Starting phenix.real_space_refine on Sat Feb 24 21:51:23 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5w5y_8771/02_2024/5w5y_8771.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5w5y_8771/02_2024/5w5y_8771.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.8 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5w5y_8771/02_2024/5w5y_8771.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5w5y_8771/02_2024/5w5y_8771.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5w5y_8771/02_2024/5w5y_8771.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5w5y_8771/02_2024/5w5y_8771.pdb" } resolution = 3.8 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.013 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: 6 Type Number sf(0) Gaussians Zn 6 6.06 5 P 102 5.49 5 S 205 5.16 5 C 29235 2.51 5 N 8048 2.21 5 O 8976 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A PHE 91": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 414": "OE1" <-> "OE2" Residue "A ARG 416": "NH1" <-> "NH2" Residue "A ARG 417": "NH1" <-> "NH2" Residue "A ARG 1003": "NH1" <-> "NH2" Residue "A ARG 1015": "NH1" <-> "NH2" Residue "B ARG 12": "NH1" <-> "NH2" Residue "G GLU 98": "OE1" <-> "OE2" Residue "O ARG 280": "NH1" <-> "NH2" Residue "O ARG 407": "NH1" <-> "NH2" Residue "O ARG 419": "NH1" <-> "NH2" Residue "O ARG 472": "NH1" <-> "NH2" Residue "O ARG 484": "NH1" <-> "NH2" Residue "O ARG 542": "NH1" <-> "NH2" Residue "O PHE 578": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "O GLU 583": "OE1" <-> "OE2" Residue "O GLU 585": "OE1" <-> "OE2" Residue "O GLU 664": "OE1" <-> "OE2" Residue "P TYR 211": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "P ARG 305": "NH1" <-> "NH2" Residue "P ARG 324": "NH1" <-> "NH2" Residue "P ARG 350": "NH1" <-> "NH2" Residue "P GLU 371": "OE1" <-> "OE2" Residue "P GLU 401": "OE1" <-> "OE2" Residue "P GLU 496": "OE1" <-> "OE2" Residue "Q PHE 2": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Q GLU 3": "OE1" <-> "OE2" Residue "Q ARG 17": "NH1" <-> "NH2" Residue "Q ARG 30": "NH1" <-> "NH2" Residue "Q ARG 33": "NH1" <-> "NH2" Residue "Q TYR 159": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Q GLU 166": "OE1" <-> "OE2" Residue "Q ARG 302": "NH1" <-> "NH2" Residue "Q GLU 363": "OE1" <-> "OE2" Time to flip residues: 0.15s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5238/modules/chem_data/mon_lib" Total number of atoms: 46572 Number of models: 1 Model: "" Number of chains: 25 Chain: "A" Number of atoms: 11542 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1461, 11542 Classifications: {'peptide': 1461} Link IDs: {'PTRANS': 59, 'TRANS': 1401} Chain breaks: 7 Chain: "B" Number of atoms: 9351 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1178, 9351 Classifications: {'peptide': 1178} Link IDs: {'PTRANS': 58, 'TRANS': 1119} Chain breaks: 2 Chain: "C" Number of atoms: 2432 Number of conformers: 1 Conformer: "" Number of residues, atoms: 306, 2432 Classifications: {'peptide': 306} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 19, 'TRANS': 286} Chain: "D" Number of atoms: 467 Number of conformers: 1 Conformer: "" Number of residues, atoms: 59, 467 Classifications: {'peptide': 59} Link IDs: {'PTRANS': 3, 'TRANS': 55} Chain breaks: 1 Chain: "E" Number of atoms: 1760 Number of conformers: 1 Conformer: "" Number of residues, atoms: 215, 1760 Classifications: {'peptide': 215} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 12, 'TRANS': 202} Chain: "F" Number of atoms: 670 Number of conformers: 1 Conformer: "" Number of residues, atoms: 83, 670 Classifications: {'peptide': 83} Link IDs: {'PTRANS': 6, 'TRANS': 76} Chain: "G" Number of atoms: 1592 Number of conformers: 1 Conformer: "" Number of residues, atoms: 201, 1592 Classifications: {'peptide': 201} Link IDs: {'PTRANS': 11, 'TRANS': 189} Chain breaks: 1 Chain: "H" Number of atoms: 1071 Number of conformers: 1 Conformer: "" Number of residues, atoms: 133, 1071 Classifications: {'peptide': 133} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 4, 'TRANS': 128} Chain breaks: 1 Chain: "I" Number of atoms: 479 Number of conformers: 1 Conformer: "" Number of residues, atoms: 65, 479 Classifications: {'peptide': 65} Link IDs: {'PTRANS': 3, 'TRANS': 61} Chain: "J" Number of atoms: 569 Number of conformers: 1 Conformer: "" Number of residues, atoms: 69, 569 Classifications: {'peptide': 69} Link IDs: {'PTRANS': 2, 'TRANS': 66} Chain: "K" Number of atoms: 811 Number of conformers: 1 Conformer: "" Number of residues, atoms: 103, 811 Classifications: {'peptide': 103} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 4, 'TRANS': 98} Chain: "L" Number of atoms: 359 Number of conformers: 1 Conformer: "" Number of residues, atoms: 45, 359 Classifications: {'peptide': 45} Modifications used: {'COO': 1} Link IDs: {'TRANS': 44} Chain: "M" Number of atoms: 841 Number of conformers: 1 Conformer: "" Number of residues, atoms: 106, 841 Classifications: {'peptide': 106} Link IDs: {'PTRANS': 5, 'TRANS': 100} Chain: "N" Number of atoms: 1254 Number of conformers: 1 Conformer: "" Number of residues, atoms: 158, 1254 Classifications: {'peptide': 158} Link IDs: {'PTRANS': 9, 'TRANS': 148} Chain: "O" Number of atoms: 5063 Number of conformers: 1 Conformer: "" Number of residues, atoms: 640, 5063 Classifications: {'peptide': 640} Incomplete info: {'truncation_to_alanine': 52} Link IDs: {'PTRANS': 19, 'TRANS': 620} Chain breaks: 4 Unresolved non-hydrogen bonds: 104 Unresolved non-hydrogen angles: 156 Unresolved non-hydrogen dihedrals: 52 Planarities with less than four sites: {'UNK:plan-1': 52} Unresolved non-hydrogen planarities: 52 Chain: "P" Number of atoms: 3238 Number of conformers: 1 Conformer: "" Number of residues, atoms: 387, 3238 Classifications: {'peptide': 387} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 17, 'TRANS': 369} Chain breaks: 4 Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 4 Unresolved non-hydrogen chiralities: 2 Chain: "Q" Number of atoms: 2923 Number of conformers: 1 Conformer: "" Number of residues, atoms: 349, 2923 Classifications: {'peptide': 349} Link IDs: {'PTRANS': 13, 'TRANS': 335} Chain breaks: 2 Chain: "R" Number of atoms: 127 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 127 Classifications: {'RNA': 6} Modifications used: {'5*END': 1, 'rna3p_pur': 4, 'rna3p_pyr': 2} Link IDs: {'rna3p': 5} Chain: "S" Number of atoms: 935 Number of conformers: 1 Conformer: "" Number of residues, atoms: 45, 935 Classifications: {'DNA': 45} Modifications used: {'5*END': 1} Link IDs: {'rna3p': 44} Chain breaks: 1 Chain: "T" Number of atoms: 1082 Number of conformers: 1 Conformer: "" Number of residues, atoms: 54, 1082 Classifications: {'DNA': 54} Modifications used: {'5*END': 1} Link IDs: {'rna3p': 53} Chain: "A" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Unusual residues: {' ZN': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "B" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} Chain: "I" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} Chain: "J" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} Chain: "L" 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 781 SG CYS A 102 174.503 82.444 82.669 1.00 0.00 S ATOM 806 SG CYS A 105 175.145 79.666 82.755 1.00 0.00 S ATOM 1605 SG CYS A 233 176.147 82.240 85.673 1.00 0.00 S ATOM 1627 SG CYS A 236 177.051 82.001 82.427 1.00 0.00 S ATOM 461 SG CYS A 62 127.549 63.316 83.214 1.00 0.00 S ATOM 480 SG CYS A 65 127.061 60.347 85.435 1.00 0.00 S ATOM 535 SG CYS A 72 126.552 63.217 86.261 1.00 0.00 S ATOM 20196 SG CYS B1104 141.602 55.595 91.699 1.00 0.00 S ATOM 20222 SG CYS B1107 142.904 58.792 91.662 1.00 0.00 S ATOM 20369 SG CYS B1128 140.433 57.247 89.597 1.00 0.00 S ATOM 20397 SG CYS B1131 143.311 55.298 89.657 1.00 0.00 S ATOM 28948 SG CYS I 10 158.831 150.475 89.442 1.00 0.00 S ATOM 28970 SG CYS I 13 156.053 148.623 88.306 1.00 0.00 S ATOM 29090 SG CYS I 30 158.806 146.948 87.457 1.00 0.00 S ATOM 29111 SG CYS I 33 158.424 150.168 86.669 1.00 0.00 S ATOM 29418 SG CYS J 7 88.151 98.304 133.007 1.00 0.00 S ATOM 29441 SG CYS J 10 85.805 96.989 134.821 1.00 0.00 S ATOM 29721 SG CYS J 45 88.250 98.788 136.269 1.00 0.00 S ATOM 29727 SG CYS J 46 84.887 99.800 135.416 1.00 0.00 S ATOM 30794 SG CYS L 31 85.692 103.780 88.997 1.00 0.00 S ATOM 30814 SG CYS L 34 82.537 104.606 89.090 1.00 0.00 S ATOM 30918 SG CYS L 48 83.761 103.264 86.676 1.00 0.00 S ATOM 30941 SG CYS L 51 85.657 105.561 86.730 1.00 0.00 S Residues with excluded nonbonded symmetry interactions: 105 residue: pdb=" N LYS A 991 " occ=0.00 ... (7 atoms not shown) pdb=" NZ LYS A 991 " occ=0.00 residue: pdb=" N PRO A 992 " occ=0.00 ... (5 atoms not shown) pdb=" CD PRO A 992 " occ=0.00 residue: pdb=" N GLN A 993 " occ=0.00 ... (7 atoms not shown) pdb=" NE2 GLN A 993 " occ=0.00 residue: pdb=" N GLU A 994 " occ=0.00 ... (7 atoms not shown) pdb=" OE2 GLU A 994 " occ=0.00 residue: pdb=" N TYR A 995 " occ=0.00 ... (10 atoms not shown) pdb=" OH TYR A 995 " occ=0.00 residue: pdb=" N TYR A 996 " occ=0.00 ... (10 atoms not shown) pdb=" OH TYR A 996 " occ=0.00 residue: pdb=" N PHE A 997 " occ=0.00 ... (9 atoms not shown) pdb=" CZ PHE A 997 " occ=0.00 residue: pdb=" N HIS A 998 " occ=0.00 ... (8 atoms not shown) pdb=" NE2 HIS A 998 " occ=0.00 residue: pdb=" N CYS A 999 " occ=0.00 ... (4 atoms not shown) pdb=" SG CYS A 999 " occ=0.00 residue: pdb=" N MET A1000 " occ=0.00 ... (6 atoms not shown) pdb=" CE MET A1000 " occ=0.00 residue: pdb=" N ALA A1001 " occ=0.00 ... (3 atoms not shown) pdb=" CB ALA A1001 " occ=0.00 residue: pdb=" N GLY A1002 " occ=0.00 ... (2 atoms not shown) pdb=" O GLY A1002 " occ=0.00 ... (remaining 93 not shown) Time building chain proxies: 24.15, per 1000 atoms: 0.52 Number of scatterers: 46572 At special positions: 0 Unit cell: (210.6, 191.1, 200.2, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) Zn 6 29.99 S 205 16.00 P 102 15.00 O 8976 8.00 N 8048 7.00 C 29235 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: 23.34 Conformation dependent library (CDL) restraints added in 8.2 seconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN A1701 " pdb="ZN ZN A1701 " - pdb=" SG CYS A 105 " pdb="ZN ZN A1701 " - pdb=" SG CYS A 102 " pdb="ZN ZN A1701 " - pdb=" SG CYS A 233 " pdb="ZN ZN A1701 " - pdb=" SG CYS A 236 " pdb=" ZN A1702 " pdb="ZN ZN A1702 " - pdb=" NE2 HIS A 75 " pdb="ZN ZN A1702 " - pdb=" SG CYS A 62 " pdb="ZN ZN A1702 " - pdb=" SG CYS A 65 " pdb="ZN ZN A1702 " - pdb=" SG CYS A 72 " pdb=" ZN B1301 " pdb="ZN ZN B1301 " - pdb=" SG CYS B1131 " pdb="ZN ZN B1301 " - pdb=" SG CYS B1107 " pdb="ZN ZN B1301 " - pdb=" SG CYS B1128 " pdb="ZN ZN B1301 " - pdb=" SG CYS B1104 " pdb=" ZN I 201 " pdb="ZN ZN I 201 " - pdb=" SG CYS I 10 " pdb="ZN ZN I 201 " - pdb=" SG CYS I 30 " pdb="ZN ZN I 201 " - pdb=" SG CYS I 13 " pdb="ZN ZN I 201 " - pdb=" SG CYS I 33 " pdb=" ZN J 101 " pdb="ZN ZN J 101 " - pdb=" SG CYS J 7 " pdb="ZN ZN J 101 " - pdb=" SG CYS J 45 " pdb="ZN ZN J 101 " - pdb=" SG CYS J 46 " pdb="ZN ZN J 101 " - pdb=" SG CYS J 10 " pdb=" ZN L 101 " pdb="ZN ZN L 101 " - pdb=" SG CYS L 51 " pdb="ZN ZN L 101 " - pdb=" SG CYS L 34 " pdb="ZN ZN L 101 " - pdb=" SG CYS L 31 " pdb="ZN ZN L 101 " - pdb=" SG CYS L 48 " Number of angles added : 33 10864 Ramachandran restraints generated. 5432 Oldfield, 0 Emsley, 5432 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 10544 Finding SS restraints... Secondary structure from input PDB file: 217 helices and 59 sheets defined 42.5% alpha, 17.0% beta 30 base pairs and 82 stacking pairs defined. Time for finding SS restraints: 15.12 Creating SS restraints... Processing helix chain 'A' and resid 20 through 28 Processing helix chain 'A' and resid 51 through 55 Processing helix chain 'A' and resid 87 through 89 No H-bonds generated for 'chain 'A' and resid 87 through 89' Processing helix chain 'A' and resid 90 through 101 Processing helix chain 'A' and resid 111 through 127 removed outlier: 3.586A pdb=" N TYR A 127 " --> pdb=" O ARG A 123 " (cutoff:3.500A) Processing helix chain 'A' and resid 129 through 136 Processing helix chain 'A' and resid 137 through 139 No H-bonds generated for 'chain 'A' and resid 137 through 139' Processing helix chain 'A' and resid 174 through 199 Processing helix chain 'A' and resid 209 through 230 removed outlier: 3.709A pdb=" N ARG A 230 " --> pdb=" O LYS A 226 " (cutoff:3.500A) Processing helix chain 'A' and resid 257 through 267 Processing helix chain 'A' and resid 316 through 331 removed outlier: 3.771A pdb=" N THR A 326 " --> pdb=" O ASN A 322 " (cutoff:3.500A) Processing helix chain 'A' and resid 331 through 339 removed outlier: 4.583A pdb=" N TYR A 337 " --> pdb=" O CYS A 333 " (cutoff:3.500A) Processing helix chain 'A' and resid 351 through 355 Processing helix chain 'A' and resid 364 through 369 removed outlier: 4.187A pdb=" N LEU A 369 " --> pdb=" O ARG A 366 " (cutoff:3.500A) Processing helix chain 'A' and resid 380 through 406 Processing helix chain 'A' and resid 415 through 439 removed outlier: 4.147A pdb=" N ILE A 419 " --> pdb=" O ASP A 415 " (cutoff:3.500A) Processing helix chain 'A' and resid 440 through 443 Processing helix chain 'A' and resid 455 through 461 Processing helix chain 'A' and resid 466 through 471 Processing helix chain 'A' and resid 498 through 505 Processing helix chain 'A' and resid 515 through 526 Processing helix chain 'A' and resid 550 through 559 Processing helix chain 'A' and resid 596 through 598 No H-bonds generated for 'chain 'A' and resid 596 through 598' Processing helix chain 'A' and resid 620 through 625 Processing helix chain 'A' and resid 640 through 650 Processing helix chain 'A' and resid 652 through 657 Processing helix chain 'A' and resid 670 through 681 removed outlier: 3.512A pdb=" N ILE A 674 " --> pdb=" O ILE A 670 " (cutoff:3.500A) Processing helix chain 'A' and resid 689 through 700 Processing helix chain 'A' and resid 701 through 705 Processing helix chain 'A' and resid 728 through 740 Processing helix chain 'A' and resid 756 through 761 Processing helix chain 'A' and resid 792 through 801 Processing helix chain 'A' and resid 802 through 824 Processing helix chain 'A' and resid 829 through 833 Processing helix chain 'A' and resid 836 through 848 Processing helix chain 'A' and resid 849 through 863 removed outlier: 3.576A pdb=" N THR A 853 " --> pdb=" O THR A 849 " (cutoff:3.500A) removed outlier: 4.236A pdb=" N ARG A 855 " --> pdb=" O VAL A 851 " (cutoff:3.500A) Processing helix chain 'A' and resid 872 through 885 Processing helix chain 'A' and resid 885 through 911 Processing helix chain 'A' and resid 911 through 916 removed outlier: 3.616A pdb=" N GLY A 915 " --> pdb=" O CYS A 911 " (cutoff:3.500A) Processing helix chain 'A' and resid 923 through 931 removed outlier: 3.559A pdb=" N ALA A 929 " --> pdb=" O MET A 925 " (cutoff:3.500A) Processing helix chain 'A' and resid 936 through 945 Processing helix chain 'A' and resid 976 through 979 Processing helix chain 'A' and resid 991 through 1012 removed outlier: 3.799A pdb=" N PHE A 997 " --> pdb=" O GLN A 993 " (cutoff:3.500A) Processing helix chain 'A' and resid 1013 through 1028 removed outlier: 4.339A pdb=" N TYR A1018 " --> pdb=" O SER A1014 " (cutoff:3.500A) removed outlier: 4.184A pdb=" N LEU A1019 " --> pdb=" O ARG A1015 " (cutoff:3.500A) removed outlier: 4.071A pdb=" N LEU A1023 " --> pdb=" O LEU A1019 " (cutoff:3.500A) removed outlier: 4.327A pdb=" N GLN A1026 " --> pdb=" O CYS A1022 " (cutoff:3.500A) Processing helix chain 'A' and resid 1049 through 1053 Processing helix chain 'A' and resid 1056 through 1064 removed outlier: 4.170A pdb=" N SER A1061 " --> pdb=" O ILE A1057 " (cutoff:3.500A) removed outlier: 7.486A pdb=" N HIS A1062 " --> pdb=" O THR A1058 " (cutoff:3.500A) removed outlier: 4.132A pdb=" N MET A1063 " --> pdb=" O LYS A1059 " (cutoff:3.500A) removed outlier: 3.919A pdb=" N THR A1064 " --> pdb=" O GLU A1060 " (cutoff:3.500A) Processing helix chain 'A' and resid 1065 through 1072 Processing helix chain 'A' and resid 1072 through 1080 Processing helix chain 'A' and resid 1081 through 1085 removed outlier: 3.726A pdb=" N ALA A1084 " --> pdb=" O ASN A1081 " (cutoff:3.500A) Processing helix chain 'A' and resid 1092 through 1108 Processing helix chain 'A' and resid 1122 through 1127 removed outlier: 3.627A pdb=" N LYS A1126 " --> pdb=" O PRO A1122 " (cutoff:3.500A) Processing helix chain 'A' and resid 1137 through 1151 Processing helix chain 'A' and resid 1162 through 1176 Processing helix chain 'A' and resid 1184 through 1195 Processing helix chain 'A' and resid 1196 through 1199 Processing helix chain 'A' and resid 1217 through 1226 Processing helix chain 'A' and resid 1247 through 1259 Processing helix chain 'A' and resid 1298 through 1307 Processing helix chain 'A' and resid 1309 through 1320 Processing helix chain 'A' and resid 1320 through 1337 Processing helix chain 'A' and resid 1440 through 1454 Processing helix chain 'A' and resid 1477 through 1481 Processing helix chain 'A' and resid 1484 through 1494 Processing helix chain 'A' and resid 1525 through 1531 removed outlier: 3.849A pdb=" N ASP A1531 " --> pdb=" O GLN A1527 " (cutoff:3.500A) Processing helix chain 'A' and resid 1537 through 1541 Processing helix chain 'A' and resid 1545 through 1554 Processing helix chain 'A' and resid 1554 through 1573 removed outlier: 3.844A pdb=" N TYR A1573 " --> pdb=" O VAL A1569 " (cutoff:3.500A) Processing helix chain 'A' and resid 1578 through 1590 removed outlier: 3.815A pdb=" N LEU A1582 " --> pdb=" O SER A1578 " (cutoff:3.500A) Processing helix chain 'A' and resid 1599 through 1605 removed outlier: 4.296A pdb=" N THR A1605 " --> pdb=" O GLN A1601 " (cutoff:3.500A) Processing helix chain 'A' and resid 1608 through 1614 Processing helix chain 'A' and resid 1617 through 1629 Processing helix chain 'A' and resid 1636 through 1643 Processing helix chain 'A' and resid 1649 through 1652 Processing helix chain 'B' and resid 18 through 27 Processing helix chain 'B' and resid 35 through 42 removed outlier: 3.725A pdb=" N GLN B 39 " --> pdb=" O PHE B 35 " (cutoff:3.500A) removed outlier: 4.112A pdb=" N VAL B 42 " --> pdb=" O LEU B 38 " (cutoff:3.500A) Processing helix chain 'B' and resid 42 through 51 removed outlier: 3.717A pdb=" N SER B 48 " --> pdb=" O PRO B 44 " (cutoff:3.500A) Processing helix chain 'B' and resid 59 through 69 removed outlier: 3.863A pdb=" N GLY B 69 " --> pdb=" O VAL B 65 " (cutoff:3.500A) Processing helix chain 'B' and resid 122 through 130 Processing helix chain 'B' and resid 147 through 149 No H-bonds generated for 'chain 'B' and resid 147 through 149' Processing helix chain 'B' and resid 170 through 175 removed outlier: 4.171A pdb=" N LYS B 174 " --> pdb=" O HIS B 171 " (cutoff:3.500A) removed outlier: 3.613A pdb=" N MET B 175 " --> pdb=" O LEU B 172 " (cutoff:3.500A) Processing helix chain 'B' and resid 176 through 183 Processing helix chain 'B' and resid 219 through 225 removed outlier: 3.689A pdb=" N ALA B 223 " --> pdb=" O ARG B 219 " (cutoff:3.500A) Processing helix chain 'B' and resid 273 through 281 removed outlier: 3.732A pdb=" N CYS B 281 " --> pdb=" O LEU B 277 " (cutoff:3.500A) Processing helix chain 'B' and resid 284 through 293 Processing helix chain 'B' and resid 299 through 317 Processing helix chain 'B' and resid 322 through 335 Processing helix chain 'B' and resid 345 through 358 Processing helix chain 'B' and resid 359 through 363 Processing helix chain 'B' and resid 366 through 387 Processing helix chain 'B' and resid 396 through 398 No H-bonds generated for 'chain 'B' and resid 396 through 398' Processing helix chain 'B' and resid 404 through 433 Processing helix chain 'B' and resid 442 through 451 Processing helix chain 'B' and resid 456 through 468 removed outlier: 3.630A pdb=" N LYS B 460 " --> pdb=" O ASN B 456 " (cutoff:3.500A) Processing helix chain 'B' and resid 474 through 478 removed outlier: 3.761A pdb=" N ASP B 477 " --> pdb=" O SER B 474 " (cutoff:3.500A) Processing helix chain 'B' and resid 492 through 500 removed outlier: 4.022A pdb=" N PHE B 500 " --> pdb=" O PHE B 496 " (cutoff:3.500A) Processing helix chain 'B' and resid 506 through 512 removed outlier: 3.537A pdb=" N LEU B 512 " --> pdb=" O PHE B 508 " (cutoff:3.500A) Processing helix chain 'B' and resid 521 through 525 Processing helix chain 'B' and resid 560 through 569 Processing helix chain 'B' and resid 573 through 577 removed outlier: 3.997A pdb=" N PHE B 577 " --> pdb=" O ALA B 573 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 573 through 577' Processing helix chain 'B' and resid 597 through 614 Processing helix chain 'B' and resid 665 through 670 removed outlier: 3.924A pdb=" N VAL B 670 " --> pdb=" O PRO B 666 " (cutoff:3.500A) Processing helix chain 'B' and resid 677 through 681 Processing helix chain 'B' and resid 692 through 697 Processing helix chain 'B' and resid 698 through 704 Processing helix chain 'B' and resid 706 through 710 removed outlier: 3.617A pdb=" N ASN B 710 " --> pdb=" O SER B 707 " (cutoff:3.500A) Processing helix chain 'B' and resid 711 through 724 Processing helix chain 'B' and resid 732 through 736 Processing helix chain 'B' and resid 754 through 760 removed outlier: 4.080A pdb=" N ASP B 758 " --> pdb=" O ALA B 754 " (cutoff:3.500A) Processing helix chain 'B' and resid 761 through 765 Processing helix chain 'B' and resid 791 through 796 Processing helix chain 'B' and resid 833 through 839 Processing helix chain 'B' and resid 950 through 952 No H-bonds generated for 'chain 'B' and resid 950 through 952' Processing helix chain 'B' and resid 953 through 958 removed outlier: 3.541A pdb=" N ARG B 957 " --> pdb=" O ALA B 953 " (cutoff:3.500A) Processing helix chain 'B' and resid 959 through 976 removed outlier: 3.753A pdb=" N PHE B 963 " --> pdb=" O THR B 959 " (cutoff:3.500A) Processing helix chain 'B' and resid 991 through 1004 Processing helix chain 'B' and resid 1039 through 1044 Processing helix chain 'B' and resid 1062 through 1066 Processing helix chain 'B' and resid 1072 through 1082 Processing helix chain 'B' and resid 1084 through 1093 Processing helix chain 'B' and resid 1173 through 1185 Proline residue: B1179 - end of helix removed outlier: 3.772A pdb=" N TYR B1184 " --> pdb=" O PHE B1180 " (cutoff:3.500A) Processing helix chain 'C' and resid 32 through 40 Processing helix chain 'C' and resid 60 through 74 Processing helix chain 'C' and resid 93 through 104 Processing helix chain 'C' and resid 109 through 113 removed outlier: 3.514A pdb=" N LEU C 113 " --> pdb=" O PRO C 110 " (cutoff:3.500A) Processing helix chain 'C' and resid 121 through 126 removed outlier: 3.773A pdb=" N PHE C 126 " --> pdb=" O ASP C 122 " (cutoff:3.500A) Processing helix chain 'C' and resid 165 through 167 No H-bonds generated for 'chain 'C' and resid 165 through 167' Processing helix chain 'C' and resid 173 through 179 