residue 46 THR Chi-restraints excluded: chain SH residue 61 ILE Chi-restraints excluded: chain SH residue 64 VAL Chi-restraints excluded: chain SH residue 95 ILE Chi-restraints excluded: chain SH residue 105 THR Chi-restraints excluded: chain SH residue 114 GLN Chi-restraints excluded: chain SH residue 172 THR Chi-restraints excluded: chain SI residue 7 ASN Chi-restraints excluded: chain SI residue 46 VAL Chi-restraints excluded: chain SI residue 77 ARG Chi-restraints excluded: chain SI residue 91 VAL Chi-restraints excluded: chain SI residue 93 THR Chi-restraints excluded: chain SI residue 144 LYS Chi-restraints excluded: chain SI residue 190 LEU Chi-restraints excluded: chain SI residue 195 LEU Chi-restraints excluded: chain SI residue 203 LYS Chi-restraints excluded: chain SK residue 22 VAL Chi-restraints excluded: chain SK residue 52 LEU Chi-restraints excluded: chain SK residue 97 SER Chi-restraints excluded: chain SL residue 19 ASN Chi-restraints excluded: chain SL residue 33 LEU Chi-restraints excluded: chain SL residue 72 ILE Chi-restraints excluded: chain SL residue 76 VAL Chi-restraints excluded: chain SL residue 124 ASP Chi-restraints excluded: chain SL residue 146 THR Chi-restraints excluded: chain SP residue 29 SER Chi-restraints excluded: chain SP residue 101 THR Chi-restraints excluded: chain SP residue 111 MET Chi-restraints excluded: chain SP residue 126 VAL Chi-restraints excluded: chain SQ residue 7 LEU Chi-restraints excluded: chain SQ residue 10 VAL Chi-restraints excluded: chain SQ residue 20 THR Chi-restraints excluded: chain SQ residue 22 VAL Chi-restraints excluded: chain SQ residue 32 ILE Chi-restraints excluded: chain SQ residue 51 LEU Chi-restraints excluded: chain SQ residue 56 LEU Chi-restraints excluded: chain SQ residue 84 ILE Chi-restraints excluded: chain SQ residue 114 GLN Chi-restraints excluded: chain SR residue 40 ILE Chi-restraints excluded: chain SR residue 50 ILE Chi-restraints excluded: chain SR residue 71 ILE Chi-restraints excluded: chain SR residue 123 THR Chi-restraints excluded: chain SS residue 10 GLN Chi-restraints excluded: chain SS residue 15 VAL Chi-restraints excluded: chain SS residue 53 THR Chi-restraints excluded: chain SS residue 58 GLU Chi-restraints excluded: chain SS residue 81 ASP Chi-restraints excluded: chain SS residue 89 ASP Chi-restraints excluded: chain SS residue 103 LEU Chi-restraints excluded: chain SS residue 112 GLU Chi-restraints excluded: chain SS residue 117 ILE Chi-restraints excluded: chain SS residue 131 VAL Chi-restraints excluded: chain ST residue 9 VAL Chi-restraints excluded: chain ST residue 37 VAL Chi-restraints excluded: chain ST residue 55 THR Chi-restraints excluded: chain ST residue 74 SER Chi-restraints excluded: chain ST residue 76 THR Chi-restraints excluded: chain SU residue 23 THR Chi-restraints excluded: chain SU residue 25 THR Chi-restraints excluded: chain SU residue 40 ILE Chi-restraints excluded: chain SU residue 81 GLN Chi-restraints excluded: chain SV residue 11 LEU Chi-restraints excluded: chain SV residue 13 VAL Chi-restraints excluded: chain SV residue 50 PHE Chi-restraints excluded: chain SV residue 62 MET Chi-restraints excluded: chain SX residue 85 VAL Chi-restraints excluded: chain SX residue 131 LEU Chi-restraints excluded: chain Sa residue 30 VAL Chi-restraints excluded: chain Sa residue 46 GLU Chi-restraints excluded: chain Sa residue 63 VAL Chi-restraints excluded: chain Sc residue 11 LEU Chi-restraints excluded: chain Sc residue 28 THR Chi-restraints excluded: chain Sc residue 34 PHE Chi-restraints excluded: chain Sc residue 46 VAL Chi-restraints excluded: chain Sc residue 58 LEU Chi-restraints excluded: chain Sg residue 21 ILE Chi-restraints excluded: chain Sg residue 30 MET Chi-restraints excluded: chain Sg residue 71 ILE Chi-restraints excluded: chain Sg residue 102 VAL Chi-restraints excluded: chain Sg residue 126 ASP Chi-restraints excluded: chain Sg residue 131 LEU Chi-restraints excluded: chain Sg residue 142 VAL Chi-restraints excluded: chain Sg residue 197 THR Chi-restraints excluded: chain SC residue 63 VAL Chi-restraints excluded: chain SC residue 91 SER Chi-restraints excluded: chain SC residue 104 ASP Chi-restraints excluded: chain SC residue 137 VAL Chi-restraints excluded: chain SC residue 147 VAL Chi-restraints excluded: chain SC residue 220 ASP Chi-restraints excluded: chain SC residue 240 THR Chi-restraints excluded: chain SG residue 16 ILE Chi-restraints excluded: chain SG residue 19 ASP Chi-restraints excluded: chain SG residue 97 VAL Chi-restraints excluded: chain SG residue 110 ASN Chi-restraints excluded: chain SG residue 113 ILE Chi-restraints excluded: chain SG residue 163 ASN Chi-restraints excluded: chain SG residue 176 ILE Chi-restraints excluded: chain SG residue 217 MET Chi-restraints excluded: chain SJ residue 2 PRO Chi-restraints excluded: chain SJ residue 62 THR Chi-restraints excluded: chain SJ residue 84 ILE Chi-restraints excluded: chain SJ residue 95 ASP Chi-restraints excluded: chain SJ residue 112 THR Chi-restraints excluded: chain SJ residue 114 VAL Chi-restraints excluded: chain SJ residue 122 SER Chi-restraints excluded: chain SJ residue 123 ILE Chi-restraints excluded: chain SJ residue 153 SER Chi-restraints excluded: chain SJ residue 160 SER Chi-restraints excluded: chain SM residue 42 LEU Chi-restraints excluded: chain SM residue 87 GLU Chi-restraints excluded: chain SN residue 22 VAL Chi-restraints excluded: chain SN residue 31 ASP Chi-restraints excluded: chain SN residue 87 ASP Chi-restraints excluded: chain SN residue 131 THR Chi-restraints excluded: chain SO residue 36 SER Chi-restraints excluded: chain SO residue 52 THR Chi-restraints excluded: chain SO residue 65 ASP Chi-restraints excluded: chain SO residue 66 ARG Chi-restraints excluded: chain SO residue 67 ASP Chi-restraints excluded: chain SO residue 105 THR Chi-restraints excluded: chain SW residue 85 ASP Chi-restraints excluded: chain SY residue 34 THR Chi-restraints excluded: chain SY residue 38 THR Chi-restraints excluded: chain SY residue 40 ILE Chi-restraints excluded: chain SY residue 51 THR Chi-restraints excluded: chain SY residue 97 TYR Chi-restraints excluded: chain SY residue 117 VAL Chi-restraints excluded: chain SZ residue 69 THR Chi-restraints excluded: chain SZ residue 76 ARG Chi-restraints excluded: chain SZ residue 77 LEU Chi-restraints excluded: chain SZ residue 107 VAL Chi-restraints excluded: chain Sb residue 33 MET Chi-restraints excluded: chain Sb residue 53 VAL Chi-restraints excluded: chain Sb residue 64 CYS Chi-restraints excluded: chain Sb residue 79 PHE Chi-restraints excluded: chain CD residue 100 LEU Chi-restraints excluded: chain CD residue 142 ASN Chi-restraints excluded: chain 3A residue 197 LEU Chi-restraints excluded: chain 3A residue 228 MET Chi-restraints excluded: chain 3A residue 230 LEU Chi-restraints excluded: chain 3A residue 349 VAL Chi-restraints excluded: chain 3A residue 452 PHE Chi-restraints excluded: chain 3A residue 498 ASN Chi-restraints excluded: chain 3B residue 467 ILE Chi-restraints excluded: chain 3B residue 517 LEU Chi-restraints excluded: chain 3B residue 528 VAL Chi-restraints excluded: chain 3B residue 541 VAL Chi-restraints excluded: chain 3B residue 544 PHE Chi-restraints excluded: chain 3C residue 76 VAL Chi-restraints excluded: chain 3C residue 77 THR Chi-restraints excluded: chain 3C residue 333 LEU Chi-restraints excluded: chain 3C residue 452 ASP Chi-restraints excluded: chain 3C residue 468 GLU Chi-restraints excluded: chain 3C residue 519 HIS Chi-restraints excluded: chain 3C residue 596 ASP Chi-restraints excluded: chain 3C residue 597 ASN Chi-restraints excluded: chain 3C residue 689 SER Chi-restraints excluded: chain 3C residue 788 LEU Chi-restraints excluded: chain 3C residue 799 TYR Chi-restraints excluded: chain 3E residue 50 MET Chi-restraints excluded: chain 3E residue 104 MET Chi-restraints excluded: chain 3E residue 201 VAL Chi-restraints excluded: chain 3F residue 202 VAL Chi-restraints excluded: chain 3G residue 244 THR Chi-restraints excluded: chain 3K residue 210 VAL Chi-restraints excluded: chain 3L residue 401 MET Chi-restraints excluded: chain 3L residue 432 HIS Chi-restraints excluded: chain 3M residue 282 PHE Chi-restraints excluded: chain 3M residue 308 VAL Chi-restraints excluded: chain 3N residue 8 VAL Chi-restraints excluded: chain 3N residue 42 VAL Chi-restraints excluded: chain 3N residue 55 TYR Chi-restraints excluded: chain 3N residue 269 VAL Chi-restraints excluded: chain 3N residue 410 ARG Chi-restraints excluded: chain 3N residue 413 LEU Chi-restraints excluded: chain 3N residue 414 ASP Chi-restraints excluded: chain 3N residue 517 ILE Chi-restraints excluded: chain 3N residue 519 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1181 random chunks: chunk 950 optimal weight: 8.9990 chunk 648 optimal weight: 0.4980 chunk 16 optimal weight: 6.9990 chunk 849 optimal weight: 9.9990 chunk 471 optimal weight: 1.9990 chunk 974 optimal weight: 30.0000 chunk 789 optimal weight: 9.9990 chunk 1 optimal weight: 0.9980 chunk 582 optimal weight: 0.3980 chunk 1024 optimal weight: 40.0000 chunk 288 optimal weight: 4.9990 overall best weight: 1.7784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** SD 57 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** SE 157 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** SF 110 GLN ** SF 203 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** SH 68 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** SK 7 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** SP 46 ASN ** SP 53 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** SP 98 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** SR 26 ASN SR 127 ASN ** SS 72 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** SS 85 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** SS 97 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ST 105 GLN ** SV 35 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Sa 25 ASN ** Sg 104 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** SC 267 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** SJ 154 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** SM 73 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** SN 36 GLN SN 49 GLN SW 24 GLN ** SW 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Sb 83 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Se 3 HIS 3A 187 GLN ** 3A 270 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 3B 518 HIS 3C 630 HIS ** 3C 637 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 3C 670 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 3C 869 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 3E 390 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** 3G 311 ASN ** 3H 261 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 3H 336 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 3L 364 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 3L 436 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 3M 199 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 3M 205 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 3N 242 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 3N 322 ASN 3N 427 ASN Total number of N/Q/H flips: 16 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7205 moved from start: 0.1870 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.051 120081 Z= 0.227 Angle : 0.681 17.683 170579 Z= 0.348 Chirality : 0.042 0.321 20688 Planarity : 0.005 0.107 15553 Dihedral : 21.510 179.740 37944 Min Nonbonded Distance : 1.927 Molprobity Statistics. All-atom Clashscore : 13.47 Ramachandran Plot: Outliers : 0.12 % Allowed : 6.24 % Favored : 93.64 % Rotamer: Outliers : 3.49 % Allowed : 18.76 % Favored : 77.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.08 % Cis-general : 0.17 % Twisted Proline : 0.54 % Twisted General : 0.05 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.93 (0.08), residues: 10145 helix: 0.74 (0.08), residues: 4553 sheet: -0.88 (0.13), residues: 1543 loop : -2.11 (0.09), residues: 4049 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.043 0.002 TRP3A 393 HIS 0.010 0.001 HIS3L 432 PHE 0.026 0.002 PHE3A 283 TYR 0.024 0.001 TYRSL 37 ARG 0.013 0.000 ARGSF 204 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 20290 Ramachandran restraints generated. 10145 Oldfield, 0 Emsley, 10145 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 20290 Ramachandran restraints generated. 10145 Oldfield, 0 Emsley, 10145 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1533 residues out of total 9059 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 267 poor density : 1266 time to evaluate : 7.494 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: Ln 9 ARG cc_start: 0.6647 (mtp85) cc_final: 0.5783 (ttp-170) REVERT: SA 158 ASP cc_start: 0.6643 (m-30) cc_final: 0.6345 (m-30) REVERT: SA 205 ARG cc_start: 0.6762 (OUTLIER) cc_final: 0.6157 (mtp-110) REVERT: SB 172 MET cc_start: 0.8571 (mtm) cc_final: 0.8310 (mtm) REVERT: SD 103 GLU cc_start: 0.6951 (OUTLIER) cc_final: 0.6456 (mt-10) REVERT: SD 128 GLU cc_start: 0.6991 (OUTLIER) cc_final: 0.6646 (pm20) REVERT: SF 51 HIS cc_start: 0.7430 (OUTLIER) cc_final: 0.7092 (t70) REVERT: SF 82 ASN cc_start: 0.8466 (OUTLIER) cc_final: 0.8046 (m110) REVERT: SI 186 ASP cc_start: 0.7564 (OUTLIER) cc_final: 0.7223 (m-30) REVERT: SP 127 LYS cc_start: 0.8594 (mtmm) cc_final: 0.8270 (ptpp) REVERT: SQ 87 SER cc_start: 0.8100 (t) cc_final: 0.7374 (p) REVERT: SS 40 TYR cc_start: 0.8306 (t80) cc_final: 0.7961 (t80) REVERT: ST 79 TYR cc_start: 0.7639 (m-80) cc_final: 0.7261 (m-80) REVERT: ST 88 MET cc_start: 0.8730 (mmt) cc_final: 0.8490 (mmm) REVERT: ST 126 GLN cc_start: 0.6783 (tp40) cc_final: 0.6472 (tp40) REVERT: SU 34 LYS cc_start: 0.7912 (pptt) cc_final: 0.7598 (pttt) REVERT: SV 1 MET cc_start: 0.7745 (ppp) cc_final: 0.7225 (ptt) REVERT: Sa 46 GLU cc_start: 0.8397 (OUTLIER) cc_final: 0.7546 (pt0) REVERT: Sa 52 ASP cc_start: 0.8039 (p0) cc_final: 0.7782 (p0) REVERT: Sc 44 ARG cc_start: 0.7730 (mmm-85) cc_final: 0.7276 (mmm160) REVERT: Sd 7 TYR cc_start: 0.8579 (t80) cc_final: 0.8361 (t80) REVERT: Sg 168 CYS cc_start: 0.8383 (p) cc_final: 0.8160 (p) REVERT: SC 254 ASP cc_start: 0.8104 (p0) cc_final: 0.7633 (p0) REVERT: SG 28 TYR cc_start: 0.8721 (m-10) cc_final: 0.8515 (m-10) REVERT: SG 32 MET cc_start: 0.7610 (ppp) cc_final: 0.7281 (ptm) REVERT: SG 126 ASP cc_start: 0.8027 (p0) cc_final: 0.7326 (p0) REVERT: SJ 154 GLN cc_start: 0.8651 (tm-30) cc_final: 0.8206 (tt0) REVERT: SN 103 GLU cc_start: 0.7051 (pp20) cc_final: 0.6660 (pp20) REVERT: Sb 33 MET cc_start: 0.8742 (OUTLIER) cc_final: 0.7798 (mmt) REVERT: CD 142 ASN cc_start: 0.8008 (OUTLIER) cc_final: 0.7049 (m110) REVERT: CD 143 TYR cc_start: 0.7808 (t80) cc_final: 0.7559 (t80) REVERT: 3A 12 LEU cc_start: 0.8652 (tp) cc_final: 0.8434 (tp) REVERT: 3B 469 ASP cc_start: 0.5364 (p0) cc_final: 0.5071 (p0) REVERT: 3B 501 ARG cc_start: -0.0480 (mmt180) cc_final: -0.1387 (tpt170) REVERT: 3B 505 ARG cc_start: 0.5526 (mtm-85) cc_final: 0.5001 (mtm180) REVERT: 3B 529 LYS cc_start: 0.6566 (mmmt) cc_final: 0.5897 (mmtt) REVERT: 3B 544 PHE cc_start: 0.3333 (OUTLIER) cc_final: 0.2376 (m-80) REVERT: 3B 549 MET cc_start: 0.1414 (mpp) cc_final: 0.0597 (mtm) REVERT: 3B 551 GLU cc_start: 0.1681 (mp0) cc_final: 0.1429 (mp0) REVERT: 3E 94 MET cc_start: 0.5030 (mmm) cc_final: 0.4736 (tpt) REVERT: 3E 104 MET cc_start: 0.4663 (OUTLIER) cc_final: 0.4150 (pmm) REVERT: 3E 314 GLU cc_start: 0.5976 (OUTLIER) cc_final: 0.5488 (pm20) REVERT: 3F 211 MET cc_start: -0.0917 (OUTLIER) cc_final: -0.2277 (mtt) REVERT: 3F 309 MET cc_start: 0.0210 (mtt) cc_final: -0.0484 (ptp) REVERT: 3K 174 MET cc_start: -0.0815 (tpp) cc_final: -0.1153 (tpt) REVERT: 3L 304 MET cc_start: -0.1054 (ptt) cc_final: -0.2074 (ptt) REVERT: 3N 413 LEU cc_start: 0.7707 (OUTLIER) cc_final: 0.7287 (pp) outliers