Starting phenix.real_space_refine on Mon Mar 18 11:59:16 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7zsa_14928/03_2024/7zsa_14928_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7zsa_14928/03_2024/7zsa_14928.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.0 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7zsa_14928/03_2024/7zsa_14928.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7zsa_14928/03_2024/7zsa_14928.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7zsa_14928/03_2024/7zsa_14928_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7zsa_14928/03_2024/7zsa_14928_updated.pdb" } resolution = 4.0 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.001 sd= 0.006 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 8 Type Number sf(0) Gaussians Fe 4 7.16 5 Zn 17 6.06 5 P 417 5.49 5 Mg 1 5.21 5 S 412 5.16 5 C 53352 2.51 5 N 15110 2.21 5 O 17075 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A PHE 224": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 356": "OD1" <-> "OD2" Residue "A TYR 383": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 440": "OD1" <-> "OD2" Residue "A ASP 555": "OD1" <-> "OD2" Residue "A PHE 614": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 678": "OE1" <-> "OE2" Residue "A GLU 846": "OE1" <-> "OE2" Residue "A TYR 852": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 1337": "OE1" <-> "OE2" Residue "B PHE 166": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 186": "OE1" <-> "OE2" Residue "B ASP 188": "OD1" <-> "OD2" Residue "B TYR 190": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 407": "OD1" <-> "OD2" Residue "B TYR 486": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 526": "OE1" <-> "OE2" Residue "B TYR 666": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 668": "OD1" <-> "OD2" Residue "B TYR 833": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 890": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 980": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 997": "OE1" <-> "OE2" Residue "B PHE 1146": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 1149": "OE1" <-> "OE2" Residue "C TYR 180": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ASP 205": "OD1" <-> "OD2" Residue "E TYR 28": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E ASP 84": "OD1" <-> "OD2" Residue "E TYR 187": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F GLU 26": "OE1" <-> "OE2" Residue "F TYR 29": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F ASP 77": "OD1" <-> "OD2" Residue "F ASP 116": "OD1" <-> "OD2" Residue "F ASP 140": "OD1" <-> "OD2" Residue "G PHE 2": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G GLU 33": "OE1" <-> "OE2" Residue "G GLU 35": "OE1" <-> "OE2" Residue "G PHE 79": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G PHE 99": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G GLU 100": "OE1" <-> "OE2" Residue "H GLU 45": "OE1" <-> "OE2" Residue "H ASP 67": "OD1" <-> "OD2" Residue "H GLU 106": "OE1" <-> "OE2" Residue "J PHE 8": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K GLU 64": "OE1" <-> "OE2" Residue "K PHE 71": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K GLU 106": "OE1" <-> "OE2" Residue "L PHE 67": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "M GLU 141": "OE1" <-> "OE2" Residue "M PHE 289": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "R ASP 301": "OD1" <-> "OD2" Residue "R PHE 304": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "V ASP 109": "OD1" <-> "OD2" Residue "X TYR 324": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "0 PHE 3": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "0 TYR 59": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "0 GLU 119": "OE1" <-> "OE2" Residue "0 GLU 166": "OE1" <-> "OE2" Residue "0 ASP 255": "OD1" <-> "OD2" Residue "0 GLU 451": "OE1" <-> "OE2" Residue "0 GLU 578": "OE1" <-> "OE2" Residue "0 TYR 629": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "0 TYR 676": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "1 PHE 91": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "1 TYR 270": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "1 ASP 363": "OD1" <-> "OD2" Residue "1 ASP 373": "OD1" <-> "OD2" Residue "2 GLU 116": "OE1" <-> "OE2" Residue "2 GLU 144": "OE1" <-> "OE2" Residue "2 PHE 182": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "2 TYR 350": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "2 PHE 491": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "3 TYR 35": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "4 GLU 31": "OE1" <-> "OE2" Residue "4 TYR 85": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "4 ASP 113": "OD1" <-> "OD2" Residue "4 GLU 123": "OE1" <-> "OE2" Residue "4 PHE 191": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "4 TYR 193": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "4 PHE 201": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "4 ASP 211": "OD1" <-> "OD2" Residue "4 GLU 314": "OE1" <-> "OE2" Residue "5 ASP 37": "OD1" <-> "OD2" Residue "6 GLU 203": "OE1" <-> "OE2" Residue "6 ASP 252": "OD1" <-> "OD2" Residue "6 TYR 282": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "6 GLU 285": "OE1" <-> "OE2" Residue "6 GLU 446": "OE1" <-> "OE2" Residue "7 PHE 113": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "7 TYR 365": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "7 GLU 542": "OE1" <-> "OE2" Residue "7 TYR 581": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "7 TYR 618": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "7 TYR 628": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "a TYR 41": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "a GLU 50": "OE1" <-> "OE2" Residue "a TYR 54": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "a GLU 73": "OE1" <-> "OE2" Residue "a TYR 99": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "b GLU 74": "OE1" <-> "OE2" Residue "c TYR 39": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "c GLU 41": "OE1" <-> "OE2" Residue "c GLU 91": "OE1" <-> "OE2" Residue "e TYR 41": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "e GLU 50": "OE1" <-> "OE2" Residue "e GLU 94": "OE1" <-> "OE2" Residue "f GLU 52": "OE1" <-> "OE2" Residue "f GLU 53": "OE1" <-> "OE2" Residue "f GLU 63": "OE1" <-> "OE2" Residue "f ASP 68": "OD1" <-> "OD2" Residue "f GLU 74": "OE1" <-> "OE2" Residue "g GLU 56": "OE1" <-> "OE2" Residue "g GLU 64": "OE1" <-> "OE2" Residue "g GLU 92": "OE1" <-> "OE2" Residue "h GLU 68": "OE1" <-> "OE2" Residue "h GLU 73": "OE1" <-> "OE2" Time to flip residues: 0.19s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib" Total number of atoms: 86388 Number of models: 1 Model: "" Number of chains: 50 Chain: "A" Number of atoms: 11221 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1426, 11221 Classifications: {'peptide': 1426} Link IDs: {'PCIS': 3, 'PTRANS': 63, 'TRANS': 1359} Chain breaks: 3 Chain: "B" Number of atoms: 9404 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1180, 9404 Classifications: {'peptide': 1180} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 52, 'TRANS': 1127} Chain breaks: 5 Chain: "C" Number of atoms: 2092 Number of conformers: 1 Conformer: "" Number of residues, atoms: 266, 2092 Classifications: {'peptide': 266} Link IDs: {'PTRANS': 11, 'TRANS': 254} Chain: "D" Number of atoms: 1343 Number of conformers: 1 Conformer: "" Number of residues, atoms: 167, 1343 Classifications: {'peptide': 167} Link IDs: {'PTRANS': 2, 'TRANS': 164} Chain breaks: 1 Chain: "E" Number of atoms: 1752 Number of conformers: 1 Conformer: "" Number of residues, atoms: 214, 1752 Classifications: {'peptide': 214} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 11, 'TRANS': 201} Chain: "F" Number of atoms: 977 Number of conformers: 1 Conformer: "" Number of residues, atoms: 118, 977 Classifications: {'peptide': 118} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 7, 'TRANS': 110} Chain breaks: 1 Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 7 Unresolved non-hydrogen dihedrals: 5 Planarities with less than four sites: {'ARG:plan': 1} Unresolved non-hydrogen planarities: 5 Chain: "G" Number of atoms: 1339 Number of conformers: 1 Conformer: "" Number of residues, atoms: 171, 1339 Classifications: {'peptide': 171} Link IDs: {'PCIS': 1, 'PTRANS': 7, 'TRANS': 162} Chain: "H" Number of atoms: 1120 Number of conformers: 1 Conformer: "" Number of residues, atoms: 140, 1120 Classifications: {'peptide': 140} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 5, 'TRANS': 134} Chain breaks: 1 Chain: "I" Number of atoms: 944 Number of conformers: 1 Conformer: "" Number of residues, atoms: 116, 944 Classifications: {'peptide': 116} Link IDs: {'PTRANS': 5, 'TRANS': 110} 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: 924 Number of conformers: 1 Conformer: "" Number of residues, atoms: 115, 924 Classifications: {'peptide': 115} Link IDs: {'PTRANS': 5, 'TRANS': 109} 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: 2379 Number of conformers: 1 Conformer: "" Number of residues, atoms: 310, 2379 Classifications: {'peptide': 310} Link IDs: {'PCIS': 1, 'PTRANS': 11, 'TRANS': 297} Chain breaks: 1 Chain: "N" Number of atoms: 4263 Number of conformers: 1 Conformer: "" Number of residues, atoms: 209, 4263 Classifications: {'DNA': 209} Modifications used: {'5*END': 1} Link IDs: {'rna3p': 208} Chain: "O" Number of atoms: 1422 Number of conformers: 1 Conformer: "" Number of residues, atoms: 181, 1422 Classifications: {'peptide': 181} Link IDs: {'PCIS': 1, 'PTRANS': 7, 'TRANS': 172} Chain: "Q" Number of atoms: 1871 Number of conformers: 1 Conformer: "" Number of residues, atoms: 221, 1871 Classifications: {'peptide': 221} Link IDs: {'PCIS': 1, 'PTRANS': 8, 'TRANS': 211} Chain breaks: 2 Chain: "R" Number of atoms: 2230 Number of conformers: 1 Conformer: "" Number of residues, atoms: 268, 2230 Classifications: {'peptide': 268} Link IDs: {'PTRANS': 10, 'TRANS': 257} Chain breaks: 1 Chain: "T" Number of atoms: 4303 Number of conformers: 1 Conformer: "" Number of residues, atoms: 209, 4303 Classifications: {'DNA': 209} Link IDs: {'rna3p': 208} Chain: "U" Number of atoms: 885 Number of conformers: 1 Conformer: "" Number of residues, atoms: 107, 885 Classifications: {'peptide': 107} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 105} Chain breaks: 2 Chain: "V" Number of atoms: 815 Number of conformers: 1 Conformer: "" Number of residues, atoms: 104, 815 Classifications: {'peptide': 104} Link IDs: {'TRANS': 103} Chain breaks: 1 Chain: "W" Number of atoms: 2473 Number of conformers: 1 Conformer: "" Number of residues, atoms: 304, 2473 Classifications: {'peptide': 304} Link IDs: {'PTRANS': 13, 'TRANS': 290} Chain breaks: 3 Chain: "X" Number of atoms: 1708 Number of conformers: 1 Conformer: "" Number of residues, atoms: 211, 1708 Classifications: {'peptide': 211} Link IDs: {'PTRANS': 9, 'TRANS': 201} Chain breaks: 1 Chain: "0" Number of atoms: 6091 Number of conformers: 1 Conformer: "" Number of residues, atoms: 752, 6091 Classifications: {'peptide': 752} Link IDs: {'PCIS': 1, 'PTRANS': 31, 'TRANS': 719} Chain: "1" Number of atoms: 4214 Number of conformers: 1 Conformer: "" Number of residues, atoms: 522, 4214 Classifications: {'peptide': 522} Link IDs: {'PCIS': 1, 'PTRANS': 17, 'TRANS': 503} Chain breaks: 6 Chain: "2" Number of atoms: 3647 Number of conformers: 1 Conformer: "" Number of residues, atoms: 452, 3647 Classifications: {'peptide': 452} Link IDs: {'PTRANS': 17, 'TRANS': 434} Chain breaks: 1 Chain: "3" Number of atoms: 1089 Number of conformers: 1 Conformer: "" Number of residues, atoms: 131, 1089 Classifications: {'peptide': 131} Link IDs: {'PTRANS': 5, 'TRANS': 125} Chain: "4" Number of atoms: 2329 Number of conformers: 1 Conformer: "" Number of residues, atoms: 301, 2329 Classifications: {'peptide': 301} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PCIS': 1, 'PTRANS': 12, 'TRANS': 287} Chain breaks: 2 Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 3 Unresolved non-hydrogen dihedrals: 1 Unresolved non-hydrogen chiralities: 1 Chain: "5" Number of atoms: 514 Number of conformers: 1 Conformer: "" Number of residues, atoms: 65, 514 Classifications: {'peptide': 65} Link IDs: {'PTRANS': 3, 'TRANS': 61} Chain: "6" Number of atoms: 3019 Number of conformers: 1 Conformer: "" Number of residues, atoms: 383, 3019 Classifications: {'peptide': 383} Link IDs: {'PCIS': 2, 'PTRANS': 19, 'TRANS': 361} Chain breaks: 1 Chain: "7" Number of atoms: 4961 Number of conformers: 1 Conformer: "" Number of residues, atoms: 616, 4961 Classifications: {'peptide': 616} Link IDs: {'PTRANS': 25, 'TRANS': 590} Chain breaks: 2 Chain: "a" Number of atoms: 826 Number of conformers: 1 Conformer: "" Number of residues, atoms: 100, 826 Classifications: {'peptide': 100} Link IDs: {'PTRANS': 4, 'TRANS': 95} Chain: "b" Number of atoms: 657 Number of conformers: 1 Conformer: "" Number of residues, atoms: 82, 657 Classifications: {'peptide': 82} Link IDs: {'PTRANS': 1, 'TRANS': 80} Chain: "c" Number of atoms: 823 Number of conformers: 1 Conformer: "" Number of residues, atoms: 107, 823 Classifications: {'peptide': 107} Link IDs: {'PTRANS': 5, 'TRANS': 101} Chain: "d" Number of atoms: 736 Number of conformers: 1 Conformer: "" Number of residues, atoms: 94, 736 Classifications: {'peptide': 94} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 2, 'TRANS': 91} Chain: "e" Number of atoms: 810 Number of conformers: 1 Conformer: "" Number of residues, atoms: 98, 810 Classifications: {'peptide': 98} Link IDs: {'PTRANS': 4, 'TRANS': 93} Chain: "f" Number of atoms: 694 Number of conformers: 1 Conformer: "" Number of residues, atoms: 86, 694 Classifications: {'peptide': 86} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 84} Chain: "g" Number of atoms: 823 Number of conformers: 1 Conformer: "" Number of residues, atoms: 107, 823 Classifications: {'peptide': 107} Link IDs: {'PTRANS': 5, 'TRANS': 101} Chain: "h" Number of atoms: 736 Number of conformers: 1 Conformer: "" Number of residues, atoms: 94, 736 Classifications: {'peptide': 94} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 2, 'TRANS': 91} Chain: "A" Number of atoms: 3 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 3 Unusual residues: {' MG': 1, ' ZN': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "B" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} Chain: "C" 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: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Unusual residues: {' ZN': 2} Classifications: {'undetermined': 2} Link IDs: {None: 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} Chain: "M" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} Chain: "W" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} Chain: "0" Number of atoms: 8 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 8 Unusual residues: {'SF4': 1} Classifications: {'undetermined': 1} Chain: "3" 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: "4" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} Chain: "6" Number of atoms: 4 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 4 Unusual residues: {' ZN': 4} Classifications: {'undetermined': 4} Link IDs: {None: 3} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 820 SG CYS A 107 98.850 117.338 129.485 1.00111.92 S ATOM 844 SG CYS A 110 101.868 119.505 128.988 1.00 92.80 S ATOM 1149 SG CYS A 148 98.504 121.060 129.832 1.00110.41 S ATOM 1287 SG CYS A 167 99.083 119.532 126.347 1.00106.70 S ATOM 515 SG CYS A 67 125.401 83.459 148.066 1.00 92.21 S ATOM 537 SG CYS A 70 127.308 84.852 151.035 1.00 93.03 S ATOM 590 SG CYS A 77 123.652 83.892 151.410 1.00 41.96 S ATOM 20131 SG CYS B1163 126.772 101.397 151.018 1.00 30.49 S ATOM 20149 SG CYS B1166 123.274 100.561 149.670 1.00 29.85 S ATOM 20274 SG CYS B1182 126.316 98.763 148.345 1.00 45.85 S ATOM 20293 SG CYS B1185 125.685 102.384 147.441 1.00 56.96 S ATOM 21278 SG CYS C 86 120.664 39.444 199.533 1.00 88.98 S ATOM 21295 SG CYS C 88 120.884 38.020 196.031 1.00103.39 S ATOM 21328 SG CYS C 92 119.373 35.989 198.048 1.00 61.86 S ATOM 21351 SG CYS C 95 117.331 39.079 197.550 1.00 59.89 S ATOM 29301 SG CYS I 7 31.543 99.116 135.696 1.00 87.81 S ATOM 29326 SG CYS I 10 34.763 97.911 133.908 1.00 91.12 S ATOM 29492 SG CYS I 29 34.733 101.327 135.283 1.00 96.92 S ATOM 29516 SG CYS I 32 32.387 100.437 132.349 1.00 94.49 S ATOM 29843 SG CYS I 75 27.276 85.328 176.984 1.00 84.45 S ATOM 29865 SG CYS I 78 24.808 82.354 177.128 1.00 87.84 S ATOM 30081 SG CYS I 103 28.237 81.886 175.648 1.00 87.90 S ATOM 30101 SG CYS I 106 25.534 83.955 173.873 1.00 83.07 S ATOM 30246 SG CYS J 7 87.385 49.958 199.374 1.00 25.04 S ATOM 30269 SG CYS J 10 88.536 48.717 202.610 1.00 16.74 S ATOM 30549 SG CYS J 45 85.639 51.173 202.623 1.00 53.41 S ATOM 30555 SG CYS J 46 85.709 47.326 201.990 1.00 23.22 S ATOM 31735 SG CYS L 31 94.138 35.074 158.524 1.00 40.58 S ATOM 31755 SG CYS L 34 93.621 31.387 159.141 1.00 58.94 S ATOM 31859 SG CYS L 48 96.022 32.481 156.441 1.00 66.01 S ATOM 31882 SG CYS L 51 92.263 33.086 155.979 1.00 83.31 S ATOM 32126 SG CYS M 24 136.125 68.244 166.570 1.00 57.64 S ATOM 32148 SG CYS M 27 137.572 65.140 168.291 1.00 80.82 S ATOM 32292 SG CYS M 45 133.930 65.152 167.222 1.00 65.38 S ATOM 32311 SG CYS M 48 135.228 67.419 170.088 1.00 57.49 S ATOM 51222 SG CYS W 124 139.215 79.892 137.565 1.00101.81 S ATOM 51243 SG CYS W 127 136.588 80.419 138.324 1.00108.81 S ATOM 51448 SG CYS W 152 136.873 77.707 140.097 1.00102.87 S ATOM 55331 SG CYS 0 115 145.025 147.840 71.418 1.00 49.08 S ATOM 55658 SG CYS 0 156 150.363 147.176 68.084 1.00 83.31 S ATOM 55473 SG CYS 0 133 150.669 147.718 74.786 1.00 57.66 S ATOM 55959 SG CYS 0 191 150.002 152.334 71.116 1.00 59.92 S ATOM 68384 SG CYS 3 13 141.882 110.471 112.069 1.00 71.97 S ATOM 68405 SG CYS 3 16 138.783 108.818 113.583 1.00 76.42 S ATOM 68600 SG CYS 3 39 140.499 111.400 115.546 1.00 64.50 S ATOM 68621 SG CYS 3 42 142.101 108.028 115.148 1.00 73.14 S ATOM 68553 SG CYS 3 34 154.634 111.198 111.420 1.00 92.50 S ATOM 68711 SG CYS 3 54 151.949 108.452 111.334 1.00 93.76 S ATOM 68749 SG CYS 3 59 155.208 107.937 109.442 1.00 82.98 S ATOM 71468 SG CYS 4 289 106.191 192.282 41.445 1.00 23.40 S ATOM 71487 SG CYS 4 292 106.396 195.617 42.486 1.00 34.26 S ATOM 71579 SG CYS 4 305 108.018 194.588 39.028 1.00 53.92 S ATOM 71597 SG CYS 4 308 109.788 193.925 42.131 1.00 46.80 S ATOM 74424 SG CYS 6 349 88.969 182.915 32.649 1.00 24.85 S ATOM 74445 SG CYS 6 352 87.825 179.769 30.742 1.00 31.38 S ATOM 74524 SG CYS 6 363 88.315 179.537 34.416 1.00 20.95 S ATOM 74543 SG CYS 6 366 91.285 179.854 32.179 1.00 23.76 S ATOM 74845 SG CYS 6 403 94.015 213.856 65.372 1.00 53.11 S ATOM 74868 SG CYS 6 406 90.458 212.887 66.440 1.00 33.97 S ATOM 75127 SG CYS 6 437 93.392 211.473 68.329 1.00 55.26 S ATOM 75148 SG CYS 6 440 92.825 210.319 64.827 1.00 41.61 S ATOM 75060 SG CYS 6 429 103.581 210.489 59.092 1.00 67.05 S ATOM 75083 SG CYS 6 432 102.045 213.734 57.910 1.00 66.96 S ATOM 75241 SG CYS 6 451 99.866 210.727 58.285 1.00 39.33 S ATOM 75258 SG CYS 6 454 102.404 210.766 55.471 1.00 47.62 S ATOM 74335 SG CYS 6 338 82.398 177.088 40.943 1.00 38.45 S ATOM 74483 SG CYS 6 357 79.526 178.931 41.615 1.00 23.83 S Time building chain proxies: 33.75, per 1000 atoms: 0.39 Number of scatterers: 86388 At special positions: 0 Unit cell: (186.9, 311.85, 254.1, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 8 Type Number sf(0) Zn 17 29.99 Fe 4 26.01 S 412 16.00 P 417 15.00 Mg 1 11.99 O 17075 8.00 N 15110 7.00 C 53352 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: 29.36 Conformation dependent library (CDL) restraints added in 11.5 seconds Dynamic metal coordination Iron sulfur cluster coordination pdb=" SF4 0 801 " pdb="FE4 SF4 0 801 " - pdb=" SG CYS 0 191 " pdb="FE1 SF4 0 801 " - pdb=" SG CYS 0 115 " pdb="FE3 SF4 0 801 " - pdb=" SG CYS 0 133 " pdb="FE2 SF4 0 801 " - pdb=" SG CYS 0 156 " Number of angles added : 12 Zn2+ tetrahedral coordination pdb=" ZN 3 401 " pdb="ZN ZN 3 401 " - pdb=" SG CYS 3 16 " pdb="ZN ZN 3 401 " - pdb=" SG CYS 3 39 " pdb="ZN ZN 3 401 " - pdb=" SG CYS 3 42 " pdb="ZN ZN 3 401 " - pdb=" SG CYS 3 13 " pdb=" ZN 3 402 " pdb="ZN ZN 3 402 " - pdb=" NE2 HIS 3 36 " pdb="ZN ZN 3 402 " - pdb=" SG CYS 3 54 " pdb="ZN ZN 3 402 " - pdb=" SG CYS 3 59 " pdb="ZN ZN 3 402 " - pdb=" SG CYS 3 34 " pdb=" ZN 4 401 " pdb="ZN ZN 4 401 " - pdb=" SG CYS 4 292 " pdb="ZN ZN 4 401 " - pdb=" SG CYS 4 289 " pdb="ZN ZN 4 401 " - pdb=" SG CYS 4 305 " pdb="ZN ZN 4 401 " - pdb=" SG CYS 4 308 " pdb=" ZN 6 501 " pdb="ZN ZN 6 501 " - pdb=" SG CYS 6 366 " pdb="ZN ZN 6 501 " - pdb=" SG CYS 6 352 " pdb="ZN ZN 6 501 " - pdb=" SG CYS 6 363 " pdb="ZN ZN 6 501 " - pdb=" SG CYS 6 349 " pdb=" ZN 6 502 " pdb="ZN ZN 6 502 " - pdb=" SG CYS 6 440 " pdb="ZN ZN 6 502 " - pdb=" SG CYS 6 437 " pdb="ZN ZN 6 502 " - pdb=" SG CYS 6 406 " pdb="ZN ZN 6 502 " - pdb=" SG CYS 6 403 " pdb=" ZN 6 503 " pdb="ZN ZN 6 503 " - pdb=" SG CYS 6 451 " pdb="ZN ZN 6 503 " - pdb=" SG CYS 6 432 " pdb="ZN ZN 6 503 " - pdb=" SG CYS 6 429 " pdb="ZN ZN 6 503 " - pdb=" SG CYS 6 454 " pdb=" ZN 6 504 " pdb="ZN ZN 6 504 " - pdb=" SG CYS 6 357 " pdb="ZN ZN 6 504 " - pdb=" SG CYS 6 338 " pdb="ZN ZN 6 504 " - pdb=" ND1 HIS 6 339 " pdb=" ZN A1801 " pdb="ZN ZN A1801 " - pdb=" SG CYS A 107 " pdb="ZN ZN A1801 " - pdb=" SG CYS A 110 " pdb="ZN ZN A1801 " - pdb=" SG CYS A 148 " pdb="ZN ZN A1801 " - pdb=" SG CYS A 167 " pdb=" ZN A1802 " pdb="ZN ZN A1802 " - pdb=" NE2 HIS A 80 " pdb="ZN ZN A1802 " - pdb=" SG CYS A 70 " pdb="ZN ZN A1802 " - pdb=" SG CYS A 67 " pdb="ZN ZN A1802 " - pdb=" SG CYS A 77 " pdb=" ZN B1301 " pdb="ZN ZN B1301 " - pdb=" SG CYS B1166 " pdb="ZN ZN B1301 " - pdb=" SG CYS B1182 " pdb="ZN ZN B1301 " - pdb=" SG CYS B1185 " pdb="ZN ZN B1301 " - pdb=" SG CYS B1163 " pdb=" ZN C 401 " pdb="ZN ZN C 401 " - pdb=" SG CYS C 92 " pdb="ZN ZN C 401 " - pdb=" SG CYS C 88 " pdb="ZN ZN C 401 " - pdb=" SG CYS C 95 " pdb="ZN ZN C 401 " - pdb=" SG CYS C 86 " pdb=" ZN I 201 " pdb="ZN ZN I 201 " - pdb=" SG CYS I 10 " pdb="ZN ZN I 201 " - pdb=" SG CYS I 32 " pdb="ZN ZN I 201 " - pdb=" SG CYS I 29 " pdb="ZN ZN I 201 " - pdb=" SG CYS I 7 " pdb=" ZN I 202 " pdb="ZN ZN I 202 " - pdb=" SG CYS I 106 " pdb="ZN ZN I 202 " - pdb=" SG CYS I 78 " pdb="ZN ZN I 202 " - pdb=" SG CYS I 103 " pdb="ZN ZN I 202 " - pdb=" SG CYS I 75 " pdb=" ZN J 101 " pdb="ZN ZN J 101 " - pdb=" SG CYS J 10 " pdb="ZN ZN J 101 " - pdb=" SG CYS J 46 " pdb="ZN ZN J 101 " - pdb=" SG CYS J 45 " pdb="ZN ZN J 101 " - pdb=" SG CYS J 7 " pdb=" ZN L 101 " pdb="ZN ZN L 101 " - pdb=" SG CYS L 31 " 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 48 " pdb=" ZN M 401 " pdb="ZN ZN M 401 " - pdb=" SG CYS M 48 " pdb="ZN ZN M 401 " - pdb=" SG CYS M 27 " pdb="ZN ZN M 401 " - pdb=" SG CYS M 24 " pdb="ZN ZN M 401 " - pdb=" SG CYS M 45 " pdb=" ZN W 501 " pdb="ZN ZN W 501 " - pdb=" SG CYS W 124 " pdb="ZN ZN W 501 " - pdb=" SG CYS W 152 " pdb="ZN ZN W 501 " - pdb=" SG CYS W 127 " Number of angles added : 84 19166 Ramachandran restraints generated. 