Processing helix chain 'C' and resid 216 through 220 Processing helix chain 'C' and resid 240 through 249 Processing helix chain 'C' and resid 269 through 273 Processing helix chain 'C' and resid 277 through 281 Processing helix chain 'C' and resid 282 through 287 removed outlier: 4.374A pdb=" N ASP C 287 " --> pdb=" O GLU C 283 " (cutoff:3.500A) Processing helix chain 'C' and resid 309 through 331 Processing helix chain 'D' and resid 32 through 49 Processing helix chain 'D' and resid 81 through 96 removed outlier: 3.824A pdb=" N SER D 85 " --> pdb=" O ASN D 81 " (cutoff:3.500A) Processing helix chain 'E' and resid 2 through 27 Processing helix chain 'E' and resid 31 through 36 Processing helix chain 'E' and resid 38 through 47 Processing helix chain 'E' and resid 54 through 59 Processing helix chain 'E' and resid 65 through 72 Processing helix chain 'E' and resid 89 through 104 Processing helix chain 'E' and resid 117 through 124 Processing helix chain 'E' and resid 138 through 142 removed outlier: 4.171A pdb=" N VAL E 142 " --> pdb=" O ALA E 139 " (cutoff:3.500A) Processing helix chain 'E' and resid 143 through 147 Processing helix chain 'E' and resid 157 through 168 Processing helix chain 'E' and resid 171 through 175 Processing helix chain 'E' and resid 182 through 189 Processing helix chain 'F' and resid 75 through 79 Processing helix chain 'F' and resid 86 through 103 Processing helix chain 'F' and resid 116 through 127 Processing helix chain 'G' and resid 10 through 20 Processing helix chain 'G' and resid 28 through 32 Processing helix chain 'G' and resid 50 through 54 removed outlier: 3.597A pdb=" N TYR G 53 " --> pdb=" O ALA G 50 " (cutoff:3.500A) Processing helix chain 'G' and resid 56 through 65 Processing helix chain 'G' and resid 150 through 152 No H-bonds generated for 'chain 'G' and resid 150 through 152' Processing helix chain 'G' and resid 160 through 162 No H-bonds generated for 'chain 'G' and resid 160 through 162' Processing helix chain 'H' and resid 88 through 92 Processing helix chain 'H' and resid 129 through 134 Processing helix chain 'I' and resid 58 through 64 Processing helix chain 'J' and resid 17 through 27 Processing helix chain 'J' and resid 31 through 40 Processing helix chain 'J' and resid 43 through 52 removed outlier: 3.503A pdb=" N ILE J 50 " --> pdb=" O CYS J 46 " (cutoff:3.500A) Processing helix chain 'J' and resid 56 through 62 removed outlier: 3.872A pdb=" N ARG J 62 " --> pdb=" O GLU J 58 " (cutoff:3.500A) Processing helix chain 'K' and resid 51 through 54 Processing helix chain 'K' and resid 69 through 82 removed outlier: 4.408A pdb=" N ALA K 75 " --> pdb=" O THR K 71 " (cutoff:3.500A) removed outlier: 3.555A pdb=" N LYS K 82 " --> pdb=" O TYR K 78 " (cutoff:3.500A) Processing helix chain 'K' and resid 95 through 98 Processing helix chain 'K' and resid 112 through 142 removed outlier: 3.517A pdb=" N MET K 142 " --> pdb=" O LYS K 138 " (cutoff:3.500A) Processing helix chain 'M' and resid 67 through 72 Processing helix chain 'M' and resid 104 through 107 removed outlier: 3.635A pdb=" N ASN M 107 " --> pdb=" O SER M 104 " (cutoff:3.500A) No H-bonds generated for 'chain 'M' and resid 104 through 107' Processing helix chain 'N' and resid 63 through 67 Processing helix chain 'N' and resid 71 through 75 Processing helix chain 'N' and resid 93 through 97 removed outlier: 3.556A pdb=" N GLU N 96 " --> pdb=" O THR N 93 " (cutoff:3.500A) Processing helix chain 'N' and resid 149 through 154 Processing helix chain 'N' and resid 176 through 180 removed outlier: 3.505A pdb=" N ASP N 179 " --> pdb=" O ASP N 176 " (cutoff:3.500A) Processing helix chain 'O' and resid 294 through 298 removed outlier: 3.569A pdb=" N ASP O 298 " --> pdb=" O VAL O 295 " (cutoff:3.500A) Processing helix chain 'O' and resid 574 through 579 removed outlier: 3.517A pdb=" N ASN O 579 " --> pdb=" O SER O 576 " (cutoff:3.500A) Processing helix chain 'O' and resid 583 through 614 Processing helix chain 'O' and resid 619 through 644 removed outlier: 3.532A pdb=" N ASP O 625 " --> pdb=" O LYS O 621 " (cutoff:3.500A) Processing helix chain 'O' and resid 671 through 686 Processing helix chain 'O' and resid 695 through 704 removed outlier: 4.047A pdb=" N LEU O 699 " --> pdb=" O GLY O 695 " (cutoff:3.500A) Processing helix chain 'O' and resid 711 through 723 removed outlier: 3.834A pdb=" N TYR O 715 " --> pdb=" O LEU O 711 " (cutoff:3.500A) removed outlier: 3.590A pdb=" N ASN O 716 " --> pdb=" O ASP O 712 " (cutoff:3.500A) Processing helix chain 'O' and resid 730 through 744 removed outlier: 3.634A pdb=" N VAL O 737 " --> pdb=" O THR O 733 " (cutoff:3.500A) Processing helix chain 'O' and resid 752 through 764 Processing helix chain 'O' and resid 765 through 777 Processing helix chain 'P' and resid 97 through 124 Processing helix chain 'P' and resid 125 through 147 removed outlier: 3.692A pdb=" N GLU P 130 " --> pdb=" O PRO P 126 " (cutoff:3.500A) removed outlier: 3.738A pdb=" N THR P 143 " --> pdb=" O LYS P 139 " (cutoff:3.500A) removed outlier: 3.554A pdb=" N ILE P 144 " --> pdb=" O ILE P 140 " (cutoff:3.500A) removed outlier: 3.623A pdb=" N ASP P 146 " --> pdb=" O LYS P 142 " (cutoff:3.500A) removed outlier: 3.528A pdb=" N GLN P 147 " --> pdb=" O THR P 143 " (cutoff:3.500A) Processing helix chain 'P' and resid 157 through 173 removed outlier: 4.039A pdb=" N THR P 161 " --> pdb=" O HIS P 157 " (cutoff:3.500A) removed outlier: 4.454A pdb=" N ILE P 162 " --> pdb=" O MET P 158 " (cutoff:3.500A) Processing helix chain 'P' and resid 177 through 188 Processing helix chain 'P' and resid 201 through 206 Processing helix chain 'P' and resid 223 through 227 removed outlier: 3.542A pdb=" N LEU P 226 " --> pdb=" O ASN P 223 " (cutoff:3.500A) Processing helix chain 'P' and resid 229 through 238 Processing helix chain 'P' and resid 238 through 243 Processing helix chain 'P' and resid 249 through 260 removed outlier: 4.152A pdb=" N LEU P 253 " --> pdb=" O CYS P 249 " (cutoff:3.500A) removed outlier: 3.732A pdb=" N CYS P 260 " --> pdb=" O LEU P 256 " (cutoff:3.500A) Processing helix chain 'P' and resid 264 through 278 removed outlier: 4.411A pdb=" N PHE P 268 " --> pdb=" O PRO P 264 " (cutoff:3.500A) Processing helix chain 'P' and resid 301 through 320 Processing helix chain 'P' and resid 327 through 339 removed outlier: 4.146A pdb=" N LEU P 332 " --> pdb=" O LEU P 328 " (cutoff:3.500A) removed outlier: 3.739A pdb=" N SER P 333 " --> pdb=" O LYS P 329 " (cutoff:3.500A) removed outlier: 3.642A pdb=" N LEU P 338 " --> pdb=" O LEU P 334 " (cutoff:3.500A) Processing helix chain 'P' and resid 345 through 355 Processing helix chain 'P' and resid 362 through 369 Processing helix chain 'P' and resid 371 through 385 Processing helix chain 'P' and resid 404 through 417 Processing helix chain 'P' and resid 437 through 449 Processing helix chain 'P' and resid 470 through 491 removed outlier: 3.616A pdb=" N HIS P 482 " --> pdb=" O ARG P 478 " (cutoff:3.500A) Processing helix chain 'P' and resid 496 through 510 removed outlier: 3.593A pdb=" N LEU P 510 " --> pdb=" O LYS P 506 " (cutoff:3.500A) Processing helix chain 'Q' and resid 12 through 35 Processing helix chain 'Q' and resid 122 through 130 Processing helix chain 'Q' and resid 159 through 167 Processing helix chain 'Q' and resid 168 through 179 removed outlier: 3.988A pdb=" N ILE Q 175 " --> pdb=" O ARG Q 171 " (cutoff:3.500A) Proline residue: Q 176 - end of helix removed outlier: 3.726A pdb=" N HIS Q 179 " --> pdb=" O ILE Q 175 " (cutoff:3.500A) Processing helix chain 'Q' and resid 181 through 192 Processing helix chain 'Q' and resid 207 through 225 removed outlier: 3.624A pdb=" N HIS Q 221 " --> pdb=" O THR Q 217 " (cutoff:3.500A) Processing helix chain 'Q' and resid 228 through 242 removed outlier: 4.341A pdb=" N LYS Q 234 " --> pdb=" O SER Q 230 " (cutoff:3.500A) removed outlier: 3.670A pdb=" N ARG Q 241 " --> pdb=" O ALA Q 237 " (cutoff:3.500A) Processing helix chain 'Q' and resid 247 through 261 removed outlier: 4.085A pdb=" N VAL Q 255 " --> pdb=" O TRP Q 251 " (cutoff:3.500A) removed outlier: 4.061A pdb=" N GLU Q 256 " --> pdb=" O GLY Q 252 " (cutoff:3.500A) removed outlier: 3.742A pdb=" N LEU Q 258 " --> pdb=" O GLY Q 254 " (cutoff:3.500A) Processing helix chain 'Q' and resid 267 through 277 Processing helix chain 'Q' and resid 306 through 322 removed outlier: 3.502A pdb=" N LYS Q 322 " --> pdb=" O ILE Q 318 " (cutoff:3.500A) Processing helix chain 'Q' and resid 340 through 351 Processing helix chain 'Q' and resid 362 through 382 removed outlier: 3.803A pdb=" N LEU Q 379 " --> pdb=" O LYS Q 375 " (cutoff:3.500A) Processing helix chain 'Q' and resid 398 through 421 removed outlier: 3.794A pdb=" N ASN Q 402 " --> pdb=" O ASP Q 398 " (cutoff:3.500A) Processing helix chain 'Q' and resid 427 through 443 removed outlier: 3.798A pdb=" N ILE Q 431 " --> pdb=" O PRO Q 427 " (cutoff:3.500A) removed outlier: 3.562A pdb=" N ARG Q 441 " --> pdb=" O SER Q 437 " (cutoff:3.500A) removed outlier: 3.522A pdb=" N LEU Q 442 " --> pdb=" O PHE Q 438 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 1631 through 1632 removed outlier: 4.396A pdb=" N SER A 13 " --> pdb=" O MET B1192 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 38 through 39 Processing sheet with id=AA3, first strand: chain 'A' and resid 77 through 79 Processing sheet with id=AA4, first strand: chain 'A' and resid 243 through 245 removed outlier: 4.396A pdb=" N ILE A 251 " --> pdb=" O ILE A 315 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 371 through 373 Processing sheet with id=AA6, first strand: chain 'A' and resid 474 through 475 Processing sheet with id=AA7, first strand: chain 'B' and resid 1045 through 1047 removed outlier: 5.653A pdb=" N ILE A 495 " --> pdb=" O ARG A 606 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 506 through 510 removed outlier: 3.826A pdb=" N GLN A 535 " --> pdb=" O TYR A 578 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'A' and resid 686 through 688 Processing sheet with id=AB1, first strand: chain 'A' and resid 749 through 752 removed outlier: 6.275A pdb=" N LEU A 770 " --> pdb=" O LEU A 777 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'A' and resid 826 through 827 removed outlier: 7.833A pdb=" N ILE B 789 " --> pdb=" O SER B 928 " (cutoff:3.500A) removed outlier: 4.620A pdb=" N LYS B 930 " --> pdb=" O ILE B 789 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'A' and resid 826 through 827 removed outlier: 4.595A pdb=" N TYR B1027 " --> pdb=" O VAL B 775 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'A' and resid 948 through 949 Processing sheet with id=AB5, first strand: chain 'A' and resid 1030 through 1032 removed outlier: 6.279A pdb=" N ASP A1040 " --> pdb=" O LEU A1045 " (cutoff:3.500A) removed outlier: 6.472A pdb=" N LEU A1045 " --> pdb=" O ASP A1040 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'A' and resid 1504 through 1508 removed outlier: 3.870A pdb=" N ARG A1506 " --> pdb=" O GLU A1522 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'A' and resid 1261 through 1262 removed outlier: 6.499A pdb=" N VAL A1261 " --> pdb=" O ILE A1498 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'A' and resid 1461 through 1462 Processing sheet with id=AB9, first strand: chain 'D' and resid 21 through 24 removed outlier: 3.768A pdb=" N VAL D 21 " --> pdb=" O TYR G 46 " (cutoff:3.500A) removed outlier: 4.026A pdb=" N LYS G 106 " --> pdb=" O PHE G 115 " (cutoff:3.500A) removed outlier: 7.574A pdb=" N TRP G 117 " --> pdb=" O LEU G 104 " (cutoff:3.500A) removed outlier: 9.667A pdb=" N LEU G 104 " --> pdb=" O TRP G 117 " (cutoff:3.500A) removed outlier: 15.236A pdb=" N HIS G 119 " --> pdb=" O GLU G 102 " (cutoff:3.500A) removed outlier: 16.797A pdb=" N GLU G 102 " --> pdb=" O HIS G 119 " (cutoff:3.500A) removed outlier: 5.267A pdb=" N VAL A1656 " --> pdb=" O ILE G 107 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'D' and resid 21 through 24 removed outlier: 3.768A pdb=" N VAL D 21 " --> pdb=" O TYR G 46 " (cutoff:3.500A) removed outlier: 6.886A pdb=" N TRP G 117 " --> pdb=" O LYS G 88 " (cutoff:3.500A) removed outlier: 6.804A pdb=" N LYS G 88 " --> pdb=" O TRP G 117 " (cutoff:3.500A) removed outlier: 5.889A pdb=" N HIS G 119 " --> pdb=" O GLY G 86 " (cutoff:3.500A) removed outlier: 6.280A pdb=" N GLY G 86 " --> pdb=" O HIS G 119 " (cutoff:3.500A) removed outlier: 6.681A pdb=" N ASN G 121 " --> pdb=" O TYR G 84 " (cutoff:3.500A) removed outlier: 4.456A pdb=" N TYR G 84 " --> pdb=" O ASN G 121 " (cutoff:3.500A) removed outlier: 6.051A pdb=" N TYR G 123 " --> pdb=" O LEU G 82 " (cutoff:3.500A) removed outlier: 3.579A pdb=" N VAL G 80 " --> pdb=" O TRP G 125 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'B' and resid 70 through 74 removed outlier: 6.557A pdb=" N LYS B 140 " --> pdb=" O GLU B 100 " (cutoff:3.500A) removed outlier: 4.770A pdb=" N VAL B 102 " --> pdb=" O LEU B 138 " (cutoff:3.500A) removed outlier: 6.783A pdb=" N LEU B 138 " --> pdb=" O VAL B 102 " (cutoff:3.500A) removed outlier: 4.848A pdb=" N ILE B 104 " --> pdb=" O LYS B 136 " (cutoff:3.500A) removed outlier: 6.988A pdb=" N LYS B 136 " --> pdb=" O ILE B 104 " (cutoff:3.500A) removed outlier: 5.135A pdb=" N GLY B 135 " --> pdb=" O GLY B 160 " (cutoff:3.500A) removed outlier: 4.330A pdb=" N GLY B 160 " --> pdb=" O GLY B 135 " (cutoff:3.500A) removed outlier: 5.419A pdb=" N LEU B 137 " --> pdb=" O CYS B 158 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'B' and resid 108 through 109 removed outlier: 3.789A pdb=" N ARG B 119 " --> pdb=" O SER B 109 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'B' and resid 194 through 196 Processing sheet with id=AC5, first strand: chain 'B' and resid 400 through 403 removed outlier: 6.615A pdb=" N MET B 205 " --> pdb=" O HIS B 504 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'B' and resid 215 through 218 removed outlier: 5.652A pdb=" N TYR B 232 " --> pdb=" O TYR B 252 " (cutoff:3.500A) removed outlier: 4.000A pdb=" N TYR B 252 " --> pdb=" O TYR B 232 " (cutoff:3.500A) removed outlier: 6.543A pdb=" N THR B 247 " --> pdb=" O SER B 263 " (cutoff:3.500A) removed outlier: 4.562A pdb=" N SER B 263 " --> pdb=" O THR B 247 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'B' and resid 550 through 551 Processing sheet with id=AC8, first strand: chain 'B' and resid 550 through 551 Processing sheet with id=AC9, first strand: chain 'B' and resid 571 through 572 removed outlier: 5.479A pdb=" N ILE B 592 " --> pdb=" O ILE B 588 " (cutoff:3.500A) removed outlier: 6.427A pdb=" N ILE B 588 " --> pdb=" O ILE B 592 " (cutoff:3.500A) removed outlier: 6.206A pdb=" N CYS B 585 " --> pdb=" O LEU B 640 " (cutoff:3.500A) removed outlier: 6.715A pdb=" N LEU B 642 " --> pdb=" O CYS B 585 " (cutoff:3.500A) removed outlier: 6.351A pdb=" N GLN B 587 " --> pdb=" O LEU B 642 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'B' and resid 740 through 744 removed outlier: 7.572A pdb=" N THR B 900 " --> pdb=" O LEU B 887 " (cutoff:3.500A) removed outlier: 5.100A pdb=" N LEU B 887 " --> pdb=" O THR B 900 " (cutoff:3.500A) removed outlier: 6.507A pdb=" N SER B 902 " --> pdb=" O VAL B 885 " (cutoff:3.500A) removed outlier: 4.276A pdb=" N VAL B 885 " --> pdb=" O SER B 902 " (cutoff:3.500A) removed outlier: 6.760A pdb=" N LYS B 904 " --> pdb=" O GLU B 883 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'B' and resid 740 through 744 removed outlier: 7.572A pdb=" N THR B 900 " --> pdb=" O LEU B 887 " (cutoff:3.500A) removed outlier: 5.100A pdb=" N LEU B 887 " --> pdb=" O THR B 900 " (cutoff:3.500A) removed outlier: 6.507A pdb=" N SER B 902 " --> pdb=" O VAL B 885 " (cutoff:3.500A) removed outlier: 4.276A pdb=" N VAL B 885 " --> pdb=" O SER B 902 " (cutoff:3.500A) removed outlier: 6.760A pdb=" N LYS B 904 " --> pdb=" O GLU B 883 " (cutoff:3.500A) removed outlier: 5.116A pdb=" N VAL B 885 " --> pdb=" O LYS L 58 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'B' and resid 752 through 753 Processing sheet with id=AD4, first strand: chain 'B' and resid 824 through 825 removed outlier: 3.666A pdb=" N CYS B 859 " --> pdb=" O LYS B 872 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'B' and resid 938 through 939 Processing sheet with id=AD6, first strand: chain 'B' and resid 1098 through 1104 Processing sheet with id=AD7, first strand: chain 'B' and resid 1113 through 1115 Processing sheet with id=AD8, first strand: chain 'B' and resid 1132 through 1134 Processing sheet with id=AD9, first strand: chain 'C' and resid 41 through 47 removed outlier: 5.380A pdb=" N VAL C 42 " --> pdb=" O ILE C 57 " (cutoff:3.500A) removed outlier: 6.662A pdb=" N ILE C 57 " --> pdb=" O VAL C 42 " (cutoff:3.500A) removed outlier: 5.276A pdb=" N ILE C 44 " --> pdb=" O ASP C 55 " (cutoff:3.500A) removed outlier: 6.727A pdb=" N ASP C 55 " --> pdb=" O ILE C 44 " (cutoff:3.500A) removed outlier: 10.013A pdb=" N ARG C 293 " --> pdb=" O ASN C 234 " (cutoff:3.500A) removed outlier: 8.939A pdb=" N ASN C 234 " --> pdb=" O ARG C 293 " (cutoff:3.500A) removed outlier: 9.845A pdb=" N ARG C 295 " --> pdb=" O GLN C 232 " (cutoff:3.500A) removed outlier: 11.139A pdb=" N GLN C 232 " --> pdb=" O ARG C 295 " (cutoff:3.500A) removed outlier: 6.876A pdb=" N HIS C 297 " --> pdb=" O LEU C 230 " (cutoff:3.500A) removed outlier: 3.544A pdb=" N THR C 224 " --> pdb=" O GLU C 303 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'C' and resid 168 through 170 removed outlier: 4.044A pdb=" N VAL C 133 " --> pdb=" O GLU C 170 " (cutoff:3.500A) removed outlier: 6.370A pdb=" N GLU C 201 " --> pdb=" O ASN C 87 " (cutoff:3.500A) removed outlier: 6.116A pdb=" N ASN C 87 " --> pdb=" O GLU C 201 " (cutoff:3.500A) removed outlier: 7.555A pdb=" N SER C 203 " --> pdb=" O PHE C 85 " (cutoff:3.500A) removed outlier: 4.813A pdb=" N PHE C 85 " --> pdb=" O SER C 203 " (cutoff:3.500A) removed outlier: 6.167A pdb=" N LYS C 205 " --> pdb=" O VAL C 83 " (cutoff:3.500A) removed outlier: 4.672A pdb=" N VAL C 83 " --> pdb=" O LYS C 205 " (cutoff:3.500A) removed outlier: 6.341A pdb=" N HIS C 207 " --> pdb=" O GLU C 81 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'C' and resid 141 through 142 Processing sheet with id=AE3, first strand: chain 'C' and resid 161 through 163 removed outlier: 6.875A pdb=" N VAL C 162 " --> pdb=" O LEU C 193 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'C' and resid 256 through 257 Processing sheet with id=AE5, first strand: chain 'E' and resid 60 through 62 removed outlier: 6.368A pdb=" N TRP E 79 " --> pdb=" O ILE E 109 " (cutoff:3.500A) removed outlier: 7.456A pdb=" N VAL E 111 " --> pdb=" O TRP E 79 " (cutoff:3.500A) removed outlier: 6.425A pdb=" N GLU E 81 " --> pdb=" O VAL E 111 " (cutoff:3.500A) Processing sheet with id=AE6, first strand: chain 'E' and resid 87 through 88 Processing sheet with id=AE7, first strand: chain 'E' and resid 152 through 155 Processing sheet with id=AE8, first strand: chain 'G' and resid 132 through 141 removed outlier: 3.629A pdb=" N TYR G 136 " --> pdb=" O LEU G 148 " (cutoff:3.500A) removed outlier: 6.017A pdb=" N GLY G 146 " --> pdb=" O PHE G 138 " (cutoff:3.500A) removed outlier: 4.612A pdb=" N GLN G 140 " --> pdb=" O HIS G 144 " (cutoff:3.500A) removed outlier: 6.784A pdb=" N HIS G 144 " --> pdb=" O GLN G 140 " (cutoff:3.500A) removed outlier: 7.099A pdb=" N ASN G 154 " --> pdb=" O VAL G 245 " (cutoff:3.500A) removed outlier: 7.610A pdb=" N GLY G 247 " --> pdb=" O ASN G 154 " (cutoff:3.500A) removed outlier: 6.530A pdb=" N SER G 156 " --> pdb=" O GLY G 247 " (cutoff:3.500A) removed outlier: 6.140A pdb=" N THR G 248 " --> pdb=" O VAL G 233 " (cutoff:3.500A) removed outlier: 5.517A pdb=" N VAL G 233 " --> pdb=" O THR G 248 " (cutoff:3.500A) Processing sheet with id=AE9, first strand: chain 'G' and resid 167 through 169 Processing sheet with id=AF1, first strand: chain 'H' and resid 4 through 16 removed outlier: 6.363A pdb=" N GLU H 27 " --> pdb=" O SER H 13 " (cutoff:3.500A) removed outlier: 4.510A pdb=" N VAL H 15 " --> pdb=" O ARG H 25 " (cutoff:3.500A) removed outlier: 6.473A pdb=" N ARG H 25 " --> pdb=" O VAL H 15 " (cutoff:3.500A) removed outlier: 4.933A pdb=" N LEU H 122 " --> pdb=" O ASP H 41 " (cutoff:3.500A) removed outlier: 3.752A pdb=" N LYS H 103 " --> pdb=" O TYR H 115 " (cutoff:3.500A) removed outlier: 6.673A pdb=" N SER H 117 " --> pdb=" O ALA H 101 " (cutoff:3.500A) removed outlier: 5.662A pdb=" N ALA H 101 " --> pdb=" O SER H 117 " (cutoff:3.500A) Processing sheet with id=AF2, first strand: chain 'I' and resid 3 through 4 Processing sheet with id=AF3, first strand: chain 'K' and resid 47 through 49 Processing sheet with id=AF4, first strand: chain 'M' and resid 10 through 11 Processing sheet with id=AF5, first strand: chain 'M' and resid 14 through 16 removed outlier: 3.608A pdb=" N LYS M 92 " --> pdb=" O GLN M 16 " (cutoff:3.500A) removed outlier: 3.558A pdb=" N SER M 87 " --> pdb=" O ASN M 82 " (cutoff:3.500A) removed outlier: 6.279A pdb=" N VAL N 53 " --> pdb=" O LYS N 135 " (cutoff:3.500A) removed outlier: 7.934A pdb=" N PHE N 137 " --> pdb=" O VAL N 53 " (cutoff:3.500A) removed outlier: 5.771A pdb=" N LEU N 55 " --> pdb=" O PHE N 137 " (cutoff:3.500A) removed outlier: 7.419A pdb=" N VAL N 139 " --> pdb=" O LEU N 55 " (cutoff:3.500A) removed outlier: 6.245A pdb=" N LYS N 57 " --> pdb=" O VAL N 139 " (cutoff:3.500A) removed outlier: 7.992A pdb=" N GLU N 141 " --> pdb=" O LYS N 57 " (cutoff:3.500A) removed outlier: 4.179A pdb=" N VAL N 136 " --> pdb=" O ASP N 92 " (cutoff:3.500A) Processing sheet with id=AF6, first strand: chain 'M' and resid 39 through 45 removed outlier: 3.730A pdb=" N VAL M 52 " --> pdb=" O TYR M 41 " (cutoff:3.500A) removed outlier: 3.821A pdb=" N GLU M 50 " --> pdb=" O LYS M 43 " (cutoff:3.500A) Processing sheet with id=AF7, first strand: chain 'O' and resid 57 through 60 removed outlier: 3.549A pdb=" N TYR O 548 " --> pdb=" O VAL O 539 " (cutoff:3.500A) removed outlier: 7.836A pdb=" N ASP O 536 " --> pdb=" O THR O 510 " (cutoff:3.500A) removed outlier: 5.313A pdb=" N THR O 510 " --> pdb=" O ASP O 536 " (cutoff:3.500A) removed outlier: 6.312A pdb=" N LEU O 538 " --> pdb=" O ILE O 508 " (cutoff:3.500A) removed outlier: 4.428A pdb=" N ILE O 508 " --> pdb=" O LEU O 538 " (cutoff:3.500A) removed outlier: 6.454A pdb=" N LYS O 540 " --> pdb=" O THR O 506 " (cutoff:3.500A) Processing sheet with id=AF8, first strand: chain 'O' and resid 201 through 205 removed outlier: 4.268A pdb=" N GLU O 201 " --> pdb=" O LEU O 219 " (cutoff:3.500A) Processing sheet with id=AF9, first strand: chain 'O' and resid 242 through 245 removed outlier: 6.629A pdb=" N ILE O 264 " --> pdb=" O LYS O 243 " (cutoff:3.500A) Processing sheet with id=AG1, first strand: chain 'O' and resid 305 through 306 Processing sheet with id=AG2, first strand: chain 'O' and resid 361 through 365 removed outlier: 3.635A pdb=" N ARG O 362 " --> pdb=" O PHE O 375 " (cutoff:3.500A) removed outlier: 3.731A pdb=" N GLU O 382 " --> pdb=" O THR O 391 " (cutoff:3.500A) Processing sheet with id=AG3, first strand: chain 'O' and resid 402 through 405 removed outlier: 6.878A pdb=" N THR O 417 " --> pdb=" O ARG O 403 " (cutoff:3.500A) Processing sheet with id=AG4, first strand: chain 'O' and resid 452 through 457 Processing sheet with id=AG5, first strand: chain 'O' and resid 452 through 457 2000 hydrogen bonds defined for protein. 