Starting phenix.real_space_refine on Mon Mar 25 14:34:53 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7zx7_15006/03_2024/7zx7_15006.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7zx7_15006/03_2024/7zx7_15006.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.4 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7zx7_15006/03_2024/7zx7_15006.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7zx7_15006/03_2024/7zx7_15006.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7zx7_15006/03_2024/7zx7_15006.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7zx7_15006/03_2024/7zx7_15006.pdb" } resolution = 3.4 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.000 sd= 0.006 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: 7 Type Number sf(0) Gaussians Zn 11 6.06 5 P 132 5.49 5 Mg 1 5.21 5 S 275 5.16 5 C 30720 2.51 5 N 8668 2.21 5 O 9470 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A ASP 146": "OD1" <-> "OD2" Residue "A PHE 592": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 657": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 994": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 1308": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 740": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 769": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 935": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 1153": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G PHE 80": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I PHE 16": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "M ARG 127": "NH1" <-> "NH2" Residue "M ARG 132": "NH1" <-> "NH2" Residue "M PHE 142": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "M TYR 146": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "M GLU 147": "OE1" <-> "OE2" Residue "M ASP 157": "OD1" <-> "OD2" Residue "M TYR 165": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "M ASP 207": "OD1" <-> "OD2" Residue "M PHE 218": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "M TYR 259": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "M GLU 267": "OE1" <-> "OE2" Residue "M TYR 293": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "M PHE 300": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "M ASP 307": "OD1" <-> "OD2" Residue "O GLU 191": "OE1" <-> "OE2" Residue "O TYR 192": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "O ARG 196": "NH1" <-> "NH2" Residue "O ARG 203": "NH1" <-> "NH2" Residue "O ARG 208": "NH1" <-> "NH2" Residue "O GLU 227": "OE1" <-> "OE2" Residue "O GLU 228": "OE1" <-> "OE2" Residue "O ARG 235": "NH1" <-> "NH2" Residue "O TYR 237": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "O PHE 246": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "O PHE 250": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "O ARG 269": "NH1" <-> "NH2" Residue "O PHE 280": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "O GLU 286": "OE1" <-> "OE2" Residue "O TYR 293": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "O ARG 294": "NH1" <-> "NH2" Residue "O ARG 299": "NH1" <-> "NH2" Residue "O ARG 318": "NH1" <-> "NH2" Residue "O GLU 323": "OE1" <-> "OE2" Residue "O GLU 326": "OE1" <-> "OE2" Residue "O ARG 336": "NH1" <-> "NH2" Residue "Q PHE 146": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "R TYR 196": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "U TYR 14": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "U ASP 35": "OD1" <-> "OD2" Residue "U GLU 47": "OE1" <-> "OE2" Residue "U ARG 363": "NH1" <-> "NH2" Residue "U ASP 364": "OD1" <-> "OD2" Residue "U TYR 365": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "U ASP 373": "OD1" <-> "OD2" Residue "V PHE 81": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "V GLU 83": "OE1" <-> "OE2" Residue "V GLU 86": "OE1" <-> "OE2" Residue "V ASP 91": "OD1" <-> "OD2" Residue "a ASP 10": "OD1" <-> "OD2" Residue "a ASP 22": "OD1" <-> "OD2" Residue "a GLU 27": "OE1" <-> "OE2" Residue "a ASP 28": "OD1" <-> "OD2" Residue "a TYR 70": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "a PHE 72": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "a ASP 105": "OD1" <-> "OD2" Residue "a GLU 106": "OE1" <-> "OE2" Residue "a PHE 120": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "a ASP 121": "OD1" <-> "OD2" Residue "a TYR 124": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "a ARG 133": "NH1" <-> "NH2" Residue "a PHE 135": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "a PHE 137": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "a GLU 179": "OE1" <-> "OE2" Residue "a PHE 213": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "b PHE 29": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "b GLU 33": "OE1" <-> "OE2" Residue "b GLU 65": "OE1" <-> "OE2" Residue "b ASP 78": "OD1" <-> "OD2" Residue "b ASP 80": "OD1" <-> "OD2" Residue "b ASP 89": "OD1" <-> "OD2" Residue "b ARG 140": "NH1" <-> "NH2" Residue "b GLU 141": "OE1" <-> "OE2" Residue "b TYR 201": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "b ASP 217": "OD1" <-> "OD2" Residue "b PHE 252": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "b GLU 276": "OE1" <-> "OE2" Residue "b GLU 279": "OE1" <-> "OE2" Residue "b GLU 318": "OE1" <-> "OE2" Residue "b ASP 325": "OD1" <-> "OD2" Residue "b ASP 369": "OD1" <-> "OD2" Residue "b GLU 374": "OE1" <-> "OE2" Residue "b GLU 392": "OE1" <-> "OE2" Residue "b TYR 402": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "c ASP 82": "OD1" <-> "OD2" Residue "c GLU 84": "OE1" <-> "OE2" Residue "c GLU 95": "OE1" <-> "OE2" Residue "c GLU 116": "OE1" <-> "OE2" Residue "c TYR 141": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "c PHE 145": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "c TYR 149": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "c GLU 178": "OE1" <-> "OE2" Residue "c ARG 203": "NH1" <-> "NH2" Residue "c GLU 225": "OE1" <-> "OE2" Residue "c GLU 239": "OE1" <-> "OE2" Residue "c ARG 257": "NH1" <-> "NH2" Residue "c ASP 262": "OD1" <-> "OD2" Residue "c GLU 264": "OE1" <-> "OE2" Residue "c GLU 272": "OE1" <-> "OE2" Residue "c GLU 279": "OE1" <-> "OE2" Residue "c GLU 300": "OE1" <-> "OE2" Residue "c GLU 301": "OE1" <-> "OE2" Residue "c GLU 323": "OE1" <-> "OE2" Residue "c PHE 331": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "c GLU 352": "OE1" <-> "OE2" Residue "c GLU 363": "OE1" <-> "OE2" Residue "c TYR 378": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "d GLU 7": "OE1" <-> "OE2" Residue "d GLU 12": "OE1" <-> "OE2" Residue "d GLU 13": "OE1" <-> "OE2" Residue "d GLU 32": "OE1" <-> "OE2" Time to flip residues: 0.14s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib" Total number of atoms: 49277 Number of models: 1 Model: "" Number of chains: 32 Chain: "A" Number of atoms: 11274 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1423, 11274 Classifications: {'peptide': 1423} Link IDs: {'PCIS': 3, 'PTRANS': 67, 'TRANS': 1352} Chain breaks: 4 Chain: "B" Number of atoms: 9076 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1136, 9076 Classifications: {'peptide': 1136} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 53, 'TRANS': 1082} Chain breaks: 2 Chain: "C" Number of atoms: 2059 Number of conformers: 1 Conformer: "" Number of residues, atoms: 257, 2059 Classifications: {'peptide': 257} Link IDs: {'PTRANS': 15, 'TRANS': 241} Chain breaks: 1 Chain: "D" Number of atoms: 1050 Number of conformers: 1 Conformer: "" Number of residues, atoms: 128, 1050 Classifications: {'peptide': 128} Link IDs: {'PTRANS': 3, 'TRANS': 124} Chain: "E" Number of atoms: 1721 Number of conformers: 1 Conformer: "" Number of residues, atoms: 209, 1721 Classifications: {'peptide': 209} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 11, 'TRANS': 197} Chain: "F" Number of atoms: 636 Number of conformers: 1 Conformer: "" Number of residues, atoms: 79, 636 Classifications: {'peptide': 79} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 5, 'TRANS': 73} Chain: "G" Number of atoms: 1351 Number of conformers: 1 Conformer: "" Number of residues, atoms: 171, 1351 Classifications: {'peptide': 171} Link IDs: {'PTRANS': 10, 'TRANS': 160} Chain: "H" Number of atoms: 1186 Number of conformers: 1 Conformer: "" Number of residues, atoms: 148, 1186 Classifications: {'peptide': 148} Link IDs: {'PTRANS': 4, 'TRANS': 143} Chain: "I" Number of atoms: 928 Number of conformers: 1 Conformer: "" Number of residues, atoms: 114, 928 Classifications: {'peptide': 114} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 5, 'TRANS': 108} Chain: "J" Number of atoms: 507 Number of conformers: 1 Conformer: "" Number of residues, atoms: 64, 507 Classifications: {'peptide': 64} Link IDs: {'PTRANS': 2, 'TRANS': 61} Chain: "K" Number of atoms: 920 Number of conformers: 1 Conformer: "" Number of residues, atoms: 115, 920 Classifications: {'peptide': 115} Link IDs: {'PTRANS': 8, 'TRANS': 106} Chain: "L" Number of atoms: 373 Number of conformers: 1 Conformer: "" Number of residues, atoms: 44, 373 Classifications: {'peptide': 44} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 42} Chain: "M" Number of atoms: 1879 Number of conformers: 1 Conformer: "" Number of residues, atoms: 242, 1879 Classifications: {'peptide': 242} Link IDs: {'PTRANS': 13, 'TRANS': 228} Chain breaks: 1 Chain: "N" Number of atoms: 1369 Number of conformers: 1 Conformer: "" Number of residues, atoms: 66, 1369 Classifications: {'DNA': 66} Link IDs: {'rna3p': 65} Chain: "O" Number of atoms: 1422 Number of conformers: 1 Conformer: "" Number of residues, atoms: 179, 1422 Classifications: {'peptide': 179} Link IDs: {'PTRANS': 9, 'TRANS': 169} Chain: "Q" Number of atoms: 1138 Number of conformers: 1 Conformer: "" Number of residues, atoms: 138, 1138 Classifications: {'peptide': 138} Link IDs: {'PTRANS': 7, 'TRANS': 130} Chain breaks: 1 Chain: "R" Number of atoms: 1788 Number of conformers: 1 Conformer: "" Number of residues, atoms: 222, 1788 Classifications: {'peptide': 222} Link IDs: {'PTRANS': 7, 'TRANS': 214} Chain breaks: 1 Chain: "T" Number of atoms: 1337 Number of conformers: 1 Conformer: "" Number of residues, atoms: 66, 1337 Classifications: {'DNA': 66} Link IDs: {'rna3p': 65} Chain: "U" Number of atoms: 734 Number of conformers: 1 Conformer: "" Number of residues, atoms: 88, 734 Classifications: {'peptide': 88} Link IDs: {'PTRANS': 1, 'TRANS': 86} Chain breaks: 1 Chain: "V" Number of atoms: 793 Number of conformers: 1 Conformer: "" Number of residues, atoms: 97, 793 Classifications: {'peptide': 97} Link IDs: {'PTRANS': 1, 'TRANS': 95} Chain: "a" Number of atoms: 1807 Number of conformers: 1 Conformer: "" Number of residues, atoms: 215, 1807 Classifications: {'peptide': 215} Link IDs: {'PCIS': 1, 'PTRANS': 6, 'TRANS': 207} Chain breaks: 1 Chain: "b" Number of atoms: 2977 Number of conformers: 1 Conformer: "" Number of residues, atoms: 365, 2977 Classifications: {'peptide': 365} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 17, 'TRANS': 347} Chain breaks: 2 Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 5 Unresolved non-hydrogen dihedrals: 3 Planarities with less than four sites: {'GLU:plan': 1} Unresolved non-hydrogen planarities: 4 Chain: "c" Number of atoms: 2516 Number of conformers: 1 Conformer: "" Number of residues, atoms: 303, 2516 Classifications: {'peptide': 303} Link IDs: {'PTRANS': 9, 'TRANS': 293} Chain breaks: 1 Chain: "d" Number of atoms: 424 Number of conformers: 1 Conformer: "" Number of residues, atoms: 52, 424 Classifications: {'peptide': 52} Link IDs: {'TRANS': 51} 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: "b" 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} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 464 SG CYS A 71 61.276 103.808 131.913 1.00230.48 S ATOM 486 SG CYS A 74 61.081 102.802 135.592 1.00231.86 S ATOM 533 SG CYS A 81 64.278 102.405 133.502 1.00233.42 S ATOM 768 SG CYS A 111 53.979 55.705 131.771 1.00356.95 S ATOM 796 SG CYS A 114 51.291 56.312 134.154 1.00360.64 S ATOM 1109 SG CYS A 154 53.208 53.071 134.356 1.00355.37 S ATOM 1132 SG CYS A 184 50.855 53.736 131.436 1.00349.72 S ATOM 19919 SG CYS B1119 55.720 91.591 145.323 1.00247.53 S ATOM 19941 SG CYS B1122 57.053 89.299 142.601 1.00241.96 S ATOM 20056 SG CYS B1137 55.469 92.583 141.633 1.00258.43 S ATOM 20077 SG CYS B1140 53.484 89.596 143.079 1.00257.62 S ATOM 21044 SG CYS C 88 110.693 146.732 142.056 1.00124.53 S ATOM 21057 SG CYS C 90 109.000 145.344 138.770 1.00121.75 S ATOM 21092 SG CYS C 94 111.788 147.750 138.796 1.00112.30 S ATOM 21114 SG CYS C 97 112.229 144.194 139.834 1.00115.62 S ATOM 28400 SG CYS I 17 118.512 28.137 108.993 1.00172.24 S ATOM 28424 SG CYS I 20 115.813 30.593 108.043 1.00187.54 S ATOM 28585 SG CYS I 39 115.484 28.577 111.159 1.00187.44 S ATOM 28610 SG CYS I 42 115.283 26.972 107.515 1.00192.40 S ATOM 28962 SG CYS I 86 151.795 48.937 129.732 1.00147.61 S ATOM 28986 SG CYS I 89 154.532 50.072 127.389 1.00152.28 S ATOM 29190 SG CYS I 114 151.521 52.140 127.779 1.00155.18 S ATOM 29225 SG CYS I 119 151.388 48.843 125.979 1.00159.53 S ATOM 29336 SG CYS J 7 131.851 119.591 141.036 1.00 89.15 S ATOM 29360 SG CYS J 10 132.741 122.199 143.570 1.00 91.16 S ATOM 29624 SG CYS J 44 133.963 118.613 143.943 1.00 98.78 S ATOM 29630 SG CYS J 45 135.303 121.023 141.550 1.00101.25 S ATOM 30750 SG CYS L 19 111.424 119.064 102.291 1.00125.53 S ATOM 30769 SG CYS L 22 113.371 121.735 100.520 1.00121.46 S ATOM 30886 SG CYS L 36 109.793 121.198 99.652 1.00137.20 S ATOM 30912 SG CYS L 39 113.048 118.234 98.750 1.00127.75 S ATOM 31094 SG CYS M 15 68.634 123.629 137.454 1.00187.93 S ATOM 31241 SG CYS M 34 71.876 124.943 135.811 1.00176.41 S ATOM 31263 SG CYS M 37 71.180 125.186 140.288 1.00178.41 S ATOM 44738 SG CYS b 221 117.475 95.488 26.106 1.00527.76 S ATOM 45535 SG CYS b 317 113.689 95.594 26.840 1.00535.97 S ATOM 45857 SG CYS b 354 129.130 74.512 27.769 1.00532.98 S ATOM 45881 SG CYS b 357 133.004 74.649 27.278 1.00541.15 S ATOM 46072 SG CYS b 380 130.625 75.335 24.419 1.00494.20 S ATOM 46093 SG CYS b 383 131.040 71.841 25.772 1.00481.70 S Time building chain proxies: 25.28, per 1000 atoms: 0.51 Number of scatterers: 49277 At special positions: 0 Unit cell: (171.15, 192.15, 225.75, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 7 Type Number sf(0) Zn 11 29.99 S 275 16.00 P 132 15.00 Mg 1 11.99 O 9470 8.00 N 8668 7.00 C 30720 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: 18.14 Conformation dependent library (CDL) restraints added in 7.8 seconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN A2001 " pdb="ZN ZN A2001 " - pdb=" NE2 HIS A 84 " pdb="ZN ZN A2001 " - pdb=" SG CYS A 81 " pdb="ZN ZN A2001 " - pdb=" SG CYS A 74 " pdb="ZN ZN A2001 " - pdb=" SG CYS A 71 " pdb=" ZN A2002 " pdb="ZN ZN A2002 " - pdb=" SG CYS A 111 " pdb="ZN ZN A2002 " - pdb=" SG CYS A 114 " pdb="ZN ZN A2002 " - pdb=" SG CYS A 184 " pdb="ZN ZN A2002 " - pdb=" SG CYS A 154 " pdb=" ZN B1201 " pdb="ZN ZN B1201 " - pdb=" SG CYS B1122 " pdb="ZN ZN B1201 " - pdb=" SG CYS B1140 " pdb="ZN ZN B1201 " - pdb=" SG CYS B1119 " pdb="ZN ZN B1201 " - pdb=" SG CYS B1137 " pdb=" ZN C 301 " pdb="ZN ZN C 301 " - pdb=" SG CYS C 90 " pdb="ZN ZN C 301 " - pdb=" SG CYS C 88 " pdb="ZN ZN C 301 " - pdb=" SG CYS C 94 " pdb="ZN ZN C 301 " - pdb=" SG CYS C 97 " pdb=" ZN I 201 " pdb="ZN ZN I 201 " - pdb=" SG CYS I 20 " pdb="ZN ZN I 201 " - pdb=" SG CYS I 17 " pdb="ZN ZN I 201 " - pdb=" SG CYS I 42 " pdb="ZN ZN I 201 " - pdb=" SG CYS I 39 " pdb=" ZN I 202 " pdb="ZN ZN I 202 " - pdb=" SG CYS I 89 " pdb="ZN ZN I 202 " - pdb=" SG CYS I 119 " pdb="ZN ZN I 202 " - pdb=" SG CYS I 114 " pdb="ZN ZN I 202 " - pdb=" SG CYS I 86 " pdb=" ZN J 101 " pdb="ZN ZN J 101 " - pdb=" SG CYS J 45 " pdb="ZN ZN J 101 " - pdb=" SG CYS J 10 " pdb="ZN ZN J 101 " - pdb=" SG CYS J 44 " pdb="ZN ZN J 101 " - pdb=" SG CYS J 7 " pdb=" ZN L 101 " pdb="ZN ZN L 101 " - pdb=" SG CYS L 22 " pdb="ZN ZN L 101 " - pdb=" SG CYS L 19 " pdb="ZN ZN L 101 " - pdb=" SG CYS L 36 " pdb="ZN ZN L 101 " - pdb=" SG CYS L 39 " pdb=" ZN M 401 " pdb="ZN ZN M 401 " - pdb=" NE2 HIS M 18 " pdb="ZN ZN M 401 " - pdb=" SG CYS M 15 " pdb="ZN ZN M 401 " - pdb=" SG CYS M 37 " pdb="ZN ZN M 401 " - pdb=" SG CYS M 34 " pdb=" ZN b 501 " pdb="ZN ZN b 501 " - pdb=" NE2 HIS b 319 " pdb="ZN ZN b 501 " - pdb=" NE2 HIS b 313 " pdb="ZN ZN b 501 " - pdb=" SG CYS b 221 " pdb="ZN ZN b 501 " - pdb=" SG CYS b 317 " pdb=" ZN b 502 " pdb="ZN ZN b 502 " - pdb=" SG CYS b 380 " pdb="ZN ZN b 502 " - pdb=" SG CYS b 383 " pdb="ZN ZN b 502 " - pdb=" SG CYS b 357 " pdb="ZN ZN b 502 " - pdb=" SG CYS b 354 " Number of angles added : 56 11430 Ramachandran restraints generated. 