9583 Oldfield, 0 Emsley, 9583 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 18464 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 360 helices and 72 sheets defined 39.8% alpha, 11.2% beta 141 base pairs and 352 stacking pairs defined. Time for finding SS restraints: 31.41 Creating SS restraints... Processing helix chain 'A' and resid 24 through 30 Processing helix chain 'A' and resid 93 through 104 removed outlier: 3.777A pdb=" N ILE A 96 " --> pdb=" O VAL A 93 " (cutoff:3.500A) removed outlier: 6.119A pdb=" N ALA A 97 " --> pdb=" O GLY A 94 " (cutoff:3.500A) Processing helix chain 'A' and resid 120 through 126 Processing helix chain 'A' and resid 131 through 142 Processing helix chain 'A' and resid 204 through 213 Processing helix chain 'A' and resid 216 through 221 Processing helix chain 'A' and resid 231 through 233 No H-bonds generated for 'chain 'A' and resid 231 through 233' Processing helix chain 'A' and resid 261 through 281 Processing helix chain 'A' and resid 286 through 304 Processing helix chain 'A' and resid 325 through 329 Processing helix chain 'A' and resid 335 through 339 Processing helix chain 'A' and resid 368 through 373 Processing helix chain 'A' and resid 382 through 394 removed outlier: 4.094A pdb=" N ILE A 385 " --> pdb=" O PRO A 382 " (cutoff:3.500A) removed outlier: 5.896A pdb=" N ASP A 386 " --> pdb=" O TYR A 383 " (cutoff:3.500A) removed outlier: 3.869A pdb=" N ARG A 387 " --> pdb=" O ASN A 384 " (cutoff:3.500A) removed outlier: 3.605A pdb=" N LEU A 388 " --> pdb=" O ILE A 385 " (cutoff:3.500A) Processing helix chain 'A' and resid 452 through 454 No H-bonds generated for 'chain 'A' and resid 452 through 454' Processing helix chain 'A' and resid 472 through 475 Processing helix chain 'A' and resid 495 through 504 Processing helix chain 'A' and resid 508 through 510 No H-bonds generated for 'chain 'A' and resid 508 through 510' Processing helix chain 'A' and resid 525 through 534 removed outlier: 3.576A pdb=" N ARG A 532 " --> pdb=" O LEU A 528 " (cutoff:3.500A) Processing helix chain 'A' and resid 543 through 551 removed outlier: 4.231A pdb=" N ASN A 548 " --> pdb=" O ASP A 544 " (cutoff:3.500A) Processing helix chain 'A' and resid 574 through 581 removed outlier: 3.680A pdb=" N VAL A 580 " --> pdb=" O GLN A 576 " (cutoff:3.500A) removed outlier: 4.108A pdb=" N ALA A 581 " --> pdb=" O ILE A 577 " (cutoff:3.500A) Processing helix chain 'A' and resid 629 through 636 Processing helix chain 'A' and resid 639 through 660 Processing helix chain 'A' and resid 666 through 669 Processing helix chain 'A' and resid 673 through 698 Processing helix chain 'A' and resid 710 through 736 Processing helix chain 'A' and resid 742 through 749 Processing helix chain 'A' and resid 755 through 762 Processing helix chain 'A' and resid 794 through 796 No H-bonds generated for 'chain 'A' and resid 794 through 796' Processing helix chain 'A' and resid 810 through 844 Processing helix chain 'A' and resid 868 through 870 No H-bonds generated for 'chain 'A' and resid 868 through 870' Processing helix chain 'A' and resid 875 through 877 No H-bonds generated for 'chain 'A' and resid 875 through 877' Processing helix chain 'A' and resid 890 through 897 Processing helix chain 'A' and resid 910 through 912 No H-bonds generated for 'chain 'A' and resid 910 through 912' Processing helix chain 'A' and resid 924 through 946 Processing helix chain 'A' and resid 960 through 970 Processing helix chain 'A' and resid 983 through 996 removed outlier: 3.600A pdb=" N GLN A 994 " --> pdb=" O VAL A 990 " (cutoff:3.500A) removed outlier: 3.716A pdb=" N GLU A 995 " --> pdb=" O LYS A 991 " (cutoff:3.500A) Processing helix chain 'A' and resid 1005 through 1025 removed outlier: 5.384A pdb=" N LEU A1017 " --> pdb=" O ASP A1013 " (cutoff:3.500A) removed outlier: 5.309A pdb=" N PHE A1018 " --> pdb=" O ALA A1014 " (cutoff:3.500A) Processing helix chain 'A' and resid 1028 through 1033 Processing helix chain 'A' and resid 1039 through 1055 Processing helix chain 'A' and resid 1064 through 1077 Proline residue: A1075 - end of helix Processing helix chain 'A' and resid 1098 through 1105 Processing helix chain 'A' and resid 1122 through 1124 No H-bonds generated for 'chain 'A' and resid 1122 through 1124' Processing helix chain 'A' and resid 1128 through 1138 Processing helix chain 'A' and resid 1164 through 1176 removed outlier: 3.763A pdb=" N GLU A1167 " --> pdb=" O PRO A1164 " (cutoff:3.500A) removed outlier: 5.738A pdb=" N GLU A1168 " --> pdb=" O GLU A1165 " (cutoff:3.500A) removed outlier: 4.024A pdb=" N ILE A1169 " --> pdb=" O ASP A1166 " (cutoff:3.500A) removed outlier: 4.022A pdb=" N ILE A1170 " --> pdb=" O GLU A1167 " (cutoff:3.500A) removed outlier: 4.300A pdb=" N GLN A1171 " --> pdb=" O GLU A1168 " (cutoff:3.500A) Processing helix chain 'A' and resid 1185 through 1187 No H-bonds generated for 'chain 'A' and resid 1185 through 1187' Processing helix chain 'A' and resid 1199 through 1204 Processing helix chain 'A' and resid 1209 through 1219 Processing helix chain 'A' and resid 1256 through 1268 Processing helix chain 'A' and resid 1332 through 1338 Processing helix chain 'A' and resid 1341 through 1358 Processing helix chain 'A' and resid 1365 through 1375 Processing helix chain 'A' and resid 1389 through 1391 No H-bonds generated for 'chain 'A' and resid 1389 through 1391' Processing helix chain 'A' and resid 1396 through 1402 removed outlier: 3.893A pdb=" N PHE A1402 " --> pdb=" O MET A1398 " (cutoff:3.500A) Processing helix chain 'A' and resid 1405 through 1415 Processing helix chain 'A' and resid 1424 through 1430 Processing helix chain 'A' and resid 1437 through 1439 No H-bonds generated for 'chain 'A' and resid 1437 through 1439' Processing helix chain 'A' and resid 1448 through 1453 Processing helix chain 'B' and resid 27 through 40 removed outlier: 3.937A pdb=" N TRP B 31 " --> pdb=" O ALA B 27 " (cutoff:3.500A) removed outlier: 4.321A pdb=" N ALA B 32 " --> pdb=" O GLU B 28 " (cutoff:3.500A) removed outlier: 3.882A pdb=" N VAL B 33 " --> pdb=" O ASP B 29 " (cutoff:3.500A) Processing helix chain 'B' and resid 45 through 56 Processing helix chain 'B' and resid 58 through 65 Processing helix chain 'B' and resid 114 through 119 Processing helix chain 'B' and resid 186 through 191 Processing helix chain 'B' and resid 282 through 288 Processing helix chain 'B' and resid 294 through 301 Processing helix chain 'B' and resid 308 through 320 Proline residue: B 316 - end of helix Processing helix chain 'B' and resid 327 through 337 removed outlier: 4.672A pdb=" N ARG B 337 " --> pdb=" O PHE B 333 " (cutoff:3.500A) Processing helix chain 'B' and resid 348 through 358 Processing helix chain 'B' and resid 371 through 389 Processing helix chain 'B' and resid 401 through 403 No H-bonds generated for 'chain 'B' and resid 401 through 403' Processing helix chain 'B' and resid 409 through 438 Processing helix chain 'B' and resid 444 through 447 No H-bonds generated for 'chain 'B' and resid 444 through 447' Processing helix chain 'B' and resid 450 through 462 Processing helix chain 'B' and resid 488 through 495 Processing helix chain 'B' and resid 516 through 518 No H-bonds generated for 'chain 'B' and resid 516 through 518' Processing helix chain 'B' and resid 552 through 559 Processing helix chain 'B' and resid 566 through 568 No H-bonds generated for 'chain 'B' and resid 566 through 568' Processing helix chain 'B' and resid 593 through 605 Processing helix chain 'B' and resid 655 through 668 Processing helix chain 'B' and resid 681 through 686 Processing helix chain 'B' and resid 697 through 700 Processing helix chain 'B' and resid 745 through 748 Processing helix chain 'B' and resid 759 through 761 No H-bonds generated for 'chain 'B' and resid 759 through 761' Processing helix chain 'B' and resid 764 through 771 Processing helix chain 'B' and resid 774 through 776 No H-bonds generated for 'chain 'B' and resid 774 through 776' Processing helix chain 'B' and resid 808 through 811 No H-bonds generated for 'chain 'B' and resid 808 through 811' Processing helix chain 'B' and resid 843 through 847 Processing helix chain 'B' and resid 1014 through 1019 Proline residue: B1018 - end of helix Processing helix chain 'B' and resid 1024 through 1038 Processing helix chain 'B' and resid 1052 through 1061 Processing helix chain 'B' and resid 1099 through 1101 No H-bonds generated for 'chain 'B' and resid 1099 through 1101' Processing helix chain 'B' and resid 1132 through 1141 Processing helix chain 'B' and resid 1145 through 1151 Processing helix chain 'B' and resid 1198 through 1209 Processing helix chain 'C' and resid 27 through 39 Processing helix chain 'C' and resid 60 through 68 Processing helix chain 'C' and resid 115 through 117 No H-bonds generated for 'chain 'C' and resid 115 through 117' Processing helix chain 'C' and resid 168 through 170 No H-bonds generated for 'chain 'C' and resid 168 through 170' Processing helix chain 'C' and resid 205 through 209 removed outlier: 3.880A pdb=" N GLU C 208 " --> pdb=" O LYS C 205 " (cutoff:3.500A) Processing helix chain 'C' and resid 240 through 266 removed outlier: 3.736A pdb=" N VAL C 244 " --> pdb=" O VAL C 240 " (cutoff:3.500A) Processing helix chain 'D' and resid 52 through 71 Processing helix chain 'D' and resid 119 through 133 Processing helix chain 'D' and resid 139 through 151 Processing helix chain 'D' and resid 157 through 170 removed outlier: 3.951A pdb=" N SER D 169 " --> pdb=" O GLN D 165 " (cutoff:3.500A) removed outlier: 4.321A pdb=" N THR D 170 " --> pdb=" O LEU D 166 " (cutoff:3.500A) Processing helix chain 'D' and resid 174 through 182 Processing helix chain 'D' and resid 188 through 194 Processing helix chain 'D' and resid 196 through 198 No H-bonds generated for 'chain 'D' and resid 196 through 198' Processing helix chain 'D' and resid 204 through 217 Processing helix chain 'E' and resid 3 through 25 Processing helix chain 'E' and resid 32 through 35 No H-bonds generated for 'chain 'E' and resid 32 through 35' Processing helix chain 'E' and resid 39 through 45 Processing helix chain 'E' and resid 66 through 71 Processing helix chain 'E' and resid 90 through 103 Processing helix chain 'E' and resid 118 through 121 No H-bonds generated for 'chain 'E' and resid 118 through 121' Processing helix chain 'E' and resid 138 through 140 No H-bonds generated for 'chain 'E' and resid 138 through 140' Processing helix chain 'E' and resid 144 through 146 No H-bonds generated for 'chain 'E' and resid 144 through 146' Processing helix chain 'E' and resid 158 through 167 Processing helix chain 'E' and resid 183 through 188 Processing helix chain 'F' and resid 25 through 31 Processing helix chain 'F' and resid 76 through 78 No H-bonds generated for 'chain 'F' and resid 76 through 78' Processing helix chain 'F' and resid 87 through 102 Processing helix chain 'F' and resid 117 through 126 Processing helix chain 'G' and resid 15 through 17 No H-bonds generated for 'chain 'G' and resid 15 through 17' Processing helix chain 'G' and resid 22 through 32 Processing helix chain 'H' and resid 89 through 92 Processing helix chain 'H' and resid 129 through 132 No H-bonds generated for 'chain 'H' and resid 129 through 132' Processing helix chain 'I' and resid 62 through 64 No H-bonds generated for 'chain 'I' and resid 62 through 64' Processing helix chain 'J' and resid 15 through 27 removed outlier: 4.097A pdb=" N TRP J 18 " --> pdb=" O GLY J 15 " (cutoff:3.500A) removed outlier: 4.835A pdb=" N GLU J 19 " --> pdb=" O ASP J 16 " (cutoff:3.500A) removed outlier: 4.264A pdb=" N SER J 20 " --> pdb=" O LYS J 17 " (cutoff:3.500A) removed outlier: 4.312A pdb=" N GLU J 27 " --> pdb=" O LEU J 24 " (cutoff:3.500A) Processing helix chain 'J' and resid 32 through 38 Processing helix chain 'J' and resid 44 through 51 removed outlier: 3.816A pdb=" N MET J 49 " --> pdb=" O CYS J 45 " (cutoff:3.500A) removed outlier: 3.694A pdb=" N ILE J 50 " --> pdb=" O CYS J 46 " (cutoff:3.500A) Processing helix chain 'J' and resid 56 through 60 Processing helix chain 'K' and resid 6 through 9 removed outlier: 3.791A pdb=" N LEU K 9 " --> pdb=" O ARG K 6 " (cutoff:3.500A) No H-bonds generated for 'chain 'K' and resid 6 through 9' Processing helix chain 'K' and resid 40 through 52 removed outlier: 3.797A pdb=" N LEU K 45 " --> pdb=" O THR K 41 " (cutoff:3.500A) Processing helix chain 'K' and resid 83 through 111 Processing helix chain 'M' and resid 104 through 115 Processing helix chain 'M' and resid 121 through 138 Processing helix chain 'M' and resid 144 through 156 Processing helix chain 'M' and resid 168 through 182 Processing helix chain 'M' and resid 189 through 195 removed outlier: 3.716A pdb=" N LEU M 195 " --> pdb=" O GLU M 191 " (cutoff:3.500A) Processing helix chain 'M' and resid 200 through 220 Processing helix chain 'M' and resid 239 through 246 Processing helix chain 'M' and resid 250 through 264 removed outlier: 4.222A pdb=" N LYS M 264 " --> pdb=" O ALA M 260 " (cutoff:3.500A) Processing helix chain 'M' and resid 274 through 289 Processing helix chain 'M' and resid 295 through 302 Processing helix chain 'M' and resid 306 through 317 Processing helix chain 'M' and resid 326 through 330 Processing helix chain 'M' and resid 336 through 338 No H-bonds generated for 'chain 'M' and resid 336 through 338' Processing helix chain 'O' and resid 82 through 88 Processing helix chain 'O' and resid 129 through 146 Processing helix chain 'O' and resid 172 through 178 Processing helix chain 'O' and resid 220 through 235 Proline residue: O 232 - end of helix Processing helix chain 'Q' and resid 24 through 34 Processing helix chain 'Q' and resid 153 through 167 Processing helix chain 'Q' and resid 337 through 345 Processing helix chain 'Q' and resid 407 through 413 removed outlier: 3.847A pdb=" N LYS Q 411 " --> pdb=" O ASP Q 407 " (cutoff:3.500A) Processing helix chain 'Q' and resid 424 through 431 Processing helix chain 'Q' and resid 437 through 449 removed outlier: 3.661A pdb=" N LYS Q 444 " --> pdb=" O ARG Q 440 " (cutoff:3.500A) Processing helix chain 'R' and resid 48 through 52 Processing helix chain 'R' and resid 62 through 65 removed outlier: 4.037A pdb=" N ASN R 65 " --> pdb=" O GLU R 62 " (cutoff:3.500A) No H-bonds generated for 'chain 'R' and resid 62 through 65' Processing helix chain 'R' and resid 75 through 80 removed outlier: 3.574A pdb=" N LYS R 80 " --> pdb=" O PHE R 76 " (cutoff:3.500A) Processing helix chain 'R' and resid 231 through 245 removed outlier: 3.842A pdb=" N HIS R 234 " --> pdb=" O PRO R 231 " (cutoff:3.500A) removed outlier: 3.584A pdb=" N VAL R 244 " --> pdb=" O ARG R 241 " (cutoff:3.500A) Processing helix chain 'R' and resid 259 through 265 removed outlier: 4.476A pdb=" N HIS R 265 " --> pdb=" O VAL R 261 " (cutoff:3.500A) Processing helix chain 'R' and resid 280 through 284 Processing helix chain 'R' and resid 296 through 309 Processing helix chain 'R' and resid 315 through 322 Processing helix chain 'R' and resid 326 through 336 removed outlier: 3.969A pdb=" N LYS R 335 " --> pdb=" O GLU R 331 " (cutoff:3.500A) removed outlier: 3.968A pdb=" N VAL R 336 " --> pdb=" O CYS R 332 " (cutoff:3.500A) Processing helix chain 'R' and resid 353 through 355 No H-bonds generated for 'chain 'R' and resid 353 through 355' Processing helix chain 'U' and resid 4 through 20 Processing helix chain 'U' and resid 22 through 28 removed outlier: 3.548A pdb=" N ALA U 28 " --> pdb=" O ASP U 24 " (cutoff:3.500A) Processing helix chain 'U' and resid 32 through 49 removed outlier: 4.018A pdb=" N ASP U 37 " --> pdb=" O THR U 34 " (cutoff:3.500A) removed outlier: 4.363A pdb=" N LEU U 38 " --> pdb=" O LEU U 35 " (cutoff:3.500A) removed outlier: 3.821A pdb=" N ILE U 41 " --> pdb=" O LEU U 38 " (cutoff:3.500A) removed outlier: 4.524A pdb=" N GLN U 43 " --> pdb=" O ASN U 40 " (cutoff:3.500A) removed outlier: 4.456A pdb=" N LYS U 44 " --> pdb=" O ILE U 41 " (cutoff:3.500A) Processing helix chain 'V' and resid 9 through 12 removed outlier: 3.802A pdb=" N ARG V 12 " --> pdb=" O LEU V 9 " (cutoff:3.500A) No H-bonds generated for 'chain 'V' and resid 9 through 12' Processing helix chain 'V' and resid 14 through 29 Processing helix chain 'V' and resid 34 through 51 Processing helix chain 'W' and resid 4 through 20 Processing helix chain 'W' and resid 23 through 34 Processing helix chain 'W' and resid 40 through 46 Processing helix chain 'W' and resid 51 through 63 Proline residue: W 56 - end of helix Processing helix chain 'W' and resid 91 through 116 Processing helix chain 'W' and resid 137 through 139 No H-bonds generated for 'chain 'W' and resid 137 through 139' Processing helix chain 'W' and resid 163 through 178 removed outlier: 4.362A pdb=" N LYS W 166 " --> pdb=" O LYS W 163 " (cutoff:3.500A) removed outlier: 4.374A pdb=" N ASP W 177 " --> pdb=" O ARG W 174 " (cutoff:3.500A) Processing helix chain 'W' and resid 180 through 190 removed outlier: 3.533A pdb=" N LYS W 188 " --> pdb=" O ASP W 184 " (cutoff:3.500A) Processing helix chain 'W' and resid 199 through 205 removed outlier: 3.777A pdb=" N ALA W 204 " --> pdb=" O GLU W 200 " (cutoff:3.500A) removed outlier: 4.250A pdb=" N ARG W 205 " --> pdb=" O ILE W 201 " (cutoff:3.500A) Processing helix chain 'W' and resid 270 through 287 Processing helix chain 'W' and resid 292 through 295 No H-bonds generated for 'chain 'W' and resid 292 through 295' Processing helix chain 'W' and resid 350 through 368 Processing helix chain 'X' and resid 107 through 115 Processing helix chain 'X' and resid 124 through 137 removed outlier: 3.713A pdb=" N ALA X 131 " --> pdb=" O LYS X 127 " (cutoff:3.500A) Processing helix chain 'X' and resid 144 through 150 Processing helix chain 'X' and resid 158 through 165 Processing helix chain 'X' and resid 189 through 197 Processing helix chain 'X' and resid 218 through 226 Processing helix chain 'X' and resid 257 through 265 Processing helix chain 'X' and resid 272 through 278 removed outlier: 4.644A pdb=" N ARG X 276 " --> pdb=" O ALA X 272 " (cutoff:3.500A) removed outlier: 4.175A pdb=" N LYS X 277 " --> pdb=" O GLU X 273 " (cutoff:3.500A) Processing helix chain 'X' and resid 315 through 317 No H-bonds generated for 'chain 'X' and resid 315 through 317' Processing helix chain '0' and resid 19 through 34 Processing helix chain '0' and resid 48 through 62 Processing helix chain '0' and resid 76 through 97 Processing helix chain '0' and resid 126 through 137 Processing helix chain '0' and resid 140 through 147 Processing helix chain '0' and resid 157 through 164 removed outlier: 3.869A pdb=" N LEU 0 162 " --> pdb=" O TYR 0 158 " (cutoff:3.500A) removed outlier: 3.982A pdb=" N TYR 0 163 " --> pdb=" O HIS 0 159 " (cutoff:3.500A) removed outlier: 4.301A pdb=" N ASN 0 164 " --> pdb=" O GLU 0 160 " (cutoff:3.500A) Processing helix chain '0' and resid 178 through 187 Processing helix chain '0' and resid 192 through 198 Processing helix chain '0' and resid 211 through 214 No H-bonds generated for 'chain '0' and resid 211 through 214' Processing helix chain '0' and resid 219 through 225 removed outlier: 4.212A pdb=" N ASN 0 224 " --> pdb=" O GLU 0 220 " (cutoff:3.500A) Processing helix chain '0' and resid 237 through 247 removed outlier: 5.493A pdb=" N ASP 0 241 " --> pdb=" O HIS 0 238 " (cutoff:3.500A) Processing helix chain '0' and resid 254 through 277 Processing helix chain '0' and resid 280 through 291 removed outlier: 4.284A pdb=" N GLU 0 285 " --> pdb=" O LYS 0 281 " (cutoff:3.500A) removed outlier: 3.685A pdb=" N GLN 0 291 " --> pdb=" O GLU 0 287 " (cutoff:3.500A) Processing helix chain '0' and resid 295 through 298 No H-bonds generated for 'chain '0' and resid 295 through 298' Processing helix chain '0' and resid 313 through 315 No H-bonds generated for 'chain '0' and resid 313 through 315' Processing helix chain '0' and resid 328 through 346 Processing helix chain '0' and resid 356 through 366 Processing helix chain '0' and resid 371 through 388 removed outlier: 3.584A pdb=" N PHE 0 376 " --> pdb=" O LYS 0 372 " (cutoff:3.500A) removed outlier: 4.720A pdb=" N SER 0 378 " --> pdb=" O LEU 0 374 " (cutoff:3.500A) removed outlier: 6.002A pdb=" N GLU 0 379 " --> pdb=" O ARG 0 375 " (cutoff:3.500A) Processing helix chain '0' and resid 397 through 411 removed outlier: 3.799A pdb=" N ASP 0 401 " --> pdb=" O THR 0 397 " (cutoff:3.500A) removed outlier: 3.617A pdb=" N ILE 0 402 " --> pdb=" O ALA 0 398 " (cutoff:3.500A) removed outlier: 4.217A pdb=" N SER 0 410 " --> pdb=" O ALA 0 406 " (cutoff:3.500A) Processing helix chain '0' and resid 443 through 452 Proline residue: 0 448 - end of helix Processing helix chain '0' and resid 466 through 472 removed outlier: 3.792A pdb=" N TYR 0 469 " --> pdb=" O LEU 0 466 " (cutoff:3.500A) Proline residue: 0 470 - end of helix No H-bonds generated for 'chain '0' and resid 466 through 472' Processing helix chain '0' and resid 510 through 512 No H-bonds generated for 'chain '0' and resid 510 through 512' Processing helix chain '0' and resid 516 through 532 Processing helix chain '0' and resid 544 through 557 Processing helix chain '0' and resid 559 through 566 removed outlier: 3.583A pdb=" N VAL 0 563 " --> pdb=" O ILE 0 559 " (cutoff:3.500A) removed outlier: 3.789A pdb=" N LYS 0 565 " --> pdb=" O ASP 0 561 " (cutoff:3.500A) removed outlier: 4.161A pdb=" N HIS 0 566 " --> pdb=" O GLU 0 562 " (cutoff:3.500A) Processing helix chain '0' and resid 576 through 591 Processing helix chain '0' and resid 614 through 617 removed outlier: 3.512A pdb=" N GLY 0 617 " --> pdb=" O HIS 0 614 " (cutoff:3.500A) No H-bonds generated for 'chain '0' and resid 614 through 617' Processing helix chain '0' and resid 633 through 645 Processing helix chain '0' and resid 650 through 667 Processing helix chain '0' and resid 687 through 692 removed outlier: 3.967A pdb=" N ARG 0 690 " --> pdb=" O SER 0 687 " (cutoff:3.500A) removed outlier: 5.110A pdb=" N SER 0 691 " --> pdb=" O ARG 0 688 " (cutoff:3.500A) Processing helix chain '0' and resid 695 through 700 Processing helix chain '0' and resid 711 through 724 Processing helix chain '0' and resid 730 through 733 Processing helix chain '0' and resid 741 through 751 Processing helix chain '1' and resid 42 through 44 No H-bonds generated for 'chain '1' and resid 42 through 44' Processing helix chain '1' and resid 94 through 120 Processing helix chain '1' and resid 171 through 176 Processing helix chain '1' and resid 178 through 187 Processing helix chain '1' and resid 190 through 198 Processing helix chain '1' and resid 206 through 211 Processing helix chain '1' and resid 214 through 225 removed outlier: 3.945A pdb=" N THR 1 224 " --> pdb=" O PHE 1 220 " (cutoff:3.500A) Processing helix chain '1' and resid 233 through 236 No H-bonds generated for 'chain '1' and resid 233 through 236' Processing helix chain '1' and resid 253 through 262 Processing helix chain '1' and resid 264 through 273 removed outlier: 3.609A pdb=" N ASP 1 272 " --> pdb=" O LYS 1 268 " (cutoff:3.500A) Processing helix chain '1' and resid 280 through 288 Processing helix chain '1' and resid 291 through 297 Processing helix chain '1' and resid 311 through 329 removed outlier: 4.399A pdb=" N THR 1 316 " --> pdb=" O ARG 1 313 " (cutoff:3.500A) Processing helix chain '1' and resid 339 through 345 Processing helix chain '1' and resid 371 through 389 removed outlier: 3.822A pdb=" N LEU 1 389 " --> pdb=" O MET 1 385 " (cutoff:3.500A) Processing helix chain '1' and resid 414 through 419 Processing helix chain '1' and resid 466 through 482 removed outlier: 3.655A pdb=" N ASN 1 482 " --> pdb=" O ASP 1 478 " (cutoff:3.500A) Processing helix chain '1' and resid 486 through 489 Processing helix chain '1' and resid 495 through 513 Processing helix chain '1' and resid 544 through 570 Processing helix chain '1' and resid 576 through 599 Processing helix chain '1' and resid 609 through 638 Proline residue: 1 618 - end of helix Processing helix chain '2' and resid 7 through 16 Processing helix chain '2' and resid 19 through 27 removed outlier: 4.201A pdb=" N THR 2 27 " --> pdb=" O ASN 2 23 " (cutoff:3.500A) Processing helix chain '2' and resid 29 through 38 removed outlier: 3.618A pdb=" N ARG 2 37 " --> pdb=" O LEU 2 33 " (cutoff:3.500A) removed outlier: 3.721A pdb=" N ILE 2 38 " --> pdb=" O ALA 2 34 " (cutoff:3.500A) Processing helix chain '2' and resid 41 through 51 Processing helix chain '2' and resid 59 through 65 Processing helix chain '2' and resid 71 through 81 Processing helix chain '2' and resid 102 through 113 Processing helix chain '2' and resid 135 through 151 Processing helix chain '2' and resid 161 through 169 Processing helix chain '2' and resid 186 through 193 Processing helix chain '2' and resid 196 through 210 Processing helix chain '2' and resid 218 through 230 Processing helix chain '2' and resid 244 through 256 Processing helix chain '2' and resid 273 through 279 removed outlier: 4.282A pdb=" N THR 2 279 " --> pdb=" O ALA 2 275 " (cutoff:3.500A) Processing helix chain '2' and resid 354 through 362 removed outlier: 3.682A pdb=" N LEU 2 362 " --> pdb=" O ALA 2 358 " (cutoff:3.500A) Processing helix chain '2' and resid 380 through 388 Processing helix chain '2' and resid 393 through 402 Processing helix chain '2' and resid 406 through 422 Processing helix chain '2' and resid 435 through 448 removed outlier: 3.822A pdb=" N LEU 2 448 " --> pdb=" O TRP 2 444 " (cutoff:3.500A) Processing helix chain '2' and resid 465 through 477 Processing helix chain '2' and resid 498 through 506 Processing helix chain '3' and resid 40 through 46 Processing helix chain '3' and resid 76 through 89 Processing helix chain '3' and resid 103 through 122 Processing helix chain '3' and resid 126 through 138 Processing helix chain '4' and resid 34 through 43 Processing helix chain '4' and resid 49 through 67 Processing helix chain '4' and resid 91 through 96 Processing helix chain '4' and resid 116 through 138 removed outlier: 3.693A pdb=" N VAL 4 121 " --> pdb=" O ARG 4 117 " (cutoff:3.500A) Processing helix chain '4' and resid 149 through 166 Processing helix chain '4' and resid 190 through 206 removed outlier: 4.349A pdb=" N ILE 4 194 " --> pdb=" O PHE 4 191 " (cutoff:3.500A) Proline residue: 4 195 - end of helix Processing helix chain '4' and resid 222 through 230 Processing helix chain '4' and resid 244 through 250 Processing helix chain '4' and resid 256 through 258 No H-bonds generated for 'chain '4' and resid 256 through 258' Processing helix chain '4' and resid 301 through 303 No H-bonds generated for 'chain '4' and resid 301 through 303' Processing helix chain '4' and resid 314 through 321 Processing helix chain '5' and resid 14 through 26 Processing helix chain '5' and resid 44 through 58 removed outlier: 3.721A pdb=" N VAL 5 47 " --> pdb=" O PRO 5 44 " (cutoff:3.500A) removed outlier: 5.670A pdb=" N GLU 5 48 " --> pdb=" O SER 5 45 " (cutoff:3.500A) removed outlier: 4.657A pdb=" N ASN 5 55 " --> pdb=" O HIS 5 52 " (cutoff:3.500A) Processing helix chain '6' and resid 83 through 85 No H-bonds generated for 'chain '6' and resid 83 through 85' Processing helix chain '6' and resid 99 through 110 removed outlier: 3.779A pdb=" N GLU 6 104 " --> pdb=" O ALA 6 100 " (cutoff:3.500A) removed outlier: 3.605A pdb=" N ALA 6 105 " --> pdb=" O SER 6 101 " (cutoff:3.500A) Processing helix chain '6' and resid 134 through 137 Processing helix chain '6' and resid 145 through 163 Processing helix chain '6' and resid 189 through 201 removed outlier: 3.766A pdb=" N LYS 6 201 " --> pdb=" O LYS 6 197 " (cutoff:3.500A) Processing helix chain '6' and resid 210 through 222 Processing helix chain '6' and resid 247 through 256 Processing helix chain '6' and resid 271 through 280 Processing helix chain '6' and resid 294 through 304 removed outlier: 3.514A pdb=" N LYS 6 298 " --> pdb=" O GLU 6 294 " (cutoff:3.500A) Processing helix chain '6' and resid 373 through 382 removed outlier: 4.102A pdb=" N SER 6 379 " --> pdb=" O HIS 6 375 " (cutoff:3.500A) removed outlier: 4.084A pdb=" N HIS 6 381 " --> pdb=" O ALA 6 377 " (cutoff:3.500A) removed outlier: 5.404A pdb=" N HIS 6 382 " --> pdb=" O ARG 6 378 " (cutoff:3.500A) Processing helix chain '6' and resid 438 through 446 removed outlier: 3.806A pdb=" N HIS 6 445 " --> pdb=" O ASP 6 441 " (cutoff:3.500A) Processing helix chain '6' and resid 452 through 456 Processing helix chain '7' and resid 109 through 112 removed outlier: 3.777A pdb=" N MET 7 112 " --> pdb=" O VAL 7 109 " (cutoff:3.500A) No H-bonds generated for 'chain '7' and resid 109 through 112' Processing helix chain '7' and resid 150 through 160 removed outlier: 3.802A pdb=" N PHE 7 156 " --> pdb=" O GLN 7 152 " (cutoff:3.500A) Processing helix chain '7' and resid 177 through 185 Processing helix chain '7' and resid 190 through 200 Processing helix chain '7' and resid 207 through 217 Processing helix chain '7' and resid 240 through 244 Processing helix chain '7' and resid 320 through 332 removed outlier: 3.598A pdb=" N VAL 7 323 " --> pdb=" O ASN 7 320 " (cutoff:3.500A) removed outlier: 5.077A pdb=" N GLU 7 324 " --> pdb=" O GLU 7 321 " (cutoff:3.500A) Processing helix chain '7' and resid 364 through 373 Processing helix chain '7' and resid 392 through 403 removed outlier: 3.847A pdb=" N GLY 7 396 " --> pdb=" O LYS 7 392 " (cutoff:3.500A) Processing helix chain '7' and resid 414 through 426 Processing helix chain '7' and resid 432 through 434 No H-bonds generated for 'chain '7' and resid 432 through 434' Processing helix chain '7' and resid 457 through 460 No H-bonds generated for 'chain '7' and resid 457 through 460' Processing helix chain '7' and resid 468 through 479 Processing helix chain '7' and resid 490 through 492 No H-bonds generated for 'chain '7' and resid 490 through 492' Processing helix chain '7' and resid 498 through 502 removed outlier: 4.205A pdb=" N VAL 7 502 " --> pdb=" O ARG 7 499 " (cutoff:3.500A) Processing helix chain '7' and resid 522 through 530 removed outlier: 4.213A pdb=" N ASN 7 528 " --> pdb=" O GLY 7 525 " (cutoff:3.500A) Processing helix chain '7' and resid 540 through 545 Processing helix chain '7' and resid 563 through 571 removed outlier: 3.549A pdb=" N ARG 7 571 " --> pdb=" O