start: 267 outliers final: 176 residues processed: 1405 average time/residue: 0.9733 time to fit residues: 2374.1034 Evaluate side-chains 1398 residues out of total 9059 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 190 poor density : 1208 time to evaluate : 7.491 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain SA residue 8 LEU Chi-restraints excluded: chain SA residue 43 SER Chi-restraints excluded: chain SA residue 81 ASN Chi-restraints excluded: chain SA residue 82 THR Chi-restraints excluded: chain SA residue 205 ARG Chi-restraints excluded: chain SB residue 60 ASP Chi-restraints excluded: chain SB residue 66 VAL Chi-restraints excluded: chain SB residue 88 THR Chi-restraints excluded: chain SD residue 51 LEU Chi-restraints excluded: chain SD residue 91 VAL Chi-restraints excluded: chain SD residue 103 GLU Chi-restraints excluded: chain SD residue 128 GLU Chi-restraints excluded: chain SD residue 164 VAL Chi-restraints excluded: chain SD residue 170 THR Chi-restraints excluded: chain SD residue 181 VAL Chi-restraints excluded: chain SE residue 81 THR Chi-restraints excluded: chain SE residue 89 VAL Chi-restraints excluded: chain SE residue 126 VAL Chi-restraints excluded: chain SF residue 51 HIS Chi-restraints excluded: chain SF residue 69 VAL Chi-restraints excluded: chain SF residue 82 ASN Chi-restraints excluded: chain SF residue 110 GLN Chi-restraints excluded: chain SF residue 113 VAL Chi-restraints excluded: chain SF residue 133 THR Chi-restraints excluded: chain SF residue 165 ASN Chi-restraints excluded: chain SF residue 182 LYS Chi-restraints excluded: chain SH residue 30 LEU Chi-restraints excluded: chain SH residue 33 ASN Chi-restraints excluded: chain SH residue 64 VAL Chi-restraints excluded: chain SH residue 105 THR Chi-restraints excluded: chain SH residue 114 GLN Chi-restraints excluded: chain SI residue 46 VAL Chi-restraints excluded: chain SI residue 93 THR Chi-restraints excluded: chain SI residue 144 LYS Chi-restraints excluded: chain SI residue 171 LEU Chi-restraints excluded: chain SI residue 186 ASP Chi-restraints excluded: chain SI residue 195 LEU Chi-restraints excluded: chain SK residue 52 LEU Chi-restraints excluded: chain SK residue 97 SER Chi-restraints excluded: chain SL residue 19 ASN Chi-restraints excluded: chain SL residue 33 LEU Chi-restraints excluded: chain SL residue 72 ILE Chi-restraints excluded: chain SL residue 124 ASP Chi-restraints excluded: chain SP residue 29 SER Chi-restraints excluded: chain SP residue 101 THR Chi-restraints excluded: chain SP residue 111 MET Chi-restraints excluded: chain SP residue 126 VAL Chi-restraints excluded: chain SQ residue 7 LEU Chi-restraints excluded: chain SQ residue 10 VAL Chi-restraints excluded: chain SQ residue 20 THR Chi-restraints excluded: chain SQ residue 22 VAL Chi-restraints excluded: chain SQ residue 32 ILE Chi-restraints excluded: chain SQ residue 56 LEU Chi-restraints excluded: chain SQ residue 84 ILE Chi-restraints excluded: chain SQ residue 114 GLN Chi-restraints excluded: chain SR residue 26 ASN Chi-restraints excluded: chain SR residue 40 ILE Chi-restraints excluded: chain SR residue 71 ILE Chi-restraints excluded: chain SR residue 93 GLN Chi-restraints excluded: chain SR residue 123 THR Chi-restraints excluded: chain SS residue 15 VAL Chi-restraints excluded: chain SS residue 53 THR Chi-restraints excluded: chain SS residue 58 GLU Chi-restraints excluded: chain SS residue 67 VAL Chi-restraints excluded: chain SS residue 81 ASP Chi-restraints excluded: chain SS residue 89 ASP Chi-restraints excluded: chain SS residue 103 LEU Chi-restraints excluded: chain SS residue 117 ILE Chi-restraints excluded: chain SS residue 131 VAL Chi-restraints excluded: chain ST residue 9 VAL Chi-restraints excluded: chain ST residue 37 VAL Chi-restraints excluded: chain ST residue 55 THR Chi-restraints excluded: chain ST residue 74 SER Chi-restraints excluded: chain ST residue 76 THR Chi-restraints excluded: chain ST residue 108 GLU Chi-restraints excluded: chain SU residue 23 THR Chi-restraints excluded: chain SU residue 25 THR Chi-restraints excluded: chain SU residue 40 ILE Chi-restraints excluded: chain SU residue 81 GLN Chi-restraints excluded: chain SV residue 13 VAL Chi-restraints excluded: chain SV residue 62 MET Chi-restraints excluded: chain SV residue 80 SER Chi-restraints excluded: chain SX residue 85 VAL Chi-restraints excluded: chain SX residue 107 ARG Chi-restraints excluded: chain Sa residue 46 GLU Chi-restraints excluded: chain Sa residue 63 VAL Chi-restraints excluded: chain Sa residue 69 VAL Chi-restraints excluded: chain Sc residue 28 THR Chi-restraints excluded: chain Sc residue 34 PHE Chi-restraints excluded: chain Sc residue 46 VAL Chi-restraints excluded: chain Sd residue 49 ASP Chi-restraints excluded: chain Sg residue 68 ASP Chi-restraints excluded: chain Sg residue 71 ILE Chi-restraints excluded: chain Sg residue 96 THR Chi-restraints excluded: chain Sg residue 102 VAL Chi-restraints excluded: chain Sg residue 126 ASP Chi-restraints excluded: chain Sg residue 131 LEU Chi-restraints excluded: chain Sg residue 197 THR Chi-restraints excluded: chain Sg residue 309 VAL Chi-restraints excluded: chain SC residue 63 VAL Chi-restraints excluded: chain SC residue 91 SER Chi-restraints excluded: chain SC residue 104 ASP Chi-restraints excluded: chain SC residue 137 VAL Chi-restraints excluded: chain SC residue 141 VAL Chi-restraints excluded: chain SC residue 220 ASP Chi-restraints excluded: chain SG residue 16 ILE Chi-restraints excluded: chain SG residue 110 ASN Chi-restraints excluded: chain SG residue 113 ILE Chi-restraints excluded: chain SG residue 163 ASN Chi-restraints excluded: chain SG residue 176 ILE Chi-restraints excluded: chain SG residue 217 MET Chi-restraints excluded: chain SJ residue 62 THR Chi-restraints excluded: chain SJ residue 84 ILE Chi-restraints excluded: chain SJ residue 95 ASP Chi-restraints excluded: chain SJ residue 102 ILE Chi-restraints excluded: chain SJ residue 112 THR Chi-restraints excluded: chain SJ residue 114 VAL Chi-restraints excluded: chain SJ residue 123 ILE Chi-restraints excluded: chain SJ residue 153 SER Chi-restraints excluded: chain SM residue 42 LEU Chi-restraints excluded: chain SM residue 66 GLU Chi-restraints excluded: chain SM residue 87 GLU Chi-restraints excluded: chain SN residue 22 VAL Chi-restraints excluded: chain SN residue 31 ASP Chi-restraints excluded: chain SN residue 87 ASP Chi-restraints excluded: chain SN residue 131 THR Chi-restraints excluded: chain SO residue 65 ASP Chi-restraints excluded: chain SO residue 66 ARG Chi-restraints excluded: chain SO residue 67 ASP Chi-restraints excluded: chain SO residue 105 THR Chi-restraints excluded: chain SW residue 85 ASP Chi-restraints excluded: chain SY residue 34 THR Chi-restraints excluded: chain SY residue 40 ILE Chi-restraints excluded: chain SY residue 117 VAL Chi-restraints excluded: chain SZ residue 69 THR Chi-restraints excluded: chain SZ residue 107 VAL Chi-restraints excluded: chain Sb residue 33 MET Chi-restraints excluded: chain Sb residue 53 VAL Chi-restraints excluded: chain Sb residue 64 CYS Chi-restraints excluded: chain Se residue 6 LEU Chi-restraints excluded: chain CD residue 100 LEU Chi-restraints excluded: chain CD residue 142 ASN Chi-restraints excluded: chain 3A residue 19 LEU Chi-restraints excluded: chain 3A residue 68 LYS Chi-restraints excluded: chain 3A residue 96 MET Chi-restraints excluded: chain 3A residue 197 LEU Chi-restraints excluded: chain 3A residue 228 MET Chi-restraints excluded: chain 3A residue 230 LEU Chi-restraints excluded: chain 3A residue 278 LYS Chi-restraints excluded: chain 3A residue 498 ASN Chi-restraints excluded: chain 3B residue 482 TRP Chi-restraints excluded: chain 3B residue 494 THR Chi-restraints excluded: chain 3B residue 517 LEU Chi-restraints excluded: chain 3B residue 541 VAL Chi-restraints excluded: chain 3B residue 544 PHE Chi-restraints excluded: chain 3C residue 76 VAL Chi-restraints excluded: chain 3C residue 77 THR Chi-restraints excluded: chain 3C residue 333 LEU Chi-restraints excluded: chain 3C residue 452 ASP Chi-restraints excluded: chain 3C residue 468 GLU Chi-restraints excluded: chain 3C residue 519 HIS Chi-restraints excluded: chain 3C residue 546 VAL Chi-restraints excluded: chain 3C residue 596 ASP Chi-restraints excluded: chain 3C residue 597 ASN Chi-restraints excluded: chain 3C residue 689 SER Chi-restraints excluded: chain 3C residue 788 LEU Chi-restraints excluded: chain 3C residue 799 TYR Chi-restraints excluded: chain 3C residue 842 VAL Chi-restraints excluded: chain 3E residue 104 MET Chi-restraints excluded: chain 3E residue 187 GLU Chi-restraints excluded: chain 3E residue 201 VAL Chi-restraints excluded: chain 3E residue 294 GLU Chi-restraints excluded: chain 3E residue 314 GLU Chi-restraints excluded: chain 3E residue 348 HIS Chi-restraints excluded: chain 3F residue 202 VAL Chi-restraints excluded: chain 3F residue 211 MET Chi-restraints excluded: chain 3G residue 244 THR Chi-restraints excluded: chain 3G residue 272 LYS Chi-restraints excluded: chain 3G residue 287 PHE Chi-restraints excluded: chain 3G residue 300 VAL Chi-restraints excluded: chain 3L residue 431 VAL Chi-restraints excluded: chain 3L residue 432 HIS Chi-restraints excluded: chain 3M residue 282 PHE Chi-restraints excluded: chain 3N residue 8 VAL Chi-restraints excluded: chain 3N residue 55 TYR Chi-restraints excluded: chain 3N residue 269 VAL Chi-restraints excluded: chain 3N residue 413 LEU Chi-restraints excluded: chain 3N residue 414 ASP Chi-restraints excluded: chain 3N residue 517 ILE Chi-restraints excluded: chain 3N residue 519 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1181 random chunks: chunk 384 optimal weight: 10.0000 chunk 1028 optimal weight: 9.9990 chunk 225 optimal weight: 0.7980 chunk 670 optimal weight: 50.0000 chunk 281 optimal weight: 3.9990 chunk 1142 optimal weight: 8.9990 chunk 948 optimal weight: 6.9990 chunk 529 optimal weight: 6.9990 chunk 95 optimal weight: 4.9990 chunk 377 optimal weight: 0.5980 chunk 599 optimal weight: 5.9990 overall best weight: 3.2786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** SD 57 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** SD 226 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** SE 157 ASN SF 110 GLN ** SF 203 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** SI 7 ASN ** SI 181 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** SK 7 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** SP 53 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** SP 98 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** SQ 114 GLN SR 127 ASN ** SS 72 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** SS 85 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** SS 97 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** SV 35 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** SX 46 HIS ** Sg 104 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** SC 178 HIS ** SC 267 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** SJ 154 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** SM 73 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** SN 36 GLN ** SN 49 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** SO 83 GLN ** SW 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** SY 94 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** Sb 83 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Se 3 HIS Sf 139 HIS 3A 187 GLN ** 3A 270 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 3C 637 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 3C 670 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 3C 837 GLN ** 3E 390 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** 3F 347 GLN ** 3G 256 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 3G 311 ASN ** 3H 141 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 3H 261 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 3H 336 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 3L 364 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 3L 436 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** 3L 443 GLN ** 3M 199 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 3M 205 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 3N 242 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 3N 322 ASN 3N 427 ASN Total number of N/Q/H flips: 18 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7247 moved from start: 0.2036 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.077 120081 Z= 0.357 Angle : 0.749 17.667 170579 Z= 0.379 Chirality : 0.045 0.332 20688 Planarity : 0.005 0.105 15553 Dihedral : 21.463 179.996 37944 Min Nonbonded Distance : 1.890 Molprobity Statistics. All-atom Clashscore : 14.07 Ramachandran Plot: Outliers : 0.13 % Allowed : 7.06 % Favored : 92.81 % Rotamer: Outliers : 3.90 % Allowed : 19.64 % Favored : 76.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.08 % Cis-general : 0.17 % Twisted Proline : 0.54 % Twisted General : 0.06 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.93 (0.08), residues: 10145 helix: 0.76 (0.08), residues: 4553 sheet: -0.88 (0.13), residues: 1514 loop : -2.12 (0.09), residues: 4078 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.039 0.002 TRP3A 393 HIS 0.010 0.001 HIS3L 432 PHE 0.027 0.002 PHESJ 147 TYR 0.024 0.002 TYRSQ 96 ARG 0.016 0.001 ARGSF 204 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 20290 Ramachandran restraints generated. 10145 Oldfield, 0 Emsley, 10145 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 20290 Ramachandran restraints generated. 