5715 Oldfield, 0 Emsley, 5715 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 10946 Finding SS restraints... Secondary structure from input PDB file: 208 helices and 53 sheets defined 43.0% alpha, 14.6% beta 56 base pairs and 112 stacking pairs defined. Time for finding SS restraints: 16.49 Creating SS restraints... Processing helix chain 'A' and resid 27 through 35 Processing helix chain 'A' and resid 99 through 109 Processing helix chain 'A' and resid 123 through 134 Processing helix chain 'A' and resid 136 through 150 removed outlier: 3.613A pdb=" N THR A 142 " --> pdb=" O LYS A 138 " (cutoff:3.500A) removed outlier: 3.880A pdb=" N LEU A 147 " --> pdb=" O HIS A 143 " (cutoff:3.500A) removed outlier: 4.049A pdb=" N GLY A 150 " --> pdb=" O ASP A 146 " (cutoff:3.500A) Processing helix chain 'A' and resid 217 through 228 removed outlier: 3.774A pdb=" N GLU A 223 " --> pdb=" O GLU A 219 " (cutoff:3.500A) removed outlier: 4.503A pdb=" N ILE A 224 " --> pdb=" O ARG A 220 " (cutoff:3.500A) Processing helix chain 'A' and resid 229 through 236 removed outlier: 3.519A pdb=" N PHE A 234 " --> pdb=" O ASP A 230 " (cutoff:3.500A) Processing helix chain 'A' and resid 244 through 249 removed outlier: 3.584A pdb=" N MET A 248 " --> pdb=" O ARG A 244 " (cutoff:3.500A) removed outlier: 4.141A pdb=" N ILE A 249 " --> pdb=" O PRO A 245 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 244 through 249' Processing helix chain 'A' and resid 274 through 297 Processing helix chain 'A' and resid 299 through 319 Processing helix chain 'A' and resid 338 through 344 removed outlier: 3.532A pdb=" N LEU A 343 " --> pdb=" O LEU A 339 " (cutoff:3.500A) Processing helix chain 'A' and resid 348 through 353 Processing helix chain 'A' and resid 382 through 388 Processing helix chain 'A' and resid 398 through 409 Processing helix chain 'A' and resid 434 through 439 removed outlier: 3.993A pdb=" N HIS A 439 " --> pdb=" O SER A 436 " (cutoff:3.500A) Processing helix chain 'A' and resid 465 through 467 No H-bonds generated for 'chain 'A' and resid 465 through 467' Processing helix chain 'A' and resid 488 through 493 Processing helix chain 'A' and resid 508 through 519 Processing helix chain 'A' and resid 521 through 524 Processing helix chain 'A' and resid 538 through 549 Processing helix chain 'A' and resid 556 through 565 Processing helix chain 'A' and resid 588 through 596 removed outlier: 3.518A pdb=" N LEU A 594 " --> pdb=" O GLN A 590 " (cutoff:3.500A) removed outlier: 3.536A pdb=" N ILE A 595 " --> pdb=" O ILE A 591 " (cutoff:3.500A) Processing helix chain 'A' and resid 612 through 616 Processing helix chain 'A' and resid 641 through 646 Processing helix chain 'A' and resid 651 through 684 removed outlier: 8.136A pdb=" N HIS A 662 " --> pdb=" O LEU A 658 " (cutoff:3.500A) removed outlier: 9.320A pdb=" N ASP A 663 " --> pdb=" O GLU A 659 " (cutoff:3.500A) removed outlier: 4.430A pdb=" N ILE A 664 " --> pdb=" O MET A 660 " (cutoff:3.500A) removed outlier: 3.871A pdb=" N LEU A 681 " --> pdb=" O ASN A 677 " (cutoff:3.500A) removed outlier: 4.177A pdb=" N ILE A 682 " --> pdb=" O ASN A 678 " (cutoff:3.500A) Processing helix chain 'A' and resid 688 through 693 removed outlier: 3.670A pdb=" N SER A 692 " --> pdb=" O GLY A 688 " (cutoff:3.500A) Processing helix chain 'A' and resid 695 through 722 Processing helix chain 'A' and resid 732 through 760 removed outlier: 3.552A pdb=" N LEU A 760 " --> pdb=" O ALA A 756 " (cutoff:3.500A) Processing helix chain 'A' and resid 764 through 772 Processing helix chain 'A' and resid 777 through 786 Processing helix chain 'A' and resid 832 through 857 removed outlier: 3.641A pdb=" N GLU A 845 " --> pdb=" O MET A 841 " (cutoff:3.500A) removed outlier: 3.803A pdb=" N GLY A 846 " --> pdb=" O GLY A 842 " (cutoff:3.500A) Processing helix chain 'A' and resid 858 through 869 removed outlier: 3.626A pdb=" N LYS A 866 " --> pdb=" O ARG A 862 " (cutoff:3.500A) removed outlier: 3.912A pdb=" N SER A 867 " --> pdb=" O ARG A 863 " (cutoff:3.500A) Processing helix chain 'A' and resid 890 through 894 Processing helix chain 'A' and resid 912 through 921 Processing helix chain 'A' and resid 926 through 934 Processing helix chain 'A' and resid 935 through 945 Processing helix chain 'A' and resid 945 through 970 removed outlier: 3.970A pdb=" N GLN A 949 " --> pdb=" O ASN A 945 " (cutoff:3.500A) Processing helix chain 'A' and resid 982 through 994 Processing helix chain 'A' and resid 1005 through 1020 Processing helix chain 'A' and resid 1027 through 1038 Processing helix chain 'A' and resid 1038 through 1049 Processing helix chain 'A' and resid 1050 through 1057 Processing helix chain 'A' and resid 1061 through 1080 removed outlier: 3.534A pdb=" N ILE A1080 " --> pdb=" O PHE A1076 " (cutoff:3.500A) Processing helix chain 'A' and resid 1086 through 1101 Proline residue: A1098 - end of helix removed outlier: 4.381A pdb=" N GLN A1101 " --> pdb=" O GLU A1097 " (cutoff:3.500A) Processing helix chain 'A' and resid 1119 through 1129 removed outlier: 3.511A pdb=" N ARG A1123 " --> pdb=" O LEU A1119 " (cutoff:3.500A) Processing helix chain 'A' and resid 1145 through 1150 removed outlier: 4.297A pdb=" N ARG A1149 " --> pdb=" O GLY A1145 " (cutoff:3.500A) Processing helix chain 'A' and resid 1150 through 1162 Processing helix chain 'A' and resid 1166 through 1169 No H-bonds generated for 'chain 'A' and resid 1166 through 1169' Processing helix chain 'A' and resid 1186 through 1197 removed outlier: 4.104A pdb=" N GLU A1191 " --> pdb=" O ALA A1187 " (cutoff:3.500A) removed outlier: 4.463A pdb=" N TRP A1192 " --> pdb=" O GLU A1188 " (cutoff:3.500A) removed outlier: 3.957A pdb=" N VAL A1195 " --> pdb=" O GLU A1191 " (cutoff:3.500A) removed outlier: 3.512A pdb=" N TYR A1196 " --> pdb=" O TRP A1192 " (cutoff:3.500A) Processing helix chain 'A' and resid 1217 through 1224 Processing helix chain 'A' and resid 1227 through 1240 removed outlier: 4.049A pdb=" N ILE A1231 " --> pdb=" O THR A1227 " (cutoff:3.500A) removed outlier: 3.577A pdb=" N ALA A1232 " --> pdb=" O MET A1228 " (cutoff:3.500A) Processing helix chain 'A' and resid 1262 through 1267 Processing helix chain 'A' and resid 1282 through 1295 removed outlier: 3.788A pdb=" N ARG A1286 " --> pdb=" O ASP A1282 " (cutoff:3.500A) removed outlier: 3.572A pdb=" N THR A1294 " --> pdb=" O SER A1290 " (cutoff:3.500A) Processing helix chain 'A' and resid 1342 through 1349 Processing helix chain 'A' and resid 1361 through 1369 Processing helix chain 'A' and resid 1370 through 1389 removed outlier: 4.574A pdb=" N ASP A1389 " --> pdb=" O VAL A1385 " (cutoff:3.500A) Processing helix chain 'A' and resid 1394 through 1407 Processing helix chain 'A' and resid 1415 through 1420 Processing helix chain 'A' and resid 1425 through 1433 Processing helix chain 'A' and resid 1434 through 1446 Processing helix chain 'A' and resid 1453 through 1460 removed outlier: 3.517A pdb=" N ASN A1457 " --> pdb=" O GLY A1453 " (cutoff:3.500A) Processing helix chain 'A' and resid 1466 through 1469 Processing helix chain 'A' and resid 1476 through 1482 removed outlier: 3.700A pdb=" N TYR A1482 " --> pdb=" O GLU A1478 " (cutoff:3.500A) Processing helix chain 'B' and resid 18 through 37 removed outlier: 4.477A pdb=" N GLN B 23 " --> pdb=" O PRO B 19 " (cutoff:3.500A) removed outlier: 5.729A pdb=" N GLU B 24 " --> pdb=" O ASP B 20 " (cutoff:3.500A) removed outlier: 3.548A pdb=" N TRP B 27 " --> pdb=" O GLN B 23 " (cutoff:3.500A) Processing helix chain 'B' and resid 40 through 53 Processing helix chain 'B' and resid 53 through 62 Processing helix chain 'B' and resid 109 through 117 Processing helix chain 'B' and resid 167 through 174 Processing helix chain 'B' and resid 248 through 253 removed outlier: 3.773A pdb=" N GLY B 253 " --> pdb=" O LYS B 249 " (cutoff:3.500A) Processing helix chain 'B' and resid 269 through 277 Processing helix chain 'B' and resid 280 through 289 removed outlier: 3.679A pdb=" N HIS B 287 " --> pdb=" O ASP B 283 " (cutoff:3.500A) Processing helix chain 'B' and resid 294 through 308 removed outlier: 3.529A pdb=" N MET B 300 " --> pdb=" O GLU B 296 " (cutoff:3.500A) removed outlier: 3.655A pdb=" N VAL B 301 " --> pdb=" O MET B 297 " (cutoff:3.500A) removed outlier: 3.535A pdb=" N LYS B 302 " --> pdb=" O MET B 298 " (cutoff:3.500A) Proline residue: B 303 - end of helix Processing helix chain 'B' and resid 313 through 324 Processing helix chain 'B' and resid 331 through 346 Processing helix chain 'B' and resid 357 through 377 Processing helix chain 'B' and resid 387 through 389 No H-bonds generated for 'chain 'B' and resid 387 through 389' Processing helix chain 'B' and resid 395 through 426 removed outlier: 3.774A pdb=" N GLY B 406 " --> pdb=" O PHE B 402 " (cutoff:3.500A) Processing helix chain 'B' and resid 430 through 435 Processing helix chain 'B' and resid 437 through 451 Processing helix chain 'B' and resid 455 through 459 Processing helix chain 'B' and resid 474 through 483 Processing helix chain 'B' and resid 489 through 496 removed outlier: 3.790A pdb=" N LYS B 494 " --> pdb=" O GLY B 490 " (cutoff:3.500A) removed outlier: 3.643A pdb=" N LEU B 495 " --> pdb=" O ARG B 491 " (cutoff:3.500A) removed outlier: 3.822A pdb=" N ALA B 496 " --> pdb=" O ASP B 492 " (cutoff:3.500A) Processing helix chain 'B' and resid 502 through 506 Processing helix chain 'B' and resid 538 through 548 Processing helix chain 'B' and resid 557 through 561 Processing helix chain 'B' and resid 579 through 594 Processing helix chain 'B' and resid 636 through 645 Processing helix chain 'B' and resid 652 through 659 removed outlier: 3.818A pdb=" N LEU B 656 " --> pdb=" O SER B 652 " (cutoff:3.500A) Processing helix chain 'B' and resid 667 through 671 Processing helix chain 'B' and resid 699 through 704 Processing helix chain 'B' and resid 713 through 717 Processing helix chain 'B' and resid 718 through 730 removed outlier: 3.887A pdb=" N LYS B 730 " --> pdb=" O SER B 726 " (cutoff:3.500A) Processing helix chain 'B' and resid 761 through 766 Processing helix chain 'B' and resid 798 through 803 Processing helix chain 'B' and resid 970 through 976 removed outlier: 4.633A pdb=" N SER B 974 " --> pdb=" O HIS B 970 " (cutoff:3.500A) removed outlier: 3.845A pdb=" N ARG B 975 " --> pdb=" O ALA B 971 " (cutoff:3.500A) Processing helix chain 'B' and resid 977 through 994 removed outlier: 3.703A pdb=" N LEU B 981 " --> pdb=" O THR B 977 " (cutoff:3.500A) Processing helix chain 'B' and resid 1007 through 1017 removed outlier: 3.636A pdb=" N ASP B1017 " --> pdb=" O ASN B1013 " (cutoff:3.500A) Processing helix chain 'B' and resid 1087 through 1098 Processing helix chain 'B' and resid 1099 through 1108 Processing helix chain 'B' and resid 1153 through 1165 Processing helix chain 'C' and resid 27 through 41 removed outlier: 3.501A pdb=" N ILE C 39 " --> pdb=" O ARG C 35 " (cutoff:3.500A) Processing helix chain 'C' and resid 60 through 70 Processing helix chain 'C' and resid 77 through 82 removed outlier: 3.943A pdb=" N LYS C 81 " --> pdb=" O ASP C 77 " (cutoff:3.500A) Processing helix chain 'C' and resid 118 through 120 No H-bonds generated for 'chain 'C' and resid 118 through 120' Processing helix chain 'C' and resid 173 through 177 Processing helix chain 'C' and resid 199 through 203 Processing helix chain 'C' and resid 240 through 271 removed outlier: 3.536A pdb=" N VAL C 245 " --> pdb=" O PRO C 241 " (cutoff:3.500A) Processing helix chain 'D' and resid 23 through 27 removed outlier: 3.539A pdb=" N GLU D 27 " --> pdb=" O LYS D 24 " (cutoff:3.500A) Processing helix chain 'D' and resid 33 through 50 removed outlier: 3.536A pdb=" N SER D 50 " --> pdb=" O GLN D 46 " (cutoff:3.500A) Processing helix chain 'D' and resid 58 through 72 removed outlier: 3.605A pdb=" N MET D 62 " --> pdb=" O SER D 58 " (cutoff:3.500A) Processing helix chain 'D' and resid 76 through 90 removed outlier: 3.590A pdb=" N LYS D 90 " --> pdb=" O LEU D 86 " (cutoff:3.500A) Processing helix chain 'D' and resid 93 through 104 Processing helix chain 'D' and resid 107 through 115 Processing helix chain 'D' and resid 116 through 119 Processing helix chain 'D' and resid 123 through 138 Processing helix chain 'E' and resid 3 through 24 removed outlier: 3.865A pdb=" N THR E 7 " --> pdb=" O ASP E 3 " (cutoff:3.500A) removed outlier: 4.283A pdb=" N TYR E 8 " --> pdb=" O GLU E 4 " (cutoff:3.500A) Processing helix chain 'E' and resid 29 through 34 Processing helix chain 'E' and resid 36 through 43 Processing helix chain 'E' and resid 83 through 98 Processing helix chain 'E' and resid 111 through 122 removed outlier: 3.893A pdb=" N GLN E 116 " --> pdb=" O PRO E 112 " (cutoff:3.500A) removed outlier: 3.617A pdb=" N VAL E 119 " --> pdb=" O LYS E 115 " (cutoff:3.500A) Processing helix chain 'E' and resid 132 through 136 Processing helix chain 'E' and resid 137 through 142 removed outlier: 6.039A pdb=" N THR E 140 " --> pdb=" O ILE E 137 " (cutoff:3.500A) Processing helix chain 'E' and resid 152 through 164 Processing helix chain 'E' and resid 166 through 170 Processing helix chain 'E' and resid 177 through 184 Processing helix chain 'F' and resid 58 through 75 Processing helix chain 'F' and resid 88 through 100 Processing helix chain 'F' and resid 121 through 123 No H-bonds generated for 'chain 'F' and resid 121 through 123' Processing helix chain 'G' and resid 14 through 18 Processing helix chain 'G' and resid 21 through 35 removed outlier: 3.540A pdb=" N THR G 32 " --> pdb=" O GLN G 28 " (cutoff:3.500A) Processing helix chain 'H' and resid 83 through 88 Processing helix chain 'H' and resid 130 through 133 removed outlier: 3.890A pdb=" N HIS H 133 " --> pdb=" O ASN H 130 " (cutoff:3.500A) No H-bonds generated for 'chain 'H' and resid 130 through 133' Processing helix chain 'I' and resid 63 through 68 removed outlier: 3.973A pdb=" N GLN I 67 " --> pdb=" O ASP I 63 " (cutoff:3.500A) Processing helix chain 'I' and resid 69 through 75 Processing helix chain 'J' and resid 17 through 27 Processing helix chain 'J' and resid 30 through 38 Processing helix chain 'J' and resid 42 through 51 removed outlier: 3.521A pdb=" N MET J 48 " --> pdb=" O CYS J 44 " (cutoff:3.500A) removed outlier: 3.625A pdb=" N LEU J 49 " --> pdb=" O CYS J 45 " (cutoff:3.500A) Processing helix chain 'J' and resid 55 through 60 Processing helix chain 'K' and resid 5 through 10 removed outlier: 3.692A pdb=" N SER K 9 " --> pdb=" O ALA K 6 " (cutoff:3.500A) Processing helix chain 'K' and resid 39 through 52 removed outlier: 3.859A pdb=" N ILE K 45 " --> pdb=" O THR K 41 " (cutoff:3.500A) Processing helix chain 'K' and resid 82 through 115 Processing helix chain 'M' and resid 47 through 52 Processing helix chain 'M' and resid 117 through 129 Processing helix chain 'M' and resid 131 through 149 Processing helix chain 'M' and resid 155 through 172 removed outlier: 3.685A pdb=" N GLY M 172 " --> pdb=" O CYS M 168 " (cutoff:3.500A) Processing helix chain 'M' and resid 176 through 182 Processing helix chain 'M' and resid 187 through 203 Processing helix chain 'M' and resid 214 through 222 Processing helix chain 'M' and resid 225 through 242 Processing helix chain 'M' and resid 249 through 265 Processing helix chain 'M' and resid 270 through 279 removed outlier: 3.513A pdb=" N ILE M 274 " --> pdb=" O THR M 270 " (cutoff:3.500A) Processing helix chain 'M' and resid 281 through 293 removed outlier: 3.672A pdb=" N LEU M 291 " --> pdb=" O GLN M 287 " (cutoff:3.500A) removed outlier: 3.953A pdb=" N ILE M 292 " --> pdb=" O SER M 288 " (cutoff:3.500A) Processing helix chain 'M' and resid 295 through 300 removed outlier: 3.711A pdb=" N LEU M 299 " --> pdb=" O ARG M 295 " (cutoff:3.500A) Processing helix chain 'O' and resid 179 through 187 Processing helix chain 'O' and resid 226 through 244 Processing helix chain 'O' and resid 269 through 277 Processing helix chain 'O' and resid 317 through 335 Proline residue: O 330 - end of helix Processing helix chain 'Q' and resid 5 through 9 Processing helix chain 'Q' and resid 34 through 36 No H-bonds generated for 'chain 'Q' and resid 34 through 36' Processing helix chain 'Q' and resid 156 through 166 removed outlier: 3.853A pdb=" N GLU Q 162 " --> pdb=" O GLU Q 158 " (cutoff:3.500A) removed outlier: 3.795A pdb=" N GLU Q 165 " --> pdb=" O GLU Q 161 " (cutoff:3.500A) removed outlier: 3.987A pdb=" N ARG Q 166 " --> pdb=" O GLU Q 162 " (cutoff:3.500A) Processing helix chain 'Q' and resid 172 through 180 removed outlier: 3.595A pdb=" N ILE Q 176 " --> pdb=" O ASN Q 172 " (cutoff:3.500A) removed outlier: 4.276A pdb=" N MET Q 177 " --> pdb=" O HIS Q 173 " (cutoff:3.500A) removed outlier: 3.619A pdb=" N GLN Q 178 " --> pdb=" O PHE Q 174 " (cutoff:3.500A) removed outlier: 3.524A pdb=" N ARG Q 180 " --> pdb=" O ILE Q 176 " (cutoff:3.500A) Processing helix chain 'R' and resid 9 through 15 Processing helix chain 'R' and resid 24 through 35 removed outlier: 3.540A pdb=" N SER R 28 " --> pdb=" O PRO R 24 " (cutoff:3.500A) removed outlier: 3.899A pdb=" N ALA R 34 " --> pdb=" O GLN R 30 " (cutoff:3.500A) Processing helix chain 'R' and resid 59 through 64 Processing helix chain 'R' and resid 121 through 136 removed outlier: 4.008A pdb=" N MET R 125 " --> pdb=" O SER R 121 " (cutoff:3.500A) removed outlier: 3.944A pdb=" N ARG R 126 " --> pdb=" O GLU R 122 " (cutoff:3.500A) removed outlier: 3.578A pdb=" N LEU R 127 " --> pdb=" O ASN R 123 " (cutoff:3.500A) Processing helix chain 'R' and resid 159 through 173 Processing helix chain 'R' and resid 179 through 192 removed outlier: 3.892A pdb=" N GLU R 192 " --> pdb=" O PHE R 188 " (cutoff:3.500A) Processing helix chain 'R' and resid 198 through 207 Processing helix chain 'R' and resid 209 through 221 removed outlier: 3.548A pdb=" N ILE R 220 " --> pdb=" O ILE R 216 " (cutoff:3.500A) Processing helix chain 'U' and resid 10 through 33 removed outlier: 4.648A pdb=" N ASP U 27 " --> pdb=" O ASN U 23 " (cutoff:3.500A) removed outlier: 4.808A pdb=" N ILE U 28 " --> pdb=" O ASP U 24 " (cutoff:3.500A) removed outlier: 3.688A pdb=" N GLY U 33 " --> pdb=" O PHE U 29 " (cutoff:3.500A) Processing helix chain 'U' and resid 35 through 51 removed outlier: 3.778A pdb=" N LEU U 39 " --> pdb=" O ASP U 35 " (cutoff:3.500A) removed outlier: 3.883A pdb=" N MET U 51 " --> pdb=" O GLU U 47 " (cutoff:3.500A) Processing helix chain 'V' and resid 9 through 25 Processing helix chain 'V' and resid 29 through 52 removed outlier: 3.859A pdb=" N VAL V 52 " --> pdb=" O LEU V 48 " (cutoff:3.500A) Processing helix chain 'a' and resid 6 through 20 Processing helix chain 'a' and resid 25 through 37 removed outlier: 3.853A pdb=" N PHE a 29 " --> pdb=" O ARG a 25 " (cutoff:3.500A) Processing helix chain 'a' and resid 38 through 43 removed outlier: 4.142A pdb=" N PHE a 42 " --> pdb=" O GLY a 39 " (cutoff:3.500A) Processing helix chain 'a' and resid 47 through 67 Processing helix chain 'a' and resid 71 through 88 Processing helix chain 'a' and resid 103 through 117 Processing helix chain 'a' and resid 119 through 132 Processing helix chain 'a' and resid 166 through 172 removed outlier: 4.253A pdb=" N LYS a 170 " --> pdb=" O ASP a 166 " (cutoff:3.500A) Processing helix chain 'a' and resid 173 through 195 removed outlier: 3.690A pdb=" N SER a 195 " --> pdb=" O LYS a 191 " (cutoff:3.500A) Processing helix chain 'a' and resid 211 through 232 Processing helix chain 'b' and resid 44 through 55 Processing helix chain 'b' and resid 77 through 91 removed outlier: 3.644A pdb=" N ARG b 81 " --> pdb=" O ALA b 77 " (cutoff:3.500A) Processing helix chain 'b' and resid 93 through 104 Processing helix chain 'b' and resid 127 through 144 Processing helix chain 'b' and resid 150 through 161 Processing helix chain 'b' and resid 192 through 197 Processing helix chain 'b' and resid 221 through 226 removed outlier: 3.697A pdb=" N GLN b 226 " --> pdb=" O SER b 223 " (cutoff:3.500A) Processing helix chain 'b' and resid 242 through 247 Processing helix chain 