GLN 7 567 " (cutoff:3.500A) Processing helix chain '7' and resid 574 through 582 removed outlier: 3.872A pdb=" N LEU 7 579 " --> pdb=" O ARG 7 575 " (cutoff:3.500A) Processing helix chain '7' and resid 585 through 600 removed outlier: 3.725A pdb=" N ARG 7 600 " --> pdb=" O GLN 7 596 " (cutoff:3.500A) Processing helix chain '7' and resid 612 through 622 Processing helix chain '7' and resid 633 through 644 Processing helix chain '7' and resid 656 through 659 Processing helix chain '7' and resid 680 through 687 removed outlier: 3.676A pdb=" N ALA 7 684 " --> pdb=" O ARG 7 680 " (cutoff:3.500A) Processing helix chain '7' and resid 694 through 697 removed outlier: 4.224A pdb=" N ASN 7 697 " --> pdb=" O LYS 7 694 " (cutoff:3.500A) No H-bonds generated for 'chain '7' and resid 694 through 697' Processing helix chain '7' and resid 714 through 729 removed outlier: 3.775A pdb=" N ALA 7 724 " --> pdb=" O THR 7 720 " (cutoff:3.500A) removed outlier: 4.913A pdb=" N PHE 7 725 " --> pdb=" O LYS 7 721 " (cutoff:3.500A) removed outlier: 4.611A pdb=" N LEU 7 726 " --> pdb=" O ARG 7 722 " (cutoff:3.500A) Processing helix chain '7' and resid 753 through 766 Processing helix chain '7' and resid 833 through 835 No H-bonds generated for 'chain '7' and resid 833 through 835' Processing helix chain 'a' and resid 45 through 56 removed outlier: 3.757A pdb=" N GLN a 55 " --> pdb=" O ILE a 51 " (cutoff:3.500A) Processing helix chain 'a' and resid 64 through 76 removed outlier: 4.093A pdb=" N GLN a 76 " --> pdb=" O ARG a 72 " (cutoff:3.500A) Processing helix chain 'a' and resid 86 through 113 Processing helix chain 'a' and resid 121 through 130 Processing helix chain 'b' and resid 31 through 41 Processing helix chain 'b' and resid 50 through 76 removed outlier: 3.783A pdb=" N ARG b 55 " --> pdb=" O TYR b 51 " (cutoff:3.500A) removed outlier: 3.624A pdb=" N ASP b 68 " --> pdb=" O ASN b 64 " (cutoff:3.500A) removed outlier: 3.634A pdb=" N ALA b 76 " --> pdb=" O TYR b 72 " (cutoff:3.500A) Processing helix chain 'b' and resid 83 through 93 Processing helix chain 'c' and resid 17 through 20 No H-bonds generated for 'chain 'c' and resid 17 through 20' Processing helix chain 'c' and resid 27 through 36 Processing helix chain 'c' and resid 45 through 73 removed outlier: 4.429A pdb=" N VAL c 49 " --> pdb=" O ALA c 45 " (cutoff:3.500A) Processing helix chain 'c' and resid 80 through 89 Processing helix chain 'c' and resid 91 through 96 Processing helix chain 'd' and resid 35 through 45 Processing helix chain 'd' and resid 53 through 81 Processing helix chain 'd' and resid 88 through 98 Processing helix chain 'd' and resid 101 through 121 removed outlier: 3.560A pdb=" N HIS d 106 " --> pdb=" O LEU d 103 " (cutoff:3.500A) removed outlier: 3.516A pdb=" N THR d 116 " --> pdb=" O LYS d 113 " (cutoff:3.500A) removed outlier: 3.551A pdb=" N ALA d 121 " --> pdb=" O TYR d 118 " (cutoff:3.500A) Processing helix chain 'e' and resid 46 through 55 Processing helix chain 'e' and resid 64 through 76 Processing helix chain 'e' and resid 86 through 114 Processing helix chain 'e' and resid 121 through 131 Processing helix chain 'f' and resid 25 through 28 Processing helix chain 'f' and resid 31 through 41 removed outlier: 3.623A pdb=" N GLY f 41 " --> pdb=" O LEU f 37 " (cutoff:3.500A) Processing helix chain 'f' and resid 48 through 76 removed outlier: 3.763A pdb=" N TYR f 51 " --> pdb=" O GLY f 48 " (cutoff:3.500A) removed outlier: 3.981A pdb=" N GLU f 52 " --> pdb=" O LEU f 49 " (cutoff:3.500A) removed outlier: 4.694A pdb=" N THR f 54 " --> pdb=" O TYR f 51 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N ILE f 66 " --> pdb=" O GLU f 63 " (cutoff:3.500A) removed outlier: 3.882A pdb=" N ARG f 67 " --> pdb=" O ASN f 64 " (cutoff:3.500A) removed outlier: 3.712A pdb=" N HIS f 75 " --> pdb=" O TYR f 72 " (cutoff:3.500A) Processing helix chain 'f' and resid 83 through 92 Processing helix chain 'g' and resid 17 through 20 No H-bonds generated for 'chain 'g' and resid 17 through 20' Processing helix chain 'g' and resid 27 through 36 Processing helix chain 'g' and resid 45 through 73 removed outlier: 4.457A pdb=" N VAL g 49 " --> pdb=" O ALA g 45 " (cutoff:3.500A) Processing helix chain 'g' and resid 80 through 89 Processing helix chain 'g' and resid 93 through 96 No H-bonds generated for 'chain 'g' and resid 93 through 96' Processing helix chain 'h' and resid 35 through 45 Processing helix chain 'h' and resid 53 through 80 Processing helix chain 'h' and resid 88 through 98 Processing helix chain 'h' and resid 101 through 119 removed outlier: 4.000A pdb=" N VAL h 108 " --> pdb=" O ALA h 104 " (cutoff:3.500A) removed outlier: 4.376A pdb=" N SER h 109 " --> pdb=" O LYS h 105 " (cutoff:3.500A) removed outlier: 3.535A pdb=" N GLY h 111 " --> pdb=" O ALA h 107 " (cutoff:3.500A) removed outlier: 3.862A pdb=" N THR h 112 " --> pdb=" O VAL h 108 " (cutoff:3.500A) Processing sheet with id= A, first strand: chain 'A' and resid 82 through 85 Processing sheet with id= B, first strand: chain 'A' and resid 151 through 153 Processing sheet with id= C, first strand: chain 'A' and resid 173 through 177 Processing sheet with id= D, first strand: chain 'A' and resid 348 through 352 Processing sheet with id= E, first strand: chain 'A' and resid 353 through 355 removed outlier: 6.107A pdb=" N PHE A 468 " --> pdb=" O SER A 354 " (cutoff:3.500A) No H-bonds generated for sheet with id= E Processing sheet with id= F, first strand: chain 'A' and resid 375 through 379 removed outlier: 3.681A pdb=" N TYR A 404 " --> pdb=" O GLU A 433 " (cutoff:3.500A) removed outlier: 6.203A pdb=" N HIS A 435 " --> pdb=" O ALA A 402 " (cutoff:3.500A) removed outlier: 6.764A pdb=" N ALA A 402 " --> pdb=" O HIS A 435 " (cutoff:3.500A) Processing sheet with id= G, first strand: chain 'A' and resid 588 through 590 removed outlier: 3.634A pdb=" N PHE A 614 " --> pdb=" O LEU A 606 " (cutoff:3.500A) removed outlier: 6.415A pdb=" N ILE A 608 " --> pdb=" O ILE A 612 " (cutoff:3.500A) removed outlier: 5.138A pdb=" N ILE A 612 " --> pdb=" O ILE A 608 " (cutoff:3.500A) Processing sheet with id= H, first strand: chain 'A' and resid 879 through 882 Processing sheet with id= I, first strand: chain 'A' and resid 1115 through 1119 removed outlier: 3.762A pdb=" N ARG A1281 " --> pdb=" O ASP A1309 " (cutoff:3.500A) Processing sheet with id= J, first strand: chain 'A' and resid 1225 through 1228 Processing sheet with id= K, first strand: chain 'B' and resid 68 through 73 Processing sheet with id= L, first strand: chain 'B' and resid 95 through 97 removed outlier: 4.003A pdb=" N GLY B 168 " --> pdb=" O LEU B 128 " (cutoff:3.500A) removed outlier: 6.896A pdb=" N VAL B 130 " --> pdb=" O PHE B 166 " (cutoff:3.500A) removed outlier: 6.139A pdb=" N PHE B 166 " --> pdb=" O VAL B 130 " (cutoff:3.500A) Processing sheet with id= M, first strand: chain 'B' and resid 101 through 103 Processing sheet with id= N, first strand: chain 'B' and resid 203 through 205 Processing sheet with id= O, first strand: chain 'B' and resid 498 through 500 removed outlier: 6.248A pdb=" N ALA B 214 " --> pdb=" O ASN B 499 " (cutoff:3.500A) Processing sheet with id= P, first strand: chain 'B' and resid 223 through 227 removed outlier: 6.957A pdb=" N LEU B 258 " --> pdb=" O SER B 235 " (cutoff:3.500A) removed outlier: 4.942A pdb=" N VAL B 237 " --> pdb=" O VAL B 256 " (cutoff:3.500A) removed outlier: 6.589A pdb=" N VAL B 256 " --> pdb=" O VAL B 237 " (cutoff:3.500A) removed outlier: 4.505A pdb=" N GLU B 239 " --> pdb=" O LEU B 254 " (cutoff:3.500A) removed outlier: 7.042A pdb=" N LEU B 254 " --> pdb=" O GLU B 239 " (cutoff:3.500A) removed outlier: 5.010A pdb=" N ARG B 241 " --> pdb=" O SER B 252 " (cutoff:3.500A) removed outlier: 6.253A pdb=" N SER B 252 " --> pdb=" O ARG B 241 " (cutoff:3.500A) removed outlier: 3.889A pdb=" N GLN B 255 " --> pdb=" O THR B 272 " (cutoff:3.500A) Processing sheet with id= Q, first strand: chain 'B' and resid 614 through 618 removed outlier: 6.815A pdb=" N ARG B 579 " --> pdb=" O LEU B 624 " (cutoff:3.500A) removed outlier: 7.797A pdb=" N ILE B 626 " --> pdb=" O ARG B 579 " (cutoff:3.500A) removed outlier: 6.389A pdb=" N PHE B 581 " --> pdb=" O ILE B 626 " (cutoff:3.500A) removed outlier: 3.882A pdb=" N GLY B 588 " --> pdb=" O VAL B 580 " (cutoff:3.500A) removed outlier: 6.408A pdb=" N VAL B 582 " --> pdb=" O TRP B 586 " (cutoff:3.500A) removed outlier: 5.338A pdb=" N TRP B 586 " --> pdb=" O VAL B 582 " (cutoff:3.500A) Processing sheet with id= R, first strand: chain 'B' and resid 634 through 638 Processing sheet with id= S, first strand: chain 'B' and resid 792 through 796 removed outlier: 3.601A pdb=" N SER B 853 " --> pdb=" O LYS B 972 " (cutoff:3.500A) removed outlier: 3.590A pdb=" N GLN B 951 " --> pdb=" O ARG B 967 " (cutoff:3.500A) removed outlier: 6.066A pdb=" N ARG B 969 " --> pdb=" O VAL B 949 " (cutoff:3.500A) removed outlier: 5.050A pdb=" N VAL B 949 " --> pdb=" O ARG B 969 " (cutoff:3.500A) Processing sheet with id= T, first strand: chain 'B' and resid 1086 through 1092 removed outlier: 4.114A pdb=" N PHE B1086 " --> pdb=" O ILE B 827 " (cutoff:3.500A) removed outlier: 6.370A pdb=" N LEU B1010 " --> pdb=" O ALA B 826 " (cutoff:3.500A) removed outlier: 7.459A pdb=" N MET B 841 " --> pdb=" O GLY B 991 " (cutoff:3.500A) removed outlier: 4.392A pdb=" N THR B 993 " --> pdb=" O MET B 841 " (cutoff:3.500A) Processing sheet with id= U, first strand: chain 'B' and resid 872 through 874 Processing sheet with id= V, first strand: chain 'B' and resid 1157 through 1163 Processing sheet with id= W, first strand: chain 'B' and resid 1172 through 1174 Processing sheet with id= X, first strand: chain 'C' and resid 176 through 180 removed outlier: 5.718A pdb=" N ILE C 21 " --> pdb=" O ILE C 10 " (cutoff:3.500A) removed outlier: 5.211A pdb=" N ILE C 10 " --> pdb=" O ILE C 21 " (cutoff:3.500A) removed outlier: 6.850A pdb=" N SER C 23 " --> pdb=" O VAL C 8 " (cutoff:3.500A) removed outlier: 5.323A pdb=" N VAL C 8 " --> pdb=" O SER C 23 " (cutoff:3.500A) Processing sheet with id= Y, first strand: chain 'C' and resid 97 through 104 removed outlier: 6.068A pdb=" N LYS C 160 " --> pdb=" O ILE C 46 " (cutoff:3.500A) removed outlier: 5.368A pdb=" N ILE C 46 " --> pdb=" O LYS C 160 " (cutoff:3.500A) removed outlier: 7.284A pdb=" N GLY C 162 " --> pdb=" O LEU C 44 " (cutoff:3.500A) removed outlier: 5.473A pdb=" N LEU C 44 " --> pdb=" O GLY C 162 " (cutoff:3.500A) Processing sheet with id= Z, first strand: chain 'C' and resid 111 through 114 Processing sheet with id= AA, first strand: chain 'D' and resid 36 through 38 Processing sheet with id= AB, first strand: chain 'E' and resid 60 through 62 removed outlier: 7.180A pdb=" N THR E 107 " --> pdb=" O TRP E 79 " (cutoff:3.500A) removed outlier: 8.598A pdb=" N GLU E 81 " --> pdb=" O THR E 107 " (cutoff:3.500A) removed outlier: 6.657A pdb=" N ILE E 109 " --> pdb=" O GLU E 81 " (cutoff:3.500A) removed outlier: 6.334A pdb=" N THR E 131 " --> pdb=" O GLY E 108 " (cutoff:3.500A) removed outlier: 7.474A pdb=" N PHE E 110 " --> pdb=" O THR E 131 " (cutoff:3.500A) removed outlier: 6.278A pdb=" N GLU E 133 " --> pdb=" O PHE E 110 " (cutoff:3.500A) removed outlier: 7.379A pdb=" N TYR E 112 " --> pdb=" O GLU E 133 " (cutoff:3.500A) removed outlier: 6.919A pdb=" N PHE E 135 " --> pdb=" O TYR E 112 " (cutoff:3.500A) Processing sheet with id= AC, first strand: chain 'E' and resid 152 through 155 Processing sheet with id= AD, first strand: chain 'F' and resid 133 through 137 Processing sheet with id= AE, first strand: chain 'G' and resid 2 through 13 removed outlier: 4.570A pdb=" N ARG G 75 " --> pdb=" O LEU G 49 " (cutoff:3.500A) removed outlier: 3.721A pdb=" N CYS G 47 " --> pdb=" O VAL G 77 " (cutoff:3.500A) removed outlier: 6.872A pdb=" N PHE G 79 " --> pdb=" O ILE G 45 " (cutoff:3.500A) removed outlier: 5.890A pdb=" N ILE G 45 " --> pdb=" O PHE G 79 " (cutoff:3.500A) Processing sheet with id= AF, first strand: chain 'G' and resid 106 through 111 removed outlier: 3.569A pdb=" N SER G 93 " --> pdb=" O GLU G 100 " (cutoff:3.500A) removed outlier: 6.134A pdb=" N GLN G 102 " --> pdb=" O VAL G 91 " (cutoff:3.500A) removed outlier: 5.836A pdb=" N VAL G 91 " --> pdb=" O GLN G 102 " (cutoff:3.500A) removed outlier: 6.829A pdb=" N ILE G 160 " --> pdb=" O GLU G 148 " (cutoff:3.500A) removed outlier: 4.605A pdb=" N CYS G 150 " --> pdb=" O HIS G 158 " (cutoff:3.500A) removed outlier: 6.651A pdb=" N HIS G 158 " --> pdb=" O CYS G 150 " (cutoff:3.500A) Processing sheet with id= AG, first strand: chain 'G' and resid 120 through 122 Processing sheet with id= AH, first strand: chain 'H' and resid 23 through 29 removed outlier: 5.388A pdb=" N LEU H 122 " --> pdb=" O ASP H 41 " (cutoff:3.500A) removed outlier: 3.977A pdb=" N LYS H 103 " --> pdb=" O TYR H 115 " (cutoff:3.500A) removed outlier: 6.734A pdb=" N SER H 117 " --> pdb=" O ALA H 101 " (cutoff:3.500A) removed outlier: 5.745A pdb=" N ALA H 101 " --> pdb=" O SER H 117 " (cutoff:3.500A) removed outlier: 7.228A pdb=" N GLU H 27 " --> pdb=" O SER H 13 " (cutoff:3.500A) removed outlier: 4.907A pdb=" N VAL H 15 " --> pdb=" O ARG H 25 " (cutoff:3.500A) removed outlier: 6.303A pdb=" N ARG H 25 " --> pdb=" O VAL H 15 " (cutoff:3.500A) Processing sheet with id= AI, first strand: chain 'I' and resid 15 through 18 removed outlier: 3.870A pdb=" N LEU I 26 " --> pdb=" O ARG I 17 " (cutoff:3.500A) Processing sheet with id= AJ, first strand: chain 'I' and resid 69 through 71 removed outlier: 3.646A pdb=" N ASN I 83 " --> pdb=" O SER I 71 " (cutoff:3.500A) Processing sheet with id= AK, first strand: chain 'K' and resid 19 through 24 removed outlier: 4.519A pdb=" N ALA K 30 " --> pdb=" O ASP K 24 " (cutoff:3.500A) Processing sheet with id= AL, first strand: chain 'L' and resid 37 through 40 Processing sheet with id= AM, first strand: chain 'M' and resid 34 through 37 removed outlier: 3.602A pdb=" N SER M 53 " --> pdb=" O VAL M 43 " (cutoff:3.500A) removed outlier: 5.960A pdb=" N CYS M 45 " --> pdb=" O VAL M 51 " (cutoff:3.500A) removed outlier: 6.479A pdb=" N VAL M 51 " --> pdb=" O CYS M 45 " (cutoff:3.500A) Processing sheet with id= AN, first strand: chain 'O' and resid 154 through 157 removed outlier: 3.656A pdb=" N ASP O 154 " --> pdb=" O THR O 75 " (cutoff:3.500A) Processing sheet with id= AO, first strand: chain 'O' and resid 193 through 197 removed outlier: 3.547A pdb=" N MET O 197 " --> pdb=" O ILE O 202 " (cutoff:3.500A) removed outlier: 4.138A pdb=" N ILE O 202 " --> pdb=" O MET O 197 " (cutoff:3.500A) removed outlier: 4.225A pdb=" N ASN O 69 " --> pdb=" O VAL O 161 " (cutoff:3.500A) removed outlier: 6.209A pdb=" N SER O 163 " --> pdb=" O LEU O 67 " (cutoff:3.500A) removed outlier: 5.518A pdb=" N LEU O 67 " --> pdb=" O SER O 163 " (cutoff:3.500A) Processing sheet with id= AP, first strand: chain 'Q' and resid 103 through 105 removed outlier: 6.313A pdb=" N PHE Q 384 " --> pdb=" O ARG Q 104 " (cutoff:3.500A) Processing sheet with id= AQ, first strand: chain 'Q' and resid 118 through 122 removed outlier: 4.730A pdb=" N ALA Q 397 " --> pdb=" O GLN Q 122 " (cutoff:3.500A) removed outlier: 3.681A pdb=" N VAL Q 392 " --> pdb=" O GLU Q 366 " (cutoff:3.500A) removed outlier: 4.174A pdb=" N TRP Q 350 " --> pdb=" O GLY Q 363 " (cutoff:3.500A) Processing sheet with id= AR, first strand: chain 'R' and resid 93 through 98 removed outlier: 4.445A pdb=" N ILE R 104 " --> pdb=" O LEU R 122 " (cutoff:3.500A) removed outlier: 3.836A pdb=" N CYS R 219 " --> pdb=" O VAL R 68 " (cutoff:3.500A) removed outlier: 7.707A pdb=" N LEU R 70 " --> pdb=" O CYS R 219 " (cutoff:3.500A) removed outlier: 4.594A pdb=" N GLU R 221 " --> pdb=" O LEU R 70 " (cutoff:3.500A) removed outlier: 6.976A pdb=" N ARG R 72 " --> pdb=" O GLU R 221 " (cutoff:3.500A) removed outlier: 4.622A pdb=" N GLN R 223 " --> pdb=" O ARG R 72 " (cutoff:3.500A) Processing sheet with id= AS, first strand: chain 'R' and resid 337 through 339 Processing sheet with id= AT, first strand: chain 'R' and resid 133 through 138 removed outlier: 3.606A pdb=" N GLY R 216 " --> pdb=" O VAL R 134 " (cutoff:3.500A) removed outlier: 6.731A pdb=" N THR R 136 " --> pdb=" O ILE R 214 " (cutoff:3.500A) removed outlier: 6.077A pdb=" N ILE R 214 " --> pdb=" O THR R 136 " (cutoff:3.500A) removed outlier: 6.860A pdb=" N GLN R 138 " --> pdb=" O THR R 212 " (cutoff:3.500A) removed outlier: 5.116A pdb=" N THR R 212 " --> pdb=" O GLN R 138 " (cutoff:3.500A) Processing sheet with id= AU, first strand: chain 'U' and resid 251 through 253 Processing sheet with id= AV, first strand: chain 'U' and resid 266 through 268 Processing sheet with id= AW, first strand: chain 'V' and resid 110 through 116 removed outlier: 3.865A pdb=" N THR V 68 " --> pdb=" O ILE V 79 " (cutoff:3.500A) removed outlier: 5.755A pdb=" N LYS V 81 " --> pdb=" O LEU V 66 " (cutoff:3.500A) removed outlier: 5.451A pdb=" N LEU V 66 " --> pdb=" O LYS V 81 " (cutoff:3.500A) Processing sheet with id= AX, first strand: chain 'V' and resid 83 through 87 removed outlier: 3.747A pdb=" N VAL V 85 " --> pdb=" O ILE V 106 " (cutoff:3.500A) removed outlier: 3.617A pdb=" N ILE V 106 " --> pdb=" O VAL V 85 " (cutoff:3.500A) removed outlier: 4.358A pdb=" N SER V 104 " --> pdb=" O VAL V 87 " (cutoff:3.500A) Processing sheet with id= AY, first strand: chain 'W' and resid 68 through 70 Processing sheet with id= AZ, first strand: chain 'W' and resid 122 through 124 Processing sheet with id= BA, first strand: chain 'X' and resid 169 through 172 removed outlier: 3.615A pdb=" N THR X 177 " --> pdb=" O ASP X 172 " (cutoff:3.500A) Processing sheet with id= BB, first strand: chain 'X' and resid 230 through 234 removed outlier: 3.846A pdb=" N TYR X 243 " --> pdb=" O LEU X 233 " (cutoff:3.500A) Processing sheet with id= BC, first strand: chain '0' and resid 2 through 5 Processing sheet with id= BD, first strand: chain '0' and resid 479 through 482 removed outlier: 3.711A pdb=" N ILE 0 39 " --> pdb=" O LEU 0 479 " (cutoff:3.500A) removed outlier: 3.789A pdb=" N LYS 0 481 " --> pdb=" O ILE 0 39 " (cutoff:3.500A) removed outlier: 7.016A pdb=" N VAL 0 232 " --> pdb=" O ILE 0 457 " (cutoff:3.500A) removed outlier: 7.581A pdb=" N THR 0 459 " --> pdb=" O VAL 0 232 " (cutoff:3.500A) removed outlier: 5.757A pdb=" N PHE 0 234 " --> pdb=" O THR 0 459 " (cutoff:3.500A) removed outlier: 3.528A pdb=" N LEU 0 106 " --> pdb=" O ILE 0 205 " (cutoff:3.500A) removed outlier: 6.706A pdb=" N GLY 0 174 " --> pdb=" O GLY 0 105 " (cutoff:3.500A) removed outlier: 8.618A pdb=" N GLY 0 107 " --> pdb=" O GLY 0 174 " (cutoff:3.500A) removed outlier: 8.156A pdb=" N PHE 0 176 " --> pdb=" O GLY 0 107 " (cutoff:3.500A) Processing sheet with id= BE, first strand: chain '0' and resid 250 through 253 Processing sheet with id= BF, first strand: chain '0' and resid 492 through 497 removed outlier: 7.002A pdb=" N GLY 0 677 " --> pdb=" O LEU 0 493 " (cutoff:3.500A) removed outlier: 7.712A pdb=" N MET 0 495 " --> pdb=" O GLY 0 677 " (cutoff:3.500A) removed outlier: 5.875A pdb=" N MET 0 679 " --> pdb=" O MET 0 495 " (cutoff:3.500A) removed outlier: 7.089A pdb=" N ILE 0 497 " --> pdb=" O MET 0 679 " (cutoff:3.500A) removed outlier: 5.994A pdb=" N LEU 0 681 " --> pdb=" O ILE 0 497 " (cutoff:3.500A) removed outlier: 3.655A pdb=" N THR 0 619 " --> pdb=" O GLY 0 536 " (cutoff:3.500A) removed outlier: 6.550A pdb=" N ALA 0 596 " --> pdb=" O MET 0 537 " (cutoff:3.500A) removed outlier: 7.890A pdb=" N VAL 0 539 " --> pdb=" O ALA 0 596 " (cutoff:3.500A) removed outlier: 6.229A pdb=" N LEU 0 598 " --> pdb=" O VAL 0 539 " (cutoff:3.500A) removed outlier: 7.417A pdb=" N PHE 0 541 " --> pdb=" O LEU 0 598 " (cutoff:3.500A) removed outlier: 6.969A pdb=" N SER 0 600 " --> pdb=" O PHE 0 541 " (cutoff:3.500A) removed outlier: 6.228A pdb=" N LEU 0 568 " --> pdb=" O ILE 0 597 " (cutoff:3.500A) removed outlier: 7.232A pdb=" N LEU 0 599 " --> pdb=" O LEU 0 568 " (cutoff:3.500A) removed outlier: 6.579A pdb=" N LEU 0 570 " --> pdb=" O LEU 0 599 " (cutoff:3.500A) removed outlier: 8.752A pdb=" N VAL 0 601 " --> pdb=" O LEU 0 570 " (cutoff:3.500A) Processing sheet with id= BG, first strand: chain '1' and resid 45 through 49 removed outlier: 6.772A pdb=" N ILE 1 63 " --> pdb=" O ASP 1 46 " (cutoff:3.500A) removed outlier: 4.474A pdb=" N LEU 1 48 " --> pdb=" O ARG 1 61 " (cutoff:3.500A) removed outlier: 6.650A pdb=" N ARG 1 61 " --> pdb=" O LEU 1 48 " (cutoff:3.500A) Processing sheet with id= BH, first strand: chain '2' and resid 87 through 92 Processing sheet with id= BI, first strand: chain '2' and resid 174 through 176 removed outlier: 3.834A pdb=" N VAL 2 176 " --> pdb=" O GLU 2 181 " (cutoff:3.500A) removed outlier: 4.089A pdb=" N GLU 2 181 " --> pdb=" O VAL 2 176 " (cutoff:3.500A) Processing sheet with id= BJ, first strand: chain '2' and resid 236 through 238 Processing sheet with id= BK, first strand: chain '2' and resid 338 through 341 removed outlier: 3.955A pdb=" N SER 2 338 " --> pdb=" O TYR 2 350 " (cutoff:3.500A) removed outlier: 6.178A pdb=" N GLN 2 377 " --> pdb=" O LEU 2 366 " (cutoff:3.500A) removed outlier: 5.178A pdb=" N LEU 2 366 " --> pdb=" O GLN 2 377 " (cutoff:3.500A) Processing sheet with id= BL, first strand: chain '2' and resid 456 through 459 removed outlier: 3.930A pdb=" N TRP 2 483 " --> pdb=" O PHE 2 492 " (cutoff:3.500A) removed outlier: 6.427A pdb=" N SER 2 494 " --> pdb=" O LEU 2 481 " (cutoff:3.500A) removed outlier: 7.333A pdb=" N LEU 2 481 " --> pdb=" O SER 2 494 " (cutoff:3.500A) Processing sheet with id= BM, first strand: chain '3' and resid 28 through 30 Processing sheet with id= BN, first strand: chain '4' and resid 82 through 87 removed outlier: 6.324A pdb=" N VAL 4 75 " --> pdb=" O LEU 4 86 " (cutoff:3.500A) removed outlier: 7.087A pdb=" N LYS 4 173 " --> pdb=" O LEU 4 25 " (cutoff:3.500A) removed outlier: 8.407A pdb=" N THR 4 27 " --> pdb=" O LYS 4 173 " (cutoff:3.500A) removed outlier: 6.644A pdb=" N ARG 4 175 " --> pdb=" O THR 4 27 " (cutoff:3.500A) removed outlier: 7.716A pdb=" N ILE 4 29 " --> pdb=" O ARG 4 175 " (cutoff:3.500A) removed outlier: 6.476A pdb=" N LEU 4 177 " --> pdb=" O ILE 4 29 " (cutoff:3.500A) removed outlier: 7.338A pdb=" N GLU 4 31 " --> pdb=" O LEU 4 177 " (cutoff:3.500A) removed outlier: 6.776A pdb=" N LEU 4 179 " --> pdb=" O GLU 4 31 " (cutoff:3.500A) removed outlier: 7.715A pdb=" N VAL 4 178 " --> pdb=" O PRO 4 209 " (cutoff:3.500A) removed outlier: 6.597A pdb=" N ASP 4 211 " --> pdb=" O VAL 4 178 " (cutoff:3.500A) removed outlier: 7.276A pdb=" N THR 4 180 " --> pdb=" O ASP 4 211 " (cutoff:3.500A) removed outlier: 6.139A pdb=" N VAL 4 213 " --> pdb=" O THR 4 180 " (cutoff:3.500A) Processing sheet with id= BO, first strand: chain '5' and resid 7 through 11 Processing sheet with id= BP, first strand: chain '6' and resid 178 through 183 removed outlier: 6.455A pdb=" N ILE 6 171 " --> pdb=" O VAL 6 182 " (cutoff:3.500A) removed outlier: 6.788A pdb=" N THR 6 229 " --> pdb=" O SER 6 125 " (cutoff:3.500A) removed outlier: 7.930A pdb=" N ILE 6 127 " --> pdb=" O THR 6 229 " (cutoff:3.500A) removed outlier: 7.202A pdb=" N GLU 6 231 " --> pdb=" O ILE 6 127 " (cutoff:3.500A) removed outlier: 7.994A pdb=" N THR 6 129 " --> pdb=" O GLU 6 231 " (cutoff:3.500A) removed outlier: 6.566A pdb=" N LEU 6 233 " --> pdb=" O THR 6 129 " (cutoff:3.500A) removed outlier: 7.957A pdb=" N ASP 6 131 " --> pdb=" O LEU 6 233 " (cutoff:3.500A) removed outlier: 7.749A pdb=" N VAL 6 235 " --> pdb=" O ASP 6 131 " (cutoff:3.500A) Processing sheet with id= BQ, first strand: chain '7' and resid 132 through 135 removed outlier: 3.750A pdb=" N ARG 7 140 " --> pdb=" O SER 7 135 " (cutoff:3.500A) removed outlier: 5.977A pdb=" N LYS 7 174 " --> pdb=" O PRO 7 163 " (cutoff:3.500A) Processing sheet with id= BR, first strand: chain '7' and resid 223 through 227 removed outlier: 3.801A pdb=" N HIS 7 314 " --> pdb=" O THR 7 236 " (cutoff:3.500A) Processing sheet with id= BS, first strand: chain '7' and resid 435 through 438 removed outlier: 6.507A pdb=" N LEU 7 452 " --> pdb=" O ALA 7 436 " (cutoff:3.500A) removed outlier: 7.490A pdb=" N PHE 7 438 " --> pdb=" O LEU 7 452 " (cutoff:3.500A) removed outlier: 6.535A pdb=" N VAL 7 454 " --> pdb=" O PHE 7 438 " (cutoff:3.500A) removed outlier: 7.079A pdb=" N VAL 7 407 " --> pdb=" O VAL 7 453 " (cutoff:3.500A) removed outlier: 8.570A pdb=" N SER 7 455 " --> pdb=" O VAL 7 407 " (cutoff:3.500A) removed outlier: 6.173A pdb=" N VAL 7 409 " --> pdb=" O SER 7 455 " (cutoff:3.500A) removed outlier: 6.863A pdb=" N PHE 7 484 " --> pdb=" O ILE 7 408 " (cutoff:3.500A) removed outlier: 8.335A pdb=" N LEU 7 410 " --> pdb=" O PHE 7 484 " (cutoff:3.500A) removed outlier: 6.554A pdb=" N ILE 7 486 " --> pdb=" O LEU 7 410 " (cutoff:3.500A) removed outlier: 6.722A pdb=" N ALA 7 509 " --> pdb=" O ILE 7 485 " (cutoff:3.500A) removed outlier: 7.587A pdb=" N LEU 7 487 " --> pdb=" O ALA 7 509 " (cutoff:3.500A) removed outlier: 6.541A pdb=" N LEU 7 511 " --> pdb=" O LEU 7 487 " (cutoff:3.500A) removed outlier: 7.057A pdb=" N GLY 7 382 " --> pdb=" O GLY 7 512 " (cutoff:3.500A) removed outlier: 8.537A pdb=" N THR 7 514 " --> pdb=" O GLY 7 382 " (cutoff:3.500A) removed outlier: 6.701A pdb=" N ILE 7 384 " --> pdb=" O THR 7 514 " (cutoff:3.500A) removed outlier: 8.906A pdb=" N VAL 7 385 " --> pdb=" O PRO 7 533 " (cutoff:3.500A) removed outlier: 8.654A pdb=" N LEU 7 535 " --> pdb=" O VAL 7 385 " (cutoff:3.500A) No H-bonds generated for sheet with id= BS Processing sheet with id= BT, first strand: chain '7' and resid 734 through 736 removed outlier: 7.078A pdb=" N ALA 7 703 " --> pdb=" O GLN 7 553 " (cutoff:3.500A) removed outlier: 7.532A pdb=" N ALA 7 555 " --> pdb=" O ALA 7 703 " (cutoff:3.500A) removed outlier: 6.297A pdb=" N PHE 7 705 " --> pdb=" O ALA 7 555 " (cutoff:3.500A) removed outlier: 7.301A pdb=" N VAL 7 557 " --> pdb=" O PHE 7 705 " (cutoff:3.500A) removed outlier: 6.315A pdb=" N SER 7 707 " --> pdb=" O VAL 7 557 " (cutoff:3.500A) removed outlier: 7.447A pdb=" N CYS 7 559 " --> pdb=" O SER 7 707 " (cutoff:3.500A) removed outlier: 6.776A pdb=" N VAL 7 709 " --> pdb=" O CYS 7 559 " (cutoff:3.500A) 2942 hydrogen bonds defined for protein. 