10145 Oldfield, 0 Emsley, 10145 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1536 residues out of total 9059 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 299 poor density : 1237 time to evaluate : 7.635 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: Ln 9 ARG cc_start: 0.6650 (mtp85) cc_final: 0.5745 (ttp-170) REVERT: SA 158 ASP cc_start: 0.6769 (m-30) cc_final: 0.6413 (m-30) REVERT: SA 205 ARG cc_start: 0.6864 (OUTLIER) cc_final: 0.6218 (mtp-110) REVERT: SB 172 MET cc_start: 0.8619 (mtm) cc_final: 0.8292 (mtm) REVERT: SD 103 GLU cc_start: 0.7079 (OUTLIER) cc_final: 0.6568 (mt-10) REVERT: SD 128 GLU cc_start: 0.7086 (OUTLIER) cc_final: 0.6764 (pm20) REVERT: SE 21 ASP cc_start: 0.8746 (OUTLIER) cc_final: 0.8283 (m-30) REVERT: SF 51 HIS cc_start: 0.7454 (OUTLIER) cc_final: 0.7146 (t70) REVERT: SF 82 ASN cc_start: 0.8392 (OUTLIER) cc_final: 0.8124 (m110) REVERT: SI 186 ASP cc_start: 0.7689 (OUTLIER) cc_final: 0.7375 (m-30) REVERT: SP 34 MET cc_start: 0.7450 (mmt) cc_final: 0.6997 (mmt) REVERT: SQ 87 SER cc_start: 0.8095 (t) cc_final: 0.7286 (p) REVERT: SR 33 ARG cc_start: 0.8295 (mmm-85) cc_final: 0.7543 (mmt-90) REVERT: SS 40 TYR cc_start: 0.8398 (t80) cc_final: 0.8020 (t80) REVERT: ST 79 TYR cc_start: 0.7688 (m-80) cc_final: 0.7343 (m-80) REVERT: ST 88 MET cc_start: 0.8714 (mmt) cc_final: 0.8453 (mmm) REVERT: ST 126 GLN cc_start: 0.6768 (tp40) cc_final: 0.6498 (tp40) REVERT: SV 1 MET cc_start: 0.7807 (ppp) cc_final: 0.7314 (ptt) REVERT: Sa 46 GLU cc_start: 0.8516 (OUTLIER) cc_final: 0.8208 (pm20) REVERT: Sa 52 ASP cc_start: 0.8100 (p0) cc_final: 0.7897 (p0) REVERT: Sc 44 ARG cc_start: 0.7782 (mmm-85) cc_final: 0.7351 (mmm160) REVERT: Sd 7 TYR cc_start: 0.8595 (t80) cc_final: 0.8317 (t80) REVERT: SC 254 ASP cc_start: 0.8152 (p0) cc_final: 0.7694 (p0) REVERT: SG 28 TYR cc_start: 0.8768 (m-10) cc_final: 0.8474 (m-10) REVERT: SG 126 ASP cc_start: 0.8038 (p0) cc_final: 0.7325 (p0) REVERT: SJ 154 GLN cc_start: 0.8730 (tm-30) cc_final: 0.8333 (tt0) REVERT: SN 103 GLU cc_start: 0.7144 (pp20) cc_final: 0.6698 (pp20) REVERT: Sb 33 MET cc_start: 0.8793 (OUTLIER) cc_final: 0.7686 (mmt) REVERT: CD 142 ASN cc_start: 0.8070 (OUTLIER) cc_final: 0.7261 (m110) REVERT: CD 143 TYR cc_start: 0.7872 (t80) cc_final: 0.7591 (t80) REVERT: 3B 469 ASP cc_start: 0.5307 (p0) cc_final: 0.4950 (p0) REVERT: 3B 501 ARG cc_start: -0.0806 (mmt180) cc_final: -0.1590 (tpt170) REVERT: 3B 505 ARG cc_start: 0.5866 (mtm-85) cc_final: 0.5402 (mtm110) REVERT: 3B 529 LYS cc_start: 0.6578 (mmmt) cc_final: 0.5902 (mmtt) REVERT: 3B 544 PHE cc_start: 0.3614 (OUTLIER) cc_final: 0.2480 (m-80) REVERT: 3B 549 MET cc_start: 0.1305 (mpp) cc_final: 0.1095 (mtm) REVERT: 3E 94 MET cc_start: 0.4956 (mmm) cc_final: 0.4698 (tpt) REVERT: 3E 104 MET cc_start: 0.4390 (OUTLIER) cc_final: 0.3798 (pmm) REVERT: 3E 314 GLU cc_start: 0.6043 (OUTLIER) cc_final: 0.5598 (pm20) REVERT: 3F 211 MET cc_start: -0.0908 (OUTLIER) cc_final: -0.2334 (mtt) REVERT: 3K 174 MET cc_start: -0.0802 (tpp) cc_final: -0.1061 (tpt) REVERT: 3L 268 MET cc_start: -0.2361 (ptt) cc_final: -0.3249 (ptt) REVERT: 3L 304 MET cc_start: -0.1192 (ptt) cc_final: -0.2223 (ptt) REVERT: 3L 326 MET cc_start: 0.0769 (ppp) cc_final: 0.0220 (ppp) REVERT: 3N 413 LEU cc_start: 0.7781 (OUTLIER) cc_final: 0.7188 (pp) outliers start: 299 outliers final: 224 residues processed: 1403 average time/residue: 0.9711 time to fit residues: 2358.1096 Evaluate side-chains 1444 residues out of total 9059 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 239 poor density : 1205 time to evaluate : 7.488 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain SA residue 8 LEU Chi-restraints excluded: chain SA residue 43 SER Chi-restraints excluded: chain SA residue 81 ASN Chi-restraints excluded: chain SA residue 82 THR Chi-restraints excluded: chain SA residue 205 ARG Chi-restraints excluded: chain SB residue 60 ASP Chi-restraints excluded: chain SB residue 66 VAL Chi-restraints excluded: chain SB residue 88 THR Chi-restraints excluded: chain SD residue 51 LEU Chi-restraints excluded: chain SD residue 91 VAL Chi-restraints excluded: chain SD residue 103 GLU Chi-restraints excluded: chain SD residue 128 GLU Chi-restraints excluded: chain SD residue 164 VAL Chi-restraints excluded: chain SD residue 170 THR Chi-restraints excluded: chain SD residue 181 VAL Chi-restraints excluded: chain SE residue 21 ASP Chi-restraints excluded: chain SE residue 48 LEU Chi-restraints excluded: chain SE residue 81 THR Chi-restraints excluded: chain SE residue 89 VAL Chi-restraints excluded: chain SE residue 126 VAL Chi-restraints excluded: chain SE residue 169 ILE Chi-restraints excluded: chain SF residue 51 HIS Chi-restraints excluded: chain SF residue 69 VAL Chi-restraints excluded: chain SF residue 82 ASN Chi-restraints excluded: chain SF residue 110 GLN Chi-restraints excluded: chain SF residue 133 THR Chi-restraints excluded: chain SF residue 182 LYS Chi-restraints excluded: chain SH residue 30 LEU Chi-restraints excluded: chain SH residue 33 ASN Chi-restraints excluded: chain SH residue 61 ILE Chi-restraints excluded: chain SH residue 64 VAL Chi-restraints excluded: chain SH residue 105 THR Chi-restraints excluded: chain SH residue 114 GLN Chi-restraints excluded: chain SI residue 46 VAL Chi-restraints excluded: chain SI residue 77 ARG Chi-restraints excluded: chain SI residue 93 THR Chi-restraints excluded: chain SI residue 144 LYS Chi-restraints excluded: chain SI residue 159 SER Chi-restraints excluded: chain SI residue 171 LEU Chi-restraints excluded: chain SI residue 186 ASP Chi-restraints excluded: chain SI residue 195 LEU Chi-restraints excluded: chain SK residue 22 VAL Chi-restraints excluded: chain SK residue 52 LEU Chi-restraints excluded: chain SK residue 97 SER Chi-restraints excluded: chain SL residue 19 ASN Chi-restraints excluded: chain SL residue 33 LEU Chi-restraints excluded: chain SL residue 66 VAL Chi-restraints excluded: chain SL residue 72 ILE Chi-restraints excluded: chain SL residue 124 ASP Chi-restraints excluded: chain SL residue 146 THR Chi-restraints excluded: chain SP residue 29 SER Chi-restraints excluded: chain SP residue 101 THR Chi-restraints excluded: chain SP residue 111 MET Chi-restraints excluded: chain SP residue 126 VAL Chi-restraints excluded: chain SQ residue 7 LEU Chi-restraints excluded: chain SQ residue 10 VAL Chi-restraints excluded: chain SQ residue 20 THR Chi-restraints excluded: chain SQ residue 22 VAL Chi-restraints excluded: chain SQ residue 32 ILE Chi-restraints excluded: chain SQ residue 56 LEU Chi-restraints excluded: chain SQ residue 57 LEU Chi-restraints excluded: chain SQ residue 84 ILE Chi-restraints excluded: chain SQ residue 114 GLN Chi-restraints excluded: chain SR residue 40 ILE Chi-restraints excluded: chain SR residue 71 ILE Chi-restraints excluded: chain SR residue 93 GLN Chi-restraints excluded: chain SR residue 99 ASP Chi-restraints excluded: chain SR residue 113 SER Chi-restraints excluded: chain SR residue 123 THR Chi-restraints excluded: chain SS residue 10 GLN Chi-restraints excluded: chain SS residue 15 VAL Chi-restraints excluded: chain SS residue 50 ILE Chi-restraints excluded: chain SS residue 53 THR Chi-restraints excluded: chain SS residue 67 VAL Chi-restraints excluded: chain SS residue 81 ASP Chi-restraints excluded: chain SS residue 103 LEU Chi-restraints excluded: chain SS residue 117 ILE Chi-restraints excluded: chain SS residue 131 VAL Chi-restraints excluded: chain SS residue 136 THR Chi-restraints excluded: chain ST residue 9 VAL Chi-restraints excluded: chain ST residue 37 VAL Chi-restraints excluded: chain ST residue 55 THR Chi-restraints excluded: chain ST residue 74 SER Chi-restraints excluded: chain ST residue 76 THR Chi-restraints excluded: chain ST residue 108 GLU Chi-restraints excluded: chain SU residue 23 THR Chi-restraints excluded: chain SU residue 24 LEU Chi-restraints excluded: chain SU residue 25 THR Chi-restraints excluded: chain SU residue 40 ILE Chi-restraints excluded: chain SU residue 65 THR Chi-restraints excluded: chain SU residue 81 GLN Chi-restraints excluded: chain SU residue 115 THR Chi-restraints excluded: chain SV residue 13 VAL Chi-restraints excluded: chain SV residue 62 MET Chi-restraints excluded: chain SX residue 4 CYS Chi-restraints excluded: chain SX residue 26 GLN Chi-restraints excluded: chain SX residue 50 ILE Chi-restraints excluded: chain SX residue 85 VAL Chi-restraints excluded: chain SX residue 107 ARG Chi-restraints excluded: chain SX residue 131 LEU Chi-restraints excluded: chain Sa residue 46 GLU Chi-restraints excluded: chain Sa residue 63 VAL Chi-restraints excluded: chain Sa residue 69 VAL Chi-restraints excluded: chain Sc residue 11 LEU Chi-restraints excluded: chain Sc residue 28 THR Chi-restraints excluded: chain Sc residue 34 PHE Chi-restraints excluded: chain Sc residue 38 THR Chi-restraints excluded: chain Sc residue 46 VAL Chi-restraints excluded: chain Sd residue 49 ASP Chi-restraints excluded: chain Sg residue 21 ILE Chi-restraints excluded: chain Sg residue 68 ASP Chi-restraints excluded: chain Sg residue 71 ILE Chi-restraints excluded: chain Sg residue 96 THR Chi-restraints excluded: chain Sg residue 102 VAL Chi-restraints excluded: chain Sg residue 126 ASP Chi-restraints excluded: chain Sg residue 131 LEU Chi-restraints excluded: chain Sg residue 142 VAL Chi-restraints excluded: chain Sg residue 197 THR Chi-restraints excluded: chain Sg residue 309 VAL Chi-restraints excluded: chain SC residue 63 VAL Chi-restraints excluded: chain SC residue 91 SER Chi-restraints excluded: chain SC residue 104 ASP Chi-restraints excluded: chain SC residue 137 VAL Chi-restraints excluded: chain SC residue 141 VAL Chi-restraints excluded: chain SC residue 147 VAL Chi-restraints excluded: chain SC residue 220 ASP Chi-restraints excluded: chain SG residue 16 ILE Chi-restraints excluded: chain SG residue 110 ASN Chi-restraints excluded: chain SG residue 113 ILE Chi-restraints excluded: chain SG residue 148 SER Chi-restraints excluded: chain SG residue 163 ASN Chi-restraints excluded: chain SG residue 176 ILE Chi-restraints excluded: chain SG residue 180 VAL Chi-restraints excluded: chain SG residue 217 MET Chi-restraints excluded: chain SJ residue 61 LEU Chi-restraints excluded: chain SJ residue 62 THR Chi-restraints excluded: chain SJ residue 84 ILE Chi-restraints excluded: chain SJ residue 95 ASP Chi-restraints excluded: chain SJ residue 102 ILE Chi-restraints excluded: chain SJ residue 112 THR Chi-restraints excluded: chain SJ residue 114 VAL Chi-restraints excluded: chain SJ residue 123 ILE Chi-restraints excluded: chain SJ residue 128 VAL Chi-restraints excluded: chain SJ residue 153 SER Chi-restraints excluded: chain SM residue 31 LEU Chi-restraints excluded: chain SM residue 42 LEU Chi-restraints excluded: chain SM residue 66 GLU Chi-restraints excluded: chain SM residue 87 GLU Chi-restraints excluded: chain SN residue 22 VAL Chi-restraints excluded: chain SN residue 31 ASP Chi-restraints excluded: chain SN residue 86 GLU Chi-restraints excluded: chain SN residue 87 ASP Chi-restraints excluded: chain SN residue 131 THR Chi-restraints excluded: chain SO residue 36 SER Chi-restraints excluded: chain SO residue 52 THR Chi-restraints excluded: chain SO residue 62 VAL Chi-restraints excluded: chain SO residue 65 ASP Chi-restraints excluded: chain SO residue 66 ARG Chi-restraints excluded: chain SO residue 67 ASP Chi-restraints excluded: chain SO residue 81 VAL Chi-restraints excluded: chain SO residue 105 THR Chi-restraints excluded: chain SO residue 132 VAL Chi-restraints excluded: chain SW residue 85 ASP Chi-restraints excluded: chain SY residue 34 THR Chi-restraints excluded: chain SY residue 40 ILE Chi-restraints excluded: chain SY residue 51 THR Chi-restraints excluded: chain SY residue 103 SER Chi-restraints excluded: chain SY residue 117 VAL Chi-restraints excluded: chain SZ residue 69 THR Chi-restraints excluded: chain SZ residue 76 ARG Chi-restraints excluded: chain SZ residue 77 LEU Chi-restraints excluded: chain SZ residue 107 VAL Chi-restraints excluded: chain Sb residue 33 MET Chi-restraints excluded: chain Sb residue 53 VAL Chi-restraints excluded: chain Sb residue 64 CYS Chi-restraints excluded: chain Se residue 6 LEU Chi-restraints excluded: chain Sf residue 148 TYR Chi-restraints excluded: chain CD residue 100 LEU Chi-restraints excluded: chain CD residue 102 ARG Chi-restraints excluded: chain CD residue 135 GLU Chi-restraints excluded: chain CD residue 142 ASN Chi-restraints excluded: chain 3A residue 19 LEU Chi-restraints excluded: chain 3A residue 68 LYS Chi-restraints excluded: chain 3A residue 96 MET Chi-restraints excluded: chain 3A residue 197 LEU Chi-restraints excluded: chain 3A residue 228 MET Chi-restraints excluded: chain 3A residue 230 LEU Chi-restraints excluded: chain 3A residue 278 LYS Chi-restraints excluded: chain 3A residue 498 ASN Chi-restraints excluded: chain 3B residue 482 TRP Chi-restraints excluded: chain 3B residue 494 THR Chi-restraints excluded: chain 3B residue 517 LEU Chi-restraints excluded: chain 3B residue 541 VAL Chi-restraints excluded: chain 3B residue 544 PHE Chi-restraints excluded: chain 3C residue 76 VAL Chi-restraints excluded: chain 3C residue 77 THR Chi-restraints excluded: chain 3C residue 333 LEU Chi-restraints excluded: chain 3C residue 446 THR Chi-restraints excluded: chain 3C residue 452 ASP Chi-restraints excluded: chain 3C residue 468 GLU Chi-restraints excluded: chain 3C residue 519 HIS Chi-restraints excluded: chain 3C residue 546 VAL Chi-restraints excluded: chain 3C residue 593 HIS Chi-restraints excluded: chain 3C residue 596 ASP Chi-restraints excluded: chain 3C residue 597 ASN Chi-restraints excluded: chain 3C residue 605 VAL Chi-restraints excluded: chain 3C residue 607 ILE Chi-restraints excluded: chain 3C residue 689 SER Chi-restraints excluded: chain 3C residue 788 LEU Chi-restraints excluded: chain 3C residue 799 TYR Chi-restraints excluded: chain 3C residue 842 VAL Chi-restraints excluded: chain 3E residue 50 MET Chi-restraints excluded: chain 3E residue 104 MET Chi-restraints excluded: chain 3E residue 187 GLU Chi-restraints excluded: chain 3E residue 201 VAL Chi-restraints excluded: chain 3E residue 294 GLU Chi-restraints excluded: chain 3E residue 314 GLU Chi-restraints excluded: chain 3E residue 348 HIS Chi-restraints excluded: chain 3F residue 202 VAL Chi-restraints excluded: chain 3F residue 211 MET Chi-restraints excluded: chain 3G residue 244 THR Chi-restraints excluded: chain 3G residue 253 THR Chi-restraints excluded: chain 3G residue 272 LYS Chi-restraints excluded: chain 3G residue 287 PHE Chi-restraints excluded: chain 3G residue 300 VAL Chi-restraints excluded: chain 3H residue 110 VAL Chi-restraints excluded: chain 3H residue 249 ARG Chi-restraints excluded: chain 3K residue 210 VAL Chi-restraints excluded: chain 3L residue 431 VAL Chi-restraints excluded: chain 3L residue 432 HIS Chi-restraints excluded: chain 3M residue 308 VAL Chi-restraints excluded: chain 3N residue 8 VAL Chi-restraints excluded: chain 3N residue 42 VAL Chi-restraints excluded: chain 3N residue 55 TYR Chi-restraints excluded: chain 3N residue 185 LEU Chi-restraints excluded: chain 3N residue 413 LEU Chi-restraints excluded: chain 3N residue 414 ASP Chi-restraints excluded: chain 3N residue 517 ILE Chi-restraints excluded: chain 3N residue 519 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1181 random chunks: chunk 1101 optimal weight: 20.0000 chunk 128 optimal weight: 9.9990 chunk 651 optimal weight: 20.0000 chunk 834 optimal weight: 50.0000 chunk 646 optimal weight: 8.9990 chunk 961 optimal weight: 4.9990 chunk 638 optimal weight: 1.9990 chunk 1138 optimal weight: 50.0000 chunk 712 optimal weight: 30.0000 chunk 693 optimal weight: 20.0000 chunk 525 optimal weight: 0.0670 overall best weight: 5.2126 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** SD 57 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** SD 226 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** SF 95 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** SF 110 GLN ** SF 203 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** SI 84 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** SK 7 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** SP 98 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** SQ 114 GLN SR 127 ASN ** SS 72 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** SS 85 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** SS 97 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** SV 35 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Sg 104 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Sg 191 HIS ** SC 267 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** SJ 154 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** SN 36 GLN ** SN 49 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** SW 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** SY 63 HIS ** SZ 89 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Sb 83 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Se 3 HIS ** 3A 209 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 3A 270 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 3B 502 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 3C 436 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 3C 600 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 3C 637 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 3C 670 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 3C 674 HIS ** 3C 762 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 3C 869 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 3E 390 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 3G 256 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 3H 141 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 3H 261 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 3H 336 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 3L 436 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 3M 199 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 3M 205 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 3N 242 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7297 moved from start: 0.2329 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.096 120081 Z= 0.525 Angle : 0.873 17.436 170579 Z= 0.436 Chirality : 0.051 0.371 20688 Planarity : 0.006 0.105 15553 Dihedral : 21.570 179.179 37944 Min Nonbonded Distance : 1.859 Molprobity Statistics. All-atom Clashscore : 15.63 Ramachandran Plot: Outliers : 0.14 % Allowed : 7.52 % Favored : 92.34 % Rotamer: Outliers : 4.40 % Allowed : 20.41 % Favored : 75.