'b' and resid 270 through 280 removed outlier: 4.150A pdb=" N ILE b 274 " --> pdb=" O LEU b 270 " (cutoff:3.500A) Processing helix chain 'b' and resid 297 through 300 Processing helix chain 'b' and resid 380 through 389 removed outlier: 3.558A pdb=" N TYR b 389 " --> pdb=" O ARG b 385 " (cutoff:3.500A) Processing helix chain 'c' and resid 82 through 123 removed outlier: 4.291A pdb=" N CYS c 86 " --> pdb=" O ASP c 82 " (cutoff:3.500A) Processing helix chain 'c' and resid 141 through 145 removed outlier: 3.576A pdb=" N HIS c 144 " --> pdb=" O TYR c 141 " (cutoff:3.500A) Processing helix chain 'c' and resid 162 through 171 Processing helix chain 'c' and resid 185 through 221 Proline residue: c 207 - end of helix Processing helix chain 'c' and resid 225 through 247 Processing helix chain 'c' and resid 249 through 255 removed outlier: 4.242A pdb=" N GLY c 255 " --> pdb=" O GLU c 251 " (cutoff:3.500A) Processing helix chain 'c' and resid 262 through 267 Processing helix chain 'c' and resid 276 through 287 Processing helix chain 'c' and resid 298 through 313 Processing helix chain 'c' and resid 316 through 324 Processing helix chain 'c' and resid 329 through 340 Processing helix chain 'c' and resid 350 through 365 Processing helix chain 'c' and resid 371 through 377 removed outlier: 3.969A pdb=" N TYR c 377 " --> pdb=" O ARG c 373 " (cutoff:3.500A) Processing helix chain 'c' and resid 383 through 394 Processing helix chain 'd' and resid 2 through 45 Processing sheet with id=AA1, first strand: chain 'A' and resid 1448 through 1449 Processing sheet with id=AA2, first strand: chain 'A' and resid 86 through 94 removed outlier: 6.664A pdb=" N THR A 251 " --> pdb=" O LEU A 90 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 190 through 194 removed outlier: 3.907A pdb=" N LEU A 198 " --> pdb=" O LEU A 216 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 263 through 266 removed outlier: 3.714A pdb=" N ALA A 270 " --> pdb=" O MET A 266 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 357 through 359 removed outlier: 3.871A pdb=" N LEU B1084 " --> pdb=" O VAL A 359 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 1060 through 1062 removed outlier: 3.632A pdb=" N THR A 365 " --> pdb=" O MET A 501 " (cutoff:3.500A) removed outlier: 7.724A pdb=" N PHE A 482 " --> pdb=" O ARG A 364 " (cutoff:3.500A) removed outlier: 6.389A pdb=" N VAL A 366 " --> pdb=" O PHE A 482 " (cutoff:3.500A) removed outlier: 7.740A pdb=" N LEU A 484 " --> pdb=" O VAL A 366 " (cutoff:3.500A) removed outlier: 6.537A pdb=" N THR A 368 " --> pdb=" O LEU A 484 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 389 through 393 removed outlier: 4.009A pdb=" N TYR A 418 " --> pdb=" O GLU A 447 " (cutoff:3.500A) removed outlier: 6.019A pdb=" N HIS A 449 " --> pdb=" O ALA A 416 " (cutoff:3.500A) removed outlier: 6.738A pdb=" N ALA A 416 " --> pdb=" O HIS A 449 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 526 through 527 removed outlier: 3.674A pdb=" N ARG A 532 " --> pdb=" O THR A 527 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'A' and resid 554 through 555 Processing sheet with id=AB1, first strand: chain 'A' and resid 579 through 581 WARNING: can't find start of bonding for strands! previous: chain 'A' and resid 579 through 581 current: chain 'H' and resid 25 through 32 WARNING: can't find start of bonding for strands! previous: chain 'H' and resid 38 through 44 current: chain 'H' and resid 111 through 118 Processing sheet with id=AB2, first strand: chain 'A' and resid 602 through 605 removed outlier: 6.810A pdb=" N VAL A 629 " --> pdb=" O ILE A 636 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'A' and resid 789 through 790 Processing sheet with id=AB4, first strand: chain 'A' and resid 792 through 793 Processing sheet with id=AB5, first strand: chain 'A' and resid 872 through 873 Processing sheet with id=AB6, first strand: chain 'A' and resid 902 through 905 Processing sheet with id=AB7, first strand: chain 'A' and resid 1307 through 1310 Processing sheet with id=AB8, first strand: chain 'A' and resid 1164 through 1165 removed outlier: 7.232A pdb=" N THR A1164 " --> pdb=" O LEU A1298 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'A' and resid 1243 through 1247 removed outlier: 4.297A pdb=" N LEU A1255 " --> pdb=" O LEU A1216 " (cutoff:3.500A) removed outlier: 3.534A pdb=" N VAL A1214 " --> pdb=" O LEU A1257 " (cutoff:3.500A) removed outlier: 6.722A pdb=" N ARG A1213 " --> pdb=" O THR A1173 " (cutoff:3.500A) removed outlier: 4.384A pdb=" N THR A1173 " --> pdb=" O ARG A1213 " (cutoff:3.500A) removed outlier: 6.531A pdb=" N GLU A1215 " --> pdb=" O ALA A1171 " (cutoff:3.500A) removed outlier: 3.970A pdb=" N TYR I 54 " --> pdb=" O ILE A1175 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'A' and resid 1319 through 1322 Processing sheet with id=AC2, first strand: chain 'A' and resid 1471 through 1475 WARNING: can't find start of bonding for strands! previous: chain 'F' and resid 115 through 119 current: chain 'G' and resid 43 through 54 WARNING: can't find start of bonding for strands! previous: chain 'G' and resid 43 through 54 current: chain 'G' and resid 66 through 77 Processing sheet with id=AC3, first strand: chain 'B' and resid 65 through 68 removed outlier: 6.241A pdb=" N ASP B 127 " --> pdb=" O GLU B 89 " (cutoff:3.500A) removed outlier: 4.408A pdb=" N ILE B 91 " --> pdb=" O TYR B 125 " (cutoff:3.500A) removed outlier: 6.596A pdb=" N TYR B 125 " --> pdb=" O ILE B 91 " (cutoff:3.500A) removed outlier: 4.484A pdb=" N LEU B 93 " --> pdb=" O PRO B 123 " (cutoff:3.500A) removed outlier: 3.588A pdb=" N GLY B 150 " --> pdb=" O LEU B 124 " (cutoff:3.500A) removed outlier: 6.286A pdb=" N VAL B 126 " --> pdb=" O PHE B 148 " (cutoff:3.500A) removed outlier: 5.348A pdb=" N PHE B 148 " --> pdb=" O VAL B 126 " (cutoff:3.500A) removed outlier: 7.493A pdb=" N ILE B 128 " --> pdb=" O LYS B 146 " (cutoff:3.500A) removed outlier: 6.885A pdb=" N LYS B 146 " --> pdb=" O ILE B 128 " (cutoff:3.500A) removed outlier: 7.566A pdb=" N LYS B 130 " --> pdb=" O HIS B 144 " (cutoff:3.500A) removed outlier: 7.240A pdb=" N HIS B 144 " --> pdb=" O LYS B 130 " (cutoff:3.500A) removed outlier: 7.457A pdb=" N VAL B 132 " --> pdb=" O THR B 142 " (cutoff:3.500A) removed outlier: 7.847A pdb=" N THR B 142 " --> pdb=" O VAL B 132 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'B' and resid 97 through 99 Processing sheet with id=AC5, first strand: chain 'B' and resid 185 through 187 Processing sheet with id=AC6, first strand: chain 'B' and resid 391 through 394 removed outlier: 6.393A pdb=" N ALA B 196 " --> pdb=" O ASN B 486 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'B' and resid 205 through 208 removed outlier: 3.502A pdb=" N TYR B 217 " --> pdb=" O MET B 239 " (cutoff:3.500A) removed outlier: 3.507A pdb=" N TRP B 236 " --> pdb=" O THR B 259 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'B' and resid 531 through 532 WARNING: can't find start of bonding for strands! previous: chain 'B' and resid 632 through 633 current: chain 'B' and resid 695 through 696 Processing sheet with id=AC9, first strand: chain 'B' and resid 550 through 552 removed outlier: 5.506A pdb=" N TRP B 573 " --> pdb=" O VAL B 569 " (cutoff:3.500A) removed outlier: 6.787A pdb=" N VAL B 569 " --> pdb=" O TRP B 573 " (cutoff:3.500A) removed outlier: 3.502A pdb=" N GLY B 575 " --> pdb=" O ILE B 567 " (cutoff:3.500A) removed outlier: 6.271A pdb=" N LYS B 566 " --> pdb=" O ILE B 612 " (cutoff:3.500A) removed outlier: 7.480A pdb=" N ILE B 614 " --> pdb=" O LYS B 566 " (cutoff:3.500A) removed outlier: 6.216A pdb=" N PHE B 568 " --> pdb=" O ILE B 614 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'B' and resid 747 through 751 removed outlier: 6.630A pdb=" N PHE B 918 " --> pdb=" O VAL B 909 " (cutoff:3.500A) removed outlier: 4.639A pdb=" N VAL B 909 " --> pdb=" O PHE B 918 " (cutoff:3.500A) removed outlier: 6.578A pdb=" N LYS B 920 " --> pdb=" O VAL B 907 " (cutoff:3.500A) removed outlier: 4.275A pdb=" N VAL B 907 " --> pdb=" O LYS B 920 " (cutoff:3.500A) removed outlier: 6.527A pdb=" N ARG B 922 " --> pdb=" O ASP B 905 " (cutoff:3.500A) removed outlier: 5.513A pdb=" N VAL B 907 " --> pdb=" O LYS L 46 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'B' and resid 759 through 760 Processing sheet with id=AD3, first strand: chain 'B' and resid 1025 through 1026 removed outlier: 7.003A pdb=" N VAL B 794 " --> pdb=" O GLY B 946 " (cutoff:3.500A) removed outlier: 6.059A pdb=" N GLN B 948 " --> pdb=" O VAL B 794 " (cutoff:3.500A) removed outlier: 6.628A pdb=" N MET B 796 " --> pdb=" O GLN B 948 " (cutoff:3.500A) removed outlier: 4.413A pdb=" N PHE B1042 " --> pdb=" O ILE B 782 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'B' and resid 827 through 829 Processing sheet with id=AD5, first strand: chain 'B' and resid 865 through 867 removed outlier: 3.728A pdb=" N ILE B 867 " --> pdb=" O THR B 894 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'B' and resid 1113 through 1119 removed outlier: 3.529A pdb=" N TYR B1114 " --> pdb=" O MET B1151 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'C' and resid 8 through 14 removed outlier: 5.736A pdb=" N VAL C 9 " --> pdb=" O GLU C 24 " (cutoff:3.500A) removed outlier: 7.138A pdb=" N GLU C 24 " --> pdb=" O VAL C 9 " (cutoff:3.500A) removed outlier: 5.214A pdb=" N ILE C 11 " --> pdb=" O ILE C 22 " (cutoff:3.500A) removed outlier: 6.546A pdb=" N ILE C 22 " --> pdb=" O ILE C 11 " (cutoff:3.500A) removed outlier: 6.584A pdb=" N TYR C 230 " --> pdb=" O PHE C 184 " (cutoff:3.500A) removed outlier: 4.223A pdb=" N PHE C 184 " --> pdb=" O TYR C 230 " (cutoff:3.500A) removed outlier: 6.155A pdb=" N ASN C 232 " --> pdb=" O VAL C 182 " (cutoff:3.500A) removed outlier: 4.384A pdb=" N VAL C 182 " --> pdb=" O ASN C 232 " (cutoff:3.500A) removed outlier: 5.812A pdb=" N GLU C 234 " --> pdb=" O ALA C 180 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'C' and resid 121 through 122 removed outlier: 7.011A pdb=" N ARG C 162 " --> pdb=" O ILE C 52 " (cutoff:3.500A) removed outlier: 5.200A pdb=" N ILE C 52 " --> pdb=" O ARG C 162 " (cutoff:3.500A) removed outlier: 7.391A pdb=" N TYR C 164 " --> pdb=" O VAL C 50 " (cutoff:3.500A) removed outlier: 5.717A pdb=" N VAL C 50 " --> pdb=" O TYR C 164 " (cutoff:3.500A) removed outlier: 6.961A pdb=" N LYS C 166 " --> pdb=" O ASP C 48 " (cutoff:3.500A) removed outlier: 5.987A pdb=" N ASP C 48 " --> pdb=" O LYS C 166 " (cutoff:3.500A) removed outlier: 6.603A pdb=" N GLY C 168 " --> pdb=" O ALA C 46 " (cutoff:3.500A) removed outlier: 6.314A pdb=" N ALA C 46 " --> pdb=" O GLY C 168 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'C' and resid 113 through 116 Processing sheet with id=AE1, first strand: chain 'E' and resid 60 through 63 removed outlier: 6.501A pdb=" N GLN E 71 " --> pdb=" O ARG E 101 " (cutoff:3.500A) removed outlier: 8.034A pdb=" N LEU E 103 " --> pdb=" O GLN E 71 " (cutoff:3.500A) removed outlier: 6.071A pdb=" N PHE E 73 " --> pdb=" O LEU E 103 " (cutoff:3.500A) removed outlier: 7.444A pdb=" N VAL E 105 " --> pdb=" O PHE E 73 " (cutoff:3.500A) removed outlier: 6.773A pdb=" N PHE E 75 " --> pdb=" O VAL E 105 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'E' and resid 81 through 82 removed outlier: 3.755A pdb=" N VAL E 82 " --> pdb=" O GLY E 109 " (cutoff:3.500A) No H-bonds generated for sheet with id=AE2 Processing sheet with id=AE3, first strand: chain 'E' and resid 147 through 151 removed outlier: 4.816A pdb=" N VAL E 190 " --> pdb=" O MET E 151 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'G' and resid 84 through 92 removed outlier: 7.015A pdb=" N PHE G 98 " --> pdb=" O THR G 90 " (cutoff:3.500A) removed outlier: 5.461A pdb=" N VAL G 92 " --> pdb=" O GLY G 96 " (cutoff:3.500A) removed outlier: 7.236A pdb=" N GLY G 96 " --> pdb=" O VAL G 92 " (cutoff:3.500A) removed outlier: 4.264A pdb=" N SER G 105 " --> pdb=" O ILE G 157 " (cutoff:3.500A) removed outlier: 3.806A pdb=" N ALA G 159 " --> pdb=" O SER G 105 " (cutoff:3.500A) removed outlier: 4.626A pdb=" N SER G 109 " --> pdb=" O GLY G 161 " (cutoff:3.500A) removed outlier: 3.791A pdb=" N ARG G 151 " --> pdb=" O PHE G 158 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N ILE G 160 " --> pdb=" O GLY G 149 " (cutoff:3.500A) removed outlier: 4.431A pdb=" N GLY G 149 " --> pdb=" O ILE G 160 " (cutoff:3.500A) removed outlier: 7.109A pdb=" N SER G 162 " --> pdb=" O ILE G 147 " (cutoff:3.500A) removed outlier: 5.938A pdb=" N ILE G 147 " --> pdb=" O SER G 162 " (cutoff:3.500A) Processing sheet with id=AE5, first strand: chain 'G' and resid 118 through 119 Processing sheet with id=AE6, first strand: chain 'I' and resid 24 through 29 removed outlier: 3.723A pdb=" N ASP I 29 " --> pdb=" O ILE I 34 " (cutoff:3.500A) removed outlier: 3.863A pdb=" N ILE I 34 " --> pdb=" O ASP I 29 " (cutoff:3.500A) removed outlier: 4.297A pdb=" N TYR I 44 " --> pdb=" O CYS I 39 " (cutoff:3.500A) Processing sheet with id=AE7, first strand: chain 'I' and resid 80 through 81 Processing sheet with id=AE8, first strand: chain 'K' and resid 19 through 23 Processing sheet with id=AE9, first strand: chain 'M' and resid 24 through 26 removed outlier: 3.580A pdb=" N MET M 32 " --> pdb=" O VAL M 41 " (cutoff:3.500A) Processing sheet with id=AF1, first strand: chain 'O' and resid 190 through 192 removed outlier: 3.665A pdb=" N THR O 209 " --> pdb=" O ILE O 204 " (cutoff:3.500A) removed outlier: 5.074A pdb=" N LEU O 165 " --> pdb=" O VAL O 259 " (cutoff:3.500A) removed outlier: 7.320A pdb=" N VAL O 259 " --> pdb=" O LEU O 165 " (cutoff:3.500A) removed outlier: 6.818A pdb=" N ASN O 167 " --> pdb=" O ASN O 257 " (cutoff:3.500A) removed outlier: 6.790A pdb=" N ASN O 257 " --> pdb=" O ASN O 167 " (cutoff:3.500A) removed outlier: 6.890A pdb=" N VAL O 169 " --> pdb=" O ILE O 255 " (cutoff:3.500A) removed outlier: 4.816A pdb=" N ILE O 255 " --> pdb=" O VAL O 169 " (cutoff:3.500A) removed outlier: 6.588A pdb=" N THR O 171 " --> pdb=" O PHE O 253 " (cutoff:3.500A) removed outlier: 4.220A pdb=" N PHE O 253 " --> pdb=" O THR O 171 " (cutoff:3.500A) removed outlier: 5.614A pdb=" N MET O 258 " --> pdb=" O GLY O 314 " (cutoff:3.500A) removed outlier: 3.885A pdb=" N GLY O 314 " --> pdb=" O MET O 258 " (cutoff:3.500A) removed outlier: 3.809A pdb=" N ILE O 300 " --> pdb=" O MET O 295 " (cutoff:3.500A) Processing sheet with id=AF2, first strand: chain 'Q' and resid 11 through 17 WARNING: can't find start of bonding for strands! previous: chain 'Q' and resid 11 through 17 current: chain 'Q' and resid 98 through 102 WARNING: can't find start of bonding for strands! previous: chain 'Q' and resid 109 through 114 current: chain 'Q' and resid 135 through 139 WARNING: can't find start of bonding for strands! previous: chain 'Q' and resid 135 through 139 current: chain 'R' and resid 52 through 58 removed outlier: 10.764A pdb=" N THR R 52 " --> pdb=" O LEU R 85 " (cutoff:3.500A) removed outlier: 7.058A pdb=" N LEU R 85 " --> pdb=" O THR R 52 " (cutoff:3.500A) removed outlier: 4.096A pdb=" N VAL R 54 " --> pdb=" O PHE R 83 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'R' and resid 81 through 86 current: chain 'R' and resid 104 through 116 Processing sheet with id=AF3, first strand: chain 'R' and resid 222 through 224 removed outlier: 3.534A pdb=" N VAL R 222 " --> pdb=" O GLU R 234 " (cutoff:3.500A) Processing sheet with id=AF4, first strand: chain 'U' and resid 334 through 344 removed outlier: 6.777A pdb=" N VAL U 334 " --> pdb=" O MET U 358 " (cutoff:3.500A) removed outlier: 4.659A pdb=" N MET U 358 " --> pdb=" O VAL U 334 " (cutoff:3.500A) removed outlier: 6.812A pdb=" N VAL U 336 " --> pdb=" O GLY U 356 " (cutoff:3.500A) removed outlier: 4.558A pdb=" N GLY U 356 " --> pdb=" O VAL U 336 " (cutoff:3.500A) removed outlier: 6.662A pdb=" N GLN U 338 " --> pdb=" O LYS U 354 " (cutoff:3.500A) removed outlier: 6.575A pdb=" N HIS U 352 " --> pdb=" O ASP U 340 " (cutoff:3.500A) removed outlier: 4.395A pdb=" N ILE U 342 " --> pdb=" O LYS U 350 " (cutoff:3.500A) removed outlier: 6.224A pdb=" N LYS U 350 " --> pdb=" O ILE U 342 " (cutoff:3.500A) removed outlier: 4.497A pdb=" N ARG U 344 " --> pdb=" O LYS U 348 " (cutoff:3.500A) removed outlier: 6.358A pdb=" N LYS U 348 " --> pdb=" O ARG U 344 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'U' and resid 363 through 367 current: chain 'V' and resid 55 through 64 WARNING: can't find start of bonding for strands! previous: chain 'V' and resid 55 through 64 current: chain 'V' and resid 71 through 82 removed outlier: 6.768A pdb=" N ASP V 91 " --> pdb=" O ASP V 78 " (cutoff:3.500A) removed outlier: 6.799A pdb=" N GLU V 80 " --> pdb=" O LYS V 89 " (cutoff:3.500A) removed outlier: 6.681A pdb=" N LYS V 89 " --> pdb=" O GLU V 80 " (cutoff:3.500A) removed outlier: 6.932A pdb=" N ARG V 82 " --> pdb=" O LEU V 87 " (cutoff:3.500A) removed outlier: 7.151A pdb=" N LEU V 87 " --> pdb=" O ARG V 82 " (cutoff:3.500A) Processing sheet with id=AF5, first strand: chain 'a' and resid 97 through 99 Processing sheet with id=AF6, first strand: chain 'b' and resid 42 through 43 Processing sheet with id=AF7, first strand: chain 'b' and resid 289 through 291 removed outlier: 3.689A pdb=" N ASN b 260 " --> pdb=" O ALA b 291 " (cutoff:3.500A) removed outlier: 6.663A pdb=" N ILE b 321 " --> pdb=" O LEU b 187 " (cutoff:3.500A) removed outlier: 7.193A pdb=" N LEU b 187 " --> pdb=" O ILE b 321 " (cutoff:3.500A) removed outlier: 5.448A pdb=" N ILE b 323 " --> pdb=" O ASN b 185 " (cutoff:3.500A) removed outlier: 6.941A pdb=" N ASN b 185 " --> pdb=" O ILE b 323 " (cutoff:3.500A) removed outlier: 4.291A pdb=" N ASP b 325 " --> pdb=" O SER b 183 " (cutoff:3.500A) removed outlier: 6.241A pdb=" N THR b 203 " --> pdb=" O ILE b 344 " (cutoff:3.500A) removed outlier: 4.114A pdb=" N LEU b 342 " --> pdb=" O LEU b 205 " (cutoff:3.500A) Processing sheet with id=AF8, first strand: chain 'b' and resid 377 through 379 2007 hydrogen bonds defined for protein. 