5475 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 65 hydrogen bonds 106 hydrogen bond angles 0 basepair planarities 30 basepair parallelities 82 stacking parallelities Total time for adding SS restraints: 27.07 Time building geometry restraints manager: 21.72 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.19 - 1.32: 7676 1.32 - 1.44: 12904 1.44 - 1.57: 26566 1.57 - 1.69: 241 1.69 - 1.82: 326 Bond restraints: 47713 Sorted by residual: bond pdb=" CA ASP O 353 " pdb=" C ASP O 353 " ideal model delta sigma weight residual 1.524 1.661 -0.137 1.26e-02 6.30e+03 1.18e+02 bond pdb=" CA LYS A1115 " pdb=" C LYS A1115 " ideal model delta sigma weight residual 1.523 1.635 -0.112 1.34e-02 5.57e+03 6.99e+01 bond pdb=" CA ARG O 584 " pdb=" C ARG O 584 " ideal model delta sigma weight residual 1.523 1.630 -0.107 1.34e-02 5.57e+03 6.37e+01 bond pdb=" CA ILE O 297 " pdb=" C ILE O 297 " ideal model delta sigma weight residual 1.523 1.621 -0.098 1.27e-02 6.20e+03 5.96e+01 bond pdb=" CA HIS P 511 " pdb=" C HIS P 511 " ideal model delta sigma weight residual 1.524 1.629 -0.105 1.40e-02 5.10e+03 5.61e+01 ... (remaining 47708 not shown) Histogram of bond angle deviations from ideal: 84.76 - 96.03: 13 96.03 - 107.30: 2670 107.30 - 118.58: 36026 118.58 - 129.85: 25911 129.85 - 141.13: 313 Bond angle restraints: 64933 Sorted by residual: angle pdb=" N VAL P 356 " pdb=" CA VAL P 356 " pdb=" C VAL P 356 " ideal model delta sigma weight residual 112.17 91.23 20.94 9.50e-01 1.11e+00 4.86e+02 angle pdb=" N HIS O 705 " pdb=" CA HIS O 705 " pdb=" C HIS O 705 " ideal model delta sigma weight residual 113.21 91.02 22.19 1.15e+00 7.56e-01 3.72e+02 angle pdb=" N LYS O 749 " pdb=" CA LYS O 749 " pdb=" C LYS O 749 " ideal model delta sigma weight residual 109.30 132.03 -22.73 1.49e+00 4.50e-01 2.33e+02 angle pdb=" C PHE P 125 " pdb=" N PRO P 126 " pdb=" CA PRO P 126 " ideal model delta sigma weight residual 119.84 138.50 -18.66 1.25e+00 6.40e-01 2.23e+02 angle pdb=" C LYS B 77 " pdb=" N PRO B 78 " pdb=" CA PRO B 78 " ideal model delta sigma weight residual 119.84 102.09 17.75 1.25e+00 6.40e-01 2.02e+02 ... (remaining 64928 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 34.89: 27955 34.89 - 69.78: 775 69.78 - 104.67: 43 104.67 - 139.56: 0 139.56 - 174.46: 1 Dihedral angle restraints: 28774 sinusoidal: 12517 harmonic: 16257 Sorted by residual: dihedral pdb=" C LYS A 410 " pdb=" N LYS A 410 " pdb=" CA LYS A 410 " pdb=" CB LYS A 410 " ideal model delta harmonic sigma weight residual -122.60 -157.53 34.93 0 2.50e+00 1.60e-01 1.95e+02 dihedral pdb=" N LYS A 410 " pdb=" C LYS A 410 " pdb=" CA LYS A 410 " pdb=" CB LYS A 410 " ideal model delta harmonic sigma weight residual 122.80 157.15 -34.35 0 2.50e+00 1.60e-01 1.89e+02 dihedral pdb=" C GLN Q 147 " pdb=" N GLN Q 147 " pdb=" CA GLN Q 147 " pdb=" CB GLN Q 147 " ideal model delta harmonic sigma weight residual -122.60 -143.29 20.69 0 2.50e+00 1.60e-01 6.85e+01 ... (remaining 28771 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.296: 7156 0.296 - 0.592: 96 0.592 - 0.889: 9 0.889 - 1.185: 2 1.185 - 1.481: 1 Chirality restraints: 7264 Sorted by residual: chirality pdb=" CA LYS A 410 " pdb=" N LYS A 410 " pdb=" C LYS A 410 " pdb=" CB LYS A 410 " both_signs ideal model delta sigma weight residual False 2.51 1.03 1.48 2.00e-01 2.50e+01 5.48e+01 chirality pdb=" CA GLN Q 147 " pdb=" N GLN Q 147 " pdb=" C GLN Q 147 " pdb=" CB GLN Q 147 " both_signs ideal model delta sigma weight residual False 2.51 1.59 0.92 2.00e-01 2.50e+01 2.13e+01 chirality pdb=" CA GLU P 246 " pdb=" N GLU P 246 " pdb=" C GLU P 246 " pdb=" CB GLU P 246 " both_signs ideal model delta sigma weight residual False 2.51 1.62 0.89 2.00e-01 2.50e+01 1.99e+01 ... (remaining 7261 not shown) Planarity restraints: 7979 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB PHE Q 188 " 0.100 2.00e-02 2.50e+03 6.14e-02 6.59e+01 pdb=" CG PHE Q 188 " -0.074 2.00e-02 2.50e+03 pdb=" CD1 PHE Q 188 " -0.058 2.00e-02 2.50e+03 pdb=" CD2 PHE Q 188 " -0.054 2.00e-02 2.50e+03 pdb=" CE1 PHE Q 188 " 0.012 2.00e-02 2.50e+03 pdb=" CE2 PHE Q 188 " 0.009 2.00e-02 2.50e+03 pdb=" CZ PHE Q 188 " 0.066 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB PHE Q 270 " 0.083 2.00e-02 2.50e+03 5.20e-02 4.74e+01 pdb=" CG PHE Q 270 " -0.056 2.00e-02 2.50e+03 pdb=" CD1 PHE Q 270 " -0.063 2.00e-02 2.50e+03 pdb=" CD2 PHE Q 270 " -0.040 2.00e-02 2.50e+03 pdb=" CE1 PHE Q 270 " 0.021 2.00e-02 2.50e+03 pdb=" CE2 PHE Q 270 " -0.000 2.00e-02 2.50e+03 pdb=" CZ PHE Q 270 " 0.055 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TYR Q 443 " 0.049 2.00e-02 2.50e+03 4.73e-02 4.48e+01 pdb=" CG TYR Q 443 " -0.004 2.00e-02 2.50e+03 pdb=" CD1 TYR Q 443 " -0.002 2.00e-02 2.50e+03 pdb=" CD2 TYR Q 443 " -0.006 2.00e-02 2.50e+03 pdb=" CE1 TYR Q 443 " -0.038 2.00e-02 2.50e+03 pdb=" CE2 TYR Q 443 " -0.042 2.00e-02 2.50e+03 pdb=" CZ TYR Q 443 " -0.054 2.00e-02 2.50e+03 pdb=" OH TYR Q 443 " 0.097 2.00e-02 2.50e+03 ... (remaining 7976 not shown) Histogram of nonbonded interaction distances: 1.01 - 1.78: 184 1.78 - 2.56: 1976 2.56 - 3.34: 64637 3.34 - 4.12: 120434 4.12 - 4.90: 211079 Nonbonded interactions: 398310 Sorted by model distance: nonbonded pdb=" NZ LYS M 45 " pdb=" OE2 GLU M 50 " model vdw 1.006 2.520 nonbonded pdb=" N VAL Q 353 " pdb=" CZ PHE Q 358 " model vdw 1.027 3.420 nonbonded pdb=" CB ALA P 195 " pdb=" CB GLU P 216 " model vdw 1.043 3.860 nonbonded pdb=" N VAL Q 353 " pdb=" CE2 PHE Q 358 " model vdw 1.052 3.420 nonbonded pdb=" OE1 GLU O 614 " pdb=" CB ALA O 670 " model vdw 1.053 3.460 ... (remaining 398305 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=0.96 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: 0.000 Normalize map: mean=0, sd=1: 1.040 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: 0.060 Extract box with map and model: 4.490 Check model and map are aligned: 0.810 Set scattering table: 0.490 Process input model: 146.680 Find NCS groups from input model: 1.170 Set up NCS constraints: 0.160 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:3.120 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 158.030 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6408 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 0.137 47713 Z= 0.420 Angle : 1.409 25.054 64933 Z= 0.902 Chirality : 0.086 1.481 7264 Planarity : 0.011 0.147 7979 Dihedral : 15.227 174.456 18230 Min Nonbonded Distance : 1.006 Molprobity Statistics. All-atom Clashscore : 83.46 Ramachandran Plot: Outliers : 4.05 % Allowed : 9.02 % Favored : 86.93 % Rotamer: Outliers : 5.40 % Allowed : 5.27 % Favored : 89.33 % Cbeta Deviations : 0.85 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.51 (0.10), residues: 5432 helix: -1.98 (0.09), residues: 1911 sheet: -1.66 (0.16), residues: 767 loop : -2.82 (0.10), residues: 2754 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.061 0.004 TRP Q 273 HIS 0.028 0.002 HIS B 875 PHE 0.100 0.003 PHE Q 188 TYR 0.097 0.007 TYR Q 443 ARG 0.095 0.011 ARG A 59 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10864 Ramachandran restraints generated. 5432 Oldfield, 0 Emsley, 5432 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10864 Ramachandran restraints generated. 5432 Oldfield, 0 Emsley, 5432 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1854 residues out of total 4950 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 267 poor density : 1587 time to evaluate : 5.770 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: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 450 LYS cc_start: 0.5507 (OUTLIER) cc_final: 0.4084 (mttm) REVERT: A 589 MET cc_start: 0.7919 (mmm) cc_final: 0.7518 (mmm) REVERT: A 635 MET cc_start: 0.7844 (ttp) cc_final: 0.7602 (ttp) REVERT: A 640 ASN cc_start: 0.7834 (t0) cc_final: 0.7568 (m-40) REVERT: A 732 ILE cc_start: 0.9115 (mm) cc_final: 0.8899 (mt) REVERT: A 994 GLU cc_start: 0.2470 (mt-10) cc_final: 0.1976 (mt-10) REVERT: A 1006 LEU cc_start: 0.1244 (mt) cc_final: 0.0687 (mt) REVERT: A 1013 THR cc_start: 0.0730 (OUTLIER) cc_final: 0.0013 (t) REVERT: A 1015 ARG cc_start: 0.1997 (mtm180) cc_final: 0.1466 (mmm-85) REVERT: A 1016 SER cc_start: 0.1841 (p) cc_final: 0.1305 (t) REVERT: A 1118 VAL cc_start: 0.5309 (OUTLIER) cc_final: 0.5059 (p) REVERT: A 1576 SER cc_start: 0.8013 (m) cc_final: 0.7729 (p) REVERT: A 1627 LEU cc_start: 0.7878 (mt) cc_final: 0.7431 (mt) REVERT: B 77 LYS cc_start: 0.5602 (OUTLIER) cc_final: 0.5380 (tptt) REVERT: B 158 CYS cc_start: 0.5829 (m) cc_final: 0.5408 (m) REVERT: B 217 ILE cc_start: 0.8898 (pt) cc_final: 0.8685 (pt) REVERT: B 450 LEU cc_start: 0.6860 (mt) cc_final: 0.6310 (mp) REVERT: B 900 THR cc_start: 0.8456 (m) cc_final: 0.8024 (p) REVERT: B 1055 LEU cc_start: 0.7794 (mt) cc_final: 0.7526 (mt) REVERT: B 1113 THR cc_start: 0.8440 (p) cc_final: 0.8080 (p) REVERT: B 1189 LEU cc_start: 0.7614 (mt) cc_final: 0.7246 (tt) REVERT: D 25 THR cc_start: 0.6313 (p) cc_final: 0.5597 (p) REVERT: E 211 TYR cc_start: 0.8225 (m-80) cc_final: 0.7770 (m-10) REVERT: F 90 ARG cc_start: 0.8317 (ttt-90) cc_final: 0.7976 (ttt-90) REVERT: F 144 GLU cc_start: 0.7149 (mt-10) cc_final: 0.6779 (mt-10) REVERT: G 53 TYR cc_start: 0.6548 (m-80) cc_final: 0.6175 (m-80) REVERT: G 100 THR cc_start: 0.6594 (OUTLIER) cc_final: 0.6249 (p) REVERT: H 25 ARG cc_start: 0.7444 (ttp80) cc_final: 0.7004 (ttp80) REVERT: I 41 GLN cc_start: 0.6762 (OUTLIER) cc_final: 0.6329 (tp-100) REVERT: K 66 VAL cc_start: 0.8732 (m) cc_final: 0.8495 (t) REVERT: K 125 MET cc_start: 0.5862 (mtp) cc_final: 0.5542 (mtp) REVERT: O 197 ARG cc_start: 0.3792 (OUTLIER) cc_final: 0.2787 (tpm170) REVERT: O 485 LYS cc_start: 0.8779 (OUTLIER) cc_final: 0.8420 (mppt) REVERT: P 312 LEU cc_start: 0.8130 (OUTLIER) cc_final: 0.7549 (mt) REVERT: P 512 ARG cc_start: 0.2231 (OUTLIER) cc_final: -0.0242 (mtm180) REVERT: Q 166 GLU cc_start: 0.7362 (tt0) cc_final: 0.7158 (pt0) REVERT: Q 214 VAL cc_start: 0.8296 (t) cc_final: 0.7477 (t) REVERT: Q 271 LEU cc_start: 0.8601 (mt) cc_final: 0.8325 (mt) outliers start: 267 outliers final: 109 residues processed: 1806 average time/residue: 0.6234 time to fit residues: 1822.5694 Evaluate side-chains 1040 residues out of total 4950 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 119 poor density : 921 time to evaluate : 5.032 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 81 LEU Chi-restraints excluded: chain A residue 413 LEU Chi-restraints excluded: chain A residue 450 LYS Chi-restraints excluded: chain A residue 721 LYS Chi-restraints excluded: chain A residue 789 SER Chi-restraints excluded: chain A residue 790 LYS Chi-restraints excluded: chain A residue 1013 THR Chi-restraints excluded: chain A residue 1114 TYR Chi-restraints excluded: chain A residue 1116 GLN Chi-restraints excluded: chain A residue 1117 SER Chi-restraints excluded: chain A residue 1118 VAL Chi-restraints excluded: chain A residue 1119 LYS Chi-restraints excluded: chain B residue 77 LYS Chi-restraints excluded: chain B residue 91 LEU Chi-restraints excluded: chain B residue 813 LEU Chi-restraints excluded: chain B residue 819 ASP Chi-restraints excluded: chain B residue 1117 VAL Chi-restraints excluded: chain B residue 1194 ILE Chi-restraints excluded: chain G residue 95 LEU Chi-restraints excluded: chain G residue 96 SER Chi-restraints excluded: chain G residue 97 LYS Chi-restraints excluded: chain G residue 100 THR Chi-restraints excluded: chain I residue 40 SER Chi-restraints excluded: chain I residue 41 GLN Chi-restraints excluded: chain M residue 47 GLU Chi-restraints excluded: chain M residue 51 PHE Chi-restraints excluded: chain M residue 113 ILE Chi-restraints excluded: chain N residue 25 ILE Chi-restraints excluded: chain N residue 128 ASN Chi-restraints excluded: chain N residue 131 LEU Chi-restraints excluded: chain O residue 197 ARG Chi-restraints excluded: chain O residue 200 THR Chi-restraints excluded: chain O residue 202 ILE Chi-restraints excluded: chain O residue 203 ILE Chi-restraints excluded: chain O residue 216 ILE Chi-restraints excluded: chain O residue 221 ARG Chi-restraints excluded: chain O residue 222 GLN Chi-restraints excluded: chain O residue 224 THR Chi-restraints excluded: chain O residue 237 GLU Chi-restraints excluded: chain O residue 260 LEU Chi-restraints excluded: chain O residue 292 LEU Chi-restraints excluded: chain O residue 350 THR Chi-restraints excluded: chain O residue 439 LYS Chi-restraints excluded: chain O residue 485 LYS Chi-restraints excluded: chain O residue 574 TRP Chi-restraints excluded: chain O residue 583 GLU Chi-restraints excluded: chain O residue 585 GLU Chi-restraints excluded: chain O residue 586 LYS Chi-restraints excluded: chain O residue 615 ASN Chi-restraints excluded: chain O residue 616 SER Chi-restraints excluded: chain O residue 617 HIS Chi-restraints excluded: chain O residue 626 LEU Chi-restraints excluded: chain O residue 637 LEU Chi-restraints excluded: chain O residue 649 ILE Chi-restraints excluded: chain O residue 650 LEU Chi-restraints excluded: chain O residue 655 SER Chi-restraints excluded: chain O residue 659 LEU Chi-restraints excluded: chain O residue 662 LEU Chi-restraints excluded: chain O residue 665 ASN Chi-restraints excluded: chain O residue 702 LEU Chi-restraints excluded: chain O residue 712 ASP Chi-restraints excluded: chain O residue 726 SER Chi-restraints excluded: chain O residue 744 LEU Chi-restraints excluded: chain O residue 772 ILE Chi-restraints excluded: chain P residue 95 LEU Chi-restraints excluded: chain P residue 147 GLN Chi-restraints excluded: chain P residue 150 GLU Chi-restraints excluded: chain P residue 151 GLU Chi-restraints excluded: chain P residue 152 LEU Chi-restraints excluded: chain P residue 154 LEU Chi-restraints excluded: chain P residue 170 THR Chi-restraints excluded: chain P residue 172 LEU Chi-restraints excluded: chain P residue 183 LYS Chi-restraints excluded: chain P residue 193 PHE Chi-restraints excluded: chain P residue 215 LEU Chi-restraints excluded: chain P residue 225 GLN Chi-restraints excluded: chain P residue 236 MET Chi-restraints excluded: chain P residue 279 THR Chi-restraints excluded: chain P residue 281 ILE Chi-restraints excluded: chain P residue 284 LEU Chi-restraints excluded: chain P residue 291 ASP Chi-restraints excluded: chain P residue 301 HIS Chi-restraints excluded: chain P residue 312 LEU Chi-restraints excluded: chain P residue 341 ARG Chi-restraints excluded: chain P residue 355 VAL Chi-restraints excluded: chain P residue 365 ASP Chi-restraints excluded: chain P residue 385 PHE Chi-restraints excluded: chain P residue 388 THR Chi-restraints excluded: chain P residue 422 GLU Chi-restraints excluded: chain P residue 444 GLU Chi-restraints excluded: chain P residue 453 PHE Chi-restraints excluded: chain P residue 493 ILE Chi-restraints excluded: chain P residue 495 LYS Chi-restraints excluded: chain P residue 497 GLN Chi-restraints excluded: chain P residue 512 ARG Chi-restraints excluded: chain Q residue 4 VAL Chi-restraints excluded: chain Q residue 27 ILE Chi-restraints excluded: chain Q residue 138 PHE Chi-restraints excluded: chain Q residue 147 GLN Chi-restraints excluded: chain Q residue 152 ILE Chi-restraints excluded: chain Q residue 155 GLN Chi-restraints excluded: chain Q residue 168 ILE Chi-restraints excluded: chain Q residue 180 CYS Chi-restraints excluded: chain Q residue 200 THR Chi-restraints excluded: chain Q residue 203 SER Chi-restraints excluded: chain Q residue 204 GLU Chi-restraints excluded: chain Q residue 206 ARG Chi-restraints excluded: chain Q residue 208 TYR Chi-restraints excluded: chain Q residue 246 GLN Chi-restraints excluded: chain Q residue 247 ILE Chi-restraints excluded: chain Q residue 248 LYS Chi-restraints excluded: chain Q residue 272 GLN Chi-restraints excluded: chain Q residue 298 GLN Chi-restraints excluded: chain Q residue 317 LEU Chi-restraints excluded: chain Q residue 364 VAL Chi-restraints excluded: chain Q residue 367 ILE Chi-restraints excluded: chain Q residue 384 VAL Chi-restraints excluded: chain Q residue 390 ASN Chi-restraints excluded: chain Q residue 393 ILE Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 556 random chunks: chunk 469 optimal weight: 8.9990 chunk 421 optimal weight: 8.9990 chunk 233 optimal weight: 20.0000 chunk 143 optimal weight: 3.9990 chunk 284 optimal weight: 5.9990 chunk 225 optimal weight: 10.0000 chunk 435 optimal weight: 6.9990 chunk 168 optimal weight: 1.9990 chunk 264 optimal weight: 8.9990 chunk 324 optimal weight: 10.0000 chunk 504 optimal weight: 5.9990 overall best weight: 4.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 43 HIS A 60 ASN ** A 76 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 93 GLN A 336 GLN ** A 383 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 384 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 432 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 580 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 656 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 738 ASN A 926 GLN A1113 HIS A1314 GLN ** A1647 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 27 ASN B 254 ASN B 398 GLN B 399 HIS ** B 504 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 532 HIS ** B 555 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 575 HIS B 636 GLN B 683 ASN B 710 ASN ** B 720 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 755 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 824 HIS B 886 ASN ** B1163 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 161 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 175 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 232 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 88 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 99 HIS ** E 113 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 36 ASN G 64 GLN ** G 128 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 237 HIS H 52 GLN H 137 GLN L 66 GLN ** M 18 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 54 HIS M 89 GLN ** N 34 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 103 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** O 239 HIS O 267 ASN ** O 308 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** O 401 ASN ** O 454 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** O 490 GLN O 579 ASN O 609 ASN ** O 635 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** O 642 GLN ** P 145 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 147 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 155 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** P 157 HIS ** P 209 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 272 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 315 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 486 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** P 511 HIS Q 22 GLN ** Q 147 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 155 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 212 HIS Q 221 HIS Q 246 GLN ** Q 272 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 276 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 287 ASN ** Q 289 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 298 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 304 HIS ** Q 339 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 372 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Q 402 ASN Total number of N/Q/H flips: 44 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6668 moved from start: 0.4195 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.079 47713 Z= 0.406 Angle : 0.989 19.456 64933 Z= 0.510 Chirality : 0.053 0.331 7264 Planarity : 0.007 0.094 7979 Dihedral : 15.419 167.821 7446 Min Nonbonded Distance : 2.037 Molprobity Statistics. All-atom Clashscore : 26.79 Ramachandran Plot: Outliers : 1.42 % Allowed : 7.93 % Favored : 90.65 % Rotamer: Outliers : 5.88 % Allowed : 14.92 % Favored : 79.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 2.07 % 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: -1.83 (0.11), residues: 5432 helix: -0.25 (0.11), residues: 1985 sheet: -1.15 (0.17), residues: 762 loop : -1.98 (0.11), residues: 2685 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.040 0.004 TRP O 399 HIS 0.022 0.002 HIS Q 212 PHE 0.040 0.003 PHE O 305 TYR 0.045 0.003 TYR O 196 ARG 0.010 0.001 ARG O 229 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10864 Ramachandran restraints generated. 5432 Oldfield, 0 Emsley, 5432 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10864 Ramachandran restraints generated. 