8139 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 340 hydrogen bonds 680 hydrogen bond angles 0 basepair planarities 141 basepair parallelities 352 stacking parallelities Total time for adding SS restraints: 50.55 Time building geometry restraints manager: 32.11 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.09 - 1.33: 15600 1.33 - 1.56: 71687 1.56 - 1.80: 1306 1.80 - 2.04: 180 2.04 - 2.28: 12 Bond restraints: 88785 Sorted by residual: bond pdb=" CG PRO R 325 " pdb=" CD PRO R 325 " ideal model delta sigma weight residual 1.503 1.088 0.415 3.40e-02 8.65e+02 1.49e+02 bond pdb=" N PRO R 325 " pdb=" CD PRO R 325 " ideal model delta sigma weight residual 1.473 1.524 -0.051 1.40e-02 5.10e+03 1.34e+01 bond pdb=" CB PRO K 23 " pdb=" CG PRO K 23 " ideal model delta sigma weight residual 1.492 1.618 -0.126 5.00e-02 4.00e+02 6.34e+00 bond pdb=" CB MET A 873 " pdb=" CG MET A 873 " ideal model delta sigma weight residual 1.520 1.447 0.073 3.00e-02 1.11e+03 5.89e+00 bond pdb=" CG ARG B 996 " pdb=" CD ARG B 996 " ideal model delta sigma weight residual 1.520 1.458 0.062 3.00e-02 1.11e+03 4.31e+00 ... (remaining 88780 not shown) Histogram of bond angle deviations from ideal: 73.67 - 85.87: 13 85.87 - 98.08: 11 98.08 - 110.28: 22341 110.28 - 122.48: 87124 122.48 - 134.68: 12147 Bond angle restraints: 121636 Sorted by residual: angle pdb=" N PRO R 325 " pdb=" CD PRO R 325 " pdb=" CG PRO R 325 " ideal model delta sigma weight residual 103.20 80.52 22.68 1.50e+00 4.44e-01 2.29e+02 angle pdb=" CA PRO R 325 " pdb=" CB PRO R 325 " pdb=" CG PRO R 325 " ideal model delta sigma weight residual 104.50 88.03 16.47 1.90e+00 2.77e-01 7.52e+01 angle pdb=" CA PRO R 325 " pdb=" N PRO R 325 " pdb=" CD PRO R 325 " ideal model delta sigma weight residual 112.00 101.24 10.76 1.40e+00 5.10e-01 5.91e+01 angle pdb=" C GLN c 24 " pdb=" N PHE c 25 " pdb=" CA PHE c 25 " ideal model delta sigma weight residual 120.68 110.39 10.29 1.52e+00 4.33e-01 4.59e+01 angle pdb=" CG1 ILE a 51 " pdb=" CB ILE a 51 " pdb=" CG2 ILE a 51 " ideal model delta sigma weight residual 110.70 90.91 19.79 3.00e+00 1.11e-01 4.35e+01 ... (remaining 121631 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.39: 51187 35.39 - 70.77: 2111 70.77 - 106.16: 63 106.16 - 141.54: 2 141.54 - 176.93: 3 Dihedral angle restraints: 53366 sinusoidal: 24925 harmonic: 28441 Sorted by residual: dihedral pdb=" CA LYS 2 238 " pdb=" C LYS 2 238 " pdb=" N ILE 2 239 " pdb=" CA ILE 2 239 " ideal model delta harmonic sigma weight residual -180.00 -144.65 -35.35 0 5.00e+00 4.00e-02 5.00e+01 dihedral pdb=" CA GLU O 108 " pdb=" C GLU O 108 " pdb=" N PRO O 109 " pdb=" CA PRO O 109 " ideal model delta harmonic sigma weight residual 180.00 150.29 29.71 0 5.00e+00 4.00e-02 3.53e+01 dihedral pdb=" CA HIS 1 87 " pdb=" C HIS 1 87 " pdb=" N MET 1 88 " pdb=" CA MET 1 88 " ideal model delta harmonic sigma weight residual -180.00 -151.06 -28.94 0 5.00e+00 4.00e-02 3.35e+01 ... (remaining 53363 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.060: 11380 0.060 - 0.120: 2063 0.120 - 0.180: 265 0.180 - 0.239: 34 0.239 - 0.299: 10 Chirality restraints: 13752 Sorted by residual: chirality pdb=" CB ILE 0 597 " pdb=" CA ILE 0 597 " pdb=" CG1 ILE 0 597 " pdb=" CG2 ILE 0 597 " both_signs ideal model delta sigma weight residual False 2.64 2.35 0.30 2.00e-01 2.50e+01 2.24e+00 chirality pdb=" CB ILE F 130 " pdb=" CA ILE F 130 " pdb=" CG1 ILE F 130 " pdb=" CG2 ILE F 130 " both_signs ideal model delta sigma weight residual False 2.64 2.35 0.30 2.00e-01 2.50e+01 2.18e+00 chirality pdb=" CG LEU A 722 " pdb=" CB LEU A 722 " pdb=" CD1 LEU A 722 " pdb=" CD2 LEU A 722 " both_signs ideal model delta sigma weight residual False -2.59 -2.30 -0.29 2.00e-01 2.50e+01 2.16e+00 ... (remaining 13749 not shown) Planarity restraints: 14134 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C GLN R 324 " 0.078 5.00e-02 4.00e+02 1.10e-01 1.93e+01 pdb=" N PRO R 325 " -0.190 5.00e-02 4.00e+02 pdb=" CA PRO R 325 " 0.053 5.00e-02 4.00e+02 pdb=" CD PRO R 325 " 0.058 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CD ARG C 66 " -0.370 9.50e-02 1.11e+02 1.66e-01 1.85e+01 pdb=" NE ARG C 66 " 0.029 2.00e-02 2.50e+03 pdb=" CZ ARG C 66 " -0.018 2.00e-02 2.50e+03 pdb=" NH1 ARG C 66 " 0.011 2.00e-02 2.50e+03 pdb=" NH2 ARG C 66 " -0.005 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C ASP K 22 " 0.068 5.00e-02 4.00e+02 9.81e-02 1.54e+01 pdb=" N PRO K 23 " -0.169 5.00e-02 4.00e+02 pdb=" CA PRO K 23 " 0.048 5.00e-02 4.00e+02 pdb=" CD PRO K 23 " 0.054 5.00e-02 4.00e+02 ... (remaining 14131 not shown) Histogram of nonbonded interaction distances: 1.36 - 2.07: 7 2.07 - 2.78: 16139 2.78 - 3.48: 118996 3.48 - 4.19: 215651 4.19 - 4.90: 363519 Nonbonded interactions: 714312 Sorted by model distance: nonbonded pdb=" CE LYS A 332 " pdb=" O PHE F 23 " model vdw 1.361 3.440 nonbonded pdb=" OE1 GLN B 776 " pdb=" CD1 PHE F 15 " model vdw 1.619 3.340 nonbonded pdb=" OE2 GLU 4 89 " pdb=" CD2 LEU 4 94 " model vdw 1.741 3.460 nonbonded pdb=" CD GLU 4 89 " pdb=" CD2 LEU 4 94 " model vdw 1.869 3.690 nonbonded pdb=" NH1 ARG A 337 " pdb=" OE2 GLU F 26 " model vdw 1.976 2.520 ... (remaining 714307 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = (chain 'a' and resid 37 through 134) selection = chain 'e' } ncs_group { reference = chain 'b' selection = (chain 'f' and resid 20 through 101) } ncs_group { reference = chain 'c' selection = chain 'g' } ncs_group { reference = chain 'd' selection = chain 'h' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=0.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 2.850 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: 0.090 Extract box with map and model: 13.170 Check model and map are aligned: 0.960 Set scattering table: 0.650 Process input model: 242.650 Find NCS groups from input model: 2.250 Set up NCS constraints: 0.450 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.020 Load rotamer database and sin/cos tables:2.830 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 265.920 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6759 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 : 0.004 0.415 88785 Z= 0.255 Angle : 0.749 22.682 121636 Z= 0.394 Chirality : 0.047 0.299 13752 Planarity : 0.006 0.166 14134 Dihedral : 16.319 176.931 34902 Min Nonbonded Distance : 1.361 Molprobity Statistics. All-atom Clashscore : 6.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.90 % Favored : 97.10 % Rotamer: Outliers : 0.00 % Allowed : 0.31 % Favored : 99.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.31 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.01 % 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: -1.01 (0.08), residues: 9583 helix: -0.50 (0.07), residues: 4060 sheet: -0.24 (0.15), residues: 1166 loop : -0.82 (0.09), residues: 4357 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.061 0.002 TRP X 214 HIS 0.010 0.001 HIS A 587 PHE 0.046 0.002 PHE J 8 TYR 0.052 0.002 TYR 4 85 ARG 0.022 0.001 ARG C 66 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 19166 Ramachandran restraints generated. 9583 Oldfield, 0 Emsley, 9583 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 19166 Ramachandran restraints generated. 9583 Oldfield, 0 Emsley, 9583 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1286 residues out of total 8648 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 1286 time to evaluate : 7.385 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: A 122 MET cc_start: 0.4926 (mmp) cc_final: 0.4506 (mmm) REVERT: A 229 SER cc_start: 0.8373 (t) cc_final: 0.8025 (t) REVERT: A 244 PRO cc_start: 0.8183 (Cg_exo) cc_final: 0.7967 (Cg_endo) REVERT: A 341 MET cc_start: 0.7692 (mtp) cc_final: 0.7357 (mmm) REVERT: A 1013 ASP cc_start: 0.5963 (t70) cc_final: 0.5713 (t70) REVERT: A 1063 MET cc_start: 0.8512 (mmm) cc_final: 0.8295 (mmm) REVERT: A 1202 MET cc_start: 0.5903 (mpp) cc_final: 0.5568 (mpp) REVERT: A 1259 MET cc_start: 0.5706 (ppp) cc_final: 0.4204 (ptp) REVERT: B 225 VAL cc_start: 0.8799 (m) cc_final: 0.8173 (t) REVERT: B 429 PHE cc_start: 0.7357 (t80) cc_final: 0.7114 (t80) REVERT: B 597 MET cc_start: 0.7554 (ppp) cc_final: 0.7287 (tmm) REVERT: B 1050 ILE cc_start: 0.8517 (mt) cc_final: 0.8272 (mt) REVERT: B 1136 ASP cc_start: 0.7020 (m-30) cc_final: 0.6744 (m-30) REVERT: E 75 MET cc_start: 0.6749 (ppp) cc_final: 0.6205 (ppp) REVERT: E 104 ASN cc_start: 0.6582 (t0) cc_final: 0.6355 (t0) REVERT: G 6 ASP cc_start: 0.7812 (m-30) cc_final: 0.7324 (m-30) REVERT: G 42 PHE cc_start: 0.8444 (m-80) cc_final: 0.8204 (m-10) REVERT: G 102 GLN cc_start: 0.6839 (tp40) cc_final: 0.6341 (pp30) REVERT: I 27 PHE cc_start: 0.3929 (m-80) cc_final: 0.3717 (m-80) REVERT: I 45 ARG cc_start: 0.7068 (ttt90) cc_final: 0.6839 (ttt90) REVERT: I 87 GLN cc_start: 0.6570 (pp30) cc_final: 0.6052 (pp30) REVERT: J 42 LYS cc_start: 0.7814 (pttm) cc_final: 0.7556 (mmmt) REVERT: K 26 LYS cc_start: 0.7903 (tptm) cc_final: 0.7603 (ttmt) REVERT: K 85 ASP cc_start: 0.7961 (m-30) cc_final: 0.7483 (m-30) REVERT: L 47 ARG cc_start: 0.6951 (mmp80) cc_final: 0.6736 (mmp80) REVERT: M 243 CYS cc_start: 0.8416 (m) cc_final: 0.8115 (m) REVERT: M 303 GLN cc_start: 0.7468 (tp40) cc_final: 0.7190 (tp40) REVERT: O 121 MET cc_start: 0.4413 (ppp) cc_final: 0.3720 (ppp) REVERT: Q 387 ILE cc_start: 0.5911 (mm) cc_final: 0.5647 (tp) REVERT: R 225 MET cc_start: 0.4304 (ppp) cc_final: 0.4014 (mmt) REVERT: R 263 MET cc_start: 0.7951 (mmp) cc_final: 0.7667 (mmp) REVERT: R 266 THR cc_start: 0.8526 (m) cc_final: 0.8201 (p) REVERT: R 294 MET cc_start: 0.0733 (pmm) cc_final: 0.0009 (pmm) REVERT: R 325 PRO cc_start: 0.2869 (Cg_endo) cc_final: 0.2215 (Cg_exo) REVERT: R 354 GLU cc_start: 0.5837 (tm-30) cc_final: 0.5182 (pt0) REVERT: W 293 TRP cc_start: 0.5394 (p90) cc_final: 0.5049 (p90) REVERT: 0 299 LEU cc_start: 0.8154 (mm) cc_final: 0.7856 (mm) REVERT: 0 547 MET cc_start: 0.8362 (ttp) cc_final: 0.7996 (ttt) REVERT: 0 712 MET cc_start: 0.5255 (ptt) cc_final: 0.5010 (ptt) REVERT: 1 58 MET cc_start: -0.1087 (mtm) cc_final: -0.2292 (mtm) REVERT: 1 192 MET cc_start: 0.6565 (mmm) cc_final: 0.6145 (mmm) REVERT: 1 254 GLU cc_start: 0.6879 (tm-30) cc_final: 0.6572 (tm-30) REVERT: 2 107 SER cc_start: 0.7837 (t) cc_final: 0.7159 (t) REVERT: 2 347 ILE cc_start: 0.8796 (mm) cc_final: 0.8574 (mm) REVERT: 2 363 PHE cc_start: 0.8365 (p90) cc_final: 0.8067 (p90) REVERT: 3 56 TYR cc_start: 0.6787 (m-80) cc_final: 0.6576 (m-80) REVERT: 3 107 ASN cc_start: 0.8712 (m-40) cc_final: 0.8433 (m-40) REVERT: 3 117 ILE cc_start: 0.9381 (mt) cc_final: 0.9104 (mm) REVERT: 4 236 LEU cc_start: 0.9059 (tp) cc_final: 0.8698 (tp) REVERT: 7 326 VAL cc_start: 0.7293 (t) cc_final: 0.7042 (t) REVERT: b 68 ASP cc_start: 0.6249 (m-30) cc_final: 0.5583 (m-30) REVERT: b 84 MET cc_start: 0.7112 (tmm) cc_final: 0.6591 (tmm) REVERT: b 92 ARG cc_start: 0.7182 (ttp80) cc_final: 0.6220 (ttp-170) REVERT: d 110 GLU cc_start: 0.6902 (tt0) cc_final: 0.6631 (tt0) REVERT: g 64 GLU cc_start: 0.6547 (tp30) cc_final: 0.6084 (tp30) REVERT: g 104 GLN cc_start: 0.7865 (mp10) cc_final: 0.7512 (mp10) REVERT: h 56 MET cc_start: 0.6113 (mmp) cc_final: 0.5677 (ppp) outliers start: 0 outliers final: 0 residues processed: 1286 average time/residue: 0.8517 time to fit residues: 1900.4346 Evaluate side-chains 1006 residues out of total 8648 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 1006 time to evaluate : 7.236 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 998 random chunks: chunk 842 optimal weight: 2.9990 chunk 756 optimal weight: 8.9990 chunk 419 optimal weight: 20.0000 chunk 258 optimal weight: 0.9980 chunk 510 optimal weight: 30.0000 chunk 404 optimal weight: 30.0000 chunk 782 optimal weight: 20.0000 chunk 302 optimal weight: 10.0000 chunk 475 optimal weight: 0.0470 chunk 582 optimal weight: 20.0000 chunk 906 optimal weight: 7.9990 overall best weight: 4.2084 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 4 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 5 GLN ** A 425 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 510 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 802 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1070 GLN A1203 ASN A1330 ASN ** A1432 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 178 ASN B 415 GLN C 24 ASN ** D 132 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 3 GLN ** E 153 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 78 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 97 HIS H 52 GLN H 137 GLN I 46 HIS K 29 ASN ** Q 150 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 43 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 36 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** W 50 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** W 133 GLN ** W 280 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** X 270 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 0 224 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 0 239 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 1 87 HIS 1 331 HIS ** 2 190 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 2 263 HIS ** 2 395 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 2 407 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 3 36 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** 3 71 GLN 4 161 ASN ** 4 246 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 4 315 HIS 5 43 ASN 6 339 HIS ** 7 761 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** b 25 ASN ** e 93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 23 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6943 moved from start: 0.1631 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.077 88785 Z= 0.446 Angle : 0.660 10.033 121636 Z= 0.354 Chirality : 0.045 0.224 13752 Planarity : 0.005 0.073 14134 Dihedral : 18.547 178.952 15190 Min Nonbonded Distance : 1.863 Molprobity Statistics. All-atom Clashscore : 12.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.06 % Favored : 96.94 % Rotamer: Outliers : 1.50 % Allowed : 8.00 % Favored : 90.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.31 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.01 % 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: -0.56 (0.08), residues: 9583 helix: 0.16 (0.08), residues: 4099 sheet: -0.40 (0.15), residues: 1208 loop : -0.77 (0.09), residues: 4276 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP Q 423 HIS 0.010 0.001 HIS A 659 PHE 0.028 0.002 PHE B 781 TYR 0.030 0.002 TYR 0 208 ARG 0.016 0.001 ARG L 54 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 19166 Ramachandran restraints generated. 9583 Oldfield, 0 Emsley, 9583 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 19166 Ramachandran restraints generated. 9583 Oldfield, 0 Emsley, 9583 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1214 residues out of total 8648 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 130 poor density : 1084 time to evaluate : 8.882 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: A 122 MET cc_start: 0.5000 (mmp) cc_final: 0.4582 (mmm) REVERT: A 229 SER cc_start: 0.8422 (t) cc_final: 0.8135 (t) REVERT: A 244 PRO cc_start: 0.8323 (Cg_exo) cc_final: 0.8023 (Cg_endo) REVERT: A 341 MET cc_start: 0.7618 (mtp) cc_final: 0.7321 (mmm) REVERT: A 555 ASP cc_start: 0.6525 (t0) cc_final: 0.6281 (t0) REVERT: A 678 GLU cc_start: 0.7946 (OUTLIER) cc_final: 0.7689 (pm20) REVERT: A 935 GLN cc_start: 0.6432 (tp40) cc_final: 0.6103 (tp-100) REVERT: A 1285 MET cc_start: 0.6747 (OUTLIER) cc_final: 0.6542 (mtm) REVERT: A 1368 MET cc_start: 0.7799 (tpp) cc_final: 0.7263 (mpp) REVERT: B 376 PHE cc_start: 0.7321 (m-10) cc_final: 0.6785 (m-10) REVERT: B 415 GLN cc_start: 0.7963 (OUTLIER) cc_final: 0.7718 (pt0) REVERT: B 566 LEU cc_start: 0.8217 (tp) cc_final: 0.7782 (tp) REVERT: B 597 MET cc_start: 0.7746 (ppp) cc_final: 0.7460 (tmm) REVERT: B 615 MET cc_start: 0.7646 (mmm) cc_final: 0.7378 (mmm) REVERT: B 776 GLN cc_start: 0.7882 (mm110) cc_final: 0.7468 (mt0) REVERT: B 863 GLU cc_start: 0.8317 (mp0) cc_final: 0.8070 (mp0) REVERT: B 1013 ASN cc_start: 0.8152 (t0) cc_final: 0.7896 (t0) REVERT: B 1210 MET cc_start: 0.8379 (mtp) cc_final: 0.7899 (mtp) REVERT: D 149 THR cc_start: 0.8731 (m) cc_final: 0.8431 (t) REVERT: E 75 MET cc_start: 0.7149 (ppp) cc_final: 0.6774 (ppp) REVERT: E 104 ASN cc_start: 0.6820 (t0) cc_final: 0.6407 (t0) REVERT: F 76 LYS cc_start: 0.7042 (mttm) cc_final: 0.6721 (mttm) REVERT: F 84 TYR cc_start: 0.7278 (m-80) cc_final: 0.6888 (m-80) REVERT: I 27 PHE cc_start: 0.3795 (m-80) cc_final: 0.3552 (m-80) REVERT: K 20 LYS cc_start: 0.8181 (tppt) cc_final: 0.7957 (tppt) REVERT: K 36 GLU cc_start: 0.7737 (tp30) cc_final: 0.7477 (tp30) REVERT: K 56 VAL cc_start: 0.9306 (t) cc_final: 0.9090 (p) REVERT: K 85 ASP cc_start: 0.8191 (m-30) cc_final: 0.7901 (m-30) REVERT: K 98 LEU cc_start: 0.8273 (pp) cc_final: 0.8006 (pp) REVERT: M 243 CYS cc_start: 0.8515 (m) cc_final: 0.8142 (m) REVERT: M 325 ASP cc_start: 0.6546 (t0) cc_final: 0.5992 (t70) REVERT: O 197 MET cc_start: 0.4054 (ptm) cc_final: 0.3795 (ptp) REVERT: Q 114 MET cc_start: 0.4050 (tmm) cc_final: 0.3837 (tmm) REVERT: R 225 MET cc_start: 0.4425 (ppp) cc_final: 0.4197 (mmt) REVERT: R 294 MET cc_start: 0.0758 (pmm) cc_final: 0.0018 (pmm) REVERT: X 246 TYR cc_start: 0.6476 (t80) cc_final: 0.6197 (t80) REVERT: 0 42 MET cc_start: 0.8472 (mmm) cc_final: 0.8084 (tpt) REVERT: 0 299 LEU cc_start: 0.8377 (mm) cc_final: 0.7963 (mm) REVERT: 0 537 MET cc_start: 0.7069 (mtt) cc_final: 0.6705 (mtt) REVERT: 0 610 ILE cc_start: 0.8980 (mm) cc_final: 0.8768 (mm) REVERT: 1 59 MET cc_start: 0.3429 (mmm) cc_final: 0.2828 (mmm) REVERT: 2 107 SER cc_start: 0.8012 (t) cc_final: 0.7716 (t) REVERT: 2 147 LEU cc_start: 0.8764 (tp) cc_final: 0.8527 (tp) REVERT: 2 200 LEU cc_start: 0.9361 (OUTLIER) cc_final: 0.9021 (mp) REVERT: 2 363 PHE cc_start: 0.8654 (p90) cc_final: 0.8275 (p90) REVERT: 3 107 ASN cc_start: 0.8773 (m-40) cc_final: 0.8562 (m-40) REVERT: 4 236 LEU cc_start: 0.9260 (tp) cc_final: 0.8781 (tp) REVERT: 6 95 MET cc_start: 0.4170 (mpp) cc_final: 0.3892 (tmm) REVERT: 6 379 SER cc_start: 0.8542 (OUTLIER) cc_final: 0.8134 (p) REVERT: 7 244 MET cc_start: 0.7175 (mpp) cc_final: 0.6858 (mpp) REVERT: c 73 ASN cc_start: 0.8757 (t0) cc_final: 0.8287 (t0) REVERT: g 101 THR cc_start: 0.8694 (m) cc_final: 0.8253 (p) REVERT: g 104 GLN cc_start: 0.8389 (mp10) cc_final: 0.8103 (mp10) outliers start: 130 outliers final: 82 residues processed: 1137 average time/residue: 0.7795 time to fit residues: 1533.2624 Evaluate side-chains 1062 residues out of total 8648 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 87 poor density : 975 time to evaluate : 7.204 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 348 SER Chi-restraints excluded: chain A residue 524 VAL Chi-restraints excluded: chain A residue 546 VAL Chi-restraints excluded: chain A residue 664 THR Chi-restraints excluded: chain A residue 678 GLU Chi-restraints excluded: chain A residue 762 SER Chi-restraints excluded: chain A residue 802 ASN Chi-restraints excluded: chain A residue 841 LEU Chi-restraints excluded: chain A residue 863 VAL Chi-restraints excluded: chain A residue 1111 MET Chi-restraints excluded: chain A residue 1284 MET Chi-restraints excluded: chain A residue 1285 MET Chi-restraints excluded: chain A residue 1291 VAL Chi-restraints excluded: chain A residue 1405 THR Chi-restraints excluded: chain A residue 1443 VAL Chi-restraints excluded: chain B residue 63 ILE Chi-restraints excluded: chain B residue 240 ILE Chi-restraints excluded: chain B residue 415 GLN Chi-restraints excluded: chain B residue 540 SER Chi-restraints excluded: chain B residue 696 GLU Chi-restraints excluded: chain B residue 782 LEU Chi-restraints excluded: chain B residue 809 MET Chi-restraints excluded: chain B residue 825 VAL Chi-restraints excluded: chain B residue 955 THR Chi-restraints excluded: chain B residue 956 THR Chi-restraints excluded: chain B residue 1186 ASP Chi-restraints excluded: chain C residue 26 ASP Chi-restraints excluded: chain E residue 182 ASP Chi-restraints excluded: chain E residue 188 LEU Chi-restraints excluded: chain F residue 16 GLU Chi-restraints excluded: chain F residue 25 ASP Chi-restraints excluded: chain G residue 91 VAL Chi-restraints excluded: chain H residue 52 GLN Chi-restraints excluded: chain H residue 107 VAL Chi-restraints excluded: chain H residue 129 TYR Chi-restraints excluded: chain I residue 46 HIS Chi-restraints excluded: chain J residue 2 ILE Chi-restraints excluded: chain J residue 52 THR Chi-restraints excluded: chain Q residue 369 ASN Chi-restraints excluded: chain R residue 347 PHE Chi-restraints excluded: chain W residue 368 GLN Chi-restraints excluded: chain X residue 251 ASN Chi-restraints excluded: chain 0 residue 6 ASP Chi-restraints excluded: chain 0 residue 110 SER Chi-restraints excluded: chain 0 residue 344 THR Chi-restraints excluded: chain 0 residue 479 LEU Chi-restraints excluded: chain 0 residue 495 MET Chi-restraints excluded: chain 0 residue 591 SER Chi-restraints excluded: chain 1 residue 204 LEU Chi-restraints excluded: chain 1 residue 485 ASP Chi-restraints excluded: chain 1 residue 610 ASN Chi-restraints excluded: chain 2 residue 97 MET Chi-restraints excluded: chain 2 residue 192 LEU Chi-restraints excluded: chain 2 residue 196 ILE Chi-restraints excluded: chain 2 residue 200 LEU Chi-restraints excluded: chain 2 residue 250 LEU Chi-restraints excluded: chain 2 residue 388 THR Chi-restraints excluded: chain 2 residue 400 LEU Chi-restraints excluded: chain 4 residue 69 SER Chi-restraints excluded: chain 4 residue 194 ILE Chi-restraints excluded: chain 4 residue 231 THR Chi-restraints excluded: chain 4 residue 257 SER Chi-restraints excluded: chain 5 residue 43 ASN Chi-restraints excluded: chain 5 residue 62 ILE Chi-restraints excluded: chain 6 residue 137 LEU Chi-restraints excluded: chain 6 residue 148 MET Chi-restraints excluded: chain 6 residue 158 HIS Chi-restraints excluded: chain 6 residue 243 ASP Chi-restraints excluded: chain 6 residue 379 SER Chi-restraints excluded: chain 7 residue 197 LEU Chi-restraints excluded: chain a residue 61 LEU Chi-restraints excluded: chain b residue 25 ASN Chi-restraints excluded: chain c residue 16 THR Chi-restraints excluded: chain c residue 87 VAL Chi-restraints excluded: chain c residue 94 ASN Chi-restraints excluded: chain c residue 110 ASN Chi-restraints excluded: chain d residue 32 GLU Chi-restraints excluded: chain d residue 66 VAL Chi-restraints excluded: chain d residue 103 LEU Chi-restraints excluded: chain d residue 108 VAL Chi-restraints excluded: chain d residue 113 LYS Chi-restraints excluded: chain e residue 58 THR Chi-restraints excluded: chain e residue 86 SER Chi-restraints excluded: chain e residue 109 LEU Chi-restraints excluded: chain g residue 79 ILE Chi-restraints excluded: chain g residue 100 VAL Chi-restraints excluded: chain h residue 112 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 998 random chunks: chunk 503 optimal weight: 20.0000 chunk 281 optimal weight: 0.0030 chunk 754 optimal weight: 1.9990 chunk 617 optimal weight: 5.9990 chunk 250 optimal weight: 0.5980 chunk 907 optimal weight: 20.0000 chunk 980 optimal weight: 0.7980 chunk 808 optimal weight: 2.9990 chunk 900 optimal weight: 0.8980 chunk 309 optimal weight: 0.0040 chunk 728 optimal weight: 0.0050 overall best weight: 0.2816 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 4 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 5 GLN ** A 510 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 768 GLN ** A 802 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 969 GLN A1432 GLN B 415 GLN B 484 ASN ** B1097 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 132 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 61 GLN ** F 78 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 102 GLN ** K 89 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 219 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** O 225 GLN Q 140 HIS Q 150 GLN R 43 ASN ** R 239 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 36 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** W 50 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** W 280 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** X 270 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 0 224 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 1 467 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 2 190 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 2 395 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 3 36 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** 5 64 ASN 7 567 GLN ** 7 646 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 7 723 GLN a 76 GLN b 25 ASN c 94 ASN e 93 GLN Total number of N/Q/H flips: 19 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6826 moved from start: 0.1578 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.040 88785 Z= 0.145 Angle : 0.518 9.153 121636 Z= 0.278 Chirality : 0.040 0.219 13752 Planarity : 0.004 0.065 14134 Dihedral : 18.505 176.642 15190 Min Nonbonded Distance : 1.696 Molprobity Statistics. All-atom Clashscore : 10.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.41 % Favored : 97.59 % Rotamer: Outliers : 1.15 % Allowed : 10.13 % Favored : 88.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.31 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.07 (0.08), residues: 9583 helix: 0.65 (0.08), residues: 4071 sheet: -0.24 (0.15), residues: 1204 loop : -0.56 (0.09), residues: 4308 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP Q 423 HIS 0.015 0.001 HIS I 46 PHE 0.021 0.001 PHE A 714 TYR 0.028 0.001 TYR 7 581 ARG 0.013 0.000 ARG F 135 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 19166 Ramachandran restraints generated. 9583 Oldfield, 0 Emsley, 9583 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 19166 Ramachandran restraints generated. 