5655 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 135 hydrogen bonds 270 hydrogen bond angles 0 basepair planarities 56 basepair parallelities 112 stacking parallelities Total time for adding SS restraints: 28.45 Time building geometry restraints manager: 19.78 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 15871 1.34 - 1.46: 11330 1.46 - 1.58: 22592 1.58 - 1.71: 262 1.71 - 1.83: 432 Bond restraints: 50487 Sorted by residual: bond pdb=" C1' DG N -7 " pdb=" N9 DG N -7 " ideal model delta sigma weight residual 1.460 1.357 0.103 2.00e-02 2.50e+03 2.65e+01 bond pdb=" C1' DG N -9 " pdb=" N9 DG N -9 " ideal model delta sigma weight residual 1.460 1.358 0.102 2.00e-02 2.50e+03 2.61e+01 bond pdb=" C1' DA N 24 " pdb=" N9 DA N 24 " ideal model delta sigma weight residual 1.460 1.362 0.098 2.00e-02 2.50e+03 2.39e+01 bond pdb=" C1' DA T -28 " pdb=" N9 DA T -28 " ideal model delta sigma weight residual 1.460 1.362 0.098 2.00e-02 2.50e+03 2.38e+01 bond pdb=" C1' DA T -9 " pdb=" N9 DA T -9 " ideal model delta sigma weight residual 1.460 1.363 0.097 2.00e-02 2.50e+03 2.36e+01 ... (remaining 50482 not shown) Histogram of bond angle deviations from ideal: 99.10 - 106.11: 1815 106.11 - 113.11: 27427 113.11 - 120.11: 17572 120.11 - 127.12: 21108 127.12 - 134.12: 800 Bond angle restraints: 68722 Sorted by residual: angle pdb=" N ASN R 152 " pdb=" CA ASN R 152 " pdb=" C ASN R 152 " ideal model delta sigma weight residual 110.23 103.28 6.95 1.45e+00 4.76e-01 2.30e+01 angle pdb=" C ASN R 152 " pdb=" CA ASN R 152 " pdb=" CB ASN R 152 " ideal model delta sigma weight residual 109.72 116.93 -7.21 1.66e+00 3.63e-01 1.88e+01 angle pdb=" O3' DG T 5 " pdb=" C3' DG T 5 " pdb=" C2' DG T 5 " ideal model delta sigma weight residual 111.50 105.11 6.39 1.50e+00 4.44e-01 1.82e+01 angle pdb=" CA PRO M 131 " pdb=" N PRO M 131 " pdb=" CD PRO M 131 " ideal model delta sigma weight residual 112.00 106.49 5.51 1.40e+00 5.10e-01 1.55e+01 angle pdb=" N GLY U 356 " pdb=" CA GLY U 356 " pdb=" C GLY U 356 " ideal model delta sigma weight residual 110.38 116.09 -5.71 1.48e+00 4.57e-01 1.49e+01 ... (remaining 68717 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 28.28: 28545 28.28 - 56.56: 1762 56.56 - 84.83: 214 84.83 - 113.11: 20 113.11 - 141.39: 2 Dihedral angle restraints: 30543 sinusoidal: 13655 harmonic: 16888 Sorted by residual: dihedral pdb=" CA VAL A 538 " pdb=" C VAL A 538 " pdb=" N GLN A 539 " pdb=" CA GLN A 539 " ideal model delta harmonic sigma weight residual 180.00 -152.04 -27.96 0 5.00e+00 4.00e-02 3.13e+01 dihedral pdb=" CA PHE c 145 " pdb=" C PHE c 145 " pdb=" N MET c 146 " pdb=" CA MET c 146 " ideal model delta harmonic sigma weight residual 180.00 -152.08 -27.92 0 5.00e+00 4.00e-02 3.12e+01 dihedral pdb=" CA TRP B 453 " pdb=" C TRP B 453 " pdb=" N GLY B 454 " pdb=" CA GLY B 454 " ideal model delta harmonic sigma weight residual 180.00 -158.20 -21.80 0 5.00e+00 4.00e-02 1.90e+01 ... (remaining 30540 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.064: 6729 0.064 - 0.127: 834 0.127 - 0.191: 45 0.191 - 0.255: 1 0.255 - 0.319: 1 Chirality restraints: 7610 Sorted by residual: chirality pdb=" C3' DA N -12 " pdb=" C4' DA N -12 " pdb=" O3' DA N -12 " pdb=" C2' DA N -12 " both_signs ideal model delta sigma weight residual False -2.66 -2.34 -0.32 2.00e-01 2.50e+01 2.54e+00 chirality pdb=" C1' DG N -9 " pdb=" O4' DG N -9 " pdb=" C2' DG N -9 " pdb=" N9 DG N -9 " both_signs ideal model delta sigma weight residual False 2.42 2.22 0.20 2.00e-01 2.50e+01 1.01e+00 chirality pdb=" C1' DG N -7 " pdb=" O4' DG N -7 " pdb=" C2' DG N -7 " pdb=" N9 DG N -7 " both_signs ideal model delta sigma weight residual False 2.42 2.23 0.19 2.00e-01 2.50e+01 8.94e-01 ... (remaining 7607 not shown) Planarity restraints: 8445 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA THR R 151 " -0.026 2.00e-02 2.50e+03 5.53e-02 3.06e+01 pdb=" C THR R 151 " 0.096 2.00e-02 2.50e+03 pdb=" O THR R 151 " -0.037 2.00e-02 2.50e+03 pdb=" N ASN R 152 " -0.032 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C LEU M 130 " -0.062 5.00e-02 4.00e+02 9.05e-02 1.31e+01 pdb=" N PRO M 131 " 0.156 5.00e-02 4.00e+02 pdb=" CA PRO M 131 " -0.046 5.00e-02 4.00e+02 pdb=" CD PRO M 131 " -0.049 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CB TYR R 153 " 0.045 2.00e-02 2.50e+03 2.55e-02 1.30e+01 pdb=" CG TYR R 153 " -0.033 2.00e-02 2.50e+03 pdb=" CD1 TYR R 153 " -0.003 2.00e-02 2.50e+03 pdb=" CD2 TYR R 153 " -0.027 2.00e-02 2.50e+03 pdb=" CE1 TYR R 153 " -0.023 2.00e-02 2.50e+03 pdb=" CE2 TYR R 153 " 0.001 2.00e-02 2.50e+03 pdb=" CZ TYR R 153 " 0.024 2.00e-02 2.50e+03 pdb=" OH TYR R 153 " 0.017 2.00e-02 2.50e+03 ... (remaining 8442 not shown) Histogram of nonbonded interaction distances: 1.38 - 2.09: 29 2.09 - 2.79: 11366 2.79 - 3.49: 70394 3.49 - 4.20: 125166 4.20 - 4.90: 217910 Nonbonded interactions: 424865 Sorted by model distance: nonbonded pdb=" OP1 DC T 9 " pdb=" CD1 TYR c 141 " model vdw 1.385 3.340 nonbonded pdb=" OP1 DG N 8 " pdb=" OG SER O 216 " model vdw 1.537 2.440 nonbonded pdb=" C5' DT T 8 " pdb=" NE2 HIS c 144 " model vdw 1.615 3.520 nonbonded pdb=" CG2 VAL O 259 " pdb=" N2 DG T -4 " model vdw 1.616 3.540 nonbonded pdb=" OP2 DA N -14 " pdb=" NE2 HIS b 347 " model vdw 1.671 2.520 ... (remaining 424860 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=0.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 4.680 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: 0.040 Extract box with map and model: 16.140 Check model and map are aligned: 0.690 Set scattering table: 0.460 Process input model: 148.860 Find NCS groups from input model: 1.500 Set up NCS constraints: 0.160 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.700 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 175.240 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7637 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 0.103 50487 Z= 0.282 Angle : 0.522 7.207 68722 Z= 0.310 Chirality : 0.042 0.319 7610 Planarity : 0.003 0.090 8445 Dihedral : 17.070 141.392 19597 Min Nonbonded Distance : 1.385 Molprobity Statistics. All-atom Clashscore : 9.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.99 % Favored : 97.01 % Rotamer: Outliers : 0.00 % Allowed : 0.21 % Favored : 99.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.56 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.17 (0.11), residues: 5715 helix: 1.89 (0.12), residues: 2195 sheet: 0.62 (0.18), residues: 855 loop : -0.05 (0.12), residues: 2665 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP B 453 HIS 0.006 0.001 HIS M 18 PHE 0.018 0.001 PHE C 63 TYR 0.045 0.001 TYR R 153 ARG 0.014 0.000 ARG E 52 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 11430 Ramachandran restraints generated. 5715 Oldfield, 0 Emsley, 5715 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 11430 Ramachandran restraints generated. 5715 Oldfield, 0 Emsley, 5715 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 707 residues out of total 5130 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 707 time to evaluate : 5.484 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 234 PHE cc_start: 0.9418 (m-80) cc_final: 0.8853 (m-80) REVERT: A 467 MET cc_start: 0.8704 (mpp) cc_final: 0.8273 (mmt) REVERT: A 865 ILE cc_start: 0.8919 (tp) cc_final: 0.8624 (mt) REVERT: A 1439 LEU cc_start: 0.9275 (mt) cc_final: 0.9062 (pp) REVERT: A 1463 LEU cc_start: 0.9325 (tp) cc_final: 0.9067 (tt) REVERT: B 144 HIS cc_start: 0.7193 (m90) cc_final: 0.6904 (m90) REVERT: B 297 MET cc_start: 0.8072 (mmm) cc_final: 0.7654 (mmt) REVERT: B 365 LEU cc_start: 0.9421 (tp) cc_final: 0.9210 (tp) REVERT: B 439 ILE cc_start: 0.8126 (mt) cc_final: 0.7818 (mt) REVERT: B 576 ILE cc_start: 0.8583 (pt) cc_final: 0.8222 (pt) REVERT: B 594 MET cc_start: 0.8362 (mtm) cc_final: 0.7628 (mmm) REVERT: B 668 LEU cc_start: 0.8896 (mt) cc_final: 0.8686 (mt) REVERT: B 778 SER cc_start: 0.8278 (m) cc_final: 0.7820 (p) REVERT: B 976 MET cc_start: 0.7892 (mtm) cc_final: 0.7570 (mtm) REVERT: B 1151 MET cc_start: 0.8807 (ptm) cc_final: 0.8605 (ptp) REVERT: B 1163 MET cc_start: 0.9156 (mtt) cc_final: 0.8900 (mpp) REVERT: E 98 ASN cc_start: 0.8365 (m-40) cc_final: 0.8033 (m-40) REVERT: E 103 LEU cc_start: 0.9446 (tp) cc_final: 0.9217 (mm) REVERT: F 65 VAL cc_start: 0.9618 (t) cc_final: 0.9386 (p) REVERT: F 66 LEU cc_start: 0.9301 (mt) cc_final: 0.8934 (mt) REVERT: I 88 LYS cc_start: 0.9340 (mttt) cc_final: 0.9122 (ttmt) REVERT: J 53 VAL cc_start: 0.7854 (t) cc_final: 0.7468 (t) REVERT: M 52 TRP cc_start: 0.5062 (m-90) cc_final: 0.4806 (m-10) REVERT: M 138 THR cc_start: 0.9160 (m) cc_final: 0.8866 (p) REVERT: M 271 GLN cc_start: 0.8725 (mt0) cc_final: 0.8496 (tt0) REVERT: O 284 GLU cc_start: 0.8293 (mm-30) cc_final: 0.8003 (mp0) REVERT: R 83 PHE cc_start: 0.6826 (m-10) cc_final: 0.6504 (m-80) REVERT: U 9 THR cc_start: 0.9128 (m) cc_final: 0.8829 (t) REVERT: U 338 GLN cc_start: 0.8782 (mt0) cc_final: 0.8427 (pm20) REVERT: U 348 LYS cc_start: 0.9361 (mppt) cc_final: 0.9131 (mmtm) REVERT: U 369 LYS cc_start: 0.9090 (tptm) cc_final: 0.8679 (pttm) REVERT: V 55 ARG cc_start: 0.9223 (ttm110) cc_final: 0.8859 (ttm110) REVERT: a 27 GLU cc_start: 0.9586 (mm-30) cc_final: 0.9283 (mp0) REVERT: a 180 MET cc_start: 0.7466 (mmp) cc_final: 0.6520 (tmm) REVERT: b 253 TYR cc_start: 0.8711 (t80) cc_final: 0.8472 (t80) REVERT: b 274 ILE cc_start: 0.9283 (mt) cc_final: 0.9066 (tp) REVERT: c 98 GLN cc_start: 0.7862 (tp40) cc_final: 0.7623 (mm110) REVERT: c 146 MET cc_start: 0.4775 (mmm) cc_final: 0.4220 (ttt) REVERT: c 150 PHE cc_start: 0.7585 (m-80) cc_final: 0.6871 (m-80) REVERT: c 209 LEU cc_start: 0.9677 (mm) cc_final: 0.9393 (mt) REVERT: c 379 MET cc_start: 0.5310 (mmm) cc_final: 0.4576 (ttm) REVERT: d 1 MET cc_start: 0.5080 (ptm) cc_final: 0.3880 (mtt) outliers start: 0 outliers final: 0 residues processed: 707 average time/residue: 0.6475 time to fit residues: 738.9636 Evaluate side-chains 409 residues out of total 5130 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 409 time to evaluate : 5.374 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 579 random chunks: chunk 488 optimal weight: 30.0000 chunk 438 optimal weight: 30.0000 chunk 243 optimal weight: 0.9980 chunk 149 optimal weight: 3.9990 chunk 296 optimal weight: 2.9990 chunk 234 optimal weight: 7.9990 chunk 453 optimal weight: 20.0000 chunk 175 optimal weight: 3.9990 chunk 275 optimal weight: 6.9990 chunk 337 optimal weight: 10.0000 chunk 525 optimal weight: 0.4980 overall best weight: 2.4986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 96 HIS ** A 341 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 671 ASN ** A 804 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A1093 GLN ** B 111 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 197 GLN B 486 ASN B 842 HIS B1053 HIS C 217 GLN ** F 49 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 4 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 53 ASN K 49 GLN ** M 18 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** M 221 ASN ** Q 44 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 129 GLN R 194 HIS ** U 352 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 39 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** a 223 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** b 198 HIS Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7983 moved from start: 0.2693 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.079 50487 Z= 0.311 Angle : 0.688 11.017 68722 Z= 0.360 Chirality : 0.044 0.216 7610 Planarity : 0.005 0.077 8445 Dihedral : 16.465 151.553 7771 Min Nonbonded Distance : 1.942 Molprobity Statistics. All-atom Clashscore : 12.15 Ramachandran Plot: Outliers : 0.02 % Allowed : 3.39 % Favored : 96.59 % Rotamer: Outliers : 0.99 % Allowed : 7.99 % Favored : 91.01 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.56 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.02 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.81 (0.11), residues: 5715 helix: 1.40 (0.11), residues: 2256 sheet: 0.55 (0.18), residues: 843 loop : -0.15 (0.12), residues: 2616 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.032 0.002 TRP a 226 HIS 0.012 0.001 HIS G 9 PHE 0.022 0.002 PHE B 769 TYR 0.029 0.002 TYR a 80 ARG 0.013 0.001 ARG U 26 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 11430 Ramachandran restraints generated. 5715 Oldfield, 0 Emsley, 5715 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 11430 Ramachandran restraints generated. 5715 Oldfield, 0 Emsley, 5715 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 491 residues out of total 5130 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 51 poor density : 440 time to evaluate : 5.297 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 78 MET cc_start: 0.8915 (tpp) cc_final: 0.8586 (mmm) REVERT: A 234 PHE cc_start: 0.9209 (m-80) cc_final: 0.8586 (m-80) REVERT: A 467 MET cc_start: 0.8784 (mpp) cc_final: 0.8299 (mmt) REVERT: A 524 MET cc_start: 0.8685 (mmp) cc_final: 0.8454 (mmm) REVERT: A 1279 MET cc_start: 0.5047 (ttt) cc_final: 0.4675 (tmm) REVERT: A 1412 MET cc_start: 0.6317 (OUTLIER) cc_final: 0.5694 (mtt) REVERT: A 1428 MET cc_start: 0.9206 (tpp) cc_final: 0.8791 (tpp) REVERT: A 1439 LEU cc_start: 0.9229 (mt) cc_final: 0.8986 (mt) REVERT: B 51 ILE cc_start: 0.9114 (mm) cc_final: 0.8838 (mm) REVERT: B 109 MET cc_start: 0.7361 (tpp) cc_final: 0.6495 (tpp) REVERT: B 144 HIS cc_start: 0.7883 (m90) cc_final: 0.7545 (m90) REVERT: B 240 LEU cc_start: 0.8343 (OUTLIER) cc_final: 0.8114 (mm) REVERT: B 345 LYS cc_start: 0.9066 (mptt) cc_final: 0.8843 (mmtm) REVERT: B 365 LEU cc_start: 0.9603 (tp) cc_final: 0.9393 (tp) REVERT: B 439 ILE cc_start: 0.8363 (mt) cc_final: 0.8157 (mt) REVERT: B 594 MET cc_start: 0.8538 (mtm) cc_final: 0.7910 (mmp) REVERT: B 606 ASP cc_start: 0.7692 (t0) cc_final: 0.7244 (t0) REVERT: B 657 VAL cc_start: 0.9165 (t) cc_final: 0.8861 (p) REVERT: B 976 MET cc_start: 0.8203 (mtm) cc_final: 0.7824 (mtm) REVERT: B 1151 MET cc_start: 0.9432 (ptm) cc_final: 0.8764 (ptp) REVERT: B 1163 MET cc_start: 0.9309 (mtt) cc_final: 0.8963 (mmm) REVERT: E 98 ASN cc_start: 0.8459 (m-40) cc_final: 0.8136 (m-40) REVERT: G 41 LYS cc_start: 0.9122 (mmmt) cc_final: 0.8884 (tppt) REVERT: L 44 MET cc_start: 0.7993 (mmm) cc_final: 0.7355 (mmm) REVERT: M 18 HIS cc_start: 0.4451 (OUTLIER) cc_final: 0.4129 (m170) REVERT: M 52 TRP cc_start: 0.5133 (m-90) cc_final: 0.4614 (m-10) REVERT: M 124 MET cc_start: 0.8744 (mtm) cc_final: 0.8520 (mtp) REVERT: Q 153 ARG cc_start: 0.9050 (mmp-170) cc_final: 0.8668 (mmp80) REVERT: R 83 PHE cc_start: 0.7009 (m-10) cc_final: 0.6784 (m-80) REVERT: R 163 ILE cc_start: 0.8909 (tp) cc_final: 0.8374 (pt) REVERT: U 358 MET cc_start: 0.8846 (ptp) cc_final: 0.8294 (ptp) REVERT: V 83 GLU cc_start: 0.8628 (tp30) cc_final: 0.8267 (tp30) REVERT: a 27 GLU cc_start: 0.9587 (mm-30) cc_final: 0.9204 (mp0) REVERT: a 31 GLU cc_start: 0.9861 (mm-30) cc_final: 0.9455 (pp20) REVERT: a 35 ASN cc_start: 0.9712 (m110) cc_final: 0.9438 (m110) REVERT: a 36 MET cc_start: 0.8772 (mtp) cc_final: 0.8404 (mpp) REVERT: a 140 MET cc_start: 0.8687 (mmm) cc_final: 0.8447 (mmm) REVERT: a 146 TYR cc_start: 0.9424 (m-80) cc_final: 0.9175 (m-10) REVERT: a 180 MET cc_start: 0.7398 (mmp) cc_final: 0.6825 (mmp) REVERT: a 190 MET cc_start: 0.2463 (ttp) cc_final: 0.2010 (tmm) REVERT: b 293 MET cc_start: 0.7241 (ttm) cc_final: 0.6597 (ptm) REVERT: d 1 MET cc_start: 0.5008 (ptm) cc_final: 0.3445 (mtt) outliers start: 51 outliers final: 24 residues processed: 474 average time/residue: 0.6295 time to fit residues: 496.2729 Evaluate side-chains 384 residues out of total 5130 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 357 time to evaluate : 6.003 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 329 MET Chi-restraints excluded: chain A residue 611 ASP Chi-restraints excluded: chain A residue 1374 VAL Chi-restraints excluded: chain A residue 1412 MET Chi-restraints excluded: chain A residue 1454 VAL Chi-restraints excluded: chain B residue 152 ILE Chi-restraints excluded: chain B residue 190 SER Chi-restraints excluded: chain B residue 240 LEU Chi-restraints excluded: chain B residue 289 ILE Chi-restraints excluded: chain B residue 373 LEU Chi-restraints excluded: chain B residue 542 LEU Chi-restraints excluded: chain B residue 598 VAL Chi-restraints excluded: chain B residue 1008 VAL Chi-restraints excluded: chain B residue 1071 ASN Chi-restraints excluded: chain C residue 112 THR Chi-restraints excluded: chain C residue 238 SER Chi-restraints excluded: chain I residue 62 VAL Chi-restraints excluded: chain J residue 28 GLU Chi-restraints excluded: chain M residue 18 HIS Chi-restraints excluded: chain M residue 168 CYS Chi-restraints excluded: chain O residue 174 LEU Chi-restraints excluded: chain Q residue 99 LEU Chi-restraints excluded: chain R residue 148 VAL Chi-restraints excluded: chain R residue 170 LYS Chi-restraints excluded: chain V residue 51 ARG Chi-restraints excluded: chain a residue 145 SER Chi-restraints excluded: chain b residue 193 HIS Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 579 random chunks: chunk 292 optimal weight: 0.9980 chunk 163 optimal weight: 8.9990 chunk 437 optimal weight: 8.9990 chunk 358 optimal weight: 10.0000 chunk 145 optimal weight: 4.9990 chunk 526 optimal weight: 0.0570 chunk 569 optimal weight: 30.0000 chunk 469 optimal weight: 10.0000 chunk 522 optimal weight: 30.0000 chunk 179 optimal weight: 0.9990 chunk 422 optimal weight: 9.9990 overall best weight: 3.2104 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 341 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 804 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 905 ASN ** A 945 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1032 GLN A1077 ASN A1146 GLN ** B 111 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 265 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 842 HIS ** B1030 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 66 HIS G 4 HIS I 84 HIS ** I 91 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** I 118 HIS M 139 ASN ** Q 44 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 48 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 352 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 39 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** a 223 HIS a 232 ASN c 270 ASN d 37 GLN Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8196 moved from start: 0.3944 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.100 50487 Z= 0.327 Angle : 0.640 12.987 68722 Z= 0.335 Chirality : 0.042 0.171 7610 Planarity : 0.005 0.082 8445 Dihedral : 16.391 145.166 7771 Min Nonbonded Distance : 1.858 Molprobity Statistics. All-atom Clashscore : 13.