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.08 % Cis-general : 0.17 % Twisted Proline : 0.54 % Twisted General : 0.07 % 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: -1.05 (0.08), residues: 10145 helix: 0.66 (0.08), residues: 4564 sheet: -0.94 (0.13), residues: 1487 loop : -2.20 (0.09), residues: 4094 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.057 0.003 TRPSg 247 HIS 0.018 0.002 HIS3C 819 PHE 0.034 0.002 PHESJ 147 TYR 0.026 0.002 TYRSL 37 ARG 0.018 0.001 ARGSF 204 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 20290 Ramachandran restraints generated. 10145 Oldfield, 0 Emsley, 10145 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 20290 Ramachandran restraints generated. 10145 Oldfield, 0 Emsley, 10145 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1538 residues out of total 9059 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 337 poor density : 1201 time to evaluate : 7.469 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: Ln 9 ARG cc_start: 0.6562 (mtp85) cc_final: 0.5668 (ttp-170) REVERT: SA 205 ARG cc_start: 0.6923 (OUTLIER) cc_final: 0.6291 (mtp-110) REVERT: SD 103 GLU cc_start: 0.7191 (OUTLIER) cc_final: 0.6672 (mt-10) REVERT: SE 21 ASP cc_start: 0.8781 (OUTLIER) cc_final: 0.8314 (m-30) REVERT: SF 51 HIS cc_start: 0.7665 (OUTLIER) cc_final: 0.7347 (t70) REVERT: SF 82 ASN cc_start: 0.8511 (OUTLIER) cc_final: 0.8086 (m110) REVERT: SI 186 ASP cc_start: 0.7806 (OUTLIER) cc_final: 0.7470 (m-30) REVERT: SL 76 VAL cc_start: 0.9057 (OUTLIER) cc_final: 0.8666 (m) REVERT: SP 34 MET cc_start: 0.7558 (mmt) cc_final: 0.6509 (mmt) REVERT: SQ 7 LEU cc_start: 0.6016 (OUTLIER) cc_final: 0.5796 (pp) REVERT: SS 40 TYR cc_start: 0.8480 (t80) cc_final: 0.8084 (t80) REVERT: ST 8 ASP cc_start: 0.6511 (p0) cc_final: 0.6307 (p0) REVERT: ST 79 TYR cc_start: 0.7617 (m-80) cc_final: 0.7319 (m-80) REVERT: ST 126 GLN cc_start: 0.6777 (tp40) cc_final: 0.6491 (tm-30) REVERT: SU 34 LYS cc_start: 0.8078 (pptt) cc_final: 0.7476 (pttt) REVERT: SV 1 MET cc_start: 0.7814 (ppp) cc_final: 0.7341 (ptt) REVERT: SV 66 ASP cc_start: 0.8356 (OUTLIER) cc_final: 0.7777 (p0) REVERT: Sa 46 GLU cc_start: 0.8543 (OUTLIER) cc_final: 0.7642 (pt0) REVERT: Sc 44 ARG cc_start: 0.7842 (mmm-85) cc_final: 0.7386 (mmm160) REVERT: Sd 7 TYR cc_start: 0.8664 (t80) cc_final: 0.8373 (t80) REVERT: SC 254 ASP cc_start: 0.8222 (p0) cc_final: 0.7793 (p0) REVERT: SG 28 TYR cc_start: 0.8836 (m-10) cc_final: 0.8363 (m-10) REVERT: SG 126 ASP cc_start: 0.8047 (p0) cc_final: 0.7299 (p0) REVERT: SO 13 GLN cc_start: 0.0279 (OUTLIER) cc_final: -0.0724 (mp10) REVERT: SW 4 MET cc_start: 0.7468 (OUTLIER) cc_final: 0.6298 (mmt) REVERT: Sb 13 GLU cc_start: 0.6947 (OUTLIER) cc_final: 0.6007 (pp20) REVERT: Sb 33 MET cc_start: 0.8786 (OUTLIER) cc_final: 0.7641 (mmt) REVERT: CD 142 ASN cc_start: 0.8013 (OUTLIER) cc_final: 0.7167 (m110) REVERT: CD 143 TYR cc_start: 0.7909 (t80) cc_final: 0.7629 (t80) REVERT: 3B 469 ASP cc_start: 0.5519 (p0) cc_final: 0.5198 (p0) REVERT: 3B 501 ARG cc_start: -0.0816 (mmt180) cc_final: -0.1658 (tpt170) REVERT: 3B 505 ARG cc_start: 0.6206 (mtm-85) cc_final: 0.5621 (mtm110) REVERT: 3B 529 LYS cc_start: 0.6675 (mmmt) cc_final: 0.5978 (mmtt) REVERT: 3B 544 PHE cc_start: 0.3842 (OUTLIER) cc_final: 0.2579 (m-80) REVERT: 3B 549 MET cc_start: 0.1599 (mpp) cc_final: 0.1214 (mtm) REVERT: 3B 551 GLU cc_start: 0.1883 (mp0) cc_final: 0.1552 (mp0) REVERT: 3E 104 MET cc_start: 0.4474 (OUTLIER) cc_final: 0.3836 (pmm) REVERT: 3E 314 GLU cc_start: 0.6257 (OUTLIER) cc_final: 0.5785 (pm20) REVERT: 3F 211 MET cc_start: -0.0708 (OUTLIER) cc_final: -0.1990 (mtt) REVERT: 3F 309 MET cc_start: -0.0133 (mtt) cc_final: -0.0743 (ptp) REVERT: 3G 292 ASP cc_start: 0.4192 (t0) cc_final: 0.1768 (t0) REVERT: 3K 174 MET cc_start: -0.0527 (tpp) cc_final: -0.0790 (tpt) REVERT: 3L 304 MET cc_start: -0.1394 (ptt) cc_final: -0.2442 (ptt) REVERT: 3L 326 MET cc_start: 0.1038 (ppp) cc_final: 0.0720 (ppp) REVERT: 3L 401 MET cc_start: -0.0380 (OUTLIER) cc_final: -0.0820 (pmm) REVERT: 3N 214 GLU cc_start: 0.4803 (OUTLIER) cc_final: 0.4526 (pm20) REVERT: 3N 413 LEU cc_start: 0.7808 (OUTLIER) cc_final: 0.7298 (pp) outliers start: 337 outliers final: 258 residues processed: 1407 average time/residue: 0.9919 time to fit residues: 2421.3967 Evaluate side-chains 1444 residues out of total 9059 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 280 poor density : 1164 time to evaluate : 7.555 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain SA residue 8 LEU Chi-restraints excluded: chain SA residue 43 SER Chi-restraints excluded: chain SA residue 68 ILE Chi-restraints excluded: chain SA residue 81 ASN Chi-restraints excluded: chain SA residue 82 THR Chi-restraints excluded: chain SA residue 205 ARG Chi-restraints excluded: chain SB residue 44 ILE Chi-restraints excluded: chain SB residue 60 ASP Chi-restraints excluded: chain SB residue 66 VAL Chi-restraints excluded: chain SB residue 78 GLU Chi-restraints excluded: chain SB residue 88 THR Chi-restraints excluded: chain SB residue 106 THR Chi-restraints excluded: chain SD residue 51 LEU Chi-restraints excluded: chain SD residue 91 VAL Chi-restraints excluded: chain SD residue 99 ILE Chi-restraints excluded: chain SD residue 103 GLU Chi-restraints excluded: chain SD residue 164 VAL Chi-restraints excluded: chain SD residue 170 THR Chi-restraints excluded: chain SD residue 177 LEU Chi-restraints excluded: chain SD residue 181 VAL Chi-restraints excluded: chain SE residue 21 ASP Chi-restraints excluded: chain SE residue 48 LEU Chi-restraints excluded: chain SE residue 81 THR Chi-restraints excluded: chain SE residue 89 VAL Chi-restraints excluded: chain SE residue 111 VAL Chi-restraints excluded: chain SE residue 126 VAL Chi-restraints excluded: chain SE residue 169 ILE Chi-restraints excluded: chain SE residue 208 VAL Chi-restraints excluded: chain SF residue 51 HIS Chi-restraints excluded: chain SF residue 69 VAL Chi-restraints excluded: chain SF residue 82 ASN Chi-restraints excluded: chain SF residue 93 VAL Chi-restraints excluded: chain SF residue 133 THR Chi-restraints excluded: chain SF residue 147 VAL Chi-restraints excluded: chain SF residue 182 LYS Chi-restraints excluded: chain SH residue 25 GLN Chi-restraints excluded: chain SH residue 30 LEU Chi-restraints excluded: chain SH residue 33 ASN Chi-restraints excluded: chain SH residue 61 ILE Chi-restraints excluded: chain SH residue 64 VAL Chi-restraints excluded: chain SH residue 80 VAL Chi-restraints excluded: chain SH residue 95 ILE Chi-restraints excluded: chain SH residue 105 THR Chi-restraints excluded: chain SH residue 114 GLN Chi-restraints excluded: chain SH residue 172 THR Chi-restraints excluded: chain SI residue 7 ASN Chi-restraints excluded: chain SI residue 46 VAL Chi-restraints excluded: chain SI residue 77 ARG Chi-restraints excluded: chain SI residue 90 LEU Chi-restraints excluded: chain SI residue 93 THR Chi-restraints excluded: chain SI residue 144 LYS Chi-restraints excluded: chain SI residue 159 SER Chi-restraints excluded: chain SI residue 171 LEU Chi-restraints excluded: chain SI residue 186 ASP Chi-restraints excluded: chain SI residue 195 LEU Chi-restraints excluded: chain SK residue 22 VAL Chi-restraints excluded: chain SK residue 52 LEU Chi-restraints excluded: chain SK residue 70 TYR Chi-restraints excluded: chain SK residue 97 SER Chi-restraints excluded: chain SL residue 19 ASN Chi-restraints excluded: chain SL residue 33 LEU Chi-restraints excluded: chain SL residue 66 VAL Chi-restraints excluded: chain SL residue 72 ILE Chi-restraints excluded: chain SL residue 76 VAL Chi-restraints excluded: chain SL residue 124 ASP Chi-restraints excluded: chain SL residue 146 THR Chi-restraints excluded: chain SP residue 22 LEU Chi-restraints excluded: chain SP residue 29 SER Chi-restraints excluded: chain SP residue 85 ILE Chi-restraints excluded: chain SP residue 101 THR Chi-restraints excluded: chain SP residue 105 VAL Chi-restraints excluded: chain SP residue 126 VAL Chi-restraints excluded: chain SQ residue 7 LEU Chi-restraints excluded: chain SQ residue 10 VAL Chi-restraints excluded: chain SQ residue 20 THR Chi-restraints excluded: chain SQ residue 22 VAL Chi-restraints excluded: chain SQ residue 32 ILE Chi-restraints excluded: chain SQ residue 51 LEU Chi-restraints excluded: chain SQ residue 56 LEU Chi-restraints excluded: chain SQ residue 57 LEU Chi-restraints excluded: chain SQ residue 84 ILE Chi-restraints excluded: chain SQ residue 114 GLN Chi-restraints excluded: chain SR residue 40 ILE Chi-restraints excluded: chain SR residue 71 ILE Chi-restraints excluded: chain SR residue 113 SER Chi-restraints excluded: chain SR residue 123 THR Chi-restraints excluded: chain SS residue 15 VAL Chi-restraints excluded: chain SS residue 50 ILE Chi-restraints excluded: chain SS residue 53 THR Chi-restraints excluded: chain SS residue 67 VAL Chi-restraints excluded: chain SS residue 81 ASP Chi-restraints excluded: chain SS residue 83 PHE Chi-restraints excluded: chain SS residue 103 LEU Chi-restraints excluded: chain SS residue 117 ILE Chi-restraints excluded: chain SS residue 131 VAL Chi-restraints excluded: chain SS residue 136 THR Chi-restraints excluded: chain ST residue 6 VAL Chi-restraints excluded: chain ST residue 9 VAL Chi-restraints excluded: chain ST residue 15 VAL Chi-restraints excluded: chain ST residue 37 VAL Chi-restraints excluded: chain ST residue 55 THR Chi-restraints excluded: chain ST residue 74 SER Chi-restraints excluded: chain ST residue 76 THR Chi-restraints excluded: chain ST residue 99 VAL Chi-restraints excluded: chain ST residue 108 GLU Chi-restraints excluded: chain SU residue 23 THR Chi-restraints excluded: chain SU residue 25 THR Chi-restraints excluded: chain SU residue 40 ILE Chi-restraints excluded: chain SU residue 65 THR Chi-restraints excluded: chain SU residue 81 GLN Chi-restraints excluded: chain SU residue 115 THR Chi-restraints excluded: chain SV residue 13 VAL Chi-restraints excluded: chain SV residue 50 PHE Chi-restraints excluded: chain SV residue 62 MET Chi-restraints excluded: chain SV residue 66 ASP Chi-restraints excluded: chain SX residue 4 CYS Chi-restraints excluded: chain SX residue 26 GLN Chi-restraints excluded: chain SX residue 50 ILE Chi-restraints excluded: chain SX residue 85 VAL Chi-restraints excluded: chain SX residue 107 ARG Chi-restraints excluded: chain SX residue 131 LEU Chi-restraints excluded: chain Sa residue 30 VAL Chi-restraints excluded: chain Sa residue 46 GLU Chi-restraints excluded: chain Sa residue 53 ILE Chi-restraints excluded: chain Sa residue 59 PHE Chi-restraints excluded: chain Sa residue 63 VAL Chi-restraints excluded: chain Sa residue 69 VAL Chi-restraints excluded: chain Sc residue 11 LEU Chi-restraints excluded: chain Sc residue 28 THR Chi-restraints excluded: chain Sc residue 34 PHE Chi-restraints excluded: chain Sc residue 38 THR Chi-restraints excluded: chain Sc residue 46 VAL Chi-restraints excluded: chain Sg residue 21 ILE Chi-restraints excluded: chain Sg residue 30 MET Chi-restraints excluded: chain Sg residue 68 ASP Chi-restraints excluded: chain Sg residue 71 ILE Chi-restraints excluded: chain Sg residue 96 THR Chi-restraints excluded: chain Sg residue 102 VAL Chi-restraints excluded: chain Sg residue 126 ASP Chi-restraints excluded: chain Sg residue 131 LEU Chi-restraints excluded: chain Sg residue 137 VAL Chi-restraints excluded: chain Sg residue 142 VAL Chi-restraints excluded: chain Sg residue 197 THR Chi-restraints excluded: chain Sg residue 309 VAL Chi-restraints excluded: chain SC residue 63 VAL Chi-restraints excluded: chain SC residue 91 SER Chi-restraints excluded: chain SC residue 104 ASP Chi-restraints excluded: chain SC residue 137 VAL Chi-restraints excluded: chain SC residue 141 VAL Chi-restraints excluded: chain SC residue 147 VAL Chi-restraints excluded: chain SC residue 163 VAL Chi-restraints excluded: chain SC residue 220 ASP Chi-restraints excluded: chain SC residue 240 THR Chi-restraints excluded: chain SG residue 16 ILE Chi-restraints excluded: chain SG residue 19 ASP Chi-restraints excluded: chain SG residue 97 VAL Chi-restraints excluded: chain SG residue 102 VAL Chi-restraints excluded: chain SG residue 106 LEU Chi-restraints excluded: chain SG residue 110 ASN Chi-restraints excluded: chain SG residue 113 ILE Chi-restraints excluded: chain SG residue 148 SER Chi-restraints excluded: chain SG residue 163 ASN Chi-restraints excluded: chain SG residue 176 ILE Chi-restraints excluded: chain SG residue 180 VAL Chi-restraints excluded: chain SG residue 181 THR Chi-restraints excluded: chain SG residue 217 MET Chi-restraints excluded: chain SJ residue 2 PRO Chi-restraints excluded: chain SJ residue 61 LEU Chi-restraints excluded: chain SJ residue 62 THR Chi-restraints excluded: chain SJ residue 84 ILE Chi-restraints excluded: chain SJ residue 95 ASP Chi-restraints excluded: chain SJ residue 112 THR Chi-restraints excluded: chain SJ residue 114 VAL Chi-restraints excluded: chain SJ residue 122 SER Chi-restraints excluded: chain SJ residue 123 ILE Chi-restraints excluded: chain SJ residue 128 VAL Chi-restraints excluded: chain SJ residue 153 SER Chi-restraints excluded: chain SM residue 31 LEU Chi-restraints excluded: chain SM residue 42 LEU Chi-restraints excluded: chain SM residue 87 GLU Chi-restraints excluded: chain SN residue 22 VAL Chi-restraints excluded: chain SN residue 31 ASP Chi-restraints excluded: chain SN residue 67 THR Chi-restraints excluded: chain SN residue 86 GLU Chi-restraints excluded: chain SN residue 87 ASP Chi-restraints excluded: chain SN residue 131 THR Chi-restraints excluded: chain SO residue 13 GLN Chi-restraints excluded: chain SO residue 36 SER Chi-restraints excluded: chain SO residue 52 THR Chi-restraints excluded: chain SO residue 62 VAL Chi-restraints excluded: chain SO residue 65 ASP Chi-restraints excluded: chain SO residue 66 ARG Chi-restraints excluded: chain SO residue 67 ASP Chi-restraints excluded: chain SO residue 105 THR Chi-restraints excluded: chain SO residue 132 VAL Chi-restraints excluded: chain SW residue 2 VAL Chi-restraints excluded: chain SW residue 4 MET Chi-restraints excluded: chain SW residue 85 ASP Chi-restraints excluded: chain SW residue 115 GLU Chi-restraints excluded: chain SY residue 34 THR Chi-restraints excluded: chain SY residue 40 ILE Chi-restraints excluded: chain SY residue 51 THR Chi-restraints excluded: chain SY residue 103 SER Chi-restraints excluded: chain SY residue 117 VAL Chi-restraints excluded: chain SZ residue 69 THR Chi-restraints excluded: chain SZ residue 76 ARG Chi-restraints excluded: chain SZ residue 77 LEU Chi-restraints excluded: chain SZ residue 107 VAL Chi-restraints excluded: chain Sb residue 13 GLU Chi-restraints excluded: chain Sb residue 33 MET Chi-restraints excluded: chain Sb residue 53 VAL Chi-restraints excluded: chain Sb residue 64 CYS Chi-restraints excluded: chain Sb residue 79 PHE Chi-restraints excluded: chain Se residue 6 LEU Chi-restraints excluded: chain Sf residue 148 TYR Chi-restraints excluded: chain CD residue 100 LEU Chi-restraints excluded: chain CD residue 102 ARG Chi-restraints excluded: chain CD residue 135 GLU Chi-restraints excluded: chain CD residue 142 ASN Chi-restraints excluded: chain 3A residue 50 ILE Chi-restraints excluded: chain 3A residue 69 GLU Chi-restraints