9583 Oldfield, 0 Emsley, 9583 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1170 residues out of total 8648 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 99 poor density : 1071 time to evaluate : 7.070 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: A 122 MET cc_start: 0.4983 (mmp) cc_final: 0.4581 (mmm) REVERT: A 229 SER cc_start: 0.8506 (t) cc_final: 0.8185 (t) REVERT: A 244 PRO cc_start: 0.8287 (Cg_exo) cc_final: 0.7989 (Cg_endo) REVERT: A 341 MET cc_start: 0.7683 (mtp) cc_final: 0.7280 (mmm) REVERT: A 555 ASP cc_start: 0.6469 (t0) cc_final: 0.6251 (t0) REVERT: A 678 GLU cc_start: 0.7745 (OUTLIER) cc_final: 0.7479 (pm20) REVERT: A 708 MET cc_start: 0.7198 (ptp) cc_final: 0.6951 (ptp) REVERT: A 960 ILE cc_start: 0.7949 (mm) cc_final: 0.7651 (mm) REVERT: A 1259 MET cc_start: 0.4679 (ppp) cc_final: 0.3764 (ptp) REVERT: A 1368 MET cc_start: 0.7579 (OUTLIER) cc_final: 0.6996 (mpp) REVERT: A 1444 MET cc_start: 0.7724 (mmt) cc_final: 0.7509 (mmt) REVERT: B 63 ILE cc_start: 0.8194 (OUTLIER) cc_final: 0.7940 (tp) REVERT: B 116 GLU cc_start: 0.7428 (tt0) cc_final: 0.7149 (pt0) REVERT: B 566 LEU cc_start: 0.8238 (tp) cc_final: 0.7736 (tp) REVERT: B 597 MET cc_start: 0.7649 (ppp) cc_final: 0.7402 (tmm) REVERT: B 1210 MET cc_start: 0.8262 (mtp) cc_final: 0.7677 (mtm) REVERT: D 149 THR cc_start: 0.8572 (m) cc_final: 0.8334 (t) REVERT: E 75 MET cc_start: 0.7131 (ppp) cc_final: 0.6659 (ppp) REVERT: E 104 ASN cc_start: 0.6794 (t0) cc_final: 0.6260 (t0) REVERT: F 76 LYS cc_start: 0.6868 (mttm) cc_final: 0.6459 (mttm) REVERT: H 40 LEU cc_start: 0.8154 (tp) cc_final: 0.7766 (tp) REVERT: I 27 PHE cc_start: 0.3837 (m-80) cc_final: 0.3602 (m-80) REVERT: I 77 LYS cc_start: 0.7238 (mmtt) cc_final: 0.7014 (tptt) REVERT: K 18 LYS cc_start: 0.8285 (tppt) cc_final: 0.8056 (tppt) REVERT: K 36 GLU cc_start: 0.7504 (tp30) cc_final: 0.7221 (tp30) REVERT: K 85 ASP cc_start: 0.8266 (m-30) cc_final: 0.7874 (m-30) REVERT: K 94 ILE cc_start: 0.8437 (tp) cc_final: 0.8089 (tp) REVERT: L 53 HIS cc_start: 0.7129 (t-90) cc_final: 0.6907 (t70) REVERT: M 243 CYS cc_start: 0.8460 (m) cc_final: 0.8110 (m) REVERT: M 325 ASP cc_start: 0.6579 (t0) cc_final: 0.5994 (t70) REVERT: Q 387 ILE cc_start: 0.5265 (OUTLIER) cc_final: 0.5030 (tt) REVERT: R 294 MET cc_start: 0.0835 (pmm) cc_final: -0.0215 (pmm) REVERT: X 246 TYR cc_start: 0.6339 (t80) cc_final: 0.6002 (t80) REVERT: 0 42 MET cc_start: 0.8308 (mmm) cc_final: 0.7969 (tpt) REVERT: 0 250 LEU cc_start: 0.8578 (tp) cc_final: 0.8341 (tp) REVERT: 0 299 LEU cc_start: 0.8342 (mm) cc_final: 0.7894 (mm) REVERT: 0 375 ARG cc_start: 0.8529 (mtp180) cc_final: 0.8255 (mtm180) REVERT: 0 610 ILE cc_start: 0.8916 (mm) cc_final: 0.8642 (mm) REVERT: 0 675 ASP cc_start: 0.7664 (t70) cc_final: 0.7417 (t70) REVERT: 1 254 GLU cc_start: 0.7076 (tm-30) cc_final: 0.6837 (tm-30) REVERT: 1 467 GLN cc_start: 0.8249 (pp30) cc_final: 0.7784 (pp30) REVERT: 1 588 ASP cc_start: 0.7720 (m-30) cc_final: 0.7341 (t0) REVERT: 2 107 SER cc_start: 0.8022 (t) cc_final: 0.7692 (t) REVERT: 2 200 LEU cc_start: 0.9299 (mm) cc_final: 0.9002 (mp) REVERT: 2 249 MET cc_start: 0.8637 (tpp) cc_final: 0.8429 (tpp) REVERT: 2 363 PHE cc_start: 0.8509 (p90) cc_final: 0.8055 (p90) REVERT: 3 107 ASN cc_start: 0.8697 (m-40) cc_final: 0.8473 (m-40) REVERT: 4 236 LEU cc_start: 0.9196 (tp) cc_final: 0.8728 (tp) REVERT: 6 158 HIS cc_start: 0.7582 (OUTLIER) cc_final: 0.7352 (t-90) REVERT: a 54 TYR cc_start: 0.7825 (m-80) cc_final: 0.7445 (m-80) REVERT: c 24 GLN cc_start: 0.8051 (pm20) cc_final: 0.6772 (pm20) REVERT: c 73 ASN cc_start: 0.8755 (t0) cc_final: 0.8218 (t0) REVERT: f 88 TYR cc_start: 0.7856 (m-10) cc_final: 0.7528 (m-10) REVERT: g 104 GLN cc_start: 0.8245 (mp10) cc_final: 0.7889 (mp10) outliers start: 99 outliers final: 54 residues processed: 1118 average time/residue: 0.7797 time to fit residues: 1510.6753 Evaluate side-chains 1056 residues out of total 8648 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 59 poor density : 997 time to evaluate : 7.182 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 546 VAL Chi-restraints excluded: chain A residue 678 GLU Chi-restraints excluded: chain A residue 802 ASN Chi-restraints excluded: chain A residue 827 THR Chi-restraints excluded: chain A residue 841 LEU Chi-restraints excluded: chain A residue 1284 MET Chi-restraints excluded: chain A residue 1291 VAL Chi-restraints excluded: chain A residue 1368 MET Chi-restraints excluded: chain B residue 63 ILE Chi-restraints excluded: chain B residue 240 ILE Chi-restraints excluded: chain B residue 388 CYS Chi-restraints excluded: chain B residue 468 GLU Chi-restraints excluded: chain B residue 480 SER Chi-restraints excluded: chain B residue 561 TRP Chi-restraints excluded: chain B residue 653 VAL Chi-restraints excluded: chain B residue 696 GLU Chi-restraints excluded: chain B residue 910 VAL Chi-restraints excluded: chain B residue 955 THR Chi-restraints excluded: chain B residue 959 ASP Chi-restraints excluded: chain B residue 1191 ILE Chi-restraints excluded: chain B residue 1213 THR Chi-restraints excluded: chain D residue 159 THR Chi-restraints excluded: chain E residue 182 ASP Chi-restraints excluded: chain E residue 188 LEU Chi-restraints excluded: chain F residue 16 GLU Chi-restraints excluded: chain F residue 130 ILE Chi-restraints excluded: chain F residue 145 ASP Chi-restraints excluded: chain G residue 91 VAL Chi-restraints excluded: chain I residue 113 ASP Chi-restraints excluded: chain J residue 2 ILE Chi-restraints excluded: chain K residue 95 ILE Chi-restraints excluded: chain Q residue 387 ILE Chi-restraints excluded: chain W residue 368 GLN Chi-restraints excluded: chain 0 residue 6 ASP Chi-restraints excluded: chain 0 residue 525 MET Chi-restraints excluded: chain 1 residue 419 LEU Chi-restraints excluded: chain 1 residue 481 ILE Chi-restraints excluded: chain 1 residue 485 ASP Chi-restraints excluded: chain 1 residue 557 CYS Chi-restraints excluded: chain 2 residue 50 MET Chi-restraints excluded: chain 2 residue 192 LEU Chi-restraints excluded: chain 2 residue 250 LEU Chi-restraints excluded: chain 2 residue 400 LEU Chi-restraints excluded: chain 4 residue 188 ASP Chi-restraints excluded: chain 6 residue 137 LEU Chi-restraints excluded: chain 6 residue 158 HIS Chi-restraints excluded: chain 7 residue 578 MET Chi-restraints excluded: chain 7 residue 622 MET Chi-restraints excluded: chain c residue 94 ASN Chi-restraints excluded: chain c residue 110 ASN Chi-restraints excluded: chain d residue 103 LEU Chi-restraints excluded: chain d residue 108 VAL Chi-restraints excluded: chain d residue 113 LYS Chi-restraints excluded: chain e residue 58 THR Chi-restraints excluded: chain e residue 74 ILE Chi-restraints excluded: chain e residue 109 LEU Chi-restraints excluded: chain g residue 79 ILE Chi-restraints excluded: chain h residue 56 MET Chi-restraints excluded: chain h residue 60 ASN Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 998 random chunks: chunk 897 optimal weight: 9.9990 chunk 682 optimal weight: 4.9990 chunk 471 optimal weight: 20.0000 chunk 100 optimal weight: 1.9990 chunk 433 optimal weight: 10.9990 chunk 609 optimal weight: 1.9990 chunk 911 optimal weight: 6.9990 chunk 964 optimal weight: 10.0000 chunk 476 optimal weight: 10.0000 chunk 863 optimal weight: 1.9990 chunk 259 optimal weight: 3.9990 overall best weight: 2.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 4 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 5 GLN ** A 451 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 510 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 802 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1070 GLN A1078 GLN B 433 GLN B 484 ASN ** B 776 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B1015 HIS ** B1097 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 132 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 3 GLN ** F 78 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 89 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** M 303 GLN ** Q 140 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 239 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 36 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** W 50 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** W 280 GLN ** 0 224 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 0 239 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 1 467 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 2 190 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 2 395 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 3 36 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** 5 43 ASN b 25 ASN c 94 ASN f 27 GLN g 112 GLN Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6927 moved from start: 0.2033 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.079 88785 Z= 0.328 Angle : 0.569 9.258 121636 Z= 0.304 Chirality : 0.042 0.218 13752 Planarity : 0.004 0.065 14134 Dihedral : 18.648 178.628 15190 Min Nonbonded Distance : 1.777 Molprobity Statistics. All-atom Clashscore : 12.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.16 % Favored : 96.84 % Rotamer: Outliers : 2.11 % Allowed : 11.15 % Favored : 86.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.31 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.04 (0.09), residues: 9583 helix: 0.75 (0.08), residues: 4093 sheet: -0.34 (0.15), residues: 1205 loop : -0.59 (0.09), residues: 4285 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP 2 483 HIS 0.011 0.001 HIS B1104 PHE 0.025 0.002 PHE B 781 TYR 0.027 0.002 TYR b 88 ARG 0.012 0.000 ARG L 54 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 19166 Ramachandran restraints generated. 9583 Oldfield, 0 Emsley, 9583 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 19166 Ramachandran restraints generated. 9583 Oldfield, 0 Emsley, 9583 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1234 residues out of total 8648 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 182 poor density : 1052 time to evaluate : 7.754 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: A 122 MET cc_start: 0.5050 (mmp) cc_final: 0.4618 (mmm) REVERT: A 229 SER cc_start: 0.8437 (t) cc_final: 0.8131 (t) REVERT: A 341 MET cc_start: 0.7615 (mtp) cc_final: 0.7343 (mmm) REVERT: A 644 LYS cc_start: 0.7508 (mmtt) cc_final: 0.7199 (ttpp) REVERT: A 678 GLU cc_start: 0.7895 (OUTLIER) cc_final: 0.7606 (pm20) REVERT: A 935 GLN cc_start: 0.6456 (tp40) cc_final: 0.6106 (tp-100) REVERT: A 1259 MET cc_start: 0.5489 (ppp) cc_final: 0.4294 (ptp) REVERT: A 1285 MET cc_start: 0.6844 (OUTLIER) cc_final: 0.6607 (mtm) REVERT: A 1368 MET cc_start: 0.7827 (OUTLIER) cc_final: 0.7238 (mpp) REVERT: B 566 LEU cc_start: 0.8245 (tp) cc_final: 0.7745 (tp) REVERT: B 597 MET cc_start: 0.7692 (ppp) cc_final: 0.7469 (tmm) REVERT: B 1013 ASN cc_start: 0.7920 (t0) cc_final: 0.7659 (t0) REVERT: B 1149 GLU cc_start: 0.7771 (mp0) cc_final: 0.7533 (mp0) REVERT: B 1210 MET cc_start: 0.8390 (mtp) cc_final: 0.8050 (mtm) REVERT: D 61 GLU cc_start: 0.7300 (mm-30) cc_final: 0.6871 (mp0) REVERT: E 104 ASN cc_start: 0.6841 (t0) cc_final: 0.6253 (t0) REVERT: F 76 LYS cc_start: 0.7011 (mttm) cc_final: 0.6639 (mttm) REVERT: F 84 TYR cc_start: 0.7287 (m-80) cc_final: 0.6796 (m-80) REVERT: H 42 ILE cc_start: 0.7577 (OUTLIER) cc_final: 0.7325 (tp) REVERT: H 97 MET cc_start: 0.7244 (mmp) cc_final: 0.7024 (mmp) REVERT: I 87 GLN cc_start: 0.6230 (pp30) cc_final: 0.5893 (pp30) REVERT: K 36 GLU cc_start: 0.7850 (tp30) cc_final: 0.7589 (tp30) REVERT: K 85 ASP cc_start: 0.8320 (m-30) cc_final: 0.7963 (m-30) REVERT: L 39 SER cc_start: 0.7543 (t) cc_final: 0.7168 (p) REVERT: M 243 CYS cc_start: 0.8465 (m) cc_final: 0.8115 (m) REVERT: M 325 ASP cc_start: 0.6580 (t0) cc_final: 0.6196 (t70) REVERT: O 228 GLU cc_start: 0.7341 (OUTLIER) cc_final: 0.7076 (tp30) REVERT: R 294 MET cc_start: 0.0610 (pmm) cc_final: -0.0202 (pmm) REVERT: 0 299 LEU cc_start: 0.8461 (mm) cc_final: 0.7975 (mm) REVERT: 0 427 ASN cc_start: 0.8388 (p0) cc_final: 0.8043 (p0) REVERT: 0 610 ILE cc_start: 0.8996 (mm) cc_final: 0.8761 (mm) REVERT: 1 254 GLU cc_start: 0.7225 (tm-30) cc_final: 0.6983 (tm-30) REVERT: 2 107 SER cc_start: 0.8006 (t) cc_final: 0.7693 (t) REVERT: 2 249 MET cc_start: 0.8640 (tpp) cc_final: 0.8421 (tpp) REVERT: 2 363 PHE cc_start: 0.8641 (p90) cc_final: 0.8205 (p90) REVERT: 3 107 ASN cc_start: 0.8734 (m-40) cc_final: 0.8491 (m-40) REVERT: 4 51 ILE cc_start: 0.8537 (OUTLIER) cc_final: 0.8163 (tp) REVERT: 4 211 ASP cc_start: 0.8389 (m-30) cc_final: 0.8177 (m-30) REVERT: 4 236 LEU cc_start: 0.9246 (tp) cc_final: 0.8848 (tp) REVERT: 4 288 ILE cc_start: 0.9107 (pt) cc_final: 0.8888 (pt) REVERT: 6 95 MET cc_start: 0.4299 (mpp) cc_final: 0.4031 (tmm) REVERT: 6 136 MET cc_start: 0.8719 (mmm) cc_final: 0.8332 (mmm) REVERT: 6 158 HIS cc_start: 0.7680 (OUTLIER) cc_final: 0.7355 (t-90) REVERT: 6 379 SER cc_start: 0.8518 (OUTLIER) cc_final: 0.8080 (p) REVERT: 7 112 MET cc_start: 0.7672 (ppp) cc_final: 0.6964 (pmm) REVERT: 7 497 MET cc_start: 0.7189 (ptt) cc_final: 0.6963 (ptt) REVERT: 7 716 MET cc_start: 0.7992 (mmm) cc_final: 0.7752 (mmm) REVERT: b 79 LYS cc_start: 0.7943 (pttt) cc_final: 0.7684 (pttt) REVERT: c 73 ASN cc_start: 0.8682 (t0) cc_final: 0.8102 (t0) REVERT: d 102 GLU cc_start: 0.7005 (tt0) cc_final: 0.6768 (tt0) REVERT: d 113 LYS cc_start: 0.8143 (OUTLIER) cc_final: 0.7898 (ptmm) REVERT: g 101 THR cc_start: 0.8693 (m) cc_final: 0.8283 (p) REVERT: g 104 GLN cc_start: 0.8448 (mp10) cc_final: 0.7976 (mp10) outliers start: 182 outliers final: 120 residues processed: 1137 average time/residue: 0.7990 time to fit residues: 1577.2734 Evaluate side-chains 1105 residues out of total 8648 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 129 poor density : 976 time to evaluate : 7.340 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 348 SER Chi-restraints excluded: chain A residue 351 THR Chi-restraints excluded: chain A residue 379 VAL Chi-restraints excluded: chain A residue 497 THR Chi-restraints excluded: chain A residue 546 VAL Chi-restraints excluded: chain A residue 678 GLU Chi-restraints excluded: chain A residue 740 LEU Chi-restraints excluded: chain A residue 762 SER Chi-restraints excluded: chain A residue 781 ASP Chi-restraints excluded: chain A residue 802 ASN Chi-restraints excluded: chain A residue 827 THR Chi-restraints excluded: chain A residue 841 LEU Chi-restraints excluded: chain A residue 863 VAL Chi-restraints excluded: chain A residue 878 ILE Chi-restraints excluded: chain A residue 886 ILE Chi-restraints excluded: chain A residue 1111 MET Chi-restraints excluded: chain A residue 1124 HIS Chi-restraints excluded: chain A residue 1284 MET Chi-restraints excluded: chain A residue 1285 MET Chi-restraints excluded: chain A residue 1291 VAL Chi-restraints excluded: chain A residue 1330 ASN Chi-restraints excluded: chain A residue 1368 MET Chi-restraints excluded: chain A residue 1405 THR Chi-restraints excluded: chain B residue 240 ILE Chi-restraints excluded: chain B residue 256 VAL Chi-restraints excluded: chain B residue 298 LEU Chi-restraints excluded: chain B residue 388 CYS Chi-restraints excluded: chain B residue 468 GLU Chi-restraints excluded: chain B residue 540 SER Chi-restraints excluded: chain B residue 543 SER Chi-restraints excluded: chain B residue 653 VAL Chi-restraints excluded: chain B residue 696 GLU Chi-restraints excluded: chain B residue 805 THR Chi-restraints excluded: chain B residue 809 MET Chi-restraints excluded: chain B residue 910 VAL Chi-restraints excluded: chain B residue 955 THR Chi-restraints excluded: chain B residue 956 THR Chi-restraints excluded: chain B residue 959 ASP Chi-restraints excluded: chain B residue 1051 THR Chi-restraints excluded: chain B residue 1186 ASP Chi-restraints excluded: chain B residue 1191 ILE Chi-restraints excluded: chain B residue 1213 THR Chi-restraints excluded: chain C residue 26 ASP Chi-restraints excluded: chain C residue 65 HIS Chi-restraints excluded: chain D residue 27 LEU Chi-restraints excluded: chain D residue 52 LEU Chi-restraints excluded: chain D residue 159 THR Chi-restraints excluded: chain E residue 3 GLN Chi-restraints excluded: chain E residue 22 MET Chi-restraints excluded: chain E residue 182 ASP Chi-restraints excluded: chain E residue 188 LEU Chi-restraints excluded: chain F residue 16 GLU Chi-restraints excluded: chain F residue 71 GLU Chi-restraints excluded: chain F residue 130 ILE Chi-restraints excluded: chain G residue 77 VAL Chi-restraints excluded: chain G residue 91 VAL Chi-restraints excluded: chain H residue 42 ILE Chi-restraints excluded: chain H residue 55 LEU Chi-restraints excluded: chain H residue 107 VAL Chi-restraints excluded: chain H residue 129 TYR Chi-restraints excluded: chain H residue 139 ASN Chi-restraints excluded: chain I residue 109 ILE Chi-restraints excluded: chain I residue 113 ASP Chi-restraints excluded: chain J residue 2 ILE Chi-restraints excluded: chain J residue 5 VAL Chi-restraints excluded: chain J residue 13 VAL Chi-restraints excluded: chain K residue 95 ILE Chi-restraints excluded: chain M residue 303 GLN Chi-restraints excluded: chain O residue 228 GLU Chi-restraints excluded: chain Q residue 99 ASN Chi-restraints excluded: chain Q residue 387 ILE Chi-restraints excluded: chain R residue 39 VAL Chi-restraints excluded: chain R residue 347 PHE Chi-restraints excluded: chain V residue 20 VAL Chi-restraints excluded: chain W residue 368 GLN Chi-restraints excluded: chain X residue 251 ASN Chi-restraints excluded: chain 0 residue 6 ASP Chi-restraints excluded: chain 0 residue 17 ILE Chi-restraints excluded: chain 0 residue 37 ASN Chi-restraints excluded: chain 0 residue 195 ILE Chi-restraints excluded: chain 0 residue 325 ILE Chi-restraints excluded: chain 0 residue 344 THR Chi-restraints excluded: chain 0 residue 495 MET Chi-restraints excluded: chain 0 residue 607 SER Chi-restraints excluded: chain 0 residue 642 MET Chi-restraints excluded: chain 0 residue 678 VAL Chi-restraints excluded: chain 1 residue 349 VAL Chi-restraints excluded: chain 1 residue 419 LEU Chi-restraints excluded: chain 1 residue 481 ILE Chi-restraints excluded: chain 1 residue 485 ASP Chi-restraints excluded: chain 2 residue 50 MET Chi-restraints excluded: chain 2 residue 192 LEU Chi-restraints excluded: chain 2 residue 196 ILE Chi-restraints excluded: chain 2 residue 250 LEU Chi-restraints excluded: chain 2 residue 388 THR Chi-restraints excluded: chain 2 residue 400 LEU Chi-restraints excluded: chain 3 residue 72 ILE Chi-restraints excluded: chain 4 residue 51 ILE Chi-restraints excluded: chain 4 residue 69 SER Chi-restraints excluded: chain 4 residue 188 ASP Chi-restraints excluded: chain 4 residue 294 CYS Chi-restraints excluded: chain 5 residue 10 VAL Chi-restraints excluded: chain 5 residue 62 ILE Chi-restraints excluded: chain 6 residue 137 LEU Chi-restraints excluded: chain 6 residue 148 MET Chi-restraints excluded: chain 6 residue 158 HIS Chi-restraints excluded: chain 6 residue 178 LEU Chi-restraints excluded: chain 6 residue 243 ASP Chi-restraints excluded: chain 6 residue 379 SER Chi-restraints excluded: chain 7 residue 197 LEU Chi-restraints excluded: chain 7 residue 453 VAL Chi-restraints excluded: chain 7 residue 516 THR Chi-restraints excluded: chain 7 residue 622 MET Chi-restraints excluded: chain b residue 25 ASN Chi-restraints excluded: chain c residue 16 THR Chi-restraints excluded: chain c residue 94 ASN Chi-restraints excluded: chain c residue 110 ASN Chi-restraints excluded: chain d residue 32 GLU Chi-restraints excluded: chain d residue 66 VAL Chi-restraints excluded: chain d residue 97 LEU Chi-restraints excluded: chain d residue 103 LEU Chi-restraints excluded: chain d residue 108 VAL Chi-restraints excluded: chain d residue 113 LYS Chi-restraints excluded: chain e residue 58 THR Chi-restraints excluded: chain e residue 124 ILE Chi-restraints excluded: chain g residue 79 ILE Chi-restraints excluded: chain h residue 56 MET Chi-restraints excluded: chain h residue 60 ASN Chi-restraints excluded: chain h residue 112 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 998 random chunks: chunk 803 optimal weight: 0.7980 chunk 547 optimal weight: 30.0000 chunk 14 optimal weight: 50.0000 chunk 718 optimal weight: 0.7980 chunk 398 optimal weight: 0.0470 chunk 823 optimal weight: 30.0000 chunk 666 optimal weight: 0.7980 chunk 1 optimal weight: 4.9990 chunk 492 optimal weight: 20.0000 chunk 865 optimal weight: 4.9990 chunk 243 optimal weight: 2.9990 overall best weight: 1.0880 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 4 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 5 GLN ** A 451 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 510 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 802 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 965 GLN A1070 GLN B 178 ASN ** B 667 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 776 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1097 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 132 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 3 GLN ** F 78 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 102 GLN H 137 GLN ** K 89 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 219 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 140 HIS ** R 239 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 36 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** W 50 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** W 280 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** X 265 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 0 224 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 0 239 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 2 190 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 2 395 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 3 36 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** 4 192 GLN 7 419 GLN 7 491 HIS c 94 ASN f 27 GLN Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6872 moved from start: 0.2083 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 88785 Z= 0.177 Angle : 0.519 10.573 121636 Z= 0.277 Chirality : 0.040 0.226 13752 Planarity : 0.004 0.065 14134 Dihedral : 18.618 177.394 15190 Min Nonbonded Distance : 1.797 Molprobity Statistics. All-atom Clashscore : 11.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.58 % Favored : 97.42 % Rotamer: Outliers : 1.69 % Allowed : 12.33 % Favored : 85.98 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.31 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.15 (0.09), residues: 9583 helix: 0.94 (0.08), residues: 4084 sheet: -0.32 (0.15), residues: 1223 loop : -0.50 (0.09), residues: 4276 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP 2 483 HIS 0.010 0.001 HIS L 53 PHE 0.021 0.001 PHE A 714 TYR 0.029 0.001 TYR B 380 ARG 0.008 0.000 ARG b 92 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 19166 Ramachandran restraints generated. 9583 Oldfield, 0 Emsley, 9583 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 19166 Ramachandran restraints generated. 9583 Oldfield, 0 Emsley, 9583 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1194 residues out of total 8648 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 146 poor density : 1048 time to evaluate : 7.382 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: A 122 MET cc_start: 0.5098 (mmp) cc_final: 0.4742 (mmm) REVERT: A 229 SER cc_start: 0.8456 (t) cc_final: 0.8192 (t) REVERT: A 332 LYS cc_start: 0.6397 (tppt) cc_final: 0.6144 (tppt) REVERT: A 341 MET cc_start: 0.7714 (mtp) cc_final: 0.7245 (mmm) REVERT: A 678 GLU cc_start: 0.7742 (OUTLIER) cc_final: 0.7448 (pm20) REVERT: A 708 MET cc_start: 0.7226 (ptp) cc_final: 0.6994 (ptp) REVERT: A 935 GLN cc_start: 0.6440 (tp40) cc_final: 0.6081 (tp-100) REVERT: A 1259 MET cc_start: 0.5103 (ppp) cc_final: 0.4363 (tmm) REVERT: A 1285 MET cc_start: 0.6809 (OUTLIER) cc_final: 0.6601 (mtm) REVERT: A 1368 MET cc_start: 0.7750 (OUTLIER) cc_final: 0.7108 (mpp) REVERT: A 1398 MET cc_start: 0.7099 (mtp) cc_final: 0.6699 (ttm) REVERT: B 63 ILE cc_start: 0.8192 (OUTLIER) cc_final: 0.7976 (tp) REVERT: B 116 GLU cc_start: 0.7483 (tt0) cc_final: 0.7206 (pt0) REVERT: B 432 MET cc_start: 0.7146 (mtm) cc_final: 0.6916 (mtm) REVERT: B 526 GLU cc_start: 0.7025 (tt0) cc_final: 0.6572 (tt0) REVERT: B 566 LEU cc_start: 0.8190 (tp) cc_final: 0.7684 (tp) REVERT: B 597 MET cc_start: 0.7663 (ppp) cc_final: 0.7387 (tmm) REVERT: B 1013 ASN cc_start: 0.7901 (t0) cc_final: 0.7679 (t0) REVERT: B 1210 MET cc_start: 0.8376 (mtp) cc_final: 0.8009 (mtm) REVERT: D 61 GLU cc_start: 0.7321 (mm-30) cc_final: 0.6945 (mp0) REVERT: E 75 MET cc_start: 0.7141 (ppp) cc_final: 0.6497 (ppp) REVERT: E 104 ASN cc_start: 0.6724 (t0) cc_final: 0.6103 (t0) REVERT: H 40 LEU cc_start: 0.8000 (tp) cc_final: 0.7799 (tp) REVERT: I 77 LYS cc_start: 0.7244 (mmtt) cc_final: 0.7036 (tptt) REVERT: K 36 GLU cc_start: 0.7759 (tp30) cc_final: 0.7515 (tp30) REVERT: K 85 ASP cc_start: 0.8292 (m-30) cc_final: 0.7910 (m-30) REVERT: L 46 VAL cc_start: 0.6616 (OUTLIER) cc_final: 0.6401 (m) REVERT: M 243 CYS cc_start: 0.8426 (m) cc_final: 0.8075 (m) REVERT: M 325 ASP cc_start: 0.6753 (t0) cc_final: 0.6312 (t70) REVERT: R 294 MET cc_start: 0.0568 (pmm) cc_final: -0.0205 (pmm) REVERT: 0 144 LYS cc_start: 0.7447 (mtmt) cc_final: 0.6884 (mtmm) REVERT: 0 250 LEU cc_start: 0.8767 (tp) cc_final: 0.8462 (tp) REVERT: 0 299 LEU cc_start: 0.8404 (mm) cc_final: 0.7908 (mm) REVERT: 0 427 ASN cc_start: 0.8353 (p0) cc_final: 0.7978 (p0) REVERT: 0 610 ILE cc_start: 0.8968 (mm) cc_final: 0.8674 (mm) REVERT: 1 192 MET cc_start: 0.7411 (mmm) cc_final: 0.7092 (tpp) REVERT: 1 254 GLU cc_start: 0.7181 (tm-30) cc_final: 0.6928 (tm-30) REVERT: 1 467 GLN cc_start: 0.8255 (pp30) cc_final: 0.7947 (pp30) REVERT: 2 107 SER cc_start: 0.8047 (t) cc_final: 0.7738 (t) REVERT: 2 249 MET cc_start: 0.8594 (tpp) cc_final: 0.8384 (tpp) REVERT: 2 363 PHE cc_start: 0.8541 (p90) cc_final: 0.8016 (p90) REVERT: 3 12 MET cc_start: 0.7633 (pmm) cc_final: 0.7238 (pmm) REVERT: 3 107 ASN cc_start: 0.8655 (m-40) cc_final: 0.8432 (m-40) REVERT: 4 128 GLU cc_start: 0.8350 (mm-30) cc_final: 0.8083 (mm-30) REVERT: 4 224 LEU cc_start: 0.8058 (OUTLIER) cc_final: 0.7829 (mt) REVERT: 4 236 LEU cc_start: 0.9167 (tp) cc_final: 0.8772 (tp) REVERT: 5 56 ARG cc_start: 0.7268 (OUTLIER) cc_final: 0.6635 (ptm-80) REVERT: 6 142 ARG cc_start: 0.7533 (mmm160) cc_final: 0.7277 (mmm160) REVERT: 7 112 MET cc_start: 0.7530 (ppp) cc_final: 0.6899 (pmm) REVERT: 7 716 MET cc_start: 0.7907 (mmm) cc_final: 0.7654 (mmm) REVERT: b 84 MET cc_start: 0.7343 (tmm) cc_final: 0.7098 (tmm) REVERT: c 73 ASN cc_start: 0.8683 (t0) cc_final: 0.8106 (t0) REVERT: d 102 GLU cc_start: 0.7059 (tt0) cc_final: 0.6752 (tt0) REVERT: f 88 TYR cc_start: 0.7894 (m-10) cc_final: 0.7674 (m-10) REVERT: g 61 GLU cc_start: 0.7327 (OUTLIER) cc_final: 0.6986 (tp30) REVERT: g 101 THR cc_start: 0.8719 (m) cc_final: 0.8348 (p) REVERT: g 104 GLN cc_start: 0.8381 (mp10) cc_final: 0.7973 (mp10) outliers start: 146 outliers final: 98 residues processed: 1123 average time/residue: 0.7794 time to fit residues: 1518.6293 Evaluate side-chains 1093 residues out of total 8648 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 106 poor density : 987 time to evaluate : 7.402 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 234 MET Chi-restraints excluded: chain A residue 329 LEU Chi-restraints excluded: chain A residue 375 THR Chi-restraints excluded: chain A residue 379 VAL Chi-restraints excluded: chain A residue 542 GLU Chi-restraints excluded: chain A residue 546 VAL Chi-restraints excluded: chain A residue 678 GLU Chi-restraints excluded: chain A residue 740 LEU Chi-restraints excluded: chain A residue 762 SER Chi-restraints excluded: chain A residue 802 ASN Chi-restraints