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.20 % Favored : 96.80 % Rotamer: Outliers : 1.46 % Allowed : 10.41 % Favored : 88.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.56 % 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: 0.77 (0.11), residues: 5715 helix: 1.42 (0.11), residues: 2276 sheet: 0.49 (0.18), residues: 840 loop : -0.22 (0.12), residues: 2599 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.026 0.002 TRP c 187 HIS 0.014 0.001 HIS I 118 PHE 0.022 0.002 PHE K 105 TYR 0.030 0.002 TYR A 924 ARG 0.014 0.001 ARG d 17 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 11430 Ramachandran restraints generated. 5715 Oldfield, 0 Emsley, 5715 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 11430 Ramachandran restraints generated. 5715 Oldfield, 0 Emsley, 5715 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 429 residues out of total 5130 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 75 poor density : 354 time to evaluate : 5.952 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 78 MET cc_start: 0.8863 (tpp) cc_final: 0.8158 (mmm) REVERT: A 99 PHE cc_start: 0.8884 (m-10) cc_final: 0.8493 (m-10) REVERT: A 234 PHE cc_start: 0.9357 (m-80) cc_final: 0.8794 (m-80) REVERT: A 549 THR cc_start: 0.9313 (OUTLIER) cc_final: 0.9000 (p) REVERT: A 1279 MET cc_start: 0.5171 (ttt) cc_final: 0.4865 (tmm) REVERT: A 1412 MET cc_start: 0.6943 (OUTLIER) cc_final: 0.6505 (ptp) REVERT: A 1428 MET cc_start: 0.9270 (tpp) cc_final: 0.8793 (tpp) REVERT: A 1439 LEU cc_start: 0.9220 (mt) cc_final: 0.9011 (mt) REVERT: B 53 MET cc_start: 0.8490 (mpp) cc_final: 0.7925 (mpp) REVERT: B 297 MET cc_start: 0.8241 (mmt) cc_final: 0.7614 (mmp) REVERT: B 594 MET cc_start: 0.8675 (mtm) cc_final: 0.8008 (mmm) REVERT: B 603 MET cc_start: 0.7520 (pmm) cc_final: 0.7187 (pmm) REVERT: B 606 ASP cc_start: 0.8229 (t0) cc_final: 0.7648 (t70) REVERT: B 680 ASP cc_start: 0.7970 (OUTLIER) cc_final: 0.7507 (p0) REVERT: B 1075 MET cc_start: 0.7891 (OUTLIER) cc_final: 0.7506 (ppp) REVERT: B 1151 MET cc_start: 0.9490 (ptm) cc_final: 0.8880 (ptp) REVERT: B 1163 MET cc_start: 0.9370 (mtt) cc_final: 0.9026 (mmm) REVERT: E 72 MET cc_start: 0.6751 (tpt) cc_final: 0.6218 (tpt) REVERT: E 98 ASN cc_start: 0.8528 (m-40) cc_final: 0.8197 (m-40) REVERT: E 103 LEU cc_start: 0.9616 (OUTLIER) cc_final: 0.9354 (mm) REVERT: F 57 MET cc_start: 0.9033 (tmm) cc_final: 0.8734 (tmm) REVERT: G 29 LYS cc_start: 0.9550 (mmmt) cc_final: 0.9133 (mmtm) REVERT: G 60 GLN cc_start: 0.8078 (tm-30) cc_final: 0.7571 (tm-30) REVERT: I 71 ASP cc_start: 0.8182 (m-30) cc_final: 0.7617 (p0) REVERT: L 44 MET cc_start: 0.8677 (mmm) cc_final: 0.7960 (mmm) REVERT: M 124 MET cc_start: 0.8781 (mtm) cc_final: 0.8495 (mtp) REVERT: M 273 GLU cc_start: 0.8725 (OUTLIER) cc_final: 0.8504 (pt0) REVERT: U 338 GLN cc_start: 0.8844 (mt0) cc_final: 0.8514 (mp10) REVERT: a 27 GLU cc_start: 0.9584 (mm-30) cc_final: 0.9303 (mp0) REVERT: a 36 MET cc_start: 0.8786 (mtp) cc_final: 0.8523 (mpp) REVERT: a 190 MET cc_start: 0.2620 (ttp) cc_final: 0.2150 (tmm) REVERT: b 293 MET cc_start: 0.6758 (ttm) cc_final: 0.6225 (ptm) REVERT: c 209 LEU cc_start: 0.9742 (mt) cc_final: 0.9418 (pp) REVERT: d 1 MET cc_start: 0.4971 (ptm) cc_final: 0.3953 (mtt) outliers start: 75 outliers final: 36 residues processed: 408 average time/residue: 0.6145 time to fit residues: 420.5832 Evaluate side-chains 346 residues out of total 5130 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 42 poor density : 304 time to evaluate : 5.513 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 549 THR Chi-restraints excluded: chain A residue 611 ASP Chi-restraints excluded: chain A residue 692 SER Chi-restraints excluded: chain A residue 1412 MET Chi-restraints excluded: chain B residue 124 LEU Chi-restraints excluded: chain B residue 152 ILE Chi-restraints excluded: chain B residue 190 SER Chi-restraints excluded: chain B residue 368 MET Chi-restraints excluded: chain B residue 598 VAL Chi-restraints excluded: chain B residue 630 LYS Chi-restraints excluded: chain B residue 680 ASP Chi-restraints excluded: chain B residue 681 ASP Chi-restraints excluded: chain B residue 817 GLN Chi-restraints excluded: chain B residue 901 THR Chi-restraints excluded: chain B residue 918 PHE Chi-restraints excluded: chain B residue 1059 ILE Chi-restraints excluded: chain B residue 1075 MET Chi-restraints excluded: chain C residue 112 THR Chi-restraints excluded: chain C residue 238 SER Chi-restraints excluded: chain D residue 90 LYS Chi-restraints excluded: chain D residue 107 THR Chi-restraints excluded: chain E residue 27 LEU Chi-restraints excluded: chain E residue 103 LEU Chi-restraints excluded: chain G residue 24 ASN Chi-restraints excluded: chain H residue 96 VAL Chi-restraints excluded: chain H residue 110 THR Chi-restraints excluded: chain I residue 62 VAL Chi-restraints excluded: chain I residue 103 ARG Chi-restraints excluded: chain J residue 38 LEU Chi-restraints excluded: chain M residue 31 ASP Chi-restraints excluded: chain M residue 37 CYS Chi-restraints excluded: chain M residue 168 CYS Chi-restraints excluded: chain M residue 273 GLU Chi-restraints excluded: chain Q residue 46 ARG Chi-restraints excluded: chain Q residue 99 LEU Chi-restraints excluded: chain Q residue 147 THR Chi-restraints excluded: chain R residue 148 VAL Chi-restraints excluded: chain R residue 170 LYS Chi-restraints excluded: chain V residue 9 THR Chi-restraints excluded: chain V residue 85 THR Chi-restraints excluded: chain b residue 128 VAL Chi-restraints excluded: chain c residue 176 PHE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 579 random chunks: chunk 520 optimal weight: 30.0000 chunk 396 optimal weight: 5.9990 chunk 273 optimal weight: 3.9990 chunk 58 optimal weight: 0.0470 chunk 251 optimal weight: 20.0000 chunk 353 optimal weight: 7.9990 chunk 528 optimal weight: 8.9990 chunk 559 optimal weight: 30.0000 chunk 276 optimal weight: 4.9990 chunk 501 optimal weight: 0.0270 chunk 150 optimal weight: 0.5980 overall best weight: 1.9340 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 313 HIS ** A 341 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 671 ASN ** A 945 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1146 GLN A1263 ASN B 98 HIS ** B 111 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 265 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 344 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 941 GLN E 92 GLN G 4 HIS ** G 93 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 138 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 91 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 100 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 113 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 18 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** M 139 ASN O 189 ASN ** U 48 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** U 343 HIS ** U 352 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 39 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 50 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8208 moved from start: 0.4389 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.065 50487 Z= 0.218 Angle : 0.575 12.431 68722 Z= 0.299 Chirality : 0.041 0.237 7610 Planarity : 0.004 0.073 8445 Dihedral : 16.201 145.147 7771 Min Nonbonded Distance : 1.975 Molprobity Statistics. All-atom Clashscore : 13.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.31 % Favored : 96.69 % Rotamer: Outliers : 1.38 % Allowed : 11.35 % Favored : 87.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.56 % 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: 0.86 (0.11), residues: 5715 helix: 1.56 (0.11), residues: 2277 sheet: 0.48 (0.18), residues: 827 loop : -0.21 (0.12), residues: 2611 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.028 0.001 TRP c 187 HIS 0.007 0.001 HIS M 18 PHE 0.022 0.001 PHE K 105 TYR 0.022 0.001 TYR b 340 ARG 0.008 0.000 ARG d 17 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 11430 Ramachandran restraints generated. 5715 Oldfield, 0 Emsley, 5715 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 11430 Ramachandran restraints generated. 5715 Oldfield, 0 Emsley, 5715 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 393 residues out of total 5130 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 71 poor density : 322 time to evaluate : 5.492 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 78 MET cc_start: 0.8864 (tpp) cc_final: 0.8181 (mmm) REVERT: A 234 PHE cc_start: 0.9339 (m-80) cc_final: 0.8813 (m-80) REVERT: A 388 MET cc_start: 0.8961 (mmm) cc_final: 0.8525 (mmt) REVERT: A 1279 MET cc_start: 0.5087 (ttt) cc_final: 0.4651 (tmm) REVERT: A 1309 MET cc_start: 0.7693 (ttt) cc_final: 0.7477 (ttt) REVERT: A 1428 MET cc_start: 0.9258 (tpp) cc_final: 0.8828 (tpp) REVERT: A 1474 LEU cc_start: 0.9393 (OUTLIER) cc_final: 0.9168 (mt) REVERT: B 300 MET cc_start: 0.7687 (mmm) cc_final: 0.6503 (tpp) REVERT: B 594 MET cc_start: 0.8714 (mtm) cc_final: 0.8071 (mmm) REVERT: B 603 MET cc_start: 0.7389 (pmm) cc_final: 0.6915 (pmm) REVERT: B 606 ASP cc_start: 0.8264 (t0) cc_final: 0.7744 (t70) REVERT: B 680 ASP cc_start: 0.7828 (OUTLIER) cc_final: 0.7451 (p0) REVERT: B 908 MET cc_start: 0.8287 (tmm) cc_final: 0.7630 (tmm) REVERT: B 909 VAL cc_start: 0.9574 (OUTLIER) cc_final: 0.9114 (p) REVERT: B 1075 MET cc_start: 0.7821 (OUTLIER) cc_final: 0.7444 (ppp) REVERT: B 1151 MET cc_start: 0.9519 (ptm) cc_final: 0.8829 (ptp) REVERT: B 1163 MET cc_start: 0.9356 (mtt) cc_final: 0.9016 (mpp) REVERT: E 72 MET cc_start: 0.7085 (tpt) cc_final: 0.6578 (tpt) REVERT: E 98 ASN cc_start: 0.8534 (m-40) cc_final: 0.8232 (m-40) REVERT: E 103 LEU cc_start: 0.9624 (tp) cc_final: 0.9373 (mm) REVERT: I 71 ASP cc_start: 0.8372 (m-30) cc_final: 0.7748 (p0) REVERT: L 44 MET cc_start: 0.8620 (mmm) cc_final: 0.8010 (mmm) REVERT: R 109 ILE cc_start: 0.8696 (pt) cc_final: 0.8455 (mp) REVERT: U 19 GLU cc_start: 0.8528 (tm-30) cc_final: 0.7951 (pp20) REVERT: V 78 ASP cc_start: 0.9545 (m-30) cc_final: 0.9018 (t0) REVERT: a 31 GLU cc_start: 0.9872 (mm-30) cc_final: 0.9614 (pp20) REVERT: a 190 MET cc_start: 0.2794 (ttp) cc_final: 0.1894 (tmm) REVERT: b 293 MET cc_start: 0.7032 (ttm) cc_final: 0.6427 (ptm) REVERT: c 98 GLN cc_start: 0.7800 (tp40) cc_final: 0.7559 (mm110) REVERT: c 146 MET cc_start: 0.5264 (mmm) cc_final: 0.4603 (ttm) REVERT: c 209 LEU cc_start: 0.9733 (mt) cc_final: 0.9468 (pp) REVERT: d 1 MET cc_start: 0.4932 (ptm) cc_final: 0.3912 (mtt) outliers start: 71 outliers final: 35 residues processed: 378 average time/residue: 0.6071 time to fit residues: 384.1397 Evaluate side-chains 336 residues out of total 5130 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 39 poor density : 297 time to evaluate : 5.549 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 329 MET Chi-restraints excluded: chain A residue 611 ASP Chi-restraints excluded: chain A residue 695 ASP Chi-restraints excluded: chain A residue 1227 THR Chi-restraints excluded: chain A residue 1454 VAL Chi-restraints excluded: chain A residue 1474 LEU Chi-restraints excluded: chain B residue 124 LEU Chi-restraints excluded: chain B residue 152 ILE Chi-restraints excluded: chain B residue 235 ILE Chi-restraints excluded: chain B residue 288 ILE Chi-restraints excluded: chain B residue 324 ARG Chi-restraints excluded: chain B residue 598 VAL Chi-restraints excluded: chain B residue 680 ASP Chi-restraints excluded: chain B residue 794 VAL Chi-restraints excluded: chain B residue 817 GLN Chi-restraints excluded: chain B residue 901 THR Chi-restraints excluded: chain B residue 909 VAL Chi-restraints excluded: chain B residue 1059 ILE Chi-restraints excluded: chain B residue 1075 MET Chi-restraints excluded: chain C residue 238 SER Chi-restraints excluded: chain D residue 90 LYS Chi-restraints excluded: chain D residue 107 THR Chi-restraints excluded: chain G residue 24 ASN Chi-restraints excluded: chain G residue 42 TYR Chi-restraints excluded: chain G residue 81 LYS Chi-restraints excluded: chain H residue 110 THR Chi-restraints excluded: chain I residue 62 VAL Chi-restraints excluded: chain I residue 103 ARG Chi-restraints excluded: chain J residue 38 LEU Chi-restraints excluded: chain M residue 37 CYS Chi-restraints excluded: chain M residue 168 CYS Chi-restraints excluded: chain Q residue 99 LEU Chi-restraints excluded: chain R residue 148 VAL Chi-restraints excluded: chain R residue 170 LYS Chi-restraints excluded: chain R residue 218 LYS Chi-restraints excluded: chain V residue 9 THR Chi-restraints excluded: chain V residue 51 ARG Chi-restraints excluded: chain V residue 53 ARG Chi-restraints excluded: chain c residue 176 PHE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 579 random chunks: chunk 466 optimal weight: 10.0000 chunk 317 optimal weight: 2.9990 chunk 8 optimal weight: 50.0000 chunk 416 optimal weight: 7.9990 chunk 230 optimal weight: 5.9990 chunk 477 optimal weight: 7.9990 chunk 386 optimal weight: 10.0000 chunk 0 optimal weight: 10.0000 chunk 285 optimal weight: 30.0000 chunk 502 optimal weight: 40.0000 chunk 141 optimal weight: 4.9990 overall best weight: 5.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 288 ASN ** A 341 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 671 ASN A 723 ASN ** A1005 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A1291 ASN ** B 111 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 265 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 344 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B1030 ASN ** B1053 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 43 HIS E 30 GLN ** E 35 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 107 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 148 HIS G 4 HIS ** G 93 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 138 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 18 GLN ** I 87 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 91 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 100 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** M 139 ASN O 189 ASN R 81 HIS ** R 144 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** R 159 HIS ** U 48 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 39 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 50 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** a 35 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8397 moved from start: 0.5699 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.096 50487 Z= 0.541 Angle : 0.789 13.031 68722 Z= 0.404 Chirality : 0.045 0.257 7610 Planarity : 0.005 0.065 8445 Dihedral : 16.304 145.003 7771 Min Nonbonded Distance : 1.852 Molprobity Statistics. All-atom Clashscore : 20.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.22 % Favored : 95.78 % Rotamer: Outliers : 2.01 % Allowed : 12.79 % Favored : 85.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.56 % 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: 0.49 (0.11), residues: 5715 helix: 1.22 (0.11), residues: 2243 sheet: 0.26 (0.18), residues: 798 loop : -0.35 (0.12), residues: 2674 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.028 0.002 TRP c 187 HIS 0.014 0.002 HIS A 465 PHE 0.039 0.002 PHE K 105 TYR 0.026 0.002 TYR B 388 ARG 0.019 0.001 ARG d 17 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 11430 Ramachandran restraints generated. 5715 Oldfield, 0 Emsley, 5715 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 11430 Ramachandran restraints generated. 