excluded: chain 3A residue 96 MET Chi-restraints excluded: chain 3A residue 197 LEU Chi-restraints excluded: chain 3A residue 228 MET Chi-restraints excluded: chain 3A residue 230 LEU Chi-restraints excluded: chain 3A residue 278 LYS Chi-restraints excluded: chain 3A residue 349 VAL Chi-restraints excluded: chain 3A residue 498 ASN Chi-restraints excluded: chain 3B residue 482 TRP Chi-restraints excluded: chain 3B residue 541 VAL Chi-restraints excluded: chain 3B residue 544 PHE Chi-restraints excluded: chain 3C residue 77 THR Chi-restraints excluded: chain 3C residue 333 LEU Chi-restraints excluded: chain 3C residue 446 THR Chi-restraints excluded: chain 3C residue 468 GLU Chi-restraints excluded: chain 3C residue 519 HIS Chi-restraints excluded: chain 3C residue 546 VAL Chi-restraints excluded: chain 3C residue 593 HIS Chi-restraints excluded: chain 3C residue 596 ASP Chi-restraints excluded: chain 3C residue 597 ASN Chi-restraints excluded: chain 3C residue 605 VAL Chi-restraints excluded: chain 3C residue 607 ILE Chi-restraints excluded: chain 3C residue 689 SER Chi-restraints excluded: chain 3C residue 788 LEU Chi-restraints excluded: chain 3C residue 799 TYR Chi-restraints excluded: chain 3C residue 842 VAL Chi-restraints excluded: chain 3E residue 50 MET Chi-restraints excluded: chain 3E residue 104 MET Chi-restraints excluded: chain 3E residue 187 GLU Chi-restraints excluded: chain 3E residue 201 VAL Chi-restraints excluded: chain 3E residue 294 GLU Chi-restraints excluded: chain 3E residue 314 GLU Chi-restraints excluded: chain 3E residue 348 HIS Chi-restraints excluded: chain 3E residue 351 ILE Chi-restraints excluded: chain 3F residue 202 VAL Chi-restraints excluded: chain 3F residue 211 MET Chi-restraints excluded: chain 3F residue 357 LEU Chi-restraints excluded: chain 3G residue 272 LYS Chi-restraints excluded: chain 3G residue 285 ILE Chi-restraints excluded: chain 3G residue 287 PHE Chi-restraints excluded: chain 3H residue 72 VAL Chi-restraints excluded: chain 3H residue 110 VAL Chi-restraints excluded: chain 3H residue 249 ARG Chi-restraints excluded: chain 3K residue 7 MET Chi-restraints excluded: chain 3K residue 210 VAL Chi-restraints excluded: chain 3L residue 401 MET Chi-restraints excluded: chain 3L residue 431 VAL Chi-restraints excluded: chain 3L residue 432 HIS Chi-restraints excluded: chain 3M residue 308 VAL Chi-restraints excluded: chain 3N residue 8 VAL Chi-restraints excluded: chain 3N residue 42 VAL Chi-restraints excluded: chain 3N residue 55 TYR Chi-restraints excluded: chain 3N residue 185 LEU Chi-restraints excluded: chain 3N residue 214 GLU Chi-restraints excluded: chain 3N residue 269 VAL Chi-restraints excluded: chain 3N residue 410 ARG Chi-restraints excluded: chain 3N residue 413 LEU Chi-restraints excluded: chain 3N residue 414 ASP Chi-restraints excluded: chain 3N residue 517 ILE Chi-restraints excluded: chain 3N residue 519 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1181 random chunks: chunk 704 optimal weight: 10.0000 chunk 454 optimal weight: 9.9990 chunk 679 optimal weight: 20.0000 chunk 342 optimal weight: 0.4980 chunk 223 optimal weight: 4.9990 chunk 220 optimal weight: 0.6980 chunk 723 optimal weight: 20.0000 chunk 775 optimal weight: 20.0000 chunk 562 optimal weight: 8.9990 chunk 106 optimal weight: 1.9990 chunk 894 optimal weight: 4.9990 overall best weight: 2.6386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** SD 57 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** SF 110 GLN ** SF 203 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** SI 99 ASN ** SK 7 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** SL 18 GLN ** SP 53 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** SP 98 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** SQ 114 GLN SR 127 ASN ** SS 72 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** SS 85 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** SS 97 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** SV 35 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Sc 26 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Sg 191 HIS ** SC 267 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** SJ 154 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** SN 36 GLN ** SN 49 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** SW 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** SY 94 HIS SY 106 GLN ** SZ 89 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Sb 83 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Se 3 HIS CD 129 GLN 3A 187 GLN ** 3A 209 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 3A 270 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 3B 502 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 3C 436 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 3C 637 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 3C 670 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 3C 819 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 3C 869 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 3E 121 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 3E 390 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 3G 256 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 3H 141 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 3H 261 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 3H 336 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 3L 366 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 3L 436 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 3M 199 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 3M 205 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** 3N 242 GLN 3N 322 ASN Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7240 moved from start: 0.2315 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.114 120081 Z= 0.300 Angle : 0.738 17.642 170579 Z= 0.374 Chirality : 0.044 0.329 20688 Planarity : 0.005 0.104 15553 Dihedral : 21.494 179.989 37944 Min Nonbonded Distance : 1.909 Molprobity Statistics. All-atom Clashscore : 14.45 Ramachandran Plot: Outliers : 0.12 % Allowed : 6.94 % Favored : 92.94 % Rotamer: Outliers : 4.03 % Allowed : 21.52 % Favored : 74.45 % Cbeta Deviations : 0.01 % Peptide Plane: Cis-proline : 1.08 % Cis-general : 0.17 % Twisted Proline : 0.54 % Twisted General : 0.05 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.91 (0.08), residues: 10145 helix: 0.78 (0.08), residues: 4562 sheet: -0.90 (0.13), residues: 1524 loop : -2.12 (0.09), residues: 4059 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.059 0.002 TRPSM 88 HIS 0.015 0.001 HIS3C 819 PHE 0.027 0.002 PHE3H 84 TYR 0.024 0.002 TYRSL 37 ARG 0.011 0.001 ARGSF 204 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 20290 Ramachandran restraints generated. 10145 Oldfield, 0 Emsley, 10145 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 20290 Ramachandran restraints generated. 10145 Oldfield, 0 Emsley, 10145 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1555 residues out of total 9059 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 309 poor density : 1246 time to evaluate : 7.570 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: Ln 9 ARG cc_start: 0.6730 (mtp85) cc_final: 0.5798 (ttp-170) REVERT: SA 205 ARG cc_start: 0.6919 (OUTLIER) cc_final: 0.6298 (mtp-110) REVERT: SB 172 MET cc_start: 0.8628 (mtm) cc_final: 0.8268 (mtm) REVERT: SD 103 GLU cc_start: 0.7043 (OUTLIER) cc_final: 0.6524 (mt-10) REVERT: SE 21 ASP cc_start: 0.8699 (OUTLIER) cc_final: 0.8236 (m-30) REVERT: SF 51 HIS cc_start: 0.7565 (OUTLIER) cc_final: 0.7262 (t70) REVERT: SF 82 ASN cc_start: 0.8513 (OUTLIER) cc_final: 0.8195 (m110) REVERT: SI 186 ASP cc_start: 0.7670 (OUTLIER) cc_final: 0.7367 (m-30) REVERT: SL 76 VAL cc_start: 0.8996 (OUTLIER) cc_final: 0.8649 (m) REVERT: SP 34 MET cc_start: 0.7662 (mmt) cc_final: 0.6753 (mmt) REVERT: SQ 7 LEU cc_start: 0.6112 (OUTLIER) cc_final: 0.5834 (pp) REVERT: SQ 87 SER cc_start: 0.8050 (t) cc_final: 0.7273 (p) REVERT: SR 33 ARG cc_start: 0.8423 (mmm-85) cc_final: 0.7674 (mmt-90) REVERT: SS 5 ILE cc_start: 0.4876 (OUTLIER) cc_final: 0.4619 (tp) REVERT: SS 40 TYR cc_start: 0.8396 (t80) cc_final: 0.8024 (t80) REVERT: ST 79 TYR cc_start: 0.7609 (m-80) cc_final: 0.7284 (m-80) REVERT: SU 34 LYS cc_start: 0.7899 (pptt) cc_final: 0.7692 (pttt) REVERT: SV 1 MET cc_start: 0.7794 (ppp) cc_final: 0.7301 (ptt) REVERT: Sa 46 GLU cc_start: 0.8534 (OUTLIER) cc_final: 0.7640 (pt0) REVERT: Sc 44 ARG cc_start: 0.7780 (mmm-85) cc_final: 0.7330 (mmm160) REVERT: Sd 7 TYR cc_start: 0.8530 (t80) cc_final: 0.8262 (t80) REVERT: SC 254 ASP cc_start: 0.8116 (p0) cc_final: 0.7677 (p0) REVERT: SG 28 TYR cc_start: 0.8777 (m-10) cc_final: 0.8376 (m-10) REVERT: SJ 59 GLU cc_start: 0.7536 (OUTLIER) cc_final: 0.7218 (tm-30) REVERT: SJ 154 GLN cc_start: 0.8683 (tm-30) cc_final: 0.8217 (tt0) REVERT: SO 13 GLN cc_start: 0.0327 (OUTLIER) cc_final: -0.0706 (mp10) REVERT: SW 4 MET cc_start: 0.7422 (OUTLIER) cc_final: 0.6280 (mmt) REVERT: SY 86 GLU cc_start: 0.8264 (tp30) cc_final: 0.7925 (tp30) REVERT: Sb 33 MET cc_start: 0.8780 (OUTLIER) cc_final: 0.7719 (mmt) REVERT: Sb 75 GLU cc_start: 0.7203 (pm20) cc_final: 0.6707 (pm20) REVERT: CD 143 TYR cc_start: 0.7900 (t80) cc_final: 0.7649 (t80) REVERT: 3B 501 ARG cc_start: -0.0700 (mmt180) cc_final: -0.1504 (tpt170) REVERT: 3B 505 ARG cc_start: 0.6011 (mtm-85) cc_final: 0.5567 (mtm110) REVERT: 3B 529 LYS cc_start: 0.6521 (mmmt) cc_final: 0.6171 (mmtt) REVERT: 3B 544 PHE cc_start: 0.3822 (OUTLIER) cc_final: 0.2864 (m-10) REVERT: 3B 549 MET cc_start: 0.1446 (mpp) cc_final: 0.1074 (mtm) REVERT: 3E 104 MET cc_start: 0.4682 (OUTLIER) cc_final: 0.3984 (pmm) REVERT: 3E 314 GLU cc_start: 0.6185 (OUTLIER) cc_final: 0.5670 (pm20) REVERT: 3E 420 MET cc_start: 0.4859 (OUTLIER) cc_final: 0.4576 (tpp) REVERT: 3F 211 MET cc_start: -0.0638 (OUTLIER) cc_final: -0.1924 (mtt) REVERT: 3F 309 MET cc_start: -0.0204 (mtt) cc_final: -0.0845 (ptp) REVERT: 3G 251 ARG cc_start: 0.6133 (mmm160) cc_final: 0.5730 (mmt-90) REVERT: 3K 174 MET cc_start: -0.0548 (tpp) cc_final: -0.0762 (tpt) REVERT: 3L 268 MET cc_start: -0.2661 (ptt) cc_final: -0.3501 (ptt) REVERT: 3L 304 MET cc_start: -0.1382 (ptt) cc_final: -0.2007 (ptt) REVERT: 3L 326 MET cc_start: 0.1171 (ppp) cc_final: 0.0933 (ppp) REVERT: 3L 401 MET cc_start: -0.0543 (OUTLIER) cc_final: -0.0784 (pmm) REVERT: 3N 413 LEU cc_start: 0.7878 (OUTLIER) cc_final: 0.7493 (pp) REVERT: 3N 522 LEU cc_start: 0.0667 (OUTLIER) cc_final: 0.0130 (mm) outliers start: 309 outliers final: 242 residues processed: 1430 average time/residue: 0.9816 time to fit residues: 2438.2553 Evaluate side-chains 1466 residues out of total 9059 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 264 poor density : 1202 time to evaluate : 7.457 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain SA residue 8 LEU Chi-restraints excluded: chain SA residue 43 SER Chi-restraints excluded: chain SA residue 81 ASN Chi-restraints excluded: chain SA residue 82 THR Chi-restraints excluded: chain SA residue 205 ARG Chi-restraints excluded: chain SB residue 60 ASP Chi-restraints excluded: chain SB residue 66 VAL Chi-restraints excluded: chain SB residue 78 GLU Chi-restraints excluded: chain SB residue 88 THR Chi-restraints excluded: chain SD residue 51 LEU Chi-restraints excluded: chain SD residue 91 VAL Chi-restraints excluded: chain SD residue 99 ILE Chi-restraints excluded: chain SD residue 103 GLU Chi-restraints excluded: chain SD residue 128 GLU Chi-restraints excluded: chain SD residue 164 VAL Chi-restraints excluded: chain SD residue 170 THR Chi-restraints excluded: chain SD residue 181 VAL Chi-restraints excluded: chain SE residue 21 ASP Chi-restraints excluded: chain SE residue 81 THR Chi-restraints excluded: chain SE residue 89 VAL Chi-restraints excluded: chain SE residue 111 VAL Chi-restraints excluded: chain SE residue 126 VAL Chi-restraints excluded: chain SF residue 51 HIS Chi-restraints excluded: chain SF residue 69 VAL Chi-restraints excluded: chain SF residue 82 ASN Chi-restraints excluded: chain SF residue 93 VAL Chi-restraints excluded: chain SF residue 110 GLN Chi-restraints excluded: chain SF residue 133 THR Chi-restraints excluded: chain SF residue 147 VAL Chi-restraints excluded: chain SF residue 165 ASN Chi-restraints excluded: chain SF residue 182 LYS Chi-restraints excluded: chain SH residue 25 GLN Chi-restraints excluded: chain SH residue 30 LEU Chi-restraints excluded: chain SH residue 33 ASN Chi-restraints excluded: chain SH residue 64 VAL Chi-restraints excluded: chain SH residue 95 ILE Chi-restraints excluded: chain SH residue 105 THR Chi-restraints excluded: chain SH residue 114 GLN Chi-restraints excluded: chain SI residue 46 VAL Chi-restraints excluded: chain SI residue 90 LEU Chi-restraints excluded: chain SI residue 91 VAL Chi-restraints excluded: chain SI residue 93 THR Chi-restraints excluded: chain SI residue 99 ASN Chi-restraints excluded: chain SI residue 144 LYS Chi-restraints excluded: chain SI residue 159 SER Chi-restraints excluded: chain SI residue 171 LEU Chi-restraints excluded: chain SI residue 186 ASP Chi-restraints excluded: chain SI residue 190 LEU Chi-restraints excluded: chain SI residue 195 LEU Chi-restraints excluded: chain SK residue 22 VAL Chi-restraints excluded: chain SK residue 52 LEU Chi-restraints excluded: chain SK residue 97 SER Chi-restraints excluded: chain SL residue 19 ASN Chi-restraints excluded: chain SL residue 33 LEU Chi-restraints excluded: chain SL residue 66 VAL Chi-restraints excluded: chain SL residue 72 ILE Chi-restraints excluded: chain SL residue 76 VAL Chi-restraints excluded: chain SL residue 124 ASP Chi-restraints excluded: chain SL residue 146 THR Chi-restraints excluded: chain SP residue 22 LEU Chi-restraints excluded: chain SP residue 29 SER Chi-restraints excluded: chain SP residue 101 THR Chi-restraints excluded: chain SP residue 126 VAL Chi-restraints excluded: chain SQ residue 7 LEU Chi-restraints excluded: chain SQ residue 10 VAL Chi-restraints excluded: chain SQ residue 20 THR Chi-restraints excluded: chain SQ residue 22 VAL Chi-restraints excluded: chain SQ residue 32 ILE Chi-restraints excluded: chain SQ residue 56 LEU Chi-restraints excluded: chain SQ residue 57 LEU Chi-restraints excluded: chain SQ residue 84 ILE Chi-restraints excluded: chain SQ residue 114 GLN Chi-restraints excluded: chain SR residue 40 ILE Chi-restraints excluded: chain SR residue 71 ILE Chi-restraints excluded: chain SR residue 93 GLN Chi-restraints excluded: chain SR residue 123 THR Chi-restraints excluded: chain SS residue 5 ILE Chi-restraints excluded: chain SS residue 15 VAL Chi-restraints excluded: chain SS residue 50 ILE Chi-restraints excluded: chain SS residue 53 THR Chi-restraints excluded: chain SS residue 67 VAL Chi-restraints excluded: chain SS residue 81 ASP Chi-restraints excluded: chain SS residue 103 LEU Chi-restraints excluded: chain SS residue 117 ILE Chi-restraints excluded: chain SS residue 131 VAL Chi-restraints excluded: chain SS residue 136 THR Chi-restraints excluded: chain ST residue 9 VAL Chi-restraints excluded: chain ST residue 15 VAL Chi-restraints excluded: chain ST residue 37 VAL Chi-restraints excluded: chain ST residue 55 THR Chi-restraints excluded: chain ST residue 66 LEU Chi-restraints excluded: chain ST residue 74 SER Chi-restraints excluded: chain ST residue 76 THR Chi-restraints excluded: chain ST residue 108 GLU Chi-restraints excluded: chain SU residue 23 THR Chi-restraints excluded: chain SU residue 24 LEU Chi-restraints excluded: chain SU residue 25 THR Chi-restraints excluded: chain SU residue 40 ILE Chi-restraints excluded: chain SU residue 47 ASN Chi-restraints excluded: chain SU residue 65 THR Chi-restraints excluded: chain SU residue 81 GLN Chi-restraints excluded: chain SV residue 13 VAL Chi-restraints excluded: chain SV residue 62 MET Chi-restraints excluded: chain