excluded: chain A residue 827 THR Chi-restraints excluded: chain A residue 841 LEU Chi-restraints excluded: chain A residue 1111 MET Chi-restraints excluded: chain A residue 1124 HIS Chi-restraints excluded: chain A residue 1284 MET Chi-restraints excluded: chain A residue 1285 MET Chi-restraints excluded: chain A residue 1291 VAL Chi-restraints excluded: chain A residue 1330 ASN Chi-restraints excluded: chain A residue 1368 MET Chi-restraints excluded: chain A residue 1432 GLN Chi-restraints excluded: chain A residue 1443 VAL Chi-restraints excluded: chain B residue 63 ILE Chi-restraints excluded: chain B residue 225 VAL Chi-restraints excluded: chain B residue 240 ILE Chi-restraints excluded: chain B residue 298 LEU Chi-restraints excluded: chain B residue 388 CYS Chi-restraints excluded: chain B residue 468 GLU Chi-restraints excluded: chain B residue 480 SER Chi-restraints excluded: chain B residue 540 SER Chi-restraints excluded: chain B residue 543 SER Chi-restraints excluded: chain B residue 696 GLU Chi-restraints excluded: chain B residue 782 LEU Chi-restraints excluded: chain B residue 910 VAL Chi-restraints excluded: chain B residue 955 THR Chi-restraints excluded: chain B residue 956 THR Chi-restraints excluded: chain B residue 959 ASP Chi-restraints excluded: chain B residue 999 MET Chi-restraints excluded: chain B residue 1156 ASP Chi-restraints excluded: chain B residue 1191 ILE Chi-restraints excluded: chain B residue 1213 THR Chi-restraints excluded: chain C residue 26 ASP Chi-restraints excluded: chain C residue 65 HIS Chi-restraints excluded: chain D residue 52 LEU Chi-restraints excluded: chain E residue 22 MET Chi-restraints excluded: chain E residue 182 ASP Chi-restraints excluded: chain E residue 188 LEU Chi-restraints excluded: chain F residue 16 GLU Chi-restraints excluded: chain F residue 71 GLU Chi-restraints excluded: chain F residue 130 ILE Chi-restraints excluded: chain G residue 77 VAL Chi-restraints excluded: chain G residue 91 VAL Chi-restraints excluded: chain H residue 42 ILE Chi-restraints excluded: chain H residue 122 LEU Chi-restraints excluded: chain H residue 139 ASN Chi-restraints excluded: chain H residue 142 LEU Chi-restraints excluded: chain I residue 109 ILE Chi-restraints excluded: chain I residue 113 ASP Chi-restraints excluded: chain J residue 2 ILE Chi-restraints excluded: chain J residue 5 VAL Chi-restraints excluded: chain J residue 13 VAL Chi-restraints excluded: chain K residue 95 ILE Chi-restraints excluded: chain L residue 46 VAL Chi-restraints excluded: chain V residue 20 VAL Chi-restraints excluded: chain W residue 261 HIS Chi-restraints excluded: chain W residue 368 GLN Chi-restraints excluded: chain X residue 251 ASN Chi-restraints excluded: chain 0 residue 6 ASP Chi-restraints excluded: chain 0 residue 37 ASN Chi-restraints excluded: chain 0 residue 44 SER Chi-restraints excluded: chain 0 residue 344 THR Chi-restraints excluded: chain 0 residue 472 MET Chi-restraints excluded: chain 0 residue 495 MET Chi-restraints excluded: chain 0 residue 525 MET Chi-restraints excluded: chain 0 residue 591 SER Chi-restraints excluded: chain 0 residue 597 ILE Chi-restraints excluded: chain 0 residue 642 MET Chi-restraints excluded: chain 0 residue 678 VAL Chi-restraints excluded: chain 1 residue 349 VAL Chi-restraints excluded: chain 1 residue 419 LEU Chi-restraints excluded: chain 1 residue 481 ILE Chi-restraints excluded: chain 1 residue 485 ASP Chi-restraints excluded: chain 1 residue 557 CYS Chi-restraints excluded: chain 2 residue 192 LEU Chi-restraints excluded: chain 2 residue 196 ILE Chi-restraints excluded: chain 2 residue 250 LEU Chi-restraints excluded: chain 2 residue 400 LEU Chi-restraints excluded: chain 4 residue 188 ASP Chi-restraints excluded: chain 4 residue 224 LEU Chi-restraints excluded: chain 5 residue 56 ARG Chi-restraints excluded: chain 6 residue 137 LEU Chi-restraints excluded: chain 6 residue 148 MET Chi-restraints excluded: chain 7 residue 197 LEU Chi-restraints excluded: chain 7 residue 453 VAL Chi-restraints excluded: chain 7 residue 516 THR Chi-restraints excluded: chain 7 residue 622 MET Chi-restraints excluded: chain c residue 110 ASN Chi-restraints excluded: chain d residue 97 LEU Chi-restraints excluded: chain d residue 103 LEU Chi-restraints excluded: chain d residue 108 VAL Chi-restraints excluded: chain e residue 58 THR Chi-restraints excluded: chain e residue 109 LEU Chi-restraints excluded: chain g residue 61 GLU Chi-restraints excluded: chain g residue 62 ILE Chi-restraints excluded: chain g residue 79 ILE Chi-restraints excluded: chain h residue 56 MET Chi-restraints excluded: chain h residue 60 ASN Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 998 random chunks: chunk 324 optimal weight: 4.9990 chunk 868 optimal weight: 20.0000 chunk 190 optimal weight: 2.9990 chunk 566 optimal weight: 4.9990 chunk 238 optimal weight: 0.8980 chunk 965 optimal weight: 2.9990 chunk 801 optimal weight: 8.9990 chunk 447 optimal weight: 10.0000 chunk 80 optimal weight: 1.9990 chunk 319 optimal weight: 4.9990 chunk 506 optimal weight: 6.9990 overall best weight: 2.7788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 4 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 5 GLN ** A 451 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 510 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 742 ASN ** A 802 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 178 ASN ** B 667 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 776 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1097 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 132 GLN D 165 GLN ** F 78 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 102 GLN ** K 89 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** M 303 GLN O 219 GLN ** Q 140 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 239 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 36 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** U 277 GLN U 280 GLN ** W 50 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** W 280 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** X 265 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 0 224 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 0 239 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 2 190 GLN 2 395 GLN ** 3 36 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** 4 45 ASN 4 192 GLN ** 5 61 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 6 212 ASN b 25 ASN c 94 ASN e 93 GLN Total number of N/Q/H flips: 18 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6930 moved from start: 0.2363 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.057 88785 Z= 0.306 Angle : 0.557 10.573 121636 Z= 0.296 Chirality : 0.041 0.240 13752 Planarity : 0.004 0.067 14134 Dihedral : 18.678 178.311 15190 Min Nonbonded Distance : 1.837 Molprobity Statistics. All-atom Clashscore : 12.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.18 % Favored : 96.82 % Rotamer: Outliers : 2.24 % Allowed : 12.83 % Favored : 84.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.31 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.09 (0.09), residues: 9583 helix: 0.91 (0.08), residues: 4095 sheet: -0.41 (0.15), residues: 1207 loop : -0.55 (0.09), residues: 4281 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP 2 483 HIS 0.009 0.001 HIS B1104 PHE 0.025 0.002 PHE B 781 TYR 0.027 0.002 TYR b 88 ARG 0.012 0.000 ARG L 54 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 19166 Ramachandran restraints generated. 9583 Oldfield, 0 Emsley, 9583 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 19166 Ramachandran restraints generated. 9583 Oldfield, 0 Emsley, 9583 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1216 residues out of total 8648 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 194 poor density : 1022 time to evaluate : 7.138 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: A 122 MET cc_start: 0.5112 (mmp) cc_final: 0.4752 (mmm) REVERT: A 229 SER cc_start: 0.8419 (t) cc_final: 0.8129 (t) REVERT: A 341 MET cc_start: 0.7607 (mtp) cc_final: 0.7274 (mmm) REVERT: A 678 GLU cc_start: 0.7772 (OUTLIER) cc_final: 0.7501 (pm20) REVERT: A 722 LEU cc_start: 0.8203 (OUTLIER) cc_final: 0.7961 (mm) REVERT: A 935 GLN cc_start: 0.6507 (tp40) cc_final: 0.6152 (tp-100) REVERT: A 1259 MET cc_start: 0.5647 (ppp) cc_final: 0.5330 (ppp) REVERT: A 1285 MET cc_start: 0.6958 (OUTLIER) cc_final: 0.6693 (mtm) REVERT: A 1368 MET cc_start: 0.7793 (OUTLIER) cc_final: 0.7168 (mpp) REVERT: A 1444 MET cc_start: 0.7726 (mmt) cc_final: 0.7526 (mmt) REVERT: B 431 TYR cc_start: 0.8088 (t80) cc_final: 0.7579 (t80) REVERT: B 432 MET cc_start: 0.7182 (mtm) cc_final: 0.6973 (mtm) REVERT: B 526 GLU cc_start: 0.7109 (tt0) cc_final: 0.6724 (tt0) REVERT: B 615 MET cc_start: 0.7870 (mpp) cc_final: 0.7428 (mpp) REVERT: B 624 LEU cc_start: 0.7703 (OUTLIER) cc_final: 0.7470 (mm) REVERT: B 1013 ASN cc_start: 0.8050 (t0) cc_final: 0.7846 (t0) REVERT: B 1210 MET cc_start: 0.8398 (mtp) cc_final: 0.8043 (mtm) REVERT: D 61 GLU cc_start: 0.7384 (mm-30) cc_final: 0.6990 (mp0) REVERT: E 104 ASN cc_start: 0.6680 (t0) cc_final: 0.6049 (t0) REVERT: I 77 LYS cc_start: 0.7285 (mmtt) cc_final: 0.7076 (tptt) REVERT: I 87 GLN cc_start: 0.6129 (pp30) cc_final: 0.5604 (pp30) REVERT: K 37 LYS cc_start: 0.8353 (tppt) cc_final: 0.8146 (tppt) REVERT: K 85 ASP cc_start: 0.8293 (m-30) cc_final: 0.7923 (m-30) REVERT: L 39 SER cc_start: 0.7581 (t) cc_final: 0.7211 (p) REVERT: M 243 CYS cc_start: 0.8481 (m) cc_final: 0.8122 (m) REVERT: M 325 ASP cc_start: 0.6799 (t0) cc_final: 0.6363 (t70) REVERT: O 104 MET cc_start: 0.6788 (ptp) cc_final: 0.6555 (ptp) REVERT: O 121 MET cc_start: 0.4468 (ppp) cc_final: 0.3740 (ppp) REVERT: R 294 MET cc_start: 0.0633 (pmm) cc_final: -0.0131 (pmm) REVERT: W 15 PHE cc_start: 0.8531 (t80) cc_final: 0.8250 (t80) REVERT: 0 76 MET cc_start: 0.7287 (ttp) cc_final: 0.7053 (tmm) REVERT: 0 299 LEU cc_start: 0.8440 (mm) cc_final: 0.7926 (mm) REVERT: 0 416 PHE cc_start: 0.9009 (m-10) cc_final: 0.8635 (m-10) REVERT: 0 427 ASN cc_start: 0.8348 (p0) cc_final: 0.8009 (p0) REVERT: 0 610 ILE cc_start: 0.8998 (mm) cc_final: 0.8749 (mm) REVERT: 1 192 MET cc_start: 0.7545 (mmm) cc_final: 0.7182 (tpp) REVERT: 1 254 GLU cc_start: 0.7254 (tm-30) cc_final: 0.6999 (tm-30) REVERT: 2 107 SER cc_start: 0.7995 (t) cc_final: 0.7721 (t) REVERT: 2 249 MET cc_start: 0.8652 (tpp) cc_final: 0.8444 (tpp) REVERT: 2 363 PHE cc_start: 0.8624 (p90) cc_final: 0.8126 (p90) REVERT: 3 107 ASN cc_start: 0.8680 (m-40) cc_final: 0.8462 (m-40) REVERT: 4 51 ILE cc_start: 0.8564 (OUTLIER) cc_final: 0.8296 (tp) REVERT: 4 236 LEU cc_start: 0.9190 (tp) cc_final: 0.8804 (tp) REVERT: 5 56 ARG cc_start: 0.7429 (OUTLIER) cc_final: 0.6811 (ptm-80) REVERT: 6 142 ARG cc_start: 0.7553 (mmm160) cc_final: 0.7300 (mmm160) REVERT: 6 379 SER cc_start: 0.8567 (OUTLIER) cc_final: 0.8138 (p) REVERT: 7 112 MET cc_start: 0.7608 (ppp) cc_final: 0.7001 (pmm) REVERT: 7 566 TYR cc_start: 0.8693 (OUTLIER) cc_final: 0.7511 (t80) REVERT: 7 716 MET cc_start: 0.7996 (mmm) cc_final: 0.7754 (mmm) REVERT: c 73 ASN cc_start: 0.8666 (t0) cc_final: 0.8111 (t0) REVERT: d 42 LEU cc_start: 0.8843 (tp) cc_final: 0.8636 (tp) REVERT: g 61 GLU cc_start: 0.7419 (OUTLIER) cc_final: 0.7092 (tp30) REVERT: g 101 THR cc_start: 0.8755 (m) cc_final: 0.8350 (p) REVERT: g 104 GLN cc_start: 0.8485 (mp10) cc_final: 0.8093 (mp10) REVERT: g 116 LEU cc_start: 0.8774 (mm) cc_final: 0.8552 (tt) REVERT: h 56 MET cc_start: 0.7961 (OUTLIER) cc_final: 0.7602 (tpp) REVERT: h 83 ARG cc_start: 0.8139 (tpp80) cc_final: 0.7551 (mtt180) outliers start: 194 outliers final: 139 residues processed: 1116 average time/residue: 0.7871 time to fit residues: 1556.8734 Evaluate side-chains 1120 residues out of total 8648 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 150 poor density : 970 time to evaluate : 7.193 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 234 MET Chi-restraints excluded: chain A residue 329 LEU Chi-restraints excluded: chain A residue 375 THR Chi-restraints excluded: chain A residue 379 VAL Chi-restraints excluded: chain A residue 500 GLU Chi-restraints excluded: chain A residue 542 GLU Chi-restraints excluded: chain A residue 546 VAL Chi-restraints excluded: chain A residue 678 GLU Chi-restraints excluded: chain A residue 722 LEU Chi-restraints excluded: chain A residue 740 LEU Chi-restraints excluded: chain A residue 762 SER Chi-restraints excluded: chain A residue 802 ASN Chi-restraints excluded: chain A residue 822 GLU Chi-restraints excluded: chain A residue 827 THR Chi-restraints excluded: chain A residue 841 LEU Chi-restraints excluded: chain A residue 863 VAL Chi-restraints excluded: chain A residue 878 ILE Chi-restraints excluded: chain A residue 886 ILE Chi-restraints excluded: chain A residue 1111 MET Chi-restraints excluded: chain A residue 1124 HIS Chi-restraints excluded: chain A residue 1284 MET Chi-restraints excluded: chain A residue 1285 MET Chi-restraints excluded: chain A residue 1291 VAL Chi-restraints excluded: chain A residue 1330 ASN Chi-restraints excluded: chain A residue 1368 MET Chi-restraints excluded: chain A residue 1377 THR Chi-restraints excluded: chain A residue 1443 VAL Chi-restraints excluded: chain B residue 30 SER Chi-restraints excluded: chain B residue 55 VAL Chi-restraints excluded: chain B residue 63 ILE Chi-restraints excluded: chain B residue 225 VAL Chi-restraints excluded: chain B residue 240 ILE Chi-restraints excluded: chain B residue 298 LEU Chi-restraints excluded: chain B residue 388 CYS Chi-restraints excluded: chain B residue 468 GLU Chi-restraints excluded: chain B residue 492 LEU Chi-restraints excluded: chain B residue 540 SER Chi-restraints excluded: chain B residue 543 SER Chi-restraints excluded: chain B residue 624 LEU Chi-restraints excluded: chain B residue 653 VAL Chi-restraints excluded: chain B residue 696 GLU Chi-restraints excluded: chain B residue 782 LEU Chi-restraints excluded: chain B residue 805 THR Chi-restraints excluded: chain B residue 809 MET Chi-restraints excluded: chain B residue 910 VAL Chi-restraints excluded: chain B residue 955 THR Chi-restraints excluded: chain B residue 956 THR Chi-restraints excluded: chain B residue 959 ASP Chi-restraints excluded: chain B residue 999 MET Chi-restraints excluded: chain B residue 1051 THR Chi-restraints excluded: chain B residue 1152 MET Chi-restraints excluded: chain B residue 1156 ASP Chi-restraints excluded: chain B residue 1169 MET Chi-restraints excluded: chain B residue 1186 ASP Chi-restraints excluded: chain B residue 1191 ILE Chi-restraints excluded: chain B residue 1213 THR Chi-restraints excluded: chain C residue 26 ASP Chi-restraints excluded: chain C residue 65 HIS Chi-restraints excluded: chain D residue 52 LEU Chi-restraints excluded: chain D residue 159 THR Chi-restraints excluded: chain E residue 22 MET Chi-restraints excluded: chain E residue 50 MET Chi-restraints excluded: chain E residue 182 ASP Chi-restraints excluded: chain E residue 188 LEU Chi-restraints excluded: chain F residue 16 GLU Chi-restraints excluded: chain F residue 71 GLU Chi-restraints excluded: chain F residue 130 ILE Chi-restraints excluded: chain G residue 77 VAL Chi-restraints excluded: chain G residue 91 VAL Chi-restraints excluded: chain H residue 49 VAL Chi-restraints excluded: chain H residue 55 LEU Chi-restraints excluded: chain H residue 88 SER Chi-restraints excluded: chain H residue 107 VAL Chi-restraints excluded: chain H residue 122 LEU Chi-restraints excluded: chain H residue 139 ASN Chi-restraints excluded: chain I residue 113 ASP Chi-restraints excluded: chain J residue 2 ILE Chi-restraints excluded: chain J residue 5 VAL Chi-restraints excluded: chain J residue 13 VAL Chi-restraints excluded: chain K residue 94 ILE Chi-restraints excluded: chain K residue 95 ILE Chi-restraints excluded: chain K residue 98 LEU Chi-restraints excluded: chain M residue 188 THR Chi-restraints excluded: chain M residue 303 GLN Chi-restraints excluded: chain Q residue 99 ASN Chi-restraints excluded: chain R residue 39 VAL Chi-restraints excluded: chain R residue 347 PHE Chi-restraints excluded: chain V residue 20 VAL Chi-restraints excluded: chain W residue 261 HIS Chi-restraints excluded: chain W residue 368 GLN Chi-restraints excluded: chain X residue 251 ASN Chi-restraints excluded: chain 0 residue 6 ASP Chi-restraints excluded: chain 0 residue 17 ILE Chi-restraints excluded: chain 0 residue 37 ASN Chi-restraints excluded: chain 0 residue 325 ILE Chi-restraints excluded: chain 0 residue 344 THR Chi-restraints excluded: chain 0 residue 487 LEU Chi-restraints excluded: chain 0 residue 495 MET Chi-restraints excluded: chain 0 residue 525 MET Chi-restraints excluded: chain 0 residue 591 SER Chi-restraints excluded: chain 0 residue 597 ILE Chi-restraints excluded: chain 0 residue 607 SER Chi-restraints excluded: chain 0 residue 642 MET Chi-restraints excluded: chain 0 residue 678 VAL Chi-restraints excluded: chain 1 residue 419 LEU Chi-restraints excluded: chain 1 residue 481 ILE Chi-restraints excluded: chain 1 residue 485 ASP Chi-restraints excluded: chain 1 residue 610 ASN Chi-restraints excluded: chain 2 residue 50 MET Chi-restraints excluded: chain 2 residue 192 LEU Chi-restraints excluded: chain 2 residue 196 ILE Chi-restraints excluded: chain 2 residue 250 LEU Chi-restraints excluded: chain 2 residue 400 LEU Chi-restraints excluded: chain 3 residue 72 ILE Chi-restraints excluded: chain 4 residue 51 ILE Chi-restraints excluded: chain 4 residue 69 SER Chi-restraints excluded: chain 4 residue 188 ASP Chi-restraints excluded: chain 4 residue 215 ILE Chi-restraints excluded: chain 4 residue 224 LEU Chi-restraints excluded: chain 5 residue 10 VAL Chi-restraints excluded: chain 5 residue 56 ARG Chi-restraints excluded: chain 5 residue 62 ILE Chi-restraints excluded: chain 6 residue 137 LEU Chi-restraints excluded: chain 6 residue 148 MET Chi-restraints excluded: chain 6 residue 178 LEU Chi-restraints excluded: chain 6 residue 243 ASP Chi-restraints excluded: chain 6 residue 379 SER Chi-restraints excluded: chain 7 residue 197 LEU Chi-restraints excluded: chain 7 residue 330 CYS Chi-restraints excluded: chain 7 residue 453 VAL Chi-restraints excluded: chain 7 residue 516 THR Chi-restraints excluded: chain 7 residue 566 TYR Chi-restraints excluded: chain 7 residue 578 MET Chi-restraints excluded: chain 7 residue 612 VAL Chi-restraints excluded: chain 7 residue 712 ASP Chi-restraints excluded: chain b residue 25 ASN Chi-restraints excluded: chain c residue 94 ASN Chi-restraints excluded: chain c residue 110 ASN Chi-restraints excluded: chain d residue 97 LEU Chi-restraints excluded: chain d residue 103 LEU Chi-restraints excluded: chain d residue 108 VAL Chi-restraints excluded: chain e residue 58 THR Chi-restraints excluded: chain e residue 65 LEU Chi-restraints excluded: chain e residue 74 ILE Chi-restraints excluded: chain e residue 109 LEU Chi-restraints excluded: chain e residue 115 LYS Chi-restraints excluded: chain g residue 61 GLU Chi-restraints excluded: chain g residue 79 ILE Chi-restraints excluded: chain h residue 56 MET Chi-restraints excluded: chain h residue 60 ASN Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 998 random chunks: chunk 930 optimal weight: 0.9990 chunk 108 optimal weight: 0.8980 chunk 550 optimal weight: 50.0000 chunk 705 optimal weight: 9.9990 chunk 546 optimal weight: 30.0000 chunk 812 optimal weight: 1.9990 chunk 539 optimal weight: 50.0000 chunk 961 optimal weight: 2.9990 chunk 601 optimal weight: 10.0000 chunk 586 optimal weight: 50.0000 chunk 444 optimal weight: 10.0000 overall best weight: 3.3788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 4 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 5 GLN ** A 451 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 510 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 802 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1432 GLN B 178 ASN B 513 GLN ** B 667 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 776 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 946 ASN ** B1097 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 165 GLN ** F 78 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 102 GLN H 137 GLN K 44 ASN ** K 89 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** M 303 GLN ** Q 140 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** R 88 HIS ** R 239 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 36 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** W 50 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** W 280 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** X 265 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** X 270 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 0 224 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 0 239 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 1 248 ASN 1 467 GLN ** 2 431 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 3 36 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** 4 192 GLN e 93 GLN f 27 GLN Total number of N/Q/H flips: 16 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6959 moved from start: 0.2643 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.071 88785 Z= 0.363 Angle : 0.592 10.593 121636 Z= 0.314 Chirality : 0.042 0.234 13752 Planarity : 0.004 0.069 14134 Dihedral : 18.789 178.264 15190 Min Nonbonded Distance : 1.909 Molprobity Statistics. All-atom Clashscore : 13.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.47 % Favored : 96.53 % Rotamer: Outliers : 2.46 % Allowed : 13.56 % Favored : 83.98 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.31 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.02 (0.09), residues: 9583 helix: 0.83 (0.08), residues: 4102 sheet: -0.48 (0.15), residues: 1210 loop : -0.62 (0.09), residues: 4271 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.027 0.002 TRP X 263 HIS 0.014 0.001 HIS B1104 PHE 0.027 0.002 PHE B 781 TYR 0.032 0.002 TYR b 88 ARG 0.013 0.000 ARG L 54 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 19166 Ramachandran restraints generated. 9583 Oldfield, 0 Emsley, 9583 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 19166 Ramachandran restraints generated. 9583 Oldfield, 0 Emsley, 9583 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1238 residues out of total 8648 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 213 poor density : 1025 time to evaluate : 8.399 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: A 122 MET cc_start: 0.5128 (mmp) cc_final: 0.4750 (mmm) REVERT: A 229 SER cc_start: 0.8386 (t) cc_final: 0.8122 (t) REVERT: A 341 MET cc_start: 0.7568 (mtp) cc_final: 0.7224 (mmm) REVERT: A 555 ASP cc_start: 0.6610 (t0) cc_final: 0.6312 (t0) REVERT: A 678 GLU cc_start: 0.7861 (OUTLIER) cc_final: 0.7555 (pm20) REVERT: A 722 LEU cc_start: 0.8170 (OUTLIER) cc_final: 0.7934 (mm) REVERT: A 935 GLN cc_start: 0.6518 (tp40) cc_final: 0.6147 (tp-100) REVERT: A 1259 MET cc_start: 0.6343 (ppp) cc_final: 0.5733 (tmm) REVERT: A 1285 MET cc_start: 0.7121 (OUTLIER) cc_final: 0.6822 (mtm) REVERT: A 1368 MET cc_start: 0.7848 (OUTLIER) cc_final: 0.7193 (mpp) REVERT: A 1417 GLU cc_start: 0.8071 (tm-30) cc_final: 0.7372 (tm-30) REVERT: A 1444 MET cc_start: 0.7777 (mmt) cc_final: 0.7575 (mmt) REVERT: B 116 GLU cc_start: 0.7690 (tt0) cc_final: 0.7344 (pt0) REVERT: B 431 TYR cc_start: 0.8100 (t80) cc_final: 0.7563 (t80) REVERT: B 432 MET cc_start: 0.7205 (mtm) cc_final: 0.6997 (mtm) REVERT: B 624 LEU cc_start: 0.7680 (OUTLIER) cc_final: 0.7463 (mm) REVERT: B 1151 LEU cc_start: 0.7977 (OUTLIER) cc_final: 0.7679 (mm) REVERT: B 1188 LYS cc_start: 0.7933 (mttp) cc_final: 0.7598 (mtmt) REVERT: B 1210 MET cc_start: 0.8419 (mtp) cc_final: 0.8061 (mtm) REVERT: C 230 MET cc_start: 0.7131 (mmm) cc_final: 0.6891 (mmm) REVERT: D 61 GLU cc_start: 0.7416 (mm-30) cc_final: 0.7094 (mp0) REVERT: E 75 MET cc_start: 0.7103 (ppp) cc_final: 0.6450 (ppp) REVERT: E 101 GLN cc_start: 0.7220 (mm-40) cc_final: 0.6995 (tp40) REVERT: E 104 ASN cc_start: 0.6742 (t0) cc_final: 0.6151 (t0) REVERT: G 74 TYR cc_start: 0.8153 (p90) cc_final: 0.7927 (p90) REVERT: I 87 GLN cc_start: 0.6014 (pp30) cc_final: 0.5584 (pp30) REVERT: I 97 MET cc_start: 0.7066 (mtp) cc_final: 0.6725 (ttt) REVERT: J 10 CYS cc_start: 0.8567 (OUTLIER) cc_final: 0.8014 (p) REVERT: K 37 LYS cc_start: 0.8380 (OUTLIER) cc_final: 0.8135 (tppt) REVERT: K 85 ASP cc_start: 0.8261 (m-30) cc_final: 0.7893 (m-30) REVERT: M 243 CYS cc_start: 0.8460 (m) cc_final: 0.8143 (m) REVERT: M 251 GLN cc_start: 0.8078 (mp10) cc_final: 0.7749 (mm-40) REVERT: M 325 ASP cc_start: 0.6774 (t0) cc_final: 0.6343 (t70) REVERT: O 104 MET cc_start: 0.6866 (ptp) cc_final: 0.6633 (ptp) REVERT: R 294 MET cc_start: 0.0670 (pmm) cc_final: -0.0088 (pmm) REVERT: W 15 PHE cc_start: 0.8524 (t80) cc_final: 0.8265 (t80) REVERT: X 197 ARG cc_start: 0.7906 (mmt-90) cc_final: 0.7702 (mmp80) REVERT: 0 76 MET cc_start: 0.7342 (ttp) cc_final: 0.7073 (tmm) REVERT: 0 299 LEU cc_start: 0.8507 (mm) cc_final: 0.7978 (mm) REVERT: 0 427 ASN cc_start: 0.8388 (p0) cc_final: 0.8045 (p0) REVERT: 0 610 ILE cc_start: 0.8995 (mm) cc_final: 0.8760 (mm) REVERT: 0 711 ASP cc_start: 0.6269 (t0) cc_final: 0.6066 (t0) REVERT: 1 1 MET cc_start: 0.6432 (tpt) cc_final: 0.6169 (tpp) REVERT: 1 30 ARG cc_start: 0.6732 (mmm160) cc_final: 0.6424 (mmm160) REVERT: 1 192 MET cc_start: 0.7537 (mmm) cc_final: 0.7138 (tpp) REVERT: 1 254 GLU cc_start: 0.7332 (tm-30) cc_final: 0.7078 (tm-30) REVERT: 1 588 ASP cc_start: 0.7673 (m-30) cc_final: 0.7283 (t0) REVERT: 1 602 ASN cc_start: 0.7772 (p0) cc_final: 0.7449 (p0) REVERT: 2 107 SER cc_start: 0.8036 (t) cc_final: 0.7749 (t) REVERT: 2 363 PHE cc_start: 0.8659 (p90) cc_final: 0.8155 (p90) REVERT: 3 107 ASN cc_start: 0.8632 (m-40) cc_final: 0.8431 (m-40) REVERT: 4 51 ILE cc_start: 0.8605 (OUTLIER) cc_final: 0.8364 (tp) REVERT: 4 236 LEU cc_start: 0.9195 (tp) cc_final: 0.8803 (tp) REVERT: 5 56 ARG cc_start: 0.7477 (OUTLIER) cc_final: 0.6769 (ptm-80) REVERT: 6 142 ARG cc_start: 0.7653 (mmm160) cc_final: 0.7415 (mmm160) REVERT: 6 379 SER cc_start: 0.8645 (OUTLIER) cc_final: 0.8229 (p) REVERT: 6 399 ARG cc_start: 0.7221 (tpp80) cc_final: 0.6975 (tpp80) REVERT: 6 409 ARG cc_start: 0.7471 (OUTLIER) cc_final: 0.7181 (tpm170) REVERT: 7 112 MET cc_start: 0.7641 (ppp) cc_final: 0.7057 (pmm) REVERT: 7 566 TYR cc_start: 0.8534 (OUTLIER) cc_final: 0.7415 (t80) REVERT: 7 610 ASP cc_start: 0.7107 (p0) cc_final: 0.6823 (p0) REVERT: 7 716 MET cc_start: 0.8001 (OUTLIER) cc_final: 0.7771 (mmm) REVERT: b 