5715 Oldfield, 0 Emsley, 5715 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 403 residues out of total 5130 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 103 poor density : 300 time to evaluate : 5.374 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 78 MET cc_start: 0.8850 (tpp) cc_final: 0.8174 (mmm) REVERT: A 99 PHE cc_start: 0.9007 (m-10) cc_final: 0.8519 (m-80) REVERT: A 234 PHE cc_start: 0.9390 (m-80) cc_final: 0.8789 (m-80) REVERT: A 467 MET cc_start: 0.8909 (mpp) cc_final: 0.8554 (mpp) REVERT: A 501 MET cc_start: 0.9127 (mmm) cc_final: 0.8894 (mmm) REVERT: A 561 MET cc_start: 0.8952 (OUTLIER) cc_final: 0.8729 (mmm) REVERT: A 1279 MET cc_start: 0.5545 (ttt) cc_final: 0.5108 (tmm) REVERT: A 1292 MET cc_start: 0.9369 (mtm) cc_final: 0.9137 (mpp) REVERT: A 1405 MET cc_start: 0.9106 (mtm) cc_final: 0.8783 (mtm) REVERT: A 1428 MET cc_start: 0.9247 (tpp) cc_final: 0.8723 (tpp) REVERT: B 155 MET cc_start: 0.9189 (ttm) cc_final: 0.8927 (ttm) REVERT: B 584 MET cc_start: 0.8864 (tpt) cc_final: 0.8563 (tpt) REVERT: B 677 MET cc_start: 0.8832 (tpp) cc_final: 0.8630 (tpp) REVERT: B 680 ASP cc_start: 0.7980 (OUTLIER) cc_final: 0.7621 (p0) REVERT: B 817 GLN cc_start: 0.8749 (OUTLIER) cc_final: 0.8533 (pm20) REVERT: B 908 MET cc_start: 0.8707 (tmm) cc_final: 0.8019 (tmm) REVERT: B 1075 MET cc_start: 0.7975 (OUTLIER) cc_final: 0.7531 (ppp) REVERT: B 1151 MET cc_start: 0.9568 (ptm) cc_final: 0.9042 (ptp) REVERT: B 1163 MET cc_start: 0.9496 (mtt) cc_final: 0.9191 (mpp) REVERT: E 18 MET cc_start: 0.8792 (mtp) cc_final: 0.8449 (ttm) REVERT: E 72 MET cc_start: 0.7301 (tpt) cc_final: 0.6817 (tpt) REVERT: E 73 PHE cc_start: 0.8578 (OUTLIER) cc_final: 0.8063 (t80) REVERT: E 98 ASN cc_start: 0.8811 (m-40) cc_final: 0.8476 (m-40) REVERT: E 103 LEU cc_start: 0.9700 (OUTLIER) cc_final: 0.9484 (mm) REVERT: F 82 GLU cc_start: 0.8947 (tp30) cc_final: 0.8635 (tp30) REVERT: G 104 MET cc_start: -0.0786 (mtt) cc_final: -0.1041 (ptp) REVERT: I 23 MET cc_start: 0.9003 (tpp) cc_final: 0.8377 (tpt) REVERT: I 71 ASP cc_start: 0.8944 (m-30) cc_final: 0.8559 (p0) REVERT: I 125 GLU cc_start: 0.7913 (mp0) cc_final: 0.7648 (mp0) REVERT: L 44 MET cc_start: 0.8899 (mmm) cc_final: 0.8270 (mmm) REVERT: L 48 ARG cc_start: 0.8516 (OUTLIER) cc_final: 0.7850 (ttm-80) REVERT: O 202 MET cc_start: 0.8844 (tpt) cc_final: 0.8619 (tpp) REVERT: Q 177 MET cc_start: 0.4960 (tmm) cc_final: 0.4087 (mmt) REVERT: R 83 PHE cc_start: 0.7327 (m-80) cc_final: 0.6854 (m-80) REVERT: U 13 LEU cc_start: 0.9577 (mp) cc_final: 0.9347 (mm) REVERT: U 15 ARG cc_start: 0.9284 (mmt-90) cc_final: 0.8946 (ttp80) REVERT: V 83 GLU cc_start: 0.8526 (tp30) cc_final: 0.7684 (tp30) REVERT: a 31 GLU cc_start: 0.9863 (mm-30) cc_final: 0.9519 (pp20) REVERT: a 36 MET cc_start: 0.8891 (mtp) cc_final: 0.8594 (mtm) REVERT: a 190 MET cc_start: 0.2220 (ttp) cc_final: 0.1671 (tmm) REVERT: b 293 MET cc_start: 0.6732 (ttm) cc_final: 0.6223 (ptm) REVERT: c 98 GLN cc_start: 0.7710 (tp40) cc_final: 0.7450 (mm110) REVERT: c 216 HIS cc_start: 0.9200 (m-70) cc_final: 0.8924 (m90) REVERT: c 356 MET cc_start: 0.9001 (ppp) cc_final: 0.8678 (ppp) REVERT: c 364 MET cc_start: 0.2035 (ttt) cc_final: 0.1616 (ttt) REVERT: c 379 MET cc_start: 0.4772 (mtt) cc_final: 0.3678 (ptp) REVERT: d 1 MET cc_start: 0.5043 (ptm) cc_final: 0.3842 (mtt) REVERT: d 12 GLU cc_start: 0.6573 (mm-30) cc_final: 0.6362 (mm-30) outliers start: 103 outliers final: 57 residues processed: 389 average time/residue: 0.6021 time to fit residues: 395.2006 Evaluate side-chains 347 residues out of total 5130 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 64 poor density : 283 time to evaluate : 5.978 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 406 VAL Chi-restraints excluded: chain A residue 458 PHE Chi-restraints excluded: chain A residue 561 MET Chi-restraints excluded: chain A residue 611 ASP Chi-restraints excluded: chain A residue 695 ASP Chi-restraints excluded: chain A residue 1227 THR Chi-restraints excluded: chain A residue 1374 VAL Chi-restraints excluded: chain A residue 1454 VAL Chi-restraints excluded: chain B residue 91 ILE Chi-restraints excluded: chain B residue 190 SER Chi-restraints excluded: chain B residue 207 VAL Chi-restraints excluded: chain B residue 218 THR Chi-restraints excluded: chain B residue 288 ILE Chi-restraints excluded: chain B residue 301 VAL Chi-restraints excluded: chain B residue 324 ARG Chi-restraints excluded: chain B residue 598 VAL Chi-restraints excluded: chain B residue 630 LYS Chi-restraints excluded: chain B residue 680 ASP Chi-restraints excluded: chain B residue 681 ASP Chi-restraints excluded: chain B residue 794 VAL Chi-restraints excluded: chain B residue 817 GLN Chi-restraints excluded: chain B residue 901 THR Chi-restraints excluded: chain B residue 918 PHE Chi-restraints excluded: chain B residue 1017 ASP Chi-restraints excluded: chain B residue 1059 ILE Chi-restraints excluded: chain B residue 1075 MET Chi-restraints excluded: chain B residue 1132 THR Chi-restraints excluded: chain C residue 112 THR Chi-restraints excluded: chain C residue 238 SER Chi-restraints excluded: chain D residue 90 LYS Chi-restraints excluded: chain D residue 107 THR Chi-restraints excluded: chain E residue 73 PHE Chi-restraints excluded: chain E residue 103 LEU Chi-restraints excluded: chain F residue 54 THR Chi-restraints excluded: chain F residue 81 VAL Chi-restraints excluded: chain G residue 24 ASN Chi-restraints excluded: chain G residue 81 LYS Chi-restraints excluded: chain G residue 93 ASN Chi-restraints excluded: chain H residue 4 ILE Chi-restraints excluded: chain H residue 96 VAL Chi-restraints excluded: chain H residue 110 THR Chi-restraints excluded: chain I residue 55 VAL Chi-restraints excluded: chain I residue 62 VAL Chi-restraints excluded: chain I residue 103 ARG Chi-restraints excluded: chain J residue 28 GLU Chi-restraints excluded: chain L residue 21 GLU Chi-restraints excluded: chain L residue 26 ASN Chi-restraints excluded: chain L residue 48 ARG Chi-restraints excluded: chain M residue 18 HIS Chi-restraints excluded: chain M residue 31 ASP Chi-restraints excluded: chain M residue 37 CYS Chi-restraints excluded: chain M residue 168 CYS Chi-restraints excluded: chain Q residue 46 ARG Chi-restraints excluded: chain Q residue 99 LEU Chi-restraints excluded: chain R residue 148 VAL Chi-restraints excluded: chain R residue 170 LYS Chi-restraints excluded: chain R residue 218 LYS Chi-restraints excluded: chain V residue 51 ARG Chi-restraints excluded: chain a residue 145 SER Chi-restraints excluded: chain b residue 128 VAL Chi-restraints excluded: chain c residue 115 GLN Chi-restraints excluded: chain c residue 144 HIS Chi-restraints excluded: chain c residue 176 PHE Chi-restraints excluded: chain d residue 13 GLU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 579 random chunks: chunk 188 optimal weight: 4.9990 chunk 504 optimal weight: 9.9990 chunk 110 optimal weight: 3.9990 chunk 328 optimal weight: 40.0000 chunk 138 optimal weight: 5.9990 chunk 560 optimal weight: 30.0000 chunk 465 optimal weight: 20.0000 chunk 259 optimal weight: 0.9990 chunk 46 optimal weight: 0.9980 chunk 185 optimal weight: 10.0000 chunk 294 optimal weight: 1.9990 overall best weight: 2.5988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 341 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 671 ASN ** A1005 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 111 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 227 ASN ** B 265 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 344 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1053 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 35 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 4 HIS ** G 60 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 93 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 138 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 91 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 100 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** O 189 ASN R 144 GLN ** U 48 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 352 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 39 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 50 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** a 35 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8343 moved from start: 0.5847 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.061 50487 Z= 0.253 Angle : 0.586 14.286 68722 Z= 0.305 Chirality : 0.041 0.193 7610 Planarity : 0.004 0.054 8445 Dihedral : 16.188 144.294 7771 Min Nonbonded Distance : 1.966 Molprobity Statistics. All-atom Clashscore : 15.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.52 % Favored : 96.48 % Rotamer: Outliers : 1.66 % Allowed : 13.75 % Favored : 84.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.56 % 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: 0.79 (0.11), residues: 5715 helix: 1.54 (0.11), residues: 2249 sheet: 0.28 (0.18), residues: 833 loop : -0.21 (0.13), residues: 2633 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.035 0.002 TRP c 187 HIS 0.007 0.001 HIS M 18 PHE 0.023 0.001 PHE K 105 TYR 0.018 0.001 TYR b 340 ARG 0.017 0.000 ARG d 17 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 11430 Ramachandran restraints generated. 5715 Oldfield, 0 Emsley, 5715 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 11430 Ramachandran restraints generated. 5715 Oldfield, 0 Emsley, 5715 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 383 residues out of total 5130 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 85 poor density : 298 time to evaluate : 5.080 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 99 PHE cc_start: 0.9042 (m-10) cc_final: 0.8691 (m-80) REVERT: A 234 PHE cc_start: 0.9326 (m-80) cc_final: 0.8737 (m-80) REVERT: A 367 ILE cc_start: 0.9750 (OUTLIER) cc_final: 0.9540 (pp) REVERT: A 388 MET cc_start: 0.8837 (mmm) cc_final: 0.8492 (mmt) REVERT: A 467 MET cc_start: 0.8925 (mpp) cc_final: 0.8614 (mpp) REVERT: A 501 MET cc_start: 0.9051 (mmm) cc_final: 0.8746 (mmm) REVERT: A 561 MET cc_start: 0.8900 (OUTLIER) cc_final: 0.8630 (mmm) REVERT: A 1085 GLU cc_start: 0.8247 (OUTLIER) cc_final: 0.7926 (mt-10) REVERT: A 1102 MET cc_start: 0.8081 (mtt) cc_final: 0.7746 (ptp) REVERT: A 1279 MET cc_start: 0.5495 (ttt) cc_final: 0.5145 (tmm) REVERT: A 1309 MET cc_start: 0.7827 (ttt) cc_final: 0.7617 (ttt) REVERT: A 1415 THR cc_start: 0.8006 (OUTLIER) cc_final: 0.7801 (p) REVERT: A 1428 MET cc_start: 0.9203 (tpp) cc_final: 0.8678 (tpp) REVERT: B 584 MET cc_start: 0.8867 (tpt) cc_final: 0.8618 (tpt) REVERT: B 680 ASP cc_start: 0.7690 (OUTLIER) cc_final: 0.7279 (p0) REVERT: B 908 MET cc_start: 0.8694 (tmm) cc_final: 0.8012 (tmm) REVERT: B 1075 MET cc_start: 0.8034 (OUTLIER) cc_final: 0.7574 (ppp) REVERT: B 1151 MET cc_start: 0.9532 (ptm) cc_final: 0.8817 (ptp) REVERT: D 119 GLU cc_start: 0.5054 (OUTLIER) cc_final: 0.4822 (mm-30) REVERT: E 18 MET cc_start: 0.8789 (mtp) cc_final: 0.8485 (ptm) REVERT: E 72 MET cc_start: 0.7310 (tpt) cc_final: 0.6936 (tpt) REVERT: E 73 PHE cc_start: 0.8524 (OUTLIER) cc_final: 0.8044 (t80) REVERT: E 98 ASN cc_start: 0.8736 (m-40) cc_final: 0.8421 (m-40) REVERT: F 57 MET cc_start: 0.8971 (tmm) cc_final: 0.8757 (tmm) REVERT: G 104 MET cc_start: -0.0580 (mtt) cc_final: -0.0851 (ptp) REVERT: G 117 MET cc_start: -0.0398 (ttp) cc_final: -0.0617 (ttp) REVERT: H 123 MET cc_start: 0.8869 (tmm) cc_final: 0.8460 (tmm) REVERT: I 23 MET cc_start: 0.9025 (tpp) cc_final: 0.8435 (tpt) REVERT: I 71 ASP cc_start: 0.8951 (m-30) cc_final: 0.8511 (p0) REVERT: I 125 GLU cc_start: 0.7854 (mp0) cc_final: 0.7531 (mp0) REVERT: L 44 MET cc_start: 0.8754 (mmm) cc_final: 0.8249 (mmm) REVERT: L 48 ARG cc_start: 0.8358 (OUTLIER) cc_final: 0.7701 (ttm-80) REVERT: Q 177 MET cc_start: 0.5000 (tmm) cc_final: 0.3968 (mmt) REVERT: R 83 PHE cc_start: 0.7383 (m-80) cc_final: 0.6945 (m-80) REVERT: V 51 ARG cc_start: 0.9517 (OUTLIER) cc_final: 0.9283 (mmm-85) REVERT: V 55 ARG cc_start: 0.9311 (ttp80) cc_final: 0.9095 (ttp80) REVERT: V 78 ASP cc_start: 0.9481 (m-30) cc_final: 0.8815 (t0) REVERT: V 83 GLU cc_start: 0.8563 (tp30) cc_final: 0.7740 (tp30) REVERT: a 31 GLU cc_start: 0.9860 (mm-30) cc_final: 0.9537 (pp20) REVERT: a 36 MET cc_start: 0.8847 (mtp) cc_final: 0.8526 (mtm) REVERT: a 190 MET cc_start: 0.2846 (ttp) cc_final: 0.2364 (tmm) REVERT: b 293 MET cc_start: 0.6794 (ttm) cc_final: 0.6275 (ptm) REVERT: c 98 GLN cc_start: 0.7665 (tp40) cc_final: 0.7414 (mm110) REVERT: c 356 MET cc_start: 0.9125 (ppp) cc_final: 0.8853 (ppp) REVERT: c 364 MET cc_start: 0.1855 (ttt) cc_final: 0.1349 (ttt) REVERT: c 379 MET cc_start: 0.5252 (mtt) cc_final: 0.4863 (mtm) REVERT: d 1 MET cc_start: 0.5142 (ptm) cc_final: 0.3903 (mtt) outliers start: 85 outliers final: 48 residues processed: 367 average time/residue: 0.6235 time to fit residues: 383.6901 Evaluate side-chains 344 residues out of total 5130 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 58 poor density : 286 time to evaluate : 5.510 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 329 MET Chi-restraints excluded: chain A residue 367 ILE Chi-restraints excluded: chain A residue 395 THR Chi-restraints excluded: chain A residue 458 PHE Chi-restraints excluded: chain A residue 561 MET Chi-restraints excluded: chain A residue 611 ASP Chi-restraints excluded: chain A residue 695 ASP Chi-restraints excluded: chain A residue 787 VAL Chi-restraints excluded: chain A residue 1085 GLU Chi-restraints excluded: chain A residue 1201 ASP Chi-restraints excluded: chain A residue 1227 THR Chi-restraints excluded: chain A residue 1374 VAL Chi-restraints excluded: chain A residue 1415 THR Chi-restraints excluded: chain A residue 1454 VAL Chi-restraints excluded: chain B residue 124 LEU Chi-restraints excluded: chain B residue 140 LEU Chi-restraints excluded: chain B residue 218 THR Chi-restraints excluded: chain B residue 324 ARG Chi-restraints excluded: chain B residue 597 ILE Chi-restraints excluded: chain B residue 680 ASP Chi-restraints excluded: chain B residue 747 LEU Chi-restraints excluded: chain B residue 865 VAL Chi-restraints excluded: chain B residue 901 THR Chi-restraints excluded: chain B residue 918 PHE Chi-restraints excluded: chain B residue 1059 ILE Chi-restraints excluded: chain B residue 1075 MET Chi-restraints excluded: chain C residue 19 VAL Chi-restraints excluded: chain C residue 238 SER Chi-restraints excluded: chain D residue 90 LYS Chi-restraints excluded: chain D residue 107 THR Chi-restraints excluded: chain D residue 119 GLU Chi-restraints excluded: chain E residue 73 PHE Chi-restraints excluded: chain G residue 24 ASN Chi-restraints excluded: chain G residue 93 ASN Chi-restraints excluded: chain H residue 96 VAL Chi-restraints excluded: chain H residue 110 THR Chi-restraints excluded: chain H residue 141 VAL Chi-restraints excluded: chain I residue 62 VAL Chi-restraints excluded: chain I residue 103 ARG Chi-restraints excluded: chain J residue 28 GLU Chi-restraints excluded: chain L residue 21 GLU Chi-restraints excluded: chain L residue 48 ARG Chi-restraints excluded: chain M residue 18 HIS Chi-restraints excluded: chain M residue 31 ASP Chi-restraints excluded: chain M residue 37 CYS Chi-restraints excluded: chain M residue 168 CYS Chi-restraints excluded: chain Q residue 46 ARG Chi-restraints excluded: chain Q residue 99 LEU Chi-restraints excluded: chain R residue 148 VAL Chi-restraints excluded: chain R residue 170 LYS Chi-restraints excluded: chain R residue 218 LYS Chi-restraints excluded: chain U residue 10 VAL Chi-restraints excluded: chain V residue 51 ARG Chi-restraints excluded: chain a residue 106 GLU Chi-restraints excluded: chain b residue 128 VAL Chi-restraints excluded: chain b residue 365 VAL Chi-restraints excluded: chain c residue 144 HIS Chi-restraints excluded: chain c residue 176 PHE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 579 random chunks: chunk 540 optimal weight: 0.0050 chunk 63 optimal weight: 3.9990 chunk 319 optimal weight: 3.9990 chunk 409 optimal weight: 7.9990 chunk 316 optimal weight: 0.9980 chunk 471 optimal weight: 1.9990 chunk 312 optimal weight: 4.9990 chunk 558 optimal weight: 8.9990 chunk 349 optimal weight: 10.0000 chunk 340 optimal weight: 1.9990 chunk 257 optimal weight: 1.9990 overall best weight: 1.4000 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 341 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 111 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 265 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 344 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1053 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 35 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 4 HIS ** G 60 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 93 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 138 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 91 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 100 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 48 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 39 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 50 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** a 35 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8327 moved from start: 0.5976 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.051 50487 Z= 0.191 Angle : 0.571 13.601 68722 Z= 0.293 Chirality : 0.041 0.220 7610 Planarity : 0.004 0.054 8445 Dihedral : 16.024 143.809 7771 Min Nonbonded Distance : 1.999 Molprobity Statistics. All-atom Clashscore : 14.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.74 % Favored : 96.26 % Rotamer: Outliers : 1.44 % Allowed : 14.25 % Favored : 84.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.56 % 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: 0.89 (0.11), residues: 5715 helix: 1.63 (0.11), residues: 2255 sheet: 0.30 (0.18), residues: 855 loop : -0.16 (0.13), residues: 2605 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.037 0.002 TRP c 187 HIS 0.009 0.001 HIS c 216 PHE 0.020 0.001 PHE B 823 TYR 0.016 0.001 TYR b 340 ARG 0.015 0.000 ARG G 63 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 11430 Ramachandran restraints generated. 5715 Oldfield, 0 Emsley, 5715 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 11430 Ramachandran restraints generated. 