SX residue 4 CYS Chi-restraints excluded: chain SX residue 26 GLN Chi-restraints excluded: chain SX residue 82 THR Chi-restraints excluded: chain SX residue 85 VAL Chi-restraints excluded: chain SX residue 107 ARG Chi-restraints excluded: chain SX residue 131 LEU Chi-restraints excluded: chain Sa residue 25 ASN Chi-restraints excluded: chain Sa residue 30 VAL Chi-restraints excluded: chain Sa residue 46 GLU Chi-restraints excluded: chain Sa residue 59 PHE Chi-restraints excluded: chain Sa residue 63 VAL Chi-restraints excluded: chain Sa residue 69 VAL Chi-restraints excluded: chain Sc residue 11 LEU Chi-restraints excluded: chain Sc residue 28 THR Chi-restraints excluded: chain Sc residue 34 PHE Chi-restraints excluded: chain Sc residue 38 THR Chi-restraints excluded: chain Sc residue 46 VAL Chi-restraints excluded: chain Sg residue 21 ILE Chi-restraints excluded: chain Sg residue 30 MET Chi-restraints excluded: chain Sg residue 68 ASP Chi-restraints excluded: chain Sg residue 71 ILE Chi-restraints excluded: chain Sg residue 92 LEU Chi-restraints excluded: chain Sg residue 96 THR Chi-restraints excluded: chain Sg residue 102 VAL Chi-restraints excluded: chain Sg residue 126 ASP Chi-restraints excluded: chain Sg residue 131 LEU Chi-restraints excluded: chain Sg residue 137 VAL Chi-restraints excluded: chain Sg residue 142 VAL Chi-restraints excluded: chain Sg residue 197 THR Chi-restraints excluded: chain Sg residue 225 LYS Chi-restraints excluded: chain Sg residue 247 TRP Chi-restraints excluded: chain Sg residue 309 VAL Chi-restraints excluded: chain SC residue 63 VAL Chi-restraints excluded: chain SC residue 91 SER Chi-restraints excluded: chain SC residue 104 ASP Chi-restraints excluded: chain SC residue 137 VAL Chi-restraints excluded: chain SC residue 141 VAL Chi-restraints excluded: chain SC residue 147 VAL Chi-restraints excluded: chain SG residue 16 ILE Chi-restraints excluded: chain SG residue 97 VAL Chi-restraints excluded: chain SG residue 102 VAL Chi-restraints excluded: chain SG residue 110 ASN Chi-restraints excluded: chain SG residue 113 ILE Chi-restraints excluded: chain SG residue 148 SER Chi-restraints excluded: chain SG residue 163 ASN Chi-restraints excluded: chain SG residue 176 ILE Chi-restraints excluded: chain SG residue 180 VAL Chi-restraints excluded: chain SG residue 181 THR Chi-restraints excluded: chain SG residue 217 MET Chi-restraints excluded: chain SJ residue 59 GLU Chi-restraints excluded: chain SJ residue 61 LEU Chi-restraints excluded: chain SJ residue 62 THR Chi-restraints excluded: chain SJ residue 84 ILE Chi-restraints excluded: chain SJ residue 95 ASP Chi-restraints excluded: chain SJ residue 112 THR Chi-restraints excluded: chain SJ residue 114 VAL Chi-restraints excluded: chain SJ residue 122 SER Chi-restraints excluded: chain SJ residue 123 ILE Chi-restraints excluded: chain SJ residue 128 VAL Chi-restraints excluded: chain SJ residue 153 SER Chi-restraints excluded: chain SJ residue 160 SER Chi-restraints excluded: chain SM residue 31 LEU Chi-restraints excluded: chain SM residue 42 LEU Chi-restraints excluded: chain SM residue 87 GLU Chi-restraints excluded: chain SN residue 22 VAL Chi-restraints excluded: chain SN residue 31 ASP Chi-restraints excluded: chain SN residue 84 LEU Chi-restraints excluded: chain SN residue 86 GLU Chi-restraints excluded: chain SN residue 87 ASP Chi-restraints excluded: chain SN residue 131 THR Chi-restraints excluded: chain SO residue 13 GLN Chi-restraints excluded: chain SO residue 52 THR Chi-restraints excluded: chain SO residue 62 VAL Chi-restraints excluded: chain SO residue 65 ASP Chi-restraints excluded: chain SO residue 66 ARG Chi-restraints excluded: chain SO residue 67 ASP Chi-restraints excluded: chain SO residue 105 THR Chi-restraints excluded: chain SO residue 132 VAL Chi-restraints excluded: chain SW residue 2 VAL Chi-restraints excluded: chain SW residue 4 MET Chi-restraints excluded: chain SW residue 85 ASP Chi-restraints excluded: chain SY residue 34 THR Chi-restraints excluded: chain SY residue 40 ILE Chi-restraints excluded: chain SY residue 51 THR Chi-restraints excluded: chain SY residue 103 SER Chi-restraints excluded: chain SY residue 117 VAL Chi-restraints excluded: chain SZ residue 69 THR Chi-restraints excluded: chain SZ residue 76 ARG Chi-restraints excluded: chain SZ residue 107 VAL Chi-restraints excluded: chain Sb residue 33 MET Chi-restraints excluded: chain Sb residue 43 ILE Chi-restraints excluded: chain Sb residue 64 CYS Chi-restraints excluded: chain Sb residue 79 PHE Chi-restraints excluded: chain Se residue 6 LEU Chi-restraints excluded: chain Sf residue 148 TYR Chi-restraints excluded: chain CD residue 100 LEU Chi-restraints excluded: chain CD residue 102 ARG Chi-restraints excluded: chain CD residue 135 GLU Chi-restraints excluded: chain CD residue 142 ASN Chi-restraints excluded: chain 3A residue 19 LEU Chi-restraints excluded: chain 3A residue 50 ILE Chi-restraints excluded: chain 3A residue 69 GLU Chi-restraints excluded: chain 3A residue 96 MET Chi-restraints excluded: chain 3A residue 197 LEU Chi-restraints excluded: chain 3A residue 228 MET Chi-restraints excluded: chain 3A residue 230 LEU Chi-restraints excluded: chain 3A residue 349 VAL Chi-restraints excluded: chain 3A residue 498 ASN Chi-restraints excluded: chain 3B residue 482 TRP Chi-restraints excluded: chain 3B residue 494 THR Chi-restraints excluded: chain 3B residue 541 VAL Chi-restraints excluded: chain 3B residue 544 PHE Chi-restraints excluded: chain 3C residue 77 THR Chi-restraints excluded: chain 3C residue 333 LEU Chi-restraints excluded: chain 3C residue 354 LEU Chi-restraints excluded: chain 3C residue 446 THR Chi-restraints excluded: chain 3C residue 452 ASP Chi-restraints excluded: chain 3C residue 453 GLU Chi-restraints excluded: chain 3C residue 468 GLU Chi-restraints excluded: chain 3C residue 519 HIS Chi-restraints excluded: chain 3C residue 546 VAL Chi-restraints excluded: chain 3C residue 596 ASP Chi-restraints excluded: chain 3C residue 597 ASN Chi-restraints excluded: chain 3C residue 605 VAL Chi-restraints excluded: chain 3C residue 684 CYS Chi-restraints excluded: chain 3C residue 689 SER Chi-restraints excluded: chain 3C residue 788 LEU Chi-restraints excluded: chain 3C residue 799 TYR Chi-restraints excluded: chain 3C residue 842 VAL Chi-restraints excluded: chain 3E residue 104 MET Chi-restraints excluded: chain 3E residue 187 GLU Chi-restraints excluded: chain 3E residue 201 VAL Chi-restraints excluded: chain 3E residue 294 GLU Chi-restraints excluded: chain 3E residue 314 GLU Chi-restraints excluded: chain 3E residue 348 HIS Chi-restraints excluded: chain 3E residue 420 MET Chi-restraints excluded: chain 3F residue 202 VAL Chi-restraints excluded: chain 3F residue 211 MET Chi-restraints excluded: chain 3F residue 253 MET Chi-restraints excluded: chain 3F residue 357 LEU Chi-restraints excluded: chain 3G residue 272 LYS Chi-restraints excluded: chain 3G residue 285 ILE Chi-restraints excluded: chain 3G residue 287 PHE Chi-restraints excluded: chain 3H residue 72 VAL Chi-restraints excluded: chain 3H residue 84 PHE Chi-restraints excluded: chain 3H residue 110 VAL Chi-restraints excluded: chain 3H residue 249 ARG Chi-restraints excluded: chain 3L residue 401 MET Chi-restraints excluded: chain 3L residue 431 VAL Chi-restraints excluded: chain 3L residue 432 HIS Chi-restraints excluded: chain 3M residue 308 VAL Chi-restraints excluded: chain 3N residue 8 VAL Chi-restraints excluded: chain 3N residue 42 VAL Chi-restraints excluded: chain 3N residue 55 TYR Chi-restraints excluded: chain 3N residue 185 LEU Chi-restraints excluded: chain 3N residue 269 VAL Chi-restraints excluded: chain 3N residue 413 LEU Chi-restraints excluded: chain 3N residue 414 ASP Chi-restraints excluded: chain 3N residue 517 ILE Chi-restraints excluded: chain 3N residue 519 VAL Chi-restraints excluded: chain 3N residue 522 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1181 random chunks: chunk 1035 optimal weight: 9.9990 chunk 1090 optimal weight: 9.9990 chunk 994 optimal weight: 40.0000 chunk 1060 optimal weight: 40.0000 chunk 638 optimal weight: 0.5980 chunk 462 optimal weight: 0.8980 chunk 832 optimal weight: 1.9990 chunk 325 optimal weight: 0.6980 chunk 958 optimal weight: 0.8980 chunk 1003 optimal weight: 30.0000 chunk 1057 optimal weight: 20.0000 overall best weight: 1.0182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: SB 76 ASN ** SD 57 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** SF 110 GLN ** SH 114 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** SI 7 ASN ** SI 181 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** SK 7 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** SP 53 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** SP 98 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** SQ 80 GLN SQ 114 GLN SR 127 ASN ** SS 72 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** SS 85 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** SS 97 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** SV 35 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Sc 26 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** SC 267 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** SJ 154 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** SN 36 GLN ** SN 49 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** SN 105 ASN SW 24 GLN ** SW 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** SY 124 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** SZ 89 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Sb 83 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Se 3 HIS ** 3A 270 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 3B 502 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 3C 637 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 3C 670 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 3C 819 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 3C 869 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 3E 121 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 3E 390 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 3G 256 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 3H 141 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 3H 261 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 3H 336 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 3L 363 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 3L 364 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 3L 366 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 3L 436 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 3M 199 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 3M 205 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7171 moved from start: 0.2379 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.104 120081 Z= 0.186 Angle : 0.681 18.096 170579 Z= 0.344 Chirality : 0.041 0.406 20688 Planarity : 0.005 0.103 15553 Dihedral : 21.368 178.564 37944 Min Nonbonded Distance : 1.975 Molprobity Statistics. All-atom Clashscore : 13.86 Ramachandran Plot: Outliers : 0.10 % Allowed : 6.55 % Favored : 93.35 % Rotamer: Outliers : 3.08 % Allowed : 22.64 % Favored : 74.28 % Cbeta Deviations : 0.01 % Peptide Plane: Cis-proline : 1.08 % Cis-general : 0.17 % Twisted Proline : 0.54 % Twisted General : 0.04 % 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: -0.72 (0.08), residues: 10145 helix: 0.92 (0.08), residues: 4571 sheet: -0.75 (0.13), residues: 1552 loop : -2.03 (0.09), residues: 4022 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.052 0.002 TRPSg 247 HIS 0.015 0.001 HIS3C 593 PHE 0.031 0.001 PHESg 27 TYR 0.022 0.001 TYRSL 37 ARG 0.008 0.000 ARGSQ 71 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 20290 Ramachandran restraints generated. 10145 Oldfield, 0 Emsley, 10145 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 20290 Ramachandran restraints generated. 10145 Oldfield, 0 Emsley, 10145 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1507 residues out of total 9059 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 236 poor density : 1271 time to evaluate : 7.526 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: Ln 9 ARG cc_start: 0.6606 (mtp85) cc_final: 0.5795 (ttp-170) REVERT: SA 14 ASP cc_start: 0.8027 (m-30) cc_final: 0.7803 (m-30) REVERT: SA 205 ARG cc_start: 0.6832 (OUTLIER) cc_final: 0.6168 (mtp-110) REVERT: SB 172 MET cc_start: 0.8623 (mtm) cc_final: 0.8318 (mtm) REVERT: SB 228 LEU cc_start: 0.7770 (tt) cc_final: 0.7159 (tt) REVERT: SD 128 GLU cc_start: 0.7123 (OUTLIER) cc_final: 0.6837 (pm20) REVERT: SE 21 ASP cc_start: 0.8564 (OUTLIER) cc_final: 0.8121 (m-30) REVERT: SF 51 HIS cc_start: 0.7506 (OUTLIER) cc_final: 0.7218 (t70) REVERT: SK 15 LEU cc_start: 0.8831 (tp) cc_final: 0.8494 (tp) REVERT: SL 76 VAL cc_start: 0.8853 (OUTLIER) cc_final: 0.8639 (m) REVERT: SP 34 MET cc_start: 0.7716 (mmt) cc_final: 0.6770 (mmt) REVERT: SQ 7 LEU cc_start: 0.6068 (OUTLIER) cc_final: 0.5815 (pp) REVERT: SQ 87 SER cc_start: 0.7979 (t) cc_final: 0.7276 (p) REVERT: SS 5 ILE cc_start: 0.4353 (OUTLIER) cc_final: 0.4147 (tp) REVERT: SS 40 TYR cc_start: 0.8288 (t80) cc_final: 0.7944 (t80) REVERT: ST 79 TYR cc_start: 0.7549 (m-80) cc_final: 0.7187 (m-80) REVERT: ST 88 MET cc_start: 0.8793 (mmt) cc_final: 0.8558 (mmm) REVERT: SU 34 LYS cc_start: 0.7746 (pptt) cc_final: 0.7385 (pttt) REVERT: SV 1 MET cc_start: 0.7709 (ppp) cc_final: 0.7205 (ptt) REVERT: Sa 46 GLU cc_start: 0.8317 (OUTLIER) cc_final: 0.8114 (pm20) REVERT: Sc 44 ARG cc_start: 0.7674 (mmm-85) cc_final: 0.7298 (mmm160) REVERT: Sd 7 TYR cc_start: 0.8483 (t80) cc_final: 0.8207 (t80) REVERT: SC 254 ASP cc_start: 0.8043 (p0) cc_final: 0.7624 (p0) REVERT: SG 28 TYR cc_start: 0.8668 (m-10) cc_final: 0.8417 (m-10) REVERT: SJ 59 GLU cc_start: 0.7557 (OUTLIER) cc_final: 0.7223 (tm-30) REVERT: SJ 144 ILE cc_start: 0.8293 (mm) cc_final: 0.7921 (mm) REVERT: SJ 154 GLN cc_start: 0.8541 (tm-30) cc_final: 0.8252 (tt0) REVERT: SW 4 MET cc_start: 0.7440 (OUTLIER) cc_final: 0.6391 (mmt) REVERT: SY 86 GLU cc_start: 0.8059 (tp30) cc_final: 0.7727 (tp30) REVERT: Sb 33 MET cc_start: 0.8639 (OUTLIER) cc_final: 0.7951 (mmt) REVERT: Sb 75 GLU cc_start: 0.6946 (pm20) cc_final: 0.6317 (pm20) REVERT: CD 143 TYR cc_start: 0.7736 (t80) cc_final: 0.7388 (t80) REVERT: 3B 529 LYS cc_start: 0.6409 (mmmt) cc_final: 0.5997 (mmtt) REVERT: 3B 544 PHE cc_start: 0.2930 (OUTLIER) cc_final: 0.2105 (m-10) REVERT: 3C 613 MET cc_start: 0.6531 (ttm) cc_final: 0.6249 (ttm) REVERT: 3E 104 MET cc_start: 0.4892 (pmm) cc_final: 0.4297 (pmm) REVERT: 3E 314 GLU cc_start: 0.6258 (OUTLIER) cc_final: 0.5786 (pm20) REVERT: 3E 420 MET cc_start: 0.4860 (tpp) cc_final: 0.4607 (tpp) REVERT: 3F 309 MET cc_start: -0.0287 (mtt) cc_final: -0.0915 (ptp) REVERT: 3L 268 MET cc_start: -0.2743 (ptt) cc_final: -0.3601 (ptt) REVERT: 3L 304 MET cc_start: -0.1389 (ptt) cc_final: -0.2292 (ptt) REVERT: 3L 377 MET cc_start: 0.4502 (mpp) cc_final: 0.4285 (mpp) REVERT: 3L 401 MET cc_start: -0.0374 (OUTLIER) cc_final: -0.0675 (pmm) REVERT: 3N 405 ASN cc_start: 0.6926 (t0) cc_final: 0.6579 (t0) REVERT: 3N 413 LEU cc_start: 0.7810 (OUTLIER) cc_final: 0.7441 (pp) REVERT: 3N 522 LEU cc_start: 0.0173 (OUTLIER) cc_final: -0.0338 (mm) outliers start: 236 outliers final: 182 residues processed: 1404 average time/residue: 0.9863 time to fit residues: 2406.2424 Evaluate side-chains 1410 residues out of total 9059 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 198 poor density : 1212 time to evaluate : 7.443 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain SA residue 8 LEU Chi-restraints excluded: chain SA residue 43 SER Chi-restraints excluded: chain SA residue 81 ASN Chi-restraints excluded: chain SA residue 205 ARG Chi-restraints excluded: chain SB residue 78 GLU Chi-restraints excluded: chain SB residue 88 THR Chi-restraints