5432 Oldfield, 0 Emsley, 5432 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1261 residues out of total 4950 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 291 poor density : 970 time to evaluate : 6.724 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: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 1 MET cc_start: 0.8098 (tpp) cc_final: 0.7805 (tpp) REVERT: A 450 LYS cc_start: 0.5857 (OUTLIER) cc_final: 0.4355 (mttm) REVERT: A 640 ASN cc_start: 0.8195 (t0) cc_final: 0.7979 (m-40) REVERT: A 790 LYS cc_start: 0.6350 (OUTLIER) cc_final: 0.6022 (tppt) REVERT: A 1009 THR cc_start: 0.1732 (m) cc_final: 0.1489 (t) REVERT: A 1015 ARG cc_start: 0.1179 (mtm180) cc_final: 0.0905 (mmm-85) REVERT: A 1497 ILE cc_start: 0.8017 (pp) cc_final: 0.7769 (pt) REVERT: B 115 SER cc_start: 0.6340 (OUTLIER) cc_final: 0.5819 (p) REVERT: B 138 LEU cc_start: 0.8105 (mt) cc_final: 0.7689 (mt) REVERT: B 388 GLU cc_start: 0.6245 (pt0) cc_final: 0.6012 (pt0) REVERT: B 759 ASP cc_start: 0.7188 (t0) cc_final: 0.6978 (t0) REVERT: B 778 TYR cc_start: 0.8414 (t80) cc_final: 0.7797 (t80) REVERT: B 816 ASN cc_start: 0.4699 (OUTLIER) cc_final: 0.4437 (m110) REVERT: B 900 THR cc_start: 0.8340 (m) cc_final: 0.8034 (p) REVERT: B 1194 ILE cc_start: 0.4014 (OUTLIER) cc_final: 0.3562 (mt) REVERT: C 71 MET cc_start: 0.7991 (ttm) cc_final: 0.7516 (ttp) REVERT: C 232 GLN cc_start: 0.6701 (tm-30) cc_final: 0.6258 (tm-30) REVERT: F 82 THR cc_start: 0.8786 (OUTLIER) cc_final: 0.8511 (p) REVERT: F 138 LEU cc_start: 0.8801 (mm) cc_final: 0.8466 (mp) REVERT: F 140 ASP cc_start: 0.7996 (p0) cc_final: 0.7700 (p0) REVERT: F 151 LEU cc_start: 0.7942 (tp) cc_final: 0.7594 (mp) REVERT: G 99 ASP cc_start: 0.5560 (p0) cc_final: 0.5295 (p0) REVERT: M 62 TYR cc_start: 0.5614 (p90) cc_final: 0.5317 (p90) REVERT: O 313 GLN cc_start: 0.5610 (OUTLIER) cc_final: 0.5398 (pp30) REVERT: O 439 LYS cc_start: 0.7476 (OUTLIER) cc_final: 0.7240 (pttm) REVERT: O 485 LYS cc_start: 0.8785 (OUTLIER) cc_final: 0.8546 (mmtt) REVERT: P 512 ARG cc_start: 0.1168 (OUTLIER) cc_final: 0.0404 (mpp-170) REVERT: Q 285 VAL cc_start: 0.4825 (OUTLIER) cc_final: 0.4553 (t) REVERT: Q 304 HIS cc_start: 0.5019 (t-90) cc_final: 0.4638 (t-90) outliers start: 291 outliers final: 132 residues processed: 1175 average time/residue: 0.6165 time to fit residues: 1207.3505 Evaluate side-chains 908 residues out of total 4950 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 143 poor density : 765 time to evaluate : 5.419 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 60 ASN Chi-restraints excluded: chain A residue 94 LEU Chi-restraints excluded: chain A residue 220 VAL Chi-restraints excluded: chain A residue 323 ILE Chi-restraints excluded: chain A residue 389 VAL Chi-restraints excluded: chain A residue 419 ILE Chi-restraints excluded: chain A residue 450 LYS Chi-restraints excluded: chain A residue 551 VAL Chi-restraints excluded: chain A residue 572 THR Chi-restraints excluded: chain A residue 599 SER Chi-restraints excluded: chain A residue 678 VAL Chi-restraints excluded: chain A residue 685 SER Chi-restraints excluded: chain A residue 721 LYS Chi-restraints excluded: chain A residue 773 ASP Chi-restraints excluded: chain A residue 790 LYS Chi-restraints excluded: chain A residue 957 VAL Chi-restraints excluded: chain A residue 962 SER Chi-restraints excluded: chain A residue 1013 THR Chi-restraints excluded: chain A residue 1033 SER Chi-restraints excluded: chain A residue 1060 GLU Chi-restraints excluded: chain A residue 1114 TYR Chi-restraints excluded: chain A residue 1118 VAL Chi-restraints excluded: chain A residue 1192 SER Chi-restraints excluded: chain A residue 1216 THR Chi-restraints excluded: chain A residue 1323 HIS Chi-restraints excluded: chain A residue 1489 VAL Chi-restraints excluded: chain A residue 1491 GLU Chi-restraints excluded: chain A residue 1543 SER Chi-restraints excluded: chain A residue 1614 SER Chi-restraints excluded: chain A residue 1634 LEU Chi-restraints excluded: chain A residue 1649 VAL Chi-restraints excluded: chain A residue 1655 ASP Chi-restraints excluded: chain B residue 35 PHE Chi-restraints excluded: chain B residue 38 LEU Chi-restraints excluded: chain B residue 75 ASP Chi-restraints excluded: chain B residue 109 SER Chi-restraints excluded: chain B residue 115 SER Chi-restraints excluded: chain B residue 163 VAL Chi-restraints excluded: chain B residue 190 ILE Chi-restraints excluded: chain B residue 218 ILE Chi-restraints excluded: chain B residue 239 VAL Chi-restraints excluded: chain B residue 255 ASP Chi-restraints excluded: chain B residue 288 ILE Chi-restraints excluded: chain B residue 455 GLU Chi-restraints excluded: chain B residue 459 SER Chi-restraints excluded: chain B residue 462 GLN Chi-restraints excluded: chain B residue 472 SER Chi-restraints excluded: chain B residue 516 THR Chi-restraints excluded: chain B residue 564 ILE Chi-restraints excluded: chain B residue 592 ILE Chi-restraints excluded: chain B residue 620 LEU Chi-restraints excluded: chain B residue 725 THR Chi-restraints excluded: chain B residue 816 ASN Chi-restraints excluded: chain B residue 821 ILE Chi-restraints excluded: chain B residue 918 SER Chi-restraints excluded: chain B residue 985 ILE Chi-restraints excluded: chain B residue 1194 ILE Chi-restraints excluded: chain C residue 328 LEU Chi-restraints excluded: chain D residue 99 LEU Chi-restraints excluded: chain E residue 93 MET Chi-restraints excluded: chain F residue 82 THR Chi-restraints excluded: chain F residue 93 ILE Chi-restraints excluded: chain F residue 142 SER Chi-restraints excluded: chain G residue 47 VAL Chi-restraints excluded: chain G residue 61 VAL Chi-restraints excluded: chain G residue 95 LEU Chi-restraints excluded: chain G residue 97 LYS Chi-restraints excluded: chain G residue 110 ASP Chi-restraints excluded: chain G residue 226 ASP Chi-restraints excluded: chain G residue 245 VAL Chi-restraints excluded: chain H residue 57 VAL Chi-restraints excluded: chain I residue 32 GLN Chi-restraints excluded: chain I residue 39 LYS Chi-restraints excluded: chain J residue 50 ILE Chi-restraints excluded: chain J residue 57 ILE Chi-restraints excluded: chain L residue 46 VAL Chi-restraints excluded: chain L residue 55 ILE Chi-restraints excluded: chain L residue 66 GLN Chi-restraints excluded: chain M residue 69 SER Chi-restraints excluded: chain N residue 25 ILE Chi-restraints excluded: chain N residue 32 CYS Chi-restraints excluded: chain N residue 63 ASP Chi-restraints excluded: chain N residue 111 VAL Chi-restraints excluded: chain N residue 128 ASN Chi-restraints excluded: chain N residue 131 LEU Chi-restraints excluded: chain N residue 160 VAL Chi-restraints excluded: chain N residue 173 THR Chi-restraints excluded: chain O residue 200 THR Chi-restraints excluded: chain O residue 202 ILE Chi-restraints excluded: chain O residue 210 THR Chi-restraints excluded: chain O residue 222 GLN Chi-restraints excluded: chain O residue 224 THR Chi-restraints excluded: chain O residue 260 LEU Chi-restraints excluded: chain O residue 274 ILE Chi-restraints excluded: chain O residue 313 GLN Chi-restraints excluded: chain O residue 329 ILE Chi-restraints excluded: chain O residue 344 ILE Chi-restraints excluded: chain O residue 405 TYR Chi-restraints excluded: chain O residue 439 LYS Chi-restraints excluded: chain O residue 442 LEU Chi-restraints excluded: chain O residue 480 VAL Chi-restraints excluded: chain O residue 485 LYS Chi-restraints excluded: chain O residue 496 THR Chi-restraints excluded: chain O residue 533 LEU Chi-restraints excluded: chain O residue 583 GLU Chi-restraints excluded: chain O residue 622 TYR Chi-restraints excluded: chain O residue 626 LEU Chi-restraints excluded: chain O residue 659 LEU Chi-restraints excluded: chain O residue 661 ASN Chi-restraints excluded: chain O residue 665 ASN Chi-restraints excluded: chain O residue 668 SER Chi-restraints excluded: chain O residue 707 ASP Chi-restraints excluded: chain O residue 726 SER Chi-restraints excluded: chain O residue 772 ILE Chi-restraints excluded: chain P residue 95 LEU Chi-restraints excluded: chain P residue 150 GLU Chi-restraints excluded: chain P residue 151 GLU Chi-restraints excluded: chain P residue 154 LEU Chi-restraints excluded: chain P residue 259 GLN Chi-restraints excluded: chain P residue 304 LEU Chi-restraints excluded: chain P residue 313 THR Chi-restraints excluded: chain P residue 317 MET Chi-restraints excluded: chain P residue 360 LYS Chi-restraints excluded: chain P residue 370 SER Chi-restraints excluded: chain P residue 388 THR Chi-restraints excluded: chain P residue 437 THR Chi-restraints excluded: chain P residue 453 PHE Chi-restraints excluded: chain P residue 512 ARG Chi-restraints excluded: chain Q residue 4 VAL Chi-restraints excluded: chain Q residue 27 ILE Chi-restraints excluded: chain Q residue 128 TRP Chi-restraints excluded: chain Q residue 138 PHE Chi-restraints excluded: chain Q residue 155 GLN Chi-restraints excluded: chain Q residue 168 ILE Chi-restraints excluded: chain Q residue 180 CYS Chi-restraints excluded: chain Q residue 247 ILE Chi-restraints excluded: chain Q residue 248 LYS Chi-restraints excluded: chain Q residue 269 ASP Chi-restraints excluded: chain Q residue 272 GLN Chi-restraints excluded: chain Q residue 285 VAL Chi-restraints excluded: chain Q residue 317 LEU Chi-restraints excluded: chain Q residue 390 ASN Chi-restraints excluded: chain Q residue 393 ILE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 556 random chunks: chunk 280 optimal weight: 9.9990 chunk 156 optimal weight: 5.9990 chunk 420 optimal weight: 20.0000 chunk 343 optimal weight: 10.0000 chunk 139 optimal weight: 4.9990 chunk 505 optimal weight: 3.9990 chunk 546 optimal weight: 0.5980 chunk 450 optimal weight: 7.9990 chunk 501 optimal weight: 20.0000 chunk 172 optimal weight: 0.9980 chunk 405 optimal weight: 10.0000 overall best weight: 3.3186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 40 ASN A 383 ASN A 384 GLN ** A 431 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 432 ASN ** A 580 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 656 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 926 GLN A1438 ASN A1647 ASN B 147 ASN ** B 339 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 422 GLN B 504 HIS ** B 555 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 636 GLN ** B 720 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 755 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B1100 GLN ** B1163 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 175 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 26 GLN ** E 54 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 26 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 56 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 64 GLN G 65 HIS ** G 128 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 139 ASN ** L 53 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 18 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 51 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 106 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 308 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 313 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** O 390 GLN ** O 401 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 454 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** O 615 ASN ** O 635 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 145 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 155 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** P 157 HIS ** P 209 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 272 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 300 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 315 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 351 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** P 486 GLN ** Q 155 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 272 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 276 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 298 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 372 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 20 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6676 moved from start: 0.5092 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.080 47713 Z= 0.286 Angle : 0.834 16.027 64933 Z= 0.430 Chirality : 0.049 0.511 7264 Planarity : 0.006 0.110 7979 Dihedral : 14.596 165.284 7279 Min Nonbonded Distance : 2.059 Molprobity Statistics. All-atom Clashscore : 21.88 Ramachandran Plot: Outliers : 0.98 % Allowed : 7.86 % Favored : 91.16 % Rotamer: Outliers : 4.89 % Allowed : 17.66 % Favored : 77.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 1.65 % Twisted General : 0.10 % 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: -1.16 (0.11), residues: 5432 helix: 0.35 (0.11), residues: 1988 sheet: -0.98 (0.17), residues: 773 loop : -1.57 (0.12), residues: 2671 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.037 0.003 TRP N 54 HIS 0.011 0.002 HIS B 183 PHE 0.032 0.002 PHE B 371 TYR 0.030 0.002 TYR Q 208 ARG 0.009 0.001 ARG G 15 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10864 Ramachandran restraints generated. 5432 Oldfield, 0 Emsley, 5432 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10864 Ramachandran restraints generated. 5432 Oldfield, 0 Emsley, 5432 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1126 residues out of total 4950 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 242 poor density : 884 time to evaluate : 5.320 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: A 450 LYS cc_start: 0.5984 (OUTLIER) cc_final: 0.4165 (mmtp) REVERT: A 461 GLU cc_start: 0.6350 (mt-10) cc_final: 0.5700 (mt-10) REVERT: A 790 LYS cc_start: 0.6568 (OUTLIER) cc_final: 0.6314 (tppt) REVERT: B 115 SER cc_start: 0.6495 (OUTLIER) cc_final: 0.6234 (p) REVERT: B 457 ILE cc_start: 0.8230 (tp) cc_final: 0.8021 (tp) REVERT: B 778 TYR cc_start: 0.8247 (t80) cc_final: 0.7642 (t80) REVERT: B 816 ASN cc_start: 0.4942 (OUTLIER) cc_final: 0.4521 (m110) REVERT: E 211 TYR cc_start: 0.8458 (m-80) cc_final: 0.8013 (m-10) REVERT: F 77 ASP cc_start: 0.6223 (p0) cc_final: 0.5987 (p0) REVERT: F 82 THR cc_start: 0.8846 (t) cc_final: 0.8521 (p) REVERT: F 111 LEU cc_start: 0.7422 (tt) cc_final: 0.7074 (tp) REVERT: F 140 ASP cc_start: 0.7881 (p0) cc_final: 0.7610 (p0) REVERT: H 14 GLU cc_start: 0.5574 (tm-30) cc_final: 0.4544 (tm-30) REVERT: H 142 LEU cc_start: 0.8125 (tp) cc_final: 0.7835 (tt) REVERT: I 15 ASP cc_start: 0.5141 (t0) cc_final: 0.4849 (t0) REVERT: K 100 LEU cc_start: 0.8141 (mm) cc_final: 0.7896 (mp) REVERT: O 313 GLN cc_start: 0.5933 (OUTLIER) cc_final: 0.5558 (pp30) REVERT: O 498 LEU cc_start: 0.6116 (mt) cc_final: 0.5886 (mt) REVERT: O 665 ASN cc_start: 0.7436 (OUTLIER) cc_final: 0.7113 (t0) REVERT: P 236 MET cc_start: 0.4274 (OUTLIER) cc_final: 0.3924 (tmm) REVERT: P 366 TYR cc_start: 0.6305 (t80) cc_final: 0.5684 (t80) REVERT: Q 304 HIS cc_start: 0.5785 (t-90) cc_final: 0.5242 (t-90) REVERT: Q 347 ASP cc_start: 0.6415 (p0) cc_final: 0.6200 (p0) outliers start: 242 outliers final: 135 residues processed: 1047 average time/residue: 0.6145 time to fit residues: 1088.6879 Evaluate side-chains 884 residues out of total 4950 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 142 poor density : 742 time to evaluate : 5.237 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 60 ASN Chi-restraints excluded: chain A residue 222 GLU Chi-restraints excluded: chain A residue 389 VAL Chi-restraints excluded: chain A residue 403 LEU Chi-restraints excluded: chain A residue 419 ILE Chi-restraints excluded: chain A residue 450 LYS Chi-restraints excluded: chain A residue 551 VAL Chi-restraints excluded: chain A residue 572 THR Chi-restraints excluded: chain A residue 599 SER Chi-restraints excluded: chain A residue 666 VAL Chi-restraints excluded: chain A residue 678 VAL Chi-restraints excluded: chain A residue 773 ASP Chi-restraints excluded: chain A residue 789 SER Chi-restraints excluded: chain A residue 790 LYS Chi-restraints excluded: chain A residue 891 ILE Chi-restraints excluded: chain A residue 947 LEU Chi-restraints excluded: chain A residue 957 VAL Chi-restraints excluded: chain A residue 1013 THR Chi-restraints excluded: chain A residue 1033 SER Chi-restraints excluded: chain A residue 1060 GLU Chi-restraints excluded: chain A residue 1063 MET Chi-restraints excluded: chain A residue 1118 VAL Chi-restraints excluded: chain A residue 1222 LEU Chi-restraints excluded: chain A residue 1491 GLU Chi-restraints excluded: chain A residue 1543 SER Chi-restraints excluded: chain A residue 1614 SER Chi-restraints excluded: chain A residue 1634 LEU Chi-restraints excluded: chain A residue 1649 VAL Chi-restraints excluded: chain B residue 35 PHE Chi-restraints excluded: chain B residue 38 LEU Chi-restraints excluded: chain B residue 75 ASP Chi-restraints excluded: chain B residue 115 SER Chi-restraints excluded: chain B residue 163 VAL Chi-restraints excluded: chain B residue 190 ILE Chi-restraints excluded: chain B residue 218 ILE Chi-restraints excluded: chain B residue 249 VAL Chi-restraints excluded: chain B residue 255 ASP Chi-restraints excluded: chain B residue 343 ASP Chi-restraints excluded: chain B residue 409 TYR Chi-restraints excluded: chain B residue 424 ILE Chi-restraints excluded: chain B residue 455 GLU Chi-restraints excluded: chain B residue 462 GLN Chi-restraints excluded: chain B residue 472 SER Chi-restraints excluded: chain B residue 489 GLU Chi-restraints excluded: chain B residue 516 THR Chi-restraints excluded: chain B residue 564 ILE Chi-restraints excluded: chain B residue 592 ILE Chi-restraints excluded: chain B residue 725 THR Chi-restraints excluded: chain B residue 779 THR Chi-restraints excluded: chain B residue 816 ASN Chi-restraints excluded: chain B residue 918 SER Chi-restraints excluded: chain C residue 73 SER Chi-restraints excluded: chain C residue 151 THR Chi-restraints excluded: chain C residue 181 ASP Chi-restraints excluded: chain C residue 201 GLU Chi-restraints excluded: chain C residue 328 LEU Chi-restraints excluded: chain D residue 14 THR Chi-restraints excluded: chain D residue 99 LEU Chi-restraints excluded: chain E residue 131 THR Chi-restraints excluded: chain F residue 93 ILE Chi-restraints excluded: chain G residue 47 VAL Chi-restraints excluded: chain G residue 61 VAL Chi-restraints excluded: chain G residue 69 LEU Chi-restraints excluded: chain G residue 87 LEU Chi-restraints excluded: chain G residue 110 ASP Chi-restraints excluded: chain G residue 226 ASP Chi-restraints excluded: chain G residue 245 VAL Chi-restraints excluded: chain G residue 246 ASP Chi-restraints excluded: chain H residue 87 ARG Chi-restraints excluded: chain H residue 139 ASN Chi-restraints excluded: chain I residue 26 SER Chi-restraints excluded: chain I residue 42 PHE Chi-restraints excluded: chain I residue 60 LEU Chi-restraints excluded: chain J residue 50 ILE Chi-restraints excluded: chain J residue 57 ILE Chi-restraints excluded: chain K residue 117 LEU Chi-restraints excluded: chain L residue 46 VAL Chi-restraints excluded: chain L residue 65 VAL Chi-restraints excluded: chain M residue 17 ASP Chi-restraints excluded: chain M residue 66 THR Chi-restraints excluded: chain M residue 69 SER Chi-restraints excluded: chain N residue 25 ILE Chi-restraints excluded: chain N residue 32 CYS Chi-restraints excluded: chain N residue 75 GLU Chi-restraints excluded: chain N residue 111 VAL Chi-restraints excluded: chain N residue 131 LEU Chi-restraints excluded: chain N residue 151 SER Chi-restraints excluded: chain N residue 160 VAL Chi-restraints excluded: chain N residue 164 GLU Chi-restraints excluded: chain N residue 173 THR Chi-restraints excluded: chain O residue 202 ILE Chi-restraints excluded: chain O residue 254 ILE Chi-restraints excluded: chain O residue 260 LEU Chi-restraints excluded: chain O residue 313 GLN Chi-restraints excluded: chain O residue 329 ILE Chi-restraints excluded: chain O residue 344 ILE Chi-restraints excluded: chain O residue 353 ASP Chi-restraints excluded: chain O residue 480 VAL Chi-restraints excluded: chain O residue 533 LEU Chi-restraints excluded: chain O residue 583 GLU Chi-restraints excluded: chain O residue 622 TYR Chi-restraints excluded: chain O residue 626 LEU Chi-restraints excluded: chain O residue 659 LEU Chi-restraints excluded: chain O residue 665 ASN Chi-restraints excluded: chain O residue 668 SER Chi-restraints excluded: chain O residue 707 ASP Chi-restraints excluded: chain O residue 726 SER Chi-restraints excluded: chain O residue 772 ILE Chi-restraints excluded: chain P residue 95 LEU Chi-restraints excluded: chain P residue 151 GLU Chi-restraints excluded: chain P residue 154 LEU Chi-restraints excluded: chain P residue 183 LYS Chi-restraints excluded: chain P residue 184 TRP Chi-restraints excluded: chain P residue 199 LEU Chi-restraints excluded: chain P residue 225 GLN Chi-restraints excluded: chain P residue 236 MET Chi-restraints excluded: chain P residue 259 GLN Chi-restraints excluded: chain P residue 262 LEU Chi-restraints excluded: chain P residue 283 ASN Chi-restraints excluded: chain P residue 304 LEU Chi-restraints excluded: chain P residue 363 SER Chi-restraints excluded: chain P residue 367 PHE Chi-restraints excluded: chain P residue 370 SER Chi-restraints excluded: chain P residue 374 THR Chi-restraints excluded: chain P residue 437 THR Chi-restraints excluded: chain Q residue 4 VAL Chi-restraints excluded: chain Q residue 10 ASN Chi-restraints excluded: chain Q residue 128 TRP Chi-restraints excluded: chain Q residue 155 GLN Chi-restraints excluded: chain Q residue 158 THR Chi-restraints excluded: chain Q residue 168 ILE Chi-restraints excluded: chain Q residue 240 ILE Chi-restraints excluded: chain Q residue 247 ILE Chi-restraints excluded: chain Q residue 248 LYS Chi-restraints excluded: chain Q residue 251 TRP Chi-restraints excluded: chain Q residue 269 ASP Chi-restraints excluded: chain Q residue 272 GLN Chi-restraints excluded: chain Q residue 285 VAL Chi-restraints excluded: chain Q residue 317 LEU Chi-restraints excluded: chain Q residue 352 TRP Chi-restraints excluded: chain Q residue 390 ASN Chi-restraints excluded: chain Q residue 401 ILE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 556 random chunks: chunk 499 optimal weight: 0.2980 chunk 380 optimal weight: 5.9990 chunk 262 optimal weight: 0.0670 chunk 55 optimal weight: 5.9990 chunk 241 optimal weight: 3.9990 chunk 339 optimal weight: 2.9990 chunk 507 optimal weight: 50.0000 chunk 537 optimal weight: 20.0000 chunk 265 optimal weight: 10.0000 chunk 481 optimal weight: 30.0000 chunk 144 optimal weight: 10.0000 overall best weight: 2.6724 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 60 ASN ** A 382 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 431 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 580 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 636 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1116 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 339 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 555 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 720 GLN ** B 755 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1163 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 175 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 88 GLN ** E 54 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 100 GLN G 36 ASN ** G 56 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 64 GLN ** G 128 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 53 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 16 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 71 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 308 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 635 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** O 642 GLN ** P 145 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** P 209 ASN ** P 272 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** P 315 ASN ** P 435 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 482 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 155 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 221 HIS ** Q 276 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 372 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6679 moved from start: 0.5619 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.070 47713 Z= 0.256 Angle : 0.805 19.571 64933 Z= 0.408 Chirality : 0.047 0.352 7264 Planarity : 0.006 0.116 7979 Dihedral : 14.310 164.206 7233 Min Nonbonded Distance : 2.029 Molprobity Statistics. All-atom Clashscore : 20.21 Ramachandran Plot: Outliers : 0.92 % Allowed : 7.07 % Favored : 92.01 % Rotamer: Outliers : 4.69 % Allowed : 18.86 % Favored : 76.