5715 Oldfield, 0 Emsley, 5715 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 370 residues out of total 5130 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 74 poor density : 296 time to evaluate : 5.575 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 99 PHE cc_start: 0.9287 (m-10) cc_final: 0.8596 (m-80) REVERT: A 234 PHE cc_start: 0.9327 (m-80) cc_final: 0.8747 (m-80) REVERT: A 367 ILE cc_start: 0.9744 (OUTLIER) cc_final: 0.9528 (pp) REVERT: A 388 MET cc_start: 0.8863 (mmm) cc_final: 0.8350 (mmt) REVERT: A 467 MET cc_start: 0.8873 (mpp) cc_final: 0.8426 (mpp) REVERT: A 501 MET cc_start: 0.9093 (mmm) cc_final: 0.8788 (mmm) REVERT: A 561 MET cc_start: 0.8876 (OUTLIER) cc_final: 0.8647 (mmm) REVERT: A 769 MET cc_start: 0.9118 (mtt) cc_final: 0.8899 (mmm) REVERT: A 1279 MET cc_start: 0.5272 (ttt) cc_final: 0.4947 (tmm) REVERT: A 1309 MET cc_start: 0.7807 (ttt) cc_final: 0.7597 (ttt) REVERT: A 1415 THR cc_start: 0.8124 (OUTLIER) cc_final: 0.7914 (p) REVERT: A 1428 MET cc_start: 0.9213 (tpp) cc_final: 0.8670 (tpp) REVERT: B 584 MET cc_start: 0.8943 (tpt) cc_final: 0.8668 (tpt) REVERT: B 594 MET cc_start: 0.8606 (mtp) cc_final: 0.8238 (mmp) REVERT: B 908 MET cc_start: 0.8711 (tmm) cc_final: 0.8044 (tmm) REVERT: B 1075 MET cc_start: 0.8116 (OUTLIER) cc_final: 0.7689 (ppp) REVERT: B 1151 MET cc_start: 0.9582 (ptm) cc_final: 0.8968 (ptp) REVERT: D 119 GLU cc_start: 0.5052 (OUTLIER) cc_final: 0.4822 (mm-30) REVERT: E 18 MET cc_start: 0.8769 (mtp) cc_final: 0.8387 (ttm) REVERT: E 72 MET cc_start: 0.6840 (tpt) cc_final: 0.6496 (tpt) REVERT: E 73 PHE cc_start: 0.8355 (OUTLIER) cc_final: 0.7940 (t80) REVERT: E 98 ASN cc_start: 0.8755 (m-40) cc_final: 0.8458 (m-40) REVERT: E 103 LEU cc_start: 0.9539 (OUTLIER) cc_final: 0.9308 (mm) REVERT: F 66 LEU cc_start: 0.9789 (OUTLIER) cc_final: 0.9588 (mm) REVERT: F 94 MET cc_start: 0.9226 (mmm) cc_final: 0.9005 (tpp) REVERT: G 104 MET cc_start: -0.0411 (mtt) cc_final: -0.0776 (ptp) REVERT: H 123 MET cc_start: 0.8854 (tmm) cc_final: 0.8444 (tmm) REVERT: I 23 MET cc_start: 0.8999 (tpp) cc_final: 0.8414 (tpt) REVERT: I 71 ASP cc_start: 0.8979 (m-30) cc_final: 0.8492 (p0) REVERT: L 44 MET cc_start: 0.8771 (mmm) cc_final: 0.8271 (mmm) REVERT: Q 162 GLU cc_start: 0.8402 (pp20) cc_final: 0.7580 (pm20) REVERT: Q 177 MET cc_start: 0.5049 (tmm) cc_final: 0.3984 (mmt) REVERT: R 83 PHE cc_start: 0.7448 (m-80) cc_final: 0.7025 (m-80) REVERT: V 51 ARG cc_start: 0.9532 (OUTLIER) cc_final: 0.9250 (mmm-85) REVERT: V 55 ARG cc_start: 0.9227 (ttp80) cc_final: 0.8811 (ttp80) REVERT: V 78 ASP cc_start: 0.9432 (m-30) cc_final: 0.8957 (t0) REVERT: V 83 GLU cc_start: 0.8545 (tp30) cc_final: 0.7702 (tp30) REVERT: a 31 GLU cc_start: 0.9859 (mm-30) cc_final: 0.9534 (pp20) REVERT: a 36 MET cc_start: 0.8807 (mtp) cc_final: 0.8531 (mtm) REVERT: a 70 TYR cc_start: 0.8865 (m-80) cc_final: 0.8593 (m-80) REVERT: a 190 MET cc_start: 0.2771 (ttp) cc_final: 0.2291 (tmm) REVERT: b 293 MET cc_start: 0.6636 (ttm) cc_final: 0.6149 (ptm) REVERT: c 98 GLN cc_start: 0.7739 (tp40) cc_final: 0.7500 (mm110) REVERT: c 216 HIS cc_start: 0.9173 (m-70) cc_final: 0.8972 (m-70) REVERT: c 356 MET cc_start: 0.9171 (ppp) cc_final: 0.8966 (ppp) REVERT: c 364 MET cc_start: 0.1754 (ttt) cc_final: 0.1163 (ttt) REVERT: d 1 MET cc_start: 0.5135 (ptm) cc_final: 0.3978 (mtt) outliers start: 74 outliers final: 48 residues processed: 355 average time/residue: 0.6288 time to fit residues: 376.9956 Evaluate side-chains 347 residues out of total 5130 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 57 poor density : 290 time to evaluate : 5.550 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 329 MET Chi-restraints excluded: chain A residue 367 ILE Chi-restraints excluded: chain A residue 458 PHE Chi-restraints excluded: chain A residue 561 MET Chi-restraints excluded: chain A residue 611 ASP Chi-restraints excluded: chain A residue 695 ASP Chi-restraints excluded: chain A residue 1201 ASP Chi-restraints excluded: chain A residue 1227 THR Chi-restraints excluded: chain A residue 1374 VAL Chi-restraints excluded: chain A residue 1415 THR Chi-restraints excluded: chain A residue 1454 VAL Chi-restraints excluded: chain B residue 124 LEU Chi-restraints excluded: chain B residue 193 VAL Chi-restraints excluded: chain B residue 218 THR Chi-restraints excluded: chain B residue 312 GLN Chi-restraints excluded: chain B residue 324 ARG Chi-restraints excluded: chain B residue 597 ILE Chi-restraints excluded: chain B residue 865 VAL Chi-restraints excluded: chain B residue 901 THR Chi-restraints excluded: chain B residue 918 PHE Chi-restraints excluded: chain B residue 964 ASP Chi-restraints excluded: chain B residue 1059 ILE Chi-restraints excluded: chain B residue 1075 MET Chi-restraints excluded: chain C residue 238 SER Chi-restraints excluded: chain D residue 90 LYS Chi-restraints excluded: chain D residue 107 THR Chi-restraints excluded: chain D residue 119 GLU Chi-restraints excluded: chain E residue 73 PHE Chi-restraints excluded: chain E residue 103 LEU Chi-restraints excluded: chain E residue 159 LEU Chi-restraints excluded: chain F residue 66 LEU Chi-restraints excluded: chain G residue 24 ASN Chi-restraints excluded: chain G residue 42 TYR Chi-restraints excluded: chain G residue 93 ASN Chi-restraints excluded: chain H residue 37 MET Chi-restraints excluded: chain H residue 96 VAL Chi-restraints excluded: chain H residue 110 THR Chi-restraints excluded: chain I residue 62 VAL Chi-restraints excluded: chain I residue 103 ARG Chi-restraints excluded: chain L residue 21 GLU Chi-restraints excluded: chain M residue 18 HIS Chi-restraints excluded: chain M residue 31 ASP Chi-restraints excluded: chain M residue 37 CYS Chi-restraints excluded: chain M residue 168 CYS Chi-restraints excluded: chain Q residue 12 THR Chi-restraints excluded: chain Q residue 99 LEU Chi-restraints excluded: chain R residue 148 VAL Chi-restraints excluded: chain R residue 170 LYS Chi-restraints excluded: chain R residue 218 LYS Chi-restraints excluded: chain U residue 340 ASP Chi-restraints excluded: chain V residue 9 THR Chi-restraints excluded: chain V residue 51 ARG Chi-restraints excluded: chain b residue 128 VAL Chi-restraints excluded: chain b residue 365 VAL Chi-restraints excluded: chain c residue 144 HIS Chi-restraints excluded: chain c residue 176 PHE Chi-restraints excluded: chain c residue 326 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 579 random chunks: chunk 345 optimal weight: 5.9990 chunk 222 optimal weight: 8.9990 chunk 333 optimal weight: 40.0000 chunk 168 optimal weight: 0.3980 chunk 109 optimal weight: 6.9990 chunk 108 optimal weight: 8.9990 chunk 354 optimal weight: 0.9980 chunk 380 optimal weight: 2.9990 chunk 275 optimal weight: 6.9990 chunk 52 optimal weight: 4.9990 chunk 438 optimal weight: 7.9990 overall best weight: 3.0786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 341 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1005 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 111 ASN ** B 265 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 344 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1053 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 35 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 4 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 93 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 138 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 91 HIS ** I 100 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** M 129 ASN ** U 48 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 39 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 50 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** a 35 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** b 198 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** b 260 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8369 moved from start: 0.6256 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.072 50487 Z= 0.292 Angle : 0.600 12.887 68722 Z= 0.308 Chirality : 0.041 0.257 7610 Planarity : 0.004 0.054 8445 Dihedral : 15.988 143.751 7771 Min Nonbonded Distance : 1.946 Molprobity Statistics. All-atom Clashscore : 15.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.99 % Favored : 96.01 % Rotamer: Outliers : 1.56 % Allowed : 14.47 % Favored : 83.97 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.56 % 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: 0.88 (0.11), residues: 5715 helix: 1.67 (0.11), residues: 2247 sheet: 0.17 (0.18), residues: 860 loop : -0.16 (0.13), residues: 2608 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.044 0.002 TRP c 187 HIS 0.007 0.001 HIS M 18 PHE 0.023 0.001 PHE K 105 TYR 0.016 0.001 TYR a 146 ARG 0.013 0.000 ARG Q 166 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 11430 Ramachandran restraints generated. 5715 Oldfield, 0 Emsley, 5715 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 11430 Ramachandran restraints generated. 5715 Oldfield, 0 Emsley, 5715 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 370 residues out of total 5130 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 80 poor density : 290 time to evaluate : 5.770 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 99 PHE cc_start: 0.9146 (m-10) cc_final: 0.8586 (m-80) REVERT: A 234 PHE cc_start: 0.9323 (m-80) cc_final: 0.8714 (m-80) REVERT: A 248 MET cc_start: 0.8548 (ptp) cc_final: 0.7519 (ppp) REVERT: A 367 ILE cc_start: 0.9749 (OUTLIER) cc_final: 0.9543 (pp) REVERT: A 388 MET cc_start: 0.8916 (mmm) cc_final: 0.8248 (mmt) REVERT: A 467 MET cc_start: 0.8888 (mpp) cc_final: 0.8500 (mpp) REVERT: A 501 MET cc_start: 0.9108 (mmm) cc_final: 0.8802 (mmm) REVERT: A 561 MET cc_start: 0.8910 (OUTLIER) cc_final: 0.8690 (mmm) REVERT: A 1124 LEU cc_start: 0.9680 (OUTLIER) cc_final: 0.9462 (tt) REVERT: A 1279 MET cc_start: 0.5257 (ttt) cc_final: 0.4893 (tmm) REVERT: A 1309 MET cc_start: 0.7933 (ttt) cc_final: 0.7696 (ttt) REVERT: A 1428 MET cc_start: 0.9201 (tpp) cc_final: 0.8671 (tpp) REVERT: B 200 MET cc_start: 0.8587 (mmm) cc_final: 0.8282 (mmm) REVERT: B 584 MET cc_start: 0.8966 (tpt) cc_final: 0.8759 (tpt) REVERT: B 594 MET cc_start: 0.8559 (mtp) cc_final: 0.8101 (mmp) REVERT: B 908 MET cc_start: 0.8747 (tmm) cc_final: 0.8071 (tmm) REVERT: B 1075 MET cc_start: 0.8131 (OUTLIER) cc_final: 0.7716 (ppp) REVERT: B 1151 MET cc_start: 0.9551 (ptm) cc_final: 0.8894 (ptp) REVERT: D 119 GLU cc_start: 0.4984 (OUTLIER) cc_final: 0.4726 (mm-30) REVERT: E 18 MET cc_start: 0.8789 (mtp) cc_final: 0.8421 (ttm) REVERT: E 72 MET cc_start: 0.6874 (tpt) cc_final: 0.6591 (tpt) REVERT: E 73 PHE cc_start: 0.8456 (OUTLIER) cc_final: 0.8044 (t80) REVERT: E 98 ASN cc_start: 0.8781 (m-40) cc_final: 0.8486 (m-40) REVERT: E 103 LEU cc_start: 0.9532 (OUTLIER) cc_final: 0.9319 (mm) REVERT: F 57 MET cc_start: 0.8852 (tmm) cc_final: 0.8612 (tmm) REVERT: F 66 LEU cc_start: 0.9807 (OUTLIER) cc_final: 0.9588 (mm) REVERT: F 94 MET cc_start: 0.9229 (mmm) cc_final: 0.8923 (tpp) REVERT: G 104 MET cc_start: -0.0421 (mtt) cc_final: -0.0803 (ptp) REVERT: G 117 MET cc_start: -0.0393 (ttp) cc_final: -0.0604 (tmm) REVERT: H 123 MET cc_start: 0.8840 (tmm) cc_final: 0.8493 (tmm) REVERT: I 23 MET cc_start: 0.9051 (tpp) cc_final: 0.8377 (tpt) REVERT: I 71 ASP cc_start: 0.9057 (m-30) cc_final: 0.8590 (p0) REVERT: I 125 GLU cc_start: 0.7899 (mp0) cc_final: 0.7466 (mp0) REVERT: L 44 MET cc_start: 0.8771 (mmm) cc_final: 0.8225 (mmm) REVERT: M 129 ASN cc_start: 0.9314 (OUTLIER) cc_final: 0.8998 (t0) REVERT: Q 177 MET cc_start: 0.4795 (tmm) cc_final: 0.3794 (mmt) REVERT: R 83 PHE cc_start: 0.7274 (m-80) cc_final: 0.6991 (m-80) REVERT: V 51 ARG cc_start: 0.9493 (OUTLIER) cc_final: 0.9178 (mmm-85) REVERT: V 55 ARG cc_start: 0.9282 (ttp80) cc_final: 0.9030 (ttp80) REVERT: V 78 ASP cc_start: 0.9417 (m-30) cc_final: 0.8937 (t0) REVERT: V 83 GLU cc_start: 0.8591 (tp30) cc_final: 0.7827 (tp30) REVERT: a 31 GLU cc_start: 0.9872 (mm-30) cc_final: 0.9557 (pp20) REVERT: a 36 MET cc_start: 0.8821 (mtp) cc_final: 0.8548 (mtm) REVERT: a 70 TYR cc_start: 0.8902 (m-80) cc_final: 0.8645 (m-80) REVERT: a 190 MET cc_start: 0.2996 (ttp) cc_final: 0.2534 (tmm) REVERT: b 293 MET cc_start: 0.6793 (ttm) cc_final: 0.6270 (ptm) REVERT: c 98 GLN cc_start: 0.7663 (tp40) cc_final: 0.7413 (mm110) REVERT: c 216 HIS cc_start: 0.9167 (m-70) cc_final: 0.8887 (m90) REVERT: c 356 MET cc_start: 0.9134 (ppp) cc_final: 0.8903 (ppp) REVERT: c 364 MET cc_start: 0.1878 (ttt) cc_final: 0.1357 (ttt) REVERT: c 379 MET cc_start: 0.5153 (mtt) cc_final: 0.4307 (ptp) REVERT: d 1 MET cc_start: 0.5110 (ptm) cc_final: 0.3949 (mtt) outliers start: 80 outliers final: 54 residues processed: 355 average time/residue: 0.6202 time to fit residues: 369.3478 Evaluate side-chains 347 residues out of total 5130 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 64 poor density : 283 time to evaluate : 5.234 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 329 MET Chi-restraints excluded: chain A residue 367 ILE Chi-restraints excluded: chain A residue 458 PHE Chi-restraints excluded: chain A residue 561 MET Chi-restraints excluded: chain A residue 611 ASP Chi-restraints excluded: chain A residue 695 ASP Chi-restraints excluded: chain A residue 1124 LEU Chi-restraints excluded: chain A residue 1227 THR Chi-restraints excluded: chain A residue 1374 VAL Chi-restraints excluded: chain A residue 1454 VAL Chi-restraints excluded: chain B residue 91 ILE Chi-restraints excluded: chain B residue 124 LEU Chi-restraints excluded: chain B residue 163 LEU Chi-restraints excluded: chain B residue 193 VAL Chi-restraints excluded: chain B residue 218 THR Chi-restraints excluded: chain B residue 312 GLN Chi-restraints excluded: chain B residue 324 ARG Chi-restraints excluded: chain B residue 597 ILE Chi-restraints excluded: chain B residue 865 VAL Chi-restraints excluded: chain B residue 901 THR Chi-restraints excluded: chain B residue 918 PHE Chi-restraints excluded: chain B residue 964 ASP Chi-restraints excluded: chain B residue 1059 ILE Chi-restraints excluded: chain B residue 1075 MET Chi-restraints excluded: chain C residue 19 VAL Chi-restraints excluded: chain C residue 238 SER Chi-restraints excluded: chain D residue 90 LYS Chi-restraints excluded: chain D residue 107 THR Chi-restraints excluded: chain D residue 119 GLU Chi-restraints excluded: chain E residue 73 PHE Chi-restraints excluded: chain E residue 103 LEU Chi-restraints excluded: chain E residue 159 LEU Chi-restraints excluded: chain F residue 66 LEU Chi-restraints excluded: chain G residue 24 ASN Chi-restraints excluded: chain G residue 93 ASN Chi-restraints excluded: chain G residue 113 ILE Chi-restraints excluded: chain H residue 4 ILE Chi-restraints excluded: chain H residue 96 VAL Chi-restraints excluded: chain H residue 110 THR Chi-restraints excluded: chain I residue 62 VAL Chi-restraints excluded: chain I residue 103 ARG Chi-restraints excluded: chain J residue 28 GLU Chi-restraints excluded: chain L residue 21 GLU Chi-restraints excluded: chain M residue 18 HIS Chi-restraints excluded: chain M residue 31 ASP Chi-restraints excluded: chain M residue 37 CYS Chi-restraints excluded: chain M residue 129 ASN Chi-restraints excluded: chain M residue 168 CYS Chi-restraints excluded: chain M residue 276 ASP Chi-restraints excluded: chain Q residue 12 THR Chi-restraints excluded: chain Q residue 46 ARG Chi-restraints excluded: chain Q residue 99 LEU Chi-restraints excluded: chain Q residue 118 VAL Chi-restraints excluded: chain R residue 148 VAL Chi-restraints excluded: chain R residue 170 LYS Chi-restraints excluded: chain R residue 218 LYS Chi-restraints excluded: chain U residue 340 ASP Chi-restraints excluded: chain V residue 51 ARG Chi-restraints excluded: chain a residue 106 GLU Chi-restraints excluded: chain b residue 128 VAL Chi-restraints excluded: chain b residue 365 VAL Chi-restraints excluded: chain c residue 144 HIS Chi-restraints excluded: chain c residue 176 PHE Chi-restraints excluded: chain c residue 326 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 579 random chunks: chunk 507 optimal weight: 40.0000 chunk 534 optimal weight: 20.0000 chunk 487 optimal weight: 50.0000 chunk 520 optimal weight: 30.0000 chunk 313 optimal weight: 2.9990 chunk 226 optimal weight: 1.9990 chunk 408 optimal weight: 6.9990 chunk 159 optimal weight: 6.9990 chunk 469 optimal weight: 10.0000 chunk 491 optimal weight: 30.0000 chunk 518 optimal weight: 0.3980 overall best weight: 3.8788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 62 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 341 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 700 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 704 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1005 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1146 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 265 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 344 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1053 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B1120 ASN C 6 GLN ** E 35 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 107 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 4 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 60 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 93 ASN ** G 138 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 41 ASN ** I 100 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** R 86 GLN ** U 48 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 39 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 50 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** a 35 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** a 73 GLN ** b 198 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** c 246 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8395 moved from start: 0.6603 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.082 50487 Z= 0.343 Angle : 0.636 18.530 68722 Z= 0.326 Chirality : 0.041 0.205 7610 Planarity : 0.004 0.054 8445 Dihedral : 16.036 143.360 7771 Min Nonbonded Distance : 1.930 Molprobity Statistics. All-atom Clashscore : 17.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.13 % Favored : 95.87 % Rotamer: Outliers : 1.54 % Allowed : 14.66 % Favored : 83.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.56 % 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: 0.82 (0.11), residues: 5715 helix: 1.61 (0.11), residues: 2253 sheet: 0.14 (0.18), residues: 857 loop : -0.19 (0.13), residues: 2605 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.049 0.002 TRP c 187 HIS 0.007 0.001 HIS A 465 PHE 0.023 0.001 PHE K 105 TYR 0.018 0.001 TYR b 340 ARG 0.011 0.000 ARG M 132 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 11430 Ramachandran restraints generated. 5715 Oldfield, 0 Emsley, 5715 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 11430 Ramachandran restraints generated. 