excluded: chain SD residue 51 LEU Chi-restraints excluded: chain SD residue 91 VAL Chi-restraints excluded: chain SD residue 128 GLU Chi-restraints excluded: chain SD residue 164 VAL Chi-restraints excluded: chain SE residue 21 ASP Chi-restraints excluded: chain SE residue 89 VAL Chi-restraints excluded: chain SE residue 126 VAL Chi-restraints excluded: chain SF residue 51 HIS Chi-restraints excluded: chain SF residue 69 VAL Chi-restraints excluded: chain SF residue 93 VAL Chi-restraints excluded: chain SF residue 110 GLN Chi-restraints excluded: chain SF residue 111 VAL Chi-restraints excluded: chain SF residue 133 THR Chi-restraints excluded: chain SH residue 25 GLN Chi-restraints excluded: chain SH residue 33 ASN Chi-restraints excluded: chain SH residue 64 VAL Chi-restraints excluded: chain SH residue 95 ILE Chi-restraints excluded: chain SH residue 114 GLN Chi-restraints excluded: chain SI residue 90 LEU Chi-restraints excluded: chain SI residue 91 VAL Chi-restraints excluded: chain SI residue 93 THR Chi-restraints excluded: chain SI residue 144 LYS Chi-restraints excluded: chain SI residue 171 LEU Chi-restraints excluded: chain SK residue 22 VAL Chi-restraints excluded: chain SK residue 77 GLN Chi-restraints excluded: chain SL residue 19 ASN Chi-restraints excluded: chain SL residue 33 LEU Chi-restraints excluded: chain SL residue 66 VAL Chi-restraints excluded: chain SL residue 72 ILE Chi-restraints excluded: chain SL residue 76 VAL Chi-restraints excluded: chain SL residue 124 ASP Chi-restraints excluded: chain SL residue 146 THR Chi-restraints excluded: chain SP residue 29 SER Chi-restraints excluded: chain SP residue 83 MET Chi-restraints excluded: chain SP residue 126 VAL Chi-restraints excluded: chain SQ residue 7 LEU Chi-restraints excluded: chain SQ residue 10 VAL Chi-restraints excluded: chain SQ residue 22 VAL Chi-restraints excluded: chain SQ residue 57 LEU Chi-restraints excluded: chain SQ residue 84 ILE Chi-restraints excluded: chain SQ residue 114 GLN Chi-restraints excluded: chain SR residue 40 ILE Chi-restraints excluded: chain SR residue 71 ILE Chi-restraints excluded: chain SR residue 93 GLN Chi-restraints excluded: chain SS residue 5 ILE Chi-restraints excluded: chain SS residue 15 VAL Chi-restraints excluded: chain SS residue 53 THR Chi-restraints excluded: chain SS residue 67 VAL Chi-restraints excluded: chain SS residue 81 ASP Chi-restraints excluded: chain SS residue 103 LEU Chi-restraints excluded: chain SS residue 131 VAL Chi-restraints excluded: chain SS residue 136 THR Chi-restraints excluded: chain ST residue 9 VAL Chi-restraints excluded: chain ST residue 15 VAL Chi-restraints excluded: chain ST residue 66 LEU Chi-restraints excluded: chain ST residue 74 SER Chi-restraints excluded: chain ST residue 76 THR Chi-restraints excluded: chain ST residue 108 GLU Chi-restraints excluded: chain SU residue 23 THR Chi-restraints excluded: chain SU residue 24 LEU Chi-restraints excluded: chain SU residue 25 THR Chi-restraints excluded: chain SU residue 40 ILE Chi-restraints excluded: chain SU residue 47 ASN Chi-restraints excluded: chain SU residue 81 GLN Chi-restraints excluded: chain SU residue 115 THR Chi-restraints excluded: chain SV residue 13 VAL Chi-restraints excluded: chain SX residue 26 GLN Chi-restraints excluded: chain SX residue 107 ARG Chi-restraints excluded: chain SX residue 131 LEU Chi-restraints excluded: chain Sa residue 30 VAL Chi-restraints excluded: chain Sa residue 46 GLU Chi-restraints excluded: chain Sa residue 69 VAL Chi-restraints excluded: chain Sc residue 28 THR Chi-restraints excluded: chain Sc residue 34 PHE Chi-restraints excluded: chain Sc residue 38 THR Chi-restraints excluded: chain Sc residue 46 VAL Chi-restraints excluded: chain Sg residue 30 MET Chi-restraints excluded: chain Sg residue 43 TRP Chi-restraints excluded: chain Sg residue 68 ASP Chi-restraints excluded: chain Sg residue 71 ILE Chi-restraints excluded: chain Sg residue 96 THR Chi-restraints excluded: chain Sg residue 102 VAL Chi-restraints excluded: chain Sg residue 126 ASP Chi-restraints excluded: chain Sg residue 137 VAL Chi-restraints excluded: chain Sg residue 142 VAL Chi-restraints excluded: chain Sg residue 197 THR Chi-restraints excluded: chain Sg residue 213 ASP Chi-restraints excluded: chain Sg residue 225 LYS Chi-restraints excluded: chain Sg residue 247 TRP Chi-restraints excluded: chain Sg residue 309 VAL Chi-restraints excluded: chain SC residue 63 VAL Chi-restraints excluded: chain SC residue 91 SER Chi-restraints excluded: chain SC residue 104 ASP Chi-restraints excluded: chain SC residue 137 VAL Chi-restraints excluded: chain SC residue 141 VAL Chi-restraints excluded: chain SC residue 147 VAL Chi-restraints excluded: chain SC residue 280 VAL Chi-restraints excluded: chain SG residue 16 ILE Chi-restraints excluded: chain SG residue 97 VAL Chi-restraints excluded: chain SG residue 110 ASN Chi-restraints excluded: chain SG residue 113 ILE Chi-restraints excluded: chain SG residue 163 ASN Chi-restraints excluded: chain SG residue 176 ILE Chi-restraints excluded: chain SG residue 180 VAL Chi-restraints excluded: chain SG residue 181 THR Chi-restraints excluded: chain SG residue 217 MET Chi-restraints excluded: chain SJ residue 59 GLU Chi-restraints excluded: chain SJ residue 62 THR Chi-restraints excluded: chain SJ residue 84 ILE Chi-restraints excluded: chain SJ residue 95 ASP Chi-restraints excluded: chain SJ residue 114 VAL Chi-restraints excluded: chain SJ residue 128 VAL Chi-restraints excluded: chain SJ residue 153 SER Chi-restraints excluded: chain SJ residue 160 SER Chi-restraints excluded: chain SM residue 42 LEU Chi-restraints excluded: chain SM residue 87 GLU Chi-restraints excluded: chain SN residue 22 VAL Chi-restraints excluded: chain SN residue 31 ASP Chi-restraints excluded: chain SN residue 84 LEU Chi-restraints excluded: chain SN residue 87 ASP Chi-restraints excluded: chain SO residue 66 ARG Chi-restraints excluded: chain SO residue 67 ASP Chi-restraints excluded: chain SO residue 105 THR Chi-restraints excluded: chain SO residue 132 VAL Chi-restraints excluded: chain SW residue 4 MET Chi-restraints excluded: chain SW residue 85 ASP Chi-restraints excluded: chain SY residue 34 THR Chi-restraints excluded: chain SY residue 40 ILE Chi-restraints excluded: chain SY residue 51 THR Chi-restraints excluded: chain SZ residue 69 THR Chi-restraints excluded: chain SZ residue 76 ARG Chi-restraints excluded: chain SZ residue 107 VAL Chi-restraints excluded: chain Sb residue 33 MET Chi-restraints excluded: chain Sb residue 43 ILE Chi-restraints excluded: chain Sb residue 64 CYS Chi-restraints excluded: chain Se residue 6 LEU Chi-restraints excluded: chain Sf residue 148 TYR Chi-restraints excluded: chain CD residue 100 LEU Chi-restraints excluded: chain CD residue 135 GLU Chi-restraints excluded: chain 3A residue 19 LEU Chi-restraints excluded: chain 3A residue 69 GLU Chi-restraints excluded: chain 3A residue 197 LEU Chi-restraints excluded: chain 3A residue 228 MET Chi-restraints excluded: chain 3A residue 230 LEU Chi-restraints excluded: chain 3A residue 498 ASN Chi-restraints excluded: chain 3B residue 482 TRP Chi-restraints excluded: chain 3B residue 494 THR Chi-restraints excluded: chain 3B residue 541 VAL Chi-restraints excluded: chain 3B residue 544 PHE Chi-restraints excluded: chain 3C residue 76 VAL Chi-restraints excluded: chain 3C residue 77 THR Chi-restraints excluded: chain 3C residue 333 LEU Chi-restraints excluded: chain 3C residue 446 THR Chi-restraints excluded: chain 3C residue 452 ASP Chi-restraints excluded: chain 3C residue 453 GLU Chi-restraints excluded: chain 3C residue 468 GLU Chi-restraints excluded: chain 3C residue 519 HIS Chi-restraints excluded: chain 3C residue 546 VAL Chi-restraints excluded: chain 3C residue 597 ASN Chi-restraints excluded: chain 3C residue 684 CYS Chi-restraints excluded: chain 3C residue 689 SER Chi-restraints excluded: chain 3C residue 788 LEU Chi-restraints excluded: chain 3C residue 799 TYR Chi-restraints excluded: chain 3C residue 842 VAL Chi-restraints excluded: chain 3E residue 187 GLU Chi-restraints excluded: chain 3E residue 201 VAL Chi-restraints excluded: chain 3E residue 294 GLU Chi-restraints excluded: chain 3E residue 314 GLU Chi-restraints excluded: chain 3E residue 348 HIS Chi-restraints excluded: chain 3E residue 351 ILE Chi-restraints excluded: chain 3F residue 202 VAL Chi-restraints excluded: chain 3F residue 253 MET Chi-restraints excluded: chain 3G residue 272 LYS Chi-restraints excluded: chain 3G residue 285 ILE Chi-restraints excluded: chain 3H residue 72 VAL Chi-restraints excluded: chain 3H residue 84 PHE Chi-restraints excluded: chain 3H residue 110 VAL Chi-restraints excluded: chain 3H residue 249 ARG Chi-restraints excluded: chain 3L residue 401 MET Chi-restraints excluded: chain 3L residue 431 VAL Chi-restraints excluded: chain 3L residue 432 HIS Chi-restraints excluded: chain 3M residue 308 VAL Chi-restraints excluded: chain 3N residue 8 VAL Chi-restraints excluded: chain 3N residue 42 VAL Chi-restraints excluded: chain 3N residue 55 TYR Chi-restraints excluded: chain 3N residue 185 LEU Chi-restraints excluded: chain 3N residue 269 VAL Chi-restraints excluded: chain 3N residue 413 LEU Chi-restraints excluded: chain 3N residue 414 ASP Chi-restraints excluded: chain 3N residue 517 ILE Chi-restraints excluded: chain 3N residue 519 VAL Chi-restraints excluded: chain 3N residue 522 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1181 random chunks: chunk 696 optimal weight: 3.9990 chunk 1121 optimal weight: 40.0000 chunk 684 optimal weight: 40.0000 chunk 532 optimal weight: 0.7980 chunk 779 optimal weight: 7.9990 chunk 1176 optimal weight: 9.9990 chunk 1082 optimal weight: 1.9990 chunk 936 optimal weight: 9.9990 chunk 97 optimal weight: 4.9990 chunk 723 optimal weight: 40.0000 chunk 574 optimal weight: 0.8980 overall best weight: 2.5386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: SB 76 ASN ** SD 57 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** SF 110 GLN SI 99 ASN ** SI 181 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** SK 7 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** SP 98 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** SQ 80 GLN SQ 114 GLN SR 127 ASN ** SS 72 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** SS 85 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** SS 97 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ST 126 GLN ** SV 35 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Sc 26 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Sg 147 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** SC 267 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** SG 155 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** SJ 154 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** SN 36 GLN SN 49 GLN SW 24 GLN ** SW 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** SZ 89 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Sb 83 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 3A 209 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 3A 270 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 3B 502 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 3C 436 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 3C 637 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 3C 670 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 3C 819 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 3C 869 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 3E 121 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 3E 390 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 3G 256 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 3H 141 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 3H 261 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 3H 336 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 3L 363 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 3L 366 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 3L 436 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 3M 199 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 3M 205 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** 3N 322 ASN 3N 479 GLN Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7225 moved from start: 0.2445 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.124 120081 Z= 0.298 Angle : 0.740 17.425 170579 Z= 0.372 Chirality : 0.044 0.366 20688 Planarity : 0.005 0.103 15553 Dihedral : 21.336 179.524 37944 Min Nonbonded Distance : 1.922 Molprobity Statistics. All-atom Clashscore : 14.35 Ramachandran Plot: Outliers : 0.11 % Allowed : 7.00 % Favored : 92.89 % Rotamer: Outliers : 2.93 % Allowed : 23.03 % Favored : 74.04 % Cbeta Deviations : 0.01 % Peptide Plane: Cis-proline : 1.08 % Cis-general : 0.17 % Twisted Proline : 0.54 % Twisted General : 0.04 % 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: -0.73 (0.08), residues: 10145 helix: 0.90 (0.08), residues: 4560 sheet: -0.74 (0.13), residues: 1533 loop : -2.02 (0.09), residues: 4052 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.053 0.003 TRP3C 749 HIS 0.014 0.001 HIS3C 593 PHE 0.053 0.002 PHE3G 287 TYR 0.029 0.001 TYRSf 140 ARG 0.009 0.001 ARGSF 204 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 20290 Ramachandran restraints generated. 10145 Oldfield, 0 Emsley, 10145 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 20290 Ramachandran restraints generated. 10145 Oldfield, 0 Emsley, 10145 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1451 residues out of total 9059 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 224 poor density : 1227 time to evaluate : 7.323 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: Ln 9 ARG cc_start: 0.6626 (mtp85) cc_final: 0.5795 (ttp-170) REVERT: SA 205 ARG cc_start: 0.6865 (OUTLIER) cc_final: 0.6233 (mtp-110) REVERT: SB 172 MET cc_start: 0.8643 (mtm) cc_final: 0.8252 (mtm) REVERT: SE 21 ASP cc_start: 0.8779 (OUTLIER) cc_final: 0.8356 (m-30) REVERT: SF 51 HIS cc_start: 0.7570 (OUTLIER) cc_final: 0.7261 (t70) REVERT: SL 76 VAL cc_start: 0.8899 (OUTLIER) cc_final: 0.8672 (m) REVERT: SP 34 MET cc_start: 0.7745 (mmt) cc_final: 0.6785 (mmt) REVERT: SP 51 ARG cc_start: 0.7370 (mmp80) cc_final: 0.7029 (mmt-90) REVERT: SP 110 GLU cc_start: 0.6192 (mp0) cc_final: 0.5535 (mm-30) REVERT: SQ 7 LEU cc_start: 0.6127 (OUTLIER) cc_final: 0.5835 (pp) REVERT: SQ 87 SER cc_start: 0.8086 (t) cc_final: 0.7314 (p) REVERT: SS 5 ILE cc_start: 0.4544 (OUTLIER) cc_final: 0.4252 (tp) REVERT: SS 40 TYR cc_start: 0.8424 (t80) cc_final: 0.8058 (t80) REVERT: ST 79 TYR cc_start: 0.7680 (m-80) cc_final: 0.7338 (m-80) REVERT: ST 88 MET cc_start: 0.8764 (mmt) cc_final: 0.8533 (mmm) REVERT: SV 1 MET cc_start: 0.7716 (ppp) cc_final: 0.7244 (ptt) REVERT: Sa 46 GLU cc_start: 0.8465 (OUTLIER) cc_final: 0.8225 (pm20) REVERT: Sc 44 ARG cc_start: 0.7905 (mmm-85) cc_final: 0.7493 (mmm160) REVERT: Sd 7 TYR cc_start: 0.8571 (t80) cc_final: 0.8304 (t80) REVERT: SC 254 ASP cc_start: 0.8025 (p0) cc_final: 0.7608 (p0) REVERT: SG 28 TYR cc_start: 0.8735 (m-10) cc_final: 0.8456 (m-10) REVERT: SJ 154 GLN cc_start: 0.8642 (tm-30) cc_final: 0.8308 (tt0) REVERT: SN 119 GLU cc_start: 0.7746 (mm-30) cc_final: 0.7114 (mm-30) REVERT: SO 13 GLN cc_start: 0.0571 (OUTLIER) cc_final: -0.0522 (mp10) REVERT: SW 4 MET cc_start: 0.7453 (OUTLIER) cc_final: 0.6330 (mmt) REVERT: Sb 33 MET cc_start: 0.8711 (OUTLIER) cc_final: 0.7659 (mmt) REVERT: Sb 75 GLU cc_start: 0.7203 (pm20) cc_final: 0.6763 (pm20) REVERT: CD 143 TYR cc_start: 0.7768 (t80) cc_final: 0.7429 (t80) REVERT: 3B 542 THR cc_start: 0.3782 (t) cc_final: 0.3272 (p) REVERT: 3C 613 MET cc_start: 0.6622 (ttm) cc_final: 0.6335 (ttm) REVERT: 3E 104 MET cc_start: 0.4906 (pmm) cc_final: 0.4295 (pmm) REVERT: 3E 314 GLU cc_start: 0.6269 (OUTLIER) cc_final: 0.5724 (pm20) REVERT: 