84 MET cc_start: 0.7272 (tmm) cc_final: 0.7032 (tmm) REVERT: b 92 ARG cc_start: 0.7633 (ttp80) cc_final: 0.7349 (tmt170) REVERT: c 73 ASN cc_start: 0.8650 (t0) cc_final: 0.8166 (t0) REVERT: d 102 GLU cc_start: 0.7003 (tt0) cc_final: 0.6719 (tt0) REVERT: d 113 LYS cc_start: 0.8388 (tmtt) cc_final: 0.8135 (tptt) REVERT: g 36 LYS cc_start: 0.8288 (tptt) cc_final: 0.8025 (tptt) REVERT: g 61 GLU cc_start: 0.7364 (OUTLIER) cc_final: 0.7150 (tp30) REVERT: g 104 GLN cc_start: 0.8513 (mp10) cc_final: 0.8148 (mp10) REVERT: h 56 MET cc_start: 0.8032 (OUTLIER) cc_final: 0.7704 (tpp) REVERT: h 83 ARG cc_start: 0.8096 (tpp80) cc_final: 0.7539 (mtt180) outliers start: 213 outliers final: 157 residues processed: 1133 average time/residue: 0.8074 time to fit residues: 1587.8251 Evaluate side-chains 1148 residues out of total 8648 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 173 poor density : 975 time to evaluate : 7.375 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 234 MET Chi-restraints excluded: chain A residue 329 LEU Chi-restraints excluded: chain A residue 351 THR Chi-restraints excluded: chain A residue 375 THR Chi-restraints excluded: chain A residue 379 VAL Chi-restraints excluded: chain A residue 381 THR Chi-restraints excluded: chain A residue 500 GLU Chi-restraints excluded: chain A residue 542 GLU Chi-restraints excluded: chain A residue 546 VAL Chi-restraints excluded: chain A residue 678 GLU Chi-restraints excluded: chain A residue 722 LEU Chi-restraints excluded: chain A residue 740 LEU Chi-restraints excluded: chain A residue 762 SER Chi-restraints excluded: chain A residue 781 ASP Chi-restraints excluded: chain A residue 802 ASN Chi-restraints excluded: chain A residue 827 THR Chi-restraints excluded: chain A residue 841 LEU Chi-restraints excluded: chain A residue 863 VAL Chi-restraints excluded: chain A residue 878 ILE Chi-restraints excluded: chain A residue 886 ILE Chi-restraints excluded: chain A residue 1015 VAL Chi-restraints excluded: chain A residue 1111 MET Chi-restraints excluded: chain A residue 1124 HIS Chi-restraints excluded: chain A residue 1284 MET Chi-restraints excluded: chain A residue 1285 MET Chi-restraints excluded: chain A residue 1291 VAL Chi-restraints excluded: chain A residue 1330 ASN Chi-restraints excluded: chain A residue 1368 MET Chi-restraints excluded: chain A residue 1377 THR Chi-restraints excluded: chain A residue 1405 THR Chi-restraints excluded: chain A residue 1411 GLU Chi-restraints excluded: chain A residue 1432 GLN Chi-restraints excluded: chain A residue 1443 VAL Chi-restraints excluded: chain B residue 30 SER Chi-restraints excluded: chain B residue 55 VAL Chi-restraints excluded: chain B residue 63 ILE Chi-restraints excluded: chain B residue 225 VAL Chi-restraints excluded: chain B residue 240 ILE Chi-restraints excluded: chain B residue 298 LEU Chi-restraints excluded: chain B residue 388 CYS Chi-restraints excluded: chain B residue 468 GLU Chi-restraints excluded: chain B residue 492 LEU Chi-restraints excluded: chain B residue 540 SER Chi-restraints excluded: chain B residue 543 SER Chi-restraints excluded: chain B residue 624 LEU Chi-restraints excluded: chain B residue 653 VAL Chi-restraints excluded: chain B residue 773 MET Chi-restraints excluded: chain B residue 782 LEU Chi-restraints excluded: chain B residue 805 THR Chi-restraints excluded: chain B residue 809 MET Chi-restraints excluded: chain B residue 825 VAL Chi-restraints excluded: chain B residue 910 VAL Chi-restraints excluded: chain B residue 955 THR Chi-restraints excluded: chain B residue 956 THR Chi-restraints excluded: chain B residue 959 ASP Chi-restraints excluded: chain B residue 999 MET Chi-restraints excluded: chain B residue 1051 THR Chi-restraints excluded: chain B residue 1151 LEU Chi-restraints excluded: chain B residue 1152 MET Chi-restraints excluded: chain B residue 1156 ASP Chi-restraints excluded: chain B residue 1169 MET Chi-restraints excluded: chain B residue 1186 ASP Chi-restraints excluded: chain B residue 1191 ILE Chi-restraints excluded: chain B residue 1213 THR Chi-restraints excluded: chain C residue 26 ASP Chi-restraints excluded: chain C residue 65 HIS Chi-restraints excluded: chain C residue 163 ILE Chi-restraints excluded: chain D residue 52 LEU Chi-restraints excluded: chain D residue 159 THR Chi-restraints excluded: chain E residue 22 MET Chi-restraints excluded: chain E residue 50 MET Chi-restraints excluded: chain E residue 182 ASP Chi-restraints excluded: chain E residue 188 LEU Chi-restraints excluded: chain F residue 16 GLU Chi-restraints excluded: chain F residue 25 ASP Chi-restraints excluded: chain F residue 71 GLU Chi-restraints excluded: chain F residue 130 ILE Chi-restraints excluded: chain G residue 77 VAL Chi-restraints excluded: chain G residue 91 VAL Chi-restraints excluded: chain H residue 49 VAL Chi-restraints excluded: chain H residue 55 LEU Chi-restraints excluded: chain H residue 88 SER Chi-restraints excluded: chain H residue 107 VAL Chi-restraints excluded: chain H residue 122 LEU Chi-restraints excluded: chain H residue 129 TYR Chi-restraints excluded: chain H residue 139 ASN Chi-restraints excluded: chain H residue 142 LEU Chi-restraints excluded: chain I residue 113 ASP Chi-restraints excluded: chain J residue 2 ILE Chi-restraints excluded: chain J residue 5 VAL Chi-restraints excluded: chain J residue 10 CYS Chi-restraints excluded: chain J residue 13 VAL Chi-restraints excluded: chain K residue 37 LYS Chi-restraints excluded: chain K residue 50 LEU Chi-restraints excluded: chain K residue 94 ILE Chi-restraints excluded: chain K residue 95 ILE Chi-restraints excluded: chain K residue 98 LEU Chi-restraints excluded: chain O residue 228 GLU Chi-restraints excluded: chain R residue 39 VAL Chi-restraints excluded: chain R residue 88 HIS Chi-restraints excluded: chain R residue 218 VAL Chi-restraints excluded: chain R residue 347 PHE Chi-restraints excluded: chain V residue 20 VAL Chi-restraints excluded: chain W residue 85 VAL Chi-restraints excluded: chain W residue 206 LEU Chi-restraints excluded: chain W residue 368 GLN Chi-restraints excluded: chain X residue 251 ASN Chi-restraints excluded: chain 0 residue 6 ASP Chi-restraints excluded: chain 0 residue 17 ILE Chi-restraints excluded: chain 0 residue 37 ASN Chi-restraints excluded: chain 0 residue 325 ILE Chi-restraints excluded: chain 0 residue 344 THR Chi-restraints excluded: chain 0 residue 487 LEU Chi-restraints excluded: chain 0 residue 495 MET Chi-restraints excluded: chain 0 residue 525 MET Chi-restraints excluded: chain 0 residue 591 SER Chi-restraints excluded: chain 0 residue 597 ILE Chi-restraints excluded: chain 0 residue 607 SER Chi-restraints excluded: chain 0 residue 642 MET Chi-restraints excluded: chain 0 residue 678 VAL Chi-restraints excluded: chain 1 residue 419 LEU Chi-restraints excluded: chain 1 residue 481 ILE Chi-restraints excluded: chain 1 residue 485 ASP Chi-restraints excluded: chain 2 residue 50 MET Chi-restraints excluded: chain 2 residue 192 LEU Chi-restraints excluded: chain 2 residue 250 LEU Chi-restraints excluded: chain 2 residue 388 THR Chi-restraints excluded: chain 2 residue 400 LEU Chi-restraints excluded: chain 3 residue 72 ILE Chi-restraints excluded: chain 4 residue 51 ILE Chi-restraints excluded: chain 4 residue 188 ASP Chi-restraints excluded: chain 4 residue 215 ILE Chi-restraints excluded: chain 4 residue 224 LEU Chi-restraints excluded: chain 4 residue 257 SER Chi-restraints excluded: chain 5 residue 10 VAL Chi-restraints excluded: chain 5 residue 56 ARG Chi-restraints excluded: chain 6 residue 137 LEU Chi-restraints excluded: chain 6 residue 148 MET Chi-restraints excluded: chain 6 residue 178 LEU Chi-restraints excluded: chain 6 residue 243 ASP Chi-restraints excluded: chain 6 residue 379 SER Chi-restraints excluded: chain 6 residue 409 ARG Chi-restraints excluded: chain 7 residue 197 LEU Chi-restraints excluded: chain 7 residue 330 CYS Chi-restraints excluded: chain 7 residue 453 VAL Chi-restraints excluded: chain 7 residue 459 MET Chi-restraints excluded: chain 7 residue 516 THR Chi-restraints excluded: chain 7 residue 566 TYR Chi-restraints excluded: chain 7 residue 583 MET Chi-restraints excluded: chain 7 residue 612 VAL Chi-restraints excluded: chain 7 residue 712 ASP Chi-restraints excluded: chain 7 residue 716 MET Chi-restraints excluded: chain a residue 64 LYS Chi-restraints excluded: chain b residue 25 ASN Chi-restraints excluded: chain b residue 66 ILE Chi-restraints excluded: chain c residue 16 THR Chi-restraints excluded: chain c residue 94 ASN Chi-restraints excluded: chain c residue 110 ASN Chi-restraints excluded: chain d residue 66 VAL Chi-restraints excluded: chain d residue 97 LEU Chi-restraints excluded: chain d residue 103 LEU Chi-restraints excluded: chain d residue 108 VAL Chi-restraints excluded: chain e residue 58 THR Chi-restraints excluded: chain e residue 65 LEU Chi-restraints excluded: chain e residue 74 ILE Chi-restraints excluded: chain e residue 86 SER Chi-restraints excluded: chain e residue 109 LEU Chi-restraints excluded: chain e residue 124 ILE Chi-restraints excluded: chain g residue 61 GLU Chi-restraints excluded: chain g residue 79 ILE Chi-restraints excluded: chain h residue 56 MET Chi-restraints excluded: chain h residue 60 ASN Chi-restraints excluded: chain h residue 77 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 998 random chunks: chunk 595 optimal weight: 20.0000 chunk 384 optimal weight: 0.0170 chunk 574 optimal weight: 9.9990 chunk 289 optimal weight: 0.0050 chunk 189 optimal weight: 3.9990 chunk 186 optimal weight: 0.8980 chunk 611 optimal weight: 4.9990 chunk 655 optimal weight: 9.9990 chunk 475 optimal weight: 10.0000 chunk 89 optimal weight: 0.1980 chunk 756 optimal weight: 0.9980 overall best weight: 0.4232 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 4 GLN A 5 GLN ** A 451 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 510 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 802 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 363 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 465 ASN B 667 GLN ** B 776 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B1076 HIS ** B1097 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 165 GLN F 78 GLN ** K 89 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 140 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** R 88 HIS ** R 239 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 36 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** U 280 GLN ** W 50 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** W 280 GLN ** X 265 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** X 270 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 0 224 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 0 239 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 0 661 HIS ** 2 431 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 3 36 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 5 61 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** a 108 ASN b 25 ASN c 94 ASN e 93 GLN Total number of N/Q/H flips: 15 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6866 moved from start: 0.2573 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.053 88785 Z= 0.154 Angle : 0.535 12.907 121636 Z= 0.282 Chirality : 0.040 0.308 13752 Planarity : 0.004 0.069 14134 Dihedral : 18.700 177.353 15190 Min Nonbonded Distance : 1.885 Molprobity Statistics. All-atom Clashscore : 11.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.59 % Favored : 97.41 % Rotamer: Outliers : 1.58 % Allowed : 14.91 % Favored : 83.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.31 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.22 (0.09), residues: 9583 helix: 1.03 (0.08), residues: 4088 sheet: -0.40 (0.15), residues: 1208 loop : -0.47 (0.10), residues: 4287 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.001 TRP X 263 HIS 0.011 0.001 HIS R 88 PHE 0.031 0.001 PHE A 714 TYR 0.026 0.001 TYR B 380 ARG 0.009 0.000 ARG G 75 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 19166 Ramachandran restraints generated. 9583 Oldfield, 0 Emsley, 9583 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 19166 Ramachandran restraints generated. 9583 Oldfield, 0 Emsley, 9583 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1180 residues out of total 8648 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 137 poor density : 1043 time to evaluate : 7.391 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: A 122 MET cc_start: 0.5118 (mmp) cc_final: 0.4759 (mmm) REVERT: A 229 SER cc_start: 0.8465 (t) cc_final: 0.8181 (t) REVERT: A 341 MET cc_start: 0.7555 (mtp) cc_final: 0.7287 (mmm) REVERT: A 644 LYS cc_start: 0.7378 (mmtt) cc_final: 0.7045 (ttpp) REVERT: A 678 GLU cc_start: 0.7699 (OUTLIER) cc_final: 0.7209 (pm20) REVERT: A 708 MET cc_start: 0.6472 (ptt) cc_final: 0.6204 (ptt) REVERT: A 722 LEU cc_start: 0.8043 (OUTLIER) cc_final: 0.7815 (mm) REVERT: A 1259 MET cc_start: 0.6277 (ppp) cc_final: 0.5687 (tmm) REVERT: A 1285 MET cc_start: 0.6907 (OUTLIER) cc_final: 0.6645 (mtm) REVERT: A 1368 MET cc_start: 0.7662 (OUTLIER) cc_final: 0.7048 (mpp) REVERT: A 1444 MET cc_start: 0.7640 (mmt) cc_final: 0.7411 (mmt) REVERT: B 116 GLU cc_start: 0.7497 (tt0) cc_final: 0.7248 (pt0) REVERT: B 431 TYR cc_start: 0.8055 (t80) cc_final: 0.7394 (t80) REVERT: B 432 MET cc_start: 0.7155 (mtm) cc_final: 0.6940 (mtm) REVERT: B 526 GLU cc_start: 0.6914 (tt0) cc_final: 0.6623 (tt0) REVERT: B 624 LEU cc_start: 0.7499 (OUTLIER) cc_final: 0.7279 (mm) REVERT: B 1188 LYS cc_start: 0.7896 (mttp) cc_final: 0.7348 (mtpp) REVERT: B 1210 MET cc_start: 0.8301 (mtp) cc_final: 0.7967 (mtm) REVERT: C 230 MET cc_start: 0.7150 (mmm) cc_final: 0.6928 (mmm) REVERT: D 61 GLU cc_start: 0.7422 (mm-30) cc_final: 0.7096 (mp0) REVERT: E 104 ASN cc_start: 0.6564 (t0) cc_final: 0.5943 (t0) REVERT: I 77 LYS cc_start: 0.7297 (mmtt) cc_final: 0.7051 (tptt) REVERT: I 81 ARG cc_start: 0.5527 (mmp-170) cc_final: 0.5297 (mmp-170) REVERT: I 87 GLN cc_start: 0.6175 (pp30) cc_final: 0.5674 (pp30) REVERT: I 97 MET cc_start: 0.6982 (mtp) cc_final: 0.6753 (ttt) REVERT: K 37 LYS cc_start: 0.8316 (OUTLIER) cc_final: 0.8058 (tppt) REVERT: K 85 ASP cc_start: 0.8204 (m-30) cc_final: 0.7843 (m-30) REVERT: M 243 CYS cc_start: 0.8439 (m) cc_final: 0.8090 (m) REVERT: M 251 GLN cc_start: 0.8072 (mp10) cc_final: 0.7705 (mm-40) REVERT: M 325 ASP cc_start: 0.6774 (t0) cc_final: 0.6448 (t70) REVERT: O 104 MET cc_start: 0.6851 (ptp) cc_final: 0.6594 (ptp) REVERT: O 121 MET cc_start: 0.4188 (ppp) cc_final: 0.3862 (ppp) REVERT: Q 114 MET cc_start: 0.3935 (tmm) cc_final: 0.3420 (tmm) REVERT: R 294 MET cc_start: 0.0643 (pmm) cc_final: -0.0271 (pmm) REVERT: R 300 LEU cc_start: 0.8089 (mt) cc_final: 0.7784 (mm) REVERT: 0 427 ASN cc_start: 0.8382 (p0) cc_final: 0.8109 (p0) REVERT: 0 610 ILE cc_start: 0.8959 (mm) cc_final: 0.8705 (mm) REVERT: 1 1 MET cc_start: 0.6248 (tpt) cc_final: 0.6007 (tpp) REVERT: 1 102 MET cc_start: 0.6878 (tmm) cc_final: 0.6656 (tmm) REVERT: 1 192 MET cc_start: 0.7497 (mmm) cc_final: 0.7133 (tpp) REVERT: 1 254 GLU cc_start: 0.7221 (tm-30) cc_final: 0.7016 (tm-30) REVERT: 1 588 ASP cc_start: 0.7614 (m-30) cc_final: 0.7237 (t0) REVERT: 2 107 SER cc_start: 0.8050 (t) cc_final: 0.7767 (t) REVERT: 2 363 PHE cc_start: 0.8535 (p90) cc_final: 0.7964 (p90) REVERT: 3 107 ASN cc_start: 0.8620 (m-40) cc_final: 0.8407 (m-40) REVERT: 4 51 ILE cc_start: 0.8449 (OUTLIER) cc_final: 0.8167 (tp) REVERT: 4 165 LYS cc_start: 0.8178 (pttt) cc_final: 0.7909 (pptt) REVERT: 4 224 LEU cc_start: 0.8043 (OUTLIER) cc_final: 0.7809 (mt) REVERT: 4 236 LEU cc_start: 0.9144 (tp) cc_final: 0.8758 (tp) REVERT: 4 311 GLN cc_start: 0.8306 (tm-30) cc_final: 0.7871 (tm-30) REVERT: 5 56 ARG cc_start: 0.7383 (OUTLIER) cc_final: 0.6741 (ptm-80) REVERT: 6 142 ARG cc_start: 0.7496 (mmm160) cc_final: 0.7238 (mmm160) REVERT: 6 300 LEU cc_start: 0.9123 (mt) cc_final: 0.8871 (mt) REVERT: 6 399 ARG cc_start: 0.7197 (tpp80) cc_final: 0.6894 (tpp80) REVERT: 6 409 ARG cc_start: 0.7436 (OUTLIER) cc_final: 0.6827 (tpm170) REVERT: 7 112 MET cc_start: 0.7456 (ppp) cc_final: 0.6942 (pmm) REVERT: 7 716 MET cc_start: 0.7909 (OUTLIER) cc_final: 0.7709 (mmm) REVERT: b 84 MET cc_start: 0.7245 (tmm) cc_final: 0.6989 (tmm) REVERT: c 73 ASN cc_start: 0.8622 (t0) cc_final: 0.8282 (t0) REVERT: d 102 GLU cc_start: 0.6765 (tt0) cc_final: 0.6497 (tt0) REVERT: d 113 LYS cc_start: 0.8397 (tmtt) cc_final: 0.8145 (tptt) REVERT: g 36 LYS cc_start: 0.8176 (tptt) cc_final: 0.7967 (tptt) REVERT: g 61 GLU cc_start: 0.7428 (OUTLIER) cc_final: 0.7223 (tp30) REVERT: g 104 GLN cc_start: 0.8389 (mp10) cc_final: 0.8026 (mp10) REVERT: h 56 MET cc_start: 0.7772 (OUTLIER) cc_final: 0.7333 (tpp) REVERT: h 83 ARG cc_start: 0.8079 (tpp80) cc_final: 0.7497 (mtt180) outliers start: 137 outliers final: 96 residues processed: 1121 average time/residue: 0.8187 time to fit residues: 1592.1004 Evaluate side-chains 1110 residues out of total 8648 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 109 poor density : 1001 time to evaluate : 7.357 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 329 LEU Chi-restraints excluded: chain A residue 351 THR Chi-restraints excluded: chain A residue 379 VAL Chi-restraints excluded: chain A residue 542 GLU Chi-restraints excluded: chain A residue 546 VAL Chi-restraints excluded: chain A residue 678 GLU Chi-restraints excluded: chain A residue 722 LEU Chi-restraints excluded: chain A residue 740 LEU Chi-restraints excluded: chain A residue 827 THR Chi-restraints excluded: chain A residue 841 LEU Chi-restraints excluded: chain A residue 1015 VAL Chi-restraints excluded: chain A residue 1111 MET Chi-restraints excluded: chain A residue 1124 HIS Chi-restraints excluded: chain A residue 1284 MET Chi-restraints excluded: chain A residue 1285 MET Chi-restraints excluded: chain A residue 1291 VAL Chi-restraints excluded: chain A residue 1330 ASN Chi-restraints excluded: chain A residue 1368 MET Chi-restraints excluded: chain A residue 1411 GLU Chi-restraints excluded: chain A residue 1443 VAL Chi-restraints excluded: chain B residue 225 VAL Chi-restraints excluded: chain B residue 240 ILE Chi-restraints excluded: chain B residue 298 LEU Chi-restraints excluded: chain B residue 388 CYS Chi-restraints excluded: chain B residue 468 GLU Chi-restraints excluded: chain B residue 492 LEU Chi-restraints excluded: chain B residue 540 SER Chi-restraints excluded: chain B residue 543 SER Chi-restraints excluded: chain B residue 624 LEU Chi-restraints excluded: chain B residue 773 MET Chi-restraints excluded: chain B residue 910 VAL Chi-restraints excluded: chain B residue 955 THR Chi-restraints excluded: chain B residue 1051 THR Chi-restraints excluded: chain B residue 1156 ASP Chi-restraints excluded: chain B residue 1191 ILE Chi-restraints excluded: chain B residue 1213 THR Chi-restraints excluded: chain C residue 26 ASP Chi-restraints excluded: chain C residue 65 HIS Chi-restraints excluded: chain D residue 52 LEU Chi-restraints excluded: chain D residue 159 THR Chi-restraints excluded: chain E residue 182 ASP Chi-restraints excluded: chain E residue 188 LEU Chi-restraints excluded: chain F residue 16 GLU Chi-restraints excluded: chain F residue 71 GLU Chi-restraints excluded: chain F residue 130 ILE Chi-restraints excluded: chain G residue 17 PHE Chi-restraints excluded: chain G residue 77 VAL Chi-restraints excluded: chain G residue 91 VAL Chi-restraints excluded: chain H residue 42 ILE Chi-restraints excluded: chain H residue 49 VAL Chi-restraints excluded: chain H residue 55 LEU Chi-restraints excluded: chain J residue 2 ILE Chi-restraints excluded: chain J residue 5 VAL Chi-restraints excluded: chain J residue 13 VAL Chi-restraints excluded: chain K residue 37 LYS Chi-restraints excluded: chain K residue 94 ILE Chi-restraints excluded: chain O residue 228 GLU Chi-restraints excluded: chain R residue 39 VAL Chi-restraints excluded: chain R residue 218 VAL Chi-restraints excluded: chain V residue 20 VAL Chi-restraints excluded: chain W residue 85 VAL Chi-restraints excluded: chain W residue 206 LEU Chi-restraints excluded: chain W residue 368 GLN Chi-restraints excluded: chain 0 residue 6 ASP Chi-restraints excluded: chain 0 residue 325 ILE Chi-restraints excluded: chain 0 residue 487 LEU Chi-restraints excluded: chain 0 residue 591 SER Chi-restraints excluded: chain 0 residue 597 ILE Chi-restraints excluded: chain 0 residue 607 SER Chi-restraints excluded: chain 0 residue 642 MET Chi-restraints excluded: chain 1 residue 419 LEU Chi-restraints excluded: chain 1 residue 481 ILE Chi-restraints excluded: chain 1 residue 485 ASP Chi-restraints excluded: chain 2 residue 192 LEU Chi-restraints excluded: chain 2 residue 244 GLU Chi-restraints excluded: chain 2 residue 250 LEU Chi-restraints excluded: chain 2 residue 388 THR Chi-restraints excluded: chain 2 residue 400 LEU Chi-restraints excluded: chain 4 residue 51 ILE Chi-restraints excluded: chain 4 residue 188 ASP Chi-restraints excluded: chain 4 residue 224 LEU Chi-restraints excluded: chain 5 residue 10 VAL Chi-restraints excluded: chain 5 residue 41 LEU Chi-restraints excluded: chain 5 residue 56 ARG Chi-restraints excluded: chain 6 residue 137 LEU Chi-restraints excluded: chain 6 residue 148 MET Chi-restraints excluded: chain 6 residue 298 LYS Chi-restraints excluded: chain 6 residue 409 ARG Chi-restraints excluded: chain 7 residue 197 LEU Chi-restraints excluded: chain 7 residue 453 VAL Chi-restraints excluded: chain 7 residue 516 THR Chi-restraints excluded: chain 7 residue 566 TYR Chi-restraints excluded: chain 7 residue 612 VAL Chi-restraints excluded: chain 7 residue 622 MET Chi-restraints excluded: chain 7 residue 716 MET Chi-restraints excluded: chain b residue 25 ASN Chi-restraints excluded: chain c residue 64 GLU Chi-restraints excluded: chain c residue 94 ASN Chi-restraints excluded: chain c residue 110 ASN Chi-restraints excluded: chain d residue 97 LEU Chi-restraints excluded: chain d residue 103 LEU Chi-restraints excluded: chain d residue 108 VAL Chi-restraints excluded: chain e residue 58 THR Chi-restraints excluded: chain e residue 74 ILE Chi-restraints excluded: chain e residue 86 SER Chi-restraints excluded: chain e residue 109 LEU Chi-restraints excluded: chain g residue 61 GLU Chi-restraints excluded: chain h residue 56 MET Chi-restraints excluded: chain h residue 60 ASN Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 998 random chunks: chunk 875 optimal weight: 20.0000 chunk 921 optimal weight: 9.9990 chunk 840 optimal weight: 0.4980 chunk 896 optimal weight: 20.0000 chunk 539 optimal weight: 0.9980 chunk 390 optimal weight: 3.9990 chunk 703 optimal weight: 0.0070 chunk 275 optimal weight: 9.9990 chunk 810 optimal weight: 0.0570 chunk 847 optimal weight: 1.9990 chunk 893 optimal weight: 10.0000 overall best weight: 0.7118 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 5 GLN ** A 451 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 510 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 802 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1432 GLN B 60 GLN ** B 363 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 465 ASN B 667 GLN ** B 776 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1097 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 78 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 102 GLN G 113 HIS H 137 GLN ** K 89 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** M 303 GLN ** Q 140 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 239 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 328 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 36 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** U 280 GLN ** W 50 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** X 265 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** X 270 GLN ** 0 224 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 0 239 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 2 431 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 3 36 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** 4 161 ASN 4 192 GLN ** a 93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** a 108 ASN c 94 ASN e 93 GLN Total number of N/Q/H flips: 16 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6864 moved from start: 0.2617 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.063 88785 Z= 0.164 Angle : 0.535 13.486 121636 Z= 0.281 Chirality : 0.040 0.332 13752 Planarity : 0.004 0.069 14134 Dihedral : 18.641 177.858 15190 Min Nonbonded Distance : 1.849 Molprobity Statistics. All-atom Clashscore : 11.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.71 % Favored : 97.29 % Rotamer: Outliers : 1.46 % Allowed : 15.36 % Favored : 83.18 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.31 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.32 (0.09), residues: 9583 helix: 1.10 (0.08), residues: 4091 sheet: -0.30 (0.15), residues: 1214 loop : -0.42 (0.10), residues: 4278 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.028 0.001 TRP X 263 HIS 0.007 0.001 HIS R 234 PHE 0.028 0.001 PHE W 20 TYR 0.026 0.001 TYR B 380 ARG 0.009 0.000 ARG 0 647 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 19166 Ramachandran restraints generated. 9583 Oldfield, 0 Emsley, 9583 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 19166 Ramachandran restraints generated. 