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 1.65 % 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: -0.91 (0.11), residues: 5432 helix: 0.57 (0.11), residues: 2005 sheet: -0.81 (0.18), residues: 749 loop : -1.46 (0.12), residues: 2678 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.044 0.002 TRP N 54 HIS 0.010 0.001 HIS B 183 PHE 0.036 0.002 PHE B 464 TYR 0.029 0.002 TYR P 211 ARG 0.009 0.001 ARG O 601 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10864 Ramachandran restraints generated. 5432 Oldfield, 0 Emsley, 5432 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10864 Ramachandran restraints generated. 5432 Oldfield, 0 Emsley, 5432 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1063 residues out of total 4950 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 232 poor density : 831 time to evaluate : 5.340 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: A 450 LYS cc_start: 0.5836 (OUTLIER) cc_final: 0.4023 (mmtm) REVERT: A 790 LYS cc_start: 0.6328 (OUTLIER) cc_final: 0.6106 (tppt) REVERT: B 115 SER cc_start: 0.6113 (OUTLIER) cc_final: 0.5657 (p) REVERT: B 743 ARG cc_start: 0.7902 (ttp-170) cc_final: 0.7630 (ttt-90) REVERT: B 778 TYR cc_start: 0.8117 (t80) cc_final: 0.7569 (t80) REVERT: B 816 ASN cc_start: 0.5125 (OUTLIER) cc_final: 0.4864 (m110) REVERT: C 71 MET cc_start: 0.7886 (ttm) cc_final: 0.7617 (ttp) REVERT: E 75 MET cc_start: 0.5648 (tpp) cc_final: 0.5046 (tpp) REVERT: E 211 TYR cc_start: 0.8451 (m-80) cc_final: 0.7986 (m-10) REVERT: F 77 ASP cc_start: 0.6349 (p0) cc_final: 0.5933 (p0) REVERT: F 78 GLN cc_start: 0.6204 (mm-40) cc_final: 0.5939 (mm-40) REVERT: F 82 THR cc_start: 0.8810 (OUTLIER) cc_final: 0.8533 (p) REVERT: F 125 LEU cc_start: 0.8641 (tp) cc_final: 0.8406 (tp) REVERT: F 140 ASP cc_start: 0.7858 (p0) cc_final: 0.7654 (p0) REVERT: J 1 MET cc_start: 0.6896 (tpp) cc_final: 0.6571 (tpt) REVERT: J 27 GLU cc_start: 0.6544 (OUTLIER) cc_final: 0.6324 (pp20) REVERT: J 47 ARG cc_start: 0.8251 (OUTLIER) cc_final: 0.7512 (mtp180) REVERT: K 81 MET cc_start: 0.6397 (mmm) cc_final: 0.6118 (mmm) REVERT: K 97 SER cc_start: 0.7938 (m) cc_final: 0.7373 (t) REVERT: K 100 LEU cc_start: 0.8174 (mm) cc_final: 0.7897 (mp) REVERT: L 67 PHE cc_start: 0.7712 (m-10) cc_final: 0.7284 (m-10) REVERT: O 311 ASP cc_start: 0.4269 (p0) cc_final: 0.3986 (p0) REVERT: O 313 GLN cc_start: 0.6159 (OUTLIER) cc_final: 0.5674 (pp30) REVERT: O 420 GLU cc_start: 0.7850 (tt0) cc_final: 0.7562 (mm-30) REVERT: P 400 MET cc_start: 0.5241 (mpp) cc_final: 0.4909 (mmm) REVERT: Q 208 TYR cc_start: 0.4979 (t80) cc_final: 0.4754 (t80) REVERT: Q 274 MET cc_start: 0.8644 (tpp) cc_final: 0.8325 (tpp) REVERT: Q 304 HIS cc_start: 0.6014 (t-90) cc_final: 0.5585 (t-90) REVERT: Q 390 ASN cc_start: 0.1784 (OUTLIER) cc_final: 0.1423 (p0) outliers start: 232 outliers final: 151 residues processed: 971 average time/residue: 0.5518 time to fit residues: 904.6545 Evaluate side-chains 886 residues out of total 4950 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 160 poor density : 726 time to evaluate : 5.244 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 94 LEU Chi-restraints excluded: chain A residue 220 VAL Chi-restraints excluded: chain A residue 222 GLU Chi-restraints excluded: chain A residue 389 VAL Chi-restraints excluded: chain A residue 403 LEU Chi-restraints excluded: chain A residue 419 ILE Chi-restraints excluded: chain A residue 450 LYS Chi-restraints excluded: chain A residue 483 VAL Chi-restraints excluded: chain A residue 551 VAL Chi-restraints excluded: chain A residue 572 THR Chi-restraints excluded: chain A residue 573 LEU Chi-restraints excluded: chain A residue 599 SER Chi-restraints excluded: chain A residue 666 VAL Chi-restraints excluded: chain A residue 678 VAL Chi-restraints excluded: chain A residue 685 SER Chi-restraints excluded: chain A residue 773 ASP Chi-restraints excluded: chain A residue 790 LYS Chi-restraints excluded: chain A residue 891 ILE Chi-restraints excluded: chain A residue 947 LEU Chi-restraints excluded: chain A residue 957 VAL Chi-restraints excluded: chain A residue 1033 SER Chi-restraints excluded: chain A residue 1060 GLU Chi-restraints excluded: chain A residue 1063 MET Chi-restraints excluded: chain A residue 1118 VAL Chi-restraints excluded: chain A residue 1222 LEU Chi-restraints excluded: chain A residue 1238 MET Chi-restraints excluded: chain A residue 1244 ASN Chi-restraints excluded: chain A residue 1323 HIS Chi-restraints excluded: chain A residue 1491 GLU Chi-restraints excluded: chain A residue 1543 SER Chi-restraints excluded: chain A residue 1607 THR Chi-restraints excluded: chain A residue 1619 CYS Chi-restraints excluded: chain A residue 1634 LEU Chi-restraints excluded: chain A residue 1649 VAL Chi-restraints excluded: chain B residue 33 SER Chi-restraints excluded: chain B residue 35 PHE Chi-restraints excluded: chain B residue 38 LEU Chi-restraints excluded: chain B residue 75 ASP Chi-restraints excluded: chain B residue 115 SER Chi-restraints excluded: chain B residue 175 MET Chi-restraints excluded: chain B residue 190 ILE Chi-restraints excluded: chain B residue 343 ASP Chi-restraints excluded: chain B residue 409 TYR Chi-restraints excluded: chain B residue 424 ILE Chi-restraints excluded: chain B residue 455 GLU Chi-restraints excluded: chain B residue 462 GLN Chi-restraints excluded: chain B residue 472 SER Chi-restraints excluded: chain B residue 489 GLU Chi-restraints excluded: chain B residue 502 MET Chi-restraints excluded: chain B residue 516 THR Chi-restraints excluded: chain B residue 564 ILE Chi-restraints excluded: chain B residue 577 PHE Chi-restraints excluded: chain B residue 592 ILE Chi-restraints excluded: chain B residue 647 SER Chi-restraints excluded: chain B residue 712 SER Chi-restraints excluded: chain B residue 725 THR Chi-restraints excluded: chain B residue 816 ASN Chi-restraints excluded: chain B residue 858 ILE Chi-restraints excluded: chain B residue 918 SER Chi-restraints excluded: chain B residue 1069 ILE Chi-restraints excluded: chain B residue 1113 THR Chi-restraints excluded: chain C residue 73 SER Chi-restraints excluded: chain C residue 151 THR Chi-restraints excluded: chain C residue 181 ASP Chi-restraints excluded: chain C residue 201 GLU Chi-restraints excluded: chain C residue 328 LEU Chi-restraints excluded: chain D residue 14 THR Chi-restraints excluded: chain D residue 88 GLN Chi-restraints excluded: chain D residue 99 LEU Chi-restraints excluded: chain E residue 131 THR Chi-restraints excluded: chain F residue 82 THR Chi-restraints excluded: chain F residue 93 ILE Chi-restraints excluded: chain G residue 47 VAL Chi-restraints excluded: chain G residue 61 VAL Chi-restraints excluded: chain G residue 69 LEU Chi-restraints excluded: chain G residue 87 LEU Chi-restraints excluded: chain G residue 110 ASP Chi-restraints excluded: chain G residue 138 PHE Chi-restraints excluded: chain G residue 226 ASP Chi-restraints excluded: chain G residue 245 VAL Chi-restraints excluded: chain G residue 246 ASP Chi-restraints excluded: chain H residue 57 VAL Chi-restraints excluded: chain H residue 61 SER Chi-restraints excluded: chain H residue 87 ARG Chi-restraints excluded: chain H residue 109 LYS Chi-restraints excluded: chain I residue 42 PHE Chi-restraints excluded: chain I residue 60 LEU Chi-restraints excluded: chain J residue 27 GLU Chi-restraints excluded: chain J residue 47 ARG Chi-restraints excluded: chain J residue 50 ILE Chi-restraints excluded: chain K residue 127 LEU Chi-restraints excluded: chain L residue 46 VAL Chi-restraints excluded: chain L residue 65 VAL Chi-restraints excluded: chain M residue 66 THR Chi-restraints excluded: chain M residue 77 VAL Chi-restraints excluded: chain M residue 88 ILE Chi-restraints excluded: chain M residue 97 VAL Chi-restraints excluded: chain N residue 24 SER Chi-restraints excluded: chain N residue 25 ILE Chi-restraints excluded: chain N residue 53 VAL Chi-restraints excluded: chain N residue 62 VAL Chi-restraints excluded: chain N residue 75 GLU Chi-restraints excluded: chain N residue 111 VAL Chi-restraints excluded: chain N residue 131 LEU Chi-restraints excluded: chain N residue 151 SER Chi-restraints excluded: chain N residue 160 VAL Chi-restraints excluded: chain N residue 173 THR Chi-restraints excluded: chain O residue 202 ILE Chi-restraints excluded: chain O residue 254 ILE Chi-restraints excluded: chain O residue 260 LEU Chi-restraints excluded: chain O residue 313 GLN Chi-restraints excluded: chain O residue 344 ILE Chi-restraints excluded: chain O residue 353 ASP Chi-restraints excluded: chain O residue 384 ASP Chi-restraints excluded: chain O residue 408 ILE Chi-restraints excluded: chain O residue 451 ILE Chi-restraints excluded: chain O residue 480 VAL Chi-restraints excluded: chain O residue 533 LEU Chi-restraints excluded: chain O residue 569 VAL Chi-restraints excluded: chain O residue 583 GLU Chi-restraints excluded: chain O residue 622 TYR Chi-restraints excluded: chain O residue 659 LEU Chi-restraints excluded: chain O residue 661 ASN Chi-restraints excluded: chain O residue 688 ASP Chi-restraints excluded: chain O residue 707 ASP Chi-restraints excluded: chain O residue 726 SER Chi-restraints excluded: chain P residue 95 LEU Chi-restraints excluded: chain P residue 154 LEU Chi-restraints excluded: chain P residue 164 ILE Chi-restraints excluded: chain P residue 180 ASP Chi-restraints excluded: chain P residue 183 LYS Chi-restraints excluded: chain P residue 184 TRP Chi-restraints excluded: chain P residue 193 PHE Chi-restraints excluded: chain P residue 225 GLN Chi-restraints excluded: chain P residue 259 GLN Chi-restraints excluded: chain P residue 262 LEU Chi-restraints excluded: chain P residue 283 ASN Chi-restraints excluded: chain P residue 304 LEU Chi-restraints excluded: chain P residue 356 VAL Chi-restraints excluded: chain P residue 367 PHE Chi-restraints excluded: chain P residue 388 THR Chi-restraints excluded: chain P residue 402 MET Chi-restraints excluded: chain P residue 408 ILE Chi-restraints excluded: chain P residue 437 THR Chi-restraints excluded: chain Q residue 4 VAL Chi-restraints excluded: chain Q residue 10 ASN Chi-restraints excluded: chain Q residue 128 TRP Chi-restraints excluded: chain Q residue 155 GLN Chi-restraints excluded: chain Q residue 158 THR Chi-restraints excluded: chain Q residue 168 ILE Chi-restraints excluded: chain Q residue 210 THR Chi-restraints excluded: chain Q residue 240 ILE Chi-restraints excluded: chain Q residue 247 ILE Chi-restraints excluded: chain Q residue 248 LYS Chi-restraints excluded: chain Q residue 251 TRP Chi-restraints excluded: chain Q residue 269 ASP Chi-restraints excluded: chain Q residue 279 SER Chi-restraints excluded: chain Q residue 285 VAL Chi-restraints excluded: chain Q residue 352 TRP Chi-restraints excluded: chain Q residue 390 ASN Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 556 random chunks: chunk 447 optimal weight: 20.0000 chunk 305 optimal weight: 9.9990 chunk 7 optimal weight: 6.9990 chunk 400 optimal weight: 10.0000 chunk 221 optimal weight: 5.9990 chunk 458 optimal weight: 50.0000 chunk 371 optimal weight: 3.9990 chunk 0 optimal weight: 10.0000 chunk 274 optimal weight: 6.9990 chunk 482 optimal weight: 40.0000 chunk 135 optimal weight: 10.0000 overall best weight: 6.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 60 ASN ** A 382 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 431 GLN A 580 HIS ** A1116 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1314 GLN ** A1319 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 128 GLN B 267 ASN B 422 GLN B 532 HIS ** B 555 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 720 GLN ** B 755 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B1100 GLN ** B1163 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 172 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 175 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 54 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 100 GLN ** G 56 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 126 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 128 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 137 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 16 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 75 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 106 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 270 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 635 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 665 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 109 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 145 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** P 194 GLN P 259 GLN ** P 272 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 351 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 435 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 482 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 150 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 155 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 207 ASN Q 276 GLN Total number of N/Q/H flips: 15 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6808 moved from start: 0.6002 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.074 47713 Z= 0.429 Angle : 0.836 15.783 64933 Z= 0.428 Chirality : 0.049 0.376 7264 Planarity : 0.006 0.125 7979 Dihedral : 14.288 163.684 7218 Min Nonbonded Distance : 2.017 Molprobity Statistics. All-atom Clashscore : 22.84 Ramachandran Plot: Outliers : 0.85 % Allowed : 7.88 % Favored : 91.27 % Rotamer: Outliers : 5.05 % Allowed : 19.79 % Favored : 75.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 1.24 % 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: -0.90 (0.11), residues: 5432 helix: 0.61 (0.11), residues: 2003 sheet: -0.81 (0.18), residues: 739 loop : -1.47 (0.12), residues: 2690 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.034 0.002 TRP A 530 HIS 0.011 0.002 HIS B 183 PHE 0.047 0.002 PHE A 437 TYR 0.028 0.002 TYR P 211 ARG 0.009 0.001 ARG A 615 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10864 Ramachandran restraints generated. 5432 Oldfield, 0 Emsley, 5432 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10864 Ramachandran restraints generated. 5432 Oldfield, 0 Emsley, 5432 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 989 residues out of total 4950 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 250 poor density : 739 time to evaluate : 5.266 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: A 450 LYS cc_start: 0.6016 (OUTLIER) cc_final: 0.4037 (mmtp) REVERT: A 530 TRP cc_start: 0.6462 (t60) cc_final: 0.6209 (t60) REVERT: A 616 LEU cc_start: 0.9019 (tp) cc_final: 0.8662 (tp) REVERT: B 115 SER cc_start: 0.6376 (OUTLIER) cc_final: 0.5987 (p) REVERT: B 778 TYR cc_start: 0.8084 (t80) cc_final: 0.7519 (t80) REVERT: B 782 ASP cc_start: 0.6238 (p0) cc_final: 0.5954 (p0) REVERT: E 75 MET cc_start: 0.5430 (tpp) cc_final: 0.4730 (tpp) REVERT: E 211 TYR cc_start: 0.8530 (m-80) cc_final: 0.8041 (m-10) REVERT: F 77 ASP cc_start: 0.6262 (p0) cc_final: 0.5802 (p0) REVERT: F 78 GLN cc_start: 0.6497 (mm-40) cc_final: 0.6218 (mm-40) REVERT: F 82 THR cc_start: 0.8821 (OUTLIER) cc_final: 0.8558 (p) REVERT: F 140 ASP cc_start: 0.7927 (p0) cc_final: 0.7712 (p0) REVERT: G 64 GLN cc_start: 0.5993 (mt0) cc_final: 0.5782 (mt0) REVERT: G 119 HIS cc_start: 0.5399 (m-70) cc_final: 0.5181 (m170) REVERT: H 14 GLU cc_start: 0.5875 (tm-30) cc_final: 0.5169 (tm-30) REVERT: I 15 ASP cc_start: 0.5684 (t0) cc_final: 0.5457 (t0) REVERT: K 89 CYS cc_start: 0.7815 (p) cc_final: 0.7587 (p) REVERT: K 97 SER cc_start: 0.8050 (m) cc_final: 0.7696 (t) REVERT: K 100 LEU cc_start: 0.8293 (mm) cc_final: 0.7906 (mt) REVERT: L 64 LEU cc_start: 0.8566 (tp) cc_final: 0.8357 (tt) REVERT: N 131 LEU cc_start: 0.7212 (OUTLIER) cc_final: 0.6286 (pp) REVERT: O 311 ASP cc_start: 0.4785 (p0) cc_final: 0.4563 (p0) REVERT: O 313 GLN cc_start: 0.6000 (OUTLIER) cc_final: 0.5473 (pp30) REVERT: P 400 MET cc_start: 0.5729 (mpp) cc_final: 0.5412 (pmm) REVERT: Q 274 MET cc_start: 0.8647 (tpp) cc_final: 0.8243 (tpp) REVERT: Q 278 TYR cc_start: 0.7183 (m-80) cc_final: 0.6894 (m-80) REVERT: Q 390 ASN cc_start: 0.1918 (OUTLIER) cc_final: 0.1592 (p0) outliers start: 250 outliers final: 169 residues processed: 905 average time/residue: 0.5591 time to fit residues: 858.2516 Evaluate side-chains 837 residues out of total 4950 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 175 poor density : 662 time to evaluate : 5.458 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 60 ASN Chi-restraints excluded: chain A residue 63 SER Chi-restraints excluded: chain A residue 94 LEU Chi-restraints excluded: chain A residue 96 ILE Chi-restraints excluded: chain A residue 220 VAL Chi-restraints excluded: chain A residue 222 GLU Chi-restraints excluded: chain A residue 323 ILE Chi-restraints excluded: chain A residue 403 LEU Chi-restraints excluded: chain A residue 419 ILE Chi-restraints excluded: chain A residue 433 ASP Chi-restraints excluded: chain A residue 450 LYS Chi-restraints excluded: chain A residue 483 VAL Chi-restraints excluded: chain A residue 551 VAL Chi-restraints excluded: chain A residue 572 THR Chi-restraints excluded: chain A residue 586 VAL Chi-restraints excluded: chain A residue 599 SER Chi-restraints excluded: chain A residue 666 VAL Chi-restraints excluded: chain A residue 678 VAL Chi-restraints excluded: chain A residue 685 SER Chi-restraints excluded: chain A residue 773 ASP Chi-restraints excluded: chain A residue 789 SER Chi-restraints excluded: chain A residue 790 LYS Chi-restraints excluded: chain A residue 891 ILE Chi-restraints excluded: chain A residue 928 MET Chi-restraints excluded: chain A residue 947 LEU Chi-restraints excluded: chain A residue 957 VAL Chi-restraints excluded: chain A residue 1008 ASP Chi-restraints excluded: chain A residue 1033 SER Chi-restraints excluded: chain A residue 1118 VAL Chi-restraints excluded: chain A residue 1222 LEU Chi-restraints excluded: chain A residue 1238 MET Chi-restraints excluded: chain A residue 1244 ASN Chi-restraints excluded: chain A residue 1323 HIS Chi-restraints excluded: chain A residue 1470 CYS Chi-restraints excluded: chain A residue 1491 GLU Chi-restraints excluded: chain A residue 1543 SER Chi-restraints excluded: chain A residue 1607 THR Chi-restraints excluded: chain A residue 1614 SER Chi-restraints excluded: chain A residue 1634 LEU Chi-restraints excluded: chain A residue 1649 VAL Chi-restraints excluded: chain B residue 33 SER Chi-restraints excluded: chain B residue 38 LEU Chi-restraints excluded: chain B residue 75 ASP Chi-restraints excluded: chain B residue 115 SER Chi-restraints excluded: chain B residue 239 VAL Chi-restraints excluded: chain B residue 249 VAL Chi-restraints excluded: chain B residue 255 ASP Chi-restraints excluded: chain B residue 288 ILE Chi-restraints excluded: chain B residue 295 ASN Chi-restraints excluded: chain B residue 343 ASP Chi-restraints excluded: chain B residue 353 VAL Chi-restraints excluded: chain B residue 409 TYR Chi-restraints excluded: chain B residue 421 LEU Chi-restraints excluded: chain B residue 424 ILE Chi-restraints excluded: chain B residue 462 GLN Chi-restraints excluded: chain B residue 472 SER Chi-restraints excluded: chain B residue 502 MET Chi-restraints excluded: chain B residue 516 THR Chi-restraints excluded: chain B residue 564 ILE Chi-restraints excluded: chain B residue 577 PHE Chi-restraints excluded: chain B residue 592 ILE Chi-restraints excluded: chain B residue 647 SER Chi-restraints excluded: chain B residue 712 SER Chi-restraints excluded: chain B residue 725 THR Chi-restraints excluded: chain B residue 858 ILE Chi-restraints excluded: chain B residue 900 THR Chi-restraints excluded: chain B residue 910 THR Chi-restraints excluded: chain B residue 918 SER Chi-restraints excluded: chain B residue 985 ILE Chi-restraints excluded: chain B residue 1069 ILE Chi-restraints excluded: chain B residue 1113 THR Chi-restraints excluded: chain B residue 1125 THR Chi-restraints excluded: chain B residue 1126 VAL Chi-restraints excluded: chain B residue 1178 ILE Chi-restraints excluded: chain B residue 1183 LYS Chi-restraints excluded: chain C residue 72 ILE Chi-restraints excluded: chain C residue 73 SER Chi-restraints excluded: chain C residue 120 LEU Chi-restraints excluded: chain C residue 122 ASP Chi-restraints excluded: chain C residue 151 THR Chi-restraints excluded: chain C residue 201 GLU Chi-restraints excluded: chain C residue 328 LEU Chi-restraints excluded: chain D residue 14 THR Chi-restraints excluded: chain D residue 18 THR Chi-restraints excluded: chain D residue 99 LEU Chi-restraints excluded: chain E residue 131 THR Chi-restraints excluded: chain F residue 82 THR Chi-restraints excluded: chain G residue 47 VAL Chi-restraints excluded: chain G residue 55 GLU Chi-restraints excluded: chain G residue 69 LEU Chi-restraints excluded: chain G residue 95 LEU Chi-restraints excluded: chain G residue 110 ASP Chi-restraints excluded: chain G residue 138 PHE Chi-restraints excluded: chain G residue 226 ASP Chi-restraints excluded: chain G residue 245 VAL Chi-restraints excluded: chain G residue 246 ASP Chi-restraints excluded: chain H residue 57 VAL Chi-restraints excluded: chain H residue 87 ARG Chi-restraints excluded: chain H residue 100 THR Chi-restraints excluded: chain H residue 109 LYS Chi-restraints excluded: chain I residue 42 PHE Chi-restraints excluded: chain I residue 60 LEU Chi-restraints excluded: chain J residue 27 GLU Chi-restraints excluded: chain K residue 105 ILE Chi-restraints excluded: chain L residue 46 VAL Chi-restraints excluded: chain L residue 50 ASP Chi-restraints excluded: chain L residue 65 VAL Chi-restraints excluded: chain M residue 12 ILE Chi-restraints excluded: chain M residue 66 THR Chi-restraints excluded: chain M residue 77 VAL Chi-restraints excluded: chain M residue 78 VAL Chi-restraints excluded: chain M residue 97 VAL Chi-restraints excluded: chain N residue 25 ILE Chi-restraints excluded: chain N residue 75 GLU Chi-restraints excluded: chain N residue 111 VAL Chi-restraints excluded: chain N residue 131 LEU Chi-restraints excluded: chain N residue 145 ILE Chi-restraints excluded: chain N residue 151 SER Chi-restraints excluded: chain N residue 155 VAL Chi-restraints excluded: chain N residue 160 VAL Chi-restraints excluded: chain N residue 173 THR Chi-restraints excluded: chain O residue 201 GLU Chi-restraints excluded: chain O residue 202 ILE Chi-restraints excluded: chain O residue 210 THR Chi-restraints excluded: chain O residue 254 ILE Chi-restraints excluded: chain O residue 258 SER Chi-restraints excluded: chain O residue 260 LEU Chi-restraints excluded: chain O residue 313 GLN Chi-restraints excluded: chain O residue 344 ILE Chi-restraints excluded: chain O residue 353 ASP Chi-restraints excluded: chain O residue 384 ASP Chi-restraints excluded: chain O residue 442 LEU Chi-restraints excluded: chain O residue 451 ILE Chi-restraints excluded: chain O residue 480 VAL Chi-restraints excluded: chain O residue 569 VAL Chi-restraints excluded: chain O residue 622 TYR Chi-restraints excluded: chain O residue 659 LEU Chi-restraints excluded: chain O residue 661 ASN Chi-restraints excluded: chain O residue 707 ASP Chi-restraints excluded: chain O residue 726 SER Chi-restraints excluded: chain O residue 770 ASP Chi-restraints excluded: chain P residue 95 LEU Chi-restraints excluded: chain P residue 154 LEU Chi-restraints excluded: chain P residue 180 ASP Chi-restraints excluded: chain P residue 183 LYS Chi-restraints excluded: chain P residue 184 TRP Chi-restraints excluded: chain P residue 193 PHE Chi-restraints excluded: chain P residue 225 GLN Chi-restraints excluded: chain P residue 244 ASN Chi-restraints excluded: chain P residue 259 GLN Chi-restraints excluded: chain P residue 262 LEU Chi-restraints excluded: chain P residue 304 LEU Chi-restraints excluded: chain P residue 356 VAL Chi-restraints excluded: chain P residue 367 PHE Chi-restraints excluded: chain P residue 378 LEU Chi-restraints excluded: chain P residue 388 THR Chi-restraints excluded: chain P residue 402 MET Chi-restraints excluded: chain P residue 408 ILE Chi-restraints excluded: chain P residue 437 THR Chi-restraints excluded: chain P residue 450 THR Chi-restraints excluded: chain P residue 480 LEU Chi-restraints excluded: chain Q residue 4 VAL Chi-restraints excluded: chain Q residue 10 ASN Chi-restraints excluded: chain Q residue 128 TRP Chi-restraints excluded: chain Q residue 155 GLN Chi-restraints excluded: chain Q residue 158 THR Chi-restraints excluded: chain Q residue 168 ILE Chi-restraints excluded: chain Q residue 240 ILE Chi-restraints excluded: chain Q residue 247 ILE Chi-restraints excluded: chain Q residue 248 LYS Chi-restraints excluded: chain Q residue 251 TRP Chi-restraints excluded: chain Q residue 269 ASP Chi-restraints excluded: chain Q residue 285 VAL Chi-restraints excluded: chain Q residue 364 VAL Chi-restraints excluded: chain Q residue 390 ASN Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 556 random chunks: chunk 180 optimal weight: 2.9990 chunk 483 optimal weight: 30.0000 chunk 106 optimal weight: 10.0000 chunk 315 optimal weight: 9.9990 chunk 132 optimal weight: 4.9990 chunk 537 optimal weight: 6.9990 chunk 446 optimal weight: 8.9990 chunk 249 optimal weight: 7.9990 chunk 44 optimal weight: 7.9990 chunk 177 optimal weight: 9.9990 chunk 282 optimal weight: 2.9990 overall best weight: 5.