3E 420 MET cc_start: 0.4812 (OUTLIER) cc_final: 0.4576 (tpp) REVERT: 3F 309 MET cc_start: -0.0665 (mtt) cc_final: -0.1054 (ptp) REVERT: 3L 268 MET cc_start: -0.2745 (ptt) cc_final: -0.3575 (ptt) REVERT: 3L 304 MET cc_start: -0.1359 (ptt) cc_final: -0.2282 (ptt) REVERT: 3L 377 MET cc_start: 0.4557 (mpp) cc_final: 0.4333 (mpp) REVERT: 3L 432 HIS cc_start: 0.2578 (OUTLIER) cc_final: 0.2375 (p90) REVERT: 3N 413 LEU cc_start: 0.7837 (OUTLIER) cc_final: 0.7481 (pp) REVERT: 3N 522 LEU cc_start: 0.0357 (OUTLIER) cc_final: -0.0177 (mm) outliers start: 224 outliers final: 194 residues processed: 1355 average time/residue: 1.0064 time to fit residues: 2368.9465 Evaluate side-chains 1399 residues out of total 9059 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 209 poor density : 1190 time to evaluate : 6.908 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain SA residue 8 LEU Chi-restraints excluded: chain SA residue 43 SER Chi-restraints excluded: chain SA residue 81 ASN Chi-restraints excluded: chain SA residue 205 ARG Chi-restraints excluded: chain SB residue 44 ILE Chi-restraints excluded: chain SB residue 66 VAL Chi-restraints excluded: chain SB residue 88 THR Chi-restraints excluded: chain SD residue 51 LEU Chi-restraints excluded: chain SD residue 91 VAL Chi-restraints excluded: chain SD residue 164 VAL Chi-restraints excluded: chain SD residue 170 THR Chi-restraints excluded: chain SE residue 21 ASP Chi-restraints excluded: chain SE residue 89 VAL Chi-restraints excluded: chain SE residue 126 VAL Chi-restraints excluded: chain SF residue 51 HIS Chi-restraints excluded: chain SF residue 69 VAL Chi-restraints excluded: chain SF residue 93 VAL Chi-restraints excluded: chain SF residue 110 GLN Chi-restraints excluded: chain SF residue 111 VAL Chi-restraints excluded: chain SF residue 133 THR Chi-restraints excluded: chain SH residue 25 GLN Chi-restraints excluded: chain SH residue 33 ASN Chi-restraints excluded: chain SH residue 64 VAL Chi-restraints excluded: chain SH residue 95 ILE Chi-restraints excluded: chain SH residue 114 GLN Chi-restraints excluded: chain SI residue 90 LEU Chi-restraints excluded: chain SI residue 91 VAL Chi-restraints excluded: chain SI residue 93 THR Chi-restraints excluded: chain SI residue 99 ASN Chi-restraints excluded: chain SI residue 144 LYS Chi-restraints excluded: chain SI residue 171 LEU Chi-restraints excluded: chain SK residue 22 VAL Chi-restraints excluded: chain SK residue 97 SER Chi-restraints excluded: chain SL residue 6 THR Chi-restraints excluded: chain SL residue 19 ASN Chi-restraints excluded: chain SL residue 33 LEU Chi-restraints excluded: chain SL residue 66 VAL Chi-restraints excluded: chain SL residue 72 ILE Chi-restraints excluded: chain SL residue 76 VAL Chi-restraints excluded: chain SL residue 87 VAL Chi-restraints excluded: chain SL residue 124 ASP Chi-restraints excluded: chain SL residue 146 THR Chi-restraints excluded: chain SP residue 29 SER Chi-restraints excluded: chain SP residue 83 MET Chi-restraints excluded: chain SP residue 85 ILE Chi-restraints excluded: chain SP residue 126 VAL Chi-restraints excluded: chain SQ residue 7 LEU Chi-restraints excluded: chain SQ residue 10 VAL Chi-restraints excluded: chain SQ residue 20 THR Chi-restraints excluded: chain SQ residue 22 VAL Chi-restraints excluded: chain SQ residue 57 LEU Chi-restraints excluded: chain SQ residue 84 ILE Chi-restraints excluded: chain SQ residue 114 GLN Chi-restraints excluded: chain SR residue 40 ILE Chi-restraints excluded: chain SR residue 71 ILE Chi-restraints excluded: chain SR residue 93 GLN Chi-restraints excluded: chain SR residue 123 THR Chi-restraints excluded: chain SS residue 5 ILE Chi-restraints excluded: chain SS residue 15 VAL Chi-restraints excluded: chain SS residue 53 THR Chi-restraints excluded: chain SS residue 67 VAL Chi-restraints excluded: chain SS residue 81 ASP Chi-restraints excluded: chain SS residue 103 LEU Chi-restraints excluded: chain SS residue 131 VAL Chi-restraints excluded: chain SS residue 136 THR Chi-restraints excluded: chain ST residue 9 VAL Chi-restraints excluded: chain ST residue 15 VAL Chi-restraints excluded: chain ST residue 66 LEU Chi-restraints excluded: chain ST residue 74 SER Chi-restraints excluded: chain ST residue 76 THR Chi-restraints excluded: chain ST residue 108 GLU Chi-restraints excluded: chain SU residue 23 THR Chi-restraints excluded: chain SU residue 25 THR Chi-restraints excluded: chain SU residue 40 ILE Chi-restraints excluded: chain SU residue 47 ASN Chi-restraints excluded: chain SU residue 81 GLN Chi-restraints excluded: chain SU residue 115 THR Chi-restraints excluded: chain SV residue 13 VAL Chi-restraints excluded: chain SX residue 26 GLN Chi-restraints excluded: chain SX residue 85 VAL Chi-restraints excluded: chain SX residue 107 ARG Chi-restraints excluded: chain SX residue 131 LEU Chi-restraints excluded: chain Sa residue 30 VAL Chi-restraints excluded: chain Sa residue 46 GLU Chi-restraints excluded: chain Sa residue 59 PHE Chi-restraints excluded: chain Sa residue 69 VAL Chi-restraints excluded: chain Sc residue 28 THR Chi-restraints excluded: chain Sc residue 34 PHE Chi-restraints excluded: chain Sc residue 38 THR Chi-restraints excluded: chain Sc residue 46 VAL Chi-restraints excluded: chain Sg residue 30 MET Chi-restraints excluded: chain Sg residue 43 TRP Chi-restraints excluded: chain Sg residue 68 ASP Chi-restraints excluded: chain Sg residue 71 ILE Chi-restraints excluded: chain Sg residue 96 THR Chi-restraints excluded: chain Sg residue 102 VAL Chi-restraints excluded: chain Sg residue 126 ASP Chi-restraints excluded: chain Sg residue 137 VAL Chi-restraints excluded: chain Sg residue 142 VAL Chi-restraints excluded: chain Sg residue 185 LYS Chi-restraints excluded: chain Sg residue 197 THR Chi-restraints excluded: chain Sg residue 225 LYS Chi-restraints excluded: chain Sg residue 247 TRP Chi-restraints excluded: chain Sg residue 309 VAL Chi-restraints excluded: chain SC residue 63 VAL Chi-restraints excluded: chain SC residue 91 SER Chi-restraints excluded: chain SC residue 104 ASP Chi-restraints excluded: chain SC residue 137 VAL Chi-restraints excluded: chain SC residue 141 VAL Chi-restraints excluded: chain SC residue 147 VAL Chi-restraints excluded: chain SC residue 280 VAL Chi-restraints excluded: chain SG residue 16 ILE Chi-restraints excluded: chain SG residue 97 VAL Chi-restraints excluded: chain SG residue 110 ASN Chi-restraints excluded: chain SG residue 113 ILE Chi-restraints excluded: chain SG residue 163 ASN Chi-restraints excluded: chain SG residue 176 ILE Chi-restraints excluded: chain SG residue 180 VAL Chi-restraints excluded: chain SG residue 181 THR Chi-restraints excluded: chain SG residue 217 MET Chi-restraints excluded: chain SJ residue 61 LEU Chi-restraints excluded: chain SJ residue 62 THR Chi-restraints excluded: chain SJ residue 84 ILE Chi-restraints excluded: chain SJ residue 95 ASP Chi-restraints excluded: chain SJ residue 114 VAL Chi-restraints excluded: chain SJ residue 128 VAL Chi-restraints excluded: chain SJ residue 153 SER Chi-restraints excluded: chain SM residue 87 GLU Chi-restraints excluded: chain SN residue 22 VAL Chi-restraints excluded: chain SN residue 31 ASP Chi-restraints excluded: chain SN residue 49 GLN Chi-restraints excluded: chain SN residue 84 LEU Chi-restraints excluded: chain SN residue 87 ASP Chi-restraints excluded: chain SO residue 13 GLN Chi-restraints excluded: chain SO residue 62 VAL Chi-restraints excluded: chain SO residue 66 ARG Chi-restraints excluded: chain SO residue 67 ASP Chi-restraints excluded: chain SO residue 105 THR Chi-restraints excluded: chain SO residue 132 VAL Chi-restraints excluded: chain SW residue 4 MET Chi-restraints excluded: chain SW residue 85 ASP Chi-restraints excluded: chain SY residue 34 THR Chi-restraints excluded: chain SY residue 40 ILE Chi-restraints excluded: chain SY residue 51 THR Chi-restraints excluded: chain SZ residue 69 THR Chi-restraints excluded: chain SZ residue 76 ARG Chi-restraints excluded: chain SZ residue 107 VAL Chi-restraints excluded: chain Sb residue 33 MET Chi-restraints excluded: chain Sb residue 43 ILE Chi-restraints excluded: chain Sb residue 53 VAL Chi-restraints excluded: chain Sb residue 64 CYS Chi-restraints excluded: chain Se residue 6 LEU Chi-restraints excluded: chain Sf residue 148 TYR Chi-restraints excluded: chain CD residue 100 LEU Chi-restraints excluded: chain CD residue 102 ARG Chi-restraints excluded: chain CD residue 135 GLU Chi-restraints excluded: chain 3A residue 19 LEU Chi-restraints excluded: chain 3A residue 69 GLU Chi-restraints excluded: chain 3A residue 197 LEU Chi-restraints excluded: chain 3A residue 228 MET Chi-restraints excluded: chain 3A residue 230 LEU Chi-restraints excluded: chain 3A residue 349 VAL Chi-restraints excluded: chain 3A residue 498 ASN Chi-restraints excluded: chain 3B residue 482 TRP Chi-restraints excluded: chain 3B residue 494 THR Chi-restraints excluded: chain 3B residue 541 VAL Chi-restraints excluded: chain 3B residue 544 PHE Chi-restraints excluded: chain 3C residue 76 VAL Chi-restraints excluded: chain 3C residue 77 THR Chi-restraints excluded: chain 3C residue 333 LEU Chi-restraints excluded: chain 3C residue 446 THR Chi-restraints excluded: chain 3C residue 453 GLU Chi-restraints excluded: chain 3C residue 468 GLU Chi-restraints excluded: chain 3C residue 519 HIS Chi-restraints excluded: chain 3C residue 546 VAL Chi-restraints excluded: chain 3C residue 597 ASN Chi-restraints excluded: chain 3C residue 684 CYS Chi-restraints excluded: chain 3C residue 689 SER Chi-restraints excluded: chain 3C residue 788 LEU Chi-restraints excluded: chain 3C residue 799 TYR Chi-restraints excluded: chain 3E residue 187 GLU Chi-restraints excluded: chain 3E residue 201 VAL Chi-restraints excluded: chain 3E residue 294 GLU Chi-restraints excluded: chain 3E residue 314 GLU Chi-restraints excluded: chain 3E residue 348 HIS Chi-restraints excluded: chain 3E residue 351 ILE Chi-restraints excluded: chain 3E residue 420 MET Chi-restraints excluded: chain 3F residue 202 VAL Chi-restraints excluded: chain 3F residue 253 MET Chi-restraints excluded: chain 3F residue 357 LEU Chi-restraints excluded: chain 3G residue 272 LYS Chi-restraints excluded: chain 3G residue 285 ILE Chi-restraints excluded: chain 3H residue 72 VAL Chi-restraints excluded: chain 3H residue 84 PHE Chi-restraints excluded: chain 3H residue 110 VAL Chi-restraints excluded: chain 3H residue 249 ARG Chi-restraints excluded: chain 3L residue 431 VAL Chi-restraints excluded: chain 3L residue 432 HIS Chi-restraints excluded: chain 3M residue 308 VAL Chi-restraints excluded: chain 3N residue 8 VAL Chi-restraints excluded: chain 3N residue 42 VAL Chi-restraints excluded: chain 3N residue 55 TYR Chi-restraints excluded: chain 3N residue 185 LEU Chi-restraints excluded: chain 3N residue 413 LEU Chi-restraints excluded: chain 3N residue 414 ASP Chi-restraints excluded: chain 3N residue 479 GLN Chi-restraints excluded: chain 3N residue 517 ILE Chi-restraints excluded: chain 3N residue 519 VAL Chi-restraints excluded: chain 3N residue 522 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1181 random chunks: chunk 744 optimal weight: 20.0000 chunk 998 optimal weight: 6.9990 chunk 287 optimal weight: 10.0000 chunk 863 optimal weight: 6.9990 chunk 138 optimal weight: 8.9990 chunk 260 optimal weight: 4.9990 chunk 938 optimal weight: 9.9990 chunk 392 optimal weight: 5.9990 chunk 963 optimal weight: 0.8980 chunk 118 optimal weight: 10.0000 chunk 172 optimal weight: 6.9990 overall best weight: 5.1788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** SB 76 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** SD 57 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** SF 29 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** SF 148 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** SI 99 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** SK 7 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** SP 98 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** SQ 80 GLN SR 127 ASN ** SS 72 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** SS 85 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** SS 97 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** ST 126 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** SV 35 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Sc 26 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Sg 147 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** SC 267 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** SG 155 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** SJ 154 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** SM 72 HIS SN 36 GLN SN 49 GLN ** SW 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** SZ 89 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Sb 83 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 3A 209 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 3A 270 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 3B 502 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 3C 436 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 3C 637 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 3C 670 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 3C 819 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 3C 869 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 3E 225 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 3E 390 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 3E 428 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 3G 256 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 3H 141 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 3H 261 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 3H 336 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 3L 363 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 3L 366 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 3L 436 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 3M 199 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 3M 205 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** 3N 322 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4132 r_free = 0.4132 target = 0.168561 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3839 r_free = 0.3839 target = 0.145900 restraints weight = 213409.432| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3761 r_free = 0.3761 target = 0.140161 restraints weight = 303423.903| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3699 r_free = 0.3699 target = 0.135869 restraints weight = 181904.255| |-----------------------------------------------------------------------------| r_work (final): 0.3695 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7137 moved from start: 0.2454 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.290 120081 Z= 0.461 Angle : 0.827 59.077 170579 Z= 0.433 Chirality : 0.049 0.903 20688 Planarity : 0.006 0.137 15553 Dihedral : 21.334 179.659 37944 Min Nonbonded Distance : 1.922 Molprobity Statistics. All-atom Clashscore : 15.51 Ramachandran Plot: Outliers : 0.13 % Allowed : 6.99 % Favored : 92.88 % Rotamer: Outliers : 3.13 % Allowed : 23.14 % Favored : 73.73 % Cbeta Deviations : 0.02 % Peptide Plane: Cis-proline : 1.08 % Cis-general : 0.17 % Twisted Proline : 0.54 % Twisted General : 0.05 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.74 (0.08), residues: 10145 helix: 0.89 (0.08), residues: 4560 sheet: -0.74 (0.13), residues: 1536 loop : -2.02 (0.09), residues: 4049 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.069 0.003 TRP3K 179 HIS 0.013 0.001 HIS3C 819 PHE 0.044 0.002 PHE3G 287 TYR 0.027 0.002 TYRSS 77 ARG 0.011 0.001 ARGSC 187 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 31557.70 seconds wall clock time: 549 minutes 15.39 seconds (32955.39 seconds total)