9583 Oldfield, 0 Emsley, 9583 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1148 residues out of total 8648 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 126 poor density : 1022 time to evaluate : 7.377 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: A 122 MET cc_start: 0.5147 (mmp) cc_final: 0.4759 (mmm) REVERT: A 229 SER cc_start: 0.8432 (t) cc_final: 0.8159 (t) REVERT: A 333 GLU cc_start: 0.5816 (pm20) cc_final: 0.5523 (pm20) REVERT: A 341 MET cc_start: 0.7501 (mtp) cc_final: 0.7297 (mmm) REVERT: A 644 LYS cc_start: 0.7404 (mmtt) cc_final: 0.7064 (ttpp) REVERT: A 678 GLU cc_start: 0.7791 (OUTLIER) cc_final: 0.7452 (pm20) REVERT: A 736 ASN cc_start: 0.6055 (t0) cc_final: 0.5827 (t160) REVERT: A 1259 MET cc_start: 0.6203 (ppp) cc_final: 0.5586 (tmm) REVERT: A 1368 MET cc_start: 0.7742 (OUTLIER) cc_final: 0.7088 (mpp) REVERT: A 1444 MET cc_start: 0.7612 (mmt) cc_final: 0.7393 (mmt) REVERT: B 116 GLU cc_start: 0.7557 (tt0) cc_final: 0.7242 (pt0) REVERT: B 431 TYR cc_start: 0.8055 (t80) cc_final: 0.7408 (t80) REVERT: B 432 MET cc_start: 0.7136 (mtm) cc_final: 0.6922 (mtm) REVERT: B 526 GLU cc_start: 0.6945 (tt0) cc_final: 0.6692 (tt0) REVERT: B 615 MET cc_start: 0.7494 (mpp) cc_final: 0.7067 (mpp) REVERT: B 624 LEU cc_start: 0.7489 (OUTLIER) cc_final: 0.7282 (mm) REVERT: B 833 TYR cc_start: 0.8493 (m-80) cc_final: 0.8124 (m-80) REVERT: B 1210 MET cc_start: 0.8248 (mtp) cc_final: 0.7903 (mtm) REVERT: C 230 MET cc_start: 0.7154 (mmm) cc_final: 0.6943 (mmm) REVERT: D 61 GLU cc_start: 0.7420 (mm-30) cc_final: 0.7177 (mp0) REVERT: E 75 MET cc_start: 0.6968 (ppp) cc_final: 0.6455 (ppp) REVERT: E 104 ASN cc_start: 0.6531 (t0) cc_final: 0.5864 (t0) REVERT: G 74 TYR cc_start: 0.8071 (p90) cc_final: 0.7722 (p90) REVERT: I 77 LYS cc_start: 0.7318 (mmtt) cc_final: 0.7094 (tptt) REVERT: I 87 GLN cc_start: 0.6233 (pp30) cc_final: 0.5762 (pp30) REVERT: K 37 LYS cc_start: 0.8316 (OUTLIER) cc_final: 0.8103 (tppt) REVERT: K 85 ASP cc_start: 0.8221 (m-30) cc_final: 0.7872 (m-30) REVERT: M 243 CYS cc_start: 0.8437 (m) cc_final: 0.8070 (m) REVERT: M 251 GLN cc_start: 0.8039 (mp10) cc_final: 0.7676 (mm-40) REVERT: M 325 ASP cc_start: 0.6794 (t0) cc_final: 0.6492 (t70) REVERT: O 104 MET cc_start: 0.6936 (ptp) cc_final: 0.6661 (ptp) REVERT: O 121 MET cc_start: 0.4162 (ppp) cc_final: 0.3804 (ppp) REVERT: Q 114 MET cc_start: 0.3877 (tmm) cc_final: 0.3450 (tmm) REVERT: Q 387 ILE cc_start: 0.4795 (mt) cc_final: 0.4534 (tt) REVERT: R 225 MET cc_start: 0.4065 (ppp) cc_final: 0.3803 (mmt) REVERT: R 263 MET cc_start: 0.7862 (mmp) cc_final: 0.7192 (mmm) REVERT: R 294 MET cc_start: 0.0536 (pmm) cc_final: -0.0204 (pmm) REVERT: R 300 LEU cc_start: 0.8082 (mt) cc_final: 0.7787 (mm) REVERT: 0 76 MET cc_start: 0.6938 (ttp) cc_final: 0.6601 (tmm) REVERT: 0 247 SER cc_start: 0.8897 (m) cc_final: 0.8677 (m) REVERT: 0 299 LEU cc_start: 0.8444 (mm) cc_final: 0.7902 (mm) REVERT: 0 427 ASN cc_start: 0.8416 (p0) cc_final: 0.8109 (p0) REVERT: 0 562 GLU cc_start: 0.7163 (tp30) cc_final: 0.6944 (tp30) REVERT: 0 610 ILE cc_start: 0.8977 (mm) cc_final: 0.8710 (mm) REVERT: 0 688 ARG cc_start: 0.7170 (mtt180) cc_final: 0.6518 (ttm-80) REVERT: 1 1 MET cc_start: 0.6241 (tpt) cc_final: 0.6030 (tpp) REVERT: 1 102 MET cc_start: 0.6821 (tmm) cc_final: 0.6612 (tmm) REVERT: 1 192 MET cc_start: 0.7483 (mmm) cc_final: 0.7163 (tpp) REVERT: 1 588 ASP cc_start: 0.7660 (m-30) cc_final: 0.7253 (t0) REVERT: 2 107 SER cc_start: 0.8013 (t) cc_final: 0.7724 (t) REVERT: 3 107 ASN cc_start: 0.8606 (m-40) cc_final: 0.8402 (m-40) REVERT: 4 51 ILE cc_start: 0.8437 (OUTLIER) cc_final: 0.8161 (tp) REVERT: 4 224 LEU cc_start: 0.8038 (OUTLIER) cc_final: 0.7830 (mt) REVERT: 4 311 GLN cc_start: 0.8218 (tm-30) cc_final: 0.7743 (tm-30) REVERT: 5 23 ILE cc_start: 0.7802 (mm) cc_final: 0.7594 (mm) REVERT: 5 56 ARG cc_start: 0.7283 (OUTLIER) cc_final: 0.6602 (ptm-80) REVERT: 6 136 MET cc_start: 0.8606 (mmm) cc_final: 0.8214 (mmm) REVERT: 6 142 ARG cc_start: 0.7482 (mmm160) cc_final: 0.7233 (mmm160) REVERT: 6 300 LEU cc_start: 0.9127 (mt) cc_final: 0.8910 (mt) REVERT: 6 399 ARG cc_start: 0.7122 (tpp80) cc_final: 0.6882 (tpp80) REVERT: 6 409 ARG cc_start: 0.7533 (OUTLIER) cc_final: 0.6804 (tpm170) REVERT: 7 112 MET cc_start: 0.7434 (ppp) cc_final: 0.6922 (pmm) REVERT: 7 474 MET cc_start: 0.7670 (ppp) cc_final: 0.7280 (ppp) REVERT: b 84 MET cc_start: 0.7307 (tmm) cc_final: 0.7062 (tmm) REVERT: c 73 ASN cc_start: 0.8630 (t0) cc_final: 0.8391 (t0) REVERT: d 102 GLU cc_start: 0.6950 (tt0) cc_final: 0.6654 (tt0) REVERT: e 109 LEU cc_start: 0.8974 (OUTLIER) cc_final: 0.8729 (tp) REVERT: g 36 LYS cc_start: 0.8225 (tptt) cc_final: 0.7960 (tptt) REVERT: g 104 GLN cc_start: 0.8394 (mp10) cc_final: 0.8025 (mp10) REVERT: h 56 MET cc_start: 0.7706 (OUTLIER) cc_final: 0.7271 (tpp) REVERT: h 83 ARG cc_start: 0.8094 (tpp80) cc_final: 0.7511 (mtt180) outliers start: 126 outliers final: 96 residues processed: 1096 average time/residue: 0.8023 time to fit residues: 1523.2556 Evaluate side-chains 1100 residues out of total 8648 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 106 poor density : 994 time to evaluate : 8.537 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 329 LEU Chi-restraints excluded: chain A residue 351 THR Chi-restraints excluded: chain A residue 379 VAL Chi-restraints excluded: chain A residue 542 GLU Chi-restraints excluded: chain A residue 546 VAL Chi-restraints excluded: chain A residue 678 GLU Chi-restraints excluded: chain A residue 740 LEU Chi-restraints excluded: chain A residue 802 ASN Chi-restraints excluded: chain A residue 827 THR Chi-restraints excluded: chain A residue 841 LEU Chi-restraints excluded: chain A residue 1111 MET Chi-restraints excluded: chain A residue 1124 HIS Chi-restraints excluded: chain A residue 1284 MET Chi-restraints excluded: chain A residue 1291 VAL Chi-restraints excluded: chain A residue 1330 ASN Chi-restraints excluded: chain A residue 1368 MET Chi-restraints excluded: chain A residue 1411 GLU Chi-restraints excluded: chain A residue 1443 VAL Chi-restraints excluded: chain B residue 55 VAL Chi-restraints excluded: chain B residue 225 VAL Chi-restraints excluded: chain B residue 240 ILE Chi-restraints excluded: chain B residue 388 CYS Chi-restraints excluded: chain B residue 468 GLU Chi-restraints excluded: chain B residue 492 LEU Chi-restraints excluded: chain B residue 540 SER Chi-restraints excluded: chain B residue 543 SER Chi-restraints excluded: chain B residue 624 LEU Chi-restraints excluded: chain B residue 773 MET Chi-restraints excluded: chain B residue 910 VAL Chi-restraints excluded: chain B residue 955 THR Chi-restraints excluded: chain B residue 989 THR Chi-restraints excluded: chain B residue 1051 THR Chi-restraints excluded: chain B residue 1156 ASP Chi-restraints excluded: chain B residue 1169 MET Chi-restraints excluded: chain B residue 1191 ILE Chi-restraints excluded: chain B residue 1213 THR Chi-restraints excluded: chain C residue 26 ASP Chi-restraints excluded: chain C residue 65 HIS Chi-restraints excluded: chain D residue 52 LEU Chi-restraints excluded: chain D residue 159 THR Chi-restraints excluded: chain E residue 182 ASP Chi-restraints excluded: chain E residue 188 LEU Chi-restraints excluded: chain F residue 16 GLU Chi-restraints excluded: chain F residue 71 GLU Chi-restraints excluded: chain F residue 130 ILE Chi-restraints excluded: chain G residue 17 PHE Chi-restraints excluded: chain G residue 77 VAL Chi-restraints excluded: chain G residue 91 VAL Chi-restraints excluded: chain G residue 102 GLN Chi-restraints excluded: chain H residue 42 ILE Chi-restraints excluded: chain H residue 49 VAL Chi-restraints excluded: chain H residue 55 LEU Chi-restraints excluded: chain H residue 122 LEU Chi-restraints excluded: chain J residue 2 ILE Chi-restraints excluded: chain J residue 5 VAL Chi-restraints excluded: chain J residue 13 VAL Chi-restraints excluded: chain K residue 37 LYS Chi-restraints excluded: chain K residue 94 ILE Chi-restraints excluded: chain M residue 303 GLN Chi-restraints excluded: chain O residue 228 GLU Chi-restraints excluded: chain R residue 39 VAL Chi-restraints excluded: chain R residue 218 VAL Chi-restraints excluded: chain V residue 20 VAL Chi-restraints excluded: chain W residue 85 VAL Chi-restraints excluded: chain W residue 206 LEU Chi-restraints excluded: chain W residue 368 GLN Chi-restraints excluded: chain 0 residue 6 ASP Chi-restraints excluded: chain 0 residue 487 LEU Chi-restraints excluded: chain 0 residue 597 ILE Chi-restraints excluded: chain 0 residue 607 SER Chi-restraints excluded: chain 0 residue 642 MET Chi-restraints excluded: chain 1 residue 419 LEU Chi-restraints excluded: chain 1 residue 481 ILE Chi-restraints excluded: chain 1 residue 485 ASP Chi-restraints excluded: chain 2 residue 192 LEU Chi-restraints excluded: chain 2 residue 250 LEU Chi-restraints excluded: chain 2 residue 400 LEU Chi-restraints excluded: chain 3 residue 72 ILE Chi-restraints excluded: chain 4 residue 51 ILE Chi-restraints excluded: chain 4 residue 188 ASP Chi-restraints excluded: chain 4 residue 215 ILE Chi-restraints excluded: chain 4 residue 224 LEU Chi-restraints excluded: chain 5 residue 10 VAL Chi-restraints excluded: chain 5 residue 41 LEU Chi-restraints excluded: chain 5 residue 56 ARG Chi-restraints excluded: chain 6 residue 137 LEU Chi-restraints excluded: chain 6 residue 148 MET Chi-restraints excluded: chain 6 residue 243 ASP Chi-restraints excluded: chain 6 residue 298 LYS Chi-restraints excluded: chain 6 residue 409 ARG Chi-restraints excluded: chain 7 residue 197 LEU Chi-restraints excluded: chain 7 residue 453 VAL Chi-restraints excluded: chain 7 residue 516 THR Chi-restraints excluded: chain 7 residue 566 TYR Chi-restraints excluded: chain 7 residue 612 VAL Chi-restraints excluded: chain 7 residue 622 MET Chi-restraints excluded: chain b residue 25 ASN Chi-restraints excluded: chain c residue 16 THR Chi-restraints excluded: chain c residue 110 ASN Chi-restraints excluded: chain d residue 97 LEU Chi-restraints excluded: chain d residue 103 LEU Chi-restraints excluded: chain d residue 108 VAL Chi-restraints excluded: chain e residue 58 THR Chi-restraints excluded: chain e residue 109 LEU Chi-restraints excluded: chain h residue 56 MET Chi-restraints excluded: chain h residue 60 ASN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 998 random chunks: chunk 588 optimal weight: 0.5980 chunk 947 optimal weight: 3.9990 chunk 578 optimal weight: 8.9990 chunk 449 optimal weight: 8.9990 chunk 658 optimal weight: 0.3980 chunk 994 optimal weight: 0.7980 chunk 915 optimal weight: 8.9990 chunk 791 optimal weight: 5.9990 chunk 82 optimal weight: 4.9990 chunk 611 optimal weight: 5.9990 chunk 485 optimal weight: 20.0000 overall best weight: 2.1584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 5 GLN ** A 451 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 802 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1432 GLN B 178 ASN B 465 ASN B 667 GLN ** B 776 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1015 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 78 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 89 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** M 303 GLN ** Q 140 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 239 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 328 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 36 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** W 50 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** X 265 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 0 224 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 0 239 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 2 431 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 3 36 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** b 25 ASN c 94 ASN g 112 GLN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6916 moved from start: 0.2756 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.067 88785 Z= 0.265 Angle : 0.578 13.569 121636 Z= 0.302 Chirality : 0.041 0.315 13752 Planarity : 0.004 0.065 14134 Dihedral : 18.660 178.343 15190 Min Nonbonded Distance : 1.858 Molprobity Statistics. All-atom Clashscore : 12.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.12 % Favored : 96.88 % Rotamer: Outliers : 1.57 % Allowed : 15.44 % Favored : 82.99 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.31 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.24 (0.09), residues: 9583 helix: 1.05 (0.08), residues: 4096 sheet: -0.36 (0.15), residues: 1215 loop : -0.47 (0.10), residues: 4272 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.001 TRP X 263 HIS 0.010 0.001 HIS B1104 PHE 0.028 0.001 PHE A 714 TYR 0.031 0.001 TYR b 88 ARG 0.009 0.000 ARG 0 647 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 19166 Ramachandran restraints generated. 9583 Oldfield, 0 Emsley, 9583 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 19166 Ramachandran restraints generated. 9583 Oldfield, 0 Emsley, 9583 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1125 residues out of total 8648 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 136 poor density : 989 time to evaluate : 7.422 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: A 122 MET cc_start: 0.5142 (mmp) cc_final: 0.4700 (mmm) REVERT: A 229 SER cc_start: 0.8406 (t) cc_final: 0.8104 (t) REVERT: A 333 GLU cc_start: 0.6047 (pm20) cc_final: 0.5740 (pm20) REVERT: A 341 MET cc_start: 0.7541 (mtp) cc_final: 0.7248 (mmm) REVERT: A 644 LYS cc_start: 0.7496 (mmtt) cc_final: 0.7038 (ttpp) REVERT: A 678 GLU cc_start: 0.7910 (OUTLIER) cc_final: 0.7615 (pm20) REVERT: A 722 LEU cc_start: 0.8144 (OUTLIER) cc_final: 0.7895 (mm) REVERT: A 935 GLN cc_start: 0.6497 (tp40) cc_final: 0.6122 (tp-100) REVERT: A 1259 MET cc_start: 0.6353 (ppp) cc_final: 0.5771 (tmm) REVERT: A 1368 MET cc_start: 0.7816 (OUTLIER) cc_final: 0.7192 (mpp) REVERT: A 1417 GLU cc_start: 0.8046 (tm-30) cc_final: 0.7396 (tm-30) REVERT: B 116 GLU cc_start: 0.7680 (tt0) cc_final: 0.7324 (pt0) REVERT: B 193 LYS cc_start: 0.8402 (mtmm) cc_final: 0.7929 (mtpt) REVERT: B 431 TYR cc_start: 0.8047 (t80) cc_final: 0.7509 (t80) REVERT: B 432 MET cc_start: 0.7196 (mtm) cc_final: 0.6974 (mtm) REVERT: B 526 GLU cc_start: 0.7111 (tt0) cc_final: 0.6748 (tt0) REVERT: B 615 MET cc_start: 0.7523 (mpp) cc_final: 0.7198 (mpp) REVERT: B 624 LEU cc_start: 0.7579 (OUTLIER) cc_final: 0.7362 (mm) REVERT: B 1037 LEU cc_start: 0.8841 (OUTLIER) cc_final: 0.8541 (mt) REVERT: B 1210 MET cc_start: 0.8259 (mtp) cc_final: 0.7921 (mtm) REVERT: D 61 GLU cc_start: 0.7427 (mm-30) cc_final: 0.7216 (mp0) REVERT: E 75 MET cc_start: 0.7038 (ppp) cc_final: 0.6442 (ppp) REVERT: E 104 ASN cc_start: 0.6422 (t0) cc_final: 0.5804 (t0) REVERT: G 1 MET cc_start: 0.7921 (ptp) cc_final: 0.7600 (ptt) REVERT: G 74 TYR cc_start: 0.8118 (p90) cc_final: 0.7879 (p90) REVERT: I 77 LYS cc_start: 0.7322 (mmtt) cc_final: 0.6958 (tppt) REVERT: I 87 GLN cc_start: 0.6165 (pp30) cc_final: 0.5757 (pp30) REVERT: J 10 CYS cc_start: 0.8562 (OUTLIER) cc_final: 0.8005 (p) REVERT: K 37 LYS cc_start: 0.8292 (OUTLIER) cc_final: 0.7966 (tppt) REVERT: K 85 ASP cc_start: 0.8230 (m-30) cc_final: 0.7888 (m-30) REVERT: L 39 SER cc_start: 0.7529 (t) cc_final: 0.7135 (p) REVERT: M 243 CYS cc_start: 0.8444 (m) cc_final: 0.8107 (m) REVERT: M 251 GLN cc_start: 0.8045 (mp10) cc_final: 0.7706 (mm-40) REVERT: M 325 ASP cc_start: 0.6847 (t0) cc_final: 0.6511 (t70) REVERT: O 104 MET cc_start: 0.6965 (ptp) cc_final: 0.6675 (ptp) REVERT: O 121 MET cc_start: 0.4150 (ppp) cc_final: 0.3794 (ppp) REVERT: Q 114 MET cc_start: 0.3844 (tmm) cc_final: 0.3474 (tmm) REVERT: Q 387 ILE cc_start: 0.4888 (mt) cc_final: 0.4628 (tt) REVERT: R 90 GLN cc_start: 0.3657 (pm20) cc_final: 0.3187 (pm20) REVERT: R 225 MET cc_start: 0.4061 (ppp) cc_final: 0.3826 (mmt) REVERT: R 263 MET cc_start: 0.7919 (mmp) cc_final: 0.7324 (mmm) REVERT: R 294 MET cc_start: 0.0464 (pmm) cc_final: -0.0302 (pmm) REVERT: R 300 LEU cc_start: 0.8133 (mt) cc_final: 0.7841 (mm) REVERT: 0 76 MET cc_start: 0.7117 (ttp) cc_final: 0.6886 (tmm) REVERT: 0 247 SER cc_start: 0.8970 (m) cc_final: 0.8752 (m) REVERT: 0 299 LEU cc_start: 0.8461 (mm) cc_final: 0.7913 (mm) REVERT: 0 427 ASN cc_start: 0.8431 (p0) cc_final: 0.8133 (p0) REVERT: 0 610 ILE cc_start: 0.9026 (mm) cc_final: 0.8771 (mm) REVERT: 0 688 ARG cc_start: 0.7267 (mtt180) cc_final: 0.6647 (ttm-80) REVERT: 1 1 MET cc_start: 0.6277 (tpt) cc_final: 0.6057 (tpp) REVERT: 1 192 MET cc_start: 0.7546 (mmm) cc_final: 0.7230 (tpp) REVERT: 1 385 MET cc_start: 0.8199 (tpp) cc_final: 0.7884 (mtt) REVERT: 1 588 ASP cc_start: 0.7700 (m-30) cc_final: 0.7250 (t0) REVERT: 2 107 SER cc_start: 0.8053 (t) cc_final: 0.7791 (t) REVERT: 2 363 PHE cc_start: 0.8511 (p90) cc_final: 0.8264 (p90) REVERT: 3 35 TYR cc_start: 0.6656 (m-80) cc_final: 0.5357 (m-80) REVERT: 4 51 ILE cc_start: 0.8523 (OUTLIER) cc_final: 0.8308 (tp) REVERT: 4 311 GLN cc_start: 0.8246 (tm-30) cc_final: 0.7784 (tm-30) REVERT: 5 56 ARG cc_start: 0.7342 (OUTLIER) cc_final: 0.6590 (ptm-80) REVERT: 6 136 MET cc_start: 0.8588 (mmm) cc_final: 0.8121 (mmm) REVERT: 6 142 ARG cc_start: 0.7515 (mmm160) cc_final: 0.7270 (mmm160) REVERT: 6 379 SER cc_start: 0.8576 (m) cc_final: 0.8156 (p) REVERT: 6 399 ARG cc_start: 0.7164 (tpp80) cc_final: 0.6925 (tpp80) REVERT: 6 409 ARG cc_start: 0.7529 (OUTLIER) cc_final: 0.7248 (tpm170) REVERT: 7 112 MET cc_start: 0.7506 (ppp) cc_final: 0.7009 (pmm) REVERT: b 79 LYS cc_start: 0.7811 (pttt) cc_final: 0.7565 (pttt) REVERT: b 84 MET cc_start: 0.7328 (tmm) cc_final: 0.7057 (tmm) REVERT: c 73 ASN cc_start: 0.8635 (t0) cc_final: 0.8417 (t0) REVERT: d 102 GLU cc_start: 0.7007 (tt0) cc_final: 0.6688 (tt0) REVERT: f 53 GLU cc_start: 0.7858 (mm-30) cc_final: 0.7472 (mm-30) REVERT: g 36 LYS cc_start: 0.8247 (tptt) cc_final: 0.7973 (tptt) REVERT: g 104 GLN cc_start: 0.8451 (mp10) cc_final: 0.8064 (mp10) REVERT: h 56 MET cc_start: 0.7896 (OUTLIER) cc_final: 0.7471 (tpp) REVERT: h 83 ARG cc_start: 0.8123 (tpp80) cc_final: 0.7546 (mtt180) outliers start: 136 outliers final: 112 residues processed: 1071 average time/residue: 0.8159 time to fit residues: 1519.9350 Evaluate side-chains 1093 residues out of total 8648 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 123 poor density : 970 time to evaluate : 7.280 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 234 MET Chi-restraints excluded: chain A residue 329 LEU Chi-restraints excluded: chain A residue 351 THR Chi-restraints excluded: chain A residue 379 VAL Chi-restraints excluded: chain A residue 546 VAL Chi-restraints excluded: chain A residue 678 GLU Chi-restraints excluded: chain A residue 722 LEU Chi-restraints excluded: chain A residue 740 LEU Chi-restraints excluded: chain A residue 762 SER Chi-restraints excluded: chain A residue 802 ASN Chi-restraints excluded: chain A residue 822 GLU Chi-restraints excluded: chain A residue 827 THR Chi-restraints excluded: chain A residue 841 LEU Chi-restraints excluded: chain A residue 1111 MET Chi-restraints excluded: chain A residue 1124 HIS Chi-restraints excluded: chain A residue 1284 MET Chi-restraints excluded: chain A residue 1291 VAL Chi-restraints excluded: chain A residue 1330 ASN Chi-restraints excluded: chain A residue 1368 MET Chi-restraints excluded: chain A residue 1411 GLU Chi-restraints excluded: chain A residue 1443 VAL Chi-restraints excluded: chain B residue 55 VAL Chi-restraints excluded: chain B residue 225 VAL Chi-restraints excluded: chain B residue 240 ILE Chi-restraints excluded: chain B residue 388 CYS Chi-restraints excluded: chain B residue 468 GLU Chi-restraints excluded: chain B residue 492 LEU Chi-restraints excluded: chain B residue 540 SER Chi-restraints excluded: chain B residue 543 SER Chi-restraints excluded: chain B residue 624 LEU Chi-restraints excluded: chain B residue 773 MET Chi-restraints excluded: chain B residue 809 MET Chi-restraints excluded: chain B residue 910 VAL Chi-restraints excluded: chain B residue 955 THR Chi-restraints excluded: chain B residue 989 THR Chi-restraints excluded: chain B residue 1037 LEU Chi-restraints excluded: chain B residue 1051 THR Chi-restraints excluded: chain B residue 1152 MET Chi-restraints excluded: chain B residue 1191 ILE Chi-restraints excluded: chain B residue 1213 THR Chi-restraints excluded: chain C residue 26 ASP Chi-restraints excluded: chain C residue 65 HIS Chi-restraints excluded: chain D residue 52 LEU Chi-restraints excluded: chain D residue 159 THR Chi-restraints excluded: chain E residue 178 ILE Chi-restraints excluded: chain E residue 182 ASP Chi-restraints excluded: chain E residue 188 LEU Chi-restraints excluded: chain F residue 16 GLU Chi-restraints excluded: chain F residue 71 GLU Chi-restraints excluded: chain F residue 130 ILE Chi-restraints excluded: chain G residue 17 PHE Chi-restraints excluded: chain G residue 77 VAL Chi-restraints excluded: chain G residue 91 VAL Chi-restraints excluded: chain H residue 42 ILE Chi-restraints excluded: chain H residue 49 VAL Chi-restraints excluded: chain H residue 55 LEU Chi-restraints excluded: chain H residue 122 LEU Chi-restraints excluded: chain H residue 142 LEU Chi-restraints excluded: chain J residue 2 ILE Chi-restraints excluded: chain J residue 5 VAL Chi-restraints excluded: chain J residue 10 CYS Chi-restraints excluded: chain J residue 13 VAL Chi-restraints excluded: chain K residue 37 LYS Chi-restraints excluded: chain K residue 94 ILE Chi-restraints excluded: chain M residue 303 GLN Chi-restraints excluded: chain O residue 228 GLU Chi-restraints excluded: chain R residue 39 VAL Chi-restraints excluded: chain R residue 218 VAL Chi-restraints excluded: chain V residue 20 VAL Chi-restraints excluded: chain W residue 85 VAL Chi-restraints excluded: chain W residue 206 LEU Chi-restraints excluded: chain W residue 368 GLN Chi-restraints excluded: chain X residue 251 ASN Chi-restraints excluded: chain 0 residue 6 ASP Chi-restraints excluded: chain 0 residue 44 SER Chi-restraints excluded: chain 0 residue 487 LEU Chi-restraints excluded: chain 0 residue 495 MET Chi-restraints excluded: chain 0 residue 591 SER Chi-restraints excluded: chain 0 residue 597 ILE Chi-restraints excluded: chain 0 residue 607 SER Chi-restraints excluded: chain 0 residue 642 MET Chi-restraints excluded: chain 0 residue 675 ASP Chi-restraints excluded: chain 1 residue 419 LEU Chi-restraints excluded: chain 1 residue 481 ILE Chi-restraints excluded: chain 1 residue 485 ASP Chi-restraints excluded: chain 2 residue 50 MET Chi-restraints excluded: chain 2 residue 192 LEU Chi-restraints excluded: chain 2 residue 244 GLU Chi-restraints excluded: chain 2 residue 250 LEU Chi-restraints excluded: chain 2 residue 400 LEU Chi-restraints excluded: chain 3 residue 72 ILE Chi-restraints excluded: chain 4 residue 51 ILE Chi-restraints excluded: chain 4 residue 188 ASP Chi-restraints excluded: chain 4 residue 215 ILE Chi-restraints excluded: chain 4 residue 224 LEU Chi-restraints excluded: chain 5 residue 10 VAL Chi-restraints excluded: chain 5 residue 41 LEU Chi-restraints excluded: chain 5 residue 56 ARG Chi-restraints excluded: chain 6 residue 137 LEU Chi-restraints excluded: chain 6 residue 148 MET Chi-restraints excluded: chain 6 residue 243 ASP Chi-restraints excluded: chain 6 residue 298 LYS Chi-restraints excluded: chain 6 residue 409 ARG Chi-restraints excluded: chain 7 residue 197 LEU Chi-restraints excluded: chain 7 residue 453 VAL Chi-restraints excluded: chain 7 residue 516 THR Chi-restraints excluded: chain 7 residue 566 TYR Chi-restraints excluded: chain 7 residue 612 VAL Chi-restraints excluded: chain 7 residue 622 MET Chi-restraints excluded: chain b residue 25 ASN Chi-restraints excluded: chain c residue 16 THR Chi-restraints excluded: chain c residue 94 ASN Chi-restraints excluded: chain c residue 110 ASN Chi-restraints excluded: chain d residue 97 LEU Chi-restraints excluded: chain d residue 103 LEU Chi-restraints excluded: chain d residue 108 VAL Chi-restraints excluded: chain e residue 58 THR Chi-restraints excluded: chain e residue 74 ILE Chi-restraints excluded: chain e residue 109 LEU Chi-restraints excluded: chain g residue 62 ILE Chi-restraints excluded: chain h residue 56 MET Chi-restraints excluded: chain h residue 60 ASN Chi-restraints excluded: chain h residue 77 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 998 random chunks: chunk 628 optimal weight: 4.9990 chunk 843 optimal weight: 0.9990 chunk 242 optimal weight: 0.4980 chunk 730 optimal weight: 6.9990 chunk 116 optimal weight: 7.9990 chunk 220 optimal weight: 0.8980 chunk 792 optimal weight: 0.4980 chunk 331 optimal weight: 0.9990 chunk 814 optimal weight: 8.9990 chunk 100 optimal weight: 5.9990 chunk 146 optimal weight: 1.9990 overall best weight: 0.7784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 5 GLN ** A 451 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 802 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1432 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 178 ASN B 465 ASN B 667 GLN ** B 776 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1015 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1097 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 78 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 89 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 140 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** R 88 HIS ** R 239 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 328 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 36 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** W 50 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** X 265 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 0 224 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 0 239 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 2 431 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 3 36 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** b 25 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** c 94 ASN ** g 112 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4241 r_free = 0.4241 target = 0.165278 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3708 r_free = 0.3708 target = 0.126541 restraints weight = 170133.820| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 50)----------------| | r_work = 0.3638 r_free = 0.3638 target = 0.122061 restraints weight = 261628.084| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3598 r_free = 0.3598 target = 0.119824 restraints weight = 216302.354| |-----------------------------------------------------------------------------| r_work (final): 0.3584 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7072 moved from start: 0.2759 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.142 88785 Z= 0.263 Angle : 0.643 59.198 121636 Z= 0.353 Chirality : 0.041 0.565 13752 Planarity : 0.004 0.136 14134 Dihedral : 18.661 178.343 15190 Min Nonbonded Distance : 1.714 Molprobity Statistics. All-atom Clashscore : 13.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.10 % Favored : 96.90 % Rotamer: Outliers : 1.55 % Allowed : 15.61 % Favored : 82.84 % Cbeta Deviations : 0.03 % Peptide Plane: Cis-proline : 3.31 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.24 (0.09), residues: 9583 helix: 1.05 (0.08), residues: 4104 sheet: -0.37 (0.15), residues: 1214 loop : -0.47 (0.10), residues: 4265 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.042 0.001 TRP 7 133 HIS 0.011 0.001 HIS A 851 PHE 0.049 0.001 PHE I 4 TYR 0.050 0.001 TYR g 57 ARG 0.022 0.000 ARG X 197 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 22365.10 seconds wall clock time: 394 minutes 26.22 seconds (23666.22 seconds total)