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 76 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 382 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 432 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 525 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1116 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 128 GLN B 251 HIS B 422 GLN ** B 555 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 720 GLN ** B 755 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1163 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 175 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 54 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 100 GLN ** G 56 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 59 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 128 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 137 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 16 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 51 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 106 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 270 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** O 454 GLN ** O 635 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 665 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 109 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 145 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 157 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 209 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 272 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 351 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 435 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 150 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 160 HIS ** Q 212 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6793 moved from start: 0.6257 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.066 47713 Z= 0.346 Angle : 0.800 15.196 64933 Z= 0.406 Chirality : 0.047 0.313 7264 Planarity : 0.006 0.123 7979 Dihedral : 14.244 161.107 7215 Min Nonbonded Distance : 2.020 Molprobity Statistics. All-atom Clashscore : 21.60 Ramachandran Plot: Outliers : 0.81 % Allowed : 7.60 % Favored : 91.59 % Rotamer: Outliers : 4.75 % Allowed : 20.57 % Favored : 74.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 1.24 % 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: -0.82 (0.11), residues: 5432 helix: 0.73 (0.12), residues: 2004 sheet: -0.85 (0.18), residues: 743 loop : -1.45 (0.12), residues: 2685 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.058 0.002 TRP N 54 HIS 0.013 0.001 HIS P 157 PHE 0.045 0.002 PHE B 464 TYR 0.028 0.002 TYR G 73 ARG 0.007 0.001 ARG A 615 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10864 Ramachandran restraints generated. 5432 Oldfield, 0 Emsley, 5432 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10864 Ramachandran restraints generated. 5432 Oldfield, 0 Emsley, 5432 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 962 residues out of total 4950 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 235 poor density : 727 time to evaluate : 5.691 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: A 450 LYS cc_start: 0.6024 (OUTLIER) cc_final: 0.4210 (mmtm) REVERT: A 790 LYS cc_start: 0.6887 (OUTLIER) cc_final: 0.6385 (tppt) REVERT: A 1624 LYS cc_start: 0.7119 (OUTLIER) cc_final: 0.6878 (mtmm) REVERT: B 115 SER cc_start: 0.5921 (OUTLIER) cc_final: 0.5562 (p) REVERT: B 464 PHE cc_start: 0.4471 (m-80) cc_final: 0.4255 (m-80) REVERT: B 778 TYR cc_start: 0.8156 (t80) cc_final: 0.7551 (t80) REVERT: C 71 MET cc_start: 0.7937 (ttm) cc_final: 0.7645 (ttp) REVERT: E 75 MET cc_start: 0.5393 (tpp) cc_final: 0.5016 (tpp) REVERT: E 211 TYR cc_start: 0.8511 (m-80) cc_final: 0.7985 (m-10) REVERT: F 77 ASP cc_start: 0.6175 (p0) cc_final: 0.5603 (p0) REVERT: F 82 THR cc_start: 0.8822 (OUTLIER) cc_final: 0.8562 (p) REVERT: K 89 CYS cc_start: 0.7893 (p) cc_final: 0.7609 (p) REVERT: K 97 SER cc_start: 0.8070 (m) cc_final: 0.7717 (t) REVERT: N 131 LEU cc_start: 0.7367 (OUTLIER) cc_final: 0.6390 (pp) REVERT: N 168 LEU cc_start: 0.7572 (OUTLIER) cc_final: 0.7257 (mt) REVERT: O 313 GLN cc_start: 0.6261 (OUTLIER) cc_final: 0.5659 (pp30) REVERT: O 420 GLU cc_start: 0.7791 (tt0) cc_final: 0.7518 (mm-30) REVERT: O 659 LEU cc_start: 0.6116 (OUTLIER) cc_final: 0.5650 (mt) REVERT: P 366 TYR cc_start: 0.7517 (t80) cc_final: 0.6857 (t80) REVERT: P 400 MET cc_start: 0.5701 (mpp) cc_final: 0.5477 (mmm) REVERT: Q 274 MET cc_start: 0.8647 (tpp) cc_final: 0.8051 (tpp) REVERT: Q 340 ASP cc_start: 0.5408 (p0) cc_final: 0.5208 (p0) outliers start: 235 outliers final: 161 residues processed: 879 average time/residue: 0.5569 time to fit residues: 835.8939 Evaluate side-chains 853 residues out of total 4950 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 170 poor density : 683 time to evaluate : 5.461 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 18 ILE Chi-restraints excluded: chain A residue 60 ASN Chi-restraints excluded: chain A residue 94 LEU Chi-restraints excluded: chain A residue 220 VAL Chi-restraints excluded: chain A residue 357 MET Chi-restraints excluded: chain A residue 403 LEU Chi-restraints excluded: chain A residue 419 ILE Chi-restraints excluded: chain A residue 433 ASP Chi-restraints excluded: chain A residue 450 LYS Chi-restraints excluded: chain A residue 483 VAL Chi-restraints excluded: chain A residue 551 VAL Chi-restraints excluded: chain A residue 572 THR Chi-restraints excluded: chain A residue 586 VAL Chi-restraints excluded: chain A residue 599 SER Chi-restraints excluded: chain A residue 666 VAL Chi-restraints excluded: chain A residue 678 VAL Chi-restraints excluded: chain A residue 685 SER Chi-restraints excluded: chain A residue 773 ASP Chi-restraints excluded: chain A residue 789 SER Chi-restraints excluded: chain A residue 790 LYS Chi-restraints excluded: chain A residue 891 ILE Chi-restraints excluded: chain A residue 928 MET Chi-restraints excluded: chain A residue 947 LEU Chi-restraints excluded: chain A residue 957 VAL Chi-restraints excluded: chain A residue 962 SER Chi-restraints excluded: chain A residue 1008 ASP Chi-restraints excluded: chain A residue 1033 SER Chi-restraints excluded: chain A residue 1060 GLU Chi-restraints excluded: chain A residue 1063 MET Chi-restraints excluded: chain A residue 1118 VAL Chi-restraints excluded: chain A residue 1192 SER Chi-restraints excluded: chain A residue 1222 LEU Chi-restraints excluded: chain A residue 1238 MET Chi-restraints excluded: chain A residue 1244 ASN Chi-restraints excluded: chain A residue 1491 GLU Chi-restraints excluded: chain A residue 1543 SER Chi-restraints excluded: chain A residue 1607 THR Chi-restraints excluded: chain A residue 1614 SER Chi-restraints excluded: chain A residue 1624 LYS Chi-restraints excluded: chain A residue 1634 LEU Chi-restraints excluded: chain A residue 1649 VAL Chi-restraints excluded: chain B residue 38 LEU Chi-restraints excluded: chain B residue 75 ASP Chi-restraints excluded: chain B residue 115 SER Chi-restraints excluded: chain B residue 125 GLU Chi-restraints excluded: chain B residue 249 VAL Chi-restraints excluded: chain B residue 255 ASP Chi-restraints excluded: chain B residue 288 ILE Chi-restraints excluded: chain B residue 295 ASN Chi-restraints excluded: chain B residue 306 LEU Chi-restraints excluded: chain B residue 343 ASP Chi-restraints excluded: chain B residue 398 GLN Chi-restraints excluded: chain B residue 409 TYR Chi-restraints excluded: chain B residue 421 LEU Chi-restraints excluded: chain B residue 424 ILE Chi-restraints excluded: chain B residue 453 VAL Chi-restraints excluded: chain B residue 462 GLN Chi-restraints excluded: chain B residue 472 SER Chi-restraints excluded: chain B residue 502 MET Chi-restraints excluded: chain B residue 516 THR Chi-restraints excluded: chain B residue 564 ILE Chi-restraints excluded: chain B residue 577 PHE Chi-restraints excluded: chain B residue 592 ILE Chi-restraints excluded: chain B residue 647 SER Chi-restraints excluded: chain B residue 712 SER Chi-restraints excluded: chain B residue 725 THR Chi-restraints excluded: chain B residue 819 ASP Chi-restraints excluded: chain B residue 835 GLU Chi-restraints excluded: chain B residue 858 ILE Chi-restraints excluded: chain B residue 898 LEU Chi-restraints excluded: chain B residue 900 THR Chi-restraints excluded: chain B residue 910 THR Chi-restraints excluded: chain B residue 918 SER Chi-restraints excluded: chain B residue 985 ILE Chi-restraints excluded: chain B residue 1069 ILE Chi-restraints excluded: chain B residue 1178 ILE Chi-restraints excluded: chain C residue 72 ILE Chi-restraints excluded: chain C residue 73 SER Chi-restraints excluded: chain C residue 92 ILE Chi-restraints excluded: chain C residue 120 LEU Chi-restraints excluded: chain C residue 122 ASP Chi-restraints excluded: chain C residue 151 THR Chi-restraints excluded: chain C residue 201 GLU Chi-restraints excluded: chain C residue 328 LEU Chi-restraints excluded: chain D residue 99 LEU Chi-restraints excluded: chain F residue 82 THR Chi-restraints excluded: chain G residue 47 VAL Chi-restraints excluded: chain G residue 69 LEU Chi-restraints excluded: chain G residue 110 ASP Chi-restraints excluded: chain G residue 226 ASP Chi-restraints excluded: chain G residue 245 VAL Chi-restraints excluded: chain G residue 246 ASP Chi-restraints excluded: chain H residue 57 VAL Chi-restraints excluded: chain H residue 87 ARG Chi-restraints excluded: chain H residue 100 THR Chi-restraints excluded: chain I residue 4 VAL Chi-restraints excluded: chain I residue 42 PHE Chi-restraints excluded: chain I residue 47 VAL Chi-restraints excluded: chain I residue 60 LEU Chi-restraints excluded: chain J residue 50 ILE Chi-restraints excluded: chain J residue 66 LEU Chi-restraints excluded: chain K residue 105 ILE Chi-restraints excluded: chain K residue 107 THR Chi-restraints excluded: chain L residue 46 VAL Chi-restraints excluded: chain L residue 50 ASP Chi-restraints excluded: chain L residue 65 VAL Chi-restraints excluded: chain M residue 12 ILE Chi-restraints excluded: chain M residue 66 THR Chi-restraints excluded: chain M residue 77 VAL Chi-restraints excluded: chain M residue 97 VAL Chi-restraints excluded: chain N residue 25 ILE Chi-restraints excluded: chain N residue 53 VAL Chi-restraints excluded: chain N residue 62 VAL Chi-restraints excluded: chain N residue 72 VAL Chi-restraints excluded: chain N residue 75 GLU Chi-restraints excluded: chain N residue 111 VAL Chi-restraints excluded: chain N residue 117 GLU Chi-restraints excluded: chain N residue 131 LEU Chi-restraints excluded: chain N residue 151 SER Chi-restraints excluded: chain N residue 160 VAL Chi-restraints excluded: chain N residue 168 LEU Chi-restraints excluded: chain N residue 173 THR Chi-restraints excluded: chain O residue 201 GLU Chi-restraints excluded: chain O residue 202 ILE Chi-restraints excluded: chain O residue 210 THR Chi-restraints excluded: chain O residue 254 ILE Chi-restraints excluded: chain O residue 258 SER Chi-restraints excluded: chain O residue 260 LEU Chi-restraints excluded: chain O residue 313 GLN Chi-restraints excluded: chain O residue 344 ILE Chi-restraints excluded: chain O residue 353 ASP Chi-restraints excluded: chain O residue 384 ASP Chi-restraints excluded: chain O residue 442 LEU Chi-restraints excluded: chain O residue 451 ILE Chi-restraints excluded: chain O residue 480 VAL Chi-restraints excluded: chain O residue 496 THR Chi-restraints excluded: chain O residue 569 VAL Chi-restraints excluded: chain O residue 601 ARG Chi-restraints excluded: chain O residue 659 LEU Chi-restraints excluded: chain O residue 688 ASP Chi-restraints excluded: chain O residue 707 ASP Chi-restraints excluded: chain P residue 95 LEU Chi-restraints excluded: chain P residue 180 ASP Chi-restraints excluded: chain P residue 183 LYS Chi-restraints excluded: chain P residue 184 TRP Chi-restraints excluded: chain P residue 193 PHE Chi-restraints excluded: chain P residue 244 ASN Chi-restraints excluded: chain P residue 259 GLN Chi-restraints excluded: chain P residue 262 LEU Chi-restraints excluded: chain P residue 304 LEU Chi-restraints excluded: chain P residue 356 VAL Chi-restraints excluded: chain P residue 367 PHE Chi-restraints excluded: chain P residue 402 MET Chi-restraints excluded: chain P residue 408 ILE Chi-restraints excluded: chain P residue 437 THR Chi-restraints excluded: chain P residue 480 LEU Chi-restraints excluded: chain Q residue 4 VAL Chi-restraints excluded: chain Q residue 10 ASN Chi-restraints excluded: chain Q residue 128 TRP Chi-restraints excluded: chain Q residue 155 GLN Chi-restraints excluded: chain Q residue 158 THR Chi-restraints excluded: chain Q residue 162 PHE Chi-restraints excluded: chain Q residue 168 ILE Chi-restraints excluded: chain Q residue 187 TYR Chi-restraints excluded: chain Q residue 240 ILE Chi-restraints excluded: chain Q residue 247 ILE Chi-restraints excluded: chain Q residue 248 LYS Chi-restraints excluded: chain Q residue 269 ASP Chi-restraints excluded: chain Q residue 364 VAL Chi-restraints excluded: chain Q residue 401 ILE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 556 random chunks: chunk 518 optimal weight: 9.9990 chunk 60 optimal weight: 1.9990 chunk 306 optimal weight: 20.0000 chunk 392 optimal weight: 0.8980 chunk 304 optimal weight: 8.9990 chunk 452 optimal weight: 40.0000 chunk 300 optimal weight: 9.9990 chunk 535 optimal weight: 9.9990 chunk 335 optimal weight: 0.8980 chunk 326 optimal weight: 5.9990 chunk 247 optimal weight: 0.9990 overall best weight: 2.1586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 60 ASN ** A 76 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 382 GLN A 432 ASN A 525 ASN A 950 GLN ** A1116 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1319 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 339 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 555 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 720 GLN B 755 ASN B1100 GLN ** B1163 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 175 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 38 GLN ** D 49 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 100 GLN ** G 56 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 59 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 128 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 137 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 16 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 34 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 51 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** N 85 HIS N 106 ASN ** O 270 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 665 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 109 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 115 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 145 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 157 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 209 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** P 259 GLN ** P 272 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 351 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 435 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 150 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 372 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6723 moved from start: 0.6490 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.066 47713 Z= 0.228 Angle : 0.771 14.518 64933 Z= 0.390 Chirality : 0.047 0.304 7264 Planarity : 0.006 0.123 7979 Dihedral : 14.125 159.571 7210 Min Nonbonded Distance : 1.986 Molprobity Statistics. All-atom Clashscore : 18.90 Ramachandran Plot: Outliers : 0.83 % Allowed : 7.18 % Favored : 91.99 % Rotamer: Outliers : 3.72 % Allowed : 21.93 % Favored : 74.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 1.24 % Twisted General : 0.02 % 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: -0.65 (0.12), residues: 5432 helix: 0.87 (0.12), residues: 1991 sheet: -0.75 (0.19), residues: 717 loop : -1.34 (0.12), residues: 2724 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.041 0.002 TRP N 54 HIS 0.017 0.001 HIS Q 212 PHE 0.038 0.002 PHE B 464 TYR 0.034 0.002 TYR G 73 ARG 0.007 0.000 ARG B 448 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10864 Ramachandran restraints generated. 5432 Oldfield, 0 Emsley, 5432 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10864 Ramachandran restraints generated. 