5715 Oldfield, 0 Emsley, 5715 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 370 residues out of total 5130 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 79 poor density : 291 time to evaluate : 5.960 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 99 PHE cc_start: 0.9225 (m-10) cc_final: 0.8902 (m-80) REVERT: A 234 PHE cc_start: 0.9346 (m-80) cc_final: 0.8757 (m-80) REVERT: A 367 ILE cc_start: 0.9754 (OUTLIER) cc_final: 0.9540 (pp) REVERT: A 388 MET cc_start: 0.8926 (mmm) cc_final: 0.8221 (mmt) REVERT: A 467 MET cc_start: 0.8916 (mpp) cc_final: 0.8478 (mpp) REVERT: A 501 MET cc_start: 0.9127 (mmm) cc_final: 0.8843 (mmm) REVERT: A 1279 MET cc_start: 0.5366 (ttt) cc_final: 0.4976 (tmm) REVERT: A 1309 MET cc_start: 0.7934 (ttt) cc_final: 0.7707 (ttt) REVERT: A 1428 MET cc_start: 0.9167 (tpp) cc_final: 0.8670 (tpp) REVERT: B 594 MET cc_start: 0.8564 (mtp) cc_final: 0.8185 (mmp) REVERT: B 908 MET cc_start: 0.8730 (tmm) cc_final: 0.8056 (tmm) REVERT: B 1075 MET cc_start: 0.8126 (OUTLIER) cc_final: 0.7723 (ppp) REVERT: B 1151 MET cc_start: 0.9531 (ptm) cc_final: 0.8642 (ptp) REVERT: B 1163 MET cc_start: 0.9427 (mmt) cc_final: 0.8940 (mmm) REVERT: D 119 GLU cc_start: 0.5019 (OUTLIER) cc_final: 0.4756 (mm-30) REVERT: E 18 MET cc_start: 0.8808 (mtp) cc_final: 0.8477 (ptm) REVERT: E 72 MET cc_start: 0.6882 (tpt) cc_final: 0.6646 (tpt) REVERT: E 73 PHE cc_start: 0.8527 (OUTLIER) cc_final: 0.8145 (t80) REVERT: E 98 ASN cc_start: 0.8840 (m-40) cc_final: 0.8543 (m-40) REVERT: E 103 LEU cc_start: 0.9555 (OUTLIER) cc_final: 0.9350 (mm) REVERT: F 57 MET cc_start: 0.8857 (tmm) cc_final: 0.8599 (tmm) REVERT: F 66 LEU cc_start: 0.9807 (OUTLIER) cc_final: 0.9591 (mm) REVERT: F 94 MET cc_start: 0.9239 (mmm) cc_final: 0.8960 (tpp) REVERT: G 104 MET cc_start: -0.0259 (mtt) cc_final: -0.0577 (ptp) REVERT: G 117 MET cc_start: -0.0123 (ttp) cc_final: -0.0344 (tmm) REVERT: H 123 MET cc_start: 0.8855 (tmm) cc_final: 0.8477 (tmm) REVERT: I 23 MET cc_start: 0.9108 (tpp) cc_final: 0.8465 (tpt) REVERT: I 41 ASN cc_start: 0.8384 (OUTLIER) cc_final: 0.7918 (p0) REVERT: I 71 ASP cc_start: 0.9108 (m-30) cc_final: 0.8701 (p0) REVERT: I 125 GLU cc_start: 0.7945 (mp0) cc_final: 0.7572 (mp0) REVERT: L 44 MET cc_start: 0.8756 (mmm) cc_final: 0.8252 (mmm) REVERT: M 263 GLN cc_start: 0.9137 (OUTLIER) cc_final: 0.8887 (mm110) REVERT: Q 162 GLU cc_start: 0.8564 (pp20) cc_final: 0.7924 (pm20) REVERT: Q 177 MET cc_start: 0.4622 (tmm) cc_final: 0.3785 (mmt) REVERT: U 338 GLN cc_start: 0.8986 (mt0) cc_final: 0.8753 (mp10) REVERT: V 51 ARG cc_start: 0.9435 (OUTLIER) cc_final: 0.9164 (mmm-85) REVERT: V 78 ASP cc_start: 0.9418 (m-30) cc_final: 0.8879 (t0) REVERT: V 83 GLU cc_start: 0.8665 (tp30) cc_final: 0.7899 (tp30) REVERT: a 31 GLU cc_start: 0.9884 (mm-30) cc_final: 0.9593 (pp20) REVERT: a 36 MET cc_start: 0.8840 (mtp) cc_final: 0.8574 (mtm) REVERT: a 70 TYR cc_start: 0.8903 (m-80) cc_final: 0.8641 (m-80) REVERT: a 190 MET cc_start: 0.3084 (ttp) cc_final: 0.2629 (tmm) REVERT: a 223 HIS cc_start: 0.8078 (t-170) cc_final: 0.7817 (t70) REVERT: b 293 MET cc_start: 0.6597 (ttm) cc_final: 0.6094 (ptm) REVERT: c 98 GLN cc_start: 0.7689 (tp40) cc_final: 0.7435 (mm110) REVERT: c 216 HIS cc_start: 0.9236 (m-70) cc_final: 0.8952 (m90) REVERT: c 356 MET cc_start: 0.9157 (ppp) cc_final: 0.8925 (ppp) REVERT: c 379 MET cc_start: 0.4963 (mtt) cc_final: 0.4202 (ptp) REVERT: d 1 MET cc_start: 0.5038 (ptm) cc_final: 0.3734 (mtt) outliers start: 79 outliers final: 60 residues processed: 354 average time/residue: 0.6125 time to fit residues: 367.1708 Evaluate side-chains 351 residues out of total 5130 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 69 poor density : 282 time to evaluate : 5.672 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 367 ILE Chi-restraints excluded: chain A residue 458 PHE Chi-restraints excluded: chain A residue 611 ASP Chi-restraints excluded: chain A residue 695 ASP Chi-restraints excluded: chain A residue 954 ARG Chi-restraints excluded: chain A residue 1227 THR Chi-restraints excluded: chain A residue 1374 VAL Chi-restraints excluded: chain A residue 1454 VAL Chi-restraints excluded: chain B residue 91 ILE Chi-restraints excluded: chain B residue 124 LEU Chi-restraints excluded: chain B residue 163 LEU Chi-restraints excluded: chain B residue 193 VAL Chi-restraints excluded: chain B residue 218 THR Chi-restraints excluded: chain B residue 288 ILE Chi-restraints excluded: chain B residue 301 VAL Chi-restraints excluded: chain B residue 312 GLN Chi-restraints excluded: chain B residue 324 ARG Chi-restraints excluded: chain B residue 597 ILE Chi-restraints excluded: chain B residue 681 ASP Chi-restraints excluded: chain B residue 747 LEU Chi-restraints excluded: chain B residue 865 VAL Chi-restraints excluded: chain B residue 901 THR Chi-restraints excluded: chain B residue 918 PHE Chi-restraints excluded: chain B residue 964 ASP Chi-restraints excluded: chain B residue 1059 ILE Chi-restraints excluded: chain B residue 1075 MET Chi-restraints excluded: chain C residue 19 VAL Chi-restraints excluded: chain C residue 238 SER Chi-restraints excluded: chain D residue 90 LYS Chi-restraints excluded: chain D residue 107 THR Chi-restraints excluded: chain D residue 119 GLU Chi-restraints excluded: chain E residue 73 PHE Chi-restraints excluded: chain E residue 103 LEU Chi-restraints excluded: chain E residue 159 LEU Chi-restraints excluded: chain F residue 54 THR Chi-restraints excluded: chain F residue 66 LEU Chi-restraints excluded: chain G residue 24 ASN Chi-restraints excluded: chain G residue 93 ASN Chi-restraints excluded: chain G residue 113 ILE Chi-restraints excluded: chain H residue 4 ILE Chi-restraints excluded: chain H residue 96 VAL Chi-restraints excluded: chain H residue 110 THR Chi-restraints excluded: chain I residue 41 ASN Chi-restraints excluded: chain I residue 62 VAL Chi-restraints excluded: chain I residue 103 ARG Chi-restraints excluded: chain J residue 28 GLU Chi-restraints excluded: chain L residue 21 GLU Chi-restraints excluded: chain M residue 18 HIS Chi-restraints excluded: chain M residue 31 ASP Chi-restraints excluded: chain M residue 37 CYS Chi-restraints excluded: chain M residue 168 CYS Chi-restraints excluded: chain M residue 263 GLN Chi-restraints excluded: chain Q residue 12 THR Chi-restraints excluded: chain Q residue 46 ARG Chi-restraints excluded: chain Q residue 99 LEU Chi-restraints excluded: chain Q residue 118 VAL Chi-restraints excluded: chain Q residue 149 LEU Chi-restraints excluded: chain R residue 148 VAL Chi-restraints excluded: chain R residue 154 LYS Chi-restraints excluded: chain R residue 170 LYS Chi-restraints excluded: chain R residue 218 LYS Chi-restraints excluded: chain U residue 340 ASP Chi-restraints excluded: chain V residue 51 ARG Chi-restraints excluded: chain a residue 24 VAL Chi-restraints excluded: chain b residue 128 VAL Chi-restraints excluded: chain b residue 365 VAL Chi-restraints excluded: chain c residue 144 HIS Chi-restraints excluded: chain c residue 176 PHE Chi-restraints excluded: chain c residue 326 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 579 random chunks: chunk 341 optimal weight: 2.9990 chunk 549 optimal weight: 9.9990 chunk 335 optimal weight: 7.9990 chunk 260 optimal weight: 0.9990 chunk 382 optimal weight: 3.9990 chunk 576 optimal weight: 9.9990 chunk 530 optimal weight: 30.0000 chunk 459 optimal weight: 20.0000 chunk 47 optimal weight: 0.7980 chunk 354 optimal weight: 6.9990 chunk 281 optimal weight: 6.9990 overall best weight: 3.1588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 62 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 341 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 700 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 704 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1005 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1146 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 265 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 344 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1053 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B1120 ASN ** E 35 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 107 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 4 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 60 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 138 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 41 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 100 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 48 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 39 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 50 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** a 35 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** b 198 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** c 246 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8393 moved from start: 0.6618 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.211 50487 Z= 0.361 Angle : 0.701 59.196 68722 Z= 0.376 Chirality : 0.042 0.550 7610 Planarity : 0.004 0.113 8445 Dihedral : 16.037 143.354 7771 Min Nonbonded Distance : 1.931 Molprobity Statistics. All-atom Clashscore : 18.21 Ramachandran Plot: Outliers : 0.02 % Allowed : 4.11 % Favored : 95.87 % Rotamer: Outliers : 1.38 % Allowed : 14.90 % Favored : 83.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.56 % 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: 0.82 (0.11), residues: 5715 helix: 1.61 (0.11), residues: 2252 sheet: 0.13 (0.18), residues: 856 loop : -0.19 (0.13), residues: 2607 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.047 0.002 TRP c 187 HIS 0.006 0.001 HIS A 465 PHE 0.024 0.001 PHE B 823 TYR 0.018 0.001 TYR b 340 ARG 0.029 0.000 ARG d 17 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 11430 Ramachandran restraints generated. 5715 Oldfield, 0 Emsley, 5715 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 11430 Ramachandran restraints generated. 5715 Oldfield, 0 Emsley, 5715 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 353 residues out of total 5130 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 71 poor density : 282 time to evaluate : 5.373 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 99 PHE cc_start: 0.9364 (m-10) cc_final: 0.8902 (m-80) REVERT: A 234 PHE cc_start: 0.9345 (m-80) cc_final: 0.8756 (m-80) REVERT: A 367 ILE cc_start: 0.9753 (OUTLIER) cc_final: 0.9538 (pp) REVERT: A 388 MET cc_start: 0.8949 (mmm) cc_final: 0.8234 (mmt) REVERT: A 467 MET cc_start: 0.8912 (mpp) cc_final: 0.8475 (mpp) REVERT: A 501 MET cc_start: 0.9127 (mmm) cc_final: 0.8835 (mmm) REVERT: A 1279 MET cc_start: 0.5366 (ttt) cc_final: 0.4974 (tmm) REVERT: A 1309 MET cc_start: 0.7933 (ttt) cc_final: 0.7711 (ttt) REVERT: A 1428 MET cc_start: 0.9166 (tpp) cc_final: 0.8668 (tpp) REVERT: B 594 MET cc_start: 0.8559 (mtp) cc_final: 0.8186 (mmp) REVERT: B 908 MET cc_start: 0.8726 (tmm) cc_final: 0.8054 (tmm) REVERT: B 1075 MET cc_start: 0.8125 (OUTLIER) cc_final: 0.7722 (ppp) REVERT: B 1151 MET cc_start: 0.9529 (ptm) cc_final: 0.8645 (ptp) REVERT: B 1163 MET cc_start: 0.9425 (mmt) cc_final: 0.8951 (mmm) REVERT: D 119 GLU cc_start: 0.5013 (OUTLIER) cc_final: 0.4756 (mm-30) REVERT: E 18 MET cc_start: 0.8805 (mtp) cc_final: 0.8473 (ptm) REVERT: E 72 MET cc_start: 0.6881 (tpt) cc_final: 0.6647 (tpt) REVERT: E 73 PHE cc_start: 0.8526 (OUTLIER) cc_final: 0.8145 (t80) REVERT: E 98 ASN cc_start: 0.8839 (m-40) cc_final: 0.8544 (m-40) REVERT: E 103 LEU cc_start: 0.9554 (OUTLIER) cc_final: 0.9350 (mm) REVERT: F 57 MET cc_start: 0.8858 (tmm) cc_final: 0.8594 (tmm) REVERT: F 66 LEU cc_start: 0.9806 (OUTLIER) cc_final: 0.9591 (mm) REVERT: F 94 MET cc_start: 0.9239 (mmm) cc_final: 0.8962 (tpp) REVERT: G 104 MET cc_start: -0.0249 (mtt) cc_final: -0.0578 (ptp) REVERT: G 117 MET cc_start: -0.0136 (ttp) cc_final: -0.0347 (tmm) REVERT: H 123 MET cc_start: 0.8849 (tmm) cc_final: 0.8479 (tmm) REVERT: I 23 MET cc_start: 0.9110 (tpp) cc_final: 0.8467 (tpt) REVERT: I 71 ASP cc_start: 0.9084 (m-30) cc_final: 0.8699 (p0) REVERT: I 125 GLU cc_start: 0.7945 (mp0) cc_final: 0.7575 (mp0) REVERT: L 44 MET cc_start: 0.8764 (mmm) cc_final: 0.8271 (mmm) REVERT: M 263 GLN cc_start: 0.9134 (OUTLIER) cc_final: 0.8884 (mm110) REVERT: Q 162 GLU cc_start: 0.8563 (pp20) cc_final: 0.7887 (pm20) REVERT: Q 177 MET cc_start: 0.4588 (tmm) cc_final: 0.3904 (mmt) REVERT: U 338 GLN cc_start: 0.8986 (mt0) cc_final: 0.8753 (mp10) REVERT: V 51 ARG cc_start: 0.9413 (OUTLIER) cc_final: 0.9163 (mmm-85) REVERT: V 78 ASP cc_start: 0.9419 (m-30) cc_final: 0.8881 (t0) REVERT: V 83 GLU cc_start: 0.8674 (tp30) cc_final: 0.7887 (tp30) REVERT: a 31 GLU cc_start: 0.9884 (mm-30) cc_final: 0.9593 (pp20) REVERT: a 36 MET cc_start: 0.8840 (mtp) cc_final: 0.8575 (mtm) REVERT: a 70 TYR cc_start: 0.8902 (m-80) cc_final: 0.8647 (m-80) REVERT: a 190 MET cc_start: 0.3093 (ttp) cc_final: 0.2634 (tmm) REVERT: b 293 MET cc_start: 0.6593 (ttm) cc_final: 0.6092 (ptm) REVERT: c 98 GLN cc_start: 0.7689 (tp40) cc_final: 0.7435 (mm110) REVERT: c 216 HIS cc_start: 0.9235 (m-70) cc_final: 0.8949 (m90) REVERT: c 356 MET cc_start: 0.9158 (ppp) cc_final: 0.8927 (ppp) REVERT: c 379 MET cc_start: 0.4987 (mtt) cc_final: 0.4191 (ptp) REVERT: d 1 MET cc_start: 0.4963 (ptm) cc_final: 0.3574 (mtt) outliers start: 71 outliers final: 60 residues processed: 338 average time/residue: 0.6238 time to fit residues: 356.6698 Evaluate side-chains 349 residues out of total 5130 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 68 poor density : 281 time to evaluate : 5.576 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 33 ARG Chi-restraints excluded: chain A residue 367 ILE Chi-restraints excluded: chain A residue 458 PHE Chi-restraints excluded: chain A residue 611 ASP Chi-restraints excluded: chain A residue 695 ASP Chi-restraints excluded: chain A residue 954 ARG Chi-restraints excluded: chain A residue 1227 THR Chi-restraints excluded: chain A residue 1374 VAL Chi-restraints excluded: chain A residue 1454 VAL Chi-restraints excluded: chain B residue 91 ILE Chi-restraints excluded: chain B residue 124 LEU Chi-restraints excluded: chain B residue 163 LEU Chi-restraints excluded: chain B residue 193 VAL Chi-restraints excluded: chain B residue 218 THR Chi-restraints excluded: chain B residue 288 ILE Chi-restraints excluded: chain B residue 301 VAL Chi-restraints excluded: chain B residue 312 GLN Chi-restraints excluded: chain B residue 324 ARG Chi-restraints excluded: chain B residue 597 ILE Chi-restraints excluded: chain B residue 681 ASP Chi-restraints excluded: chain B residue 747 LEU Chi-restraints excluded: chain B residue 865 VAL Chi-restraints excluded: chain B residue 901 THR Chi-restraints excluded: chain B residue 918 PHE Chi-restraints excluded: chain B residue 964 ASP Chi-restraints excluded: chain B residue 1059 ILE Chi-restraints excluded: chain B residue 1075 MET Chi-restraints excluded: chain C residue 19 VAL Chi-restraints excluded: chain C residue 238 SER Chi-restraints excluded: chain D residue 90 LYS Chi-restraints excluded: chain D residue 107 THR Chi-restraints excluded: chain D residue 119 GLU Chi-restraints excluded: chain E residue 73 PHE Chi-restraints excluded: chain E residue 103 LEU Chi-restraints excluded: chain E residue 159 LEU Chi-restraints excluded: chain F residue 54 THR Chi-restraints excluded: chain F residue 66 LEU Chi-restraints excluded: chain G residue 24 ASN Chi-restraints excluded: chain G residue 113 ILE Chi-restraints excluded: chain H residue 4 ILE Chi-restraints excluded: chain H residue 96 VAL Chi-restraints excluded: chain H residue 110 THR Chi-restraints excluded: chain I residue 62 VAL Chi-restraints excluded: chain I residue 103 ARG Chi-restraints excluded: chain J residue 28 GLU Chi-restraints excluded: chain L residue 21 GLU Chi-restraints excluded: chain M residue 18 HIS Chi-restraints excluded: chain M residue 31 ASP Chi-restraints excluded: chain M residue 37 CYS Chi-restraints excluded: chain M residue 168 CYS Chi-restraints excluded: chain M residue 263 GLN Chi-restraints excluded: chain Q residue 12 THR Chi-restraints excluded: chain Q residue 46 ARG Chi-restraints excluded: chain Q residue 99 LEU Chi-restraints excluded: chain Q residue 118 VAL Chi-restraints excluded: chain Q residue 149 LEU Chi-restraints excluded: chain R residue 148 VAL Chi-restraints excluded: chain R residue 154 LYS Chi-restraints excluded: chain R residue 170 LYS Chi-restraints excluded: chain R residue 218 LYS Chi-restraints excluded: chain U residue 340 ASP Chi-restraints excluded: chain V residue 51 ARG Chi-restraints excluded: chain a residue 24 VAL Chi-restraints excluded: chain b residue 128 VAL Chi-restraints excluded: chain b residue 365 VAL Chi-restraints excluded: chain c residue 144 HIS Chi-restraints excluded: chain c residue 176 PHE Chi-restraints excluded: chain c residue 326 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 579 random chunks: chunk 364 optimal weight: 4.9990 chunk 489 optimal weight: 40.0000 chunk 140 optimal weight: 0.2980 chunk 423 optimal weight: 10.0000 chunk 67 optimal weight: 6.9990 chunk 127 optimal weight: 7.9990 chunk 460 optimal weight: 10.0000 chunk 192 optimal weight: 2.9990 chunk 472 optimal weight: 0.8980 chunk 58 optimal weight: 5.9990 chunk 84 optimal weight: 4.9990 overall best weight: 2.8386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 62 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 341 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 700 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 704 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1005 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1146 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 265 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 344 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1053 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B1120 ASN ** E 35 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 107 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 4 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 138 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 41 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 100 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 48 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 39 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 50 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** a 35 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** b 198 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** c 246 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3973 r_free = 0.3973 target = 0.071337 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3186 r_free = 0.3186 target = 0.046536 restraints weight = 331368.098| |-----------------------------------------------------------------------------| r_work (start): 0.2931 rms_B_bonded: 5.28 r_work (final): 0.2931 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8464 moved from start: 0.6620 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.211 50487 Z= 0.361 Angle : 0.701 59.196 68722 Z= 0.376 Chirality : 0.042 0.550 7610 Planarity : 0.004 0.113 8445 Dihedral : 16.037 143.354 7771 Min Nonbonded Distance : 1.931 Molprobity Statistics. All-atom Clashscore : 18.80 Ramachandran Plot: Outliers : 0.02 % Allowed : 4.11 % Favored : 95.87 % Rotamer: Outliers : 1.33 % Allowed : 14.95 % Favored : 83.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.56 % 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: 0.82 (0.11), residues: 5715 helix: 1.61 (0.11), residues: 2252 sheet: 0.13 (0.18), residues: 856 loop : -0.19 (0.13), residues: 2607 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.047 0.002 TRP c 187 HIS 0.006 0.001 HIS A 465 PHE 0.024 0.001 PHE B 823 TYR 0.018 0.001 TYR b 340 ARG 0.029 0.000 ARG d 17 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 10467.16 seconds wall clock time: 190 minutes 42.86 seconds (11442.86 seconds total)