5432 Oldfield, 0 Emsley, 5432 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 973 residues out of total 4950 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 184 poor density : 789 time to evaluate : 5.637 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: A 433 ASP cc_start: 0.4890 (OUTLIER) cc_final: 0.4674 (t0) REVERT: A 450 LYS cc_start: 0.6073 (OUTLIER) cc_final: 0.4336 (mmtt) REVERT: A 590 ASN cc_start: 0.8721 (t0) cc_final: 0.8288 (t0) REVERT: A 790 LYS cc_start: 0.6429 (OUTLIER) cc_final: 0.5954 (tppt) REVERT: A 1624 LYS cc_start: 0.6960 (OUTLIER) cc_final: 0.6703 (mtmm) REVERT: B 115 SER cc_start: 0.5442 (OUTLIER) cc_final: 0.5033 (p) REVERT: B 778 TYR cc_start: 0.8014 (t80) cc_final: 0.7525 (t80) REVERT: C 94 ASP cc_start: 0.6188 (t0) cc_final: 0.5902 (t0) REVERT: D 45 ASP cc_start: 0.4776 (t0) cc_final: 0.4372 (t0) REVERT: E 75 MET cc_start: 0.5140 (tpp) cc_final: 0.4883 (tpp) REVERT: E 211 TYR cc_start: 0.8444 (m-80) cc_final: 0.7910 (m-10) REVERT: F 77 ASP cc_start: 0.6236 (p0) cc_final: 0.5773 (p0) REVERT: F 82 THR cc_start: 0.8768 (OUTLIER) cc_final: 0.8560 (p) REVERT: K 45 GLU cc_start: 0.6777 (pm20) cc_final: 0.6577 (pm20) REVERT: K 97 SER cc_start: 0.8047 (m) cc_final: 0.7632 (t) REVERT: L 67 PHE cc_start: 0.7821 (m-10) cc_final: 0.7313 (m-10) REVERT: N 131 LEU cc_start: 0.7395 (OUTLIER) cc_final: 0.6585 (pp) REVERT: N 168 LEU cc_start: 0.7198 (OUTLIER) cc_final: 0.6943 (mt) REVERT: O 659 LEU cc_start: 0.6190 (OUTLIER) cc_final: 0.5870 (mt) REVERT: P 311 MET cc_start: 0.7465 (ppp) cc_final: 0.6336 (pmm) REVERT: P 400 MET cc_start: 0.5601 (mpp) cc_final: 0.5354 (mmm) REVERT: Q 274 MET cc_start: 0.8533 (tpp) cc_final: 0.8164 (tpp) outliers start: 184 outliers final: 135 residues processed: 901 average time/residue: 0.5936 time to fit residues: 916.7513 Evaluate side-chains 843 residues out of total 4950 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 144 poor density : 699 time to evaluate : 5.350 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 18 ILE Chi-restraints excluded: chain A residue 60 ASN Chi-restraints excluded: chain A residue 94 LEU Chi-restraints excluded: chain A residue 222 GLU Chi-restraints excluded: chain A residue 357 MET Chi-restraints excluded: chain A residue 403 LEU Chi-restraints excluded: chain A residue 419 ILE Chi-restraints excluded: chain A residue 433 ASP Chi-restraints excluded: chain A residue 438 ILE Chi-restraints excluded: chain A residue 450 LYS Chi-restraints excluded: chain A residue 483 VAL Chi-restraints excluded: chain A residue 495 ILE Chi-restraints excluded: chain A residue 551 VAL Chi-restraints excluded: chain A residue 572 THR Chi-restraints excluded: chain A residue 599 SER Chi-restraints excluded: chain A residue 666 VAL Chi-restraints excluded: chain A residue 678 VAL Chi-restraints excluded: chain A residue 685 SER Chi-restraints excluded: chain A residue 773 ASP Chi-restraints excluded: chain A residue 790 LYS Chi-restraints excluded: chain A residue 891 ILE Chi-restraints excluded: chain A residue 947 LEU Chi-restraints excluded: chain A residue 957 VAL Chi-restraints excluded: chain A residue 962 SER Chi-restraints excluded: chain A residue 1033 SER Chi-restraints excluded: chain A residue 1060 GLU Chi-restraints excluded: chain A residue 1118 VAL Chi-restraints excluded: chain A residue 1238 MET Chi-restraints excluded: chain A residue 1244 ASN Chi-restraints excluded: chain A residue 1543 SER Chi-restraints excluded: chain A residue 1607 THR Chi-restraints excluded: chain A residue 1614 SER Chi-restraints excluded: chain A residue 1619 CYS Chi-restraints excluded: chain A residue 1624 LYS Chi-restraints excluded: chain A residue 1634 LEU Chi-restraints excluded: chain A residue 1649 VAL Chi-restraints excluded: chain B residue 38 LEU Chi-restraints excluded: chain B residue 75 ASP Chi-restraints excluded: chain B residue 115 SER Chi-restraints excluded: chain B residue 125 GLU Chi-restraints excluded: chain B residue 249 VAL Chi-restraints excluded: chain B residue 295 ASN Chi-restraints excluded: chain B residue 306 LEU Chi-restraints excluded: chain B residue 343 ASP Chi-restraints excluded: chain B residue 409 TYR Chi-restraints excluded: chain B residue 421 LEU Chi-restraints excluded: chain B residue 424 ILE Chi-restraints excluded: chain B residue 455 GLU Chi-restraints excluded: chain B residue 472 SER Chi-restraints excluded: chain B residue 502 MET Chi-restraints excluded: chain B residue 516 THR Chi-restraints excluded: chain B residue 547 HIS Chi-restraints excluded: chain B residue 564 ILE Chi-restraints excluded: chain B residue 577 PHE Chi-restraints excluded: chain B residue 712 SER Chi-restraints excluded: chain B residue 725 THR Chi-restraints excluded: chain B residue 739 ASN Chi-restraints excluded: chain B residue 789 ILE Chi-restraints excluded: chain B residue 819 ASP Chi-restraints excluded: chain B residue 858 ILE Chi-restraints excluded: chain B residue 901 VAL Chi-restraints excluded: chain B residue 918 SER Chi-restraints excluded: chain B residue 1069 ILE Chi-restraints excluded: chain B residue 1113 THR Chi-restraints excluded: chain B residue 1178 ILE Chi-restraints excluded: chain B residue 1183 LYS Chi-restraints excluded: chain C residue 73 SER Chi-restraints excluded: chain C residue 92 ILE Chi-restraints excluded: chain C residue 151 THR Chi-restraints excluded: chain C residue 201 GLU Chi-restraints excluded: chain C residue 328 LEU Chi-restraints excluded: chain D residue 14 THR Chi-restraints excluded: chain D residue 99 LEU Chi-restraints excluded: chain E residue 178 ILE Chi-restraints excluded: chain F residue 82 THR Chi-restraints excluded: chain G residue 47 VAL Chi-restraints excluded: chain G residue 69 LEU Chi-restraints excluded: chain G residue 110 ASP Chi-restraints excluded: chain G residue 138 PHE Chi-restraints excluded: chain G residue 226 ASP Chi-restraints excluded: chain G residue 245 VAL Chi-restraints excluded: chain G residue 246 ASP Chi-restraints excluded: chain H residue 87 ARG Chi-restraints excluded: chain H residue 137 GLN Chi-restraints excluded: chain I residue 42 PHE Chi-restraints excluded: chain I residue 60 LEU Chi-restraints excluded: chain J residue 28 ASP Chi-restraints excluded: chain J residue 66 LEU Chi-restraints excluded: chain K residue 105 ILE Chi-restraints excluded: chain L residue 46 VAL Chi-restraints excluded: chain L residue 65 VAL Chi-restraints excluded: chain M residue 36 THR Chi-restraints excluded: chain M residue 66 THR Chi-restraints excluded: chain M residue 78 VAL Chi-restraints excluded: chain N residue 25 ILE Chi-restraints excluded: chain N residue 53 VAL Chi-restraints excluded: chain N residue 54 TRP Chi-restraints excluded: chain N residue 72 VAL Chi-restraints excluded: chain N residue 75 GLU Chi-restraints excluded: chain N residue 111 VAL Chi-restraints excluded: chain N residue 131 LEU Chi-restraints excluded: chain N residue 160 VAL Chi-restraints excluded: chain N residue 168 LEU Chi-restraints excluded: chain N residue 173 THR Chi-restraints excluded: chain O residue 201 GLU Chi-restraints excluded: chain O residue 202 ILE Chi-restraints excluded: chain O residue 210 THR Chi-restraints excluded: chain O residue 254 ILE Chi-restraints excluded: chain O residue 258 SER Chi-restraints excluded: chain O residue 344 ILE Chi-restraints excluded: chain O residue 353 ASP Chi-restraints excluded: chain O residue 384 ASP Chi-restraints excluded: chain O residue 442 LEU Chi-restraints excluded: chain O residue 451 ILE Chi-restraints excluded: chain O residue 480 VAL Chi-restraints excluded: chain O residue 569 VAL Chi-restraints excluded: chain O residue 601 ARG Chi-restraints excluded: chain O residue 659 LEU Chi-restraints excluded: chain O residue 661 ASN Chi-restraints excluded: chain O residue 688 ASP Chi-restraints excluded: chain O residue 707 ASP Chi-restraints excluded: chain P residue 95 LEU Chi-restraints excluded: chain P residue 154 LEU Chi-restraints excluded: chain P residue 184 TRP Chi-restraints excluded: chain P residue 193 PHE Chi-restraints excluded: chain P residue 244 ASN Chi-restraints excluded: chain P residue 259 GLN Chi-restraints excluded: chain P residue 262 LEU Chi-restraints excluded: chain P residue 304 LEU Chi-restraints excluded: chain P residue 356 VAL Chi-restraints excluded: chain P residue 437 THR Chi-restraints excluded: chain P residue 480 LEU Chi-restraints excluded: chain Q residue 6 ILE Chi-restraints excluded: chain Q residue 128 TRP Chi-restraints excluded: chain Q residue 155 GLN Chi-restraints excluded: chain Q residue 158 THR Chi-restraints excluded: chain Q residue 168 ILE Chi-restraints excluded: chain Q residue 187 TYR Chi-restraints excluded: chain Q residue 240 ILE Chi-restraints excluded: chain Q residue 247 ILE Chi-restraints excluded: chain Q residue 248 LYS Chi-restraints excluded: chain Q residue 269 ASP Chi-restraints excluded: chain Q residue 401 ILE Chi-restraints excluded: chain Q residue 424 PHE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 556 random chunks: chunk 331 optimal weight: 7.9990 chunk 214 optimal weight: 0.8980 chunk 320 optimal weight: 7.9990 chunk 161 optimal weight: 0.6980 chunk 105 optimal weight: 9.9990 chunk 103 optimal weight: 30.0000 chunk 340 optimal weight: 6.9990 chunk 365 optimal weight: 7.9990 chunk 264 optimal weight: 0.5980 chunk 49 optimal weight: 10.0000 chunk 421 optimal weight: 3.9990 overall best weight: 2.6384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 382 GLN ** A1116 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1319 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 339 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 555 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 720 GLN ** B1163 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 175 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 49 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 5 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 100 GLN ** G 56 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 59 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 137 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 16 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 71 GLN ** N 34 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 51 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 270 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 313 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 665 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 109 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 145 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 157 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 209 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 272 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 351 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 435 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 150 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 286 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 372 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6732 moved from start: 0.6691 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.066 47713 Z= 0.249 Angle : 0.781 14.463 64933 Z= 0.395 Chirality : 0.047 0.356 7264 Planarity : 0.006 0.124 7979 Dihedral : 14.024 158.772 7207 Min Nonbonded Distance : 1.992 Molprobity Statistics. All-atom Clashscore : 19.91 Ramachandran Plot: Outliers : 0.75 % Allowed : 7.29 % Favored : 91.96 % Rotamer: Outliers : 3.54 % Allowed : 23.14 % Favored : 73.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 1.24 % Twisted General : 0.02 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.61 (0.12), residues: 5432 helix: 0.92 (0.12), residues: 1993 sheet: -0.69 (0.19), residues: 732 loop : -1.35 (0.12), residues: 2707 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.042 0.002 TRP N 54 HIS 0.024 0.001 HIS Q 212 PHE 0.054 0.002 PHE B1167 TYR 0.034 0.002 TYR P 357 ARG 0.007 0.000 ARG A 59 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10864 Ramachandran restraints generated. 5432 Oldfield, 0 Emsley, 5432 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10864 Ramachandran restraints generated. 5432 Oldfield, 0 Emsley, 5432 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 927 residues out of total 4950 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 175 poor density : 752 time to evaluate : 5.794 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: A 450 LYS cc_start: 0.5977 (OUTLIER) cc_final: 0.4281 (mmtt) REVERT: A 471 MET cc_start: 0.7445 (mtp) cc_final: 0.7197 (mtp) REVERT: A 549 MET cc_start: 0.5703 (ttm) cc_final: 0.5491 (ttm) REVERT: B 778 TYR cc_start: 0.8025 (t80) cc_final: 0.7570 (t80) REVERT: C 71 MET cc_start: 0.7866 (ttm) cc_final: 0.7514 (ttp) REVERT: E 75 MET cc_start: 0.5333 (tpp) cc_final: 0.5060 (tpp) REVERT: E 211 TYR cc_start: 0.8463 (m-80) cc_final: 0.7958 (m-10) REVERT: F 77 ASP cc_start: 0.6050 (p0) cc_final: 0.5585 (p0) REVERT: F 82 THR cc_start: 0.8785 (OUTLIER) cc_final: 0.8557 (p) REVERT: K 45 GLU cc_start: 0.6830 (pm20) cc_final: 0.6584 (pm20) REVERT: K 97 SER cc_start: 0.8069 (m) cc_final: 0.7628 (t) REVERT: L 67 PHE cc_start: 0.7883 (m-10) cc_final: 0.7448 (m-10) REVERT: N 131 LEU cc_start: 0.7719 (OUTLIER) cc_final: 0.7108 (pp) REVERT: N 168 LEU cc_start: 0.7348 (OUTLIER) cc_final: 0.7081 (mt) REVERT: O 478 MET cc_start: 0.7941 (ppp) cc_final: 0.7687 (ppp) REVERT: O 659 LEU cc_start: 0.6191 (OUTLIER) cc_final: 0.5961 (mt) REVERT: Q 212 HIS cc_start: 0.5526 (m-70) cc_final: 0.4519 (m-70) REVERT: Q 274 MET cc_start: 0.8564 (tpp) cc_final: 0.8153 (tpp) outliers start: 175 outliers final: 132 residues processed: 864 average time/residue: 0.6099 time to fit residues: 905.5554 Evaluate side-chains 827 residues out of total 4950 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 137 poor density : 690 time to evaluate : 5.348 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 94 LEU Chi-restraints excluded: chain A residue 220 VAL Chi-restraints excluded: chain A residue 222 GLU Chi-restraints excluded: chain A residue 357 MET Chi-restraints excluded: chain A residue 403 LEU Chi-restraints excluded: chain A residue 419 ILE Chi-restraints excluded: chain A residue 438 ILE Chi-restraints excluded: chain A residue 450 LYS Chi-restraints excluded: chain A residue 483 VAL Chi-restraints excluded: chain A residue 495 ILE Chi-restraints excluded: chain A residue 551 VAL Chi-restraints excluded: chain A residue 599 SER Chi-restraints excluded: chain A residue 666 VAL Chi-restraints excluded: chain A residue 678 VAL Chi-restraints excluded: chain A residue 685 SER Chi-restraints excluded: chain A residue 773 ASP Chi-restraints excluded: chain A residue 790 LYS Chi-restraints excluded: chain A residue 891 ILE Chi-restraints excluded: chain A residue 947 LEU Chi-restraints excluded: chain A residue 957 VAL Chi-restraints excluded: chain A residue 962 SER Chi-restraints excluded: chain A residue 1033 SER Chi-restraints excluded: chain A residue 1060 GLU Chi-restraints excluded: chain A residue 1118 VAL Chi-restraints excluded: chain A residue 1222 LEU Chi-restraints excluded: chain A residue 1238 MET Chi-restraints excluded: chain A residue 1244 ASN Chi-restraints excluded: chain A residue 1543 SER Chi-restraints excluded: chain A residue 1607 THR Chi-restraints excluded: chain A residue 1614 SER Chi-restraints excluded: chain A residue 1634 LEU Chi-restraints excluded: chain A residue 1649 VAL Chi-restraints excluded: chain B residue 33 SER Chi-restraints excluded: chain B residue 38 LEU Chi-restraints excluded: chain B residue 75 ASP Chi-restraints excluded: chain B residue 249 VAL Chi-restraints excluded: chain B residue 295 ASN Chi-restraints excluded: chain B residue 306 LEU Chi-restraints excluded: chain B residue 343 ASP Chi-restraints excluded: chain B residue 409 TYR Chi-restraints excluded: chain B residue 421 LEU Chi-restraints excluded: chain B residue 424 ILE Chi-restraints excluded: chain B residue 453 VAL Chi-restraints excluded: chain B residue 462 GLN Chi-restraints excluded: chain B residue 472 SER Chi-restraints excluded: chain B residue 489 GLU Chi-restraints excluded: chain B residue 502 MET Chi-restraints excluded: chain B residue 516 THR Chi-restraints excluded: chain B residue 547 HIS Chi-restraints excluded: chain B residue 564 ILE Chi-restraints excluded: chain B residue 577 PHE Chi-restraints excluded: chain B residue 712 SER Chi-restraints excluded: chain B residue 725 THR Chi-restraints excluded: chain B residue 739 ASN Chi-restraints excluded: chain B residue 789 ILE Chi-restraints excluded: chain B residue 819 ASP Chi-restraints excluded: chain B residue 858 ILE Chi-restraints excluded: chain B residue 910 THR Chi-restraints excluded: chain B residue 918 SER Chi-restraints excluded: chain B residue 1069 ILE Chi-restraints excluded: chain B residue 1113 THR Chi-restraints excluded: chain B residue 1125 THR Chi-restraints excluded: chain B residue 1178 ILE Chi-restraints excluded: chain C residue 73 SER Chi-restraints excluded: chain C residue 92 ILE Chi-restraints excluded: chain C residue 151 THR Chi-restraints excluded: chain C residue 201 GLU Chi-restraints excluded: chain C residue 328 LEU Chi-restraints excluded: chain D residue 14 THR Chi-restraints excluded: chain D residue 99 LEU Chi-restraints excluded: chain E residue 178 ILE Chi-restraints excluded: chain F residue 82 THR Chi-restraints excluded: chain G residue 47 VAL Chi-restraints excluded: chain G residue 69 LEU Chi-restraints excluded: chain G residue 110 ASP Chi-restraints excluded: chain G residue 226 ASP Chi-restraints excluded: chain G residue 245 VAL Chi-restraints excluded: chain H residue 137 GLN Chi-restraints excluded: chain I residue 42 PHE Chi-restraints excluded: chain I residue 60 LEU Chi-restraints excluded: chain J residue 66 LEU Chi-restraints excluded: chain K residue 105 ILE Chi-restraints excluded: chain L residue 46 VAL Chi-restraints excluded: chain L residue 65 VAL Chi-restraints excluded: chain M residue 36 THR Chi-restraints excluded: chain M residue 66 THR Chi-restraints excluded: chain M residue 78 VAL Chi-restraints excluded: chain M residue 97 VAL Chi-restraints excluded: chain N residue 25 ILE Chi-restraints excluded: chain N residue 53 VAL Chi-restraints excluded: chain N residue 54 TRP Chi-restraints excluded: chain N residue 72 VAL Chi-restraints excluded: chain N residue 75 GLU Chi-restraints excluded: chain N residue 111 VAL Chi-restraints excluded: chain N residue 131 LEU Chi-restraints excluded: chain N residue 160 VAL Chi-restraints excluded: chain N residue 168 LEU Chi-restraints excluded: chain N residue 173 THR Chi-restraints excluded: chain O residue 201 GLU Chi-restraints excluded: chain O residue 202 ILE Chi-restraints excluded: chain O residue 210 THR Chi-restraints excluded: chain O residue 254 ILE Chi-restraints excluded: chain O residue 258 SER Chi-restraints excluded: chain O residue 344 ILE Chi-restraints excluded: chain O residue 353 ASP Chi-restraints excluded: chain O residue 384 ASP Chi-restraints excluded: chain O residue 408 ILE Chi-restraints excluded: chain O residue 442 LEU Chi-restraints excluded: chain O residue 480 VAL Chi-restraints excluded: chain O residue 496 THR Chi-restraints excluded: chain O residue 569 VAL Chi-restraints excluded: chain O residue 601 ARG Chi-restraints excluded: chain O residue 659 LEU Chi-restraints excluded: chain O residue 688 ASP Chi-restraints excluded: chain O residue 707 ASP Chi-restraints excluded: chain P residue 95 LEU Chi-restraints excluded: chain P residue 154 LEU Chi-restraints excluded: chain P residue 184 TRP Chi-restraints excluded: chain P residue 193 PHE Chi-restraints excluded: chain P residue 201 LYS Chi-restraints excluded: chain P residue 262 LEU Chi-restraints excluded: chain P residue 304 LEU Chi-restraints excluded: chain P residue 356 VAL Chi-restraints excluded: chain P residue 378 LEU Chi-restraints excluded: chain P residue 437 THR Chi-restraints excluded: chain P residue 480 LEU Chi-restraints excluded: chain Q residue 10 ASN Chi-restraints excluded: chain Q residue 128 TRP Chi-restraints excluded: chain Q residue 155 GLN Chi-restraints excluded: chain Q residue 158 THR Chi-restraints excluded: chain Q residue 168 ILE Chi-restraints excluded: chain Q residue 187 TYR Chi-restraints excluded: chain Q residue 240 ILE Chi-restraints excluded: chain Q residue 247 ILE Chi-restraints excluded: chain Q residue 269 ASP Chi-restraints excluded: chain Q residue 401 ILE Chi-restraints excluded: chain Q residue 424 PHE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 556 random chunks: chunk 487 optimal weight: 8.9990 chunk 513 optimal weight: 3.9990 chunk 468 optimal weight: 8.9990 chunk 499 optimal weight: 5.9990 chunk 300 optimal weight: 10.0000 chunk 217 optimal weight: 10.0000 chunk 392 optimal weight: 20.0000 chunk 153 optimal weight: 20.0000 chunk 451 optimal weight: 5.9990 chunk 472 optimal weight: 8.9990 chunk 497 optimal weight: 7.9990 overall best weight: 6.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 60 ASN ** A 383 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 706 HIS ** A1116 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1191 GLN ** A1319 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 128 GLN ** B 339 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 398 GLN ** B 555 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 720 GLN ** B 899 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B1100 GLN ** B1163 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 172 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 175 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 49 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 5 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 100 GLN F 104 ASN ** G 56 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 59 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 64 GLN ** G 128 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 137 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 16 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 71 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 34 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 51 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 270 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 313 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 109 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 145 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 157 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 209 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 272 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 351 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 435 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 150 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 260 ASN ** Q 286 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 321 GLN Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6836 moved from start: 0.6858 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.076 47713 Z= 0.419 Angle : 0.842 14.575 64933 Z= 0.429 Chirality : 0.049 0.361 7264 Planarity : 0.006 0.126 7979 Dihedral : 14.097 158.635 7203 Min Nonbonded Distance : 1.979 Molprobity Statistics. All-atom Clashscore : 23.54 Ramachandran Plot: Outliers : 0.74 % Allowed : 7.97 % Favored : 91.29 % Rotamer: Outliers : 3.52 % Allowed : 23.61 % Favored : 72.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 1.24 % Twisted General : 0.02 % 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: -0.79 (0.12), residues: 5432 helix: 0.80 (0.12), residues: 1997 sheet: -0.86 (0.18), residues: 748 loop : -1.46 (0.12), residues: 2687 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.038 0.002 TRP N 54 HIS 0.015 0.002 HIS P 157 PHE 0.065 0.002 PHE B1167 TYR 0.049 0.002 TYR A 618 ARG 0.008 0.001 ARG A 615 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10864 Ramachandran restraints generated. 5432 Oldfield, 0 Emsley, 5432 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10864 Ramachandran restraints generated. 5432 Oldfield, 0 Emsley, 5432 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 858 residues out of total 4950 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 174 poor density : 684 time to evaluate : 5.597 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: A 68 ASP cc_start: 0.6077 (p0) cc_final: 0.5578 (p0) REVERT: A 450 LYS cc_start: 0.6264 (OUTLIER) cc_final: 0.4499 (mmtt) REVERT: A 549 MET cc_start: 0.5925 (ttm) cc_final: 0.5572 (ttm) REVERT: B 778 TYR cc_start: 0.8170 (t80) cc_final: 0.7530 (t80) REVERT: B 782 ASP cc_start: 0.6295 (p0) cc_final: 0.6026 (p0) REVERT: C 71 MET cc_start: 0.7924 (ttm) cc_final: 0.7497 (ttp) REVERT: E 211 TYR cc_start: 0.8509 (m-80) cc_final: 0.7997 (m-10) REVERT: F 77 ASP cc_start: 0.6324 (p0) cc_final: 0.5650 (p0) REVERT: F 82 THR cc_start: 0.8709 (OUTLIER) cc_final: 0.8474 (p) REVERT: K 45 GLU cc_start: 0.7026 (pm20) cc_final: 0.6824 (pm20) REVERT: K 97 SER cc_start: 0.8027 (m) cc_final: 0.7736 (t) REVERT: N 131 LEU cc_start: 0.7190 (OUTLIER) cc_final: 0.6574 (pp) REVERT: N 168 LEU cc_start: 0.7317 (OUTLIER) cc_final: 0.7030 (mt) REVERT: O 478 MET cc_start: 0.7904 (ppp) cc_final: 0.7696 (ppp) REVERT: O 552 LEU cc_start: 0.8186 (mt) cc_final: 0.7771 (tt) REVERT: O 570 ASP cc_start: 0.7054 (p0) cc_final: 0.6615 (p0) REVERT: Q 8 LEU cc_start: 0.7614 (OUTLIER) cc_final: 0.7297 (pp) REVERT: Q 274 MET cc_start: 0.8567 (tpp) cc_final: 0.8115 (tpp) outliers start: 174 outliers final: 148 residues processed: 802 average time/residue: 0.5668 time to fit residues: 773.4400 Evaluate side-chains 810 residues out of total 4950 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 153 poor density : 657 time to evaluate : 5.391 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 18 ILE Chi-restraints excluded: chain A residue 94 LEU Chi-restraints excluded: chain A residue 220 VAL Chi-restraints excluded: chain A residue 222 GLU Chi-restraints excluded: chain A residue 357 MET Chi-restraints excluded: chain A residue 403 LEU Chi-restraints excluded: chain A residue 419 ILE Chi-restraints excluded: chain A residue 433 ASP Chi-restraints excluded: chain A residue 438 ILE Chi-restraints excluded: chain A residue 450 LYS Chi-restraints excluded: chain A residue 483 VAL Chi-restraints excluded: chain A residue 495 ILE Chi-restraints excluded: chain A residue 551 VAL Chi-restraints excluded: chain A residue 666 VAL Chi-restraints excluded: chain A residue 678 VAL Chi-restraints excluded: chain A residue 685 SER Chi-restraints excluded: chain A residue 773 ASP Chi-restraints excluded: chain A residue 790 LYS Chi-restraints excluded: chain A residue 947 LEU Chi-restraints excluded: chain A residue 957 VAL Chi-restraints excluded: chain A residue 962 SER Chi-restraints excluded: chain A residue 1033 SER Chi-restraints excluded: chain A residue 1060 GLU Chi-restraints excluded: chain A residue 1118 VAL Chi-restraints excluded: chain A residue 1192 SER Chi-restraints excluded: chain A residue 1222 LEU Chi-restraints excluded: chain A residue 1238 MET Chi-restraints excluded: chain A residue 1491 GLU Chi-restraints excluded: chain A residue 1543 SER Chi-restraints excluded: chain A residue 1607 THR Chi-restraints excluded: chain A residue 1614 SER Chi-restraints excluded: chain A residue 1649 VAL Chi-restraints excluded: chain B residue 33 SER Chi-restraints excluded: chain B residue 38 LEU Chi-restraints excluded: chain B residue 57 ASP Chi-restraints excluded: chain B residue 75 ASP Chi-restraints excluded: chain B residue 121 VAL Chi-restraints excluded: chain B residue 249 VAL Chi-restraints excluded: chain B residue 295 ASN Chi-restraints excluded: chain B residue 306 LEU Chi-restraints excluded: chain B residue 343 ASP Chi-restraints excluded: chain B residue 374 LEU Chi-restraints excluded: chain B residue 398 GLN Chi-restraints excluded: chain B residue 409 TYR Chi-restraints excluded: chain B residue 421 LEU Chi-restraints excluded: chain B residue 424 ILE Chi-restraints excluded: chain B residue 453 VAL Chi-restraints excluded: chain B residue 455 GLU Chi-restraints excluded: chain B residue 462 GLN Chi-restraints excluded: chain B residue 472 SER Chi-restraints excluded: chain B residue 502 MET Chi-restraints excluded: chain B residue 516 THR Chi-restraints excluded: chain B residue 547 HIS Chi-restraints excluded: chain B residue 564 ILE Chi-restraints excluded: chain B residue 577 PHE Chi-restraints excluded: chain B residue 712 SER Chi-restraints excluded: chain B residue 725 THR Chi-restraints excluded: chain B residue 739 ASN Chi-restraints excluded: chain B residue 789 ILE Chi-restraints excluded: chain B residue 819 ASP Chi-restraints excluded: chain B residue 900 THR Chi-restraints excluded: chain B residue 901 VAL Chi-restraints excluded: chain B residue 910 THR Chi-restraints excluded: chain B residue 918 SER Chi-restraints excluded: chain B residue 934 ILE Chi-restraints excluded: chain B residue 1033 TYR Chi-restraints excluded: chain B residue 1069 ILE Chi-restraints excluded: chain B residue 1110 ILE Chi-restraints excluded: chain B residue 1113 THR Chi-restraints excluded: chain B residue 1125 THR Chi-restraints excluded: chain B residue 1178 ILE Chi-restraints excluded: chain C residue 72 ILE Chi-restraints excluded: chain C residue 73 SER Chi-restraints excluded: chain C residue 92 ILE Chi-restraints excluded: chain C residue 151 THR Chi-restraints excluded: chain C residue 201 GLU Chi-restraints excluded: chain C residue 328 LEU Chi-restraints excluded: chain D residue 14 THR Chi-restraints excluded: chain D residue 15 THR Chi-restraints excluded: chain D residue 99 LEU Chi-restraints excluded: chain E residue 178 ILE Chi-restraints excluded: chain E residue 199 ILE Chi-restraints excluded: chain F residue 82 THR Chi-restraints excluded: chain G residue 47 VAL Chi-restraints excluded: chain G residue 69 LEU Chi-restraints excluded: chain G residue 104 LEU Chi-restraints excluded: chain G residue 110 ASP Chi-restraints excluded: chain G residue 226 ASP Chi-restraints excluded: chain G residue 245 VAL Chi-restraints excluded: chain H residue 87 ARG Chi-restraints excluded: chain H residue 100 THR Chi-restraints excluded: chain H residue 109 LYS Chi-restraints excluded: chain H residue 137 GLN Chi-restraints excluded: chain I residue 4 VAL Chi-restraints excluded: chain I residue 42 PHE Chi-restraints excluded: chain I residue 47 VAL Chi-restraints excluded: chain I residue 60 LEU Chi-restraints excluded: chain J residue 50 ILE Chi-restraints excluded: chain J residue 66 LEU Chi-restraints excluded: chain K residue 105 ILE Chi-restraints excluded: chain L residue 46 VAL Chi-restraints excluded: chain L residue 50 ASP Chi-restraints excluded: chain L residue 65 VAL Chi-restraints excluded: chain M residue 36 THR Chi-restraints excluded: chain M residue 66 THR Chi-restraints excluded: chain M residue 78 VAL Chi-restraints excluded: chain M residue 88 ILE Chi-restraints excluded: chain M residue 97 VAL Chi-restraints excluded: chain N residue 25 ILE Chi-restraints excluded: chain N residue 54 TRP Chi-restraints excluded: chain N residue 72 VAL Chi-restraints excluded: chain N residue 75 GLU Chi-restraints excluded: chain N residue 87 TYR Chi-restraints excluded: chain N residue 111 VAL Chi-restraints excluded: chain N residue 131 LEU Chi-restraints excluded: chain N residue 151 SER Chi-restraints excluded: chain N residue 155 VAL Chi-restraints excluded: chain N residue 160 VAL Chi-restraints excluded: chain N residue 168 LEU Chi-restraints excluded: chain N residue 173 THR Chi-restraints excluded: chain O residue 201 GLU Chi-restraints excluded: chain O residue 202 ILE Chi-restraints excluded: chain O residue 210 THR Chi-restraints excluded: chain O residue 254 ILE Chi-restraints excluded: chain O residue 300 LEU Chi-restraints excluded: chain O residue 344 ILE Chi-restraints excluded: chain O residue 353 ASP Chi-restraints excluded: chain O residue 383 ILE Chi-restraints excluded: chain O residue 384 ASP Chi-restraints excluded: chain O residue 442 LEU Chi-restraints excluded: chain O residue 480 VAL Chi-restraints excluded: chain O residue 569 VAL Chi-restraints excluded: chain O residue 601 ARG Chi-restraints excluded: chain O residue 688 ASP Chi-restraints excluded: chain P residue 95 LEU Chi-restraints excluded: chain P residue 154 LEU Chi-restraints excluded: chain P residue 184 TRP Chi-restraints excluded: chain P residue 193 PHE Chi-restraints excluded: chain P residue 201 LYS Chi-restraints excluded: chain P residue 244 ASN Chi-restraints excluded: chain P residue 262 LEU Chi-restraints excluded: chain P residue 304 LEU Chi-restraints excluded: chain P residue 356 VAL Chi-restraints excluded: chain P residue 378 LEU Chi-restraints excluded: chain P residue 437 THR Chi-restraints excluded: chain P residue 480 LEU Chi-restraints excluded: chain Q residue 8 LEU Chi-restraints excluded: chain Q residue 10 ASN Chi-restraints excluded: chain Q residue 155 GLN Chi-restraints excluded: chain Q residue 158 THR Chi-restraints excluded: chain Q residue 168 ILE Chi-restraints excluded: chain Q residue 269 ASP Chi-restraints excluded: chain Q residue 424 PHE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 556 random chunks: chunk 327 optimal weight: 6.9990 chunk 528 optimal weight: 2.9990 chunk 322 optimal weight: 4.9990 chunk 250 optimal weight: 4.9990 chunk 367 optimal weight: 4.9990 chunk 553 optimal weight: 30.0000 chunk 509 optimal weight: 50.0000 chunk 441 optimal weight: 8.9990 chunk 45 optimal weight: 10.0000 chunk 340 optimal weight: 3.9990 chunk 270 optimal weight: 7.9990 overall best weight: 4.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 383 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1116 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1319 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 128 GLN ** B 339 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 398 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 555 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 720 GLN ** B 899 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1163 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 175 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 49 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 5 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 100 GLN ** G 56 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 59 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 64 GLN ** H 137 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 16 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 34 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 270 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 313 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 109 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 145 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 209 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 272 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 351 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 435 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 150 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 212 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 286 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6795 moved from start: 0.7003 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.068 47713 Z= 0.315 Angle : 0.812 15.014 64933 Z= 0.410 Chirality : 0.048 0.461 7264 Planarity : 0.006 0.126 7979 Dihedral : 14.075 155.871 7199 Min Nonbonded Distance : 2.007 Molprobity Statistics. All-atom Clashscore : 21.79 Ramachandran Plot: Outliers : 0.72 % Allowed : 7.73 % Favored : 91.55 % Rotamer: Outliers : 3.27 % Allowed : 24.17 % Favored : 72.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 1.24 % Twisted General : 0.02 % 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: -0.71 (0.12), residues: 5432 helix: 0.87 (0.12), residues: 1987 sheet: -0.78 (0.18), residues: 737 loop : -1.41 (0.12), residues: 2708 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.038 0.002 TRP N 54 HIS 0.011 0.001 HIS Q 372 PHE 0.075 0.002 PHE B1167 TYR 0.059 0.002 TYR Q 208 ARG 0.007 0.001 ARG A 615 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10864 Ramachandran restraints generated. 5432 Oldfield, 0 Emsley, 5432 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10864 Ramachandran restraints generated. 5432 Oldfield, 0 Emsley, 5432 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 869 residues out of total 4950 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 162 poor density : 707 time to evaluate : 5.055 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: A 68 ASP cc_start: 0.5995 (p0) cc_final: 0.5576 (p0) REVERT: A 450 LYS cc_start: 0.6167 (OUTLIER) cc_final: 0.4331 (mmtt) REVERT: A 790 LYS cc_start: 0.6734 (OUTLIER) cc_final: 0.6340 (tppt) REVERT: B 778 TYR cc_start: 0.8107 (t80) cc_final: 0.7493 (t80) REVERT: C 71 MET cc_start: 0.7930 (ttm) cc_final: 0.7553 (ttp) REVERT: E 211 TYR cc_start: 0.8462 (m-80) cc_final: 0.7891 (m-10) REVERT: F 77 ASP cc_start: 0.6284 (p0) cc_final: 0.5663 (p0) REVERT: F 82 THR cc_start: 0.8648 (OUTLIER) cc_final: 0.8417 (p) REVERT: F 85 MET cc_start: 0.7933 (tpp) cc_final: 0.7678 (tpp) REVERT: K 45 GLU cc_start: 0.6986 (pm20) cc_final: 0.6784 (pm20) REVERT: K 97 SER cc_start: 0.7940 (m) cc_final: 0.7691 (t) REVERT: N 168 LEU cc_start: 0.7240 (OUTLIER) cc_final: 0.6939 (mt) REVERT: O 285 MET cc_start: 0.7084 (pmm) cc_final: 0.6817 (pmm) REVERT: O 380 MET cc_start: 0.7350 (tpp) cc_final: 0.6860 (tpt) REVERT: Q 274 MET cc_start: 0.8471 (tpp) cc_final: 0.8070 (tpp) outliers start: 162 outliers final: 138 residues processed: 815 average time/residue: 0.6096 time to fit residues: 849.0378 Evaluate side-chains 824 residues out of total 4950 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 142 poor density : 682 time to evaluate : 5.256 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 18 ILE Chi-restraints excluded: chain A residue 94 LEU Chi-restraints excluded: chain A residue 220 VAL Chi-restraints excluded: chain A residue 222 GLU Chi-restraints excluded: chain A residue 357 MET Chi-restraints excluded: chain A residue 403 LEU Chi-restraints excluded: chain A residue 419 ILE Chi-restraints excluded: chain A residue 433 ASP Chi-restraints excluded: chain A residue 438 ILE Chi-restraints excluded: chain A residue 450 LYS Chi-restraints excluded: chain A residue 483 VAL Chi-restraints excluded: chain A residue 551 VAL Chi-restraints excluded: chain A residue 666 VAL Chi-restraints excluded: chain A residue 678 VAL Chi-restraints excluded: chain A residue 685 SER Chi-restraints excluded: chain A residue 773 ASP Chi-restraints excluded: chain A residue 790 LYS Chi-restraints excluded: chain A residue 947 LEU Chi-restraints excluded: chain A residue 957 VAL Chi-restraints excluded: chain A residue 962 SER Chi-restraints excluded: chain A residue 1033 SER Chi-restraints excluded: chain A residue 1060 GLU Chi-restraints excluded: chain A residue 1118 VAL Chi-restraints excluded: chain A residue 1222 LEU Chi-restraints excluded: chain A residue 1238 MET Chi-restraints excluded: chain A residue 1491 GLU Chi-restraints excluded: chain A residue 1543 SER Chi-restraints excluded: chain A residue 1607 THR Chi-restraints excluded: chain A residue 1614 SER Chi-restraints excluded: chain A residue 1649 VAL Chi-restraints excluded: chain B residue 33 SER Chi-restraints excluded: chain B residue 38 LEU Chi-restraints excluded: chain B residue 75 ASP Chi-restraints excluded: chain B residue 121 VAL Chi-restraints excluded: chain B residue 249 VAL Chi-restraints excluded: chain B residue 295 ASN Chi-restraints excluded: chain B residue 306 LEU Chi-restraints excluded: chain B residue 343 ASP Chi-restraints excluded: chain B residue 374 LEU Chi-restraints excluded: chain B residue 409 TYR Chi-restraints excluded: chain B residue 421 LEU Chi-restraints excluded: chain B residue 424 ILE Chi-restraints excluded: chain B residue 453 VAL Chi-restraints excluded: chain B residue 455 GLU Chi-restraints excluded: chain B residue 462 GLN Chi-restraints excluded: chain B residue 472 SER Chi-restraints excluded: chain B residue 502 MET Chi-restraints excluded: chain B residue 516 THR Chi-restraints excluded: chain B residue 547 HIS Chi-restraints excluded: chain B residue 564 ILE Chi-restraints excluded: chain B residue 577 PHE Chi-restraints excluded: chain B residue 647 SER Chi-restraints excluded: chain B residue 712 SER Chi-restraints excluded: chain B residue 725 THR Chi-restraints excluded: chain B residue 739 ASN Chi-restraints excluded: chain B residue 789 ILE Chi-restraints excluded: chain B residue 819 ASP Chi-restraints excluded: chain B residue 835 GLU Chi-restraints excluded: chain B residue 900 THR Chi-restraints excluded: chain B residue 901 VAL Chi-restraints excluded: chain B residue 910 THR Chi-restraints excluded: chain B residue 918 SER Chi-restraints excluded: chain B residue 934 ILE Chi-restraints excluded: chain B residue 1069 ILE Chi-restraints excluded: chain B residue 1096 SER Chi-restraints excluded: chain B residue 1113 THR Chi-restraints excluded: chain B residue 1125 THR Chi-restraints excluded: chain B residue 1178 ILE Chi-restraints excluded: chain C residue 73 SER Chi-restraints excluded: chain C residue 151 THR Chi-restraints excluded: chain C residue 201 GLU Chi-restraints excluded: chain C residue 328 LEU Chi-restraints excluded: chain D residue 15 THR Chi-restraints excluded: chain D residue 99 LEU Chi-restraints excluded: chain E residue 178 ILE Chi-restraints excluded: chain E residue 199 ILE Chi-restraints excluded: chain E residue 202 SER Chi-restraints excluded: chain F residue 82 THR Chi-restraints excluded: chain F residue 89 GLU Chi-restraints excluded: chain G residue 47 VAL Chi-restraints excluded: chain G residue 69 LEU Chi-restraints excluded: chain G residue 104 LEU Chi-restraints excluded: chain G residue 110 ASP Chi-restraints excluded: chain G residue 226 ASP Chi-restraints excluded: chain H residue 87 ARG Chi-restraints excluded: chain H residue 100 THR Chi-restraints excluded: chain H residue 137 GLN Chi-restraints excluded: chain I residue 4 VAL Chi-restraints excluded: chain I residue 42 PHE Chi-restraints excluded: chain I residue 47 VAL Chi-restraints excluded: chain I residue 60 LEU Chi-restraints excluded: chain J residue 28 ASP Chi-restraints excluded: chain J residue 66 LEU Chi-restraints excluded: chain K residue 105 ILE Chi-restraints excluded: chain L residue 46 VAL Chi-restraints excluded: chain L residue 65 VAL Chi-restraints excluded: chain M residue 23 VAL Chi-restraints excluded: chain M residue 36 THR Chi-restraints excluded: chain M residue 66 THR Chi-restraints excluded: chain M residue 78 VAL Chi-restraints excluded: chain M residue 88 ILE Chi-restraints excluded: chain M residue 97 VAL Chi-restraints excluded: chain N residue 25 ILE Chi-restraints excluded: chain N residue 54 TRP Chi-restraints excluded: chain N residue 72 VAL Chi-restraints excluded: chain N residue 75 GLU Chi-restraints excluded: chain N residue 87 TYR Chi-restraints excluded: chain N residue 111 VAL Chi-restraints excluded: chain N residue 151 SER Chi-restraints excluded: chain N residue 155 VAL Chi-restraints excluded: chain N residue 160 VAL Chi-restraints excluded: chain N residue 168 LEU Chi-restraints excluded: chain N residue 173 THR Chi-restraints excluded: chain O residue 201 GLU Chi-restraints excluded: chain O residue 202 ILE Chi-restraints excluded: chain O residue 210 THR Chi-restraints excluded: chain O residue 254 ILE Chi-restraints excluded: chain O residue 300 LEU Chi-restraints excluded: chain O residue 344 ILE Chi-restraints excluded: chain O residue 353 ASP Chi-restraints excluded: chain O residue 384 ASP Chi-restraints excluded: chain O residue 434 ARG Chi-restraints excluded: chain O residue 442 LEU Chi-restraints excluded: chain O residue 480 VAL Chi-restraints excluded: chain O residue 569 VAL Chi-restraints excluded: chain O residue 601 ARG Chi-restraints excluded: chain O residue 688 ASP Chi-restraints excluded: chain P residue 95 LEU Chi-restraints excluded: chain P residue 184 TRP Chi-restraints excluded: chain P residue 201 LYS Chi-restraints excluded: chain P residue 262 LEU Chi-restraints excluded: chain P residue 304 LEU Chi-restraints excluded: chain P residue 356 VAL Chi-restraints excluded: chain P residue 378 LEU Chi-restraints excluded: chain P residue 437 THR Chi-restraints excluded: chain P residue 480 LEU Chi-restraints excluded: chain Q residue 10 ASN Chi-restraints excluded: chain Q residue 155 GLN Chi-restraints excluded: chain Q residue 158 THR Chi-restraints excluded: chain Q residue 168 ILE Chi-restraints excluded: chain Q residue 269 ASP Chi-restraints excluded: chain Q residue 411 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 556 random chunks: chunk 350 optimal weight: 8.9990 chunk 469 optimal weight: 20.0000 chunk 135 optimal weight: 4.9990 chunk 406 optimal weight: 10.0000 chunk 65 optimal weight: 1.9990 chunk 122 optimal weight: 10.0000 chunk 441 optimal weight: 0.6980 chunk 184 optimal weight: 0.9990 chunk 453 optimal weight: 50.0000 chunk 55 optimal weight: 4.9990 chunk 81 optimal weight: 10.0000 overall best weight: 2.7388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 383 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1116 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1319 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1438 ASN ** B 339 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 398 GLN ** B 555 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 720 GLN ** B 899 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1163 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 175 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 49 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 5 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 56 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 59 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 119 HIS ** H 137 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 16 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 34 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 270 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 109 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 145 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 209 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 272 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 351 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 435 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 497 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 150 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 212 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 286 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3906 r_free = 0.3906 target = 0.116723 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3235 r_free = 0.3235 target = 0.083849 restraints weight = 143767.991| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3295 r_free = 0.3295 target = 0.086574 restraints weight = 68749.057| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 25)----------------| | r_work = 0.3313 r_free = 0.3313 target = 0.087433 restraints weight = 40484.146| |-----------------------------------------------------------------------------| r_work (final): 0.3265 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7774 moved from start: 0.7155 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.068 47713 Z= 0.252 Angle : 0.807 15.708 64933 Z= 0.405 Chirality : 0.047 0.448 7264 Planarity : 0.006 0.127 7979 Dihedral : 14.017 154.531 7197 Min Nonbonded Distance : 2.029 Molprobity Statistics. All-atom Clashscore : 20.28 Ramachandran Plot: Outliers : 0.63 % Allowed : 7.66 % Favored : 91.72 % Rotamer: Outliers : 2.83 % Allowed : 24.90 % Favored : 72.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 1.24 % 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: -0.68 (0.12), residues: 5432 helix: 0.90 (0.12), residues: 2000 sheet: -0.77 (0.18), residues: 734 loop : -1.42 (0.12), residues: 2698 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.054 0.002 TRP Q 141 HIS 0.011 0.001 HIS P 157 PHE 0.072 0.002 PHE B1167 TYR 0.062 0.002 TYR Q 208 ARG 0.014 0.001 ARG A1105 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 14383.63 seconds wall clock time: 259 minutes 25.94 seconds (15565.94 seconds total)